Next Issue
Volume 9, September
Previous Issue
Volume 9, March

Table of Contents

Life, Volume 9, Issue 2 (June 2019) – 23 articles

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Readerexternal link to open them.
Cover Story (view full-size image) Carbonaceous chondrites are considered as primitive meteorites due their relatively high carbon [...] Read more.
Order results
Result details
Select all
Export citation of selected articles as:
Open AccessFeature PaperArticle
Molecular Diversity and Network Complexity in Growing Protocells
Life 2019, 9(2), 53; https://doi.org/10.3390/life9020053 - 20 Jun 2019
Viewed by 1458
Abstract
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address the essential role of the huge diversity of cellular components, we studied a model of protocells that convert resources into catalysts with [...] Read more.
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address the essential role of the huge diversity of cellular components, we studied a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources were limited, the diversity in the intracellular components was found to be increased to allow the use of diverse resources for cellular growth. A scaling relation was demonstrated between resource abundances and molecular diversity. In the present study, we examined how the molecular species diversify and how complex catalytic reaction networks develop through an evolutionary course. At some generations, molecular species first appear as parasites that do not contribute to the replication of other molecules. Later, the species turn into host species that contribute to the replication of other species, with further diversification of molecular species. Thus, a complex joint network evolves with this successive increase in species. The present study sheds new light on the origin of molecular diversity and complex reaction networks at the primitive stage of a cell. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
Show Figures

Figure 1

Open AccessArticle
Prebiotic Sugar Formation Under Nonaqueous Conditions and Mechanochemical Acceleration
Life 2019, 9(2), 52; https://doi.org/10.3390/life9020052 - 20 Jun 2019
Cited by 8 | Viewed by 2487
Abstract
Monosaccharides represent one of the major building blocks of life. One of the plausible prebiotic synthesis routes is the formose network, which generates sugars from C1 and C2 carbon sources in basic aqueous solution. We report on the feasibility of the formation of [...] Read more.
Monosaccharides represent one of the major building blocks of life. One of the plausible prebiotic synthesis routes is the formose network, which generates sugars from C1 and C2 carbon sources in basic aqueous solution. We report on the feasibility of the formation of monosaccharides under physical forces simulated in a ball mill starting from formaldehyde, glycolaldehyde, DL-glyceraldehyde as prebiotically available substrates using catalytically active, basic minerals. We investigated the influence of the mechanic energy input on our model system using calcium hydroxide in an oscillatory ball mill. We show that the synthesis of monosaccharides is kinetically accelerated under mechanochemical conditions. The resulting sugar mixture contains monosaccharides with straight and branched carbon chains as well as decomposition products. In comparison to the sugar formation in water, the monosaccharides formed under mechanochemical conditions are more stable and selectively synthesized. Our results imply the possibility of a prebiotic monosaccharide origin in geochemical environments scant or devoid of water promoted by mechanochemical forces such as meteorite impacts or lithospheric activity. Full article
Show Figures

Graphical abstract

Open AccessArticle
Emergence of a “Cyclosome” in a Primitive Network Capable of Building “Infinite” Proteins
Life 2019, 9(2), 51; https://doi.org/10.3390/life9020051 - 18 Jun 2019
Cited by 12 | Viewed by 1760
Abstract
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These [...] Read more.
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included “infinite” proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon’s synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
Show Figures

