151
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Abstract
Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.
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152
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Zhu QZ, Wegener G, Hinrichs KU, Elvert M. Activity of Ancillary Heterotrophic Community Members in Anaerobic Methane-Oxidizing Cultures. Front Microbiol 2022; 13:912299. [PMID: 35722308 PMCID: PMC9201399 DOI: 10.3389/fmicb.2022.912299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria mediate the anaerobic oxidation of methane (AOM) in marine sediments. However, even sediment-free cultures contain a substantial number of additional microorganisms not directly related to AOM. To track the heterotrophic activity of these community members and their possible relationship with AOM, we amended meso- (37°C) and thermophilic (50°C) AOM cultures (dominated by ANME-1 archaea and their partner bacteria of the Seep-SRB2 clade or Candidatus Desulfofervidus auxilii) with L-leucine-3-13C (13C-leu). Various microbial lipids incorporated the labeled carbon from this amino acid, independent of the presence of methane as an energy source, specifically bacterial fatty acids, such as iso and anteiso-branched C15:0 and C17:0, as well as unsaturated C18:1ω9 and C18:1ω7. In natural methane-rich environments, these bacterial fatty acids are strongly 13C-depleted. We, therefore, suggest that those fatty acids are produced by ancillary bacteria that grow on 13C-depleted necromass or cell exudates/lysates of the AOM core communities. Candidates that likely benefit from AOM biomass are heterotrophic bacterial members of the Spirochetes and Anaerolineae—known to produce abundant branched fatty acids and present in all the AOM enrichment cultures. For archaeal lipids, we observed minor 13C-incorporation, but still suggesting some 13C-leu anabolism. Based on their relatively high abundance in the culture, the most probable archaeal candidates are Bathyarchaeota, Thermoplasmatales, and Lokiarchaeota. The identified heterotrophic bacterial and archaeal ancillary members are likely key players in organic carbon recycling in anoxic marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
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153
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Hatano T, Palani S, Papatziamou D, Salzer R, Souza DP, Tamarit D, Makwana M, Potter A, Haig A, Xu W, Townsend D, Rochester D, Bellini D, Hussain HMA, Ettema TJG, Löwe J, Baum B, Robinson NP, Balasubramanian M. Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery. Nat Commun 2022; 13:3398. [PMID: 35697693 PMCID: PMC9192718 DOI: 10.1038/s41467-022-30656-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 05/10/2022] [Indexed: 11/23/2022] Open
Abstract
The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.
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Grants
- MC_U105184326 Medical Research Council
- MC_UP_1201/27 Medical Research Council
- 203276/Z/16/Z Wellcome Trust
- Wellcome Trust
- WT101885MA Wellcome Trust
- Wellcome Trust (Wellcome)
- Leverhulme Trust
- Svenska Forskningsrådet Formas (Swedish Research Council Formas)
- Above funding attributed to the authors as follows (from paper acknowledgements): Computational analysis was facilitated by resources provided by the Swedish National Infrastructure for Computing (SNIC) at the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank the Warwick Proteomics RTP for mass spectrometry. MKB was supported by the Wellcome Trust (WT101885MA) and the European Research Council (ERC-2014-ADG No. 671083). Work by the NR laboratory was supported by start-up funds from the Division of Biomedical and Life Sciences (BLS, Lancaster University) and a Leverhulme Research Project Grant (RPG-2019-297). NR would like to thank Johanna Syrjanen for performing trial expressions of the Odinarchaeota ESCRT proteins, and Joseph Maman for helpful discussion regarding the SEC-MALS. NR, WX and AP would like to thank Charley Lai and Siu-Kei Yau for assistance with initial Odinarchaeota ESCRT protein purifications. DPS and BB would like to thank Chris Johnson at the MRC LMB Biophysics facility for performing the SEC-MALS assay on Heimdallarchaeotal Vps22. TH, HH, MB, RS, JL, D Tamarit, TE, DPS and BB received support from a Wellcome Trust collaborative award (203276/Z/16/Z). BB and DPS were supported by the MRC. D Tamarit was supported by the Swedish Research Council (International Postdoc grant 2018-06609).
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Affiliation(s)
- Tomoyuki Hatano
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Saravanan Palani
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Dimitra Papatziamou
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Ralf Salzer
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Diorge P Souza
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Daniel Tamarit
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Mehul Makwana
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Antonia Potter
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Alexandra Haig
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Wenjue Xu
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - David Townsend
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - David Rochester
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Hamdi M A Hussain
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Nicholas P Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK.
| | - Mohan Balasubramanian
- Centre for Mechanochemical Cell Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
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154
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Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol 2022; 6:1007-1023. [PMID: 35680998 PMCID: PMC7613034 DOI: 10.1038/s41559-022-01771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Bernd Franz Lang
- Robert Cedergren Centre in Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-Garcia
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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155
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Gophna U, Altman-Price N. Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution. Annu Rev Microbiol 2022; 76:481-502. [PMID: 35667126 DOI: 10.1146/annurev-micro-040820-124627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; ,
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; , .,Department of Natural and Life Sciences, The Open University of Israel, Raanana, Israel
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156
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McGrath C. Highlight: Unraveling the Origins of LUCA and LECA on the Tree of Life. Genome Biol Evol 2022. [PMCID: PMC9168435 DOI: 10.1093/gbe/evac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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157
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Cai M, Duan C, Zhang X, Pan J, Liu Y, Zhang C, Li M. Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1222-1234. [PMID: 34668130 DOI: 10.1007/s11427-021-1996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
Theionarchaea is a recently described archaeal class within the Euryarchaeota. While it is widely distributed in sediment ecosystems, little is known about its metabolic potential and ecological features. Here, we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes, which were further divided into two subgroups, from coastal mangrove sediments of China and seawater columns of the Yap Trench. Genomic analysis revealed that apart from the canonical sulfhydrogenase, Theionarchaea harbor genes encoding heliorhodopsin, group 4 [NiFe]-hydrogenase, and flagellin, in which genes for heliorhodopsin and group 4 [NiFe]-hydrogenase were transcribed in mangrove sediment. Further, the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics, and the potential carbon substrates include detrital proteins, hemicellulose, ethanol, and CO2. The genes for organic substrate metabolism (mainly detrital protein and amino acid metabolism genes) have relatively higher transcripts in the top sediment layers in mangrove wetlands. In addition, co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters (e.g., Chloroflexi) and methanogens. Collectively, these observations expand the current knowledge of the metabolic potential of Theionarchaea, and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.
