Life | March 2015 - Browse Articles

3 pages, 353 KiB

Open AccessEditorial

Hypotheses, Limits, Models and Life

by William Bains

Rufus Scientific Ltd., 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK

Life 2015, 5(1), 1-3; https://doi.org/10.3390/life5010001 - 29 Dec 2014

Cited by 4 | Viewed by 5554

Abstract

Life is launching a new section, called Hypotheses in the Life Sciences. The new Section will complement the other sections of Life, providing a feedstock of ideas whose tests can be published in the wider Life family, and elsewhere. We will [...] Read more.

Life is launching a new section, called Hypotheses in the Life Sciences. The new Section will complement the other sections of Life, providing a feedstock of ideas whose tests can be published in the wider Life family, and elsewhere. We will consider hypotheses that are supported by real world, rigorous evidence, by clear arguments, and which provide a potential solution to a genuine gap in our understanding of any aspect of the life sciences. Full article

(This article belongs to the Special Issue The Physico-Chemical Limits of Life)

21 pages, 4977 KiB

Open AccessArticle

Occurrence of Far-Red Light Photoacclimation (FaRLiP) in Diverse Cyanobacteria

by Fei Gan¹, Gaozhong Shen¹ and Donald A. Bryant^1,2,*

¹ Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA

² Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA

Life 2015, 5(1), 4-24; https://doi.org/10.3390/life5010004 - 29 Dec 2014

Cited by 163 | Viewed by 16136

Abstract

Cyanobacteria have evolved a number of acclimation strategies to sense and respond to changing nutrient and light conditions. Leptolyngbya sp. JSC-1 was recently shown to photoacclimate to far-red light by extensively remodeling its photosystem (PS) I, PS II and phycobilisome complexes, thereby gaining [...] Read more.

Cyanobacteria have evolved a number of acclimation strategies to sense and respond to changing nutrient and light conditions. Leptolyngbya sp. JSC-1 was recently shown to photoacclimate to far-red light by extensively remodeling its photosystem (PS) I, PS II and phycobilisome complexes, thereby gaining the ability to grow in far-red light. A 21-gene photosynthetic gene cluster (rfpA/B/C, apcA2/B2/D2/E2/D3, psbA3/D3/C2/B2/ H2/A4, psaA2/B2/L2/I2/F2/J2) that is specifically expressed in far-red light encodes the core subunits of the three major photosynthetic complexes. The growth responses to far-red light were studied here for five additional cyanobacterial strains, each of which has a gene cluster similar to that in Leptolyngbya sp. JSC-1. After acclimation all five strains could grow continuously in far-red light. Under these growth conditions each strain synthesizes chlorophylls d, f and a after photoacclimation, and each strain produces modified forms of PS I, PS II (and phycobiliproteins) that absorb light between 700 and 800 nm. We conclude that these photosynthetic gene clusters are diagnostic of the capacity to photoacclimate to and grow in far-red light. Given the diversity of terrestrial environments from which these cyanobacteria were isolated, it is likely that FaRLiP plays an important role in optimizing photosynthesis in terrestrial environments. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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25 pages, 1029 KiB

Open AccessReview

Salt Acclimation of Cyanobacteria and Their Application in Biotechnology

by Nadin Pade and Martin Hagemann^*

Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany

Life 2015, 5(1), 25-49; https://doi.org/10.3390/life5010025 - 29 Dec 2014

Cited by 133 | Viewed by 11563

Abstract

The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the [...] Read more.

The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the accumulation of compatible solutes. Cyanobacterial salt acclimation has been characterized in much detail using selected model cyanobacteria, but their salt sensing and regulatory mechanisms are less well understood. Here, we briefly review recent advances in the identification of salt acclimation processes and the essential genes/proteins involved in acclimation to high salt. This knowledge is of increasing importance because the necessary mass cultivation of cyanobacteria for future use in biotechnology will be performed in sea water. In addition, cyanobacterial salt resistance genes also can be applied to improve the salt tolerance of salt sensitive organisms, such as crop plants. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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15 pages, 851 KiB

Open AccessArticle

Does a Barcoding Gap Exist in Prokaryotes? Evidences from Species Delimitation in Cyanobacteria

by Ester M. Eckert^*, Diego Fontaneto, Manuela Coci and Cristiana Callieri

Microbial Ecology Group, Institute of Ecosystem Study, National Research Council, Largo Tonolli 50, 28922 Verbania, Italy

Life 2015, 5(1), 50-64; https://doi.org/10.3390/life5010050 - 31 Dec 2014

Cited by 18 | Viewed by 11256

Abstract

The amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may [...] Read more.

The amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results. Here we tests for the existence of a barcoding gap in several groups of Cyanobacteria, defining units of diversity according to clear differences between within-species and among-species genetic distances in 16S rRNA. The application of a tool developed for animal DNA taxonomy, the Automatic Barcode Gap Detector (ABGD), revealed that a barcoding gap could actually be found in almost half of the datasets that we tested. The identification of units of diversity through this method provided results that were not compatible with those obtained with the identification of OTUs with threshold of similarity in genetic distances of 97% or 99%. The main message of our results is a call for caution in the estimate of diversity from 16S sequences only, given that different subjective choices in the method to delimit units could provide different results. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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20 pages, 1347 KiB

Open AccessArticle

Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth

by Chaitanya V. Mungi and Sudha Rajamani^*

Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India

Life 2015, 5(1), 65-84; https://doi.org/10.3390/life5010065 - 5 Jan 2015

Cited by 46 | Viewed by 13063

Abstract

Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches [...] Read more.

Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in “prebiotic phosphodiester polymers” prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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17 pages, 705 KiB

Open AccessArticle

Pilin Processing Follows a Different Temporal Route than That of Archaellins in Methanococcus maripaludis

by Divya B. Nair and Ken F. Jarrell^*

Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada

Life 2015, 5(1), 85-101; https://doi.org/10.3390/life5010085 - 5 Jan 2015

Cited by 7 | Viewed by 9189

Abstract

Methanococcus maripaludis has two different surface appendages: type IV-like pili and archaella. Both structures are believed to be assembled using a bacterial type IV pilus mechanism. Each structure is composed of multiple subunits, either pilins or archaellins. Both pilins and archaellins are made [...] Read more.

Methanococcus maripaludis has two different surface appendages: type IV-like pili and archaella. Both structures are believed to be assembled using a bacterial type IV pilus mechanism. Each structure is composed of multiple subunits, either pilins or archaellins. Both pilins and archaellins are made initially as preproteins with type IV pilin-like signal peptides, which must be removed by a prepilin peptidase-like enzyme. This enzyme is FlaK for archaellins and EppA for pilins. In addition, both pilins and archaellins are modified with N-linked glycans. The archaellins possess an N-linked tetrasaccharide while the pilins have a pentasaccharide which consists of the archaellin tetrasaccharide but with an additional sugar, an unidentified hexose, attached to the linking sugar. In this report, we show that archaellins can be processed by FlaK in the absence of N-glycosylation and N-glycosylation can occur on archaellins that still retain their signal peptides. In contrast, pilins are not glycosylated unless they have been acted on by EppA to have the signal peptide removed. However, EppA can still remove signal peptides from non-glycosylated pilins. These findings indicate that there is a difference in the order of the posttranslational modifications of pilins and archaellins even though both are type IV pilin-like proteins. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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25 pages, 1703 KiB

Open AccessReview

Sucrose in Cyanobacteria: From a Salt-Response Molecule to Play a Key Role in Nitrogen Fixation

by María A. Kolman, Carolina N. Nishi, Macarena Perez-Cenci and Graciela L. Salerno^*

Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata B7600DHN, Argentina

Life 2015, 5(1), 102-126; https://doi.org/10.3390/life5010102 - 6 Jan 2015

Cited by 47 | Viewed by 12134

Abstract

In the biosphere, sucrose is mainly synthesized in oxygenic photosynthetic organisms, such as cyanobacteria, green algae and land plants, as part of the carbon dioxide assimilation pathway. Even though its central position in the functional biology of plants is well documented, much less [...] Read more.

In the biosphere, sucrose is mainly synthesized in oxygenic photosynthetic organisms, such as cyanobacteria, green algae and land plants, as part of the carbon dioxide assimilation pathway. Even though its central position in the functional biology of plants is well documented, much less is known about the role of sucrose in cyanobacteria. In those prokaryotes, sucrose accumulation has been associated with salt acclimation, and considered as a compatible solute in low-salt tolerant strains. In the last years, functional characterizations of sucrose metabolizing enzymes, metabolic control analysis, cellular localization of gene expressions, and reverse genetic experiments have revealed that sucrose metabolism is crucial in the diazotrophic growth of heterocystic strains, and besides, that it can be connected to glycogen synthesis. This article briefly summarizes the current state of knowledge of sucrose physiological functions in modern cyanobacteria and how they might have evolved taking into account the phylogenetic analyses of sucrose enzymes. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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3 pages, 312 KiB

Open AccessEditorial

Acknowledgement to Reviewers of Life in 2014

by Life Editorial Office

Life Editorial Office, MDPI AG, Klybeckstrasse 64, CH-4057 Basel, Switzerland

Life 2015, 5(1), 127-129; https://doi.org/10.3390/life5010127 - 7 Jan 2015

Viewed by 3583

Abstract

The editors of Life would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2014:[...] Full article

34 pages, 1238 KiB

Open AccessArticle

The Anabaena sp. PCC 7120 Exoproteome: Taking a Peek outside the Box

by Paulo Oliveira^1,2,*,†

, Nuno M. Martins^1,2,3,†, Marina Santos^1,2, Narciso A. S. Couto⁴, Phillip C. Wright⁴ and Paula Tamagnini^1,2,5

¹ Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4150-180, Portugal

² IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal

³ Laboratoire du Biologie du Noyau, Institut de Biologie & de Médecine Moléculaire, Université Libre de Bruxelles, Charleroi B-6041, Belgium

⁴ ChELSI Institute, Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK

⁵ Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto 4169-007, Portugal

^† These authors contributed equally to this work.

