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Life, Volume 4, Issue 4 (December 2014) – 27 articles , Pages 535-1116

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3162 KiB  
Review
Synthetic Biology: A Bridge between Artificial and Natural Cells
by Yunfeng Ding, Fan Wu and Cheemeng Tan
Life 2014, 4(4), 1092-1116; https://doi.org/10.3390/life4041092 - 19 Dec 2014
Cited by 33 | Viewed by 18249
Abstract
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation [...] Read more.
Artificial cells are simple cell-like entities that possess certain properties of natural cells. In general, artificial cells are constructed using three parts: (1) biological membranes that serve as protective barriers, while allowing communication between the cells and the environment; (2) transcription and translation machinery that synthesize proteins based on genetic sequences; and (3) genetic modules that control the dynamics of the whole cell. Artificial cells are minimal and well-defined systems that can be more easily engineered and controlled when compared to natural cells. Artificial cells can be used as biomimetic systems to study and understand natural dynamics of cells with minimal interference from cellular complexity. However, there remain significant gaps between artificial and natural cells. How much information can we encode into artificial cells? What is the minimal number of factors that are necessary to achieve robust functioning of artificial cells? Can artificial cells communicate with their environments efficiently? Can artificial cells replicate, divide or even evolve? Here, we review synthetic biological methods that could shrink the gaps between artificial and natural cells. The closure of these gaps will lead to advancement in synthetic biology, cellular biology and biomedical applications. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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1005 KiB  
Article
The Place of RNA in the Origin and Early Evolution of the Genetic Machinery
by Günter Wächtershäuser
Life 2014, 4(4), 1050-1091; https://doi.org/10.3390/life4041050 - 19 Dec 2014
Cited by 20 | Viewed by 10711
Abstract
The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence [...] Read more.
The extant genetic machinery revolves around three interrelated polymers: RNA, DNA and proteins. Two evolutionary views approach this vital connection from opposite perspectives. The RNA World theory posits that life began in a cold prebiotic broth of monomers with the de novo emergence of replicating RNA as functionally self-contained polymer and that subsequent evolution is characterized by RNA → DNA memory takeover and ribozyme → enzyme catalyst takeover. The FeS World theory posits that life began as an autotrophic metabolism in hot volcanic-hydrothermal fluids and evolved with organic products turning into ligands for transition metal catalysts thereby eliciting feedback and feed-forward effects. In this latter context it is posited that the three polymers of the genetic machinery essentially coevolved from monomers through oligomers to polymers, operating functionally first as ligands for ligand-accelerated transition metal catalysis with later addition of base stacking and base pairing, whereby the functional dichotomy between hereditary DNA with stability on geologic time scales and transient, catalytic RNA with stability on metabolic time scales existed since the dawn of the genetic machinery. Both approaches are assessed comparatively for chemical soundness. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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539 KiB  
Review
Droplets: Unconventional Protocell Model with Life-Like Dynamics and Room to Grow
by Martin M Hanczyc
Life 2014, 4(4), 1038-1049; https://doi.org/10.3390/life4041038 - 17 Dec 2014
Cited by 40 | Viewed by 10061
Abstract
Over the past few decades, several protocell models have been developed that mimic certain essential characteristics of living cells. These protocells tend to be highly reductionist simplifications of living cells with prominent bilayer membrane boundaries, encapsulated metabolisms and/or encapsulated biologically-derived polymers as potential [...] Read more.
Over the past few decades, several protocell models have been developed that mimic certain essential characteristics of living cells. These protocells tend to be highly reductionist simplifications of living cells with prominent bilayer membrane boundaries, encapsulated metabolisms and/or encapsulated biologically-derived polymers as potential sources of information coding. In parallel with this conventional work, a novel protocell model based on droplets is also being developed. Such water-in-oil and oil-in-water droplet systems can possess chemical and biochemical transformations and biomolecule production, self-movement, self-division, individuality, group dynamics, and perhaps the fundamentals of intelligent systems and evolution. Given the diverse functionality possible with droplets as mimics of living cells, this system has the potential to be the first true embodiment of artificial life that is an orthologous departure from the one familiar type of biological life. This paper will synthesize the recent activity to develop droplets as protocell models. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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1178 KiB  
Article
Distribution and Ecology of Cyanobacteria in the Rocky Littoral of an English Lake District Water Body, Devoke Water
by Allan Pentecost
Life 2014, 4(4), 1026-1037; https://doi.org/10.3390/life4041026 - 16 Dec 2014
Cited by 3 | Viewed by 6146
Abstract
Cyanobacteria were sampled along two vertical and two horizontal transects in the littoral of Devoke Water, English Lake District. Profiles of cyanobacterium diversity and abundance showed that both attained a maximum close to the water line, but declined rapidly 20–40 cm above it. [...] Read more.