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Affiliation(s)
- Mingwei Cai
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Changhai Duan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China
| | - Xinxu Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jie Pan
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Cuijing Zhang
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Meng Li
- Archaeal Biology Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China.
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158
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Bell PJL. Eukaryogenesis: The Rise of an Emergent Superorganism. Front Microbiol 2022; 13:858064. [PMID: 35633668 PMCID: PMC9130767 DOI: 10.3389/fmicb.2022.858064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/15/2022] [Indexed: 12/11/2022] Open
Abstract
Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.
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159
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Bremer N, Tria FDK, Skejo J, Garg SG, Martin WF. Ancestral state reconstructions trace mitochondria but not phagocytosis to the last eukaryotic common ancestor. Genome Biol Evol 2022; 14:6596370. [PMID: 35642316 PMCID: PMC9185374 DOI: 10.1093/gbe/evac079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Two main theories have been put forward to explain the origin of mitochondria in eukaryotes: phagotrophic engulfment (undigested food) and microbial symbiosis (physiological interactions). The two theories generate mutually exclusive predictions about the order in which mitochondria and phagocytosis arose. To discriminate the alternatives, we have employed ancestral state reconstructions (ASR) for phagocytosis as a trait, phagotrophy as a feeding habit, the presence of mitochondria, the presence of plastids, and the multinucleated organization across major eukaryotic lineages. To mitigate the bias introduced by assuming a particular eukaryotic phylogeny, we reconstructed the appearance of these traits across 1789 different rooted gene trees, each having species from opisthokonts, mycetozoa, hacrobia, excavate, archeplastida, and Stramenopiles, Alveolates and Rhizaria. The trees reflect conflicting relationships and different positions of the root. We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.
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Affiliation(s)
- Nico Bremer
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - Josip Skejo
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf 40225 Düsseldorf, Germany
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160
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Liu Y, Li M. The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea. MLIFE 2022; 1:218-222. [PMID: 38817676 PMCID: PMC10989867 DOI: 10.1002/mlf2.12020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/24/2022] [Accepted: 04/18/2022] [Indexed: 06/01/2024]
Abstract
The applications of marker gene concatenation have been advanced to resolve the key questions in the Tree of Life. However, the interphylum evolutionary relationship between Korarchaeota of TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) and Asgard archaea remains uncertain. We applied a marker gene ranking procedure to examine their evolutionary history. Our updated trees showed confident placements of (1) Korarchaeota as the basal branch to other TACK archaea and as a sister group to Asgard archaea; (2) Njordarchaeota at basal branch to Korarchaeota instead of within Asgard archaea. They highlight the importance of evaluating marker genes for phylogeny inference of the Archaea domain.
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Affiliation(s)
- Yang Liu
- Archaeal Biology Center, Institute for Advanced StudyShenzhen UniversityShenzhenChina
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced StudyShenzhen UniversityShenzhenChina
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced StudyShenzhen UniversityShenzhenChina
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced StudyShenzhen UniversityShenzhenChina
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161
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Yin X, Zhou G, Cai M, Zhu QZ, Richter-Heitmann T, Aromokeye DA, Liu Y, Nimzyk R, Zheng Q, Tang X, Elvert M, Li M, Friedrich MW. Catabolic protein degradation in marine sediments confined to distinct archaea. THE ISME JOURNAL 2022; 16:1617-1626. [PMID: 35220398 PMCID: PMC9123169 DOI: 10.1038/s41396-022-01210-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/03/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
Abstract
Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating 13C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.
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Affiliation(s)
- Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. .,Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Guowei Zhou
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany. .,School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China.
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Rolf Nimzyk
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Qingfei Zheng
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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162
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Spang A, Mahendrarajah TA, Offre P, Stairs CW. Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere. Genome Biol Evol 2022; 14:evac034. [PMID: 35218347 PMCID: PMC9169541 DOI: 10.1093/gbe/evac034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 11/14/2022] Open
Abstract
The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
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Affiliation(s)
- Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
| | - Courtney W Stairs
- Department of Biology, Microbiology research group, Lund University, Lund, Sweden
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163
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Heinrichs ME, Heyerhoff B, Arslan-Gatz BS, Seidel M, Niggemann J, Engelen B. Deciphering the Virus Signal Within the Marine Dissolved Organic Matter Pool. Front Microbiol 2022; 13:863686. [PMID: 35694303 PMCID: PMC9184803 DOI: 10.3389/fmicb.2022.863686] [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: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are ubiquitously distributed in the marine environment, influencing microbial population dynamics and biogeochemical cycles on a large scale. Due to their small size, they fall into the oceanographic size-class definition of dissolved organic matter (DOM; <0.7 μm). The purpose of our study was to investigate if there is a detectable imprint of virus particles in natural DOM following standard sample preparation and molecular analysis routines using ultrahigh-resolution mass spectrometry (FT-ICR-MS). Therefore, we tested if a molecular signature deriving from virus particles can be detected in the DOM fingerprint of a bacterial culture upon prophage induction and of seawater containing the natural microbial community. Interestingly, the virus-mediated lysate of the infected bacterial culture differed from the cell material of a physically disrupted control culture in its molecular composition. Overall, a small subset of DOM compounds correlated significantly with virus abundances in the bacterial culture setup, accounting for <1% of the detected molecular formulae and <2% of the total signal intensity of the DOM dataset. These were phosphorus- and nitrogen-containing compounds and they were partially also detected in DOM samples from other studies that included high virus abundances. While some of these formulae matched with typical biomolecules that are constituents of viruses, others matched with bacterial cell wall components. Thus, the identified DOM molecular formulae were probably not solely derived from virus particles but were partially also derived from processes such as the virus-mediated bacterial cell lysis. Our results indicate that a virus-derived DOM signature is part of the natural DOM and barely detectable within the analytical window of ultrahigh-resolution mass spectrometry when a high natural background is present.
