Life | September 2016 - Browse Articles

3220 KiB

Open AccessArticle

Functional Annotations of Paralogs: A Blessing and a Curse

by Rémi Zallot, Katherine J. Harrison, Bryan Kolaczkowski and Valérie De Crécy-Lagard

Life 2016, 6(3), 39; https://doi.org/10.3390/life6030039 - 08 Sep 2016

Cited by 39 | Viewed by 11319

Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately [...] Read more.

Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines. Here we describe how integrating evolutionary and functional information such as genome context, phylogeny, metabolic reconstruction and signature motifs may be required to correctly annotate multifunctional families. These integrative analyses can also lead to the discovery of novel gene functions, as hints from specific subgroups can guide the functional characterization of other members of the family. We demonstrate how careful manual curation processes using comparative genomics can disambiguate subgroups within large multifunctional families and discover their functions. We present the COG0720 protein family as a case study. We also discuss strategies to automate this process to improve the accuracy of genome functional annotation pipelines. Full article

(This article belongs to the Section Genetics and Genomics)

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1496 KiB

Open AccessArticle

Evidence Supporting the Uptake and Genomic Incorporation of Environmental DNA in the “Ancient Asexual” Bdelloid Rotifer Philodina roseola

by Olaf R. P. Bininda-Emonds, Claus Hinz and Wilko H. Ahlrichs

Life 2016, 6(3), 38; https://doi.org/10.3390/life6030038 - 06 Sep 2016

Cited by 3 | Viewed by 6010

Abstract

Increasing evidence suggests that bdelloid rotifers regularly undergo horizontal gene transfer, apparently as a surrogate mechanism of genetic exchange in the absence of true sexual reproduction, in part because of their ability to withstand desiccation. We provide empirical support for this latter hypothesis [...] Read more.

Increasing evidence suggests that bdelloid rotifers regularly undergo horizontal gene transfer, apparently as a surrogate mechanism of genetic exchange in the absence of true sexual reproduction, in part because of their ability to withstand desiccation. We provide empirical support for this latter hypothesis using the bdelloid Philodina roseola, which we demonstrate to readily internalize environmental DNA in contrast to a representative monogonont rotifer (Brachionus rubens), which, like other monogononts, is facultative sexual and cannot withstand desiccation. In addition, environmental DNA that was more similar to the host DNA was retained more often and for a longer period of time. Indirect evidence (increased variance in the reproductive output of the untreated F1 generation) suggests that environmental DNA can be incorporated into the genome during desiccation and is thus heritable. Our observed fitness effects agree with sexual theory and also occurred when the animals were desiccated in groups (thereby acting as DNA donors), but not individually, indicating the mechanism could occur in nature. Thus, although DNA uptake and its genomic incorporation appears proximally related to anhydrobiosis in bdelloids, it might also facilitate accidental genetic exchange with closely related taxa, thereby maintaining higher levels of genetic diversity than is otherwise expected for this group of “ancient asexuals”. Full article

(This article belongs to the Section Genetics and Genomics)

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2396 KiB

Open AccessArticle

Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea

by Daniel L. Jones and Bonnie K. Baxter

Life 2016, 6(3), 37; https://doi.org/10.3390/life6030037 - 02 Sep 2016

Cited by 12 | Viewed by 8018

Abstract

Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional [...] Read more.

Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions. However, this speculation overlooks the other bipyrimidine sequences, all of which capable of forming photolesions to varying degrees. Therefore, we designed a program to determine the frequencies of the four bipyrimidine pairs (5’ to 3’: TT, TC, CT, and CC) within genomes of halophilic archaea and four other randomized sample groups for comparison. The outputs for each sampled genome were weighted by the intrinsic photoreactivities of each dinucleotide pair. Statistical methods were employed to investigate intergroup differences. Our findings indicate that the UV-resistance seen in halophilic archaea can be attributed in part to a genomic strategy: high G + C content and the resulting bipyrimidine signature reduces the genomic photoreactivity. Full article

(This article belongs to the Special Issue Proceedings from the 11th Conference on Halophilic Microorganisms Halophiles 2016)

