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Kita A, Ishida Y, Shimosaka T, Michimori Y, Makarova K, Koonin E, Atomi H, Miki K. Crystal structure of GTP-dependent dephospho-coenzyme A kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis. Proteins 2024; 92:768-775. [PMID: 38235908 DOI: 10.1002/prot.26666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/17/2023] [Accepted: 01/01/2024] [Indexed: 01/19/2024]
Abstract
The biosynthesis pathways of coenzyme A (CoA) in most archaea involve several unique enzymes including dephospho-CoA kinase (DPCK) that converts dephospho-CoA to CoA in the final step of CoA biosynthesis in all domains of life. The archaeal DPCK is unrelated to the analogous bacterial and eukaryotic enzymes and shows no significant sequence similarity to any proteins with known structures. Unusually, the archaeal DPCK utilizes GTP as the phosphate donor although the analogous bacterial and eukaryotic enzymes are ATP-dependent kinases. Here, we report the crystal structure of DPCK and its complex with GTP and a magnesium ion from the archaeal hyperthermophile Thermococcus kodakarensis. The crystal structure demonstrates why GTP is the preferred substrate of this kinase. We also report the activity analyses of site-directed mutants of crucial residues determined based on sequence conservation and the crystal structure. From these results, the key residues involved in the reaction of phosphoryl transfer and the possible dephospho-CoA binding site are inferred.
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Affiliation(s)
- Akiko Kita
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Yuna Ishida
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Takahiro Shimosaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kira Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Eugene Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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2
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Ding S, Hamm JN, Bale NJ, Sinninghe Damsté JS, Spang A. Selective lipid recruitment by an archaeal DPANN symbiont from its host. Nat Commun 2024; 15:3405. [PMID: 38649682 PMCID: PMC11035636 DOI: 10.1038/s41467-024-47750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus - Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e., nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.
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Affiliation(s)
- Su Ding
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Joshua N Hamm
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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Tittes C, Nijland J, Schoentag AMC, Hackl T, Di Cianni N, Marchfelder A, Quax TEF. Development of a genetic system for Haloferax gibbonsii LR2-5, model host for halo archaeal viruses. Appl Environ Microbiol 2024; 90:e0012924. [PMID: 38470030 PMCID: PMC11022537 DOI: 10.1128/aem.00129-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Archaeal viruses are among the most enigmatic members of the virosphere, and their diverse morphologies raise many questions about their infection mechanisms. The study of molecular mechanisms underlying virus-host interactions hinges upon robust model organisms with a system for gene expression and deletion. Currently, there are only a limited number of archaea that have associated viruses and have a well-developed genetic system. Here, we report the development of a genetic system for the euryarchaeon Haloferax gibbonsii LR2-5. This strain can be infected by multiple viruses and is a model for the study of virus-host interactions. We created a Hfx. gibbonsii LR2-5 ∆pyrE strain, resulting in uracil auxotrophy, which could be used as a selection marker. An expression plasmid carrying a pyrE gene from the well-established Haloferax volcanii system was tested for functionality. Expression of a GFP-MinD fusion under a tryptophan inducible promoter was fully functional and showed similar cellular localization as in Hfx. volcanii. Thus, the plasmids of the Hfx. volcanii system can be used directly for the Hfx. gibbonsii LR2-5 genetic system, facilitating the transfer of tools between the two. Finally, we tested for the functionality of gene deletions by knocking out two genes of the archaeal motility structure, the archaellum. These deletion mutants were as expected non-motile and the phenotype of one deletion could be rescued by the expression of the deleted archaellum gene from a plasmid. Thus, we developed a functional genetic toolbox for the euryarchaeal virus host Hfx. gibbonsii LR2-5, which will propel future studies on archaeal viruses. IMPORTANCE Species from all domains of life are infected by viruses. In some environments, viruses outnumber their microbial hosts by a factor of 10, and viruses are the most important predators of microorganisms. While much has been discovered about the infection mechanisms of bacterial and eukaryotic viruses, archaeal viruses remain understudied. Good model systems are needed to study their virus-host interactions in detail. The salt-loving archaeon Haloferax gibbonsii LR2-5 has been shown to be infected by a variety of different viruses and, thus, is an excellent model to study archaeal viruses. By establishing a genetic system, we have significantly expanded the toolbox for this model organism, which will fuel our understanding of infection strategies of the underexplored archaeal viruses.
