1
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Kato S, Tahara YO, Nishimura Y, Uematsu K, Arai T, Nakane D, Ihara A, Nishizaka T, Iwasaki W, Itoh T, Miyata M, Ohkuma M. Cell surface architecture of the cultivated DPANN archaeon Nanobdella aerobiophila. J Bacteriol 2024; 206:e0035123. [PMID: 38289045 PMCID: PMC10882981 DOI: 10.1128/jb.00351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 02/23/2024] Open
Abstract
The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon Nanobdella aerobiophila strain MJ1T and its host Metallosphaera sedula strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1T were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1T gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1T and MJ1HA were motile, but sole MJ1T cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila.IMPORTANCEDPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon, Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Yuki Nishimura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | | | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Ayaka Ihara
- Department of Physics, Gakushuin University, Tokyo, Japan
| | | | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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2
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Tessmer I, Margison GP. The DNA Alkyltransferase Family of DNA Repair Proteins: Common Mechanisms, Diverse Functions. Int J Mol Sci 2023; 25:463. [PMID: 38203633 PMCID: PMC10779285 DOI: 10.3390/ijms25010463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
DNA alkyltransferase and alkyltransferase-like family proteins are responsible for the repair of highly mutagenic and cytotoxic O6-alkylguanine and O4-alkylthymine bases in DNA. Their mechanism involves binding to the damaged DNA and flipping the base out of the DNA helix into the active site pocket in the protein. Alkyltransferases then directly and irreversibly transfer the alkyl group from the base to the active site cysteine residue. In contrast, alkyltransferase-like proteins recruit nucleotide excision repair components for O6-alkylguanine elimination. One or more of these proteins are found in all kingdoms of life, and where this has been determined, their overall DNA repair mechanism is strictly conserved between organisms. Nevertheless, between species, subtle as well as more extensive differences that affect target lesion preferences and/or introduce additional protein functions have evolved. Examining these differences and their functional consequences is intricately entwined with understanding the details of their DNA repair mechanism(s) and their biological roles. In this review, we will present and discuss various aspects of the current status of knowledge on this intriguing protein family.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Geoffrey P. Margison
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
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3
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Chen B, Yu K, Fu L, Wei Y, Liang J, Liao Z, Qin Z, Yu X, Deng C, Han M, Ma H. The diversity, community dynamics, and interactions of the microbiome in the world's deepest blue hole: insights into extreme environmental response patterns and tolerance of marine microorganisms. Microbiol Spectr 2023; 11:e0053123. [PMID: 37861344 PMCID: PMC10883803 DOI: 10.1128/spectrum.00531-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE This study comprehensively examined the community dynamics, functional profiles, and interactions of the microbiome in the world's deepest blue hole. The findings revealed a positive correlation between the α-diversities of Symbiodiniaceae and archaea, indicating the potential reliance of Symbiodiniaceae on archaea in an extreme environment resulting from a partial niche overlap. The negative association between the α-diversity and β-diversity of the bacterial community suggested that the change rule of the bacterial community was consistent with the Anna Karenina effects. The core microbiome comprised nine microbial taxa, highlighting their remarkable tolerance and adaptability to sharp environmental gradient variations. Bacteria and archaea played significant roles in carbon, nitrogen, and sulfur cycles, while fungi contributed to carbon metabolism. This study advanced our understanding of the community dynamics, response patterns, and resilience of microorganisms populating the world's deepest blue hole, thereby facilitating further ecological and evolutional exploration of microbiomes in diverse extreme environments.
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Affiliation(s)
- Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute Co. Ltd. , Qionghai, China
| | - Yuxin Wei
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University , Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Chuanqi Deng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Minwei Han
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Honglin Ma
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University , Nanning, China
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4
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Arcadi E, Rizzo C, Calogero R, Sciutteri V, Fabiano F, Consoli P, Andaloro F, Romeo T. Microbial communities inhabiting shallow hydrothermal vents as sentinels of acidification processes. Front Microbiol 2023; 14:1233893. [PMID: 37727286 PMCID: PMC10505797 DOI: 10.3389/fmicb.2023.1233893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023] Open
Abstract
Introduction Shallow hydrothermal vents are considered natural laboratories to study the effects of acidification on biota, due to the consistent CO2 emissions with a consequent decrease in the local pH. Methods Here the microbial communities of water and sediment samples from Levante Bay (Vulcano Island) with different pH and redox conditions were explored by Next Generation Sequencing techniques. The taxonomic structure was elucidated and compared with previous studies from the same area in the last decades. Results and discussion The results revealed substantial shifts in the taxonomic structure of both bacterial and archaeal communities, with special relevance in the sediment samples, where the effects of external parameters probably act for a long time. The study demonstrates that microbial communities could be used as indicators of acidification processes, by shaping the entire biogeochemical balance of the ecosystem in response to stress factors. The study contributes to understanding how much these communities can tell us about future changes in marine ecosystems.
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Affiliation(s)
- Erika Arcadi
- Department of Biology and Evolution of Marine Organism, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Carmen Rizzo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Valentina Sciutteri
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Francesco Fabiano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
| | - Pierpaolo Consoli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
- National Institute for Environmental Protection and Research, Milazzo, Italy
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5
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Pichard-Kostuch A, Da Cunha V, Oberto J, Sauguet L, Basta T. The universal Sua5/TsaC family evolved different mechanisms for the synthesis of a key tRNA modification. Front Microbiol 2023; 14:1204045. [PMID: 37415821 PMCID: PMC10321239 DOI: 10.3389/fmicb.2023.1204045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
TsaC/Sua5 family of enzymes catalyzes the first step in the synthesis of N6-threonyl-carbamoyl adenosine (t6A) one of few truly ubiquitous tRNA modifications important for translation accuracy. TsaC is a single domain protein while Sua5 proteins contains a TsaC-like domain and an additional SUA5 domain of unknown function. The emergence of these two proteins and their respective mechanisms for t6A synthesis remain poorly understood. Here, we performed phylogenetic and comparative sequence and structure analysis of TsaC and Sua5 proteins. We confirm that this family is ubiquitous but the co-occurrence of both variants in the same organism is rare and unstable. We further find that obligate symbionts are the only organisms lacking sua5 or tsaC genes. The data suggest that Sua5 was the ancestral version of the enzyme while TsaC arose via loss of the SUA5 domain that occurred multiple times in course of evolution. Multiple losses of one of the two variants in combination with horizontal gene transfers along a large range of phylogenetic distances explains the present day patchy distribution of Sua5 and TsaC. The loss of the SUA5 domain triggered adaptive mutations affecting the substrate binding in TsaC proteins. Finally, we identified atypical Sua5 proteins in Archaeoglobi archaea that seem to be in the process of losing the SUA5 domain through progressive gene erosion. Together, our study uncovers the evolutionary path for emergence of these homologous isofunctional enzymes and lays the groundwork for future experimental studies on the function of TsaC/Sua5 proteins in maintaining faithful translation.
