1
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Rork AM, Bala AS, Renner T. Dynamic evolution of the mTHF gene family associated with primary metabolism across life. BMC Genomics 2024; 25:432. [PMID: 38693486 PMCID: PMC11064299 DOI: 10.1186/s12864-024-10159-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 02/25/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND The folate cycle of one-carbon (C1) metabolism, which plays a central role in the biosynthesis of nucleotides and amino acids, demonstrates the significance of metabolic adaptation. We investigated the evolutionary history of the methylenetetrahydrofolate dehydrogenase (mTHF) gene family, one of the main drivers of the folate cycle, across life. RESULTS Through comparative genomic and phylogenetic analyses, we found that several lineages of Archaea lacked domains vital for folate cycle function such as the mTHF catalytic and NAD(P)-binding domains of FolD. Within eukaryotes, the mTHF gene family diversified rapidly. For example, several duplications have been observed in lineages including the Amoebozoa, Opisthokonta, and Viridiplantae. In a common ancestor of Opisthokonta, FolD and FTHFS underwent fusion giving rise to the gene MTHFD1, possessing the domains of both genes. CONCLUSIONS Our evolutionary reconstruction of the mTHF gene family associated with a primary metabolic pathway reveals dynamic evolution, including gene birth-and-death, gene fusion, and potential horizontal gene transfer events and/or amino acid convergence.
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Affiliation(s)
- Adam M Rork
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA.
- Department of Entomology, Purdue University, West Lafayette, Indiana, 47907, USA.
| | - Arthi S Bala
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, 20007, USA
- School of Medicine, Georgetown University, Washington, DC, 20007, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA.
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2
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Shen L, Liu Y, Chen L, Lei T, Ren P, Ji M, Song W, Lin H, Su W, Wang S, Rooman M, Pucci F. Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group. THE ISME JOURNAL 2024; 18:wrad020. [PMID: 38365240 PMCID: PMC10837837 DOI: 10.1093/ismejo/wrad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.
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Affiliation(s)
- Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu 241000, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tingting Lei
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wei Su
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
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3
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Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat Commun 2022; 13:4110. [PMID: 35840579 PMCID: PMC9287336 DOI: 10.1038/s41467-022-31847-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/06/2022] [Indexed: 11/09/2022] Open
Abstract
The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota. Phylum-level analysis reveals that Thermoplasmatota evolution had been punctuated by several periods of high levels of novel gene family acquisition. Several essential metabolisms, such as aerobic respiration and acid tolerance, were likely acquired independently by divergent lineages through convergent evolution rather than inherited from a common ancestor. Ultimately, this study describes the terrestrially prevalent Lutacidiciplasmatales and highlights convergent evolution as an important driving force in the evolution of archaeal lineages.
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4
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Gophna U, Altman-Price N. Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution. Annu Rev Microbiol 2022; 76:481-502. [PMID: 35667126 DOI: 10.1146/annurev-micro-040820-124627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; ,
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; , .,Department of Natural and Life Sciences, The Open University of Israel, Raanana, Israel
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5
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Prostova M, Shilkin E, Kulikova AA, Makarova A, Ryazansky S, Kulbachinskiy A. Noncanonical prokaryotic X family DNA polymerases lack polymerase activity and act as exonucleases. Nucleic Acids Res 2022; 50:6398-6413. [PMID: 35657103 PMCID: PMC9226535 DOI: 10.1093/nar/gkac461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/12/2022] Open
Abstract
The X family polymerases (PolXs) are specialized DNA polymerases that are found in all domains of life. While the main representatives of eukaryotic PolXs, which have dedicated functions in DNA repair, were studied in much detail, the functions and diversity of prokaryotic PolXs have remained largely unexplored. Here, by combining a comprehensive bioinformatic analysis of prokaryotic PolXs and biochemical experiments involving selected recombinant enzymes, we reveal a previously unrecognized group of PolXs that seem to be lacking DNA polymerase activity. The noncanonical PolXs contain substitutions of the key catalytic residues and deletions in their polymerase and dNTP binding sites in the palm and fingers domains, but contain functional nuclease domains, similar to canonical PolXs. We demonstrate that representative noncanonical PolXs from the Deinococcus genus are indeed inactive as DNA polymerases but are highly efficient as 3'-5' exonucleases. We show that both canonical and noncanonical PolXs are often encoded together with the components of the non-homologous end joining pathway and may therefore participate in double-strand break repair, suggesting an evolutionary conservation of this PolX function. This is a remarkable example of polymerases that have lost their main polymerase activity, but retain accessory functions in DNA processing and repair.