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Affiliation(s)
- Mara E. Heinrichs
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Benedikt Heyerhoff
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Berin S. Arslan-Gatz
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Michael Seidel
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Bert Engelen
- Benthic Microbiology Group, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
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164
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Morales DP, Robinson AJ, Pawlowski AC, Ark C, Kelliher JM, Junier P, Werner JH, Chain PSG. Advances and Challenges in Fluorescence in situ Hybridization for Visualizing Fungal Endobacteria. Front Microbiol 2022; 13:892227. [PMID: 35722318 PMCID: PMC9199388 DOI: 10.3389/fmicb.2022.892227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022] Open
Abstract
Several bacteria have long been known to interact intimately with fungi, but molecular approaches have only recently uncovered how cosmopolitan these interactions are in nature. Currently, bacterial–fungal interactions (BFI) are inferred based on patterns of co-occurrence in amplicon sequencing investigations. However, determining the nature of these interactions, whether the bacteria are internally or externally associated, remains a grand challenge in BFI research. Fluorescence in situ hybridization (FISH) is a robust method that targets unique sequences of interest which can be employed for visualizing intra-hyphal targets, such as mitochondrial organelles or, as in this study, bacteria. We evaluate the challenges and employable strategies to resolve intra-hyphal BFI to address pertinent criteria in BFI research, such as culturing media, spatial distribution of bacteria, and abundance of bacterial 16S rRNA copies for fluorescent labeling. While these experimental factors influence labeling and detection of endobacteria, we demonstrate how to overcome these challenges thorough permeabilization, appropriate media choice, and targeted amplification using hybridization chain reaction FISH. Such microscopy imaging approaches can now be utilized by the broader research community to complement sequence-based investigations and provide more conclusive evidence on the nature of specific bacterial–fungal relationships.
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Affiliation(s)
- Demosthenes P. Morales
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, United States
- *Correspondence: Demosthenes P. Morales,
| | - Aaron J. Robinson
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andrew C. Pawlowski
- Department of Genetics, Harvard Medical School, Boston, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Caitlyn Ark
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| | - Julia M. Kelliher
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - James H. Werner
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Patrick S. G. Chain
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM, United States
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165
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Aravind L, Iyer LM, Burroughs AM. Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. Annu Rev Biomed Data Sci 2022; 5:367-391. [PMID: 35609893 DOI: 10.1146/annurev-biodatasci-122220-101119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biological replicators, from genes within a genome to whole organisms, are locked in conflicts. Comparative genomics has revealed a staggering diversity of molecular armaments and mechanisms regulating their deployment, collectively termed biological conflict systems. These encompass toxins used in inter- and intraspecific interactions, self/nonself discrimination, antiviral immune mechanisms, and counter-host effectors deployed by viruses and intragenomic selfish elements. These systems possess shared syntactical features in their organizational logic and a set of effectors targeting genetic information flow through the Central Dogma, certain membranes, and key molecules like NAD+. These principles can be exploited to discover new conflict systems through sensitive computational analyses. This has led to significant advances in our understanding of the biology of these systems and furnished new biotechnological reagents for genome editing, sequencing, and beyond. We discuss these advances using specific examples of toxins, restriction-modification, apoptosis, CRISPR/second messenger-regulated systems, and other enigmatic nucleic acid-targeting systems. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA;
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166
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Guéguen N, Maréchal E. Origin of cyanobacterial thylakoids via a non-vesicular glycolipid phase transition and their impact on the Great Oxygenation Event. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2721-2734. [PMID: 35560194 DOI: 10.1093/jxb/erab429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/16/2021] [Indexed: 06/15/2023]
Abstract
The appearance of oxygenic photosynthesis in cyanobacteria is a major event in evolution. It had an irreversible impact on the Earth, promoting the Great Oxygenation Event (GOE) ~2.4 billion years ago. Ancient cyanobacteria predating the GOE were Gloeobacter-type cells lacking thylakoids, which hosted photosystems in their cytoplasmic membrane. The driver of the GOE was proposed to be the transition from unicellular to filamentous cyanobacteria. However, the appearance of thylakoids expanded the photosynthetic surface to such an extent that it introduced a multiplier effect, which would be more coherent with an impact on the atmosphere. Primitive thylakoids self-organize as concentric parietal uninterrupted multilayers. There is no robust evidence for an origin of thylakoids via a vesicular-based scenario. This review reports studies supporting that hexagonal II-forming glucolipids and galactolipids at the periphery of the cytosolic membrane could be turned, within nanoseconds and without any external source of energy, into membrane multilayers. Comparison of lipid biosynthetic pathways shows that ancient cyanobacteria contained only one anionic lamellar-forming lipid, phosphatidylglycerol. The acquisition of sulfoquinovosyldiacylglycerol biosynthesis correlates with thylakoid emergence, possibly enabling sufficient provision of anionic lipids to trigger a hexagonal II-to-lamellar phase transition. With this non-vesicular lipid-phase transition, a framework is also available to re-examine the role of companion proteins in thylakoid biogenesis.