Life 2015, 5(1), 130-163; https://doi.org/10.3390/life5010130 - 8 Jan 2015

Cited by 42 | Viewed by 10091

Abstract

The interest in examining the subset of proteins present in the extracellular milieu, the exoproteome, has been growing due to novel insights highlighting their role on extracellular matrix organization and biofilm formation, but also on homeostasis and development. The cyanobacterial exoproteome is poorly [...] Read more.

The interest in examining the subset of proteins present in the extracellular milieu, the exoproteome, has been growing due to novel insights highlighting their role on extracellular matrix organization and biofilm formation, but also on homeostasis and development. The cyanobacterial exoproteome is poorly studied, and the role of cyanobacterial exoproteins on cell wall biogenesis, morphology and even physiology is largely unknown. Here, we present a comprehensive examination of the Anabaena sp. PCC 7120 exoproteome under various growth conditions. Altogether, 139 proteins belonging to 16 different functional categories have been identified. A large fraction (48%) of the identified proteins is classified as “hypothetical”, falls into the “other categories” set or presents no similarity to other proteins. The evidence presented here shows that Anabaena sp. PCC 7120 is capable of outer membrane vesicle formation and that these vesicles are likely to contribute to the exoproteome profile. Furthermore, the activity of selected exoproteins associated with oxidative stress has been assessed, suggesting their involvement in redox homeostasis mechanisms in the extracellular space. Finally, we discuss our results in light of other cyanobacterial exoproteome studies and focus on the potential of exploring cyanobacteria as cell factories to produce and secrete selected proteins. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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17 pages, 2311 KiB

Open AccessReview

Biosynthesis and Function of Extracellular Glycans in Cyanobacteria

by Jan-Christoph Kehr^* and Elke Dittmann

University of Potsdam, Institute for Biochemistry and Biology, Department of Microbiology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam-Golm, Germany

Life 2015, 5(1), 164-180; https://doi.org/10.3390/life5010164 - 12 Jan 2015

Cited by 103 | Viewed by 11142

Abstract

The cell surface of cyanobacteria is covered with glycans that confer versatility and adaptability to a multitude of environmental factors. The complex carbohydrates act as barriers against different types of stress and play a role in intra- as well as inter-species interactions. In [...] Read more.

The cell surface of cyanobacteria is covered with glycans that confer versatility and adaptability to a multitude of environmental factors. The complex carbohydrates act as barriers against different types of stress and play a role in intra- as well as inter-species interactions. In this review, we summarize the current knowledge of the chemical composition, biosynthesis and biological function of exo- and lipo-polysaccharides from cyanobacteria and give an overview of sugar-binding lectins characterized from cyanobacteria. We discuss similarities with well-studied enterobacterial systems and highlight the unique features of cyanobacteria. We pay special attention to colony formation and EPS biosynthesis in the bloom-forming cyanobacterium, Microcystis aeruginosa. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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31 pages, 1444 KiB

Open AccessArticle

Emergent Chemical Behavior in Variable-Volume Protocells

by Ben Shirt-Ediss^1,2, Ricard V. Solé^1,3 and Kepa Ruiz-Mirazo^2,4,*

¹ ICREA-Complex Systems Lab, Institut de Biologia Evolutiva, CSIC-UPF, 08003 Barcelona, Spain

² Logic and Philosophy of Science Department, University of The Basque Country, Avda. Tolosa 70, 20018 Donostia-San Sebastian, Gipuzkoa, Spain

³ Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA

⁴ Biophysics Unit (CSIC, UPV/EHU), University of The Basque Country, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain

Life 2015, 5(1), 181-211; https://doi.org/10.3390/life5010181 - 13 Jan 2015

Cited by 20 | Viewed by 8158

Abstract

Artificial protocellular compartments and lipid vesicles have been used as model systems to understand the origins and requirements for early cells, as well as to design encapsulated reactors for biotechnology. One prominent feature of vesicles is the semi-permeable nature of their membranes, able [...] Read more.

Artificial protocellular compartments and lipid vesicles have been used as model systems to understand the origins and requirements for early cells, as well as to design encapsulated reactors for biotechnology. One prominent feature of vesicles is the semi-permeable nature of their membranes, able to support passive diffusion of individual solute species into/out of the compartment, in addition to an osmotic water flow in the opposite direction to the net solute concentration gradient. Crucially, this water flow affects the internal aqueous volume of the vesicle in response to osmotic imbalances, in particular those created by ongoing reactions within the system. In this theoretical study, we pay attention to this often overlooked aspect and show, via the use of a simple semi-spatial vesicle reactor model, that a changing solvent volume introduces interesting non-linearities into an encapsulated chemistry. Focusing on bistability, we demonstrate how a changing volume compartment can degenerate existing bistable reactions, but also promote emergent bistability from very simple reactions, which are not bistable in bulk conditions. One particularly remarkable effect is that two or more chemically-independent reactions, with mutually exclusive reaction kinetics, are able to couple their dynamics through the variation of solvent volume inside the vesicle. Our results suggest that other chemical innovations should be expected when more realistic and active properties of protocellular compartments are taken into account. Full article

(This article belongs to the Special Issue Protocells - Designs for Life)

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2 pages, 285 KiB

Open AccessEditorial

Message from the Editor-in-Chief

by Pabulo Henrique Rampelotto

Center of Biotechnology and PPGBCM, Federal University of Rio Grande do Sul, Bento Gonçalves Avenue, P.O. Box 15005, 91501-970, Porto Alegre—RS, Brazil

Life 2015, 5(1), 212-213; https://doi.org/10.3390/life5010212 - 13 Jan 2015

Cited by 2 | Viewed by 4505

Abstract

One year after I assumed the position of Editor in Chief of Life, it is my great pleasure to write this editorial highlighting our achievements during this period, which were so many! As I wrote in the first editorial, my commitment was [...] Read more.

One year after I assumed the position of Editor in Chief of Life, it is my great pleasure to write this editorial highlighting our achievements during this period, which were so many! As I wrote in the first editorial, my commitment was to make the journal a success, with the launch of exciting special issues, publication of high quality papers as well as inclusion of the journal in major indexing and abstracting services [1]. Basically, throughout 2014, all these commitments have been accomplished. Several eminent team leaders have joined our editorial board [2], timely special issues have been launched [3], and the journal already was indexed in PubMed [4]; now, it is just a matter of time to be indexed in Web of Science. The feedback from the scientific community already has been quite positive. With timely special issues lined up for 2015, the journal is developing quite fast.[...] Full article

16 pages, 1455 KiB

Open AccessReview

Nanoporous Silica-Based Protocells at Multiple Scales for Designs of Life and Nanomedicine

by Jie Sun¹, Eric Jakobsson¹, Yingxiao Wang² and C. Jeffrey Brinker^3,4,*

¹ Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

² Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA

³ Department of Chemical and Nuclear Engineering, Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NW 87106, USA

⁴ Sandia National Laboratories (SNL), Albuquerque, NW 87185, USA

Life 2015, 5(1), 214-229; https://doi.org/10.3390/life5010214 - 19 Jan 2015

Cited by 17 | Viewed by 10442

Abstract

Various protocell models have been constructed de novo with the bottom-up approach. Here we describe a silica-based protocell composed of a nanoporous amorphous silica core encapsulated within a lipid bilayer built by self-assembly that provides for independent definition of cell interior and the [...] Read more.

Various protocell models have been constructed de novo with the bottom-up approach. Here we describe a silica-based protocell composed of a nanoporous amorphous silica core encapsulated within a lipid bilayer built by self-assembly that provides for independent definition of cell interior and the surface membrane. In this review, we will first describe the essential features of this architecture and then summarize the current development of silica-based protocells at both micro- and nanoscale with diverse functionalities. As the structure of the silica is relatively static, silica-core protocells do not have the ability to change shape, but their interior structure provides a highly crowded and, in some cases, authentic scaffold upon which biomolecular components and systems could be reconstituted. In basic research, the larger protocells based on precise silica replicas of cells could be developed into geometrically realistic bioreactor platforms to enable cellular functions like coupled biochemical reactions, while in translational research smaller protocells based on mesoporous silica nanoparticles are being developed for targeted nanomedicine. Ultimately we see two different motivations for protocell research and development: (1) to emulate life in order to understand it; and (2) to use biomimicry to engineer desired cellular interactions. Full article

(This article belongs to the Special Issue Protocells - Designs for Life)

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17 pages, 738 KiB

Open AccessReview

How Amino Acids and Peptides Shaped the RNA World

by Peter T.S. Van der Gulik¹ and Dave Speijer^2,*

¹ Centrum Wiskunde & Informatica, Science Park 123, 1098 SJ Amsterdam, The Netherlands

² Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands

Life 2015, 5(1), 230-246; https://doi.org/10.3390/life5010230 - 19 Jan 2015

Cited by 49 | Viewed by 13040

Abstract

The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and [...] Read more.