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Affiliation(s)
| | - Evgeniy Shilkin
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Alexandra A Kulikova
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Alena Makarova
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 4991960015; Fax: +7 4991960015;
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6
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Nobs SJ, MacLeod FI, Wong HL, Burns BP. Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life? Trends Microbiol 2021; 30:421-431. [PMID: 34863611 DOI: 10.1016/j.tim.2021.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
One of the most significant events in the evolution of life is the origin of the eukaryotic cell, an increase in cellular complexity that occurred approximately 2 billion years ago. Ground-breaking research has centered around unraveling the characteristics of the Last Eukaryotic Common Ancestor (LECA) and the nuanced archaeal and bacterial contributions in eukaryogenesis, resulting in fundamental changes in our understanding of the Tree of Life. The archaeal and bacterial roles are covered by theories of endosymbiogenesis wherein an ancestral host archaeon and a bacterial endosymbiont merged to create a new complex cell type - Eukarya - and its mitochondrion. Eukarya is often regarded as a unique and distinct domain due to complex innovations not found in archaea or bacteria, despite housing a chimeric genome containing genes of both archaeal and bacterial origin. However, the discovery of complex cell machineries in recently described Asgard archaeal lineages, and the growing support for diverse bacterial gene transfers prior to and during the time of LECA, is redefining our understanding of eukaryogenesis. Indeed, the uniqueness of Eukarya, as a domain, is challenged. It is likely that many microbial syntrophies, encompassing a 'microbial village', were required to 'raise' a eukaryote during the process of eukaryogenesis.
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Affiliation(s)
- Stephanie-Jane Nobs
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia.
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7
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Watson AK, Lopez P, Bapteste E. Hundreds of out-of-frame remodelled gene families in the E. coli pangenome. Mol Biol Evol 2021; 39:6430988. [PMID: 34792602 PMCID: PMC8788219 DOI: 10.1093/molbev/msab329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.
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Affiliation(s)
- Andrew K Watson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
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8
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Tria FDK, Martin WF. Gene Duplications Are At Least 50 Times Less Frequent than Gene Transfers in Prokaryotic Genomes. Genome Biol Evol 2021; 13:6380140. [PMID: 34599337 PMCID: PMC8536544 DOI: 10.1093/gbe/evab224] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 12/20/2022] Open
Abstract
The contribution of gene duplications to the evolution of eukaryotic genomes is well studied. By contrast, studies of gene duplications in prokaryotes are scarce and generally limited to a handful of genes or careful analysis of a few prokaryotic lineages. Systematic broad-scale studies of prokaryotic genomes that sample available data are lacking, leaving gaps in our understanding of the contribution of gene duplications as a source of genetic novelty in the prokaryotic world. Here, we report conservative and robust estimates for the frequency of recent gene duplications within prokaryotic genomes relative to recent lateral gene transfer (LGT), as mechanisms to generate multiple copies of related sequences in the same genome. We obtain our estimates by focusing on evolutionarily recent events among 5,655 prokaryotic genomes, thereby avoiding vagaries of deep phylogenetic inference and confounding effects of ancient events and differential loss. We find that recent, genome-specific gene duplications are at least 50 times less frequent and probably 100 times less frequent than recent, genome-specific, gene acquisitions via LGT. The frequency of gene duplications varies across lineages and functional categories. The findings improve our understanding of genome evolution in prokaryotes and have far-reaching implications for evolutionary models that entail LGT to gene duplications ratio as a parameter.
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Affiliation(s)
- Fernando D K Tria
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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9
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Watson AK, Lopez P, Bapteste E. Retracing lineage history: time to emphasize genetic turnover. Trends Microbiol 2021; 29:957-958. [PMID: 34452802 DOI: 10.1016/j.tim.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/07/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Andrew K Watson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, 75005 Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, 75005 Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, 75005 Paris, France.