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Affiliation(s)
- Adeline Pichard-Kostuch
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Violette Da Cunha
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jacques Oberto
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Tamara Basta
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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6
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Schneider A, Bergsch J, Lipps G. The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically. Nucleic Acids Res 2023; 51:5087-5105. [PMID: 37099378 PMCID: PMC10250227 DOI: 10.1093/nar/gkad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/27/2023] Open
Abstract
The marine thermophilic archaeon Nanoarchaeum equitans possesses a monomeric primase encompassing the conserved domains of the small catalytic and the large regulatory subunits of archaeoeukaryotic heterodimeric primases in one protein chain. The recombinant protein primes on templates containing a triplet with a central thymidine, thus displaying a pronounced sequence specificity typically observed with bacterial type primases only. The N. equitans primase (NEQ395) is a highly active primase enzyme synthesizing short RNA primers. Termination occurs preferentially at about nine nucleotides, as determined by HPLC analysis and confirmed with mass spectrometry. Possibly, the compact monomeric primase NEQ395 represents the minimal archaeoeukaryotic primase and could serve as a functional and structural model of the heterodimeric archaeoeukaryotic primases, whose study is hindered by engagement in protein assemblies and rather low activity.
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Affiliation(s)
- Andy Schneider
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Jan Bergsch
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Georg Lipps
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, 4132 Muttenz, Switzerland
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7
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van Wolferen M, Pulschen AA, Baum B, Gribaldo S, Albers SV. The cell biology of archaea. Nat Microbiol 2022; 7:1744-1755. [PMID: 36253512 PMCID: PMC7613921 DOI: 10.1038/s41564-022-01215-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Buzz Baum
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institute Pasteur, Paris, France.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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8
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Kato S, Ogasawara A, Itoh T, Sakai HD, Shimizu M, Yuki M, Kaneko M, Takashina T, Ohkuma M. Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A co-culture of a novel thermoacidophilic, obligate symbiotic archaeon, designated as strain MJ1T, with its specific host archaeon
Metallosphaera sedula
strain MJ1HA was obtained from a terrestrial hot spring in Japan. Strain MJ1T grew in the co-culture under aerobic conditions. Coccoid cells of strain MJ1T were 200–500 nm in diameter, and attached to the MJ1HA cells in the co-culture. The ranges and optima of the growth temperature and pH of strain MJ1T in the co-culture were 60–75 °C (optimum, 65–70 °C) and pH 1.0–4.0 (optimum, pH 2.5), respectively. Core lipids of dialkyl glycerol tetraethers (GDGT)−3 and GDGT-4 were highly abundant in MJ1T cells concentrated from the co-culture. Strain MJ1T has a small genome (0.67 Mbp) lacking genes for biosynthesis of essential biomolecules, such as nucleotides, lipids and ATP. The genomic DNA G+C content was 24.9 mol%. The 16S rRNA gene sequence of strain MJ1T was most closely related to that of the cultivated species, ‘Nanopusillus acidilobi’ strain N7A (85.8 % similarity). Based on phylogenetic and physiological characteristics, we propose the name Nanobdella aerobiophila gen. nov., sp. nov. to accommodate the strain MJ1T (=JCM 33616T=DSM 111728T). In addition, we propose the names Nanobdellaceae fam. nov., Nanobdellales ord. nov., and Nanobdellia class. nov. to accommodate the novel genus.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ayaka Ogasawara
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroyuki D. Sakai
- Present address: Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Hachioji, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Michiru Shimizu
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Kaneko
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Tomonori Takashina
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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9
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Krause S, Gfrerer S, von Kügelgen A, Reuse C, Dombrowski N, Villanueva L, Bunk B, Spröer C, Neu TR, Kuhlicke U, Schmidt-Hohagen K, Hiller K, Bharat TAM, Rachel R, Spang A, Gescher J. The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host. Nat Commun 2022; 13:1735. [PMID: 35365607 PMCID: PMC8975820 DOI: 10.1038/s41467-022-29263-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 02/28/2022] [Indexed: 01/05/2023] Open
Abstract
Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.
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Affiliation(s)
- Susanne Krause
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany
| | - Sabrina Gfrerer
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Carsten Reuse
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Thomas R Neu
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Ute Kuhlicke
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Kerstin Schmidt-Hohagen
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom.,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Reinhard Rachel
- Center for Electron Microscopy, University of Regensburg, Regensburg, Germany
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Gescher
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany. .,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Institute of Technical Microbiology, Technical University of Hamburg, Hamburg, Germany.
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10
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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11
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Ataeian M, Liu Y, Kouris A, Hawley AK, Strous M. Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration. Front Microbiol 2022; 13:780346. [PMID: 35222325 PMCID: PMC8880816 DOI: 10.3389/fmicb.2022.780346] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Yihua Liu
- Department Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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12
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Hassani Y, Saad J, Terrer E, Aboudharam G, Giancarlo B, Silvestri F, Raoult D, Drancourt M, Grine G. Introducing clinical nanorachaeaology: Isolation by co-culture of Nanopusillus massiliensis sp. nov. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100100. [PMID: 35005659 PMCID: PMC8718826 DOI: 10.1016/j.crmicr.2021.100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
The first ever detection in human microbiota of nanoarchaea. Detection and co-isolation of nanoarchaea new species in human oral microbiota. These data suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology. Extended our knowledge of human microbiota diversity. Opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.
Background Nanoarchaeota, obligate symbiont of some environmental archaea with reduced genomes, have been described in marine thermal vent environments, yet never detected in hosts, including humans. Methods Here, using laboratory tools geared towards the detection of nanoarchaea including PCR-sequencing, WGS, microscopy and culture. Results We discovered a novel nanoarchaea, Nanopusillus massiliensis, detected in dental plate samples by specific PCR-based assays. Combining fluorescent in situ hybridization (FISH) with scanning electron microscopy disclosed close contacts between N. massiliensis and the archaea Methanobrevibacter oralis in these samples. Culturing one sample yielded co-isolation of M. oralis and N. massiliensis with a 606,935-bp genome, with 23.6% GC encoded 16 tRNA, 3 rRNA and 942 coding DNA sequences, of which 400 were assigned to clusters of orthologous groups. Conclusion The discovery of N. massiliensis, made publicly available in collection, extended our knowledge of human microbiota diversity, opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.