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Affiliation(s)
- Nolwenn Guéguen
- Laboratoire de Physiologie Cellulaire et Végétale; INRAE, CNRS, CEA, Université Grenoble Alpes; IRIG; CEA Grenoble, 17 rue des Martyrs, 38000 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale; INRAE, CNRS, CEA, Université Grenoble Alpes; IRIG; CEA Grenoble, 17 rue des Martyrs, 38000 Grenoble, France
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167
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Wang Y, Hong H, Qian L, Wang Q, Li J, Huang Q, Jiang Y, Lu H, Liu J, Dong Y, Li J, Yan C. Polycyclic aromatic hydrocarbons at subcritical levels as novel indicators of microbial adaptation in a pre-industrial river delta. CHEMOSPHERE 2022; 295:133858. [PMID: 35124082 DOI: 10.1016/j.chemosphere.2022.133858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/21/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Marine sediment is considered a vast sink for organic pollutants including polycyclic aromatic hydrocarbons (PAHs). However, little is known about the relationship between subcritical PAH allocation and benthic microbial patterns. Thus, we carried out a field investigation at the abandoned Yellow River Delta (AYRD) to deepen the understanding of PAHs' horizontal distribution and ecological roles on the continental shelf. The PAH level in the AYRD is relatively low and distance-independent, indicating it resulted from long-term, chronic, anthropogenic input. The combined application of diagnostic molecular ratios reported inconsistent PAH sources, which might be due to the low PAH concentrations and the complexity of contributing sources. Positive Matrix Factorization provided a more robust source classification and identified three main PAH sources-coal combustion and vehicle emissions, petrogenic process, and fossil fuels. The benthic microbiome did not show a significant response to PAHs in terms of microbial assemblage or alpha-diversity. However, Operational Taxonomic Units in some specific phyla, like Thaumarchaeota, Proteobacteria, Acidobacteria, and Chytridiomycota, correlated with the PAH source indicators, supporting the notion that PAH source indicators can act as a novel environmental indicator for microbial adaption. What's more, Microbial Ecological Networks show more connection at sites identified as biomass combustion by both Fluoranthene/(Fluoranthene + Pyrene) and Indeno(1,2,3-cd)pyrene/(Indeno(1,2,3-cd)pyrene + Benzo(ghi)perylene) compared to the ones identified as biomass combustion by Fluoranthene/(Fluoranthene + Pyrene) and petroleum combustion by Indeno(1,2,3-cd)pyrene/(Indeno(1,2,3-cd)pyrene + Benzo(ghi)perylene). Herein, we demonstrate that the PAHs' source indicator can serve as a novel indicator of the interactions between microorganisms, and thus, should be applied to the sustainable management effort in the offshore area.
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Affiliation(s)
- Yazhi Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China; Academy of Environmental Planning and Design, Nanjing University, Nanjing, 210000, Jiangsu, China.
| | - Hualong Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Lu Qian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Qiang Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China; State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Junwei Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China; Key Laboratory of the Ministry of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Guilin, 541004, Guangxi, China.
| | - Qi Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Yongcan Jiang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Haoliang Lu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Jingchun Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Yunwei Dong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China; The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao, China.
| | - Jian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Chongling Yan
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, 361102, Fujian, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China.
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168
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Eukaryogenesis and oxygen in Earth history. Nat Ecol Evol 2022; 6:520-532. [PMID: 35449457 DOI: 10.1038/s41559-022-01733-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/15/2022] [Indexed: 02/07/2023]
Abstract
The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H2 exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.
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169
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Zachar I, Boza G. The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.798045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.
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170
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Jüttner M, Ferreira-Cerca S. Looking through the Lens of the Ribosome Biogenesis Evolutionary History: Possible Implications for Archaeal Phylogeny and Eukaryogenesis. Mol Biol Evol 2022; 39:msac054. [PMID: 35275997 PMCID: PMC8997704 DOI: 10.1093/molbev/msac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.
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Affiliation(s)
- Michael Jüttner
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Regensburg, Germany
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171
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Meyer BH, Adam PS, Wagstaff BA, Kolyfetis GE, Probst AJ, Albers SV, Dorfmueller HC. Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes. eLife 2022; 11:e67448. [PMID: 35394422 PMCID: PMC8993221 DOI: 10.7554/elife.67448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/13/2022] [Indexed: 11/13/2022] Open
Abstract
Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.
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Affiliation(s)
- Benjamin H Meyer
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbial Ecology, University of Duisburg-EssenEssenGermany
- Division of Molecular Microbiology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
- Molecular Biology of Archaea, Faculty of Biology, University of FreiburgFreiburgGermany
| | - Panagiotis S Adam
- Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, Faculty of Chemistry University Duisburg-EssenEssenGermany
| | - Ben A Wagstaff
- Division of Molecular Microbiology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - George E Kolyfetis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of AthensAthensGreece
| | - Alexander J Probst
- Centre of Water and Environmental Research (ZWU), University of Duisburg-EssenEssenGermany
| | - Sonja V Albers
- Molecular Biology of Archaea, Faculty of Biology, University of FreiburgFreiburgGermany
| | - Helge C Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of DundeeDundeeUnited Kingdom
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172
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Van Etten J, Keddis R, Lisa J, Rauschenbach I. The Diverse World of Protists-an Ideal Community with which to Introduce Microscopy in the Microbiology Teaching Laboratory. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2022; 23:e00142-21. [PMID: 35340451 PMCID: PMC8943629 DOI: 10.1128/jmbe.00142-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Protists and other eukaryotes are present in diverse terrestrial and aquatic environments. They can easily be collected from local ponds and streams. Although they are typically larger in size than prokaryotes, making them easy to study with even basic microscopes, microbiology laboratory courses often do not discuss them in detail and may only dedicate a short time to observing preserved samples. This laboratory exercise allows students to develop microscope skills, experience real world application of collecting and processing field samples, and delve deeper into the diverse world of protists and other microbial eukaryotes. Students may also engage by sharing their findings on the website iNaturalist to contribute to the scientific knowledge collected around the world. This laboratory module was initially designed for in-person learning but has been successfully adapted to remote learning and can also be applied to a complete online learning environment.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, New Jersey, USA
| | - Ramaydalis Keddis
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Jessica Lisa
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
- Department of Biology, Georgian Court University, Lakewood, New Jersey, USA
| | - Ines Rauschenbach
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
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173
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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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174
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Xie R, Wang Y, Huang D, Hou J, Li L, Hu H, Zhao X, Wang F. Expanding Asgard members in the domain of Archaea sheds new light on the origin of eukaryotes. SCIENCE CHINA. LIFE SCIENCES 2022; 65:818-829. [PMID: 34378142 DOI: 10.1007/s11427-021-1969-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota-Wukongarchaeota branch from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. However, our understanding is still limited in terms of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe three previously unknown phylum-level Asgard archaeal lineages, tentatively named Sigyn-, Freyr- and Njordarchaeota. Additional members in Wukongarchaeota and Baldrarchaeota from distinct environments are also reported here, further expanding their ecological roles and metabolic capacities. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Asgard archaea and a new lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that Njordarchaeota may have a heterotrophic lifestyle with capability of peptides and amino acids utilization, while Sigynarchaeota and Freyrarchaeota also have the potentials to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Freyrarchaeota and Wukongrarchaeota, respectively. Some previously unidentified eukaryotic signature proteins for intracellular membrane trafficking system, and the homologue of mu/sigma subunit of adaptor protein complex, were identified in Freyrarchaeota. This study expands the Asgard superphylum, sheds new light on the evolution of eukaryotes and improves our understanding of ecological functions of the Asgard archaea.