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10
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Kozlowski LP. IPC 2.0: prediction of isoelectric point and pKa dissociation constants. Nucleic Acids Res 2021; 49:W285-W292. [PMID: 33905510 PMCID: PMC8262712 DOI: 10.1093/nar/gkab295] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/03/2021] [Accepted: 04/12/2021] [Indexed: 01/05/2023] Open
Abstract
The isoelectric point is the pH at which a particular molecule is electrically neutral due to the equilibrium of positive and negative charges. In proteins and peptides, this depends on the dissociation constant (pKa) of charged groups of seven amino acids and NH+ and COO− groups at polypeptide termini. Information regarding isoelectric point and pKa is extensively used in two-dimensional gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), crystallisation, and mass spectrometry. Therefore, there is a strong need for the in silico prediction of isoelectric point and pKa values. In this paper, I present Isoelectric Point Calculator 2.0 (IPC 2.0), a web server for the prediction of isoelectric points and pKa values using a mixture of deep learning and support vector regression models. The prediction accuracy (RMSD) of IPC 2.0 for proteins and peptides outperforms previous algorithms: 0.848 versus 0.868 and 0.222 versus 0.405, respectively. Moreover, the IPC 2.0 prediction of pKa using sequence information alone was better than the prediction from structure-based methods (0.576 versus 0.826) and a few folds faster. The IPC 2.0 webserver is freely available at www.ipc2-isoelectric-point.org
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Affiliation(s)
- Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Mazovian Voivodeship 02-097, Poland
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11
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Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP. The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biol Evol 2021; 13:6320066. [PMID: 34255041 PMCID: PMC8350355 DOI: 10.1093/gbe/evab166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2021] [Indexed: 12/12/2022] Open
Abstract
Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; whereas the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (distantly related groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/noncatalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN.
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Affiliation(s)
- Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Neri
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Sean Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Artemis S Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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12
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Aldeguer-Riquelme B, Ramos-Barbero MD, Santos F, Antón J. Environmental dissolved DNA harbours meaningful biological information on microbial community structure. Environ Microbiol 2021; 23:2669-2682. [PMID: 33817941 DOI: 10.1111/1462-2920.15510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/03/2021] [Indexed: 01/21/2023]
Abstract
Extracellular DNA (eDNA) comprises all the DNA molecules outside cells. This component of microbial ecosystems may serve as a source of nutrients and genetic information. Hypersaline environments harbour one of the highest concentrations of eDNA reported for natural systems, which has been attributed to the physicochemical preservative effect of salts and to high viral abundance. Here, we compared centrifugation and filtration protocols for the extraction of dissolved DNA (dDNA, as opposed to eDNA that also includes DNA from free viral particles) from a solar saltern crystallizer pond (CR30) water sample. The crystallizer dDNA fraction has been characterized, for the first time, and compared with cellular and viral metagenomes from the same location. High-speed centrifugation affected CR30 dDNA concentration and composition due to cell lysis, highlighting that protocol optimization should be the first step in dDNA studies. Crystallizer dDNA, which accounted for lower concentrations than those previously reported for hypersaline anoxic sediments, had a mixed viral and cellular origin, was enriched in archaeal DNA and had a distinctive taxonomic composition compared to that from the cellular assemblage of the same sample. Bioinformatic analyses indicated that nanohaloarchaeal viruses could be a cause for these differences.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain
| | | | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain.,Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, 03080, Spain
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13
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Abaramak G, Porras-Domínguez JR, Janse van Rensburg HC, Lescrinier E, Toksoy Öner E, Kırtel O, Van den Ende W. Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase. Microorganisms 2021; 9:microorganisms9040749. [PMID: 33918392 PMCID: PMC8066391 DOI: 10.3390/microorganisms9040749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/30/2022] Open
Abstract
Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.
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Affiliation(s)
- Gülbahar Abaramak
- IBSB-Industrial Biotechnology and Systems Biology Research Group, Bioengineering Department, Marmara University, Istanbul 34722, Turkey; (G.A.); (E.T.Ö.)
| | - Jaime Ricardo Porras-Domínguez
- Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium; (J.R.P.-D.); (H.C.J.v.R.)
| | | | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, P.O. Box 1041, 3000 Leuven, Belgium;
| | - Ebru Toksoy Öner
- IBSB-Industrial Biotechnology and Systems Biology Research Group, Bioengineering Department, Marmara University, Istanbul 34722, Turkey; (G.A.); (E.T.Ö.)
| | - Onur Kırtel
- IBSB-Industrial Biotechnology and Systems Biology Research Group, Bioengineering Department, Marmara University, Istanbul 34722, Turkey; (G.A.); (E.T.Ö.)
- Correspondence: (O.K.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium; (J.R.P.-D.); (H.C.J.v.R.)