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1229 KiB

Open AccessEditorial

The Genetic Code: Francis Crick’s Legacy and Beyond

by Koji Tamura

Life 2016, 6(3), 36; https://doi.org/10.3390/life6030036 - 25 Aug 2016

Cited by 7 | Viewed by 8291

Abstract

Francis Crick (Figure 1) was born on 8 June 1916, in Northampton, England, and passed away on 28 July 2004, in La Jolla, California, USA.[...] Full article

(This article belongs to the Special Issue The Origin and Evolution of the Genetic Code: 100th Anniversary Year of the Birth of Francis Crick)

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Open AccessArticle

The Use of a Fractional Factorial Design to Determine the Factors That Impact 1,3-Propanediol Production from Glycerol by Halanaerobium hydrogeniformans

by Shivani Kalia, Jordan Trager, Oliver C. Sitton and Melanie R. Mormile

Life 2016, 6(3), 35; https://doi.org/10.3390/life6030035 - 20 Aug 2016

Cited by 1 | Viewed by 4999

Abstract

In recent years, biodiesel, a substitute for fossil fuels, has led to the excessive production of crude glycerol. The resulting crude glycerol can possess a high concentration of salts and an alkaline pH. Moreover, current crude glycerol purification methods are expensive, rendering this [...] Read more.

In recent years, biodiesel, a substitute for fossil fuels, has led to the excessive production of crude glycerol. The resulting crude glycerol can possess a high concentration of salts and an alkaline pH. Moreover, current crude glycerol purification methods are expensive, rendering this former commodity a waste product. However, Halanaerobium hydrogeniformans, a haloalkaliphilic bacterium, possesses the metabolic capability to convert glycerol into 1,3-propanediol, a valuable commodity compound, without the need for salt dilution or adjusting pH when grown on this waste. Experiments were performed with different combinations of 24 medium components to determine their impact on the production of 1,3-propanediol by using a fractional factorial design. Tested medium components were selected based on data from the organism’s genome. Analysis of HPLC data revealed enhanced production of 1,3-propanediol with additional glycerol, pH, vitamin B₁₂, ammonium ions, sodium sulfide, cysteine, iron, and cobalt. However, other selected components; nitrate ions, phosphate ions, sulfate ions, sodium:potassium ratio, chloride, calcium, magnesium, silicon, manganese, zinc, borate, nickel, molybdenum, tungstate, copper and aluminum, did not enhance 1,3-propanediol production. The use of a fractional factorial design enabled the quick and efficient assessment of the impact of 24 different medium components on 1,3-propanediol production from glycerol from a haloalkaliphilic bacterium. Full article

(This article belongs to the Special Issue Proceedings from the 11th Conference on Halophilic Microorganisms Halophiles 2016)

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1724 KiB

Open AccessConcept Paper

Pressure as a Limiting Factor for Life

by Rachael Hazael, Filip Meersman, Fumihisa Ono and Paul F. McMillan

Life 2016, 6(3), 34; https://doi.org/10.3390/life6030034 - 17 Aug 2016

Cited by 20 | Viewed by 6147

Abstract

Facts concerning the stability and functioning of key biomolecular components suggest that cellular life should no longer be viable above a few thousand atmospheres (200–300 MPa). However, organisms are seen to survive in the laboratory to much higher pressures, extending into the GPa [...] Read more.

Facts concerning the stability and functioning of key biomolecular components suggest that cellular life should no longer be viable above a few thousand atmospheres (200–300 MPa). However, organisms are seen to survive in the laboratory to much higher pressures, extending into the GPa or even tens of GPa ranges. This is causing main questions to be posed concerning the survival mechanisms of simple to complex organisms. Understanding the ultimate pressure survival of organisms is critical for food sterilization and agricultural products conservation technologies. On Earth the deep biosphere is limited in its extent by geothermal gradients but if life forms exist in cooler habitats elsewhere then survival to greater depths must be considered. The extent of pressure resistance and survival appears to vary greatly with the timescale of the exposure. For example, shock experiments on nanosecond timescales reveal greatly enhanced survival rates extending to higher pressure. Some organisms could survive bolide impacts thus allowing successful transport between planetary bodies. We summarize some of the main questions raised by recent results and their implications for the survival of life under extreme compression conditions and its possible extent in the laboratory and throughout the universe. Full article

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

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2149 KiB

Open AccessReview

A Self-Assembled Aggregate Composed of a Fatty Acid Membrane and the Building Blocks of Biological Polymers Provides a First Step in the Emergence of Protocells

by Roy A. Black and Matthew C. Blosser

Life 2016, 6(3), 33; https://doi.org/10.3390/life6030033 - 11 Aug 2016

Cited by 37 | Viewed by 12809

Abstract

We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of [...] Read more.