Figure 1

Open AccessReview
Evolutionary Steps in the Analytics of Primordial Metabolic Evolution
Life 2019, 9(2), 50; https://doi.org/10.3390/life9020050 - 18 Jun 2019
Cited by 3 | Viewed by 2039
Abstract
Experimental studies of primordial metabolic evolution are based on multi-component reactions which typically result in highly complex product mixtures. The detection and structural assignment of these products crucially depends on sensitive and selective analytical procedures. Progress in the instrumentation of these methods steadily [...] Read more.
Experimental studies of primordial metabolic evolution are based on multi-component reactions which typically result in highly complex product mixtures. The detection and structural assignment of these products crucially depends on sensitive and selective analytical procedures. Progress in the instrumentation of these methods steadily lowered the detection limits to concentrations in the pico molar range. At the same time, conceptual improvements in chromatography, nuclear magnetic resonance (NMR) and mass spectrometry dramatically increased the resolution power as well as throughput, now, allowing the simultaneous detection and structural determination of hundreds to thousands of compounds in complex mixtures. In retrospective, the development of these analytical methods occurred stepwise in a kind of evolutionary process that is reminiscent of steps occurring in the evolution of metabolism under chemoautotrophic conditions. This can be nicely exemplified in the analytical procedures used in our own studies that are based on Wächtershäuser’s theory for metabolic evolution under Fe/Ni-catalyzed volcanic aqueous conditions. At the onset of these studies, gas chromatography (GC) and GC-MS (mass spectrometry) was optimized to detect specific low molecular weight products (<200 Da) in a targeted approach, e.g., methyl thioacetate, amino acids, hydroxy acids, and closely related molecules. Liquid chromatography mass spectrometry (LC-MS) was utilized for the detection of larger molecules including peptides exceeding a molecular weight of 200 Da. Although being less sensitive than GC-MS or LC-MS, NMR spectroscopy benefitted the structural determination of relevant products, such as intermediates involved in a putative primordial peptide cycle. In future, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) seems to develop as a complementary method to analyze the compositional space of the products and reaction clusters in a non-targeted approach at unprecedented sensitivity and mass resolution (700,000 for m/z 250). Stable isotope labeling was important to differentiate between reaction products and artifacts but also to reveal the mechanisms of product formation. In this review; we summarize some of the developmental steps and key improvements in analytical procedures mainly used in own studies of metabolic evolution. Full article
(This article belongs to the Special Issue Analytical Chemistry in Astrobiology)
Show Figures

Figure 1

Open AccessReview
Investigating Prebiotic Protocells for a Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective
Life 2019, 9(2), 49; https://doi.org/10.3390/life9020049 - 07 Jun 2019
Cited by 7 | Viewed by 2211
Abstract
Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films [...] Read more.
Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
Show Figures

Figure 1

Open AccessArticle
Profiling Murchison Soluble Organic Matter for New Organic Compounds with APPI- and ESI-FT-ICR MS
Life 2019, 9(2), 48; https://doi.org/10.3390/life9020048 - 06 Jun 2019
Cited by 1 | Viewed by 2228
Abstract
The investigation of the abundant organic matter in primitive meteorite such as carbonaceous chondrites is of major interest in the field of origin of life. In this study, the soluble organic fraction of the Murchison meteorite was analyzed by atmospheric pressure photoionization (APPI) [...] Read more.
The investigation of the abundant organic matter in primitive meteorite such as carbonaceous chondrites is of major interest in the field of origin of life. In this study, the soluble organic fraction of the Murchison meteorite was analyzed by atmospheric pressure photoionization (APPI) and electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), in both detection modes. Such an approach ensured that we obtained an extensive description of the organic matter of the CM2 meteorite. Indeed, while in total close to 16,000 unique features were assigned, only 4% are common to all analyses, illustrating the complementarity of both the detection modes and the ionization sources. ESI FT-ICR MS analysis, in negative-ion mode, ensured to observe specifically CHOS and CHNOS species, whereas the positive-ion mode is more dedicated to the detection of CHNO and CHN species. Moreover, new organomagnesium components were observed in (+) ESI. Eventually, (+) APPI FT-ICR MS analysis was a preferred method for the detection of less polar or nonpolar species such as polycyclic aromatic hydrocarbons but also heteroatom aromatic species composing the organic matter of Murchison. Full article
(This article belongs to the Special Issue Analytical Chemistry in Astrobiology)
Show Figures