- Correspondence: (O.K.); (W.V.d.E.)
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14
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Makkay AM, Louyakis AS, Ram-Mohan N, Gophna U, Gogarten JP, Papke RT. Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon. Sci Rep 2020; 10:22297. [PMID: 33339886 PMCID: PMC7749143 DOI: 10.1038/s41598-020-79296-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/19/2020] [Indexed: 12/16/2022] Open
Abstract
Horizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating in Hfx. volcanii.
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Affiliation(s)
- Andrea M Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Artemis S Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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15
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Gaba S, Kumari A, Medema M, Kaushik R. Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order. Sci Rep 2020; 10:21205. [PMID: 33273480 PMCID: PMC7713125 DOI: 10.1038/s41598-020-77723-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Halobacteria, a class of Euryarchaeota are extremely halophilic archaea that can adapt to a wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl. It consists of the orders: Halobacteriales, Haloferaciales and Natriabales. Pan-genome analysis of class Halobacteria was done to explore the core (300) and variable components (Softcore: 998, Cloud:36531, Shell:11784). The core component revealed genes of replication, transcription, translation and repair, whereas the variable component had a major portion of environmental information processing. The pan-gene matrix was mapped onto the core-gene tree to find the ancestral (44.8%) and derived genes (55.1%) of the Last Common Ancestor of Halobacteria. A High percentage of derived genes along with presence of transformation and conjugation genes indicate the occurrence of horizontal gene transfer during the evolution of Halobacteria. A Core and pan-gene tree were also constructed to infer a phylogeny which implicated on the new super-order comprising of Natrialbales and Halobacteriales.
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Affiliation(s)
- Sonam Gaba
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.,Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Abha Kumari
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Marnix Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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16
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Bapteste E, Papale F. Modeling the evolution of interconnected processes: It is the song and the singers: Tracking units of selection with interaction networks. Bioessays 2020; 43:e2000077. [PMID: 33165956 DOI: 10.1002/bies.202000077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 01/04/2023]
Abstract
Recently, Doolittle and Inkpen formulated a thought provoking theory, asserting that evolution by natural selection was responsible for the sideways evolution of two radically different kinds of selective units (also called Domains). The former entities, termed singers, correspond to the usual objects studied by evolutionary biologists (gene, genomes, individuals, species, etc.), whereas the later, termed songs, correspond to re-produced biological and ecosystemic functions, processes, information, and memes. Singers perform songs through selected patterns of interactions, meaning that a wealth of critical phenomena might receive novel evolutionary explanations. However, this theory did not provide an empirical approach to study evolution in such a broadened context. Here, we show that analyzing songs and singers, using patterns of interaction networks as a common ontology for both, offers a novel, actionable, inclusive and mathematical way to analyze not only the re-production but also the evolution and fitness of biological and ecosystemic interconnected processes.
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Affiliation(s)
- Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Bâtiment A 4ème étage, pièce 427, Paris, 75005, France
| | - François Papale
- Departement of Philosophy, University of Montreal, 2910 Édouard-Montpetit blvd, Montréal, QC, H3C 3J7, Canada
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17
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Martijn J, Schön ME, Lind AE, Vosseberg J, Williams TA, Spang A, Ettema TJG. Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition. Nat Commun 2020; 11:5490. [PMID: 33127909 PMCID: PMC7599335 DOI: 10.1038/s41467-020-19200-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/01/2020] [Indexed: 01/09/2023] Open
Abstract
Halobacteria (henceforth: Haloarchaea) are predominantly aerobic halophiles that are thought to have evolved from anaerobic methanogens. This remarkable transformation most likely involved an extensive influx of bacterial genes. Whether it entailed a single massive transfer event or a gradual stream of transfers remains a matter of debate. To address this, genomes that descend from methanogen-to-halophile intermediates are necessary. Here, we present five such near-complete genomes of Marine Group IV archaea (Hikarchaeia), the closest known relatives of Haloarchaea. Their inclusion in gene tree-aware ancestral reconstructions reveals an intermediate stage that had already lost a large number of genes, including nearly all of those involved in methanogenesis and the Wood-Ljungdahl pathway. In contrast, the last Haloarchaea common ancestor gained a large number of genes and expanded its aerobic respiration and salt/UV resistance gene repertoire. Our results suggest that complex and gradual patterns of gain and loss shaped the methanogen-to-halophile transition.