Cyanobacteria were sampled along two vertical and two horizontal transects in the littoral of Devoke Water, English Lake District. Profiles of cyanobacterium diversity and abundance showed that both attained a maximum close to the water line, but declined rapidly 20–40 cm above it. The distribution of individual species with height together with species and site ordinations showed that several taxa occurred in well-defined zones. A narrow “black zone” in the supralittoral was colonised mainly by species of Calothrix, Dichothrix and Gloeocapsa with pigmented sheaths. There was no evidence of lateral variation of species around the lake, but the height of the black zone correlated positively with wind exposure. The flora of Devoke Water is that of a base-poor mountain lake with some elements of a lowland, more alkaline water-body. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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1051 KiB  
Review
The Stereochemical Basis of the Genetic Code and the (Mostly) Autotrophic Origin of Life
by Juan C. Fontecilla-Camps
Life 2014, 4(4), 1013-1025; https://doi.org/10.3390/life4041013 - 16 Dec 2014
Cited by 12 | Viewed by 7798
Abstract
Spark-tube experiments and analysis of meteorite contents have led to the widespread notion that abiotic organic molecules were the first life components. However, there is a contradiction between the abundance of simple molecules, such as the amino acids glycine and alanine, observed in [...] Read more.
Spark-tube experiments and analysis of meteorite contents have led to the widespread notion that abiotic organic molecules were the first life components. However, there is a contradiction between the abundance of simple molecules, such as the amino acids glycine and alanine, observed in these studies, and the minimal functional complexity that even the least sophisticated living system should require. I will argue that although simple abiotic molecules must have primed proto-metabolic pathways, only Darwinian evolving systems could have generated life. This condition may have been initially fulfilled by both replicating RNAs and autocatalytic reaction chains, such as the reductive citric acid cycle. The interactions between nucleotides and biotic amino acids, which conferred new functionalities to the former, also resulted in the progressive stereochemical recognition of the latter by cognate anticodons. At this point only large enough amino acids would be recognized by the primordial RNA adaptors and could polymerize forming the first peptides. The gene duplication of RNA adaptors was a crucial event. By removing one of the anticodons from the acceptor stem the new RNA adaptor liberated itself from the stereochemical constraint and could be acylated by smaller amino acids. The emergence of messenger RNA and codon capture followed. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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1774 KiB  
Review
Mitigating Harmful Cyanobacterial Blooms in a Human- and Climatically-Impacted World
by Hans W. Paerl
Life 2014, 4(4), 988-1012; https://doi.org/10.3390/life4040988 - 15 Dec 2014
Cited by 223 | Viewed by 19329
Abstract
Bloom-forming harmful cyanobacteria (CyanoHABs) are harmful from environmental, ecological and human health perspectives by outcompeting beneficial phytoplankton, creating low oxygen conditions (hypoxia, anoxia), and by producing cyanotoxins. Cyanobacterial genera exhibit optimal growth rates and bloom potentials at relatively high water temperatures; hence, global [...] Read more.
Bloom-forming harmful cyanobacteria (CyanoHABs) are harmful from environmental, ecological and human health perspectives by outcompeting beneficial phytoplankton, creating low oxygen conditions (hypoxia, anoxia), and by producing cyanotoxins. Cyanobacterial genera exhibit optimal growth rates and bloom potentials at relatively high water temperatures; hence, global warming plays a key role in their expansion and persistence. CyanoHABs are regulated by synergistic effects of nutrient (nitrogen:N and phosphorus:P) supplies, light, temperature, vertical stratification, water residence times, and biotic interactions. In most instances, nutrient control strategies should focus on reducing both N and P inputs. Strategies based on physical, chemical (nutrient) and biological manipulations can be effective in reducing CyanoHABs; however, these strategies are largely confined to relatively small systems, and some are prone to ecological and environmental drawbacks, including enhancing release of cyanotoxins, disruption of planktonic and benthic communities and fisheries habitat. All strategies should consider and be adaptive to climatic variability and change in order to be effective for long-term control of CyanoHABs. Rising temperatures and greater hydrologic variability will increase growth rates and alter critical nutrient thresholds for CyanoHAB development; thus, nutrient reductions for bloom control may need to be more aggressively pursued in response to climatic changes globally. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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1164 KiB  
Article
Ecology and Physiology of the Pathogenic Cyanobacterium Roseofilum reptotaenium
by Laurie L. Richardson, Dina Stanić, Amanda May, Abigael Brownell, Miroslav Gantar and Shawn R. Campagna
Life 2014, 4(4), 968-987; https://doi.org/10.3390/life4040968 - 15 Dec 2014
Cited by 17 | Viewed by 11103
Abstract
Roseofilum reptotaenium is a gliding, filamentous, phycoerythrin-rich cyanobacterium that has been found only in the horizontally migrating, pathogenic microbial mat, black band disease (BBD) on Caribbean corals. R. reptotaenium dominates the BBD mat in terms of biomass and motility, and the filaments form [...] Read more.
