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Life, Volume 5, Issue 2 (June 2015) , Pages 1019-1471

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Open AccessReview
Acetate Metabolism in Anaerobes from the Domain Archaea
Life 2015, 5(2), 1454-1471; https://doi.org/10.3390/life5021454
Received: 16 April 2015 / Accepted: 1 June 2015 / Published: 9 June 2015
Cited by 7 | Viewed by 3095 | PDF Full-text (1040 KB) | HTML Full-text | XML Full-text
Abstract
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth’s biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle [...] Read more.
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth’s biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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Open AccessConference Report
The Routes of Emergence of Life from LUCA during the RNA and Viral World: A Conspectus
Life 2015, 5(2), 1445-1453; https://doi.org/10.3390/life5021445
Received: 13 April 2015 / Accepted: 20 May 2015 / Published: 5 June 2015
Cited by 7 | Viewed by 3662 | PDF Full-text (787 KB) | HTML Full-text | XML Full-text
Abstract
How did life emerge on Earth? The aim of the Network of Researchers on Horizontal Gene Transfer and the Last Universal Cellular Ancestor (NoR HGT & LUCA) is to understand how the genetics of LUCAs were reorganised prior to the advent of the [...] Read more.
How did life emerge on Earth? The aim of the Network of Researchers on Horizontal Gene Transfer and the Last Universal Cellular Ancestor (NoR HGT & LUCA) is to understand how the genetics of LUCAs were reorganised prior to the advent of the three domains of life. This paper reports the research of eminent scientists who have come together within the network and are making significant contributions to the wider knowledge base surrounding this, one of science’s remaining mysteries. I also report on their relevance in relation to LUCAs and life’s origins, as well as ask a question: what next? Full article
(This article belongs to the Section Life Sciences)
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Open AccessArticle
A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes
Life 2015, 5(2), 1427-1444; https://doi.org/10.3390/life5021427
Received: 2 April 2015 / Revised: 22 May 2015 / Accepted: 25 May 2015 / Published: 2 June 2015
Cited by 6 | Viewed by 3190 | PDF Full-text (909 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. [...] Read more.
Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis, Haloquadratum walsbyi strains HBSQ001 and C23, Natrialba magadii, Haloarcula marismortui and Har. hispanica, and Halohasta litchfieldiae). Genomes are checked for missing genes, start codon misassignments, and disrupted genes. Assignments of a specific function are preferably based on experimentally characterized homologs (Gold Standard Proteins). To avoid overannotation, which is a major source of database errors, we restrict annotation to only general function assignments when support for a specific substrate assignment is insufficient. This strategy results in annotations that are resistant to the plethora of errors that compromise public databases. Annotation consistency is rigorously validated for ortholog pairs from the genomes surveyed. The annotation is regularly crosschecked against the UniProt database to further improve annotations and increase the level of standardization. Enhanced genome annotations are submitted to public databases (EMBL/GenBank, UniProt), to the benefit of the scientific community. The enhanced annotations are also publically available via HaloLex. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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Open AccessReview
Horizontal Gene Transfer, Dispersal and Haloarchaeal Speciation
Life 2015, 5(2), 1405-1426; https://doi.org/10.3390/life5021405
Received: 7 April 2015 / Revised: 8 May 2015 / Accepted: 11 May 2015 / Published: 19 May 2015
Cited by 5 | Viewed by 2698 | PDF Full-text (465 KB) | HTML Full-text | XML Full-text
Abstract
The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to [...] Read more.
The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
Open AccessArticle
Freshwater Ammonia-Oxidizing Archaea Retain amoA mRNA and 16S rRNA during Ammonia Starvation
Life 2015, 5(2), 1396-1404; https://doi.org/10.3390/life5021396
Received: 18 March 2015 / Revised: 12 May 2015 / Accepted: 12 May 2015 / Published: 19 May 2015
Cited by 5 | Viewed by 1873 | PDF Full-text (722 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to [...] Read more.