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Affiliation(s)
- Colin Tittes
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jeroen Nijland
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Anna M. C. Schoentag
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Thomas Hackl
- Microbial Ecology Cluster, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | | | | | - Tessa E. F. Quax
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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van Wolferen M, Ithurbide S, Santiago-Martínez MG, Charles-Orszag A. Editorial: Molecular Biology of Archaea - 2022. Front Microbiol 2024; 15:1393932. [PMID: 38655083 PMCID: PMC11035895 DOI: 10.3389/fmicb.2024.1393932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, Freiburg, Germany
| | - Solenne Ithurbide
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Michel Geovanni Santiago-Martínez
- The Microbial Ecophysiology Laboratory, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Arthur Charles-Orszag
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, United States
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Janhvi S, Saini S, Singh V, Sharma T, Rao A. ProGlycProt V3.0: updated insights into prokaryotic glycoproteins and their glycosyltransferases. Glycobiology 2024; 34:cwad103. [PMID: 38153163 DOI: 10.1093/glycob/cwad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023] Open
Abstract
ProGlycProt is a comprehensive database of experimentally validated information about protein glycosylation in prokaryotes, including the glycoproteins, glycosyltransferases, and their accessory enzymes. The first release of ProGlycProt featured experimentally validated information on glycoproteins only. For the second release in 2019, the size and scope of the database were expanded twofold, and experimental data on cognate glycosyltransferases and their accessory proteins was incorporated. The growing research and technology interest in microbial glycoproteins and their enzymes is evident from the steady rise in academic publications and patents in this area. Accordingly, the third update comprises a new section on patents related to glycosylation methods, novel glycosyltransferases, and technologies developed therefrom. The structure gallery is reorganized, wherein the number and quality of the models are upgraded with the help of AlphaFold2. Over the years, the influx of experimental proteomics data into public repositories like PRIDE has surged. Harnessing this legacy data for in-silico glycoprotein identification is a smart approach. Version 3.0 adds 45 N-glycoprotein entries annotated from MS datasets available on PRIDE and reviewed by independent research groups. With a 67% rise in entries corresponding to 119 genera of prokaryotes, the ProGlycProt continues to be the exclusive database of experimentally validated comprehensive information about protein glycosylation in prokaryotes.
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Affiliation(s)
- Shreya Janhvi
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Shikha Saini
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Vaidhvi Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Tarun Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
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Wang J, Wu S, Ye K. Complicated target recognition by archaeal box C/D guide RNAs. Sci China Life Sci 2024; 67:631-644. [PMID: 38041781 DOI: 10.1007/s11427-022-2412-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/14/2022] [Indexed: 12/03/2023]
Abstract
Box C/D RNAs guide the site-specific formation of 2'-O-methylated nucleotides (Nm) of RNAs in eukaryotes and archaea. Although C/D RNAs have been profiled in several archaea, their targets have not been experimentally determined. Here, we mapped Nm in rRNAs, tRNAs, and abundant small RNAs (sRNAs) and profiled C/D RNAs in the crenarchaeon Sulfolobus islandicus. The targets of C/D RNAs were assigned by analysis of base-pairing interactions, in vitro modification assays, and gene deletion experiments, revealing a complicated landscape of C/D RNA-target interactions. C/D RNAs widely use dual antisense elements to target adjacent sites in rRNAs, enhancing modification at weakly bound sites. Two consecutive sites can be guided with the same antisense element upstream of box D or D', a phenomenon known as double-specificity that is exclusive to internal box D' in eukaryotic C/D RNAs. Several C/D RNAs guide modification at a single non-canonical site. This study reveals the global landscape of RNA-guided 2'-O-methylation in an archaeon and unexpected targeting rules employed by C/D RNA.