The “RNA world” hypothesis is seen as one of the main contenders for a viable theory on the origin of life. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis. However, this view is incomplete at best. The modern protein-RNA ribosome most probably is not a distorted form of a “pure RNA ribosome” evolution started out with. Though the oldest center of the ribosome seems “RNA only”, we cannot conclude from this that it ever functioned in an environment without amino acids and/or peptides. Very small RNAs (versatile and stable due to basepairing) and amino acids, as well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. With the rise of the “RNA world” view of early life, the pendulum seems to have swung too much towards the ribozymatic part of early biochemistry. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus. We argue that an RNA world completely independent of amino acids never existed. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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22 pages, 1124 KiB

Open AccessReview

RNA Synthesis by in Vitro Selected Ribozymes for Recreating an RNA World

by Lyssa L. Martin¹, Peter J. Unrau^1,* and Ulrich F. Müller^2,*

¹ Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada

² Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA

Life 2015, 5(1), 247-268; https://doi.org/10.3390/life5010247 - 20 Jan 2015

Cited by 39 | Viewed by 13605

Abstract

The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs [...] Read more.

The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme’s possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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25 pages, 959 KiB

Open AccessReview

Terpenoids and Their Biosynthesis in Cyanobacteria

by Bagmi Pattanaik and Pia Lindberg^*

Department of Chemistry—Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden

Life 2015, 5(1), 269-293; https://doi.org/10.3390/life5010269 - 21 Jan 2015

Cited by 134 | Viewed by 24985

Abstract

Terpenoids, or isoprenoids, are a family of compounds with great structural diversity which are essential for all living organisms. In cyanobacteria, they are synthesized from the methylerythritol-phosphate (MEP) pathway, using glyceraldehyde 3-phosphate and pyruvate produced by photosynthesis as substrates. The products of the [...] Read more.

Terpenoids, or isoprenoids, are a family of compounds with great structural diversity which are essential for all living organisms. In cyanobacteria, they are synthesized from the methylerythritol-phosphate (MEP) pathway, using glyceraldehyde 3-phosphate and pyruvate produced by photosynthesis as substrates. The products of the MEP pathway are the isomeric five-carbon compounds isopentenyl diphosphate and dimethylallyl diphosphate, which in turn form the basic building blocks for formation of all terpenoids. Many terpenoid compounds have useful properties and are of interest in the fields of pharmaceuticals and nutrition, and even potentially as future biofuels. The MEP pathway, its function and regulation, and the subsequent formation of terpenoids have not been fully elucidated in cyanobacteria, despite its relevance for biotechnological applications. In this review, we summarize the present knowledge about cyanobacterial terpenoid biosynthesis, both regarding the native metabolism and regarding metabolic engineering of cyanobacteria for heterologous production of non-native terpenoids. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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27 pages, 2914 KiB

Open AccessReview

What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention

by Charles W. Carter, Jr.

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA

Life 2015, 5(1), 294-320; https://doi.org/10.3390/life5010294 - 23 Jan 2015

Cited by 72 | Viewed by 16387

Abstract

We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged [...] Read more.

We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code. A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA. Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene. Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily. Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. That scenario documents a path to increasing complexity that obviates the need for a single polymer to act both catalytically and as an informational molecule. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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11 pages, 1095 KiB

Open AccessReview

Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution

by Akio Kanai^1,2

¹ Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan

² Faculty of Environment and Information Studies, Keio University, Fujisawa 252-8520, Japan

Life 2015, 5(1), 321-331; https://doi.org/10.3390/life5010321 - 26 Jan 2015

Cited by 35 | Viewed by 12322

Abstract

Transfer RNAs (tRNAs) are small non-coding RNAs with lengths of approximately 70–100 nt. They are directly involved in protein synthesis by carrying amino acids to the ribosome. In this sense, tRNAs are key molecules that connect the RNA world and the protein world. [...] Read more.

Transfer RNAs (tRNAs) are small non-coding RNAs with lengths of approximately 70–100 nt. They are directly involved in protein synthesis by carrying amino acids to the ribosome. In this sense, tRNAs are key molecules that connect the RNA world and the protein world. Thus, study of the evolution of tRNA molecules may reveal the processes that led to the establishment of the central dogma: genetic information flows from DNA to RNA to protein. Thanks to the development of DNA sequencers in this century, we have determined a huge number of nucleotide sequences from complete genomes as well as from transcriptomes in many species. Recent analyses of these large data sets have shown that particular tRNA genes, especially in Archaea, are disrupted in unique ways: some tRNA genes contain multiple introns and some are split genes. Even tRNA molecules themselves are fragmented post-transcriptionally in many species. These fragmented small RNAs are known as tRNA-derived fragments (tRFs). In this review, I summarize the progress of research into the disrupted tRNA genes and the tRFs, and propose a possible model for the molecular evolution of tRNAs based on the concept of the combination of fragmented tRNA halves. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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16 pages, 5709 KiB

Open AccessReview

Portrait of a Geothermal Spring, Hunter’s Hot Springs, Oregon

by Richard W. Castenholz

Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA

Life 2015, 5(1), 332-347; https://doi.org/10.3390/life5010332 - 27 Jan 2015

Cited by 20 | Viewed by 7616

Abstract

Although alkaline Hunter’s Hot Springs in southeastern Oregon has been studied extensively for over 40 years, most of these studies and the subsequent publications were before the advent of molecular methods. However, there are many field observations and laboratory experiments that reveal the [...] Read more.

Although alkaline Hunter’s Hot Springs in southeastern Oregon has been studied extensively for over 40 years, most of these studies and the subsequent publications were before the advent of molecular methods. However, there are many field observations and laboratory experiments that reveal the major aspects of the phototrophic species composition within various physical and chemical gradients of these springs. Relatively constant temperature boundaries demark the upper boundary of the unicellular cyanobacterium, Synechococcus at 73–74 °C (the world-wide upper limit for photosynthesis), and 68–70 °C the upper limit for Chloroflexus. The upper limit for the cover of the filamentous cyanobacterium, Geitlerinema (Oscillatoria) is at 54–55 °C, and the in situ lower limit at 47–48 °C for all three of these phototrophs due to the upper temperature limit for the grazing ostracod, Thermopsis. The in situ upper limit for the cyanobacteria Pleurocapsa and Calothrix is at ~47–48 °C, which are more grazer-resistant and grazer dependent. All of these demarcations are easily visible in the field. In addition, there is a biosulfide production in some sections of the springs that have a large impact on the microbiology. Most of the temperature and chemical limits have been explained by field and laboratory experiments. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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24 pages, 2201 KiB

Open AccessReview

Regulation of CO₂ Concentrating Mechanism in Cyanobacteria

by Robert L. Burnap^1,*,†, Martin Hagemann^2,† and Aaron Kaplan^3,†

¹ Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA

² Institute Biosciences, Department Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, Rostock D-18059, Germany

³ Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem 91904, Israel

^† These authors contributed equally to this work.

Life 2015, 5(1), 348-371; https://doi.org/10.3390/life5010348 - 28 Jan 2015

Cited by 164 | Viewed by 14754

Abstract

In this chapter, we mainly focus on the acclimation of cyanobacteria to the changing ambient CO₂ and discuss mechanisms of inorganic carbon (C_i) uptake, photorespiration, and the regulation among the metabolic fluxes involved in photoautotrophic, photomixotrophic and heterotrophic growth. The [...] Read more.

In this chapter, we mainly focus on the acclimation of cyanobacteria to the changing ambient CO₂ and discuss mechanisms of inorganic carbon (C_i) uptake, photorespiration, and the regulation among the metabolic fluxes involved in photoautotrophic, photomixotrophic and heterotrophic growth. The structural components for several of the transport and uptake mechanisms are described and the progress towards elucidating their regulation is discussed in the context of studies, which have documented metabolomic changes in response to changes in C_i availability. Genes for several of the transport and uptake mechanisms are regulated by transcriptional regulators that are in the LysR-transcriptional regulator family and are known to act in concert with small molecule effectors, which appear to be well-known metabolites. Signals that trigger changes in gene expression and enzyme activity correspond to specific “regulatory metabolites” whose concentrations depend on the ambient C_i availability. Finally, emerging evidence for an additional layer of regulatory complexity involving small non-coding RNAs is discussed. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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13 pages, 1086 KiB

Open AccessArticle

From Formamide to RNA, the Path Is Tenuous but Continuous

by Samanta Pino¹, Judit E. Sponer^2,3, Giovanna Costanzo⁴, Raffaele Saladino⁵ and Ernesto Di Mauro^1,*

¹ Fondazione "Istituto Pasteur-Fondazione Cenci-Bolognetti" c/o Dipartimento di Biologia e Biotecnologie "Charles Darwin", "Sapienza" Università di Roma, P.le Aldo Moro, 5, 00185 Rome, Italy

² Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic

³ CEITEC-Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic

⁴ Istituto di Biologia e Patologia Molecolari, CNR, P.le Aldo Moro, 5, 00185 Rome, Italy

⁵ Dipartimento di Scienze Ecologiche e Biologiche Università della Tuscia Via San Camillo De Lellis, 01100 Viterbo, Italy

Life 2015, 5(1), 372-384; https://doi.org/10.3390/life5010372 - 30 Jan 2015

Cited by 36 | Viewed by 11171

Abstract

Reactions of formamide (NH₂COH) in the presence of catalysts of both terrestrial and meteoritic origin yield, in plausible and variegated conditions, a large panel of precursors of (pre)genetic and (pre)metabolic interest. Formamide chemistry potentially satisfies all of the steps from the [...] Read more.