Graphical abstract

Open AccessReview
Methodologies for Analyzing Soluble Organic Compounds in Extraterrestrial Samples: Amino Acids, Amines, Monocarboxylic Acids, Aldehydes, and Ketones
Life 2019, 9(2), 47; https://doi.org/10.3390/life9020047 - 06 Jun 2019
Cited by 3 | Viewed by 2018
Abstract
Soluble organic compositions of extraterrestrial samples offer valuable insights into the prebiotic organic chemistry of the solar system. This review provides a summary of the techniques commonly used for analyzing amino acids, amines, monocarboxylic acids, aldehydes, and ketones in extraterrestrial samples. Here, we [...] Read more.
Soluble organic compositions of extraterrestrial samples offer valuable insights into the prebiotic organic chemistry of the solar system. This review provides a summary of the techniques commonly used for analyzing amino acids, amines, monocarboxylic acids, aldehydes, and ketones in extraterrestrial samples. Here, we discuss possible effects of various experimental factors (e.g., extraction protocols, derivatization methods, and chromatographic techniques) in order to highlight potential influences on the results obtained from different methodologies. This detailed summary and assessment of current techniques is intended to serve as a basic guide for selecting methodologies for soluble organic analyses and to emphasize some key considerations for future method development. Full article
(This article belongs to the Special Issue Analytical Chemistry in Astrobiology)
Show Figures

Figure 1

Open AccessArticle
Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations
Life 2019, 9(2), 46; https://doi.org/10.3390/life9020046 - 04 Jun 2019
Cited by 2 | Viewed by 1638
Abstract
The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation [...] Read more.
The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history. Full article
Show Figures

Figure 1

Open AccessReview
Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior
Life 2019, 9(2), 45; https://doi.org/10.3390/life9020045 - 03 Jun 2019
Cited by 6 | Viewed by 1516
Abstract
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent [...] Read more.
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of these simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
Show Figures

Figure 1

Open AccessArticle
A Mineralogical Context for the Organic Matter in the Paris Meteorite Determined by A Multi-Technique Analysis
Life 2019, 9(2), 44; https://doi.org/10.3390/life9020044 - 30 May 2019
Viewed by 1427
Abstract
This study is a multi-technique investigation of the Paris carbonaceous chondrite directly applied on two selected 500 × 500 µm² areas of a millimetric fragment, without any chemical extraction. By mapping the partial hydration of the amorphous silicate phase dominating the meteorite sample [...] Read more.
This study is a multi-technique investigation of the Paris carbonaceous chondrite directly applied on two selected 500 × 500 µm² areas of a millimetric fragment, without any chemical extraction. By mapping the partial hydration of the amorphous silicate phase dominating the meteorite sample matrix, infrared spectroscopy gave an interesting glimpse into the way the fluid may have circulated into the sample and partially altered it. The TOF-SIMS in-situ analysis allowed the studying and mapping of the wide diversity of chemical moieties composing the meteorite organic content. The results of the combined techniques show that at the micron scale, the organic matter was always spatially associated with the fine-grained and partially-hydrated amorphous silicates and to the presence of iron in different chemical states. These systematic associations, illustrated in previous studies of other carbonaceous chondrites, were further supported by the identification by TOF-SIMS of cyanide and/or cyanate salts that could be direct remnants of precursor ices that accreted with dust during the parent body formation, and by the detection of different metal-containing large organic ions. Finally, the results obtained emphasized the importance of studying the specific interactions taking place between organic and mineral phases in the chondrite matrix, in order to investigate their role in the evolution story of primitive organic matter in meteorite parent bodies. Full article
(This article belongs to the Special Issue Analytical Chemistry in Astrobiology)
Show Figures