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Affiliation(s)
- Joran Martijn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Max E Schön
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Anders E Lind
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Julian Vosseberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Anja Spang
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Thijs J G Ettema
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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18
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Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments. mBio 2020; 11:mBio.02371-20. [PMID: 33051370 PMCID: PMC7554672 DOI: 10.1128/mbio.02371-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unlike all other archaeal lineages, ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread and abundant in all moderate and oxic environments on Earth. The evolutionary adaptations that led to such unprecedented ecological success of a microbial clade characterized by highly conserved energy and carbon metabolisms have, however, remained underexplored. Here, we reconstructed the genomic content and growth temperature of the ancestor of all AOA, as well as the ancestors of the marine and soil lineages, based on 39 available complete or nearly complete genomes of AOA. Our evolutionary scenario depicts an extremely thermophilic, autotrophic, aerobic ancestor from which three independent lineages of a marine and two terrestrial groups radiated into moderate environments. Their emergence was paralleled by (i) a continuous acquisition of an extensive collection of stress tolerance genes mostly involved in redox maintenance and oxygen detoxification, (ii) an expansion of regulatory capacities in transcription and central metabolic functions, and (iii) an extended repertoire of cell appendages and modifications related to adherence and interactions with the environment. Our analysis provides insights into the evolutionary transitions and key processes that enabled the conquest of the diverse environments in which contemporary AOA are found.
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19
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Arroyo AS, Lannes R, Bapteste E, Ruiz-Trillo I. Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition. Genome Biol Evol 2020; 12:1664-1678. [PMID: 32533833 PMCID: PMC7533066 DOI: 10.1093/gbe/evaa117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
The Holozoa clade comprises animals and several unicellular lineages (choanoflagellates, filastereans, and teretosporeans). Understanding their full diversity is essential to address the origins of animals and other evolutionary questions. However, they are poorly known. To provide more insights into the real diversity of holozoans and check for undiscovered diversity, we here analyzed 18S rDNA metabarcoding data from the global Tara Oceans expedition. To overcome the low phylogenetic information contained in the metabarcoding data set (composed of sequences from the short V9 region of the gene), we used similarity networks by combining two data sets: unknown environmental sequences from Tara Oceans and known reference sequences from GenBank. We then calculated network metrics to compare environmental sequences with reference sequences. These metrics reflected the divergence between both types of sequences and provided an effective way to search for evolutionary relevant diversity, further validated by phylogenetic placements. Our results showed that the percentage of unicellular holozoan diversity remains hidden. We found novelties in several lineages, especially in Acanthoecida choanoflagellates. We also identified a potential new holozoan group that could not be assigned to any of the described extant clades. Data on geographical distribution showed that, although ubiquitous, each unicellular holozoan lineage exhibits a different distribution pattern. We also identified a positive association between new animal hosts and the ichthyosporean symbiont Creolimax fragrantissima, as well as for other holozoans previously reported as free-living. Overall, our analyses provide a fresh perspective into the diversity and ecology of unicellular holozoans, highlighting the amount of undescribed diversity.
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Affiliation(s)
- Alicia S Arroyo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Romain Lannes
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Departament de Genètica, Microbiologia I Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Spain
- ICREA, Barcelona, Spain
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20
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Skejo J, Franjević D. Eukaryotes Are a Holophyletic Group of Polyphyletic Origin. Front Microbiol 2020; 11:1380. [PMID: 32714303 PMCID: PMC7343848 DOI: 10.3389/fmicb.2020.01380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/28/2020] [Indexed: 12/02/2022] Open
Affiliation(s)
- Josip Skejo
- Institute of Molecular Evolution, Heinrich–Heine University Düsseldorf, Düsseldorf, Germany
- Evolution Lab, Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Damjan Franjević
- Evolution Lab, Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- *Correspondence: Damjan Franjević
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21
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Papale F, Saget J, Bapteste É. Networks Consolidate the Core Concepts of Evolution by Natural Selection. Trends Microbiol 2019; 28:254-265. [PMID: 31866140 DOI: 10.1016/j.tim.2019.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023]
Abstract
Microbiology has unraveled rich evidence of ongoing reticulate evolutionary processes and complex interactions both within and between cells. These phenomena feature real biological networks, which can logically be analyzed using network-based tools. It is thus not surprising that network sciences, a field independent from evolutionary biology and microbiology, have recently pervasively infused their methods into both fields. Importantly, network tools bring forward observations enhancing the understanding of three core evolutionary concepts: variation, fitness, and heredity. Consequently, our work shows how network sciences can enhance evolutionary theory by explaining the evolution by natural selection of a broad diversity of units of selection, while updating the popular figure of Darwin's tree of life with a comprehensive sketch of the networks of evolution.