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Affiliation(s)
- Y. Hassani
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - J. Saad
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - E. Terrer
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
| | - G. Aboudharam
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
| | - B Giancarlo
- Private practice Marseille France, Marseille, France
| | - F. Silvestri
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
| | - D. Raoult
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - M. Drancourt
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - G. Grine
- Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France
- Faculté de médecine dentaire, Aix-Marseille Université, Marseille 13005, France
- Corresponding author at: Aix-Marseille-Univ., IRD, MEPHI, IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille 13005, France.
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13
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Pawłowski PH. The Codon Usage in the Minimal Natural Cell. ORIGINS LIFE EVOL B 2021; 51:215-230. [PMID: 34694559 DOI: 10.1007/s11084-021-09616-1] [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: 07/28/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
A statistical analysis of the variation in contents with the size of the current known smallest genomes, N. deltocephalinicola, C. ruddii, N. equitans, and M. genitalium, enabled the indication of a minimal set of codons capable of naturally building a modern-type free-living unicellular organism in an early stage of evolution. Using a linear regression model, the potential codon distribution in the minimal natural cell was predicted and compared to the composition of the smallest synthetic, JCVI-Syn3.0. The distribution of the molecular weight of potentially coded amino acids was also calculated. The main differences in the features of the minimal natural cell and H. Sapiens genome were analyzed. In this regard, the content percentage of respective amino acids and their polarization charge properties were reported and compared. The fractions of occurring nucleotides were calculated, too. Then, the estimated numbers of codons in a minimal natural cell were related to the expected numbers for random distribution. Shown increase, or decrease in the contents, relative to the calculated random filling was related to the evolutionary preferences, varying with the subsequent eras of the evolution of genetic code.
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Affiliation(s)
- Piotr H Pawłowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland.
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14
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Horikoshi T, Noguchi H, Umehara T, Mutsuro-Aoki H, Kurihara R, Noguchi R, Hashimoto T, Watanabe Y, Ando T, Kamata K, Park SY, Tamura K. Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNA Tyr with an extra guanosine residue at the 5'-terminus. Biochem Biophys Res Commun 2021; 575:90-95. [PMID: 34461441 DOI: 10.1016/j.bbrc.2021.08.070] [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: 08/05/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/24/2022]
Abstract
tRNATyr of Nanoarchaeum equitans has a remarkable feature with an extra guanosine residue at the 5'-terminus. However, the N. equitans tRNATyr mutant without extra guanosine at the 5'-end was tyrosylated by tyrosyl-tRNA synthase (TyrRS). We solved the crystal structure of N. equitans TyrRS at 2.80 Å resolution. By comparing the present solved structure with the complex structures TyrRS with tRNATyr of Thermus thermophilus and Methanocaldococcus jannaschii, an arginine substitution mutant of N. equitans TyrRS at Ile200 (I200R), which is the putative closest candidate to the 5'-phosphate of C1 of N. equitans tRNATyr, was prepared. The I200R mutant tyrosylated not only wild-type tRNATyr but also the tRNA without the G-1 residue. Further tyrosylation analysis revealed that the second base of the anticodon (U35), discriminator base (A73), and C1:G72 base pair are strong recognition sites.
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Affiliation(s)
- Tatsuya Horikoshi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiroki Noguchi
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Takuya Umehara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiromi Mutsuro-Aoki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryodai Kurihara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryohei Noguchi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Takahiro Hashimoto
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Yuki Watanabe
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kenichi Kamata
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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15
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Vázquez-Campos X, Kinsela AS, Bligh MW, Payne TE, Wilkins MR, Waite TD. Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. Front Microbiol 2021; 12:732575. [PMID: 34737728 PMCID: PMC8561730 DOI: 10.3389/fmicb.2021.732575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022] Open
Abstract
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.
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Affiliation(s)
- Xabier Vázquez-Campos
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Andrew S. Kinsela
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Mark W. Bligh
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Timothy E. Payne
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW, Australia
| | - Marc R. Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - T. David Waite
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
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16
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Li YX, Rao YZ, Qi YL, Qu YN, Chen YT, Jiao JY, Shu WS, Jiang H, Hedlund BP, Hua ZS, Li WJ. Deciphering Symbiotic Interactions of " Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks. mSystems 2021; 6:e0060621. [PMID: 34313464 PMCID: PMC8407114 DOI: 10.1128/msystems.00606-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022] Open
Abstract
"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.
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Affiliation(s)
- Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Ya-Ting Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People’s Republic of China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People’s Republic of China
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People’s Republic of China
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Abstract
DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.
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18
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Archaea: An Agro-Ecological Perspective. Curr Microbiol 2021; 78:2510-2521. [PMID: 34019119 DOI: 10.1007/s00284-021-02537-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Microorganisms inhabiting bulk soil and rhizosphere play an important role in soil biogeochemical cycles leading to enhanced plant growth and productivity. In this context, the role of bacteria is well established, however, not much reports are available about the role archaea plays in this regard. Literature suggests that archaea also play a greater role in nutrient cycling of carbon, nitrogen, sulfur, and other minerals, possess various plant growth promoting attributes, and can impart tolerance to various abiotic stresses (especially osmotic and oxidative) in areas of high salinity, low and high temperatures and hydrogen ion concentrations. Thermoacidophilic archaea have been found to potentially involve in bioleaching of mineral ores and bioremediation of chemical pollutants and aromatic compounds. Looking at immense potential of archaea in promoting plant growth, alleviating abiotic stresses, and remediating contaminated sites, detailed studies are required to establish their role in different ecological processes, and their interactions in rhizosphere with plant and other microflora (bacteria and fungi) in different ecosystems. In this review, a brief discussion on archaea from the agro-ecological point of view is presented.
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19
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Nottebaum S, Weinzierl ROJ. Transcribing Genes the Hard Way: In Vitro Reconstitution of Nanoarchaeal RNA Polymerase Reveals Unusual Active Site Properties. Front Mol Biosci 2021; 8:669314. [PMID: 34141723 PMCID: PMC8204694 DOI: 10.3389/fmolb.2021.669314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Nanoarchaea represent a highly diverged archaeal phylum that displays many unusual biological features. The Nanoarchaeum equitans genome encodes a complete set of RNA polymerase (RNAP) subunits and basal factors. Several of the standard motifs in the active center contain radical substitutions that are normally expected to render the polymerase catalytically inactive. Here we show that, despite these unusual features, a RNAP reconstituted from recombinant Nanoarchaeum subunits is transcriptionally active. Using a sparse-matrix high-throughput screening method we identified an atypical stringent requirement for fluoride ions to maximize its activity under in vitro transcription conditions.