Roseofilum reptotaenium is a gliding, filamentous, phycoerythrin-rich cyanobacterium that has been found only in the horizontally migrating, pathogenic microbial mat, black band disease (BBD) on Caribbean corals. R. reptotaenium dominates the BBD mat in terms of biomass and motility, and the filaments form the mat fabric. This cyanobacterium produces the cyanotoxin microcystin, predominately MC-LR, and can tolerate high levels of sulfide produced by sulfate reducing bacteria (SRB) that are also associated with BBD. Laboratory cultures of R. reptotaenium infect coral fragments, suggesting that the cyanobacterium is the primary pathogen of BBD, but since this species cannot grow axenically and Koch’s Postulates cannot be fulfilled, it cannot be proposed as a primary pathogen. However, R. reptotaenium does play several major pathogenic roles in this polymicrobial disease. Here, we provide an overview of the ecology of this coral pathogen and present new information on R. reptotaenium ecophysiology, including roles in the infection process, chemotactic and other motility responses, and the effect of pH on growth and motility. Additionally, we show, using metabolomics, that exposure of the BBD microbial community to the cyanotoxin MC-LR affects community metabolite profiles, in particular those associated with nucleic acid biosynthesis. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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1995 KiB  
Review
Regulation of Three Nitrogenase Gene Clusters in the Cyanobacterium Anabaena variabilis ATCC 29413
by Teresa Thiel and Brenda S. Pratte
Life 2014, 4(4), 944-967; https://doi.org/10.3390/life4040944 - 11 Dec 2014
Cited by 42 | Viewed by 12093
Abstract
The filamentous cyanobacterium Anabaena variabilis ATCC 29413 fixes nitrogen under aerobic conditions in specialized cells called heterocysts that form in response to an environmental deficiency in combined nitrogen. Nitrogen fixation is mediated by the enzyme nitrogenase, which is very sensitive to oxygen. Heterocysts [...] Read more.
The filamentous cyanobacterium Anabaena variabilis ATCC 29413 fixes nitrogen under aerobic conditions in specialized cells called heterocysts that form in response to an environmental deficiency in combined nitrogen. Nitrogen fixation is mediated by the enzyme nitrogenase, which is very sensitive to oxygen. Heterocysts are microxic cells that allow nitrogenase to function in a filament comprised primarily of vegetative cells that produce oxygen by photosynthesis. A. variabilis is unique among well-characterized cyanobacteria in that it has three nitrogenase gene clusters that encode different nitrogenases, which function under different environmental conditions. The nif1 genes encode a Mo-nitrogenase that functions only in heterocysts, even in filaments grown anaerobically. The nif2 genes encode a different Mo-nitrogenase that functions in vegetative cells, but only in filaments grown under anoxic conditions. An alternative V-nitrogenase is encoded by vnf genes that are expressed only in heterocysts in an environment that is deficient in Mo. Thus, these three nitrogenases are expressed differentially in response to environmental conditions. The entire nif1 gene cluster, comprising at least 15 genes, is primarily under the control of the promoter for the first gene, nifB1. Transcriptional control of many of the downstream nif1 genes occurs by a combination of weak promoters within the coding regions of some downstream genes and by RNA processing, which is associated with increased transcript stability. The vnf genes show a similar pattern of transcriptional and post-transcriptional control of expression suggesting that the complex pattern of regulation of the nif1 cluster is conserved in other cyanobacterial nitrogenase gene clusters. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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1534 KiB  
Article
Reconciling Ligase Ribozyme Activity with Fatty Acid Vesicle Stability
by Fabrizio Anella and Christophe Danelon
Life 2014, 4(4), 929-943; https://doi.org/10.3390/life4040929 - 11 Dec 2014
Cited by 7 | Viewed by 7332
Abstract
The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, in [...] Read more.
The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, in particular Mg2+, with respect to optimal ribozyme activity, fatty acid vesicle stability and protection against RNA strand cleavage. Here, we report on the activity of a short L1 ligase ribozyme in the presence of myristoleic acid (MA) vesicles at varying concentrations of Mg2+. The ligation rate is significantly lower at low-Mg2+ conditions. However, the loss of activity is overcompensated by the increased stability of RNA leading to a larger amount of intact ligated substrate after long reaction periods. Combining RNA ligation assays with fatty acid vesicles we found that MA vesicles made of 5 mM amphiphile are stable and do not impair ligase ribozyme activity in the presence of approximately 2 mM Mg2+. These results provide a scenario in which catalytic RNA and primordial membrane assembly can coexist in the same environment. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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536 KiB  
Review
Toward Spatially Regulated Division of Protocells: Insights into the E. coli Min System from in Vitro Studies
by Simon Kretschmer and Petra Schwille
Life 2014, 4(4), 915-928; https://doi.org/10.3390/life4040915 - 11 Dec 2014
Cited by 15 | Viewed by 8112
Abstract
For reconstruction of controlled cell division in a minimal cell model, or protocell, a positioning mechanism that spatially regulates division is indispensable. In Escherichia coli, the Min proteins oscillate from pole to pole to determine the division site by inhibition of the [...] Read more.
For reconstruction of controlled cell division in a minimal cell model, or protocell, a positioning mechanism that spatially regulates division is indispensable. In Escherichia coli, the Min proteins oscillate from pole to pole to determine the division site by inhibition of the primary divisome protein FtsZ anywhere but in the cell middle. Remarkably, when reconstituted under defined conditions in vitro, the Min proteins self-organize into spatiotemporal patterns in the presence of a lipid membrane and ATP. We review recent progress made in studying the Min system in vitro, particularly focusing on the effects of various physicochemical parameters and boundary conditions on pattern formation. Furthermore, we discuss implications and challenges for utilizing the Min system for division site placement in protocells. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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580 KiB  
Article
Consequences of Decreased Light Harvesting Capability on Photosystem II Function in Synechocystis sp. PCC 6803
by Aparna Nagarajan, Lawrence E. Page, Michelle Liberton and Himadri B. Pakrasi
Life 2014, 4(4), 903-914; https://doi.org/10.3390/life4040903 - 11 Dec 2014
Cited by 13 | Viewed by 8035
Abstract
Cyanobacteria use large pigment-protein complexes called phycobilisomes to harvest light energy primarily for photosystem II (PSII). We used a series of mutants with partial to complete reduction of phycobilisomes to examine the effects of antenna truncation on photosystem function in Synechocystis sp. PCC [...] Read more.