In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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Open AccessReview
Altiarchaeales”: Uncultivated Archaea from the Subsurface
Life 2015, 5(2), 1381-1395; https://doi.org/10.3390/life5021381
Received: 30 March 2015 / Revised: 1 May 2015 / Accepted: 5 May 2015 / Published: 12 May 2015
Cited by 8 | Viewed by 2810 | PDF Full-text (4058 KB) | HTML Full-text | XML Full-text
Abstract
Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings [...] Read more.
Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes “Candidatus Altiarchaeum hamiconexum” as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the “hami”) and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth’s crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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Open AccessArticle
Toxic Cyanobacterial Bloom Triggers in Missisquoi Bay, Lake Champlain, as Determined by Next-Generation Sequencing and Quantitative PCR
Life 2015, 5(2), 1346-1380; https://doi.org/10.3390/life5021346
Received: 27 January 2015 / Revised: 4 May 2015 / Accepted: 5 May 2015 / Published: 12 May 2015
Cited by 6 | Viewed by 2238 | PDF Full-text (2493 KB) | HTML Full-text | XML Full-text
Abstract
Missisquoi Bay (MB) is a temperate eutrophic freshwater lake that frequently experiences toxic Microcystis-dominated cyanobacterial blooms. Non-point sources are responsible for the high concentrations of phosphorus and nitrogen in the bay. This study combined data from environmental parameters, E. coli counts, high-throughput [...] Read more.
Missisquoi Bay (MB) is a temperate eutrophic freshwater lake that frequently experiences toxic Microcystis-dominated cyanobacterial blooms. Non-point sources are responsible for the high concentrations of phosphorus and nitrogen in the bay. This study combined data from environmental parameters, E. coli counts, high-throughput sequencing of 16S rRNA gene amplicons, quantitative PCR (16S rRNA and mcyD genes) and toxin analyses to identify the main bloom-promoting factors. In 2009, nutrient concentrations correlated with E. coli counts, abundance of total cyanobacterial cells, Microcystis 16S rRNA and mcyD genes and intracellular microcystin. Total and dissolved phosphorus also correlated significantly with rainfall. The major cyanobacterial taxa were members of the orders Chroococcales and Nostocales. The genus Microcystis was the main mcyD-carrier and main microcystin producer. Our results suggested that increasing nutrient concentrations and total nitrogen:total phosphorus (TN:TP) ratios approaching 11:1, coupled with an increase in temperature, promoted Microcystis-dominated toxic blooms. Although the importance of nutrient ratios and absolute concentrations on cyanobacterial and Microcystis dynamics have been documented in other laboratories, an optimum TN:TP ratio for Microcystis dominance has not been previously observed in situ. This observation provides further support that nutrient ratios are an important determinant of species composition in natural phytoplankton assemblages. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessReview
Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Life 2015, 5(2), 1333-1345; https://doi.org/10.3390/life5021333
Received: 13 March 2015 / Revised: 27 April 2015 / Accepted: 28 April 2015 / Published: 5 May 2015
Cited by 12 | Viewed by 2743 | PDF Full-text (680 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Archaea are well-recognized components of the human microbiome. However, they appear to be drastically underrepresented compared to the high diversity of bacterial taxa which can be found on various human anatomic sites, such as the gastrointestinal environment, the oral cavity and the skin. [...] Read more.