Reactions of formamide (NH₂COH) in the presence of catalysts of both terrestrial and meteoritic origin yield, in plausible and variegated conditions, a large panel of precursors of (pre)genetic and (pre)metabolic interest. Formamide chemistry potentially satisfies all of the steps from the very initial precursors to RNA. Water chemistry enters the scene in RNA non-enzymatic synthesis and recombination. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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18 pages, 1649 KiB

Open AccessReview

Haloarchaea and the Formation of Gas Vesicles

by Felicitas Pfeifer

Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany

Life 2015, 5(1), 385-402; https://doi.org/10.3390/life5010385 - 2 Feb 2015

Cited by 50 | Viewed by 12709

Abstract

Halophilic Archaea (Haloarchaea) thrive in salterns containing sodium chloride concentrations up to saturation. Many Haloarchaea possess genes encoding gas vesicles, but only a few species, such as Halobacterium salinarum and Haloferax mediterranei, produce these gas-filled, proteinaceous nanocompartments. Gas vesicles increase the buoyancy [...] Read more.

Halophilic Archaea (Haloarchaea) thrive in salterns containing sodium chloride concentrations up to saturation. Many Haloarchaea possess genes encoding gas vesicles, but only a few species, such as Halobacterium salinarum and Haloferax mediterranei, produce these gas-filled, proteinaceous nanocompartments. Gas vesicles increase the buoyancy of cells and enable them to migrate vertically in the water body to regions with optimal conditions. Their synthesis depends on environmental factors, such as light, oxygen supply, temperature and salt concentration. Fourteen gas vesicle protein (gvp) genes are involved in their formation, and regulation of gvp gene expression occurs at the level of transcription, including the two regulatory proteins, GvpD and GvpE, but also at the level of translation. The gas vesicle wall is solely formed of proteins with the two major components, GvpA and GvpC, and seven additional accessory proteins are also involved. Except for GvpI and GvpH, all of these are required to form the gas permeable wall. The applications of gas vesicles include their use as an antigen presenter for viral or pathogen proteins, but also as a stable ultrasonic reporter for biomedical purposes. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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15 pages, 578 KiB

Open AccessArticle

The RUBISCO to Photosystem II Ratio Limits the Maximum Photosynthetic Rate in Picocyanobacteria

by Jackie K. Zorz^†, Jessica R. Allanach^†, Cole D. Murphy, Mitchell S. Roodvoets, Douglas A. Campbell and Amanda M. Cockshutt^*

¹ Department of Chemistry & Biochemistry, Mount Allison University, Sackville, New Brunswick, E4L 1G8, Canada

^† These authors contributed equally to this work.

Life 2015, 5(1), 403-417; https://doi.org/10.3390/life5010403 - 4 Feb 2015

Cited by 38 | Viewed by 7574

Abstract

Marine Synechococcus and Prochlorococcus are picocyanobacteria predominating in subtropical, oligotrophic marine environments, a niche predicted to expand with climate change. When grown under common low light conditions Synechococcus WH 8102 and Prochlorococcus MED 4 show similar Cytochrome b₆f and Photosystem I [...] Read more.

Marine Synechococcus and Prochlorococcus are picocyanobacteria predominating in subtropical, oligotrophic marine environments, a niche predicted to expand with climate change. When grown under common low light conditions Synechococcus WH 8102 and Prochlorococcus MED 4 show similar Cytochrome b₆f and Photosystem I contents normalized to Photosystem II content, while Prochlorococcus MIT 9313 has twice the Cytochrome b₆f content and four times the Photosystem I content of the other strains. Interestingly, the Prochlorococcus strains contain only one third to one half of the RUBISCO catalytic subunits compared to the marine Synechococcus strain. The maximum Photosystem II electron transport rates were similar for the two Prochlorococcus strains but higher for the marine Synechococcus strain. Photosystem II electron transport capacity is highly correlated to the molar ratio of RUBISCO active sites to Photosystem II but not to the ratio of cytochrome b₆f to Photosystem II, nor to the ratio of Photosystem I: Photosystem II. Thus, the catalytic capacity for the rate-limiting step of carbon fixation, the ultimate electron sink, appears to limit electron transport rates. The high abundance of Cytochrome b₆f and Photosystem I in MIT 9313, combined with the slower flow of electrons away from Photosystem II and the relatively low level of RUBISCO, are consistent with cyclic electron flow around Photosystem I in this strain. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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14 pages, 585 KiB

Open AccessReview

Long-Term Changes in Cyanobacteria Populations in Lake Kinneret (Sea of Galilee), Israel: An Eco-Physiological Outlook

by Ora Hadas^1,*,†, Aaron Kaplan^2,† and Assaf Sukenik^3,†

¹ The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel

² Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel

³ The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel

^† These authors contributed equally to this work.

Life 2015, 5(1), 418-431; https://doi.org/10.3390/life5010418 - 5 Feb 2015

Cited by 30 | Viewed by 7091

Abstract

The long-term record of cyanobacteria abundance in Lake Kinneret (Sea of Galilee), Israel, demonstrates changes in cyanobacteria abundance and composition in the last five decades. New invasive species of the order Nostocales (Aphanizomenon ovalisporum and Cylindrospermopsis raciborskii) became part of the [...] Read more.

The long-term record of cyanobacteria abundance in Lake Kinneret (Sea of Galilee), Israel, demonstrates changes in cyanobacteria abundance and composition in the last five decades. New invasive species of the order Nostocales (Aphanizomenon ovalisporum and Cylindrospermopsis raciborskii) became part of the annual phytoplankton assemblage during summer-autumn. Concomitantly, bloom events of Microcystis sp. (Chroococcales) during winter-spring intensified. These changes in cyanobacteria pattern may be partly attributed to the management policy in Lake Kinneret’s vicinity and watershed aimed to reduce effluent discharge to the lake and partly to climate changes in the region; i.e., increased water column temperature, less wind and reduced precipitation. The gradual decrease in the concentration of total and dissolved phosphorus and total and dissolved nitrogen and an increase in alkalinity, pH and salinity, combined with the physiological features of cyanobacteria, probably contributed to the success of cyanobacteria. The data presented here indicate that the trend of the continuous decline of nutrients may not be sufficient to reduce and to control the abundance and proliferation of toxic and non-toxic cyanobacteria. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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15 pages, 3103 KiB

Open AccessArticle

Functional Characterization of the FNT Family Nitrite Transporter of Marine Picocyanobacteria

by Shin-ichi Maeda^1,2,*, Akio Murakami^2,3, Hisashi Ito^2,4, Ayumi Tanaka^2,4 and Tatsuo Omata^1,2

¹ Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan

² CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076 Japan

³ Research Center for Inland Seas, Kobe University, Awaji, Hyogo 656-2401, Japan

⁴ Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo 060-0819, Japan

Life 2015, 5(1), 432-446; https://doi.org/10.3390/life5010432 - 9 Feb 2015

Cited by 21 | Viewed by 7054

Abstract

Many of the cyanobacterial species found in marine and saline environments have a gene encoding a putative nitrite transporter of the formate/nitrite transporter (FNT) family. The presumed function of the gene (designated nitM) was confirmed by functional expression of the gene from [...] Read more.

Many of the cyanobacterial species found in marine and saline environments have a gene encoding a putative nitrite transporter of the formate/nitrite transporter (FNT) family. The presumed function of the gene (designated nitM) was confirmed by functional expression of the gene from the coastal marine species Synechococcus sp. strain PCC7002 in the nitrite-transport-less mutant (NA4) of the freshwater cyanobacterium Synechococcus elongatus strain PCC7942. The NitM-mediated nitrite uptake showed an apparent K_m (NO₂⁻) of about 8 μM and was not inhibited by nitrate, cyanate or formate. Of the nitM orthologs from the three oceanic cyanobacterial species, which are classified as α-cyanobacteria on the basis of the occurrence of Type 1a RuBisCO, the one from Synechococcus sp. strain CC9605 conferred nitrite uptake activity on NA4, but those from Synechococcus sp. strain CC9311 and Prochlorococcus marinus strain MIT9313 did not. A strongly conserved hydrophilic amino acid sequence was found at the C-termini of the deduced NitM sequences from α-cyanobacteria, with a notable exception of the Synechococcus sp. strain CC9605 NitM protein, which entirely lacked the C-terminal amino acids. The C-terminal sequence was not conserved in the NitM proteins from β-cyanobacteria carrying the Type 1b RuBisCO, including the one from Synechococcus sp. strain PCC7002. Expression of the truncated nitM genes from Synechococcus sp. strain CC9311 and Prochlorococcus marinus strain MIT9313, encoding the proteins lacking the conserved C-terminal region, conferred nitrite uptake activity on the NA4 mutant, indicating that the C-terminal region of α-cyanobacterial NitM proteins inhibits the activity of the transporter. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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12 pages, 455 KiB

Open AccessConcept Paper

Protocells: At the Interface of Life and Non-Life

by Wentao Ma^* and Yu Feng

College of Life Sciences, Wuhan University, Wuhan 430072, China

Life 2015, 5(1), 447-458; https://doi.org/10.3390/life5010447 - 9 Feb 2015

Cited by 8 | Viewed by 8225

Abstract

The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one “correct” structure to perform one special function (e.g., an enzyme), and thus [...] Read more.