Cyanobacteria use large pigment-protein complexes called phycobilisomes to harvest light energy primarily for photosystem II (PSII). We used a series of mutants with partial to complete reduction of phycobilisomes to examine the effects of antenna truncation on photosystem function in Synechocystis sp. PCC 6803. The antenna mutants CB, CK, and PAL expressed increasing levels of functional PSII centers to compensate for the loss of phycobilisomes, with a concomitant decrease in photosystem I (PSI). This increased PSII titer led to progressively higher oxygen evolution rates on a per chlorophyll basis. The mutants also exhibited impaired S-state transition profiles for oxygen evolution. Additionally, P700+ re-reduction rates were impacted by antenna reduction. Thus, a decrease in antenna size resulted in overall physiological changes in light harvesting and delivery to PSII as well as changes in downstream electron transfer to PSI. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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1122 KiB  
Review
Looked at Life from Both Sides Now
by Jillian E. Smith, Allisandra K. Mowles, Anil K. Mehta and David G. Lynn
Life 2014, 4(4), 887-902; https://doi.org/10.3390/life4040887 - 11 Dec 2014
Cited by 23 | Viewed by 9259
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, [...] Read more.
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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1491 KiB  
Review
Metals in Cyanobacteria: Analysis of the Copper, Nickel, Cobalt and Arsenic Homeostasis Mechanisms
by María José Huertas, Luis López-Maury, Joaquín Giner-Lamia, Ana María Sánchez-Riego and Francisco Javier Florencio
Life 2014, 4(4), 865-886; https://doi.org/10.3390/life4040865 - 9 Dec 2014
Cited by 128 | Viewed by 13573
Abstract
Traces of metal are required for fundamental biochemical processes, such as photosynthesis and respiration. Cyanobacteria metal homeostasis acquires an important role because the photosynthetic machinery imposes a high demand for metals, making them a limiting factor for cyanobacteria, especially in the open oceans. [...] Read more.
Traces of metal are required for fundamental biochemical processes, such as photosynthesis and respiration. Cyanobacteria metal homeostasis acquires an important role because the photosynthetic machinery imposes a high demand for metals, making them a limiting factor for cyanobacteria, especially in the open oceans. On the other hand, in the last two centuries, the metal concentrations in marine environments and lake sediments have increased as a result of several industrial activities. In all cases, cells have to tightly regulate uptake to maintain their intracellular concentrations below toxic levels. Mechanisms to obtain metal under limiting conditions and to protect cells from an excess of metals are present in cyanobacteria. Understanding metal homeostasis in cyanobacteria and the proteins involved will help to evaluate the use of these microorganisms in metal bioremediation. Furthermore, it will also help to understand how metal availability impacts primary production in the oceans. In this review, we will focus on copper, nickel, cobalt and arsenic (a toxic metalloid) metabolism, which has been mainly analyzed in model cyanobacterium Synechocystis sp. PCC 6803. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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683 KiB  
Article
Growth and Division in a Dynamic Protocell Model
by Marco Villani, Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Timoteo Carletti and Roberto Serra
Life 2014, 4(4), 837-864; https://doi.org/10.3390/life4040837 - 3 Dec 2014
Cited by 22 | Viewed by 8843
Abstract
In this paper a new model of growing and dividing protocells is described, whose main features are (i) a lipid container that grows according to the composition of the molecular milieu (ii) a set of “genetic memory molecules” (GMMs) that undergo catalytic reactions [...] Read more.
In this paper a new model of growing and dividing protocells is described, whose main features are (i) a lipid container that grows according to the composition of the molecular milieu (ii) a set of “genetic memory molecules” (GMMs) that undergo catalytic reactions in the internal aqueous phase and (iii) a set of stochastic kinetic equations for the GMMs. The mass exchange between the external environment and the internal phase is described by simulating a semipermeable membrane and a flow driven by the differences in chemical potentials, thereby avoiding to resort to sometimes misleading simplifications, e.g., that of a flow reactor. Under simple assumptions, it is shown that synchronization takes place between the rate of replication of the GMMs and that of the container, provided that the set of reactions hosts a so-called RAF (Reflexive Autocatalytic, Food-generated) set whose influence on synchronization is hereafter discussed. It is also shown that a slight modification of the basic model that takes into account a rate-limiting term, makes possible the growth of novelties, allowing in such a way suitable evolution: so the model represents an effective basis for understanding the main abstract properties of populations of protocells. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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2056 KiB  
Article
Cellular Dynamics Drives the Emergence of Supracellular Structure in the Cyanobacterium, Phormidium sp. KS
by Naoki Sato, Yutaro Katsumata, Kaoru Sato and Naoyuki Tajima
Life 2014, 4(4), 819-836; https://doi.org/10.3390/life4040819 - 28 Nov 2014
Cited by 13 | Viewed by 9765
Abstract
Motile filamentous cyanobacteria, such as Oscillatoria, Phormidium and Arthrospira, are ubiquitous in terrestrial and aquatic environments. As noted by Nägeli in 1860, many of them form complex three-dimensional or two-dimensional structures, such as biofilm, weed-like thalli, bundles of filaments and [...] Read more.