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Affiliation(s)
- Sven Nottebaum
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Orthomol Pharmazeutische Vertriebs GmbH, Langenfeld, Germany
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20
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Koonin EV, Makarova KS, Wolf YI. Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century. Trends Microbiol 2021; 29:582-592. [PMID: 33541841 DOI: 10.1016/j.tim.2021.01.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/20/2022]
Abstract
Prokaryote genomics started in earnest in 1995, with the complete sequences of two small bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium. During the next quarter century, the prokaryote genome database has been growing exponentially, with no saturation in sight. For most of these 25 years, genome sequencing remained limited to cultivable microbes. Together with next-generation sequencing methods, advances in metagenomics and single-cell genomics have lifted this limitation, providing for an increasingly unbiased characterization of the global prokaryote diversity. Advances in computational genomics followed the progress of genome sequencing, even if occasionally lagging behind. Several major new branches of bacteria and archaea were discovered, including Asgard archaea, the apparent closest relatives of eukaryotes and expansive groups of bacteria and archaea with small genomes thought to be symbionts of other prokaryotes. Comparative analysis of numerous prokaryote genomes spanning a wide range of evolutionary distances changed the conceptual foundations of microbiology, supplanting the notion of species genomes with fixed gene sets with that of dynamic pangenomes and the notion of a single Tree of Life (ToL) with a statistical tree-like trend among individual gene trees. Strides were also made towards a theory and quantitative laws of prokaryote genome evolution.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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Perez-Garcia P, Kobus S, Gertzen CGW, Hoeppner A, Holzscheck N, Strunk CH, Huber H, Jaeger KE, Gohlke H, Kovacic F, Smits SHJ, Streit WR, Chow J. A promiscuous ancestral enzyme´s structure unveils protein variable regions of the highly diverse metallo-β-lactamase family. Commun Biol 2021; 4:132. [PMID: 33514861 PMCID: PMC7846560 DOI: 10.1038/s42003-021-01671-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
The metallo-β-lactamase fold is an ancient protein structure present in numerous enzyme families responsible for diverse biological processes. The crystal structure of the hyperthermostable crenarchaeal enzyme Igni18 from Ignicoccus hospitalis was solved at 2.3 Å and could resemble a possible first archetype of a multifunctional metallo-β-lactamase. Ancestral enzymes at the evolutionary origin are believed to be promiscuous all-rounders. Consistently, Igni18´s activity can be cofactor-dependently directed from β-lactamase to lactonase, lipase, phosphodiesterase, phosphotriesterase or phospholipase. Its core-domain is highly conserved within metallo-β-lactamases from Bacteria, Archaea and Eukarya and gives insights into evolution and function of enzymes from this superfamily. Structural alignments with diverse metallo-β-lactamase-fold-containing enzymes allowed the identification of Protein Variable Regions accounting for modulation of activity, specificity and oligomerization patterns. Docking of different substrates within the active sites revealed the basis for the crucial cofactor dependency of this enzyme superfamily.
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Affiliation(s)
- Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Astrid Hoeppner
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Nicholas Holzscheck
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Harald Huber
- Institute for Microbiology and Archaeal Center, Regensburg University, 93035, Regensburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany.
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Kirschning A. The coenzyme/protein pair and the molecular evolution of life. Nat Prod Rep 2020; 38:993-1010. [PMID: 33206101 DOI: 10.1039/d0np00037j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Zentrum für Biomolekulare Wirkstoffchemie (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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James P, Isupov MN, De Rose SA, Sayer C, Cole IS, Littlechild JA. A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans: Structure and Biochemical Characterization. Front Microbiol 2020; 11:592353. [PMID: 33193259 PMCID: PMC7661550 DOI: 10.3389/fmicb.2020.592353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
A novel transketolase has been reconstituted from two separate polypeptide chains encoded by a ‘split-gene’ identified in the genome of the hyperthermophilic bacterium, Carboxydothermus hydrogenoformans. The reconstituted active α2β2 tetrameric enzyme has been biochemically characterized and its activity has been determined using a range of aldehydes including glycolaldehyde, phenylacetaldehyde and cyclohexanecarboxaldehyde as the ketol acceptor and hydroxypyruvate as the donor. This reaction proceeds to near 100% completion due to the release of the product carbon dioxide and can be used for the synthesis of a range of sugars of interest to the pharmaceutical industry. This novel reconstituted transketolase is thermally stable with no loss of activity after incubation for 1 h at 70°C and is stable after 1 h incubation with 50% of the organic solvents methanol, ethanol, isopropanol, DMSO, acetonitrile and acetone. The X-ray structure of the holo reconstituted α2β2 tetrameric transketolase has been determined to 1.4 Å resolution. In addition, the structure of an inactive tetrameric β4 protein has been determined to 1.9 Å resolution. The structure of the active reconstituted α2β2 enzyme has been compared to the structures of related enzymes; the E1 component of the pyruvate dehydrogenase complex and D-xylulose-5-phosphate synthase, in an attempt to rationalize differences in structure and substrate specificity between these enzymes. This is the first example of a reconstituted ‘split-gene’ transketolase to be biochemically and structurally characterized allowing its potential for industrial biocatalysis to be evaluated.
