1
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Marques E, Kramer R, Ryan DG. Multifaceted mitochondria in innate immunity. NPJ METABOLIC HEALTH AND DISEASE 2024; 2:6. [PMID: 38812744 PMCID: PMC11129950 DOI: 10.1038/s44324-024-00008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/14/2024] [Indexed: 05/31/2024]
Abstract
The ability of mitochondria to transform the energy we obtain from food into cell phosphorylation potential has long been appreciated. However, recent decades have seen an evolution in our understanding of mitochondria, highlighting their significance as key signal-transducing organelles with essential roles in immunity that extend beyond their bioenergetic function. Importantly, mitochondria retain bacterial motifs as a remnant of their endosymbiotic origin that are recognised by innate immune cells to trigger inflammation and participate in anti-microbial defence. This review aims to explore how mitochondrial physiology, spanning from oxidative phosphorylation (OxPhos) to signalling of mitochondrial nucleic acids, metabolites, and lipids, influences the effector functions of phagocytes. These myriad effector functions include macrophage polarisation, efferocytosis, anti-bactericidal activity, antigen presentation, immune signalling, and cytokine regulation. Strict regulation of these processes is critical for organismal homeostasis that when disrupted may cause injury or contribute to disease. Thus, the expanding body of literature, which continues to highlight the central role of mitochondria in the innate immune system, may provide insights for the development of the next generation of therapies for inflammatory diseases.
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Affiliation(s)
- Eloïse Marques
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Robbin Kramer
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Dylan G. Ryan
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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2
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Liu M, Liu Y, Song T, Yang L, Qi L, Zhang YZ, Wang Y, Shen QT. Three-dimensional architecture of ESCRT-III flat spirals on the membrane. Proc Natl Acad Sci U S A 2024; 121:e2319115121. [PMID: 38709931 PMCID: PMC11098116 DOI: 10.1073/pnas.2319115121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/01/2024] [Indexed: 05/08/2024] Open
Abstract
The endosomal sorting complexes required for transport (ESCRTs) are responsible for membrane remodeling in many cellular processes, such as multivesicular body biogenesis, viral budding, and cytokinetic abscission. ESCRT-III, the most abundant ESCRT subunit, assembles into flat spirals as the primed state, essential to initiate membrane invagination. However, the three-dimensional architecture of ESCRT-III flat spirals remained vague for decades due to highly curved filaments with a small diameter and a single preferred orientation on the membrane. Here, we unveiled that yeast Snf7, a component of ESCRT-III, forms flat spirals on the lipid monolayers using cryogenic electron microscopy. We developed a geometry-constrained Euler angle-assigned reconstruction strategy and obtained moderate-resolution structures of Snf7 flat spirals with varying curvatures. Our analyses showed that Snf7 subunits recline on the membrane with N-terminal motifs α0 as anchors, adopt an open state with fused α2/3 helices, and bend α2/3 gradually from the outer to inner parts of flat spirals. In all, we provide the orientation and conformations of ESCRT-III flat spirals on the membrane and unveil the underlying assembly mechanism, which will serve as the initial step in understanding how ESCRTs drive membrane abscission.
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Affiliation(s)
- Mingdong Liu
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Yunhui Liu
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
| | - Tiefeng Song
- College of Life Sciences, Zhejiang University, Hangzhou310058, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining314400, China
| | - Liuyan Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao266237, China
| | - Lei Qi
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
- Biomedical Research Center for Structural Analysis, Shandong University, Jinan250012, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao266237, China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou310058, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining314400, China
| | - Qing-Tao Shen
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
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3
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Yu Y, Li YP, Ren K, Hao X, Fru EC, Rønn R, Rivera WL, Becker K, Feng R, Yang J, Rensing C. A brief history of metal recruitment in protozoan predation. Trends Microbiol 2024; 32:465-476. [PMID: 38103995 DOI: 10.1016/j.tim.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Metals and metalloids are used as weapons for predatory feeding by unicellular eukaryotes on prokaryotes. This review emphasizes the role of metal(loid) bioavailability over the course of Earth's history, coupled with eukaryogenesis and the evolution of the mitochondrion to trace the emergence and use of the metal(loid) prey-killing phagosome as a feeding strategy. Members of the genera Acanthamoeba and Dictyostelium use metals such as zinc (Zn) and copper (Cu), and possibly metalloids, to kill their bacterial prey after phagocytosis. We provide a potential timeline on when these capacities first evolved and how they correlate with perceived changes in metal(loid) bioavailability through Earth's history. The origin of phagotrophic eukaryotes must have postdated the Great Oxidation Event (GOE) in agreement with redox-dependent modification of metal(loid) bioavailability for phagotrophic poisoning. However, this predatory mechanism is predicted to have evolved much later - closer to the origin of the multicellular metazoans and the evolutionary development of the immune systems.
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Affiliation(s)
- Yanshuang Yu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuan-Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Kexin Ren
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiuli Hao
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Ernest Chi Fru
- Centre for Geobiology and Geochemistry, School of Earth and Ocean Sciences, Cardiff University, CF10 3AT Cardiff, UK
| | - Regin Rønn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Karsten Becker
- Friedrich Loeffler-Institute for Medical Microbiology, University Medicine Greifswald, D-17489 Greifswald, Germany
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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4
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van der Gulik PTS, Hoff WD, Speijer D. The contours of evolution: In defence of Darwin's tree of life paradigm. Bioessays 2024; 46:e2400012. [PMID: 38436469 DOI: 10.1002/bies.202400012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.
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Affiliation(s)
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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5
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Eme L, Tamarit D. Microbial Diversity and Open Questions about the Deep Tree of Life. Genome Biol Evol 2024; 16:evae053. [PMID: 38620144 PMCID: PMC11018274 DOI: 10.1093/gbe/evae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2024] [Indexed: 04/17/2024] Open
Abstract
In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring debates surrounding various aspects of the microbial Tree of Life, focusing on recent advances in some of its deepest nodes, such as the roots of bacteria, archaea, and eukaryotes. We also bring forth current limitations in genome recovery and phylogenomic methodology, as well as new avenues of research to uncover additional key microbial lineages and resolve the shape of the Tree of Life.
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Affiliation(s)
- Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif sur-Yvette, France
| | - Daniel Tamarit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584CH, The Netherlands
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6
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Asnicar F, Thomas AM, Passerini A, Waldron L, Segata N. Machine learning for microbiologists. Nat Rev Microbiol 2024; 22:191-205. [PMID: 37968359 DOI: 10.1038/s41579-023-00984-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/17/2023]
Abstract
Machine learning is increasingly important in microbiology where it is used for tasks such as predicting antibiotic resistance and associating human microbiome features with complex host diseases. The applications in microbiology are quickly expanding and the machine learning tools frequently used in basic and clinical research range from classification and regression to clustering and dimensionality reduction. In this Review, we examine the main machine learning concepts, tasks and applications that are relevant for experimental and clinical microbiologists. We provide the minimal toolbox for a microbiologist to be able to understand, interpret and use machine learning in their experimental and translational activities.