The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one “correct” structure to perform one special function (e.g., an enzyme), and thus molecular cooperation is inevitable. While this is particularly true for advanced life with complex functions, it should have already been true for life at its outset with only limited functions, which entailed some sort of primitive cellular form—“protocells”. At the very beginning, the protocells may have even been unable to intervene in the growth of their own membrane, which can be called “pseudo-protocells”. Then, the ability to synthesize membrane components (amphiphiles) may have emerged under selective pressure, leading to “true-protocells”. The emergence of a “chromosome” (with genes linked together)—thus avoiding “gene-loss” during the protocell division, was another key event in the evolution of protocells. Such “unitary-protocells”, containing a central genetic molecule, may have appeared as a milestone—in principle, since then life could evolve endlessly, “gaining” more and more functions by introducing new genes. To synthesize in laboratory these different types of protocells, which stand at the interface between life and non-life, would greatly enhance our understanding on the essence of life. Full article

(This article belongs to the Special Issue Protocells - Designs for Life)

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8 pages, 768 KiB

Open AccessShort Note

Does DNA Exert an Active Role in Generating Cell-Sized Spheres in an Aqueous Solution with a Crowding Binary Polymer?

by Kanta Tsumoto¹, Masafumi Arai², Naoki Nakatani², Shun N. Watanabe² and Kenichi Yoshikawa^2,*

¹ Graduate School of Engineering, Mie University, Mie, 514-8507, Japan

² Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan

Life 2015, 5(1), 459-466; https://doi.org/10.3390/life5010459 - 9 Feb 2015

Cited by 25 | Viewed by 8587

Abstract

We report the spontaneous generation of a cell-like morphology in an environment crowded with the polymers dextran and polyethylene glycol (PEG) in the presence of DNA. DNA molecules were selectively located in the interior of dextran-rich micro-droplets, when the composition of an aqueous [...] Read more.

We report the spontaneous generation of a cell-like morphology in an environment crowded with the polymers dextran and polyethylene glycol (PEG) in the presence of DNA. DNA molecules were selectively located in the interior of dextran-rich micro-droplets, when the composition of an aqueous two-phase system (ATPS) was near the critical condition of phase-segregation. The resulting micro-droplets could be controlled by the use of optical tweezers. As an example of laser manipulation, the dynamic fusion of two droplets is reported, which resembles the process of cell division in time-reverse. A hypothetical scenario for the emergence of a primitive cell with DNA is briefly discussed. Full article

(This article belongs to the Special Issue Protocells - Designs for Life)

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39 pages, 1413 KiB

Open AccessHypothesis

The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

by Brian R. Francis

Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA

Life 2015, 5(1), 467-505; https://doi.org/10.3390/life5010467 - 11 Feb 2015

Cited by 16 | Viewed by 9523

Abstract

Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin [...] Read more.

Although analysis of the genetic code has allowed explanations for its evolution to be proposed, little evidence exists in biochemistry and molecular biology to offer an explanation for the origin of the genetic code. In particular, two features of biology make the origin of the genetic code difficult to understand. First, nucleic acids are highly complicated polymers requiring numerous enzymes for biosynthesis. Secondly, proteins have a simple backbone with a set of 20 different amino acid side chains synthesized by a highly complicated ribosomal process in which mRNA sequences are read in triplets. Apparently, both nucleic acid and protein syntheses have extensive evolutionary histories. Supporting these processes is a complex metabolism and at the hub of metabolism are the carboxylic acid cycles. This paper advances the hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles. In the β-linked polyester, the side chains are carboxylic acid groups capable of forming interstrand double hydrogen bonds. Evolution of the nucleic acids involved changes to the backbone and side chain of poly(β-d-malic acid). Conversion of the side chain carboxylic acid into a carboxamide or a longer side chain bearing a carboxamide group, allowed information polymers to form amide pairs between polyester chains. Aminoacylation of the hydroxyl groups of malic acid and its derivatives with simple amino acids such as glycine and alanine allowed coupling of polyester synthesis and protein synthesis. Use of polypeptides containing glycine and l-alanine for activation of two different monomers with either glycine or l-alanine allowed simple coded autocatalytic synthesis of polyesters and polypeptides and established the first genetic code. A primitive cell capable of supporting electron transport, thioester synthesis, reduction reactions, and synthesis of polyesters and polypeptides is proposed. The cell consists of an iron-sulfide particle enclosed by tholin, a heterogeneous organic material that is produced by Miller-Urey type experiments that simulate conditions on the early Earth. As the synthesis of nucleic acids evolved from β-linked polyesters, the singlet coding system for replication evolved into a four nucleotide/four amino acid process (AMP = aspartic acid, GMP = glycine, UMP = valine, CMP = alanine) and then into the triplet ribosomal process that permitted multiple copies of protein to be synthesized independent of replication. This hypothesis reconciles the “genetics first” and “metabolism first” approaches to the origin of life and explains why there are four bases in the genetic alphabet. Full article

(This article belongs to the Section Origin of Life)

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15 pages, 658 KiB

Open AccessArticle

pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements

by Xiaoyu Xiang^†, Xiaoxing Huang^†, Haina Wang^† and Li Huang^*

¹ State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China

^† These authors contributed equally to this work.

Life 2015, 5(1), 506-520; https://doi.org/10.3390/life5010506 - 12 Feb 2015

Cited by 3 | Viewed by 6659

Abstract

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 [...] Read more.

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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17 pages, 829 KiB

Open AccessReview

The Adaptive Immune System of Haloferax volcanii

by Lisa-Katharina Maier¹, Mike Dyall-Smith² and Anita Marchfelder^1,*

¹ Department of Biology II, Ulm University, 89069 Ulm, Germany

² School of Biomedical Sciences, Charles Sturt University, 2650 NSW, Australia

Life 2015, 5(1), 521-537; https://doi.org/10.3390/life5010521 - 16 Feb 2015

Cited by 25 | Viewed by 9643

Abstract

To fight off invading genetic elements, prokaryotes have developed an elaborate defence system that is both adaptable and heritable—the CRISPR-Cas system (CRISPR is short for: clustered regularly interspaced short palindromic repeats and Cas: CRISPR associated). Comprised of proteins and multiple small RNAs, this [...] Read more.

To fight off invading genetic elements, prokaryotes have developed an elaborate defence system that is both adaptable and heritable—the CRISPR-Cas system (CRISPR is short for: clustered regularly interspaced short palindromic repeats and Cas: CRISPR associated). Comprised of proteins and multiple small RNAs, this prokaryotic defence system is present in 90% of archaeal and 40% of bacterial species, and enables foreign intruders to be eliminated in a sequence-specific manner. There are three major types (I–III) and at least 14 subtypes of this system, with only some of the subtypes having been analysed in detail, and many aspects of the defence reaction remaining to be elucidated. Few archaeal examples have so far been analysed. Here we summarize the characteristics of the CRISPR-Cas system of Haloferax volcanii, an extremely halophilic archaeon originally isolated from the Dead Sea. It carries a single CRISPR-Cas system of type I-B, with a Cascade like complex composed of Cas proteins Cas5, Cas6b and Cas7. Cas6b is essential for CRISPR RNA (crRNA) maturation but is otherwise not required for the defence reaction. A systematic search revealed that six protospacer adjacent motif (PAM) sequences are recognised by the Haloferax defence system. For successful invader recognition, a non-contiguous seed sequence of 10 base-pairs between the crRNA and the invader is required. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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16 pages, 961 KiB

Open AccessReview

A Prokaryotic Twist on Argonaute Function

by Sarah Willkomm¹, Adrian Zander², Alexander Gust² and Dina Grohmann^2,*

¹ Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, University of Lübeck, 23538 Lübeck, Germany

² Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106 Braunschweig, Germany

Life 2015, 5(1), 538-553; https://doi.org/10.3390/life5010538 - 16 Feb 2015

Cited by 29 | Viewed by 11945

Abstract

Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic [...] Read more.

Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive. This review discusses new findings in the field that shed light on the structure and function of Argonaute. We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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14 pages, 921 KiB

Open AccessCommunication

Modes of Fatty Acid Desaturation in Cyanobacteria: An Update

by Dmitry A. Los^*

and Kirill S. Mironov

Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street, Moscow 127276, Russia

Life 2015, 5(1), 554-567; https://doi.org/10.3390/life5010554 - 16 Feb 2015

Cited by 77 | Viewed by 9566

Abstract

Fatty acid composition of individual species of cyanobacteria is conserved and it may be used as a phylogenetic marker. The previously proposed classification system was based solely on biochemical data. Today, new genomic data are available, which support a need to update a [...] Read more.

Fatty acid composition of individual species of cyanobacteria is conserved and it may be used as a phylogenetic marker. The previously proposed classification system was based solely on biochemical data. Today, new genomic data are available, which support a need to update a previously postulated FA-based classification of cyanobacteria. These changes are necessary in order to adjust and synchronize biochemical, physiological and genomic data, which may help to establish an adequate comprehensive taxonomic system for cyanobacteria in the future. Here, we propose an update to the classification system of cyanobacteria based on their fatty acid composition. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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19 pages, 1163 KiB

Open AccessReview

Volcanogenic Fluvial-Lacustrine Environments in Iceland and Their Utility for Identifying Past Habitability on Mars

by Claire Cousins

UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK

Life 2015, 5(1), 568-586; https://doi.org/10.3390/life5010568 - 16 Feb 2015

Cited by 19 | Viewed by 9423

Abstract

The search for once-habitable locations on Mars is increasingly focused on environments dominated by fluvial and lacustrine processes, such as those investigated by the Mars Science Laboratory Curiosity rover. The availability of liquid water coupled with the potential longevity of such systems renders [...] Read more.