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Affiliation(s)
- Paul James
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Isobel S Cole
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, United Kingdom
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Metabolic Diversity and Evolutionary History of the Archaeal Phylum " Candidatus Micrarchaeota" Uncovered from a Freshwater Lake Metagenome. Appl Environ Microbiol 2020; 86:AEM.02199-20. [PMID: 32978130 DOI: 10.1128/aem.02199-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Acidophilic archaea of the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group from the uncultured candidate phylum "Candidatus Micrarchaeota" have small genomes and cell sizes and are known to be metabolically dependent and physically associated with their Thermoplasmatales hosts. However, phylogenetically diverse "Ca Micrarchaeota" are widely distributed in various nonacidic environments, and it remains uncertain because of the lack of complete genomes whether they are also devoted to a partner-dependent lifestyle. Here, we obtained nine metagenome-assembled genomes of "Ca Micrarchaeota" from the sediments of a meromictic freshwater lake, including a complete, closed 1.2 Mbp genome of "Ca Micrarchaeota" Sv326, an archaeon phylogenetically distant from the ARMAN lineage. Genome analysis revealed that, contrary to ARMAN "Ca Micrarchaeota," the Sv326 archaeon has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation reactions, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacked an aerobic respiratory chain. We suppose that Sv326 is a free-living scavenger rather than an obligate parasite/symbiont. Comparative analysis of "Ca Micrarchaeota" genomes representing different order-level divisions indicated that evolution of the "Ca Micrarchaeota" from a free-living "Candidatus Diapherotrites"-like ancestor involved losses of important metabolic pathways in different lineages and gains of specific functions in the course of adaptation to a partner-dependent lifestyle and specific environmental conditions. The ARMAN group represents the most pronounced case of genome reduction and gene loss, while the Sv326 lineage appeared to be rather close to the ancestral state of the "Ca Micrarchaeota" in terms of metabolic potential.IMPORTANCE The recently described superphylum DPANN includes several phyla of uncultivated archaea with small cell sizes, reduced genomes, and limited metabolic capabilities. One of these phyla, "Ca Micrarchaeota," comprises an enigmatic group of archaea found in acid mine drainage environments, the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group. Analysis of their reduced genomes revealed the absence of key metabolic pathways consistent with their partner-associated lifestyle, and physical associations of ARMAN cells with their hosts were documented. However, "Ca Micrarchaeota" include several lineages besides the ARMAN group found in nonacidic environments, and none of them have been characterized. Here, we report a complete genome of "Ca Micrarchaeota" from a non-ARMAN lineage. Analysis of this genome revealed the presence of metabolic capacities lost in ARMAN genomes that could enable a free-living lifestyle. These results expand our understanding of genetic diversity, lifestyle, and evolution of "Ca Micrarchaeota."
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Rose S, Auxilien S, Havelund JF, Kirpekar F, Huber H, Grosjean H, Douthwaite S. The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications. Nucleic Acids Res 2020; 48:6906-6918. [PMID: 32459340 PMCID: PMC7337903 DOI: 10.1093/nar/gkaa411] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/19/2020] [Accepted: 05/06/2020] [Indexed: 01/31/2023] Open
Abstract
The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis grow physically coupled under identical hyperthermic conditions. We report here two fundamentally different routes by which these archaea modify the key conserved nucleotide U54 within their tRNA T-loops. In N. equitans, this nucleotide is methylated by the S-adenosylmethionine-dependent enzyme NEQ053 to form m5U54, and a recombinant version of this enzyme maintains specificity for U54 in Escherichia coli. In N. equitans, m5U54 is subsequently thiolated to form m5s2U54. In contrast, I. hospitalis isomerizes U54 to pseudouridine prior to methylating its N1-position and thiolating the O4-position of the nucleobase to form the previously uncharacterized nucleotide m1s4Ψ. The methyl and thiol groups in m1s4Ψ and m5s2U are presented within the T-loop in a spatially identical manner that stabilizes the 3′-endo-anti conformation of nucleotide-54, facilitating stacking onto adjacent nucleotides and reverse-Hoogsteen pairing with nucleotide m1A58. Thus, two distinct structurally-equivalent solutions have evolved independently and convergently to maintain the tertiary fold of tRNAs under extreme hyperthermic conditions.
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Affiliation(s)
- Simon Rose
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Sylvie Auxilien
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jesper F Havelund
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Finn Kirpekar
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Harald Huber
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Henri Grosjean
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stephen Douthwaite
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Colombet J, Fuster M, Billard H, Sime-Ngando T. Femtoplankton: What's New? Viruses 2020; 12:E881. [PMID: 32806713 PMCID: PMC7472349 DOI: 10.3390/v12080881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 01/01/2023] Open
Abstract
Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010-2020) of high abundances of biomimetic mineral-organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.
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Affiliation(s)
- Jonathan Colombet
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (M.F.); (H.B.); (T.S.-N.)
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Bayer K, Busch K, Kenchington E, Beazley L, Franzenburg S, Michels J, Hentschel U, Slaby BM. Microbial Strategies for Survival in the Glass Sponge Vazella pourtalesii. mSystems 2020; 5:e00473-20. [PMID: 32788407 PMCID: PMC7426153 DOI: 10.1128/msystems.00473-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/23/2020] [Indexed: 01/04/2023] Open
Abstract
Few studies have explored the microbiomes of glass sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the glass sponge Vazella pourtalesii and the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling toward this goal. Microscopic imaging revealed that the host and microbial cells appeared within dense biomass patches that are presumably syncytial tissue aggregates. Based on abundances in amplicon libraries and metagenomic data, SAR324 bacteria, Crenarchaeota, Patescibacteria, and Nanoarchaeota were identified as abundant members of the V. pourtalesii microbiome; thus, their genomic potentials were analyzed in detail. A general pattern emerged in that the V. pourtalesii symbionts had very small genome sizes, in the range of 0.5 to 2.2 Mb, and low GC contents, even below those of seawater relatives. Based on functional analyses of metagenome-assembled genomes (MAGs), we propose two major microbial strategies: the "givers," namely, Crenarchaeota and SAR324, heterotrophs and facultative anaerobes, produce and partly secrete all required amino acids and vitamins. The "takers," Nanoarchaeota and Patescibacteria, are anaerobes with reduced genomes that tap into the microbial community for resources, e.g., lipids and DNA, likely using pilus-like structures. We posit that the existence of microbial cells in sponge syncytia together with the low-oxygen conditions in the seawater environment are factors that shape the unique compositional and functional properties of the microbial community associated with V. pourtalesii IMPORTANCE We investigated the microbial community of V. pourtalesii that forms globally unique, monospecific sponge grounds under low-oxygen conditions on the Scotian Shelf, where it plays a key role in its vulnerable ecosystem. The microbial community was found to be concentrated within biomass patches and is dominated by small cells (<1 μm). MAG analyses showed consistently small genome sizes and low GC contents, which is unusual compared to known sponge symbionts. These properties, as well as the (facultatively) anaerobic metabolism and a high degree of interdependence between the dominant symbionts regarding amino acid and vitamin synthesis, are likely adaptations to the unique conditions within the syncytial tissue of their hexactinellid host and the low-oxygen environment.