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Affiliation(s)
- Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Andrew Maltez Thomas
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Andrea Passerini
- Department of Information Engineering and Computer Science, University of Trento, Trento, Italy
| | - Levi Waldron
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- Department of Epidemiology and Biostatistics, City University of New York, New York, NY, USA.
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy.
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7
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Zhu P, Hou J, Xiong Y, Xie R, Wang Y, Wang F. Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis. Microorganisms 2024; 12:707. [PMID: 38674651 PMCID: PMC11052028 DOI: 10.3390/microorganisms12040707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.
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Affiliation(s)
- Pengfei Zhu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Jialin Hou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Yixuan Xiong
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Ruize Xie
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Fengping Wang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education, School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; (P.Z.); (J.H.); (Y.X.); (R.X.)
- 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 519080, China
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8
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Charles-Orszag A, Petek-Seoane NA, Mullins RD. Archaeal actins and the origin of a multi-functional cytoskeleton. J Bacteriol 2024; 206:e0034823. [PMID: 38391233 PMCID: PMC10955848 DOI: 10.1128/jb.00348-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
Actin and actin-like proteins form filamentous polymers that carry out important cellular functions in all domains of life. In this review, we sketch a map of the function and regulation of actin-like proteins across bacteria, archaea, and eukarya, marking some of the terra incognita that remain in this landscape. We focus particular attention on archaea because mapping the structure and function of cytoskeletal systems across this domain promises to help us understand the evolutionary relationship between the (mostly) mono-functional actin-like filaments found in bacteria and the multi-functional actin cytoskeletons that characterize eukaryotic cells.
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Affiliation(s)
- Arthur Charles-Orszag
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA
| | - Natalie A. Petek-Seoane
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA
| | - R. Dyche Mullins
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA
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9
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Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Diversity, origin, and evolution of the ESCRT systems. mBio 2024; 15:e0033524. [PMID: 38380930 PMCID: PMC10936438 DOI: 10.1128/mbio.00335-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Endosomal sorting complexes required for transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold and using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The last archaeal common ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.IMPORTANCEAll eukaryotic cells possess complex intracellular membrane organization. Endosomal sorting complexes required for transport (ESCRT) play a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the last archaeal common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved toward greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Victor Tobiasson
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Zhongyi Lu
- 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
| | - 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
| | - Siyu Zhang
- 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
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université de Paris, Paris, France
| | - 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
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
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10
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Tran LT, Akıl C, Senju Y, Robinson RC. The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea. Commun Biol 2024; 7:273. [PMID: 38472392 DOI: 10.1038/s42003-024-05888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.
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Affiliation(s)
- Linh T Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
- Division of Structural Biology, University of Oxford, Oxford, England
| | - Yosuke Senju
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, 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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11
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Qiu Z, Yuan L, Lian CA, Lin B, Chen J, Mu R, Qiao X, Zhang L, Xu Z, Fan L, Zhang Y, Wang S, Li J, Cao H, Li B, Chen B, Song C, Liu Y, Shi L, Tian Y, Ni J, Zhang T, Zhou J, Zhuang WQ, Yu K. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nat Commun 2024; 15:2179. [PMID: 38467684 PMCID: PMC10928208 DOI: 10.1038/s41467-024-46539-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Li Yuan
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Bin Lin
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
| | - Jie Chen
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Liyu Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Zheng Xu
- Southern University of Sciences and Technology Yantian Hospital, Shenzhen, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Junyi Li
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Huiluo Cao
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Bing Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Wuhan Benagen Technology Co., Ltd, Wuhan, China
| | - Yongxin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lili Shi
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yonghong Tian
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Jinren Ni
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - Tong Zhang
- Department of Civil Engineering, University of Hong Kong, Hong Kong, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wei-Qin Zhuang
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Auckland, Auckland, New Zealand
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China.
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12
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Mills J, Gebhard LJ, Schubotz F, Shevchenko A, Speth DR, Liao Y, Duggin IG, Marchfelder A, Erdmann S. Extracellular vesicle formation in Euryarchaeota is driven by a small GTPase. Proc Natl Acad Sci U S A 2024; 121:e2311321121. [PMID: 38408251 DOI: 10.1073/pnas.2311321121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/14/2024] [Indexed: 02/28/2024] Open
Abstract
Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms interact with their extracellular world. EVs are able to traffic a diverse array of molecules across different species and even domains, facilitating numerous functions. In this study, we investigate EV production in Euryarchaeota, using the model organism Haloferax volcanii. We uncover that EVs enclose RNA, with specific transcripts preferentially enriched, including those with regulatory potential, and conclude that EVs can act as an RNA communication system between haloarchaea. We demonstrate the key role of an EV-associated small GTPase for EV formation in H. volcanii that is also present across other diverse evolutionary branches of Archaea. We propose the name, ArvA, for the identified family of archaeal vesiculating GTPases. Additionally, we show that two genes in the same operon with arvA (arvB and arvC) are also involved in EV formation. Both, arvB and arvC, are closely associated with arvA in the majority of other archaea encoding ArvA. Our work demonstrates that small GTPases involved in membrane deformation and vesiculation, ubiquitous in Eukaryotes, are also present in Archaea and are widely distributed across diverse archaeal phyla.
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Affiliation(s)
- Joshua Mills
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - L Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen 28359, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Daan R Speth
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Yan Liao
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Iain G Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | | | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
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13
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Hocher A, Warnecke T. Nucleosomes at the Dawn of Eukaryotes. Genome Biol Evol 2024; 16:evae029. [PMID: 38366053 PMCID: PMC10919886 DOI: 10.1093/gbe/evae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/09/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024] Open
Abstract
Genome regulation in eukaryotes revolves around the nucleosome, the fundamental building block of eukaryotic chromatin. Its constituent parts, the four core histones (H3, H4, H2A, H2B), are universal to eukaryotes. Yet despite its exceptional conservation and central role in orchestrating transcription, repair, and other DNA-templated processes, the origins and early evolution of the nucleosome remain opaque. Histone-fold proteins are also found in archaea, but the nucleosome we know-a hetero-octameric complex composed of histones with long, disordered tails-is a hallmark of eukaryotes. What were the properties of the earliest nucleosomes? Did ancestral histones inevitably assemble into nucleosomes? When and why did the four core histones evolve? This review will look at the evolution of the eukaryotic nucleosome from the vantage point of archaea, focusing on the key evolutionary transitions required to build a modern nucleosome. We will highlight recent work on the closest archaeal relatives of eukaryotes, the Asgardarchaea, and discuss what their histones can and cannot tell us about the early evolution of eukaryotic chromatin. We will also discuss how viruses have become an unexpected source of information about the evolutionary path toward the nucleosome. Finally, we highlight the properties of early nucleosomes as an area where new tools and data promise tangible progress in the not-too-distant future.