We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then explain how the conformational constraints and altered chemical environment due to binding of the components to the membrane could facilitate the formation of nucleosides, oligonucleotides and peptides. We conclude by discussing how the resulting oligomers, even if short and random, could have increased vesicle stability and growth more than their building blocks did, and how competition among these vesicles could have led to longer polymers with complex functions. Full article

(This article belongs to the Special Issue Origin of Cellular Life)

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1317 KiB

Open AccessOpinion

Ultra Large Gene Families: A Matter of Adaptation or Genomic Parasites?

by Philipp H. Schiffer, Jan Gravemeyer, Martina Rauscher and Thomas Wiehe

Life 2016, 6(3), 32; https://doi.org/10.3390/life6030032 - 08 Aug 2016

Cited by 7 | Viewed by 5953

Abstract

Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly) deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution [...] Read more.

Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly) deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR)-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome. We were interested to see whether such a tight clustering is characteristic for ultra large gene families. Our data reconfirm that most gene family inflations are lineage-specific, but we can only identify very few gene clusters. Based on our observations we hypothesise that, beyond a certain size threshold, ultra large gene families continue to proliferate in a mechanism we term “run-away evolution”. This process might ultimately lead to the failure of genomic integrity and drive species to extinction. Full article

(This article belongs to the Special Issue Structure and Evolution of Genome)

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2470 KiB

Open AccessArticle

AglM and VNG1048G, Two Haloarchaeal UDP-Glucose Dehydrogenases, Show Different Salt-Related Behaviors

by Lina Kandiba and Jerry Eichler

Life 2016, 6(3), 31; https://doi.org/10.3390/life6030031 - 03 Aug 2016

Viewed by 4290

Abstract

Haloferax volcanii AglM and Halobacterium salinarum VNG1048G are UDP-glucose dehydrogenases involved in N-glycosylation in each species. Despite sharing >60% sequence identity and the ability of VNG1048G to functionally replace AglM in vivo, these proteins behaved differently as salinity changed. Whereas AglM was [...] Read more.

Haloferax volcanii AglM and Halobacterium salinarum VNG1048G are UDP-glucose dehydrogenases involved in N-glycosylation in each species. Despite sharing >60% sequence identity and the ability of VNG1048G to functionally replace AglM in vivo, these proteins behaved differently as salinity changed. Whereas AglM was active in 2–4 M NaCl, VNG1048G lost much of its activity when salinity dropped below 3 M NaCl. To understand the molecular basis of this phenomenon, each protein was examined by size exclusion chromatrography in 2 M NaCl. Whereas AglM appeared as a dodecamer, VNG1048G was essentially detected as a dodecamer and a dimer. The specific activity of the VNG1048G dodecamer was only a sixth of that of AglM, while the dimer was inactive. As such, not only was the oligomeric status of VNG1048G affected by lowered salinity, so was the behavior of the individual dodecamer subunits. Analyzing surface-exposed residues in homology models of the two UDP-glucose dehydrogenases revealed the more acidic and less basic VNG1048G surface, further explaining the greater salt-dependence of the Hbt. salinarum enzyme. Full article

(This article belongs to the Special Issue Proceedings from the 11th Conference on Halophilic Microorganisms Halophiles 2016)

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984 KiB

Open AccessArticle

Gene-Family Extension Measures and Correlations

by Gon Carmi and Alexander Bolshoy

Life 2016, 6(3), 30; https://doi.org/10.3390/life6030030 - 03 Aug 2016

Cited by 1 | Viewed by 4948

Abstract

The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that [...] Read more.