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Affiliation(s)
- Kristina Bayer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
| | - Ellen Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Lindsay Beazley
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Sören Franzenburg
- Institute for Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Jan Michels
- Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Kiel, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
- Kiel University, Kiel, Germany
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
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Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, Rinke C, Spang A. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat Commun 2020; 11:3939. [PMID: 32770105 PMCID: PMC7414124 DOI: 10.1038/s41467-020-17408-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023] Open
Abstract
The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jun-Hoe Lee
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Bui Quang Minh
- Research School of Computer Science and Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands.
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden.
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Host Species Determines the Composition of the Prokaryotic Microbiota in Phlebotomus Sandflies. Pathogens 2020; 9:pathogens9060428. [PMID: 32485988 PMCID: PMC7350354 DOI: 10.3390/pathogens9060428] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
Phlebotomine sandflies are vectors of the humans' and mammals' parasite Leishmania spp. Although the role of gut microbiome in the biological cycle of insects is acknowledged, we still know little about the factors modulating the composition of the gut microbiota of sandflies. We tested whether host species impose a strong structural effect on the gut microbiota of Phlebotomus spp. Sandflies were collected from the island of Leros, Greece, and classified to P. papatasi, P. neglectus, P. tobbi, and P. similis, all being negative to Leishmania spp. The prokaryotic gut microbiota was determined via 16S rRNA gene amplicon sequencing. Phlebotomus species supported distinct microbial communities (p < 0.001). P. papatasi microbiota was the most distinct over-dominated by three Spiroplasma, Wolbachia and Paenibacillus operational taxonomic units (OTUs), while another Wolbachia OTU prevailed in P. neglectus. Conversely, the microbiota of P. tobbi and P. similis was composed of several less dominant OTUs. Archaea showed low presence with the dominant OTUs belonging to methanogenic Euryarcheota, ammonia-oxidizing Thaumarcheota, and Nanoarchaeota. We provide first insights into the composition of the bacterial and archaeal community of Phlebotomus sandflies and showed that, in the absence of Leishmania, host genotype is the major modulator of Phlebotomus sandfly gut microbiota.
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Choi IY, Kwon EC, Kim NS. The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy. Genes Genomics 2020; 42:699-714. [DOI: 10.1007/s13258-020-00941-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
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Arutaki M, Kurihara R, Matsuoka T, Inami A, Tokunaga K, Ohno T, Takahashi H, Takano H, Ando T, Mutsuro-Aoki H, Umehara T, Tamura K. G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases. J Mol Evol 2020; 88:501-509. [DOI: 10.1007/s00239-020-09945-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/28/2020] [Indexed: 11/25/2022]
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Diversity, ecology and evolution of Archaea. Nat Microbiol 2020; 5:887-900. [PMID: 32367054 DOI: 10.1038/s41564-020-0715-z] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/30/2020] [Indexed: 12/23/2022]
Abstract
Compared to bacteria, our knowledge of archaeal biology is limited. Historically, microbiologists have mostly relied on culturing and single-gene diversity surveys to understand Archaea in nature. However, only six of the 27 currently proposed archaeal phyla have cultured representatives. Advances in genomic sequencing and computational approaches are revolutionizing our understanding of Archaea. The recovery of genomes belonging to uncultured groups from the environment has resulted in the description of several new phyla, many of which are globally distributed and are among the predominant organisms on the planet. In this Review, we discuss how these genomes, together with long-term enrichment studies and elegant in situ measurements, are providing insights into the metabolic capabilities of the Archaea. We also debate how such studies reveal how important Archaea are in mediating an array of ecological processes, including global carbon and nutrient cycles, and how this increase in archaeal diversity has expanded our view of the tree of life and early archaeal evolution, and has provided new insights into the origin of eukaryotes.
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Probst AJ, Elling FJ, Castelle CJ, Zhu Q, Elvert M, Birarda G, Holman HYN, Lane KR, Ladd B, Ryan MC, Woyke T, Hinrichs KU, Banfield JF. Lipid analysis of CO 2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME JOURNAL 2020; 14:1547-1560. [PMID: 32203118 PMCID: PMC7242380 DOI: 10.1038/s41396-020-0624-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 11/09/2022]
Abstract
Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.
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Affiliation(s)
- Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA. .,Institute for Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Felix J Elling
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. .,Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA.
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Qingzeng Zhu
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Giovanni Birarda
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163,5 Basovizza, 34149, Trieste, Italy.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hoi-Ying N Holman
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine R Lane
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Bethany Ladd
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.,Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - M Cathryn Ryan
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, MA, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA.
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35
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Thermotogales origin scenario of eukaryogenesis. J Theor Biol 2020; 492:110192. [PMID: 32044287 DOI: 10.1016/j.jtbi.2020.110192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
How eukaryotes were generated is an enigma of evolutionary biology. Widely accepted archaeal-origin eukaryogenesis scenarios, based on similarities of genes and related characteristics between archaea and eukaryotes, cannot explain several eukaryote-specific features of the last eukaryotic common ancestor, such as glycerol-3-phosphate-type membrane lipids, large cells and genomes, and endomembrane formation. Thermotogales spheroids, having multicopy-integrated large nucleoids and producing progeny in periplasm, may explain all of these features as well as endoplasmic reticulum-type signal cleavage sites, although they cannot divide. We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). We propose that Thermotogales ancestor spheroids came to divide owing to the archaeal cell division genes horizontally transferred via virus-related particles, forming the first eukaryotic common ancestor (FECA). Referring to the hypothesis, the archaeal information-processing system would have been established in FECA by random joining DNAs excised from the MILG, which contained horizontally transferred archaeal and bacterial DNAs, followed by reorganization by the MILG-enabled homologous recombination. Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. The random joining of DNAs likely provided the basic mechanisms for eukaryotic evolution: producing the diversity by the formations of supergroups, novel genes, and introns that are involved in exon shuffling.
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36
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Mayer C. Life in The Context of Order and Complexity. Life (Basel) 2020; 10:life10010005. [PMID: 31963637 PMCID: PMC7175320 DOI: 10.3390/life10010005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/06/2020] [Accepted: 01/16/2020] [Indexed: 11/17/2022] Open
Abstract
It is generally accepted that life requires structural complexity. However, a chaotic mixture of organic compounds like the one formed by extensive reaction sequences over time may be extremely complex, but could just represent a static asphalt-like dead end situation. Likewise, it is accepted that life requires a certain degree of structural order. However, even extremely ordered structures like mineral crystals show no tendency to be alive. So neither complexity nor order alone can characterize a living organism. In order to come close to life, and in order for life to develop to higher organisms, both conditions have to be fulfilled and advanced simultaneously. Only a combination of the two requirements, complexity and structural order, can mark the difference between living and dead matter. It is essential for the development of prebiotic chemistry into life and characterizes the course and the result of Darwinian evolution. For this reason, it is worthwhile to define complexity and order as an essential pair of characteristics of life and to use them as fundamental parameters to evaluate early steps in prebiotic development. A combination of high order and high complexity also represents a universal type of biosignature which could be used to identify unknown forms of life or remnants thereof.