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Affiliation(s)
- Antoine Hocher
- Medical Research Council Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Tobias Warnecke
- Medical Research Council Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Trinity College, University of Oxford, Oxford, UK
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14
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Bozdag GO, Szeinbaum N, Conlin PL, Chen K, Fos SM, Garcia A, Penev PI, Schaible GA, Trubl G. Chapter 5: Major Biological Innovations in the History of Life on Earth. ASTROBIOLOGY 2024; 24:S107-S123. [PMID: 38498818 PMCID: PMC11071111 DOI: 10.1089/ast.2021.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/14/2023] [Indexed: 03/20/2024]
Abstract
All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.
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Affiliation(s)
- G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L. Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin–Madison, Wisconsin, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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15
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Batista M, Langendijk-Genevaux P, Kwapisz M, Canal I, Phung DK, Plassart L, Capeyrou R, Moalic Y, Jebbar M, Flament D, Fichant G, Bouvier M, Clouet-d'Orval B. Evolutionary and functional insights into the Ski2-like helicase family in Archaea: a comparison of Thermococcales ASH-Ski2 and Hel308 activities. NAR Genom Bioinform 2024; 6:lqae026. [PMID: 38500564 PMCID: PMC10946056 DOI: 10.1093/nargab/lqae026] [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: 05/10/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5'-3' aRNase J exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3'-5' polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ΔASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.
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Affiliation(s)
- Manon Batista
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | | | - Marta Kwapisz
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Isabelle Canal
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Duy Khanh Phung
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Laura Plassart
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Régine Capeyrou
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Yann Moalic
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Didier Flament
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Gwennaele Fichant
- LMGM, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Marie Bouvier
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Béatrice Clouet-d'Orval
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
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16
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Whitman WB, Chuvochina M, Hedlund BP, Konstantinidis KT, Palmer M, Rodriguez‐R LM, Sutcliffe I, Wang F. Why and how to use the SeqCode. MLIFE 2024; 3:1-13. [PMID: 38827511 PMCID: PMC11139209 DOI: 10.1002/mlf2.12092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/16/2023] [Accepted: 11/01/2023] [Indexed: 06/04/2024]
Abstract
The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.
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Affiliation(s)
| | - Maria Chuvochina
- School of Chemistry and Molecular Biosciences, Australian Centre for EcogenomicsThe University of QueenslandSt LuciaAustralia
| | | | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Marike Palmer
- Department of MicrobiologyUniversity of ManitobaWinnipegManitobaCanada
- School of Life SciencesUniversity of Nevada Las VegasLas VegasNevadaUSA
| | - Luis M. Rodriguez‐R
- Department of Microbiology and Digital Science Center (DiSC)University of InnsbruckInnsbruckAustria
| | - Iain Sutcliffe
- Faculty of Health & Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Fengping Wang
- School of Oceanography, International Center for Deep Life InvestigationShanghai Jiao Tong UniversityShanghaiChina
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17
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Zhao P, Bi X, Wang X, Feng X, Shen Y, Yuan G, She Q. Rational design of unrestricted pRN1 derivatives and their application in the construction of a dual plasmid vector system for Saccharolobus islandicus. MLIFE 2024; 3:119-128. [PMID: 38827506 PMCID: PMC11139203 DOI: 10.1002/mlf2.12107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/26/2023] [Accepted: 11/25/2023] [Indexed: 06/04/2024]
Abstract
Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools, which include efficient genome editing, gene silencing, and robust protein expression systems. However, plasmid vectors constructed for this crenarchaeon thus far are based solely on the pRN2 cryptic plasmid. Although this plasmid coexists with pRN1 in its original host, early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for Sa. islandicus. We hypothesized that this failure could be due to the occurrence of CRISPR immunity against pRN1 in this archaeon. We identified a putative target sequence in orf904 encoding a putative replicase on pRN1 (target N1). Mutated targets (N1a, N1b, and N1c) were then designed and tested for their capability to escape the host CRISPR immunity by using a plasmid interference assay. The results revealed that the original target triggered CRISPR immunity in this archaeon, whereas all three mutated targets did not, indicating that all the designed target mutations evaded host immunity. These mutated targets were then incorporated into orf904 individually, yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed (pN1aSD, pN1bSD, and pN1cSD). Sa. islandicus transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors, but pN1cSD lost the capability for replication. These results indicate that the missense mutations in the conserved helicase domain in pN1c inactivated the replicase. We further showed that pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination, and this yielded a dual plasmid system for genetic study with this important archaeal model.
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Affiliation(s)
- Pengpeng Zhao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina
| | - Xiaonan Bi
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina
| | - Xiaoning Wang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina
| | - Xu Feng
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina
| | - Guanhua Yuan
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology InstituteShandong UniversityQingdaoChina
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18
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Lu Z, Zhang S, Liu Y, Xia R, Li M. Origin of eukaryotic-like Vps23 shapes an ancient functional interplay between ESCRT and ubiquitin system in Asgard archaea. Cell Rep 2024; 43:113781. [PMID: 38358888 DOI: 10.1016/j.celrep.2024.113781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
Functional interplay between the endosomal sorting complexes required for transport (ESCRT) and the ubiquitin system underlies the ubiquitin-dependent cargo-sorting pathway of the eukaryotic endomembrane system, yet its evolutionary origin remains unclear. Here, we show that a UEV-Vps23 protein family, which contains UEV and Vps23 domains, mediates an ancient ESCRT and ubiquitin system interplay in Asgard archaea. The UEV binds ubiquitin with high affinity, making the UEV-Vps23 a sensor for sorting ubiquitinated cargo. A steadiness box in the Vps23 domain undergoes ubiquitination through an Asgard E1, E2, and RING E3 cascade. The UEV-Vps23 switches between autoinhibited and active forms, regulating the ESCRT and ubiquitin system interplay. Furthermore, the shared sequence and structural homology among the UEV-Vps23, eukaryotic Vps23, and archaeal CdvA suggest a common evolutionary origin. Together, this work expands our understanding of the ancient ESCRT and ubiquitin system interplay that likely arose antedating divergent evolution between Asgard archaea and eukaryotes.