Motile filamentous cyanobacteria, such as Oscillatoria, Phormidium and Arthrospira, are ubiquitous in terrestrial and aquatic environments. As noted by Nägeli in 1860, many of them form complex three-dimensional or two-dimensional structures, such as biofilm, weed-like thalli, bundles of filaments and spirals, which we call supracellular structures. In all of these structures, individual filaments incessantly move back and forth. The structures are, therefore, macroscopic, dynamic structures that are continuously changing their microscopic arrangement of filaments. In the present study, we analyzed quantitatively the movement of individual filaments of Phormidium sp. KS grown on agar plates. Junctional pores, which have been proposed to drive cell movement by mucilage/slime secretion, were found to align on both sides of each septum. The velocity of movement was highest just after the reversal of direction and, then, attenuated exponentially to a final value before the next reversal of direction. This kinetics is compatible with the “slime gun” model. A higher agar concentration restricts the movement more severely and, thus, resulted in more spiral formation. The spiral is a robust form compatible with non-homogeneous movements of different parts of a long filament. We propose a model of spiral formation based on the microscopic movement of filaments. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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551 KiB  
Review
RNA Sociology: Group Behavioral Motifs of RNA Consortia
by Guenther Witzany
Life 2014, 4(4), 800-818; https://doi.org/10.3390/life4040800 - 24 Nov 2014
Cited by 14 | Viewed by 10417
Abstract
RNA sociology investigates the behavioral motifs of RNA consortia from the social science perspective. Besides the self-folding of RNAs into single stem loop structures, group building of such stem loops results in a variety of essential agents that are highly active in regulatory [...] Read more.
RNA sociology investigates the behavioral motifs of RNA consortia from the social science perspective. Besides the self-folding of RNAs into single stem loop structures, group building of such stem loops results in a variety of essential agents that are highly active in regulatory processes in cellular and non-cellular life. RNA stem loop self-folding and group building do not depend solely on sequence syntax; more important are their contextual (functional) needs. Also, evolutionary processes seem to occur through RNA stem loop consortia that may act as a complement. This means the whole entity functions only if all participating parts are coordinated, although the complementary building parts originally evolved for different functions. If complementary groups, such as rRNAs and tRNAs, are placed together in selective pressure contexts, new evolutionary features may emerge. Evolution initiated by competent agents in natural genome editing clearly contrasts with statistical error replication narratives. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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996 KiB  
Article
On the Contribution of Protein Spatial Organization to the Physicochemical Interconnection between Proteins and Their Cognate mRNAs
by Andreas Beier, Bojan Zagrovic and Anton A. Polyansky
Life 2014, 4(4), 788-799; https://doi.org/10.3390/life4040788 - 21 Nov 2014
Cited by 10 | Viewed by 8951
Abstract
Early-stage evolutionary development of the universal genetic code remains a fundamental, open problem. One of the possible scenarios suggests that the code evolved in response to direct interactions between peptides and RNA oligonucleotides in the primordial environment. Recently, we have revealed a strong [...] Read more.
Early-stage evolutionary development of the universal genetic code remains a fundamental, open problem. One of the possible scenarios suggests that the code evolved in response to direct interactions between peptides and RNA oligonucleotides in the primordial environment. Recently, we have revealed a strong matching between base-binding preferences of modern protein sequences and the composition of their cognate mRNA coding sequences. These results point directly at the physicochemical foundation behind the code’s origin, but also support the possibility of direct complementary interactions between proteins and their cognate mRNAs, especially if the two are unstructured. Here, we analyze molecular-surface mapping of knowledge-based amino-acid/nucleobase interaction preferences for a set of complete, high-resolution protein structures and show that the connection between the two biopolymers could remain relevant even for structured, folded proteins. Specifically, protein surface loops are strongly enriched in residues with a high binding propensity for guanine and cytosine, while adenine- and uracil-preferring residues are uniformly distributed throughout protein structures. Moreover, compositional complementarity of cognate protein and mRNA sequences remains strong even after weighting protein sequence profiles by residue solvent exposure. Our results support the possibility that protein/mRNA sequence complementarity may also translate to cognate interactions between structured biopolymers. Full article
(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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754 KiB  
Article
The Effects of Dark Incubation on Cellular Metabolism of the Wild Type Cyanobacterium Synechocystis sp. PCC 6803 and a Mutant Lacking the Transcriptional Regulator cyAbrB2
by Masamitsu Hanai, Yusuke Sato, Atsuko Miyagi, Maki Kawai-Yamada, Kyoko Tanaka, Yasuko Kaneko, Yoshitaka Nishiyama and Yukako Hihara
Life 2014, 4(4), 770-787; https://doi.org/10.3390/life4040770 - 21 Nov 2014
Cited by 19 | Viewed by 7513
Abstract
The cyAbrB2 transcriptional regulator is essential for active sugar catabolism in Synechocystis sp. PCC 6803 grown under light conditions. In the light-grown cyabrB2-disrupted mutant, glycogen granules and sugar phosphates corresponding to early steps in the glycolytic pathway accumulated to higher levels than [...] Read more.