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Affiliation(s)
- Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Danyue Huang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haining Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoxiao Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fengping Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China.
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175
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Frohn BP, Härtel T, Cox J, Schwille P. Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures. PLoS One 2022; 17:e0266395. [PMID: 35358274 PMCID: PMC8970359 DOI: 10.1371/journal.pone.0266395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/18/2022] [Indexed: 11/19/2022] Open
Abstract
The Endosomal Sorting Complex Required for Transport (ESCRT) system is a multi-protein machinery that is involved in cell division of both Eukaryotes and Archaea. This spread across domains of life suggests that a precursor ESCRT machinery existed already at an evolutionary early stage of life, making it a promising candidate for the (re)construction of a minimal cell division machinery. There are, however, only few experimental data about ESCRT machineries in Archaea, due to high technical challenges in cultivation and microscopy. Here, we analyse the proteins of ESCRT machineries in archaea bioinformatically on a protein domain level, to enable mechanistical comparison without such challenging experiments. First, we infer that there are at least three different cell division mechanisms utilizing ESCRT proteins in archaea, probably similar in their constriction mechanisms but different in membrane tethering. Second, we show that ESCRT proteins in the archaeal super-phylum Asgard are highly similar to eukaryotic ESCRT proteins, strengthening the recently developed idea that all Eukaryotes descended from archaea. Third, we reconstruct a plausible evolutionary development of ESCRT machineries and suggest that a simple ESCRT-based constriction machinery existed in the last archaeal common ancestor. These findings not only give very interesting insights into the likely evolution of cell division in Archaea and Eukaryotes, but also offer new research avenues by suggesting hypothesis-driven experiments for both, cell biology and bottom-up synthetic biology.
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Affiliation(s)
- Béla P. Frohn
- Department of Cellular and Molecular Biophysics, Max-Planck Institute of Biochemistry, Martinsried, Germany
- Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Tobias Härtel
- Department of Cellular and Molecular Biophysics, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
- Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max-Planck Institute of Biochemistry, Martinsried, Germany
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176
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Kambara H, Shinno T, Matsuura N, Matsushita S, Aoi Y, Kindaichi T, Ozaki N, Ohashi A. Environmental Factors Affecting the Community of Methane-oxidizing Bacteria. Microbes Environ 2022; 37. [PMID: 35342121 PMCID: PMC8958294 DOI: 10.1264/jsme2.me21074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB. To investigate the environmental factors affecting the dominant type in the MOB community, we performed MOB enrichment using down-flow hanging sponge reactors under 38 different environmental conditions with a wide range of methane (0.01–80%) and ammonium concentrations (0.001–2,000 mg N L–1) and pH 4–7. Enrichment results revealed that pH was a crucial factor influencing the MOB type enriched. Type II was dominantly enriched at low pH (4–5), whereas Type I was dominant around neutral pH (6–7). However, there were some unusual cultivated biomass samples. Even though high methane oxidation activity was observed, very few or zero conventional MOB were detected using common FISH probes and primer sets for the 16S rRNA gene and pmoA gene amplification. Mycobacterium mostly dominated the microbial community in the biomass cultivated at very high NH4+ concentrations, strongly implying that it exhibits methane oxidation activity. Collectively, the present results revealed the presence of many unknown phylogenetic groups with the capacity for methane oxidation other than the reported MOB.
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Affiliation(s)
- Hiromi Kambara
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University
| | - Takahiro Shinno
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University
| | | | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute
| | - Yoshiteru Aoi
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Noriatsu Ozaki
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
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177
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Akıl C, Ali S, Tran LT, Gaillard J, Li W, Hayashida K, Hirose M, Kato T, Oshima A, Fujishima K, Blanchoin L, Narita A, Robinson RC. Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. SCIENCE ADVANCES 2022; 8:eabm2225. [PMID: 35333570 PMCID: PMC8956254 DOI: 10.1126/sciadv.abm2225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.
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Affiliation(s)
- Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
| | - Samson Ali
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Linh T. Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Jérémie Gaillard
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210093 Nanjing, China
| | - Kenichi Hayashida
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kosuke Fujishima
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Laurent Blanchoin
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
- Université de Paris, INSERM, CEA, Institut de Recherche Saint Louis, U 976, CytoMorpho Lab, 75010 Paris, France
| | - Akihiro Narita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Robert C. Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
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178
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Hammond M, Dorrell RG, Speijer D, Lukeš J. Eukaryotic cellular intricacies shape mitochondrial proteomic complexity. Bioessays 2022; 44:e2100258. [PMID: 35318703 DOI: 10.1002/bies.202100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022]
Abstract
Mitochondria have been fundamental to the eco-physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories.
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Affiliation(s)
- Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dave Speijer
- Medical Biochemistry, UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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179
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Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids. Nat Commun 2022; 13:1545. [PMID: 35318330 PMCID: PMC8941075 DOI: 10.1038/s41467-022-29264-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/07/2022] [Indexed: 01/08/2023] Open
Abstract
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-deleted mutant in Sulfolobus acidocaldarius were unsuccessful, suggesting that the gene is essential in this organism. Heterologous expression of tes homologues leads to production of GDGT and structurally related lipids in the methanogen Methanococcus maripaludis (which otherwise does not synthesize GDGTs and lacks a tes homolog, but produces a putative GDGT precursor, archaeol). Tes homologues are encoded in the genomes of many archaea, as well as in some bacteria, in which they might be involved in the synthesis of bacterial branched glycerol dialkyl glycerol tetraethers.
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180
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Abstract
Healthy development and function of essentially all physiological systems and organs, including the brain, require exposure to the microbiota of our mothers and of the natural environment, especially in early life. We also know that some infections, if we survive them, modulate the immune system in relevant ways. If we study the evolution of the immune and metabolic systems, we can understand how these requirements developed and the nature of the organisms that we need to encounter. We can then begin to identify the mechanisms of the beneficial effects of these exposures. Against this evolutionary background, we can analyze the ways in which the modern urban lifestyle, particularly for individuals experiencing low socioeconomic status (SES), results in deficient or distorted microbial exposures and microbiomes. Thus, an evolutionary approach facilitates the identification of practical solutions to the growing scandal of health disparities linked to inequality.