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Affiliation(s)
- Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Runyue Xia
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
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19
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Romero H, Aguilar PS, Graña M, Langleib M, Gudiño V, Podbilewicz B. Membrane fusion and fission during eukaryogenesis. Curr Opin Cell Biol 2024; 86:102321. [PMID: 38219525 DOI: 10.1016/j.ceb.2023.102321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/16/2024]
Abstract
All eukaryotes can be traced back to a single shared ancestral lineage that emerged from interactions between different prokaryotic cells. Current models of eukaryogenesis describe various selective forces and evolutionary mechanisms that contributed to the formation of eukaryotic cells. Central to this process were significant changes in cellular structure, resulting in the configuration of a new cell type characterized by internal membrane compartments. Additionally, eukaryogenesis results in a life cycle that relies on cell-cell fusion. We discuss the potential roles of proteins involved in remodeling cellular membranes, highlighting two critical stages in the evolution of eukaryotes: the internalization of symbiotic partners and a scenario wherein the emergence of sexual reproduction is linked to a polyploid ancestor generated by cell-cell fusion.
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Affiliation(s)
- Héctor Romero
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias/CURE, Universidad de la República, Uruguay; Centro Interdisciplinario de Ciencia de Datos y Aprendizaje Automático (CICADA), Espacio Interdisciplinario, Universidad de la República, Uruguay.
| | - Pablo S Aguilar
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Buenos Aires, Argentina.
| | - Martin Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mauricio Langleib
- Laboratorio de Genómica Evolutiva, Facultad de Ciencias/CURE, Universidad de la República, Uruguay; Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Virginia Gudiño
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Buenos Aires, Argentina
| | - Benjamin Podbilewicz
- Department of Biology, Technion Israel Institute of Technology, Haifa, Israel; Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
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20
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Kazan R, Bourgeois G, Lazennec-Schurdevin C, Coureux PD, Mechulam Y, Schmitt E. Structural insights into the evolution of late steps of translation initiation in the three domains of life. Biochimie 2024; 217:31-41. [PMID: 36773835 DOI: 10.1016/j.biochi.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. These two factors are also orthologous to the bacterial IF2 and IF1 proteins, respectively. Recent cryo-EM studies showed how e/aIF5B and e/aIF1A cooperate on the small ribosomal subunit to favor the binding of the large ribosomal subunit and the formation of a ribosome competent for elongation. In this review, pioneering studies and recent biochemical and structural results providing new insights into the role of a/eIF5B in archaea and eukaryotes will be presented. Recent structures will also be compared to orthologous bacterial initiation complexes to highlight domain-specific features and the evolution of initiation mechanisms.
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Affiliation(s)
- Ramy Kazan
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Christine Lazennec-Schurdevin
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Pierre-Damien Coureux
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
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21
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Zong G, Desfougères Y, Portela-Torres P, Kwon YU, Saiardi A, Shears SB, Wang H. Biochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus. EMBO J 2024; 43:462-480. [PMID: 38216735 PMCID: PMC10897400 DOI: 10.1038/s44318-023-00005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024] Open
Abstract
Kinases that synthesize inositol phosphates (IPs) and pyrophosphates (PP-IPs) control numerous biological processes in eukaryotic cells. Herein, we extend this cellular signaling repertoire to viruses. We have biochemically and structurally characterized a minimalist inositol phosphate kinase (i.e., TvIPK) encoded by Terrestrivirus, a nucleocytoplasmic large ("giant") DNA virus (NCLDV). We show that TvIPK can synthesize inositol pyrophosphates from a range of scyllo- and myo-IPs, both in vitro and when expressed in yeast cells. We present multiple crystal structures of enzyme/substrate/nucleotide complexes with individual resolutions from 1.95 to 2.6 Å. We find a heart-shaped ligand binding pocket comprising an array of positively charged and flexible side chains, underlying the observed substrate diversity. A crucial arginine residue in a conserved "G-loop" orients the γ-phosphate of ATP to allow substrate pyrophosphorylation. We highlight additional conserved catalytic and architectural features in TvIPK, and support their importance through site-directed mutagenesis. We propose that NCLDV inositol phosphate kinases may have assisted evolution of inositol pyrophosphate signaling, and we discuss the potential biogeochemical significance of TvIPK in soil niches.
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Affiliation(s)
- Guangning Zong
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Yann Desfougères
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Paloma Portela-Torres
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Yong-Uk Kwon
- Department of Chemistry and Nanoscience, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK.
| | - Stephen B Shears
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
| | - Huanchen Wang
- Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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22
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Harish A. Protein structures unravel the signatures and patterns of deep time evolution. QRB DISCOVERY 2024; 5:e3. [PMID: 38616890 PMCID: PMC11016368 DOI: 10.1017/qrd.2024.4] [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: 08/18/2023] [Revised: 11/13/2023] [Accepted: 12/12/2023] [Indexed: 04/16/2024] Open
Abstract
The formulation and testing of hypotheses using 'big biology data' often lie at the interface of computational biology and structural biology. The Protein Data Bank (PDB), which was established about 50 years ago, catalogs three-dimensional (3D) shapes of organic macromolecules and showcases a structural view of biology. The comparative analysis of the structures of homologs, particularly of proteins, from different species has significantly improved the in-depth analyses of molecular and cell biological questions. In addition, computational tools that were developed to analyze the 'protein universe' are providing the means for efficient resolution of longstanding debates in cell and molecular evolution. In celebrating the golden jubilee of the PDB, much has been written about the transformative impact of PDB on a broad range of fields of scientific inquiry and how structural biology transformed the study of the fundamental processes of life. Yet, the transforming influence of PDB on one field of inquiry of fundamental interest-the reconstruction of the distant biological past-has gone almost unnoticed. Here, I discuss the recent advances to highlight how insights and tools of structural biology are bearing on the data required for the empirical resolution of vigorously debated and apparently contradicting hypotheses in evolutionary biology. Specifically, I show that evolutionary characters defined by protein structure are superior compared to conventional sequence characters for reliable, data-driven resolution of competing hypotheses about the origins of the major clades of life and evolutionary relationship among those clades. Since the better quality data unequivocally support two primary domains of life, it is imperative that the primary classification of life be revised accordingly.
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23
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Novikova PV, Bhanu Busi S, Probst AJ, May P, Wilmes P. Functional prediction of proteins from the human gut archaeome. ISME COMMUNICATIONS 2024; 4:ycad014. [PMID: 38486809 PMCID: PMC10939349 DOI: 10.1093/ismeco/ycad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 03/17/2024]
Abstract
The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.
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Affiliation(s)
- Polina V Novikova
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- UK Centre for Ecology and Hydrology, Wallingford, OX10 8 BB, United Kingdom
| | - Alexander J Probst
- Environmental Metagenomics, Department of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, for Environmental Microbiology and Biotechnology, University Duisburg-Essen, Duisburg 47057, Germany
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Paul Wilmes
- Systems Ecology, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
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24
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Göker M, Oren A. Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38252124 DOI: 10.1099/ijsem.0.006242] [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: 01/23/2024] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
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25
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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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26
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Betancurt-Anzola L, Martínez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L. Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun 2023; 14:8306. [PMID: 38097591 PMCID: PMC10721889 DOI: 10.1038/s41467-023-44125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.