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Affiliation(s)
- Jiayin Wang
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keqiong Ye
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Kuehnast T, Kumpitsch C, Mohammadzadeh R, Weichhart T, Moissl-Eichinger C, Heine H. Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system. FEBS J 2024. [PMID: 38555566 DOI: 10.1111/febs.17123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.
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Affiliation(s)
- Torben Kuehnast
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Christina Kumpitsch
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Rokhsareh Mohammadzadeh
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Thomas Weichhart
- Institute of Medical Genetics, Medical University of Vienna, Austria
| | - Christine Moissl-Eichinger
- D&R Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
- BioTechMed Graz, Austria
| | - Holger Heine
- Research Center Borstel - Leibniz Lung Center, Division of Innate Immunity, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
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Zhang IH, Borer B, Zhao R, Wilbert S, Newman DK, Babbin AR. Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential. mBio 2024; 15:e0291823. [PMID: 38380943 PMCID: PMC10936187 DOI: 10.1128/mbio.02918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
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Affiliation(s)
- Irene H. Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Benedict Borer
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Steven Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Sato Y, Sato R, Fukui E, Yoshizawa F. Impact of rumen microbiome on cattle carcass traits. Sci Rep 2024; 14:6064. [PMID: 38480864 PMCID: PMC10937913 DOI: 10.1038/s41598-024-56603-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
Rumen microbes are crucial in the anaerobic fermentation of plant polysaccharides to produce volatile fatty acids. However, limited information exists about the specific microbial species and strains in the rumen that affect carcass traits, and it is unclear whether there is a relationship between rumen metabolic functions and these traits. This study investigated the relationship between the rumen microbiome and carcass traits in beef cattle using 16S rRNA amplicon and shotgun sequencing. Metagenomic sequencing was used to compare the rumen microbiome between high-carcass weight (HW) and low-carcass weight (LW) cattle, and high-marbling (HM) and low-marbling (LM) cattle. Prokaryotic communities in the rumen of HW vs. LW and HM vs. LM were separated using 16S rRNA amplicon sequencing. Notably, shotgun metagenomic sequencing revealed that HW cattle had more methane-producing bacteria and ciliate protozoa, suggesting higher methane emissions. Additionally, variations were observed in the abundances of certain glycoside hydrolases and polysaccharide lyases involved in the ruminal degradation of plant polysaccharides between HW and LW. From our metagenome dataset, 807 non-redundant metagenome-assembled genomes (MAGs) of medium to high quality were obtained. Among these, 309 and 113 MAGs were associated with carcass weight and marbling, respectively.
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Affiliation(s)
- Yoshiaki Sato
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan.
| | - Ruki Sato
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan
| | - Emiko Fukui
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan
| | - Fumiaki Yoshizawa
- Department of Agrobiology and Bioresources, School of Agriculture, Utsunomiya University, Tochigi, Japan
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Huuki H, Vilkki J, Vanhatalo A, Tapio I. Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health. Front Microbiol 2024; 15:1353874. [PMID: 38505558 PMCID: PMC10949896 DOI: 10.3389/fmicb.2024.1353874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
Early-life modulation of rumen microbiota holds promise for enhancing calf growth, health, and long-term production in ruminants. However, limited attention has been given to the impact of rumen microbiota modulation on the establishment of hindgut microbiota. In this study, fecal microbiota development was examined in identical twin calves for 12 months. The treatment group (T-group) received adult cow fresh rumen liquid inoculum during the pre-weaning period, while the control group did not (C-group). The effects of inoculum were assessed on calf gut health and as microbial seeding route into the hindgut. The early rumen modulation had no effect on age-related fecal microbiota development. The fecal bacterial community evolved gradually following dietary changes and categorized into pre-weaning and post-weaning communities. Bacterial richness increased with age and stabilized at month 9, while between-sample variation reduced in post-weaning samples. Archaeal load in fecal samples increased after month 4, while archaeal richness increased and stabilized in both groups by month 9. Between-sample similarity was higher during the pre-weaning period, with increased dissimilarity from month 4 onward. Anaerobic fungi were detected in feces at month 4, with richness peaking at month 7. Before month 6, fungal community composition distinctly differed from mature communities. When colostrum, calf rumen, and donor inoculum were evaluated as seeding sources for hindgut colonization, the calf's own rumen was identified as the primary seeding source for fecal bacteria and fungi. Colostrum was a source for several bacteria detected in feces, but these were of temporary importance until weaning. The donor inoculum had limited impact on gut health as diarrhea rates were similar between the T-group and C-group. In conclusion, early-life microbiota modulation shows potential in ruminant development. However, a more targeted approach with bacteria adapted to the hindgut environment may be necessary to modulate hindgut effectively. This research contributes to our understanding of the complex relationship between gut microbiota and calf health and growth.