Archaea are well-recognized components of the human microbiome. However, they appear to be drastically underrepresented compared to the high diversity of bacterial taxa which can be found on various human anatomic sites, such as the gastrointestinal environment, the oral cavity and the skin. As our “microbial” view of the human body, including the methodological concepts used to describe them, has been traditionally biased on bacteria, the question arises whether our current knowledge reflects the actual ratio of archaea versus bacteria or whether we have failed so far to unravel the full diversity of human-associated archaea. This review article hypothesizes that distinct archaeal lineages within humans exist, which still await our detection. First, previously unrecognized taxa might be quite common but they have eluded conventional detection methods. Two recent prime examples are described that demonstrate that this might be the case for specific archaeal lineages. Second, some archaeal taxa might be overlooked because they are rare and/or in low abundance. Evidence for this exists for a broad range of phylogenetic lineages, however we currently do not know whether these sporadically appearing organisms are mere transients or important members of the so called “rare biosphere” with probably basic ecosystem functions. Lastly, evidence exists that different human populations harbor different archaeal taxa and/or the abundance and activity of shared archaeal taxa may differ and thus their impact on the overall microbiome. This research line is rather unexplored and warrants further investigation. While not recapitulating exhaustively all studies on archaeal diversity in humans, this review highlights pertinent recent findings that show that the choice of appropriate methodological approaches and the consideration of different human populations may lead to the detection of archaeal lineages previously not associated with humans. This in turn will help understand variations found in the overall microbiomes from different individuals and ultimately may lead to the emergence of novel concepts/mechanisms impacting human health. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
Open AccessArticle
Genetic Code Evolution Reveals the Neutral Emergence of Mutational Robustness, and Information as an Evolutionary Constraint
Life 2015, 5(2), 1301-1332; https://doi.org/10.3390/life5021301
Received: 2 March 2015 / Revised: 2 April 2015 / Accepted: 3 April 2015 / Published: 24 April 2015
Cited by 18 | Viewed by 2391 | PDF Full-text (981 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its [...] Read more.
The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of “neutral emergence”. The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these “pseudaptations”, and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an “unfreezing” of the codon – amino acid mapping that defines the genetic code, consistent with Crick’s Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content between organisms, a selective pressure in the evolution of sexual reproduction, and differences in translational fidelity. Lastly, the utility of the concept of an informational constraint to other diverse fields of research is explored. Full article
(This article belongs to the Section Life Sciences)
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Open AccessArticle
Amino Acid Transporters and Release of Hydrophobic Amino Acids in the Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120
Life 2015, 5(2), 1282-1300; https://doi.org/10.3390/life5021282
Received: 18 March 2015 / Revised: 16 April 2015 / Accepted: 20 April 2015 / Published: 23 April 2015
Cited by 6 | Viewed by 2651 | PDF Full-text (1231 KB) | HTML Full-text | XML Full-text
Abstract
Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can use inorganic compounds such as nitrate or ammonium as nitrogen sources. In the absence of combined nitrogen, it can fix N2 in differentiated cells called heterocysts. Anabaena also shows substantial activities [...] Read more.
Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can use inorganic compounds such as nitrate or ammonium as nitrogen sources. In the absence of combined nitrogen, it can fix N2 in differentiated cells called heterocysts. Anabaena also shows substantial activities of amino acid uptake, and three ABC-type transporters for amino acids have been previously characterized. Seven new loci encoding predicted amino acid transporters were identified in the Anabaena genomic sequence and inactivated. Two of them were involved in amino acid uptake. Locus alr2535-alr2541 encodes the elements of a hydrophobic amino acid ABC-type transporter that is mainly involved in the uptake of glycine. ORF all0342 encodes a putative transporter from the dicarboxylate/amino acid:cation symporter (DAACS) family whose inactivation resulted in an increased uptake of a broad range of amino acids. An assay to study amino acid release from Anabaena filaments to the external medium was set up. Net release of the alanine analogue α-aminoisobutyric acid (AIB) was observed when transport system N-I (a hydrophobic amino acid ABC-type transporter) was engaged in the uptake of a specific substrate. The rate of AIB release was directly proportional to the intracellular AIB concentration, suggesting leakage from the cells by diffusion. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessArticle
The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets
Life 2015, 5(2), 1264-1281; https://doi.org/10.3390/life5021264
Received: 21 January 2015 / Revised: 23 March 2015 / Accepted: 15 April 2015 / Published: 21 April 2015
Cited by 3 | Viewed by 2462 | PDF Full-text (1140 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism. Sm-based regulation is diverse and can range in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in these processes being mediated by [...] Read more.