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Affiliation(s)
- Leonardo Betancurt-Anzola
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
- New England Biolabs France, 5 Rue Henri Auguste Desbruères, 91000, Évry-Courcouronnes, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Kelly M Zatopek
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Andrew F Gardner
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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27
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Rafiq M, Hassan N, Rehman M, Hayat M, Nadeem G, Hassan F, Iqbal N, Ali H, Zada S, Kang Y, Sajjad W, Jamal M. Challenges and Approaches of Culturing the Unculturable Archaea. BIOLOGY 2023; 12:1499. [PMID: 38132325 PMCID: PMC10740628 DOI: 10.3390/biology12121499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.
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Affiliation(s)
- Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- FF Institute (Huzhou) Co., Ltd., Huzhou 313000, China
| | - Noor Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Maliha Rehman
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Muhammad Hayat
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Jinan 266101, China
| | - Gullasht Nadeem
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Farwa Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Naveed Iqbal
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Sahib Zada
- Guangzhou Institute of Energy Conservation, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou, Guiyang 550025, China
- Key Laboratory of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Wasim Sajjad
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan 23200, Pakistan
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28
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Carlton JG, Baum B. Roles of ESCRT-III polymers in cell division across the tree of life. Curr Opin Cell Biol 2023; 85:102274. [PMID: 37944425 PMCID: PMC7615534 DOI: 10.1016/j.ceb.2023.102274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Every cell becomes two through a carefully orchestrated process of division. Prior to division, contractile machinery must first be assembled at the cell midzone to ensure that the cut, when it is made, bisects the two separated copies of the genetic material. Second, this contractile machinery must be dynamically tethered to the limiting plasma membrane so as to bring the membrane with it as it constricts. Finally, the connecting membrane must be severed to generate two physically separate daughter cells. In several organisms across the tree of life, Endosomal Sorting Complex Required for Transport (ESCRT)-III family proteins aid cell division by forming composite polymers that function together with the Vps4 AAA-ATPase to constrict and cut the membrane tube connecting nascent daughter cells from the inside. In this review, we discuss unique features of ESCRT-III that enable it to play this role in division in many archaea and eukaryotes.
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Affiliation(s)
- Jeremy Graham Carlton
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, Guy's Hospital, London, SE1 1UL, UK; Organelle Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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29
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Notaro A, Zaretsky M, Molinaro A, De Castro C, Eichler J. N-glycosylation in Archaea: Unusual sugars and unique modifications. Carbohydr Res 2023; 534:108963. [PMID: 37890267 DOI: 10.1016/j.carres.2023.108963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Archaea are microorganisms that comprise a distinct branch of the universal tree of life and which are best known as extremophiles, residing in a variety of environments characterized by harsh physical conditions. One seemingly universal trait of Archaea is the ability to perform N-glycosylation. At the same time, archaeal N-linked glycans present variety in terms of both composition and architecture not seen in the parallel eukaryal or bacterial processes. In this mini-review, many of the unique and unusual sugars found in archaeal N-linked glycans as identified by nuclear magnetic resonance spectroscopy are described.
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Affiliation(s)
- Anna Notaro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy
| | - Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel.
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30
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Vulcano F, Hribovšek P, Denny EO, Steen IH, Stokke R. Potential for homoacetogenesis via the Wood-Ljungdahl pathway in Korarchaeia lineages from marine hydrothermal vents. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:698-707. [PMID: 37218095 PMCID: PMC10667645 DOI: 10.1111/1758-2229.13168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
The Wood-Ljungdahl pathway (WLP) is a key metabolic component of acetogenic bacteria where it acts as an electron sink. In Archaea, despite traditionally being linked to methanogenesis, the pathway has been found in several Thermoproteota and Asgardarchaeota lineages. In Bathyarchaeia and Lokiarchaeia, its presence has been linked to a homoacetogenic metabolism. Genomic evidence from marine hydrothermal genomes suggests that lineages of Korarchaeia could also encode the WLP. In this study, we reconstructed 50 Korarchaeia genomes from marine hydrothermal vents along the Arctic Mid-Ocean Ridge, substantially expanding the Korarchaeia class with several taxonomically novel genomes. We identified a complete WLP in several deep-branching lineages, showing that the presence of the WLP is conserved at the root of the Korarchaeia. No methyl-CoM reductases were encoded by genomes with the WLP, indicating that the WLP is not linked to methanogenesis. By assessing the distribution of hydrogenases and membrane complexes for energy conservation, we show that the WLP is likely used as an electron sink in a fermentative homoacetogenic metabolism. Our study confirms previous hypotheses that the WLP has evolved independently from the methanogenic metabolism in Archaea, perhaps due to its propensity to be combined with heterotrophic fermentative metabolisms.
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Affiliation(s)
- Francesca Vulcano
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
| | - Petra Hribovšek
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
- Department of Earth Science, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
| | - Emily Olesin Denny
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
- Department of Informatics, Computational Biological UnitUniversity of BergenBergenNorway
| | - Ida H. Steen
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
| | - Runar Stokke
- Department of Biological Sciences, Centre for Deep Sea ResearchUniversity of BergenBergenNorway
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31
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Palacios-Pérez M, José MV. A Proposal of the Ur-RNAome. Genes (Basel) 2023; 14:2158. [PMID: 38136981 PMCID: PMC10743229 DOI: 10.3390/genes14122158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
It is widely accepted that the earliest RNA molecules were folded into hairpins or mini-helixes. Herein, we depict the 2D and 3D conformations of those earliest RNA molecules with only RNY triplets, which Eigen proposed as the primeval genetic code. We selected 26 species (13 bacteria and 13 archaea). We found that the free energy of RNY hairpins was consistently lower than that of their corresponding shuffled controls. We found traces of the three ribosomal RNAs (16S, 23S, and 5S), tRNAs, 6S RNA, and the RNA moieties of RNase P and the signal recognition particle. Nevertheless, at this stage of evolution there was no genetic code (as seen in the absence of the peptidyl transferase centre and any vestiges of the anti-Shine-Dalgarno sequence). Interestingly, we detected the anticodons of both glycine (GCC) and threonine (GGU) in the hairpins of proto-tRNA.
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Affiliation(s)
- Miryam Palacios-Pérez
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Network of Researchers on the Chemical Emergence of Life (NoRCEL), Leeds LS7 3RB, UK
- NoRCEL’s Latin America Hub, 113 Philosophy Hall, University of California, Berkeley, CA 94720, USA
| | - Marco V. José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Network of Researchers on the Chemical Emergence of Life (NoRCEL), Leeds LS7 3RB, UK
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32
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Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
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Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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33
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Zheng J, Mallon J, Lammers A, Rados T, Litschel T, Moody ERR, Ramirez-Diaz DA, Schmid A, Williams TA, Bisson-Filho AW, Garner E. Salactin, a dynamically unstable actin homolog in Haloarchaea. mBio 2023; 14:e0227223. [PMID: 37966230 PMCID: PMC10746226 DOI: 10.1128/mbio.02272-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.