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Affiliation(s)
- Hanna Huuki
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Johanna Vilkki
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Aila Vanhatalo
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ilma Tapio
- Production Systems, Genomics and Breeding, Natural Resources Institute Finland (Luke), Jokioinen, Finland
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhu QZ, Elvert M, Meador TB, Schröder JM, Doeana KD, Becker KW, Elling FJ, Lipp JS, Heuer VB, Zabel M, Hinrichs KU. Comprehensive molecular-isotopic characterization of archaeal lipids in the Black Sea water column and underlying sediments. Geobiology 2024; 22:e12589. [PMID: 38465505 DOI: 10.1111/gbi.12589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The Black Sea is a permanently anoxic, marine basin serving as model system for the deposition of organic-rich sediments in a highly stratified ocean. In such systems, archaeal lipids are widely used as paleoceanographic and biogeochemical proxies; however, the diverse planktonic and benthic sources as well as their potentially distinct diagenetic fate may complicate their application. To track the flux of archaeal lipids and to constrain their sources and turnover, we quantitatively examined the distributions and stable carbon isotopic compositions (δ13 C) of intact polar lipids (IPLs) and core lipids (CLs) from the upper oxic water column into the underlying sediments, reaching deposits from the last glacial. The distribution of IPLs responded more sensitively to the geochemical zonation than the CLs, with the latter being governed by the deposition from the chemocline. The isotopic composition of archaeal lipids indicates CLs and IPLs in the deep anoxic water column have negligible influence on the sedimentary pool. Archaeol substitutes tetraether lipids as the most abundant IPL in the deep anoxic water column and the lacustrine methanic zone. Its elevated IPL/CL ratios and negative δ13 C values indicate active methane metabolism. Sedimentary CL- and IPL-crenarchaeol were exclusively derived from the water column, as indicated by non-variable δ13 C values that are identical to those in the chemocline and by the low BIT (branched isoprenoid tetraether index). By contrast, in situ production accounts on average for 22% of the sedimentary IPL-GDGT-0 (glycerol dibiphytanyl glycerol tetraether) based on isotopic mass balance using the fermentation product lactate as an endmember for the dissolved substrate pool. Despite the structural similarity, glycosidic crenarchaeol appears to be more recalcitrant in comparison to its non-cycloalkylated counterpart GDGT-0, as indicated by its consistently higher IPL/CL ratio in sediments. The higher TEX86 , CCaT, and GDGT-2/-3 values in glacial sediments could plausibly result from selective turnover of archaeal lipids and/or an archaeal ecology shift during the transition from the glacial lacustrine to the Holocene marine setting. Our in-depth molecular-isotopic examination of archaeal core and intact polar lipids provided new constraints on the sources and fate of archaeal lipids and their applicability in paleoceanographic and biogeochemical studies.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Travis B Meador
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Biology Centre CAS, Soil and Water Research Infrastructure, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan M Schröder
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Katiana D Doeana
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kevin W Becker
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Felix J Elling
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Matthias Zabel
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
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Abstract
The surface layer of Sulfolobus acidocaldarius consists of a flexible but stable outer protein layer that interacts with an inner, membrane-bound protein.