Figure 1

Open AccessArticle
Phosphates as Energy Sources to Expand Metabolic Networks
Life 2019, 9(2), 43; https://doi.org/10.3390/life9020043 - 22 May 2019
Cited by 3 | Viewed by 1813
Abstract
Phosphates are essential for modern metabolisms. A recent study reported a phosphate-free metabolic network and suggested that thioesters, rather than phosphates, could alleviate thermodynamic bottlenecks of network expansion. As a result, it was considered that a phosphorus-independent metabolism could exist before the phosphate-based [...] Read more.
Phosphates are essential for modern metabolisms. A recent study reported a phosphate-free metabolic network and suggested that thioesters, rather than phosphates, could alleviate thermodynamic bottlenecks of network expansion. As a result, it was considered that a phosphorus-independent metabolism could exist before the phosphate-based genetic coding system. To explore the origin of phosphorus-dependent metabolism, the present study constructs a protometabolic network that contains phosphates prebiotically available using computational systems biology approaches. It is found that some primitive phosphorylated intermediates could greatly alleviate thermodynamic bottlenecks of network expansion. Moreover, the phosphorus-dependent metabolic network exhibits several ancient features. Taken together, it is concluded that phosphates played a role as important as that of thioesters during the origin and evolution of metabolism. Both phosphorus and sulfur are speculated to be critical to the origin of life. Full article
Show Figures

Figure 1

Open AccessArticle
Mathematical Analysis of a Prototypical Autocatalytic Reaction Network
Life 2019, 9(2), 42; https://doi.org/10.3390/life9020042 - 20 May 2019
Cited by 1 | Viewed by 1720
Abstract
Network autocatalysis, which is autocatalysis whereby a catalyst is not directly produced in a catalytic cycle, is likely to be more common in chemistry than direct autocatalysis is. Nevertheless, the kinetics of autocatalytic networks often does not exactly follow simple quadratic or cubic [...] Read more.
Network autocatalysis, which is autocatalysis whereby a catalyst is not directly produced in a catalytic cycle, is likely to be more common in chemistry than direct autocatalysis is. Nevertheless, the kinetics of autocatalytic networks often does not exactly follow simple quadratic or cubic rate laws and largely depends on the structure of the network. In this article, we analyzed one of the simplest and most chemically plausible autocatalytic networks where a catalytic cycle is coupled to an ancillary reaction that produces the catalyst. We analytically analyzed deviations in the kinetics of this network from its exponential growth and numerically studied the competition between two networks for common substrates. Our results showed that when quasi-steady-state approximation is applicable for at least one of the components, the deviation from the exponential growth is small. Numerical simulations showed that competition between networks results in the mutual exclusion of autocatalysts; however, the presence of a substantial noncatalytic conversion of substrates will create broad regions where autocatalysts can coexist. Thus, we should avoid the accumulation of intermediates and the noncatalytic conversion of the substrate when designing experimental systems that need autocatalysis as a source of positive feedback or as a source of evolutionary pressure. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
Show Figures

Graphical abstract

Open AccessEditorial
Exploring the Kamchatka Geothermal Region in the Context of Life’s Beginning
Life 2019, 9(2), 41; https://doi.org/10.3390/life9020041 - 16 May 2019
Viewed by 1438
Abstract
This article is a brief review of research in the Kamchatka geothermal region initiated by David Deamer and the author in 1999. Results obtained over the last 20 years are described, including a seminal experiment in which biologically important organic compounds were dispersed [...] Read more.
This article is a brief review of research in the Kamchatka geothermal region initiated by David Deamer and the author in 1999. Results obtained over the last 20 years are described, including a seminal experiment in which biologically important organic compounds were dispersed in a hot spring to determine their fate. Other investigations include ionic and organic composition of hydrothermal water, the source of hydrothermally generated oil, and pressure–temperature oscillations in hydrothermal systems. The relation of these results to research on the origin of life is discussed. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
Show Figures