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Affiliation(s)
- Jenny Zheng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - John Mallon
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Alex Lammers
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Department of Biomedical Engineering, The Biological Design Center, Boston University, Boston, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Theopi Rados
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Thomas Litschel
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Edmund R. R. Moody
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Diego A. Ramirez-Diaz
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amy Schmid
- Department of Biology, Duke University, Durham, North Carolina, USA
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexandre W. Bisson-Filho
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
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Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
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35
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Marinov GK, Bagdatli ST, Wu T, He C, Kundaje A, Greenleaf WJ. The chromatin landscape of the euryarchaeon Haloferax volcanii. Genome Biol 2023; 24:253. [PMID: 37932847 PMCID: PMC10626798 DOI: 10.1186/s13059-023-03095-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes, not all archaea possess histones and it is not clear if histones are a main packaging component for all that do. Despite increased interest in archaeal chromatin in recent years, its properties have been little studied using genomic tools. RESULTS Here, we adapt the ATAC-seq assay to archaea and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA) and find that while H. volcanii promoters exist in a preferentially accessible state, unlike most eukaryotes, modulation of transcriptional activity is not associated with changes in promoter accessibility. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii and find that Haloferax chromatin is similarly or only slightly more accessible, in aggregate, than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. CONCLUSIONS Our results provide the first comprehensive maps of chromatin accessibility and active transcription in Haloferax across conditions and thus a foundation for future functional studies of archaeal chromatin.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Tong Wu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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36
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Pfitzner AK, Zivkovic H, Bernat-Silvestre C, West M, Peltier T, Humbert F, Odorizzi G, Roux A. Vps60 initiates alternative ESCRT-III filaments. J Cell Biol 2023; 222:e202206028. [PMID: 37768378 PMCID: PMC10538557 DOI: 10.1083/jcb.202206028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 03/08/2023] [Accepted: 06/12/2023] [Indexed: 09/29/2023] Open
Abstract
Endosomal sorting complex required for transport-III (ESCRT-III) participates in essential cellular functions, from cell division to endosome maturation. The remarkable increase of its subunit diversity through evolution may have enabled the acquisition of novel functions. Here, we characterize a novel ESCRT-III copolymer initiated by Vps60. Membrane-bound Vps60 polymers recruit Vps2, Vps24, Did2, and Ist1, as previously shown for Snf7. Snf7- and Vps60-based filaments can coexist on membranes without interacting as their polymerization and recruitment of downstream subunits remain spatially and biochemically separated. In fibroblasts, Vps60/CHMP5 and Snf7/CHMP4 are both recruited during endosomal functions and cytokinesis, but their localization is segregated and their recruitment dynamics are different. Contrary to Snf7/CHMP4, Vps60/CHMP5 is not recruited during nuclear envelope reformation. Taken together, our results show that Vps60 and Snf7 form functionally distinct ESCRT-III polymers, supporting the notion that diversification of ESCRT-III subunits through evolution is linked to the acquisition of new cellular functions.
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Affiliation(s)
| | - Henry Zivkovic
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | | | - Matt West
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Tanner Peltier
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Frédéric Humbert
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Greg Odorizzi
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
- National Center of Competence in Research in Chemical Biology, University of Geneva, Geneva, Switzerland
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37
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Fernando LD, Pérez-Llano Y, Dickwella Widanage MC, Jacob A, Martínez-Ávila L, Lipton AS, Gunde-Cimerman N, Latgé JP, Batista-García RA, Wang T. Structural adaptation of fungal cell wall in hypersaline environment. Nat Commun 2023; 14:7082. [PMID: 37925437 PMCID: PMC10625518 DOI: 10.1038/s41467-023-42693-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023] Open
Abstract
Halophilic fungi thrive in hypersaline habitats and face a range of extreme conditions. These fungal species have gained considerable attention due to their potential applications in harsh industrial processes, such as bioremediation and fermentation under unfavorable conditions of hypersalinity, low water activity, and extreme pH. However, the role of the cell wall in surviving these environmental conditions remains unclear. Here we employ solid-state NMR spectroscopy to compare the cell wall architecture of Aspergillus sydowii across salinity gradients. Analyses of intact cells reveal that A. sydowii cell walls contain a rigid core comprising chitin, β-glucan, and chitosan, shielded by a surface shell composed of galactomannan and galactosaminogalactan. When exposed to hypersaline conditions, A. sydowii enhances chitin biosynthesis and incorporates α-glucan to create thick, stiff, and hydrophobic cell walls. Such structural rearrangements enable the fungus to adapt to both hypersaline and salt-deprived conditions, providing a robust mechanism for withstanding external stress. These molecular principles can aid in the optimization of halophilic strains for biotechnology applications.
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Affiliation(s)
- Liyanage D Fernando
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yordanis Pérez-Llano
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Malitha C Dickwella Widanage
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anand Jacob
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Andrew S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology, University of Crete, Heraklion, Greece
- Fungal Respiratory Infections Research Unit, University of Angers, Angers, France
| | | | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA.
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38
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Marinov GK, Doughty B, Kundaje A, Greenleaf WJ. The landscape of the histone-organized chromatin of Bdellovibrionota bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564843. [PMID: 37961278 PMCID: PMC10634947 DOI: 10.1101/2023.10.30.564843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, histone proteins have recently been identified in a few bacterial clades, most notably the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that, similar to what is observed in some archaea and in eukaryotes with compact genomes such as yeast, Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions. Similar to eukaryotes, chromatin accessibility in Bacteriovorax positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that unlike in yeast, but similar to the state of mammalian and fly promoters, Bacteriovorax promoters exhibit very strong polymerase pausing. Finally, similar to that of other bacteria without histones, the Bacteriovorax genome exists in a three-dimensional (3D) configuration organized by the parABS system along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the functional diversity in chromatin organization across the tree of life.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Benjamin Doughty
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Arc Institute, Palo Alto, California, USA
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39
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Schlösser L, Sachse C, Low HH, Schneider D. Conserved structures of ESCRT-III superfamily members across domains of life. Trends Biochem Sci 2023; 48:993-1004. [PMID: 37718229 DOI: 10.1016/j.tibs.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/19/2023]
Abstract
Structural and evolutionary studies of cyanobacterial phage shock protein A (PspA) and inner membrane-associated protein of 30 kDa (IM30) have revealed that these proteins belong to the endosomal sorting complex required for transport-III (ESCRT-III) superfamily, which is conserved across all three domains of life. PspA and IM30 share secondary and tertiary structures with eukaryotic ESCRT-III proteins, whilst also oligomerizing via conserved interactions. Here, we examine the structures of bacterial ESCRT-III-like proteins and compare the monomeric and oligomerized forms with their eukaryotic counterparts. We discuss conserved interactions used for self-assembly and highlight key hinge regions that mediate oligomer ultrastructure versatility. Finally, we address the differences in nomenclature assigned to equivalent structural motifs in both the bacterial and eukaryotic fields and suggest a common nomenclature applicable across the ESCRT-III superfamily.