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Affiliation(s)
- Bernhard Schuster
- Institute of Synthetic Bioarchitectures, Department of Bionanosciences, University of Natural Resources and Life Sciences, ViennaViennaAustria
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14
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Hallberg ZF, Nicolas AM, Alvarez-Aponte ZI, Mok KC, Sieradzki ET, Pett-Ridge J, Banfield JF, Carlson HK, Firestone MK, Taga ME. Vitamin B 12 variants structure soil microbial communities despite soil's vast reservoir of B 12. bioRxiv 2024:2024.02.12.580003. [PMID: 38405713 PMCID: PMC10888822 DOI: 10.1101/2024.02.12.580003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B12. Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids show distinct shifts in bacterial 16S composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.
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Affiliation(s)
- Zachary F. Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Alexa M. Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Zoila I. Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Kenny C. Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Ella T. Sieradzki
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
| | - Jillian F. Banfield
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720 USA
- Innovative Genomics Institute, Berkeley, CA, 94720 USA
| | | | - Mary K. Firestone
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michiko E. Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720 USA
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15
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Kato S, Tahara YO, Nishimura Y, Uematsu K, Arai T, Nakane D, Ihara A, Nishizaka T, Iwasaki W, Itoh T, Miyata M, Ohkuma M. Cell surface architecture of the cultivated DPANN archaeon Nanobdella aerobiophila. J Bacteriol 2024; 206:e0035123. [PMID: 38289045 PMCID: PMC10882981 DOI: 10.1128/jb.00351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 02/23/2024] Open
Abstract
The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon Nanobdella aerobiophila strain MJ1T and its host Metallosphaera sedula strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1T were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1T gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1T and MJ1HA were motile, but sole MJ1T cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila.IMPORTANCEDPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon, Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Yuhei O. Tahara
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Yuki Nishimura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | | | | | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Ayaka Ihara
- Department of Physics, Gakushuin University, Tokyo, Japan
| | | | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
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16
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McNair K, Salamon P, Edwards RA, Segall AM. PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes. BMC Bioinformatics 2024; 25:82. [PMID: 38389044 PMCID: PMC10885494 DOI: 10.1186/s12859-024-05701-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence and shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain. More importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the original in-frame amino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation. RESULTS Here we present PRFect, an innovative machine-learning method for the detection and prediction of PRFs in coding genes of various types. PRFect combines advanced machine learning techniques with the integration of multiple complex cellular properties, such as secondary structure, codon usage, ribosomal binding site interference, direction, and slippery site motif. Calculating and incorporating these diverse properties posed significant challenges, but through extensive research and development, we have achieved a user-friendly approach. The code for PRFect is freely available, open-source, and can be easily installed via a single command in the terminal. Our comprehensive evaluations on diverse organisms, including bacteria, archaea, and phages, demonstrate PRFect's strong performance, achieving high sensitivity, specificity, and an accuracy exceeding 90%. The code for PRFect is freely available and installs with a single terminal command. CONCLUSION PRFect represents a significant advancement in the field of PRF detection and prediction, offering a powerful tool for researchers and scientists to unravel the intricacies of programmed ribosomal frameshifting in coding genes.
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Affiliation(s)
- Katelyn McNair
- Computational Science Research Center, San Diego State University, San Diego, CA, USA.
- Department of Computational Science, University of California Irvine, Irvine, CA, USA.