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Affiliation(s)
- Christian Mayer
- Institute of Physical Chemistry, CENIDE, University of Duisburg-Essen, 45141 Essen, Germany
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37
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Abstract
The ribosome and RNase P are cellular ribonucleoprotein complexes that perform peptide bond synthesis and phosphodiester bond cleavage, respectively. Both are ancient biological assemblies that were already present in the last universal common ancestor of all life. The large subunit rRNA in the ribosome and the RNA subunit of RNase P are the ribozyme components required for catalysis. Here, we explore the idea that these two large ribozymes may have begun their evolutionary odyssey as an assemblage of RNA "fragments" smaller than the contemporary full-length versions and that they transitioned through distinct stages along a pathway that may also be relevant for the evolution of other non-coding RNAs.
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Affiliation(s)
- Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210.
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Abstract
In recent years, split inteins have seen widespread use as molecular platforms for the design of a variety of peptide and protein chemistry technologies, most notably protein ligation. The development of these approaches is dependent on the identification and/or design of split inteins with robust activity, stability, and solubility. Here, we describe two approaches to characterize and compare the activities of newly identified or engineered split inteins. The first assay employs an E. coli-based selection system to rapidly screen the activities of many inteins and can be repurposed for directed evolution. The second assay utilizes reverse-phase high-performance liquid chromatography (RP-HPLC) to provide insights into individual chemical steps in the protein splicing reaction, information that can guide further engineering efforts. These techniques provide useful alternatives to common assays that utilize SDS-PAGE to analyze splicing reaction progress.
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Romero-Casañas A, Gordo V, Castro J, Ribó M. Protein Splicing: From the Foundations to the Development of Biotechnological Applications. Methods Mol Biol 2020; 2133:15-29. [PMID: 32144661 DOI: 10.1007/978-1-0716-0434-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Expressed protein ligation is a simple and powerful method in protein engineering to introduce sequences of unnatural amino acids, posttranslational modifications, and biophysical probes into proteins of any size. This methodology has been developed based on the knowledge obtained from protein splicing. Protein splicing is a multistep biochemical reaction that includes the concomitant cleavage and formation of peptide bonds carried out by self-processing domains named inteins. The natural substrates of protein splicing are essential proteins found in intein-containing organisms; inteins are also functional in nonnative frameworks and can be used to alter nearly any protein's primary amino acid sequence. Accordingly, different reactivity features of inteins have been largely exploited to manipulate proteins in countless methods encompassing fields from biochemical research to the development of biotechnological applications including the study of disease progression and validation of potential drug candidates. Here, we review almost three decades of research to uncover the chemical and biochemical enigmas of protein splicing and the development of inteins as potent protein engineering tools.
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Affiliation(s)
- Alejandro Romero-Casañas
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain
| | - Verónica Gordo
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain
| | - Jessica Castro
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, Girona, Spain.
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Schwank K, Bornemann TLV, Dombrowski N, Spang A, Banfield JF, Probst AJ. An archaeal symbiont-host association from the deep terrestrial subsurface. THE ISME JOURNAL 2019; 13:2135-2139. [PMID: 31048756 PMCID: PMC6776059 DOI: 10.1038/s41396-019-0421-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/26/2019] [Accepted: 03/29/2019] [Indexed: 01/27/2023]
Abstract
DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.
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Affiliation(s)
- Katrin Schwank
- Department of Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Duisburg, Germany
| | - Till L V Bornemann
- Department of Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Duisburg, Germany
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry (MMB), Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry (MMB), Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Jillian F Banfield
- Department for Earth and Planetary Sciences, University of California, Berkeley, USA
| | - Alexander J Probst
- Department of Chemistry, Biofilm Centre, Group for Aquatic Microbial Ecology (GAME), University of Duisburg-Essen, Duisburg, Germany.
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41
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Costa Brandão Cruz D, Lima Santana L, Siqueira Guedes A, Teodoro de Souza J, Arthur Santos Marbach P. Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes. Genome Biol Evol 2019; 11:1235-1249. [PMID: 30785193 PMCID: PMC6486802 DOI: 10.1093/gbe/evz035] [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] [Accepted: 02/16/2019] [Indexed: 01/27/2023] Open
Abstract
The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. Based on the results, we propose that the gene purO was present in the common ancestor of all living beings, whereas the gene encoding PurP emerged after the divergence of Archaea and Bacteria and their isoforms originated in duplication events in the common ancestor of phyla Crenarchaeota and Euryarchaeota. The results reported here expand our understanding of the diversity and evolution of the last two steps of the purine biosynthetic pathway in prokaryotes.
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Affiliation(s)
| | - Lenon Lima Santana
- CCAAB, Biological Sciences, Recôncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil
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43
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Gill S, Catchpole R, Forterre P. Extracellular membrane vesicles in the three domains of life and beyond. FEMS Microbiol Rev 2019; 43:273-303. [PMID: 30476045 PMCID: PMC6524685 DOI: 10.1093/femsre/fuy042] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Cells from all three domains of life, Archaea, Bacteria and Eukarya, produce extracellular vesicles (EVs) which are sometimes associated with filamentous structures known as nanopods or nanotubes. The mechanisms of EV biogenesis in the three domains remain poorly understood, although studies in Bacteria and Eukarya indicate that the regulation of lipid composition plays a major role in initiating membrane curvature. EVs are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. They have been implicated in many aspects of cell physiology such as stress response, intercellular competition, lateral gene transfer (via RNA or DNA), pathogenicity and detoxification. Their role in various human pathologies and aging has aroused much interest in recent years. EVs can be used as decoys against viral attack but virus-infected cells also produce EVs that boost viral infection. Here, we review current knowledge on EVs in the three domains of life and their interactions with the viral world.