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Affiliation(s)
- Lukas Schlösser
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institute for Biological Information Processing/IBI-6 Cellular Structural Biology, Jülich, Germany; Department of Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, UK
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany.
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40
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Aktürk Dizman Y. Codon usage bias analysis of the gene encoding NAD +-dependent DNA ligase protein of Invertebrate iridescent virus 6. Arch Microbiol 2023; 205:352. [PMID: 37812231 DOI: 10.1007/s00203-023-03688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD+-dependent DNA ligases. The 615-amino acid open reading frame (ORF 205R) consists of several domains, including an N-terminal domain Ia, followed by an adenylation domain, an OB-fold domain, a helix-hairpin-helix (HhH) domain, and a BRCT domain. Notably, the zinc finger domain, typically present in NAD+-dependent DNA ligases, is absent in ORF 205R. Since the protein encoded by ORF 205R (IIV6 DNA ligase gene) is involved in critical functions such as DNA replication, modification, and repair, it is crucial to comprehend the codon usage associated with this gene. In this paper, the codon usage bias (CUB) in DNA ligase gene of IIV6 and 11 reference iridoviruses was analyzed by comparing the nucleotide contents, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), relative abundance of dinucleotides and other indices. Both the base content and the RCSU analysis indicated that the A- and T-ending codons were mostly favored in the DNA ligase gene of IIV6. The ENC value of 35.64 implied a high CUB in the IIV6 DNA ligase gene. The ENC plot, neutrality plot, parity rule 2 plot, correspondence analysis revealed that mutation pressure and natural selection had an impact on the CUB of the IIVs DNA ligase genes. Additionally, the analysis of codon adaptation index demonstrated that the IIV6 DNA ligase gene is strongly adapted to its host. These findings will improve our comprehension of the CUB of IIV6 DNA ligase and reference genes, which may provide the required information for a fundamental evolutionary analysis of these genes.
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Affiliation(s)
- Yeşim Aktürk Dizman
- Department of Biology, Faculty of Arts and Sciences, Recep Tayyip Erdogan University, 53100, Rize, Turkey.
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41
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Rangel LT, Fournier GP. Fast-Evolving Alignment Sites Are Highly Informative for Reconstructions of Deep Tree of Life Phylogenies. Microorganisms 2023; 11:2499. [PMID: 37894157 PMCID: PMC10609509 DOI: 10.3390/microorganisms11102499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
The trimming of fast-evolving sites, often known as "slow-fast" analysis, is broadly used in microbial phylogenetic reconstruction under the assumption that fast-evolving sites do not retain an accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here, we show that, contrary to this assumption, even the fastest-evolving sites present in the conserved proteins often used in Tree of Life studies contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site-specific substitution rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we also show that both slow- and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have a substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of the Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.
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Affiliation(s)
- L. Thibério Rangel
- Department of Earth, Atmospheric, & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
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42
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Esposti MD. Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis. FEBS Lett 2023; 597:2484-2496. [PMID: 37507225 DOI: 10.1002/1873-3468.14708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.
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43
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Tirumalai MR, Sivaraman RV, Kutty LA, Song EL, Fox GE. Ribosomal Protein Cluster Organization in Asgard Archaea. ARCHAEA (VANCOUVER, B.C.) 2023; 2023:5512414. [PMID: 38314098 PMCID: PMC10833476 DOI: 10.1155/2023/5512414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 02/06/2024]
Abstract
It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | | | | | | | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
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44
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Lim Y, Yang SJ, Kang I, Cho JC. Metagenomic data from surface seawater of the east coast of South Korea. Sci Data 2023; 10:647. [PMID: 37737276 PMCID: PMC10517112 DOI: 10.1038/s41597-023-02556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
The East Sea, also known as the Sea of Japan, is a marginal sea located in the western Pacific Ocean, displaying comparable characteristics to Earth's oceans, thereby meriting its recognition as a "miniature ocean". The East Sea exhibits a range of annually-recurring biogeochemical features in accordance with seasonal fluctuations, such as phytoplankton blooms during the spring and autumn seasons. Despite ongoing monitoring efforts focused on water quality and physicochemical parameters, the investigation of prokaryotic assemblages in the East Sea, encompassing seasonal variations, has been infrequently pursued. Here, we present a monthly time-series metagenomic dataset spanning a one-year period in 2009, obtained from surface (10 m) seawater samples collected off the coast of the East Sea. The dataset encompasses 12 metagenomes, amounting 195 Gbp, with 14.73-22.52 Gbp per sample. This dataset is accompanied by concurrently measured physicochemical parameters. Our anticipation is that these metagenomes will facilitate extensive investigations aimed at elucidating various aspects of the marine microbial ecosystems in the East Sea.
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Affiliation(s)
- Yeonjung Lim
- Center for Molecular and Cell Biology, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea
| | - Seung-Jo Yang
- CJ Bioscience, Inc., Sejong-daero 14, Seoul, 04527, Republic of Korea
| | - Ilnam Kang
- Center for Molecular and Cell Biology, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
- Department of Biological Sciences and Bioengineering, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Inha-ro 100, Incheon, 22212, Republic of Korea.
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45
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Abstract
The origin of modern eukaryotes is one of the key transitions in life's history, and also one of the least understood. Although the fossil record provides the most direct view of this process, interpreting the fossils of early eukaryotes and eukaryote-grade organisms is not straightforward. We present two end-member models for the evolution of modern (i.e., crown) eukaryotes-one in which modern eukaryotes evolved early, and another in which they evolved late-and interpret key fossils within these frameworks, including where they might fit in eukaryote phylogeny and what they may tell us about the evolution of eukaryotic cell biology and ecology. Each model has different implications for understanding the rise of complex life on Earth, including different roles of Earth surface oxygenation, and makes different predictions that future paleontological studies can test.
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Affiliation(s)
- Susannah M Porter
- Department of Earth Science, University of California at Santa Barbara, Santa Barbara, California, USA;
| | - Leigh Anne Riedman
- Department of Earth Science, University of California at Santa Barbara, Santa Barbara, California, USA;
- Earth Research Institute, University of California at Santa Barbara, Santa Barbara, California, USA;
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46
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Donoghue PCJ, Kay C, Spang A, Szöllősi G, Nenarokova A, Moody ERR, Pisani D, Williams TA. Defining eukaryotes to dissect eukaryogenesis. Curr Biol 2023; 33:R919-R929. [PMID: 37699353 DOI: 10.1016/j.cub.2023.07.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The origin of eukaryotes is among the most contentious debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryotic characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically, and that doing so clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which cannot currently be distinguished phylogenetically. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryotic traits, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to emergence of the last eukaryotic common ancestor. In this way, it may finally be possible to distinguish heat from light in the debate over eukaryogenesis.