| | - Peter Salamon
- Computational Science Research Center, San Diego State University, San Diego, CA, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, USA
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Anca M Segall
- Computational Science Research Center, San Diego State University, San Diego, CA, USA
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, USA
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17
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Luo H, Qu X, Deng X, He L, Wu Y, Liu Y, He D, Yin J, Wang B, Gan F, Tang B, Tang XF. HtrAs are essential for the survival of the haloarchaeon Natrinema gari J7-2 in response to heat, high salinity, and toxic substances. Appl Environ Microbiol 2024; 90:e0204823. [PMID: 38289131 PMCID: PMC10880668 DOI: 10.1128/aem.02048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/24/2023] [Indexed: 02/22/2024] Open
Abstract
Bacterial and eukaryotic HtrAs can act as an extracytoplasmic protein quality control (PQC) system to help cells survive in stress conditions, but the functions of archaeal HtrAs remain unknown. Particularly, haloarchaea route most secretory proteins to the Tat pathway, enabling them to fold properly in well-controlled cytoplasm with cytosolic PQC systems before secretion. It is unclear whether HtrAs are required for haloarchaeal survival and stress response. The haloarchaeon Natrinema gari J7-2 encodes three Tat signal peptide-bearing HtrAs (NgHtrA, NgHtrB, and NgHtrC), and the signal peptides of NgHtrA and NgHtrC contain a lipobox. Here, the in vitro analysis reveals that the three HtrAs show different profiles of temperature-, salinity-, and metal ion-dependent proteolytic activities and could exhibit chaperone-like activities to prevent the aggregation of reduced lysozyme when their proteolytic activities are inhibited at low temperatures or the active site is disrupted. The gene deletion and complementation assays reveal that NgHtrA and NgHtrC are essential for the survival of strain J7-2 at elevated temperature and/or high salinity and contribute to the resistance of this haloarchaeon to zinc and inhibitory substances generated from tryptone. Mutational analysis shows that the lipobox mediates membrane anchoring of NgHtrA or NgHtrC, and both the membrane-anchored and free extracellular forms of the two enzymes are involved in the stress resistance of strain J7-2, depending on the stress conditions. Deletion of the gene encoding NgHtrB in strain J7-2 causes no obvious growth defect, but NgHtrB can functionally substitute for NgHtrA or NgHtrC under some conditions.IMPORTANCEHtrA-mediated protein quality control plays an important role in the removal of aberrant proteins in the extracytoplasmic space of living cells, and the action mechanisms of HtrAs have been extensively studied in bacteria and eukaryotes; however, information about the function of archaeal HtrAs is scarce. Our results demonstrate that three HtrAs of the haloarchaeon Natrinema gari J7-2 possess both proteolytic and chaperone-like activities, confirming that the bifunctional nature of HtrAs is conserved across all three domains of life. Moreover, we found that NgHtrA and NgHtrC are essential for the survival of strain J7-2 under stress conditions, while NgHtrB can serve as a substitute for the other two HtrAs under certain circumstances. This study provides the first biochemical and genetic evidence of the importance of HtrAs for the survival of haloarchaea in response to stresses.
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Affiliation(s)
- Hongyi Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoyi Qu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xi Deng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Liping He
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan He
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bingxue Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fei Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation, Ministry of Education and Hubei Province, Wuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation, Ministry of Education and Hubei Province, Wuhan, China
| | - Xiao-Feng Tang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation, Ministry of Education and Hubei Province, Wuhan, China
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18
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Liman GLS, Garcia AA, Fluke KA, Anderson HR, Davidson SC, Welander PV, Santangelo TJ. Tetraether archaeal lipids promote long-term survival in extreme conditions. Mol Microbiol 2024. [PMID: 38372181 DOI: 10.1111/mmi.15240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The sole unifying feature of the incredibly diverse Archaea is their isoprenoid-based ether-linked lipid membranes. Unique lipid membrane composition, including an abundance of membrane-spanning tetraether lipids, impart resistance to extreme conditions. Many questions remain, however, regarding the synthesis and modification of tetraether lipids and how dynamic changes to archaeal lipid membrane composition support hyperthermophily. Tetraether membranes, termed glycerol dibiphytanyl glycerol tetraethers (GDGTs), are generated by tetraether synthase (Tes) by joining the tails of two bilayer lipids known as archaeol. GDGTs are often further specialized through the addition of cyclopentane rings by GDGT ring synthase (Grs). A positive correlation between relative GDGT abundance and entry into stationary phase growth has been observed, but the physiological impact of inhibiting GDGT synthesis has not previously been reported. Here, we demonstrate that the model hyperthermophile Thermococcus kodakarensis remains viable when Tes (TK2145) or Grs (TK0167) are deleted, permitting phenotypic and lipid analyses at different temperatures. The absence of cyclopentane rings in GDGTs does not impact growth in T. kodakarensis, but an overabundance of rings due to ectopic Grs expression is highly fitness negative at supra-optimal temperatures. In contrast, deletion of Tes resulted in the loss of all GDGTs, cyclization of archaeol, and loss of viability upon transition to the stationary phase in this model archaea. These results demonstrate the critical roles of highly specialized, dynamic, isoprenoid-based lipid membranes for archaeal survival at high temperatures.