The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. Additionally, it was found that several atypical microbes deviated from the observed general trend. In this study, we reexamined these associations on a larger dataset consisting of 1484 prokaryotic genomes and using several ranking approaches. We applied ranking methods in such a way that genomes with lower numbers of gene copies would have lower rank. Until now only simple ranking methods were used; we applied the Kemeny optimal aggregation approach as well. Regression and correlation analysis were utilized in order to accurately quantify and characterize the relationships between measures of paralog indices and genome size. In addition, boxplot analysis was employed as a method for outlier detection. We found that, in general, all paralog indexes positively correlate with an increase of genome size. As expected, different groups of atypical prokaryotic genomes were found for different types of paralog quantities. Mycoplasmataceae and Halobacteria appeared to be among the most interesting candidates for further research of evolution through gene duplication. Full article

(This article belongs to the Special Issue Structure and Evolution of Genome)

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2451 KiB

Open AccessArticle

A Hypothesis: Life Initiated from Two Genes, as Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems

by Kunio Kawamura

Life 2016, 6(3), 29; https://doi.org/10.3390/life6030029 - 02 Aug 2016

Cited by 7 | Viewed by 9802

Abstract

RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of [...] Read more.

RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life. For instance, an RNA-based life-like system should possess enough stability to resist environmental perturbations, by developing a cell-like compartment, for instance. Here, a conceptual viewpoint is summarized to provide a realistic life-like system that is compatible with the primitive Earth environment and the capabilities of RNA molecules. According to the empirical and conceptual analysis, I propose the hypothesis that the first life-like system could have initiated from only two genes. Full article

(This article belongs to the Special Issue Origin of Cellular Life)

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Open AccessArticle

Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis

by David S. Ross and David Deamer

Life 2016, 6(3), 28; https://doi.org/10.3390/life6030028 - 26 Jul 2016

Cited by 94 | Viewed by 8062

Abstract

The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how [...] Read more.

The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium N_m + N_n ↔ N_m+n + H₂O is endoergic by about 3.3 kcal/mol for polynucleotide formation, and the system thus lies far to the left in the starting solutions. Kinetic simulations of the evaporation showed that simple Le Châtelier’s principle shifts were insufficient, but the introduction of oligomer-stabilizing factors of 5–10 kcal/mol both moved the process to the right and respectively boosted and retarded the elongation and hydrolysis rates. Molecular crowding and excluded volume effects in present-day cells yield stabilizing factors of that order, and we argue here that the crowded conditions in the evaporites generate similar effects. Oligomer formation is thus energetically preferred in those settings, but the process is thwarted in each evaporation step as diffusion becomes rate limiting. Rehydration dissipates disordered oligomer clusters in the evaporites, however, and subsequent dry/wet cycling accordingly “ratchets up” the system to an ultimate population of kinetically trappedthermodynamically preferred biopolymers. Full article

(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)

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1058 KiB

Open AccessArticle

Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals

by Diana Chernikova, David Managadze, Galina V. Glazko, Wojciech Makalowski and Igor B. Rogozin

Life 2016, 6(3), 27; https://doi.org/10.3390/life6030027 - 15 Jul 2016

Cited by 10 | Viewed by 6517

Abstract

The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which [...] Read more.

The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important. Full article

(This article belongs to the Special Issue Structure and Evolution of Genome)

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1854 KiB

Open AccessReview

Constructive Approaches for Understanding the Origin of Self-Replication and Evolution

by Norikazu Ichihashi and Tetsuya Yomo

Life 2016, 6(3), 26; https://doi.org/10.3390/life6030026 - 13 Jul 2016

Cited by 20 | Viewed by 8500

Abstract

The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is [...] Read more.

The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules. Using this approach, we are able to employ design principles to reproduce life-specific functions, and the knowledge gained through the reproduction process provides clues as to their origins. In this mini-review, we introduce recent insights gained using this approach, and propose important future directions for advancing our understanding of the origins of life. Full article

(This article belongs to the Special Issue Origin of Cellular Life)

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300 KiB

Open AccessEssay

The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life

by William Bains and Dirk Schulze-Makuch

Life 2016, 6(3), 25; https://doi.org/10.3390/life6030025 - 30 Jun 2016

Cited by 28 | Viewed by 22894

Abstract

Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key [...] Read more.

Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe. Full article

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