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Mei R, Kaneko M, Imachi H, Nobu MK. The origin and evolution of methanogenesis and Archaea are intertwined. PNAS NEXUS 2023; 2:pgad023. [PMID: 36874274 PMCID: PMC9982363 DOI: 10.1093/pnasnexus/pgad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/20/2023] [Indexed: 02/01/2023]
Abstract
Methanogenesis has been widely accepted as an ancient metabolism, but the precise evolutionary trajectory remains hotly debated. Disparate theories exist regarding its emergence time, ancestral form, and relationship with homologous metabolisms. Here, we report the phylogenies of anabolism-involved proteins responsible for cofactor biosynthesis, providing new evidence for the antiquity of methanogenesis. Revisiting the phylogenies of key catabolism-involved proteins further suggests that the last Archaea common ancestor (LACA) was capable of versatile H2-, CO2-, and methanol-utilizing methanogenesis. Based on phylogenetic analyses of the methyl/alkyl-S-CoM reductase family, we propose that, in contrast to current paradigms, substrate-specific functions emerged through parallel evolution traced back to a nonspecific ancestor, which likely originated from protein-free reactions as predicted from autocatalytic experiments using cofactor F430. After LACA, inheritance/loss/innovation centered around methanogenic lithoautotrophy coincided with ancient lifestyle divergence, which is clearly reflected by genomically predicted physiologies of extant archaea. Thus, methanogenesis is not only a hallmark metabolism of Archaea, but the key to resolve the enigmatic lifestyle that ancestral archaea took and the transition that led to physiologies prominent today.
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Affiliation(s)
- Ran Mei
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Masanori Kaneko
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8567, Japan
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan.,Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
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2
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Kurth JM, Nobu MK, Tamaki H, de Jonge N, Berger S, Jetten MSM, Yamamoto K, Mayumi D, Sakata S, Bai L, Cheng L, Nielsen JL, Kamagata Y, Wagner T, Welte CU. Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. THE ISME JOURNAL 2021; 15:3549-3565. [PMID: 34145392 PMCID: PMC8630106 DOI: 10.1038/s41396-021-01025-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 02/05/2023]
Abstract
Methane-generating archaea drive the final step in anaerobic organic compound mineralization and dictate the carbon flow of Earth's diverse anoxic ecosystems in the absence of inorganic electron acceptors. Although such Archaea were presumed to be restricted to life on simple compounds like hydrogen (H2), acetate or methanol, an archaeon, Methermicoccus shengliensis, was recently found to convert methoxylated aromatic compounds to methane. Methoxylated aromatic compounds are important components of lignin and coal, and are present in most subsurface sediments. Despite the novelty of such a methoxydotrophic archaeon its metabolism has not yet been explored. In this study, transcriptomics and proteomics reveal that under methoxydotrophic growth M. shengliensis expresses an O-demethylation/methyltransferase system related to the one used by acetogenic bacteria. Enzymatic assays provide evidence for a two step-mechanisms in which the methyl-group from the methoxy compound is (1) transferred on cobalamin and (2) further transferred on the C1-carrier tetrahydromethanopterin, a mechanism distinct from conventional methanogenic methyl-transfer systems which use coenzyme M as final acceptor. We further hypothesize that this likely leads to an atypical use of the methanogenesis pathway that derives cellular energy from methyl transfer (Mtr) rather than electron transfer (F420H2 re-oxidation) as found for methylotrophic methanogenesis.
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Affiliation(s)
- Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Stefanie Berger
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Utrecht, The Netherlands
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Liping Bai
- Key Laboratory of Energy Microbiology and Its Application of Ministry of Agriculture, Biogas Institute of Ministry of Agriculture, Chengdu, China
| | - Lei Cheng
- Key Laboratory of Energy Microbiology and Its Application of Ministry of Agriculture, Biogas Institute of Ministry of Agriculture, Chengdu, China
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg East, Denmark
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Tristan Wagner
- Microbial Metabolism research group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands.