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181
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Da Cunha V, Gaïa M, Forterre P. The expanding Asgard archaea and their elusive relationships with Eukarya. MLIFE 2022; 1:3-12. [PMID: 38818326 PMCID: PMC10989751 DOI: 10.1002/mlf2.12012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 06/01/2024]
Abstract
The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.
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Affiliation(s)
- Violette Da Cunha
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Morgan Gaïa
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRSUniv. Evry, Université Paris‐SaclayEvryFrance
| | - Patrick Forterre
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
- Département de Microbiologie, Institut PasteurParisFrance
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182
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Smith D, Palacios-Pérez M, Jheeta S. The Enclosed Intestinal Microbiome: Semiochemical Signals from the Precambrian and Their Disruption by Heavy Metal Pollution. Life (Basel) 2022; 12:287. [PMID: 35207574 PMCID: PMC8879143 DOI: 10.3390/life12020287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
It is increasingly likely that many non-communicable diseases of humans and associated animals are due to the degradation of their intestinal microbiomes, a situation often referred to as dysbiosis. An analysis of the resultant diseases offers an opportunity to probe the function of these microbial partners of multicellular animals. In our view, it now seems likely that vertebrate animals and their microbiomes have coevolved throughout the Ediacaran-Cambrian transition and beyond, operating by semiochemical messaging between the multicellular host and its microbial community guest. A consideration of the overall role of the mutualistic intestinal microbiome as an enclosed bioreactor throws up a variety of challenging concepts. In particular: the significance of the microbiome with respect to the immune system suggests that microeukaryotes could act as microbial sentinel cells; the ubiquity of bacteriophage viruses implies the rapid turnover of microbial composition by a viral-shunt mechanism; and high microbial diversity is needed to ensure that horizontal gene transfer allows valuable genetic functions to be expressed. We have previously postulated that microbes of sufficient diversity must be transferred from mother to infant by seemingly accidental contamination during the process of natural birth. We termed this maternal microbial inheritance and suggested that it operates alongside parental genetic inheritance to modify gene expression. In this way, the adjustment of the neonate immune system by the microbiome may represent one of the ways in which the genome of a vertebrate animal interacts with its microbial environment. The absence of such critical functions in the neonate may help to explain the observation of persistent immune-system problems in affected adults. Equally, granted that the survival of the guest microbiome depends on the viability of its host, one function of microbiome-generated semiochemicals could be to facilitate the movement of food through the digestive tract, effectively partitioning nutrition between host and guest. In the event of famine, downregulation of microbial growth and therefore of semiochemical production would allow all available food to be consumed by the host. Although it is often thought that non-communicable diseases, such as type 2 diabetes, are caused by consumption of food containing insufficient dietary fibre, our hypothesis suggests that poor-quality food is not the prime cause but that the tendency for disease follows the degradation of the intestinal microbiome, when fat build-up occurs because the relevant semiochemicals can no longer be produced. It is the purpose of this paper to highlight the possibility that the origins of the microbiome lie in the Precambrian and that the disconnection of body and microbiome gives rise to non-communicable disease through the loss of semiochemical signalling. We further surmise that this disconnect has been largely brought about by heavy metal poisoning, potentially illuminating a facet of the exposome, the sum total of environmental insults that influence the expression of the genetic inheritance of an animal.
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Affiliation(s)
- David Smith
- Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds LS7 3RB, UK
| | - Miryam Palacios-Pérez
- Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds LS7 3RB, UK
- Theoretical Biology Group, Institute of Biomedical Research, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Sohan Jheeta
- Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds LS7 3RB, UK
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183
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Medina-Chávez NO, Travisano M. Archaeal Communities: The Microbial Phylogenomic Frontier. Front Genet 2022; 12:693193. [PMID: 35154237 PMCID: PMC8826477 DOI: 10.3389/fgene.2021.693193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Michael Travisano
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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184
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Nishizawa H, Yamanaka M, Igarashi K. Ferroptosis: regulation by competition between NRF2 and BACH1 and propagation of the death signal. FEBS J 2022; 290:1688-1704. [PMID: 35107212 DOI: 10.1111/febs.16382] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 12/15/2022]
Abstract
Ferroptosis is triggered by a chain of intracellular labile iron-dependent peroxidation of cell membrane phospholipids. Ferroptosis is important not only as a cause of ischaemic and neurodegenerative diseases but also as a mechanism of cancer suppression, and a better understanding of its regulatory mechanism is required. It has become clear that ferroptosis is finely controlled by two oxidative stress-responsive transcription factors, NRF2 (NF-E2-related factor 2) and BACH1 (BTB and CNC homology 1). NRF2 and BACH1 inhibit and promote ferroptosis, respectively, by activating or suppressing the expression of genes in the major regulatory pathways of ferroptosis: intracellular labile iron metabolism, the GSH (glutathione) -GPX4 (glutathione peroxidase 4) pathway and the FSP1 (ferroptosis suppressor protein 1)-CoQ (coenzyme Q) pathway. In addition to this, NRF2 and BACH1 control ferroptosis through the regulation of lipid metabolism and cell differentiation. This multifaceted regulation of ferroptosis by NRF2 and BACH1 is considered to have been acquired during the evolution of multicellular organisms, allowing the utilization of ferroptosis for maintaining homeostasis, including cancer suppression. In terms of cell-cell interaction, it has been revealed that ferroptosis has the property of propagating to surrounding cells along with lipid peroxidation. The regulation of ferroptosis by NRF2 and BACH1 and the propagation phenomenon could be used to realize anticancer cell therapy in the future. In this review, these points will be summarized and discussed.