Figure 1

Open AccessCommunication
Chemistry of Homocysteine Thiolactone in A Prebiotic Perspective
Life 2019, 9(2), 40; https://doi.org/10.3390/life9020040 - 16 May 2019
Cited by 4 | Viewed by 1437
Abstract
Homocysteine is a non-proteinogenic sulfur-containing amino acid. Like cysteine, it can form disulfide bridges and complex metallic cations. It is also closely related to methionine, the first amino acid in the synthesis of all contemporary proteins. Furthermore, its cyclized form, a five-membered ring [...] Read more.
Homocysteine is a non-proteinogenic sulfur-containing amino acid. Like cysteine, it can form disulfide bridges and complex metallic cations. It is also closely related to methionine, the first amino acid in the synthesis of all contemporary proteins. Furthermore, its cyclized form, a five-membered ring thiolactone, is stable in acidic and neutral water. Here, we demonstrate that this thiolactone may have been formed in the primitive ocean directly from the Strecker precursor of homocysteine, an aminonitrile. Even though it is poorly reactive, this thiolactone may be open by some amines, yielding amides which, in turn, could be the precursors of longer peptides. Full article
Show Figures

Graphical abstract

Open AccessEditorial
Developmental Biology in Cyanobacteria
Life 2019, 9(2), 39; https://doi.org/10.3390/life9020039 - 10 May 2019
Viewed by 1584
Abstract
Filamentous, heterocyst-forming cyanobacteria are phototrophic multicellular organisms in which N2-fixing heterocysts and CO2-fixing vegetative cells exchange regulators and nutrients [...] Full article
(This article belongs to the Special Issue Developmental Biology in Cyanobacteria)
Open AccessReview
Protobiotic Systems Chemistry Analyzed by Molecular Dynamics
Life 2019, 9(2), 38; https://doi.org/10.3390/life9020038 - 10 May 2019
Cited by 9 | Viewed by 2130
Abstract
Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer [...] Read more.
Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
Show Figures

Figure 1

Open AccessReview
A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code
Life 2019, 9(2), 37; https://doi.org/10.3390/life9020037 - 04 May 2019
Cited by 10 | Viewed by 2988
Abstract
Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by sequence. Specifically, structural class IA aaRS enzymes derive from class [...] Read more.
Pathways of standard genetic code evolution remain conserved and apparent, particularly upon analysis of aminoacyl-tRNA synthetase (aaRS) lineages. Despite having incompatible active site folds, class I and class II aaRS are homologs by sequence. Specifically, structural class IA aaRS enzymes derive from class IIA aaRS enzymes by in-frame extension of the protein N-terminus and by an alternate fold nucleated by the N-terminal extension. The divergence of aaRS enzymes in the class I and class II clades was analyzed using the Phyre2 protein fold recognition server. The class I aaRS radiated from the class IA enzymes, and the class II aaRS radiated from the class IIA enzymes. The radiations of aaRS enzymes bolster the coevolution theory for evolution of the amino acids, tRNAomes, the genetic code, and aaRS enzymes and support a tRNA anticodon-centric perspective. We posit that second- and third-position tRNA anticodon sequence preference (C>(U~G)>A) powerfully selected the sectoring pathway for the code. GlyRS-IIA appears to have been the primordial aaRS from which all aaRS enzymes evolved, and glycine appears to have been the primordial amino acid around which the genetic code evolved. Full article
(This article belongs to the Section Hypotheses in the Life Sciences)
Show Figures

Figure 1

Open AccessEditorial
David Deamer: Five Decades of Research on the Question of How Life Can Begin
Life 2019, 9(2), 36; https://doi.org/10.3390/life9020036 - 02 May 2019
Cited by 1 | Viewed by 2305
Abstract
In commemoration of his 80th birthday, this interview article engages David Deamer in some personal and scientific insights into his fifty year quest surrounding the question of “how can life begin” on the Earth or other worlds. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
Show Figures