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Affiliation(s)
- François Papale
- Departement of Philosophy, University of Montreal, Montréal, QC, H3C 3J7, Canada; Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 75005 Paris, France
| | - Jordane Saget
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 75005 Paris, France
| | - Éric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 75005 Paris, France.
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22
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Willson BJ, Chapman LNM, Thomas GH. Evolutionary dynamics of membrane transporters and channels: enhancing function through fusion. Curr Opin Genet Dev 2019; 58-59:76-86. [DOI: 10.1016/j.gde.2019.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 02/05/2023]
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23
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Subirana JA, Messeguer X. Satellites in the prokaryote world. BMC Evol Biol 2019; 19:181. [PMID: 31533616 PMCID: PMC6749651 DOI: 10.1186/s12862-019-1504-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/28/2019] [Indexed: 11/10/2022] Open
Abstract
Background Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on their occurrence. For this reason we present here an overview of the distribution and properties of satellites in a set of representative species. Our results provide novel insights into the evolutionary relationship between eukaryotes, Archaea and Bacteria. Results We have searched all possible satellites present in the NCBI reference group of genomes in Archaea (142 species) and in Bacteria (119 species), detecting 2735 satellites in Archaea and 1067 in Bacteria. We have found that the distribution of satellites is very variable in different organisms. The archaeal Methanosarcina class stands out for the large amount of satellites in their genomes. Satellites from a few species have similar characteristics to those in eukaryotes, but most species have very few satellites: only 21 species in Archaea and 18 in Bacteria have more than 4 satellites/Mb. The distribution of satellites in these species is reminiscent of what is found in eukaryotes, but we find two significant differences: most satellites have a short length and many of them correspond to segments of genes coding for amino acid repeats. Transposition of non-coding satellites throughout the genome occurs rarely: only in the bacteria Leptospira interrogans and the archaea Methanocella conradii we have detected satellite families of transposed satellites with long repeats. Conclusions Our results demonstrate that the presence of satellites in the genome is not an exclusive feature of eukaryotes. We have described a few prokaryotes which do contain satellites. We present a discussion on their eventual evolutionary significance. Electronic supplementary material The online version of this article (10.1186/s12862-019-1504-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan A Subirana
- Department of Computer Science, Universitat Politècnica de Catalunya, Jordi Girona 1-3, 08034, Barcelona, Spain.
| | - Xavier Messeguer
- Department of Computer Science, Universitat Politècnica de Catalunya, Jordi Girona 1-3, 08034, Barcelona, Spain
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24
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Kırtel O, Lescrinier E, Van den Ende W, Toksoy Öner E. Discovery of fructans in Archaea. Carbohydr Polym 2019; 220:149-156. [DOI: 10.1016/j.carbpol.2019.05.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023]
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25
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Ou Y, McInerney JO. Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites. Genes (Basel) 2019; 10:genes10090648. [PMID: 31466252 PMCID: PMC6769587 DOI: 10.3390/genes10090648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/18/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022] Open
Abstract
The formation of new genes by combining parts of existing genes is an important evolutionary process. Remodelled genes, which we call composites, have been investigated in many species, however, their distribution across all of life is still unknown. We set out to examine the extent to which genomes from cells and mobile genetic elements contain composite genes. We identify composite genes as those that show partial homology to at least two unrelated component genes. In order to identify composite and component genes, we constructed sequence similarity networks (SSNs) of more than one million genes from all three domains of life, as well as viruses and plasmids. We identified non-transitive triplets of nodes in this network and explored the homology relationships in these triplets to see if the middle nodes were indeed composite genes. In total, we identified 221,043 (18.57%) composites genes, which were distributed across all genomic and functional categories. In particular, the presence of composite genes is statistically more likely in eukaryotes than prokaryotes.
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Affiliation(s)
- Yaqing Ou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.
| | - James O McInerney
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
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26
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Exaptation at the molecular genetic level. SCIENCE CHINA-LIFE SCIENCES 2018; 62:437-452. [PMID: 30798493 DOI: 10.1007/s11427-018-9447-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.
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Abstract
All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.
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