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism. Sm-based regulation is diverse and can range in scope from eukaryotic mRNA splicing to bacterial quorum sensing, with at least one step in these processes being mediated by an RNA-associated molecular assembly built on Sm proteins. Despite the availability of several 3D-structures of Sm-like archaeal proteins (SmAPs), their function has remained elusive. The aim of this study was to shed light on the function of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso). Using co-purification followed by RNASeq different classes of non-coding RNAs and mRNAs were identified that co-purified either with both paralogues or solely with Sso-SmAP1 or Sso-SmAP2. The large number of associated intron-containing tRNAs and tRNA/rRNA modifying RNAs may suggest a role of the two Sso-SmAPs in tRNA/rRNA processing. Moreover, the 3D structure of Sso-SmAP2 was elucidated. Like Sso-SmAP1, Sso-SmAP2 forms homoheptamers. The binding of both proteins to distinct RNA substrates is discussed in terms of surface conservation, structural differences in the RNA binding sites and differences in the electrostatic surface potential of the two Sso-SmAP proteins. Taken together, this study may hint to common and different functions of both Sso-SmAPs in Sso RNA metabolism. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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Open AccessReview
Current Ideas about Prebiological Compartmentalization
Life 2015, 5(2), 1239-1263; https://doi.org/10.3390/life5021239
Received: 3 March 2015 / Revised: 1 April 2015 / Accepted: 2 April 2015 / Published: 10 April 2015
Cited by 28 | Viewed by 3089 | PDF Full-text (328 KB) | HTML Full-text | XML Full-text
Abstract
Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell’s interior and the environment. Since such compartmentalization is [...] Read more.
Contemporary biological cells are highly sophisticated dynamic compartment systems which separate an internal volume from the external medium through a boundary, which controls, in complex ways, the exchange of matter and energy between the cell’s interior and the environment. Since such compartmentalization is a fundamental principle of all forms of life, scenarios have been elaborated about the emergence of prebiological compartments on early Earth, in particular about their likely structural characteristics and dynamic features. Chemical systems that consist of potentially prebiological compartments and chemical reaction networks have been designed to model pre-cellular systems. These systems are often referred to as “protocells”. Past and current protocell model systems are presented and compared. Since the prebiotic formation of cell-like compartments is directly linked to the prebiotic availability of compartment building blocks, a few aspects on the likely chemical inventory on the early Earth are also summarized. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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Open AccessReview
Role of Cyanobacterial Exopolysaccharides in Phototrophic Biofilms and in Complex Microbial Mats
Life 2015, 5(2), 1218-1238; https://doi.org/10.3390/life5021218
Received: 18 December 2014 / Revised: 21 March 2015 / Accepted: 26 March 2015 / Published: 1 April 2015
Cited by 62 | Viewed by 3397 | PDF Full-text (3064 KB) | HTML Full-text | XML Full-text
Abstract
Exopolysaccharides (EPSs) are an important class of biopolymers with great ecological importance. In natural environments, they are a common feature of microbial biofilms, where they play key protective and structural roles. As the primary colonizers of constrained environments, such as desert soils and [...] Read more.