The search for once-habitable locations on Mars is increasingly focused on environments dominated by fluvial and lacustrine processes, such as those investigated by the Mars Science Laboratory Curiosity rover. The availability of liquid water coupled with the potential longevity of such systems renders these localities prime targets for the future exploration of Martian biosignatures. Fluvial-lacustrine environments associated with basaltic volcanism are highly relevant to Mars, but their terrestrial counterparts have been largely overlooked as a field analogue. Such environments are common in Iceland, where basaltic volcanism interacts with glacial ice and surface snow to produce large volumes of meltwater within an otherwise cold and dry environment. This meltwater can be stored to create subglacial, englacial, and proglacial lakes, or be released as catastrophic floods and proglacial fluvial systems. Sedimentary deposits produced by the resulting fluvial-lacustrine activity are extensive, with lithologies dominated by basaltic minerals, low-temperature alteration assemblages (e.g., smectite clays, calcite), and amorphous, poorly crystalline phases (basaltic glass, palagonite, nanophase iron oxides). This paper reviews examples of these environments, including their sedimentary deposits and microbiology, within the context of utilising these localities for future Mars analogue studies and instrument testing. Full article

(This article belongs to the Special Issue Planetary Exploration: Habitats and Terrestrial Analogs)

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17 pages, 391 KiB

Open AccessArticle

Regulation of Genes Involved in Heterocyst Differentiation in the Cyanobacterium Anabaena sp. Strain PCC 7120 by a Group 2 Sigma Factor SigC

by Shigeki Ehira^1,2,* and Shogo Miyazaki¹

¹ Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan

² Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan

Life 2015, 5(1), 587-603; https://doi.org/10.3390/life5010587 - 16 Feb 2015

Cited by 18 | Viewed by 7681

Abstract

The filamentous cyanobacterium Anabaena sp. strain PCC 7120 differentiates specialized cells for nitrogen fixation called heterocysts upon limitation of combined nitrogen in the medium. During heterocyst differentiation, expression of approximately 500 genes is upregulated with spatiotemporal regulation. In the present study, we investigated [...] Read more.

The filamentous cyanobacterium Anabaena sp. strain PCC 7120 differentiates specialized cells for nitrogen fixation called heterocysts upon limitation of combined nitrogen in the medium. During heterocyst differentiation, expression of approximately 500 genes is upregulated with spatiotemporal regulation. In the present study, we investigated the functions of sigma factors of RNA polymerase in the regulation of heterocyst differentiation. The transcript levels of sigC, sigE, and sigG were increased during heterocyst differentiation, while expression of sigJ was downregulated. We carried out DNA microarray analysis to identify genes regulated by SigC, SigE, and SigG. It was indicated that SigC regulated the expression of genes involved in heterocyst differentiation and functions. Moreover, genes regulated by SigC partially overlapped with those regulated by SigE, and deficiency of SigC was likely to be compensated by SigE. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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33 pages, 3684 KiB

Open AccessReview

The Origin and Evolution of Ribonucleotide Reduction

by Daniel Lundin^1,*, Gustav Berggren^1,†, Derek T. Logan² and Britt-Marie Sjöberg¹

¹ Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden

² Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden

^† Current address: Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden

Life 2015, 5(1), 604-636; https://doi.org/10.3390/life5010604 - 27 Feb 2015

Cited by 64 | Viewed by 13655

Abstract

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a [...] Read more.

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B₁₂-dependent mechanism in modern class II RNRs. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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14 pages, 837 KiB

Open AccessReview

Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

by Hideo Hashizume

National Institute for Materials Science, Tsukuba 305-0044, Japan

Life 2015, 5(1), 637-650; https://doi.org/10.3390/life5010637 - 27 Feb 2015

Cited by 35 | Viewed by 9247

Abstract

Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role [...] Read more.

Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the “RNA world”. The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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25 pages, 6411 KiB

Open AccessReview

From Vesicles to Protocells: The Roles of Amphiphilic Molecules

by Yuka Sakuma and Masayuki Imai^*

Department of Physics, Tohoku University, Aoba, Sendai 980-8578, Japan

Life 2015, 5(1), 651-675; https://doi.org/10.3390/life5010651 - 2 Mar 2015

Cited by 51 | Viewed by 13590

Abstract

It is very challenging to construct protocells from molecular assemblies. An important step in this challenge is the achievement of vesicle dynamics that are relevant to cellular functions, such as membrane trafficking and self-reproduction, using amphiphilic molecules. Soft matter physics will play an [...] Read more.

It is very challenging to construct protocells from molecular assemblies. An important step in this challenge is the achievement of vesicle dynamics that are relevant to cellular functions, such as membrane trafficking and self-reproduction, using amphiphilic molecules. Soft matter physics will play an important role in the development of vesicles that have these functions. Here, we show that simple binary phospholipid vesicles have the potential to reproduce the relevant functions of adhesion, pore formation and self-reproduction of vesicles, by coupling the lipid geometries (spontaneous curvatures) and the phase separation. This achievement will elucidate the pathway from molecular assembly to cellular life. Full article

(This article belongs to the Special Issue Protocells - Designs for Life)

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24 pages, 4166 KiB

Open AccessArticle

Mechanisms of High Temperature Resistance of Synechocystis sp. PCC 6803: An Impact of Histidine Kinase 34

by Jan Červený^1,†, Maria A. Sinetova^2,*,†, Tomáš Zavřel¹ and Dmitry A. Los²

¹ Department of Adaptation Biotechnologies, Global Change Research Centre, Academy of Sciences of the Czech Republic, Drásov 470, CZ-66424 Drásov, Czech Republic

² Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia

^† These authors contributed equally to this work.

Life 2015, 5(1), 676-699; https://doi.org/10.3390/life5010676 - 2 Mar 2015

Cited by 37 | Viewed by 10896

Abstract

Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying responses and acclimation to different abiotic stresses. Changes in transcriptome, proteome, lipidome, and photosynthesis in response to short term heat stress are well studied in this organism, and histidine kinase 34 [...] Read more.

Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying responses and acclimation to different abiotic stresses. Changes in transcriptome, proteome, lipidome, and photosynthesis in response to short term heat stress are well studied in this organism, and histidine kinase 34 (Hik34) is shown to play an important role in mediating such response. Corresponding data on long term responses, however, are fragmentary and vary depending on parameters of experiments and methods of data collection, and thus are hard to compare. In order to elucidate how the early stress responses help cells to sustain long-term heat stress, as well as the role of Hik34 in prolonged acclimation, we examined the resistance to long-term heat stress of wild-type and ΔHik34 mutant of Synechocystis. In this work, we were able to precisely control the long term experimental conditions by cultivating Synechocystis in automated photobioreactors, measuring selected physiological parameters within a time range of minutes. In addition, morphological and ultrastructural changes in cells were analyzed and western blotting of individual proteins was used to study the heat stress-affected protein expression. We have shown that the majority of wild type cell population was able to recover after 24 h of cultivation at 44 °C. In contrast, while ΔHik34 mutant cells were resistant to heat stress within its first hours, they could not recover after 24 h long high temperature treatment. We demonstrated that the early induction of HspA expression and maintenance of high amount of other HSPs throughout the heat incubation is critical for successful adaptation to long-term stress. In addition, it appears that histidine kinase Hik34 is an essential component for the long term high temperature resistance. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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16 pages, 1467 KiB

Open AccessReview

Appendages of the Cyanobacterial Cell

by Nils Schuergers and Annegret Wilde^*

University of Freiburg, Institute of Biology III, Schänzlestr. 1, 79104 Freiburg, Germany

Life 2015, 5(1), 700-715; https://doi.org/10.3390/life5010700 - 4 Mar 2015

Cited by 59 | Viewed by 9844

Abstract

Extracellular non-flagellar appendages, called pili or fimbriae, are widespread in gram-negative bacteria. They are involved in many different functions, including motility, adhesion, biofilm formation, and uptake of DNA. Sequencing data for a large number of cyanobacterial genomes revealed that most of them contain [...] Read more.

Extracellular non-flagellar appendages, called pili or fimbriae, are widespread in gram-negative bacteria. They are involved in many different functions, including motility, adhesion, biofilm formation, and uptake of DNA. Sequencing data for a large number of cyanobacterial genomes revealed that most of them contain genes for pili synthesis. However, only for a very few cyanobacteria structure and function of these appendages have been analyzed. Here, we review the structure and function of type IV pili in Synechocystis sp. PCC 6803 and analyze the distribution of type IV pili associated genes in other cyanobacteria. Further, we discuss the role of the RNA-chaperone Hfq in pilus function and the presence of genes for the chaperone-usher pathway of pilus assembly in cyanobacteria. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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28 pages, 1623 KiB

Open AccessReview

Cyanobacterial Oxygenic Photosynthesis is Protected by Flavodiiron Proteins

by Yagut Allahverdiyeva, Janne Isojärvi, Pengpeng Zhang^† and Eva-Mari Aro^*

¹ Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland

^† Current position: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Life 2015, 5(1), 716-743; https://doi.org/10.3390/life5010716 - 9 Mar 2015

Cited by 133 | Viewed by 12340

Abstract

Flavodiiron proteins (FDPs, also called flavoproteins, Flvs) are modular enzymes widely present in Bacteria and Archaea. The evolution of cyanobacteria and oxygenic photosynthesis occurred in concert with the modulation of typical bacterial FDPs. Present cyanobacterial FDPs are composed of three domains, the β-lactamase-like, [...] Read more.