The cyAbrB2 transcriptional regulator is essential for active sugar catabolism in Synechocystis sp. PCC 6803 grown under light conditions. In the light-grown cyabrB2-disrupted mutant, glycogen granules and sugar phosphates corresponding to early steps in the glycolytic pathway accumulated to higher levels than those in the wild-type (WT) strain, whereas the amounts of 3-phosphoglycerate, phosphoenolpyruvate and ribulose 1,5-bisphosphate were significantly lower. We further determined that accumulated glycogen granules in the mutant could be actively catabolized under dark conditions. Differences in metabolite levels between WT and the mutant became less substantial during dark incubation due to a general quantitative decrease in metabolite levels. Notable exceptions, however, were increases in 2-oxoglutarate, histidine, ornithine and citrulline in the WT but not in the mutant. The amounts of cyAbrBs were highly responsive to the availability of light both in transcript and protein levels. When grown under light-dark cycle conditions, diurnal oscillatory pattern of glycogen content of the mutant was lost after the second dark period. These observations indicate that cyAbrB2 is dispensable for activation of sugar catabolism under dark conditions but involved in the proper switching between day and night metabolisms. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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1170 KiB  
Review
Survival Strategies in the Aquatic and Terrestrial World: The Impact of Second Messengers on Cyanobacterial Processes
by Marco Agostoni and Beronda L. Montgomery
Life 2014, 4(4), 745-769; https://doi.org/10.3390/life4040745 - 18 Nov 2014
Cited by 28 | Viewed by 11728
Abstract
Second messengers are intracellular substances regulated by specific external stimuli globally known as first messengers. Cells rely on second messengers to generate rapid responses to environmental changes and the importance of their roles is becoming increasingly realized in cellular signaling research. Cyanobacteria are [...] Read more.
Second messengers are intracellular substances regulated by specific external stimuli globally known as first messengers. Cells rely on second messengers to generate rapid responses to environmental changes and the importance of their roles is becoming increasingly realized in cellular signaling research. Cyanobacteria are photooxygenic bacteria that inhabit most of Earth’s environments. The ability of cyanobacteria to survive in ecologically diverse habitats is due to their capacity to adapt and respond to environmental changes. This article reviews known second messenger-controlled physiological processes in cyanobacteria. Second messengers used in these systems include the element calcium (Ca2+), nucleotide-based guanosine tetraphosphate or pentaphosphate (ppGpp or pppGpp, represented as (p)ppGpp), cyclic adenosine 3’,5’-monophosphate (cAMP), cyclic dimeric GMP (c-di-GMP), cyclic guanosine 3’,5’-monophosphate (cGMP), and cyclic dimeric AMP (c-di-AMP), and the gaseous nitric oxide (NO). The discussion focuses on processes central to cyanobacteria, such as nitrogen fixation, light perception, photosynthesis-related processes, and gliding motility. In addition, we address future research trajectories needed to better understand the signaling networks and cross talk in the signaling pathways of these molecules in cyanobacteria. Second messengers have significant potential to be adapted as technological tools and we highlight possible novel and practical applications based on our understanding of these molecules and the signaling networks that they control. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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1263 KiB  
Article
Photosynthesis in Hydrogen-Dominated Atmospheres
by William Bains, Sara Seager and Andras Zsom
Life 2014, 4(4), 716-744; https://doi.org/10.3390/life4040716 - 18 Nov 2014
Cited by 26 | Viewed by 12539
Abstract
The diversity of extrasolar planets discovered in the last decade shows that we should not be constrained to look for life in environments similar to early or present-day Earth. Super-Earth exoplanets are being discovered with increasing frequency, and some will be able to [...] Read more.
The diversity of extrasolar planets discovered in the last decade shows that we should not be constrained to look for life in environments similar to early or present-day Earth. Super-Earth exoplanets are being discovered with increasing frequency, and some will be able to retain a stable, hydrogen-dominated atmosphere. We explore the possibilities for photosynthesis on a rocky planet with a thin H2-dominated atmosphere. If a rocky, H2-dominated planet harbors life, then that life is likely to convert atmospheric carbon into methane. Outgassing may also build an atmosphere in which methane is the principal carbon species. We describe the possible chemical routes for photosynthesis starting from methane and show that less energy and lower energy photons could drive CH4-based photosynthesis as compared with CO2-based photosynthesis. We find that a by-product biosignature gas is likely to be H2, which is not distinct from the hydrogen already present in the environment. Ammonia is a potential biosignature gas of hydrogenic photosynthesis that is unlikely to be generated abiologically. We suggest that the evolution of methane-based photosynthesis is at least as likely as the evolution of anoxygenic photosynthesis on Earth and may support the evolution of complex life. Full article
(This article belongs to the Special Issue Planetary Exploration: Habitats and Terrestrial Analogs)
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1298 KiB  
Review
Viruses of Haloarchaea
by Alison W. S. Luk, Timothy J. Williams, Susanne Erdmann, R. Thane Papke and Ricardo Cavicchioli
Life 2014, 4(4), 681-715; https://doi.org/10.3390/life4040681 - 13 Nov 2014
Cited by 48 | Viewed by 14043
Abstract
In hypersaline environments, haloarchaea (halophilic members of the Archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. Since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing [...] Read more.