Exopolysaccharides (EPSs) are an important class of biopolymers with great ecological importance. In natural environments, they are a common feature of microbial biofilms, where they play key protective and structural roles. As the primary colonizers of constrained environments, such as desert soils and lithic and exposed substrates, cyanobacteria are the first contributors to the synthesis of the EPSs constituting the extracellular polymeric matrix that favors the formation of microbial associations with varying levels of complexity called biofilms. Cyanobacterial colonization represents the first step for the formation of biofilms with different levels of complexity. In all of the possible systems in which cyanobacteria are involved, the synthesis of EPSs contributes a structurally-stable and hydrated microenvironment, as well as chemical/physical protection against biotic and abiotic stress factors. Notwithstanding the important roles of cyanobacterial EPSs, many aspects related to their roles and the relative elicited biotic and abiotic factors have still to be clarified. The aim of this survey is to outline the state-of-the-art of the importance of the cyanobacterial EPS excretion, both for the producing cells and for the microbial associations in which cyanobacteria are a key component. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessArticle
Modeling the Role of pH on Baltic Sea Cyanobacteria
Life 2015, 5(2), 1204-1217; https://doi.org/10.3390/life5021204
Received: 28 January 2015 / Revised: 24 March 2015 / Accepted: 26 March 2015 / Published: 30 March 2015
Cited by 4 | Viewed by 1965 | PDF Full-text (1075 KB) | HTML Full-text | XML Full-text
Abstract
We simulate pH-dependent growth of cyanobacteria with an ecosystem model for the central Baltic Sea. Four model components—a life cycle model of cyanobacteria, a biogeochemical model, a carbonate chemistry model and a water column model—are coupled via the framework for aquatic biogeochemical models. [...] Read more.
We simulate pH-dependent growth of cyanobacteria with an ecosystem model for the central Baltic Sea. Four model components—a life cycle model of cyanobacteria, a biogeochemical model, a carbonate chemistry model and a water column model—are coupled via the framework for aquatic biogeochemical models. The coupled model is forced by the output of a regional climate model, based on the A1B emission scenario. With this coupled model, we perform simulations for the period 1968–2098. Our simulation experiments suggest that in the future, cyanobacteria growth is hardly affected by the projected pH decrease. However, in the simulation phase prior to 1980, cyanobacteria growth and N2-fixation are limited by the relatively high pH. The observed absence of cyanobacteria before the 1960s may thus be explained not only by lower eutrophication levels, but also by a higher alkalinity. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessReview
Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments
Life 2015, 5(2), 1172-1203; https://doi.org/10.3390/life5021172
Received: 10 November 2014 / Revised: 23 March 2015 / Accepted: 24 March 2015 / Published: 30 March 2015
Cited by 9 | Viewed by 2683 | PDF Full-text (1992 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Chlorophyll a (Chl) is a light-absorbing tetrapyrrole pigment that is essential for photosynthesis. The molecule is produced from glutamate via a complex biosynthetic pathway comprised of at least 15 enzymatic steps. The first half of the Chl pathway is shared with heme biosynthesis, [...] Read more.
Chlorophyll a (Chl) is a light-absorbing tetrapyrrole pigment that is essential for photosynthesis. The molecule is produced from glutamate via a complex biosynthetic pathway comprised of at least 15 enzymatic steps. The first half of the Chl pathway is shared with heme biosynthesis, and the latter half, called the Mg-branch, is specific to Mg-containing Chl a. Bilin pigments, such as phycocyanobilin, are additionally produced from heme, so these light-harvesting pigments also share many common biosynthetic steps with Chl biosynthesis. Some of these common steps in the biosynthetic pathways of heme, Chl and bilins require molecular oxygen for catalysis, such as oxygen-dependent coproporphyrinogen III oxidase. Cyanobacteria thrive in diverse environments in terms of oxygen levels. To cope with Chl deficiency caused by low-oxygen conditions, cyanobacteria have developed elaborate mechanisms to maintain Chl production, even under microoxic environments. The use of enzymes specialized for low-oxygen conditions, such as oxygen-independent coproporphyrinogen III oxidase, constitutes part of a mechanism adapted to low-oxygen conditions. Another mechanism adaptive to hypoxic conditions is mediated by the transcriptional regulator ChlR that senses low oxygen and subsequently activates the transcription of genes encoding enzymes that work under low-oxygen tension. In diazotrophic cyanobacteria, this multilayered regulation also contributes in Chl biosynthesis by supporting energy production for nitrogen fixation that also requires low-oxygen conditions. We will also discuss the evolutionary implications of cyanobacterial tetrapyrrole biosynthesis and regulation, because low oxygen-type enzymes also appear to be evolutionarily older than oxygen-dependent enzymes. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessArticle
Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component
Life 2015, 5(2), 1141-1171; https://doi.org/10.3390/life5021141
Received: 5 December 2014 / Revised: 9 March 2015 / Accepted: 16 March 2015 / Published: 27 March 2015
Cited by 17 | Viewed by 4126 | PDF Full-text (10902 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α [...] Read more.