Flavodiiron proteins (FDPs, also called flavoproteins, Flvs) are modular enzymes widely present in Bacteria and Archaea. The evolution of cyanobacteria and oxygenic photosynthesis occurred in concert with the modulation of typical bacterial FDPs. Present cyanobacterial FDPs are composed of three domains, the β-lactamase-like, flavodoxin-like and flavin-reductase like domains. Cyanobacterial FDPs function as hetero- and homodimers and are involved in the regulation of photosynthetic electron transport. Whilst Flv2 and Flv4 proteins are limited to specific cyanobacterial species (β-cyanobacteria) and function in photoprotection of Photosystem II, Flv1 and Flv3 proteins, functioning in the “Mehler-like” reaction and safeguarding Photosystem I under fluctuating light conditions, occur in nearly all cyanobacteria and additionally in green algae, mosses and lycophytes. Filamentous cyanobacteria have additional FDPs in heterocyst cells, ensuring a microaerobic environment for the function of the nitrogenase enzyme under the light. Here, the evolution, occurrence and functional mechanisms of various FDPs in oxygenic photosynthetic organisms are discussed. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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26 pages, 2114 KiB

Open AccessArticle

CaCO₃ Precipitation in Multilayered Cyanobacterial Mats: Clues to Explain the Alternation of Micrite and Sparite Layers in Calcareous Stromatolites

by Józef Kaźmierczak^1,*, Tom Fenchel², Michael Kühl², Stephan Kempe³, Barbara Kremer¹, Bożena Łącka⁴ and Krzysztof Małkowski¹

¹ Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland

² Marine Biological Laboratory, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark

³ Institute of Applied Geosciences, Technische Universität Darmstadt, Schnittspahnstr. 9, 64287 Darmstadt, Germany

⁴ Institute of Geological Sciences, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland

Life 2015, 5(1), 744-769; https://doi.org/10.3390/life5010744 - 9 Mar 2015

Cited by 57 | Viewed by 12115

Abstract

Marine cyanobacterial mats were cultured on coastal sediments (Nivå Bay, Øresund, Denmark) for over three years in a closed system. Carbonate particles formed in two different modes in the mat: (i) through precipitation of submicrometer-sized grains of Mg calcite within the mucilage near [...] Read more.

Marine cyanobacterial mats were cultured on coastal sediments (Nivå Bay, Øresund, Denmark) for over three years in a closed system. Carbonate particles formed in two different modes in the mat: (i) through precipitation of submicrometer-sized grains of Mg calcite within the mucilage near the base of living cyanobacterial layers, and (ii) through precipitation of a variety of mixed Mg calcite/aragonite morphs in layers of degraded cyanobacteria dominated by purple sulfur bacteria. The d¹³C values were about 2‰ heavier in carbonates from the living cyanobacterial zones as compared to those generated in the purple bacterial zones. Saturation indices calculated with respect to calcite, aragonite, and dolomite inside the mats showed extremely high values across the mat profile. Such high values were caused by high pH and high carbonate alkalinity generated within the mats in conjunction with increased concentrations of calcium and magnesium that were presumably stored in sheaths and extracellular polymer substances (EPS) of the living cyanobacteria and liberated during their post-mortem degradation. The generated CaCO₃ morphs were highly similar to morphs reported from heterotrophic bacterial cultures, and from bacterially decomposed cyanobacterial biomass emplaced in Ca-rich media. They are also similar to CaCO₃ morphs precipitated from purely inorganic solutions. No metabolically (enzymatically) controlled formation of particular CaCO3 morphs by heterotrophic bacteria was observed in the studied mats. The apparent alternation of in vivo and post-mortem generated calcareous layers in the studied cyanobacterial mats may explain the alternation of fine-grained (micritic) and coarse-grained (sparitic) laminae observed in modern and fossil calcareous cyanobacterial microbialites as the result of a probably similar multilayered mat organization. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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13 pages, 668 KiB

Open AccessCommunication

Haloferax volcanii, as a Novel Tool for Producing Mammalian Olfactory Receptors Embedded in Archaeal Lipid Bilayer

by Simona Lobasso¹, Rita Vitale¹, Patrizia Lopalco¹ and Angela Corcelli^1,2,*

¹ Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, I-70124 Bari, Italy

² Institute for Chemical-Physical Processes, National Research Council (IPCF-CNR), Bari Unit, via Orabona 4, I-70126 Bari, Italy

Life 2015, 5(1), 770-782; https://doi.org/10.3390/life5010770 - 9 Mar 2015

Cited by 6 | Viewed by 6254

Abstract

The aim of this study was to explore the possibility of using an archaeal microorganism as a host system for expressing mammalian olfactory receptors (ORs). We have selected the archaeon Haloferax volcanii as a cell host system and one of the most extensively [...] Read more.

The aim of this study was to explore the possibility of using an archaeal microorganism as a host system for expressing mammalian olfactory receptors (ORs). We have selected the archaeon Haloferax volcanii as a cell host system and one of the most extensively investigated OR, namely I7-OR, whose preferred ligands are short-chain aldehydes, such as octanal, heptanal, nonanal. A novel plasmid has been constructed to express the rat I7-OR, fused with a hexahistidine-tag for protein immunodetection. The presence of the recombinant receptor at a membrane level was demonstrated by immunoblot of the membranes isolated from the transgenic archaeal strain. In addition, the lipid composition of archaeonanosomes containing ORs has been characterized in detail by High-Performance Thin-Layer Chromatography (HPTLC) in combination with Matrix-Assisted Laser Desorption Ionization—Time-Of-Flight/Mass Spectrometry (MALDI-TOF/MS) analysis. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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35 pages, 1491 KiB

Open AccessReview

CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity

by Roger A. Garrett^1,*, Shiraz A. Shah¹, Susanne Erdmann², Guannan Liu¹, Marzieh Mousaei¹, Carlos León-Sobrino¹, Wenfang Peng¹, Soley Gudbergsdottir¹, Ling Deng¹, Gisle Vestergaard³, Xu Peng¹ and Qunxin She¹

¹ Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark

² School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney NSW, Australia

³ Helmholtz Zentrum München, Research Unit Environmental Genomics, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany

Life 2015, 5(1), 783-817; https://doi.org/10.3390/life5010783 - 10 Mar 2015

Cited by 43 | Viewed by 9402

Abstract

The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional [...] Read more.

The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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23 pages, 1297 KiB

Open AccessArticle

Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales

by Kira S. Makarova^*, Yuri I. Wolf

and Eugene V. Koonin

National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA

Life 2015, 5(1), 818-840; https://doi.org/10.3390/life5010818 - 10 Mar 2015

Cited by 191 | Viewed by 14156

Abstract

With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection [...] Read more.

With the continuously accelerating genome sequencing from diverse groups of archaea and bacteria, accurate identification of gene orthology and availability of readily expandable clusters of orthologous genes are essential for the functional annotation of new genomes. We report an update of the collection of archaeal Clusters of Orthologous Genes (arCOGs) to cover, on average, 91% of the protein-coding genes in 168 archaeal genomes. The new arCOGs were constructed using refined algorithms for orthology identification combined with extensive manual curation, including incorporation of the results of several completed and ongoing research projects in archaeal genomics. A new level of classification is introduced, superclusters that untie two or more arCOGs and more completely reflect gene family evolution than individual, disconnected arCOGs. Assessment of the current archaeal genome annotation in public databases indicates that consistent use of arCOGs can significantly improve the annotation quality. In addition to their utility for genome annotation, arCOGs also are a platform for phylogenomic analysis. We explore this aspect of arCOGs by performing a phylogenomic study of the Thermococci that are traditionally viewed as the basal branch of the Euryarchaeota. The results of phylogenomic analysis that involved both comparison of multiple phylogenetic trees and a search for putative derived shared characters by using phyletic patterns extracted from the arCOGs reveal a likely evolutionary relationship between the Thermococci, Methanococci, and Methanobacteria. The arCOGs are expected to be instrumental for a comprehensive phylogenomic study of the archaea. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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20 pages, 1406 KiB

Open AccessArticle

A Comparative Study of Iron Uptake Rates and Mechanisms amongst Marine and Fresh Water Cyanobacteria: Prevalence of Reductive Iron Uptake

by Hagar Lis^1,2,*, Chana Kranzler^1,3, Nir Keren³ and Yeala Shaked^1,2

¹ Interuniversity Institute for Marine Sciences in Eilat, Israel

² The Freddy and Nadine Herrmann Institute of Earth Sciences, Edmond J. Safra Campus, Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel

³ Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel

Life 2015, 5(1), 841-860; https://doi.org/10.3390/life5010841 - 11 Mar 2015

Cited by 61 | Viewed by 8955

Abstract

In this contribution, we address the question of iron bioavailability to cyanobacteria by measuring Fe uptake rates and probing for a reductive uptake pathway in diverse cyanobacterial species. We examined three Fe-substrates: dissolved inorganic iron (Fe') and the Fe-siderophores Ferrioxamine B (FOB) and [...] Read more.

In this contribution, we address the question of iron bioavailability to cyanobacteria by measuring Fe uptake rates and probing for a reductive uptake pathway in diverse cyanobacterial species. We examined three Fe-substrates: dissolved inorganic iron (Fe') and the Fe-siderophores Ferrioxamine B (FOB) and FeAerobactin (FeAB). In order to compare across substrates and strains, we extracted uptake rate constants (k_in = uptake rate/[Fe-substrate]). Fe' was the most bioavailable Fe form to cyanobacteria, with k_in values higher than those of other substrates. When accounting for surface area (SA), all strains acquired Fe' at similar rates, as their k_in/SA were similar. We also observed homogeneity in the uptake of FOB among strains, but with 10,000 times lower k_in/SA values than Fe'. Uniformity in k_in/SA suggests similarity in the mechanism of uptake and indeed, all strains were found to employ a reductive step in the uptake of Fe' and FOB. In contrast, different uptake pathways were found for FeAB along with variations in k_in/SA. Our data supports the existence of a common reductive Fe uptake pathway amongst cyanobacteria, functioning alone or in addition to siderophore-mediated uptake. Cyanobacteria combining both uptake strategies benefit from increased flexibility in accessing different Fe-substrates. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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11 pages, 515 KiB

Open AccessCommunication

The Role of Active Site Residues in ATP Binding and Catalysis in the Methanosarcina thermophila Acetate Kinase

by Cheryl Ingram-Smith^*, Jeffrey Wharton, Christian Reinholz^†, Tara Doucet^†, Rachel Hesler^† and Kerry Smith^*

¹ Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA

^† These authors contributed equally to this work.