In hypersaline environments, haloarchaea (halophilic members of the Archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. Since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing Myoviridae, Siphoviridae, Podoviridae, Pleolipoviridae, Sphaerolipoviridae and Fuselloviridae families. This review overviews current knowledge of haloarchaeoviruses, providing information about classification, morphotypes, macromolecules, life cycles, genetic manipulation and gene regulation, and host-virus responses. In so doing, the review incorporates knowledge from laboratory studies of isolated viruses, field-based studies of environmental samples, and both genomic and metagenomic analyses of haloarchaeoviruses. What emerges is that some haloarchaeoviruses possess unique morphological and life cycle properties, while others share features with other viruses (e.g., bacteriophages). Their interactions with hosts influence community structure and evolution of populations that exist in hypersaline environments as diverse as seawater evaporation ponds, to hot desert or Antarctic lakes. The discoveries of their wide-ranging and important roles in the ecology and evolution of hypersaline communities serves as a strong motivator for future investigations of both laboratory-model and environmental systems. Full article
(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)
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1860 KiB  
Review
Function and Regulation of Ferredoxins in the Cyanobacterium, Synechocystis PCC6803: Recent Advances
by Corinne Cassier-Chauvat and Franck Chauvat
Life 2014, 4(4), 666-680; https://doi.org/10.3390/life4040666 - 7 Nov 2014
Cited by 83 | Viewed by 9979
Abstract
Ferredoxins (Fed), occurring in most organisms, are small proteins that use their iron-sulfur cluster to distribute electrons to various metabolic pathways, likely including hydrogen production. Here, we summarize the current knowledge on ferredoxins in cyanobacteria, the prokaryotes regarded as important producers of the [...] Read more.
Ferredoxins (Fed), occurring in most organisms, are small proteins that use their iron-sulfur cluster to distribute electrons to various metabolic pathways, likely including hydrogen production. Here, we summarize the current knowledge on ferredoxins in cyanobacteria, the prokaryotes regarded as important producers of the oxygenic atmosphere and biomass for the food chain, as well as promising cell factories for biofuel production. Most studies of ferredoxins were performed in the model strain, Synechocystis PCC6803, which possesses nine highly-conserved ferredoxins encoded by monocistronic or operonic genes, some of which are localized in conserved genome regions. Fed1, encoded by a light-inducible gene, is a highly abundant protein essential to photosynthesis. Fed2-Fed9, encoded by genes differently regulated by trophic conditions, are low-abundant proteins that play prominent roles in the tolerance to environmental stresses. Concerning the selectivity/redundancy of ferredoxin, we report that Fed1, Fed7 and Fed9 belong to ferredoxin-glutaredoxin-thioredoxin crosstalk pathways operating in the protection against oxidative and metal stresses. Furthermore, Fed7 specifically interacts with a DnaJ-like protein, an interaction that has been conserved in photosynthetic eukaryotes in the form of a composite protein comprising DnaJ- and Fed7-like domains. Fed9 specifically interacts with the Flv3 flavodiiron protein acting in the photoreduction of O2 to H2O. Full article
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
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4364 KiB  
Review
Microgravity-Induced Fluid Shift and Ophthalmic Changes
by Emily S. Nelson, Lealem Mulugeta and Jerry G. Myers
Life 2014, 4(4), 621-665; https://doi.org/10.3390/life4040621 - 7 Nov 2014
Cited by 135 | Viewed by 22056
Abstract
Although changes to visual acuity in spaceflight have been observed in some astronauts since the early days of the space program, the impact to the crew was considered minor. Since that time, missions to the International Space Station have extended the typical duration [...] Read more.
Although changes to visual acuity in spaceflight have been observed in some astronauts since the early days of the space program, the impact to the crew was considered minor. Since that time, missions to the International Space Station have extended the typical duration of time spent in microgravity from a few days or weeks to many months. This has been accompanied by the emergence of a variety of ophthalmic pathologies in a significant proportion of long-duration crewmembers, including globe flattening, choroidal folding, optic disc edema, and optic nerve kinking, among others. The clinical findings of affected astronauts are reminiscent of terrestrial pathologies such as idiopathic intracranial hypertension that are characterized by high intracranial pressure. As a result, NASA has placed an emphasis on determining the relevant factors and their interactions that are responsible for detrimental ophthalmic response to space. This article will describe the Visual Impairment and Intracranial Pressure syndrome, link it to key factors in physiological adaptation to the microgravity environment, particularly a cephalad shifting of bodily fluids, and discuss the implications for ocular biomechanics and physiological function in long-duration spaceflight. Full article
(This article belongs to the Special Issue Response of Terrestrial Life to Space Conditions)
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2220 KiB  
Review
Synergism and Mutualism in Non-Enzymatic RNA Polymerization
by Hussein Kaddour and Nita Sahai
Life 2014, 4(4), 598-620; https://doi.org/10.3390/life4040598 - 3 Nov 2014
Cited by 16 | Viewed by 14787
Abstract
The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the “RNA world” and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. [...] Read more.