Graphical abstract

Open AccessArticle
Data-Driven UPLC-Orbitrap MS Analysis in Astrochemistry
Life 2019, 9(2), 35; https://doi.org/10.3390/life9020035 - 02 May 2019
Cited by 3 | Viewed by 1877
Abstract
Meteorites have been found to be rich and highly diverse in organic compounds. Next to previous direct infusion high resolution mass spectrometry experiments (DI-HR-MS), we present here data-driven strategies to evaluate UPLC-Orbitrap MS analyses. This allows a comprehensive mining of structural isomers extending [...] Read more.
Meteorites have been found to be rich and highly diverse in organic compounds. Next to previous direct infusion high resolution mass spectrometry experiments (DI-HR-MS), we present here data-driven strategies to evaluate UPLC-Orbitrap MS analyses. This allows a comprehensive mining of structural isomers extending the level of information on the molecular diversity in astrochemical materials. As a proof-of-concept study, Murchison and Allende meteorites were analyzed. Both, global organic fingerprint and specific isomer analyses are discussed. Up to 31 different isomers per molecular composition are present in Murchison suggesting the presence of ≈440,000 different compounds detected therein. By means of this time-resolving high resolution mass spectrometric method, we go one step further toward the characterization of chemical structures within complex extraterrestrial mixtures, enabling a better understanding of organic chemical evolution, from interstellar ices toward small bodies in the Solar System. Full article
(This article belongs to the Special Issue Analytical Chemistry in Astrobiology)
Show Figures

Graphical abstract

Open AccessArticle
Production of Carbamic Acid Dimer from Ammonia-Carbon Dioxide Ices: Matching Observed and Computed IR Spectra
Life 2019, 9(2), 34; https://doi.org/10.3390/life9020034 - 23 Apr 2019
Cited by 1 | Viewed by 1501
Abstract
The production of complex molecules in ammonia–carbon dioxide ices is presumed to pass through species of formula H3N:CO2 with further addition of ammonia and carbon dioxide. One possible landmark, carbamic acid, H2NCOOH, has been implicated among the products [...] Read more.
The production of complex molecules in ammonia–carbon dioxide ices is presumed to pass through species of formula H3N:CO2 with further addition of ammonia and carbon dioxide. One possible landmark, carbamic acid, H2NCOOH, has been implicated among the products of warming and irradiation of such ices. Experimental study of the IR spectra of residues has suggested the presence of related species, including weakly bound 1:1 and 2:1 complexes of ammonia with carbon dioxide, zwitterionic carbamic acid, ammonium carbamate, and the dimer of carbamic acid. We computed the energetics and vibrational spectra of these species as well as the complex between ammonia and carbamic acid for gas and condensed phases. By means of a new spectrum-matching scoring between computed and observed vibrational spectra, we infer species that are most probably present. The leading candidates are ammonium carbamate, the carbamic acid–ammonia complex, and the carbamic acid dimer. Full article
Show Figures

Figure 1

Open AccessArticle
Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions
Life 2019, 9(2), 33; https://doi.org/10.3390/life9020033 - 04 Apr 2019
Cited by 1 | Viewed by 2035
Abstract
The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible [...] Read more.
The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible pathway for life emergence, and is by no means be a demonstration of how life really emerged. The best we can hope for is to indicate plausible chemical–physical conditions and mechanisms that might lead to self-organizing and autopoietic systems. Here we present a stochastic simulation, based on chemical reactions already observed in prebiotic environments, that might help in the design of new experiments. We will show how the definition of simple rules for the synthesis of random peptides may lead to the appearance of networks of autocatalytic cycles and the emergence of memory. Full article
Show Figures

Graphical abstract

Open AccessReview
Metalloproteins in the Biology of Heterocysts
Life 2019, 9(2), 32; https://doi.org/10.3390/life9020032 - 03 Apr 2019
Cited by 7 | Viewed by 2025
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N2 fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological [...] Read more.
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N2 fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O2 evolution and CO2 fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N2 fixation, H2 metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts. Full article
(This article belongs to the Special Issue Developmental Biology in Cyanobacteria)
Show Figures

Figure 1

Open AccessEditorial
Extreme-Fungi and the Benefits of A Stressing Life
Life 2019, 9(2), 31; https://doi.org/10.3390/life9020031 - 27 Mar 2019
Cited by 1 | Viewed by 1374
Abstract
A stress-free condition is considered for humans to be related to relaxation or happiness [...] Full article
(This article belongs to the Special Issue Fungi from Extreme Environments)
Previous Issue
Next Issue
Back to TopTop