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Affiliation(s)
- Sukhvinder Gill
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
| | - Ryan Catchpole
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), Biologie Cellulaire des Archées (BCA), CEA, CNRS, Université Paris-Sud, 91405 Orsay cedex, France
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, F75015 Paris, France
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44
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Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation. Biochem Biophys Res Commun 2019; 511:228-233. [PMID: 30771900 DOI: 10.1016/j.bbrc.2019.01.142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 11/23/2022]
Abstract
This study reports the X-ray crystallographic structure of the glycyl-tRNA synthetase (GlyRS) of Nanoarchaeum equitans - a hyperthermophilic archaeal species. This is the first archaeal GlyRS crystal structure elucidated. The GlyRS comprises an N-terminal catalytic domain and a C-terminal anticodon-binding domain with a long β-sheet inserted between these domains. An unmodified transcript of the wild-type N. equitans tRNAGly was successfully glycylated using GlyRS. Substitution of the discriminator base A73 of tRNAGly with any other nucleotide caused a significant decrease in glycylation activity. Mutational analysis of the second base-pair C2G71 of the acceptor stem of tRNAGly elucidated the importance of the base-pair, especially G71, as an identity element for recognition by GlyRS. Glycylation assays using tRNAGly G71 substitution mutants and a GlyRS mutant where Arg223 is mutated to alanine strengthen the possibility that the carbonyl oxygen at position 6 of G71 would hydrogen-bond with the guanidine nitrogen of Arg223 in N. equitans GlyRS.
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45
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Kobus S, Perez-Garcia P, Hoeppner A, Holzscheck N, Kovacic F, Streit WR, Jaeger KE, Chow J, Smits SHJ. Igni18, a novel metallo-hydrolase from the hyperthermophilic archaeon Ignicoccus hospitalis KIN4/I: cloning, expression, purification and X-ray analysis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:307-311. [PMID: 30950832 DOI: 10.1107/s2053230x19002851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022]
Abstract
The hyperthermophilic crenarchaeon Ignicoccus hospitalis KIN4/I possesses at least 35 putative genes encoding enzymes that belong to the α/β-hydrolase superfamily. One of those genes, the metallo-hydrolase-encoding igni18, was cloned and heterologously expressed in Pichia pastoris. The enzyme produced was purified in its catalytically active form. The recombinant enzyme was successfully crystallized and the crystal diffracted to a resolution of 2.3 Å. The crystal belonged to space group R32, with unit-cell parameters a = b = 67.42, c = 253.77 Å, α = β = 90.0, γ = 120.0°. It is suggested that it contains one monomer of Igni18 within the asymmetric unit.
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Affiliation(s)
- Stefanie Kobus
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Astrid Hoeppner
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Nicholas Holzscheck
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426 Jülich, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Karl Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426 Jülich, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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St John E, Flores GE, Meneghin J, Reysenbach AL. Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:262-270. [PMID: 30768760 DOI: 10.1111/1758-2229.12740] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Ectosymbiotic Nanoarchaeota live on the surface of diverse archaeal hosts. Despite being broadly distributed in global geothermal systems, only three Nanoarchaeota have been successfully co-cultivated with their hosts, and until now no nanoarchaeotal cultures or genomes have been described from deep-sea hydrothermal vents. We recovered three nanoarchaeotal metagenome-assembled genomes (MAGs) from deep-sea hydrothermal vent sites at the Eastern Lau Spreading Center (M10-121), Guaymas Basin (Gua-46) and the Mid-Cayman Rise (MC-1). Based on average amino acid identity analysis, M10-121 is a novel species in the candidate genus Nanoclepta, while the other two MAGs represent novel genera in the Nanoarchaeota. Like previously sequenced Nanoarchaeota, each MAG encodes at least one split protein-coding gene. The MAGs also contain a mosaic of key nanoarchaeotal features, including CRISPR repeat regions and marker genes for gluconeogenesis and archaeal flagella. MC-1 also encodes the pentose bisphosphate pathway, which may allow the nanoarchaeote to bypass several steps in glycolysis and produce ATP.
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Affiliation(s)
- Emily St John
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Gilberto E Flores
- Department of Biology, California State University, Northridge, CA 91330, USA
| | - Jennifer Meneghin
- Department of Biology, Portland State University, Portland, OR 97201, USA
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47
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Claverie JM, Abergel C, Legendre M. [Giant viruses that create their own genes]. Med Sci (Paris) 2019; 34:1087-1091. [PMID: 30623766 DOI: 10.1051/medsci/2018300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Since 2003 and the discovery of Mimivirus, the saga of giant viruses continues with the isolation of new amoeba viruses, which are now divided into seven distinct families, the origin (s) of which are still mysterious and controversial. Thanks to the isolation of 3 new members of the Pandoraviridae family, whose micrometric particles and genomes of more than 2 megabases encroach on the cellular world, we carried out a stringent re-analysis of their gene contents, using a combination of transcriptomic, proteomic and bioinformatic approaches. We concluded that the only scenario capable of accounting for the distribution and the huge proportion of orphan genes ("ORFans") that characterize Pandoraviruses is that they were created de novo within the intergenic regions. This process, perhaps shared among other large DNA viruses, challenges the central paradigm of molecular evolution according to which all genes / proteins have an ancestry history.
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Affiliation(s)
- Jean-Michel Claverie
- Aix-Marseille université et CNRS, Information génomique et structurale (IGS), UMR7256, Institut de microbiologie de la Méditerranée-IMM-FR 3479, parc scientifique de Luminy, 163, avenue de Luminy, case 934, 13288 Marseille Cedex 09, France
| | - Chantal Abergel
- Aix-Marseille université et CNRS, Information génomique et structurale (IGS), UMR7256, Institut de microbiologie de la Méditerranée-IMM-FR 3479, parc scientifique de Luminy, 163, avenue de Luminy, case 934, 13288 Marseille Cedex 09, France
| | - Matthieu Legendre
- Aix-Marseille université et CNRS, Information génomique et structurale (IGS), UMR7256, Institut de microbiologie de la Méditerranée-IMM-FR 3479, parc scientifique de Luminy, 163, avenue de Luminy, case 934, 13288 Marseille Cedex 09, France
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48
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Dombrowski N, Lee JH, Williams TA, Offre P, Spang A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol Lett 2019; 366:5281434. [PMID: 30629179 PMCID: PMC6349945 DOI: 10.1093/femsle/fnz008] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Jun-Hoe Lee
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, Bristol BS8 1TQ, UK
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
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Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018; 42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Yves Quentin
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
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Genome size evolution in the Archaea. Emerg Top Life Sci 2018; 2:595-605. [PMID: 33525826 PMCID: PMC7289037 DOI: 10.1042/etls20180021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/17/2022]
Abstract
What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.
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