The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in three model organisms and show that CsoS2 is vital for α-carboxysome biogenesis. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle (M)-, and C-terminal region. Repetitive motifs can be identified in the N- and M-regions. Multiple lines of evidence suggest CsoS2 is highly flexible, possibly an intrinsically disordered protein. Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome. Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessArticle
Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality
Life 2015, 5(2), 1127-1140; https://doi.org/10.3390/life5021127
Received: 13 February 2015 / Revised: 17 March 2015 / Accepted: 19 March 2015 / Published: 27 March 2015
Cited by 5 | Viewed by 2410 | PDF Full-text (976 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships [...] Read more.
Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessArticle
Enhancing Alkane Production in Cyanobacterial Lipid Droplets: A Model Platform for Industrially Relevant Compound Production
Life 2015, 5(2), 1111-1126; https://doi.org/10.3390/life5021111
Received: 27 December 2014 / Revised: 10 March 2015 / Accepted: 19 March 2015 / Published: 26 March 2015
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Abstract
Cyanobacterial lipid droplets (LDs) are packed with hydrophobic energy-dense compounds and have great potential for biotechnological expression and the compartmentalization of high value compounds. Nostoc punctiforme normally accumulates LDs containing neutral lipids, and small amounts of heptadecane, during the stationary phase of growth. [...] Read more.
Cyanobacterial lipid droplets (LDs) are packed with hydrophobic energy-dense compounds and have great potential for biotechnological expression and the compartmentalization of high value compounds. Nostoc punctiforme normally accumulates LDs containing neutral lipids, and small amounts of heptadecane, during the stationary phase of growth. In this study, we further enhanced heptadecane production in N. punctiforme by introducing extrachromosomal copies of aar/adc genes, and report the discovery of a putative novel lipase encoded by Npun_F5141, which further enhanced alkane production. Extra copies of all three genes in high light conditions resulted in a 16-fold higher accumulation of heptadecane compared to the wild type strain in the exponential phase. LD accumulation during exponential phase also increased massively to accommodate the heptadecane production. A large number of small, less fluorescent LDs were observed at the cell periphery in exponential growth phase, whereas fewer number of highly fluorescent, much larger LDs were localized towards the center of the cell in the stationary phase. These advances demonstrate that cyanobacterial LDs are an ideal model platform to make industrially relevant compounds, such as alkanes, during exponential growth, and provide insight into LD formation in cyanobacteria. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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Open AccessArticle
Bending Elasticity Modulus of Giant Vesicles Composed of Aeropyrum Pernix K1 Archaeal Lipid
Life 2015, 5(2), 1101-1110; https://doi.org/10.3390/life5021101
Received: 21 December 2014 / Revised: 8 March 2015 / Accepted: 19 March 2015 / Published: 26 March 2015
Cited by 2 | Viewed by 2081 | PDF Full-text (1357 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Thermally induced shape fluctuations were used to study elastic properties of giant vesicles composed of archaeal lipids C25,25-archetidyl (glucosyl) inositol and C25,25-archetidylinositol isolated from lyophilised Aeropyrum pernix K1 cells. Giant vesicles were created by electroformation in pure water environment. [...] Read more.