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Affiliation(s)
- Hironari Nishizawa
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mie Yamanaka
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai, Japan
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185
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Wu F, Speth DR, Philosof A, Crémière A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoshechkin IA, Orphan VJ. Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. Nat Microbiol 2022; 7:200-212. [PMID: 35027677 PMCID: PMC8813620 DOI: 10.1038/s41564-021-01039-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022]
Abstract
Eukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation-decentralized innovation-hierarchical import model that accounts for the emergence of eukaryotic complexity.
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Affiliation(s)
- Fabai Wu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alon Philosof
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Antoine Crémière
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Aditi Narayanan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Igor A Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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186
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Abstract
Light is a ubiquitous energy source and environmental signal that broadly impacts the lifestyle of a large number of photosynthetic/nonphotosynthetic microorganisms living in the euphotic layer. However, the responses of deep-sea microbes to light are largely unknown, even though blue light is proposed to be distributed in the deep ocean. Here, we successfully cultured a novel bacterial species, named Spongiibacter nanhainus CSC3.9, from deep-sea cold seep samples by a blue light induction approach. The growth of strain CSC3.9 was obviously promoted by the illumination of blue light. We next determined BLUF (a typical blue light photoreceptor) was the most essential factor directing light sensing of strain CSC3.9 through a combined proteomic and genetic method. The function of light sensing mediated by BLUF was further confirmed by the in vitro-synthesized protein. Notably, homologs of BLUF widely existed across the marine microorganisms (containing Spongiibacter species) derived from different environments, including cold seeps. This strongly indicates that the distribution of light utilization by the nonphototrophic bacteria living in the ocean is broad and has been substantially underestimated. IMPORTANCE Extensive studies have been conducted to explore the mechanisms of light sensing and utilization by microorganisms that live in the photic zone. Strikingly, accumulated evidence shows that light is distributed in the deep biosphere. However, the existence and process of light sensing and utilization by microbes inhabiting the deep ocean have been seldom reported. In the present study, a novel bacterial strain, Spongiibacter nanhainus CSC3.9, was enriched and purified from a deep-sea cold seep sample through a blue light induction method. Combined with genomic, proteomic, genetic, and biochemical approaches, the mechanism of this novel strain sensing blue light through a BLUF-dependent pathway was detailed. Our study provides a good model to study the mechanisms of light sensing mediated by deep-sea nonphototrophic bacteria.
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187
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Albers S, Ashmore J, Pollard T, Spang A, Zhou J. Origin of eukaryotes: What can be learned from the first successfully isolated Asgard archaeon. Fac Rev 2022; 11:3. [PMID: 35174363 PMCID: PMC8815363 DOI: 10.12703/r-01-000005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024] Open
Abstract
The origin of cellular complexity characterizing eukaryotic cells remains a central unresolved issue in the study of diversification of cellular life on Earth. The isolation by Imachi et al.1 of a member of the Asgard archaea2 - a contemporary relative of organisms thought to have given rise to eukaryotic cells about 2 billion years ago - now promises new insight. The complete genome sequence of the isolated Lokiarchaeum strain confirms that the eukaryotic signature proteins (ESPs) previously identified in the Lokiarchaeota3 and other Asgard archaea2 are indeed encoded by these archaeal genomes and do not represent contamination from eukaryotes. These ESPs encode homologs of eukaryotic actins, small GTPases and the ESCRT complex proteins and are required for the functioning of complex eukaryotic cells. The new, slowly growing, anaerobic laboratory strain allows a first direct look at these organisms and provides key insights into the morphology and metabolism of an Asgard archaeal organism. The work has provided valuable information for other laboratories that aim to isolate and characterize related organisms from other environments.
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Affiliation(s)
| | | | | | - Anja Spang
- Netherlands Institute of Sea Research (NIOZ)
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188
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La SR, Ndhlovu A, Durand PM. The Ancient Origins of Death Domains Support the 'Original Sin' Hypothesis for the Evolution of Programmed Cell Death. J Mol Evol 2022; 90:95-113. [PMID: 35084524 DOI: 10.1007/s00239-021-10044-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2022]
Abstract
The discovery of caspase homologs in bacteria highlighted the relationship between programmed cell death (PCD) evolution and eukaryogenesis. However, the origin of PCD genes in prokaryotes themselves (bacteria and archaea) is poorly understood and a source of controversy. Whether archaea also contain C14 peptidase enzymes and other death domains is largely unknown because of a historical dearth of genomic data. Archaeal genomic databases have grown significantly in the last decade, which allowed us to perform a detailed comparative study of the evolutionary histories of PCD-related death domains in major archaeal phyla, including the deepest branching phyla of Candidatus Aenigmarchaeota, Candidatus Woesearchaeota, and Euryarchaeota. We identified death domains associated with executioners of PCD, like the caspase homologs of the C14 peptidase family, in 321 archaea sequences. Of these, 15.58% were metacaspase type I orthologues and 84.42% were orthocaspases. Maximum likelihood phylogenetic analyses revealed a scattered distribution of orthocaspases and metacaspases in deep-branching bacteria and archaea. The tree topology was incongruent with the prokaryote 16S phylogeny suggesting a common ancestry of PCD genes in prokaryotes and subsequent massive horizontal gene transfer coinciding with the divergence of archaea and bacteria. Previous arguments for the origin of PCD were philosophical in nature with two popular propositions being the "addiction" and 'original sin' hypotheses. Our data support the 'original sin' hypothesis, which argues for a pleiotropic origin of the PCD toolkit with pro-life and pro-death functions tracing back to the emergence of cellular life-the Last Universal Common Ancestor State.
