Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling
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Title
Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling
Authors
Keywords
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Journal
Science Advances
Volume 8, Issue 44, Pages -
Publisher
American Association for the Advancement of Science (AAAS)
Online
2022-11-05
DOI
10.1126/sciadv.abm9651
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Note: Only part of the references are listed.- Crystallographic snapshots of a B12-dependent radical SAM methyltransferase
- (2022) Cameron D. Fyfe et al. NATURE
- A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea
- (2022) Olivier N. Lemaire et al. BIOCHEMISTRY
- Diversity and Evolution of Methane-Related Pathways in Archaea
- (2022) Pierre Simon Garcia et al. Annual Review of Microbiology
- Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway
- (2021) Jia-Wei Zhang et al. ISME Journal
- Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis
- (2021) Hui Qi Loh et al. Frontiers in Microbiology
- Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
- (2021) Ivica Letunic et al. NUCLEIC ACIDS RESEARCH
- Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways
- (2021) Valerie De Anda et al. Nature Communications
- Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications
- (2021) Julia Maria Kurth et al. Microorganisms
- Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds
- (2021) Julia M. Kurth et al. ISME Journal
- Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals
- (2021) Suha Naser-Khdour et al. SYSTEMATIC BIOLOGY
- A standardized archaeal taxonomy for the Genome Taxonomy Database
- (2021) Christian Rinke et al. Nature Microbiology
- Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex
- (2021) Tadeo Moreno Chicano et al. Nature Microbiology
- A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism
- (2021) Yinzhao Wang et al. Science Advances
- Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in “ Candidatus Bathyarchaeia”
- (2021) Yan-Ling Qi et al. mSystems
- Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily
- (2021) Seiya Watanabe et al. Communications Biology
- Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species
- (2021) Zhuo Zhou et al. NATURE
- Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments
- (2020) Ibrahim F. Farag et al. ISME Journal
- IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
- (2020) Bui Quang Minh et al. MOLECULAR BIOLOGY AND EVOLUTION
- Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans
- (2020) Dipti D. Nayak et al. PLOS BIOLOGY
- Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment
- (2020) Zhichao Zhou et al. mSystems
- New methods to calculate concordance factors for phylogenomic datasets
- (2020) Bui Quang Minh et al. MOLECULAR BIOLOGY AND EVOLUTION
- A complete domain-to-species taxonomy for Bacteria and Archaea
- (2020) Donovan H. Parks et al. NATURE BIOTECHNOLOGY
- “Candidatus Ethanoperedens,” a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane
- (2020) Cedric Jasper Hahn et al. mBio
- Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi
- (2020) Yi-Fan Liu et al. mSystems
- Several ways one goal—methanogenesis from unconventional substrates
- (2020) Julia M. Kurth et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Anaerobic degradation of paraffins by thermophilic Actinobacteria under methanogenic conditions
- (2020) Yifan Liu et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
- A widely distributed hydrogenase oxidises atmospheric H2 during bacterial growth
- (2020) Zahra F. Islam et al. ISME Journal
- Roadmap for naming uncultivated Archaea and Bacteria
- (2020) Alison E. Murray et al. Nature Microbiology
- Conexivisphaera calida gen. nov., sp. nov., a thermophilic sulfur- and iron-reducing archaeon, and proposal of Conexivisphaeraceae fam. nov., Conexivisphaerales ord. nov., and Conexivisphaeria class. nov. in the phylum Thaumarchaeota
- (2020) Shingo Kato et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
- (2020) Jacob L. Steenwyk et al. PLOS BIOLOGY
- Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi
- (2019) Joel A. Boyd et al. ISME Journal
- Expanding anaerobic alkane metabolism in the domain of Archaea
- (2019) Yinzhao Wang et al. Nature Microbiology
- Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea
- (2019) Guillaume Borrel et al. Nature Microbiology
- Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota
- (2019) Luke J. McKay et al. Nature Microbiology
- Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens
- (2019) Bojk A. Berghuis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep
- (2019) Song-Can Chen et al. NATURE
- Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere
- (2019) Stephanie A. Carr et al. ISME Journal
- Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution
- (2019) Minglei Ren et al. ISME Journal
- Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin
- (2019) Matthew I. Radle et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Asgard archaea capable of anaerobic hydrocarbon cycling
- (2019) Kiley W. Seitz et al. Nature Communications
- An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy
- (2019) Panagiotis S. Adam et al. Nature Microbiology
- GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
- (2019) Pierre-Alain Chaumeil et al. BIOINFORMATICS
- Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea
- (2019) Zheng-Shuang Hua et al. Nature Communications
- GeneSpy, a user-friendly and flexible genomic context visualizer
- (2018) Pierre Simon Garcia et al. BIOINFORMATICS
- Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota
- (2018) Yang Liu et al. ISME Journal
- Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model
- (2018) Stephanie J Spielman et al. MOLECULAR BIOLOGY AND EVOLUTION
- dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
- (2018) Han Zhang et al. NUCLEIC ACIDS RESEARCH
- Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes
- (2018) Panagiotis S. Adam et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The importance of designating type material for uncultured taxa
- (2018) Maria Chuvochina et al. SYSTEMATIC AND APPLIED MICROBIOLOGY
- Identification of a unique Radical SAM methyltransferase required for the sp3-C-methylation of an arginine residue of methyl-coenzyme M reductase
- (2018) Darja Deobald et al. Scientific Reports
- Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
- (2018) Christian M. K. Sieber et al. Nature Microbiology
- Genome-centric view of carbon processing in thawing permafrost
- (2018) Ben J. Woodcroft et al. NATURE
- A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
- (2018) Donovan H Parks et al. NATURE BIOTECHNOLOGY
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
- (2018) Jaime Huerta-Cepas et al. NUCLEIC ACIDS RESEARCH
- The Pfam protein families database in 2019
- (2018) Sara El-Gebali et al. NUCLEIC ACIDS RESEARCH
- Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments
- (2018) Nina Dombrowski et al. Nature Communications
- metaSPAdes: a new versatile metagenomic assembler
- (2017) Sergey Nurk et al. GENOME RESEARCH
- dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
- (2017) Matthew R Olm et al. ISME Journal
- The growing tree of Archaea: new perspectives on their diversity, evolution and ecology
- (2017) Panagiotis S Adam et al. ISME Journal
- UFBoot2: Improving the Ultrafast Bootstrap Approximation
- (2017) Diep Thi Hoang et al. MOLECULAR BIOLOGY AND EVOLUTION
- Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- (2017) Robert M Bowers et al. NATURE BIOTECHNOLOGY
- ModelFinder: fast model selection for accurate phylogenetic estimates
- (2017) Subha Kalyaanamoorthy et al. NATURE METHODS
- The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database
- (2017) Neil D Rawlings et al. NUCLEIC ACIDS RESEARCH
- Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
- (2017) Huai-Chun Wang et al. SYSTEMATIC BIOLOGY
- Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea
- (2017) Dipti D Nayak et al. eLife
- Respiratory Ammonification of Nitrate Coupled to Anaerobic Oxidation of Elemental Sulfur in Deep-Sea Autotrophic Thermophilic Bacteria
- (2017) Galina B. Slobodkina et al. Frontiers in Microbiology
- Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates
- (2017) Dariya K. Sydykova et al. PeerJ
- Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids
- (2017) Sean P. Jungbluth et al. Scientific Data
- Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis
- (2017) Dimitry Y. Sorokin et al. Nature Microbiology
- Phylogenetic rooting using minimal ancestor deviation
- (2017) Fernando Domingues Kümmel Tria et al. Nature Ecology & Evolution
- Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
- (2017) Uyen Mai et al. PLoS One
- Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations
- (2016) Alexander J. Probst et al. ENVIRONMENTAL MICROBIOLOGY
- OrthoANI: An improved algorithm and software for calculating average nucleotide identity
- (2016) Imchang Lee et al. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
- Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt
- (2016) Sean P Jungbluth et al. ISME Journal
- Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen
- (2016) Masaru Konishi Nobu et al. ISME Journal
- BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
- (2016) Minoru Kanehisa et al. JOURNAL OF MOLECULAR BIOLOGY