Thermally induced shape fluctuations were used to study elastic properties of giant vesicles composed of archaeal lipids C25,25-archetidyl (glucosyl) inositol and C25,25-archetidylinositol isolated from lyophilised Aeropyrum pernix K1 cells. Giant vesicles were created by electroformation in pure water environment. Stroboscopic illumination using a xenon flash lamp was implemented to remove the blur effect due to the finite integration time of the camera and to obtain an instant picture of the fluctuating vesicle shape. The mean weighted value of the bending elasticity modulus kc of the archaeal membrane determined from the measurements meeting the entire set of qualification criteria was (1.89 ± 0.18) × 10−19 J, which is similar to the values obtained for a membrane composed of the eukaryotic phospholipids SOPC (1.88 ± 0.17) × 10−19 J and POPC (2.00 ± 0.21) ´ 10−19 J. We conclude that membranes composed of archaeal lipids isolated from Aeropyrum pernix K1 cells have similar elastic properties as membranes composed of eukaryotic lipids. This fact, together with the importance of the elastic properties for the normal circulation through blood system, provides further evidence in favor of expectations that archaeal lipids could be appropriate for the design of drug delivery systems. Full article
(This article belongs to the Section Life Sciences)
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Open AccessArticle
Prediction of the Maximum Temperature for Life Based on the Stability of Metabolites to Decomposition in Water
Life 2015, 5(2), 1054-1100; https://doi.org/10.3390/life5021054
Received: 30 January 2015 / Revised: 3 March 2015 / Accepted: 5 March 2015 / Published: 26 March 2015
Cited by 8 | Viewed by 2287 | PDF Full-text (8800 KB) | HTML Full-text | XML Full-text
Abstract
The components of life must survive in a cell long enough to perform their function in that cell. Because the rate of attack by water increases with temperature, we can, in principle, predict a maximum temperature above which an active terrestrial metabolism cannot [...] Read more.
The components of life must survive in a cell long enough to perform their function in that cell. Because the rate of attack by water increases with temperature, we can, in principle, predict a maximum temperature above which an active terrestrial metabolism cannot function by analysis of the decomposition rates of the components of life, and comparison of those rates with the metabolites’ minimum metabolic half-lives. The present study is a first step in this direction, providing an analytical framework and method, and analyzing the stability of 63 small molecule metabolites based on literature data. Assuming that attack by water follows a first order rate equation, we extracted decomposition rate constants from literature data and estimated their statistical reliability. The resulting rate equations were then used to give a measure of confidence in the half-life of the metabolite concerned at different temperatures. There is little reliable data on metabolite decomposition or hydrolysis rates in the literature, the data is mostly confined to a small number of classes of chemicals, and the data available are sometimes mutually contradictory because of varying reaction conditions. However, a preliminary analysis suggests that terrestrial biochemistry is limited to environments below ~150–180 °C. We comment briefly on why pressure is likely to have a small effect on this. Full article
(This article belongs to the Special Issue The Physico-Chemical Limits of Life)
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Open AccessReview
Engineering Protocells: Prospects for Self-Assembly and Nanoscale Production-Lines
Life 2015, 5(2), 1019-1053; https://doi.org/10.3390/life5021019
Received: 1 January 2015 / Revised: 9 March 2015 / Accepted: 16 March 2015 / Published: 25 March 2015
Cited by 14 | Viewed by 2997 | PDF Full-text (1156 KB) | HTML Full-text | XML Full-text
Abstract
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic “organisms” with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis [...] Read more.
The increasing ease of producing nucleic acids and proteins to specification offers potential for design and fabrication of artificial synthetic “organisms” with a myriad of possible capabilities. The prospects for these synthetic organisms are significant, with potential applications in diverse fields including synthesis of pharmaceuticals, sources of renewable fuel and environmental cleanup. Until now, artificial cell technology has been largely restricted to the modification and metabolic engineering of living unicellular organisms. This review discusses emerging possibilities for developing synthetic protocell “machines” assembled entirely from individual biological components. We describe a host of recent technological advances that could potentially be harnessed in design and construction of synthetic protocells, some of which have already been utilized toward these ends. More elaborate designs include options for building self-assembling machines by incorporating cellular transport and assembly machinery. We also discuss production in miniature, using microfluidic production lines. While there are still many unknowns in the design, engineering and optimization of protocells, current technologies are now tantalizingly close to the capabilities required to build the first prototype protocells with potential real-world applications. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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