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Affiliation(s)
- Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | - Chris Kay
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg 1790 AB, The Netherlands
| | - Gergely Szöllősi
- Department of Biological Physics, Eötvös Lorand University, H-1117 Budapest, Hungary; MTA-ELTE "Lendü let" Evolutionary Genomics Research Group, H-1117 Budapest, Hungary; Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Hungary
| | - Anna Nenarokova
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK; Bristol Palaeobiology Group, School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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47
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Cezanne A, Hoogenberg B, Baum B. Probing archaeal cell biology: exploring the use of dyes in the imaging of Sulfolobus cells. Front Microbiol 2023; 14:1233032. [PMID: 37731920 PMCID: PMC10508906 DOI: 10.3389/fmicb.2023.1233032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023] Open
Abstract
Archaea are key players in many critical ecological processes. In comparison to eukaryotes and bacteria, however, our understanding of both the cell biology and diversity of archaea remains limited. While archaea inhabit a wide range of environmental conditions, many species are extremophiles, surviving in extreme temperature, salt or pH conditions, making their cell biology hard to study. Recently, our understanding of archaeal cell biology has been advanced significantly by the advent of live cell imaging in extremis as well as the development of genetic tools to exogenously express fluorescent proteins in some mesophilic archaeal model systems, e.g., Haloferax volcanii. However, for most archaeal species, especially thermophilic species or emerging model systems without well characterized genetic tools, live cell imaging remains dependent on fluorescent chemical probes to label and track the dynamics of living cells. While a wide range of fluorescent stains and markers that label different components of the cell are available commercially, their use has usually been optimized for use in a small number of eukaryotic cell systems. Here we report the successes and failures of the application of membrane, DNA, S-layer and cytoplasm markers in live cell imaging of archaea, as well as the optimization of fixation and immunolabelling approaches. We have applied these markers to the thermoacidophilic archaeon Sulfolobus acidocaldarius, but expect some to work in other archaeal species. Furthermore, those procedures that failed in S. acidocaldarius may still prove useful for imaging archaea that grow at a more neutral pH and/or at a less extreme temperature.
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Affiliation(s)
- Alice Cezanne
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Baukje Hoogenberg
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Buzz Baum
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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48
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Ferrelli ML, Pidre ML, García-Domínguez R, Alberca LN, Del Saz-Navarro DM, Santana-Molina C, Devos DP. Prokaryotic membrane coat - like proteins: An update. J Struct Biol 2023; 215:107987. [PMID: 37343709 DOI: 10.1016/j.jsb.2023.107987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Membrane coat proteins are essential players in the eukaryotic endomembrane traffic system. Previous work identified proteins with the membrane-coat architecture in prokaryotes, specifically in the Planctomycetes, Verrucomicrobia and Chlamydiae (PVC) superphylum, bacteria that display the most developed prokaryotic endomembrane system. Hence, the membrane coat-like (MCL) proteins are predicted to play a central role in this system but their actual function is still unknown. In this work we strengthened previous structure predictions for these prokaryotic MCL proteins. We also detected new putative MCL proteins in the Planctomycete Gemmata obscuriglobus. Structural analysis of these revealed the presence of additional domains apart from the β-propeller and α-solenoid combination, characteristic of the membrane-coat architecture. Functions associated with these domains include some related to carbohydrate or membrane/lipid binding. Using homology-based methods, we found MCL proteins in other bacterial phyla, but the most abundant hits are still restricted to Planctomycetes and Verrucomicrobia. Detailed inspection of neighbouring genes of MCL in G. obscuriglobus supports the idea that the function of these proteins is related to membrane manipulation. No significant hits were found in Archaea, including Asgard archaea. More than 10 years after their original detection, PVC bacteria are still uniquely linked to eukaryotes through the structure of the MCL proteins sustaining their endomembrane system.
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Affiliation(s)
- M Leticia Ferrelli
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Pablo de Olavide (UPO), 41013 Seville, Spain
| | - Matías L Pidre
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Pablo de Olavide (UPO), 41013 Seville, Spain
| | - Ruben García-Domínguez
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Pablo de Olavide (UPO), 41013 Seville, Spain
| | - Lucas N Alberca
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Pablo de Olavide (UPO), 41013 Seville, Spain
| | - DMaría Del Saz-Navarro
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Pablo de Olavide (UPO), 41013 Seville, Spain
| | - Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Pablo de Olavide (UPO), 41013 Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Pablo de Olavide (UPO), 41013 Seville, Spain.
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49
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Carreira LAM, Szadkowski D, Lometto S, Hochberg GKA, Søgaard-Andersen L. Molecular basis and design principles of switchable front-rear polarity and directional migration in Myxococcus xanthus. Nat Commun 2023; 14:4056. [PMID: 37422455 PMCID: PMC10329633 DOI: 10.1038/s41467-023-39773-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
During cell migration, front-rear polarity is spatiotemporally regulated; however, the underlying design of regulatory interactions varies. In rod-shaped Myxococcus xanthus cells, a spatial toggle switch dynamically regulates front-rear polarity. The polarity module establishes front-rear polarity by guaranteeing front pole-localization of the small GTPase MglA. Conversely, the Frz chemosensory system, by acting on the polarity module, causes polarity inversions. MglA localization depends on the RomR/RomX GEF and MglB/RomY GAP complexes that localize asymmetrically to the poles by unknown mechanisms. Here, we show that RomR and the MglB and MglC roadblock domain proteins generate a positive feedback by forming a RomR/MglC/MglB complex, thereby establishing the rear pole with high GAP activity that is non-permissive to MglA. MglA at the front engages in negative feedback that breaks the RomR/MglC/MglB positive feedback allosterically, thus ensuring low GAP activity at this pole. These findings unravel the design principles of a system for switchable front-rear polarity.
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Affiliation(s)
| | - Dobromir Szadkowski
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Stefano Lometto
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University, 35043, Marburg, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University, 35043, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
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50
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Carlton JD, Langwig MV, Gong X, Aguilar-Pine EJ, Vázquez-Rosas-Landa M, Seitz KW, Baker BJ, De Anda V. Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles. ISME COMMUNICATIONS 2023; 3:64. [PMID: 37355707 PMCID: PMC10290634 DOI: 10.1038/s43705-023-00269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.
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Affiliation(s)
- John D Carlton
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Xianzhe Gong
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Emily J Aguilar-Pine
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mirna Vázquez-Rosas-Landa
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Unidad Académica de Ecologia y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Kiley W Seitz
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- EMBL Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
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