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3
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Wang Y, Wegener G, Williams TA, Xie R, Hou J, Tian C, Zhang Y, Wang F, Xiao X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. SCIENCE ADVANCES 2021; 7:eabj1453. [PMID: 34215592 PMCID: PMC11057702 DOI: 10.1126/sciadv.abj1453] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TH Bristol, UK
| | - Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Tian
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Fuchs ACD, Ammelburg M, Martin J, Schmitz RA, Hartmann MD, Lupas AN. Archaeal Connectase is a specific and efficient protein ligase related to proteasome β subunits. Proc Natl Acad Sci U S A 2021; 118:e2017871118. [PMID: 33688044 PMCID: PMC7980362 DOI: 10.1073/pnas.2017871118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Sequence-specific protein ligations are widely used to produce customized proteins "on demand." Such chimeric, immobilized, fluorophore-conjugated or segmentally labeled proteins are generated using a range of chemical, (split) intein, split domain, or enzymatic methods. Where short ligation motifs and good chemoselectivity are required, ligase enzymes are often chosen, although they have a number of disadvantages, for example poor catalytic efficiency, low substrate specificity, and side reactions. Here, we describe a sequence-specific protein ligase with more favorable characteristics. This ligase, Connectase, is a monomeric homolog of 20S proteasome subunits in methanogenic archaea. In pulldown experiments with Methanosarcina mazei cell extract, we identify a physiological substrate in methyltransferase A (MtrA), a key enzyme of archaeal methanogenesis. Using microscale thermophoresis and X-ray crystallography, we show that only a short sequence of about 20 residues derived from MtrA and containing a highly conserved KDPGA motif is required for this high-affinity interaction. Finally, in quantitative activity assays, we demonstrate that this recognition tag can be repurposed to allow the ligation of two unrelated proteins. Connectase catalyzes such ligations at substantially higher rates, with higher yields, but without detectable side reactions when compared with a reference enzyme. It thus presents an attractive tool for the development of new methods, for example in the preparation of selectively labeled proteins for NMR, the covalent and geometrically defined attachment of proteins on surfaces for cryo-electron microscopy, or the generation of multispecific antibodies.
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Affiliation(s)
- Adrian C D Fuchs
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Moritz Ammelburg
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian Albrecht University of Kiel, 24118 Kiel, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
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Gong P, Lei P, Wang S, Zeng A, Lou H. Post-Translational Modifications Aid Archaeal Survival. Biomolecules 2020; 10:biom10040584. [PMID: 32290118 PMCID: PMC7226565 DOI: 10.3390/biom10040584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/22/2022] Open
Abstract
Since the pioneering work of Carl Woese, Archaea have fascinated biologists of almost all areas given their unique evolutionary status, wide distribution, high diversity, and ability to grow in special environments. Archaea often thrive in extreme conditions such as high temperature, high/low pH, high salinity, and anoxic ecosystems. All of these are threats to the stability and proper functioning of biological molecules, especially proteins and nucleic acids. Post-translational modifications (PTMs), such as phosphorylation, methylation, acetylation, and glycosylation, are reportedly widespread in Archaea and represent a critical adaptive mechanism to extreme habitats. Here, we summarize our current understanding of the contributions of PTMs to aid in extremophile survival, with a particular focus on the maintenance of genome stability.
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Affiliation(s)
- Ping Gong
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
- Correspondence: (P.G.); (H.L.)
| | - Ping Lei
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Shengping Wang
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Ao Zeng
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No.2 Yuan-Ming-Yuan West Road, Beijing 100193, China
- Correspondence: (P.G.); (H.L.)
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Phylogenomic analysis demonstrates a pattern of rare and long-lasting concerted evolution in prokaryotes. Commun Biol 2018; 1:12. [PMID: 30271899 PMCID: PMC6053082 DOI: 10.1038/s42003-018-0014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/11/2018] [Indexed: 12/15/2022] Open
Abstract
Concerted evolution, where paralogs in the same species show higher sequence similarity to each other than to orthologs in other species, is widely found in many species. However, cases of concerted evolution that last for hundreds of millions of years are very rare. By genome-wide analysis of a broad selection of prokaryotes, we provide strong evidence of recurrent concerted evolution in 26 genes, most of which have lasted more than ~500 million years. We find that most concertedly evolving genes are key members of important pathways, and encode proteins from the same complexes and/or pathways, suggesting coevolution of genes via concerted evolution to maintain gene balance. We also present LRCE-DB, a comprehensive online repository of long-lasting concerted evolution. Collectively, our study reveals that although most duplicated genes may diverge in sequence over a long period, on rare occasions this constraint can be breached, leading to unexpected long-lasting concerted evolution in a recurrent manner. Sishuo Wang and Youhua Chen present an analysis of concerted evolution in prokaryotes using a new computational pipeline, iSeeCE. They find evidence in 26 genes for recurrent concerted evolution, most of which last more than ~500 million years, and provide a database, LRCE-DB, for data exploration.
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