- Computing the Internode Certainty and Related Measures from Partial Gene Trees
- (2016) Kassian Kobert et al. MOLECULAR BIOLOGY AND EVOLUTION
- Thermophilic archaea activate butane via alkyl-coenzyme M formation
- (2016) Rafael Laso-Pérez et al. NATURE
- Measurement of bacterial replication rates in microbial communities
- (2016) Christopher T Brown et al. NATURE BIOTECHNOLOGY
- Causes of evolutionary rate variation among protein sites
- (2016) Julian Echave et al. NATURE REVIEWS GENETICS
- The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea
- (2016) Kaiyuan Zheng et al. SCIENCE
- Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments
- (2016) Y. He et al. Nature Microbiology
- Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
- (2016) Inka Vanwonterghem et al. Nature Microbiology
- HydDB: A web tool for hydrogenase classification and analysis
- (2016) Dan Søndergaard et al. Scientific Reports
- MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
- (2015) Yu-Wei Wu et al. BIOINFORMATICS
- CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- (2015) Donovan H. Parks et al. GENOME RESEARCH
- Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life
- (2015) Céline Petitjean et al. MOLECULAR BIOLOGY AND EVOLUTION
- The Phyre2 web portal for protein modeling, prediction and analysis
- (2015) Lawrence A Kelley et al. Nature Protocols
- The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides
- (2015) Konstantinos D. Tsirigos et al. NUCLEIC ACIDS RESEARCH
- The two-domain tree of life is linked to a new root for the Archaea
- (2015) Kasie Raymann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
- (2015) P. N. Evans et al. SCIENCE
- Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus
- (2015) Jie Li et al. Scientific Reports
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Elucidating the Process of Activation of Methyl-Coenzyme M Reductase
- (2014) D. Prakash et al. JOURNAL OF BACTERIOLOGY
- Fast and sensitive protein alignment using DIAMOND
- (2014) Benjamin Buchfink et al. NATURE METHODS
- UniProt: a hub for protein information
- (2014) NUCLEIC ACIDS RESEARCH
- PhyloSift: phylogenetic analysis of genomes and metagenomes
- (2014) Aaron E. Darling et al. PeerJ
- SyntTax: a web server linking synteny to prokaryotic taxonomy
- (2013) Jacques Oberto BMC BIOINFORMATICS
- Phenotypic evidence that the function of the [Fe]-hydrogenase Hmd inMethanococcus maripaludisrequires sevenhcg(hmdco-occurring genes) but nothmdII
- (2013) Thomas J. Lie et al. FEMS MICROBIOLOGY LETTERS
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- CD-HIT: accelerated for clustering the next-generation sequencing data
- (2012) Limin Fu et al. BIOINFORMATICS
- Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis
- (2012) T. J. Lie et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Phylogeny and evolution of the Archaea: one hundred genomes later
- (2011) Celine Brochier-Armanet et al. CURRENT OPINION IN MICROBIOLOGY
- Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically
- (2011) Seigo Shima et al. NATURE
- HMMER web server: interactive sequence similarity searching
- (2011) R. D. Finn et al. NUCLEIC ACIDS RESEARCH
- Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
- (2011) Maria Anisimova et al. SYSTEMATIC BIOLOGY
- More Than 200 Genes Required for Methane Formation from H2and CO2and Energy Conservation Are Present inMethanothermobacter marburgensisandMethanothermobacter thermautotrophicus
- (2011) Anne-Kristin Kaster et al. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL
- DUFs: families in search of function
- (2010) Alex Bateman et al. Acta Crystallographica Section F-Structural Biology and Crystallization Communications
- BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
- (2010) Alexis Criscuolo et al. BMC EVOLUTIONARY BIOLOGY
- Characterization of Energy-Conserving Hydrogenase B in Methanococcus maripaludis
- (2010) T. A. Major et al. JOURNAL OF BACTERIOLOGY
- Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea
- (2010) Yoshiho Ikeuchi et al. Nature Chemical Biology
- New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
- (2010) Stéphane Guindon et al. SYSTEMATIC BIOLOGY
- SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
- (2009) M. Gouy et al. MOLECULAR BIOLOGY AND EVOLUTION
- Preliminary structural studies on the MtxX protein fromMethanococcus jannaschii
- (2008) Dong Hae Shin Acta Crystallographica Section F-Structural Biology and Crystallization Communications
- Structure of an F430 Variant from Archaea Associated with Anaerobic Oxidation of Methane
- (2008) Stefan Mayr et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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