Life 2015, 5(1), 861-871; https://doi.org/10.3390/life5010861 - 12 Mar 2015

Cited by 3 | Viewed by 6779

Abstract

Acetate kinase (ACK), which catalyzes the reversible phosphorylation of acetate by ATP, is a member of the acetate and sugar kinase/heat shock cognate/actin (ASKHA) superfamily. ASKHA family members share a common core fold that includes an ATPase domain with five structural motifs. The [...] Read more.

Acetate kinase (ACK), which catalyzes the reversible phosphorylation of acetate by ATP, is a member of the acetate and sugar kinase/heat shock cognate/actin (ASKHA) superfamily. ASKHA family members share a common core fold that includes an ATPase domain with five structural motifs. The PHOSPHATE1 motif has previously been shown to be important for catalysis. We have investigated the role of two of these motifs in the Methanosarcina thermophila ACK (MtACK) and have shown that residues projecting into the ACK active site from the PHOSPHATE2 and ADENOSINE loops and a third highly conserved loop designated here as LOOP3 play key roles in nucleotide triphosphate (NTP) selection and utilization. Alteration of Asn211 of PHOSPHATE2, Gly239 of LOOP3, and Gly331 of ADENOSINE greatly reduced catalysis. In particular, Gly331, which is highly conserved throughout the ASKHA superfamily, has the greatest effect on substrate selection. Alteration at this site strongly skewed MtACK toward utilization of purines over pyrimidines, unlike the wild type enzyme that shows broad NTP utilization. Further investigation into differences between the ATPase domain in MtACK and other acetate kinases that show different substrate preferences will provide us with a better understanding of the diversity of phosphoryl donor selection in this enzyme family. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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16 pages, 1643 KiB

Open AccessArticle

Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life

by Bruce Damer^1,2,*

and David Deamer¹

¹ Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA

² DigitalSpace Research, Boulder Creek, CA 95006, USA

Life 2015, 5(1), 872-887; https://doi.org/10.3390/life5010872 - 13 Mar 2015

Cited by 221 | Viewed by 24448

Abstract

Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial [...] Read more.

Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an “experiment” in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life. Full article

(This article belongs to the Special Issue Protocells - Designs for Life)

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17 pages, 914 KiB

Open AccessArticle

Nitrogen Starvation Acclimation in Synechococcus elongatus: Redox-Control and the Role of Nitrate Reduction as an Electron Sink

by Alexander Klotz^1,†, Edgar Reinhold^1,†, Sofía Doello^1,2 and Karl Forchhammer^1,*

¹ Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany

² Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, 96822 HI, USA

^† These authors contributed equally to this work.

Life 2015, 5(1), 888-904; https://doi.org/10.3390/life5010888 - 13 Mar 2015

Cited by 32 | Viewed by 8727

Abstract

Nitrogen starvation acclimation in non-diazotrophic cyanobacteria is characterized by a process termed chlorosis, where the light harvesting pigments are degraded and the cells gradually tune down photosynthetic and metabolic activities. The chlorosis response is governed by a complex and poorly understood regulatory network, [...] Read more.

Nitrogen starvation acclimation in non-diazotrophic cyanobacteria is characterized by a process termed chlorosis, where the light harvesting pigments are degraded and the cells gradually tune down photosynthetic and metabolic activities. The chlorosis response is governed by a complex and poorly understood regulatory network, which converges at the expression of the nblA gene, the triggering factor for phycobiliprotein degradation. This study established a method that allows uncoupling metabolic and redox-signals involved in nitrogen-starvation acclimation. Inhibition of glutamine synthetase (GS) by a precise dosage of l-methionine-sulfoximine (MSX) mimics the metabolic situation of nitrogen starvation. Addition of nitrate to such MSX-inhibited cells eliminates the associated redox-stress by enabling electron flow towards nitrate/nitrite reduction and thereby, prevents the induction of nblA expression and the associated chlorosis response. This study demonstrates that nitrogen starvation is perceived not only through metabolic signals, but requires a redox signal indicating over-reduction of PSI-reduced electron acceptors. It further establishes a cryptic role of nitrate/nitrite reductases as electron sinks to balance conditions of over-reduction. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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16 pages, 4257 KiB

Open AccessArticle

The Expansion of Animal MicroRNA Families Revisited

by Jana Hertel¹ and Peter F. Stadler^{1,2,3,4,5,6,7,*}

¹ Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16–18, D-04107 Leipzig, Germany

² German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103 Leipzig, Germany

³ Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany

⁴ Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany

⁵ Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria

⁶ Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark

⁷ Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA

Life 2015, 5(1), 905-920; https://doi.org/10.3390/life5010905 - 13 Mar 2015

Cited by 45 | Viewed by 8755

Abstract

MicroRNAs are important regulatory small RNAs in many eukaryotes. Due to their small size and simple structure, they are readily innovated de novo. Throughout the evolution of animals, the emergence of novel microRNA families traces key morphological innovations. Here, we use a computational [...] Read more.

MicroRNAs are important regulatory small RNAs in many eukaryotes. Due to their small size and simple structure, they are readily innovated de novo. Throughout the evolution of animals, the emergence of novel microRNA families traces key morphological innovations. Here, we use a computational approach based on homology search and parsimony-based presence/absence analysis to draw a comprehensive picture of microRNA evolution in 159 animal species. We confirm previous observations regarding bursts of innovations accompanying the three rounds of genome duplications in vertebrate evolution and in the early evolution of placental mammals. With a much better resolution for the invertebrate lineage compared to large-scale studies, we observe additional bursts of innovation, e.g., in Rhabditoidea. More importantly, we see clear evidence that loss of microRNA families is not an uncommon phenomenon. The Enoplea may serve as a second dramatic example beyond the tunicates. The large-scale analysis presented here also highlights several generic technical issues in the analysis of very large gene families that will require further research. Full article

(This article belongs to the Section Origin of Life)

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28 pages, 2730 KiB

Open AccessArticle

Highly Iterated Palindromic Sequences (HIPs) and Their Relationship to DNA Methyltransferases

by Jeff Elhai

Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA

Life 2015, 5(1), 921-948; https://doi.org/10.3390/life5010921 - 17 Mar 2015

Cited by 17 | Viewed by 8321

Abstract

The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency in cyanobacterial genomes. An important clue to its function may be the presence of two orphan DNA methyltransferases that recognize internal sequences GATC and CGATCG. An examination of genomes from [...] Read more.

The sequence GCGATCGC (Highly Iterated Palindrome, HIP1) is commonly found in high frequency in cyanobacterial genomes. An important clue to its function may be the presence of two orphan DNA methyltransferases that recognize internal sequences GATC and CGATCG. An examination of genomes from 97 cyanobacteria, both free-living and obligate symbionts, showed that there are exceptional cases in which HIP1 is at a low frequency or nearly absent. In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs. When HIP1 is at a high frequency, GATC- and CGATCG-specific methyltransferases are generally present in the genome. When an alternate HIP is at high frequency, a methyltransferase specific for that sequence is present. The pattern of 1-nt deviations from HIP1 sequences is biased towards the first and last nucleotides, i.e., those distinguish CGATCG from HIP1. Taken together, the results point to a role of DNA methylation in the creation or functioning of HIP sites. A model is presented that postulates the existence of a G^meC-dependent mismatch repair system whose activity creates and maintains HIP sequences. Full article

(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)

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20 pages, 1019 KiB

Open AccessArticle

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis

by Guanghong Zuo¹, Zhao Xu² and Bailin Hao^1,*

¹ Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China

² Thermo Fisher Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080, USA

Life 2015, 5(1), 949-968; https://doi.org/10.3390/life5010949 - 17 Mar 2015

Cited by 22 | Viewed by 11993

Abstract

A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the [...] Read more.

A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey’s Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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28 pages, 2953 KiB

Open AccessArticle

Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes

by Erica D'Aguanno^1,2,†, Emiliano Altamura^1,3,†, Fabio Mavelli³, Alfred Fahr², Pasquale Stano^1,* and Pier Luigi Luisi^1,*

¹ Science Department, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy

² Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Lessingstraße 8, D-07743 Jena, Germany

³ Chemistry Department, University of Bari, Via E. Orabona 4, I-70125 Bari, Italy

^† These authors contributed equally to this work.

Life 2015, 5(1), 969-996; https://doi.org/10.3390/life5010969 - 18 Mar 2015

Cited by 23 | Viewed by 8592

Abstract

How did primitive living cells originate? The formation of early cells, which were probably solute-filled vesicles capable of performing a rudimentary metabolism (and possibly self-reproduction), is still one of the big unsolved questions in origin of life. We have recently used lipid vesicles [...] Read more.

How did primitive living cells originate? The formation of early cells, which were probably solute-filled vesicles capable of performing a rudimentary metabolism (and possibly self-reproduction), is still one of the big unsolved questions in origin of life. We have recently used lipid vesicles (liposomes) as primitive cell models, aiming at the study of the physical mechanisms for macromolecules encapsulation. We have reported that proteins and ribosomes can be encapsulated very efficiently, against statistical expectations, inside a small number of liposomes. Moreover the transcription-translation mixture, which realistically mimics a sort of minimal metabolic network, can be functionally reconstituted in liposomes owing to a self-concentration mechanism. Here we firstly summarize the recent advancements in this research line, highlighting how these results open a new vista on the phenomena that could have been important for the formation of functional primitive cells. Then, we present new evidences on the non-random entrapment of macromolecules (proteins, dextrans) in phospholipid vesicle, and in particular we show how enzymatic reactions can be accelerated because of the enhancement of their concentration inside liposomes. Full article

(This article belongs to the Special Issue Protocells - Designs for Life)

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Life, Volume 5, Issue 1 (March 2015) – 53 articles , Pages 1-1018

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