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Affiliation(s)
- So Ri La
- Evolutionary Studies Institute, University of Witwatersrand, Braamfontein, Johannesburg, South Africa.
| | - Andrew Ndhlovu
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Pierre M Durand
- Evolutionary Studies Institute, University of Witwatersrand, Braamfontein, Johannesburg, South Africa
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189
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Hedlund BP, Zhang C, Wang F, Rinke C, Martin WF. Editorial: Ecology, Metabolism and Evolution of Archaea-Perspectives From Proceedings of the International Workshop on Geo-Omics of Archaea. Front Microbiol 2022; 12:827229. [PMID: 35126338 PMCID: PMC8816317 DOI: 10.3389/fmicb.2021.827229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai JiaoTong University, Shanghai, China
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - William F. Martin
- Institute for Molecular Evolution, University of Dusseldorf Medical School, Düsseldorf, Germany
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190
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Gogoi J, Bhatnagar A, Ann KJ, Pottabathini S, Singh R, Mazeed M, Kuncha SK, Kruparani SP, Sankaranarayanan R. Switching a conflicted bacterial DTD-tRNA code is essential for the emergence of mitochondria. SCIENCE ADVANCES 2022; 8:eabj7307. [PMID: 35020439 PMCID: PMC8754408 DOI: 10.1126/sciadv.abj7307] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/17/2021] [Indexed: 06/09/2023]
Abstract
Mitochondria emerged through an endosymbiotic event involving a proteobacterium and an archaeal host. However, the process of optimization of cellular processes required for the successful evolution and survival of mitochondria, which integrates components from two evolutionarily distinct ancestors as well as novel eukaryotic elements, is not well understood. We identify two key switches in the translational machinery—one in the discriminator recognition code of a chiral proofreader DTD [d-aminoacyl–transfer RNA (tRNA) deacylase] and the other in mitochondrial tRNAGly—that enable the compatibility between disparate elements essential for survival. Notably, the mito-tRNAGly discriminator element is the only one to switch from pyrimidine to purine during the bacteria-to-mitochondria transition. We capture this code transition in the Jakobida, an early diverging eukaryotic clade bearing the most bacterial-like mito-genome, wherein both discriminator elements are present. This study underscores the need to explore the fundamental integration strategies critical for mitochondrial and eukaryotic evolution.
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Affiliation(s)
- Jotin Gogoi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Akshay Bhatnagar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Kezia. J. Ann
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | | | - Raghvendra Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Mohd Mazeed
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Santosh Kumar Kuncha
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Shobha P. Kruparani
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR–CCMB Campus, Uppal Road, Hyderabad 500007, India
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191
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192
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Medina M, Baker DM, Baltrus DA, Bennett GM, Cardini U, Correa AMS, Degnan SM, Christa G, Kim E, Li J, Nash DR, Marzinelli E, Nishiguchi M, Prada C, Roth MS, Saha M, Smith CI, Theis KR, Zaneveld J. Grand Challenges in Coevolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.618251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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193
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Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, Garcia SL. A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Front Microbiol 2022; 12:761869. [PMID: 35069467 PMCID: PMC8767057 DOI: 10.3389/fmicb.2021.761869] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/15/2021] [Indexed: 01/09/2023] Open
Abstract
Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Julia K. Nuy
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Sarahi L. Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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194
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Aouad M, Flandrois JP, Jauffrit F, Gouy M, Gribaldo S, Brochier-Armanet C. A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea. BMC Ecol Evol 2022; 22:1. [PMID: 34986784 PMCID: PMC8734073 DOI: 10.1186/s12862-021-01952-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022] Open
Abstract
Background The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal. Results We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study. Conclusions We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01952-0.
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Affiliation(s)
- Monique Aouad
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France.,École Supérieure de Biologie-Biochimie-Biotechnologies, Université Catholique de Lyon, 10 place des archives, 69002, Lyon, France
| | - Jean-Pierre Flandrois
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Frédéric Jauffrit
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France.,Technology Research Department, Innovation Unit, bioMérieux SA, Marcy Étoile, France
| | - Manolo Gouy
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Simonetta Gribaldo
- Department of Microbiology, Unit "Evolutionary Biology of the Microbial Cell", UMR2001, Institut Pasteur, Paris, France.
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622, Villeurbanne, France.
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195
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Mukai T, Amikura K, Fu X, Söll D, Crnković A. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Front Genet 2022; 12:794509. [PMID: 35047015 PMCID: PMC8762117 DOI: 10.3389/fgene.2021.794509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/18/2021] [Indexed: 01/23/2023] Open
Abstract
Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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196
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Adam PS, Bornemann TLV, Probst AJ. Progress and Challenges in Studying the Ecophysiology of Archaea. Methods Mol Biol 2022; 2522:469-486. [PMID: 36125771 DOI: 10.1007/978-1-0716-2445-6_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.
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Affiliation(s)
- Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany.
| | - Till L V Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, UniversitätsstraÔe, Essen, Germany.
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197
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198
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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199
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Werner F. Progress and Challenges in Archaeal Molecular Biology. Methods Mol Biol 2022; 2522:205-207. [PMID: 36125751 DOI: 10.1007/978-1-0716-2445-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Archaea are a key feature of the terran biosphere. Since their early characterization in the 1970s, we have learned much about the fascinating organism, most recently by applying genome-, transcriptome-, proteome-, and metabolome-scale methods. This chapter describes seminal contributions that elaborate on the study of archaeal biology at the systems level.
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Affiliation(s)
- Finn Werner
- RNAP laboratory, Institute of Structural and Molecular Biology, University College London, London, UK.
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200
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Abstract
The rebuttal of the prokaryote-eukaryote dichotomy and the elaboration of the three domains concept by Carl Woese and colleagues has been a breakthrough in biology. With the methodologies available at this time, they have shown that a single molecule, the 16S ribosomal RNA, could reveal the global organization of the living world. Later on, mining archaeal genomes led to major discoveries in archaeal molecular biology, providing a third model for comparative molecular biology. These analyses revealed the strong eukaryal flavor of the basic molecular fabric of Archaea and support rooting the universal tree between Bacteria and Arcarya (the clade grouping Archaea and Eukarya). However, in contradiction with this conclusion, it remains to understand why the archaeal and bacterial mobilomes are so similar and so different from the eukaryal one. These last years, the number of recognized archaea lineages (phyla?) has exploded. The archaeal nomenclature is now in turmoil and debates about the nature of the last universal common ancestor, the last archaeal common ancestor, and the topology of the tree of life are still going on. Interestingly, the expansion of the archaeal eukaryome, especially in the Asgard archaea, has provided new opportunities to study eukaryogenesis. In recent years, the application to Archaea of the new methodologies described in the various chapters of this book have opened exciting avenues to study the molecular biology and the physiology of these fascinating microorganisms.
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Affiliation(s)
- Patrick Forterre
- Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France.
- Institute for Integrative biology of the Cell. université Paris-Saclay, Gif sur Yvette, France.
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