The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the “RNA world” and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life’s building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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1501 KiB  
Article
Compartmentalization and Cell Division through Molecular Discreteness and Crowding in a Catalytic Reaction Network
by Atsushi Kamimura and Kunihiko Kaneko
Life 2014, 4(4), 586-597; https://doi.org/10.3390/life4040586 - 29 Oct 2014
Cited by 4 | Viewed by 5776
Abstract
Explanation of the emergence of primitive cellular structures from a set of chemical reactions is necessary to unveil the origin of life and to experimentally synthesize protocells. By simulating a cellular automaton model with a two-species hypercycle, we demonstrate the reproduction of a [...] Read more.
Explanation of the emergence of primitive cellular structures from a set of chemical reactions is necessary to unveil the origin of life and to experimentally synthesize protocells. By simulating a cellular automaton model with a two-species hypercycle, we demonstrate the reproduction of a localized cluster; that is, a protocell with a growth-division process emerges when the replication and degradation speeds of one species are respectively slower than those of the other species, because of overcrowding of molecules as a natural outcome of the replication. The protocell exhibits synchrony between its division process and replication of the minority molecule. We discuss the effects of the crowding molecule on the formation of primitive structures. The generality of this result is demonstrated through the extension of our model to a hypercycle with three molecular species, where a localized layered structure of molecules continues to divide, triggered by the replication of a minority molecule at the center. Full article
(This article belongs to the Special Issue Protocells - Designs for Life)
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2556 KiB  
Article
Mud Volcanoes of Trinidad as Astrobiological Analogs for Martian Environments
by Riad Hosein, Shirin Haque and Denise M. Beckles
Life 2014, 4(4), 566-585; https://doi.org/10.3390/life4040566 - 13 Oct 2014
Cited by 14 | Viewed by 17018
Abstract
Eleven onshore mud volcanoes in the southern region of Trinidad have been studied as analog habitats for possible microbial life on Mars. The profiles of the 11 mud volcanoes are presented in terms of their physical, chemical, mineralogical, and soil properties. The mud [...] Read more.
Eleven onshore mud volcanoes in the southern region of Trinidad have been studied as analog habitats for possible microbial life on Mars. The profiles of the 11 mud volcanoes are presented in terms of their physical, chemical, mineralogical, and soil properties. The mud volcanoes sampled all emitted methane gas consistently at 3% volume. The average pH for the mud volcanic soil was 7.98. The average Cation Exchange Capacity (CEC) was found to be 2.16 kg/mol, and the average Percentage Water Content was 34.5%. Samples from three of the volcanoes, (i) Digity; (ii) Piparo and (iii) Devil’s Woodyard were used to culture bacterial colonies under anaerobic conditions indicating possible presence of methanogenic microorganisms. The Trinidad mud volcanoes can serve as analogs for the Martian environment due to similar geological features found extensively on Mars in Acidalia Planitia and the Arabia Terra region. Full article
(This article belongs to the Special Issue Planetary Exploration: Habitats and Terrestrial Analogs)
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1535 KiB  
Review
Biota and Biomolecules in Extreme Environments on Earth: Implications for Life Detection on Mars
by Joost W. Aerts, Wilfred F.M. Röling, Andreas Elsaesser and Pascale Ehrenfreund
Life 2014, 4(4), 535-565; https://doi.org/10.3390/life4040535 - 13 Oct 2014
Cited by 36 | Viewed by 14422
Abstract
The three main requirements for life as we know it are the presence of organic compounds, liquid water, and free energy. Several groups of organic compounds (e.g., amino acids, nucleobases, lipids) occur in all life forms on Earth and are used as diagnostic [...] Read more.
The three main requirements for life as we know it are the presence of organic compounds, liquid water, and free energy. Several groups of organic compounds (e.g., amino acids, nucleobases, lipids) occur in all life forms on Earth and are used as diagnostic molecules, i.e., biomarkers, for the characterization of extant or extinct life. Due to their indispensability for life on Earth, these biomarkers are also prime targets in the search for life on Mars. Biomarkers degrade over time; in situ environmental conditions influence the preservation of those molecules. Nonetheless, upon shielding (e.g., by mineral surfaces), particular biomarkers can persist for billions of years, making them of vital importance in answering questions about the origins and limits of life on early Earth and Mars. The search for organic material and biosignatures on Mars is particularly challenging due to the hostile environment and its effect on organic compounds near the surface. In support of life detection on Mars, it is crucial to investigate analogue environments on Earth that resemble best past and present Mars conditions. Terrestrial extreme environments offer a rich source of information allowing us to determine how extreme conditions affect life and molecules associated with it. Extremophilic organisms have adapted to the most stunning conditions on Earth in environments with often unique geological and chemical features. One challenge in detecting biomarkers is to optimize extraction, since organic molecules can be low in abundance and can strongly adsorb to mineral surfaces. Methods and analytical tools in the field of life science are continuously improving. Amplification methods are very useful for the detection of low concentrations of genomic material but most other organic molecules are not prone to amplification methods. Therefore, a great deal depends on the extraction efficiency. The questions “what to look for”, “where to look”, and “how to look for it” require more of our attention to ensure the success of future life detection missions on Mars. Full article
(This article belongs to the Special Issue Planetary Exploration: Habitats and Terrestrial Analogs)
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