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Affiliation(s)
- Geraldy Lie Stefanus Liman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Andy A Garcia
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Kristin A Fluke
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA
| | - Hayden R Anderson
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Sarah C Davidson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Paula V Welander
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, Colorado, USA
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19
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Makarova KS, Zhang C, Wolf YI, Karamycheva S, Whitaker RJ, Koonin EV. Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea. mBio 2024; 15:e0309223. [PMID: 38189270 PMCID: PMC10865827 DOI: 10.1128/mbio.03092-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
The identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes. However, interpretation of the LKP is complicated because a substantial fraction of the genes with this phenotype remains poorly functionally characterized. Furthermore, many genes can exhibit LKP not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes (conditionally essential genes). We analyzed the sets of LKP genes for two archaea, Methanococcus maripaludis and Sulfolobus islandicus, using a variety of computational approaches aiming to differentiate between essential and conditionally essential genes and to predict at least a general function for as many of the proteins encoded by these genes as possible. This analysis allowed us to predict the functions of several LKP genes including previously uncharacterized subunit of the GINS protein complex with an essential function in genome replication and of the KEOPS complex that is responsible for an essential tRNA modification as well as GRP protease implicated in protein quality control. Additionally, several novel antitoxins (conditionally essential genes) were predicted, and this prediction was experimentally validated by showing that the deletion of these genes together with the adjacent genes apparently encoding the cognate toxins caused no growth defect. We applied principal component analysis based on sequence and comparative genomic features showing that this approach can separate essential genes from conditionally essential ones and used it to predict essential genes in other archaeal genomes.IMPORTANCEOnly a relatively small fraction of the genes in any bacterium or archaeon is essential for survival as demonstrated by the lethal effect of their disruption. The identification of essential genes and their functions is crucial for understanding fundamental cell biology. However, many of the genes with a lethal knockout phenotype remain poorly functionally characterized, and furthermore, many genes can exhibit this phenotype not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes. We applied state-of-the-art computational methods to predict the functions of a number of uncharacterized genes with the lethal knockout phenotype in two archaeal species and developed a computational approach to predict genes involved in essential functions. These findings advance the current understanding of key functionalities of archaeal cells.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Rachel J. Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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20
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Brunk CF, Marshall CR. Opinion: The Key Steps in the Origin of Life to the Formation of the Eukaryotic Cell. Life (Basel) 2024; 14:226. [PMID: 38398735 PMCID: PMC10890422 DOI: 10.3390/life14020226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The path from life's origin to the emergence of the eukaryotic cell was long and complex, and as such it is rarely treated in one publication. Here, we offer a sketch of this path, recognizing that there are points of disagreement and that many transitions are still shrouded in mystery. We assume life developed within microchambers of an alkaline hydrothermal vent system. Initial simple reactions were built into more sophisticated reflexively autocatalytic food-generated networks (RAFs), laying the foundation for life's anastomosing metabolism, and eventually for the origin of RNA, which functioned as a genetic repository and as a catalyst (ribozymes). Eventually, protein synthesis developed, leading to life's biology becoming dominated by enzymes and not ribozymes. Subsequent enzymatic innovation included ATP synthase, which generates ATP, fueled by the proton gradient between the alkaline vent flux and the acidic sea. This gradient was later internalized via the evolution of the electron transport chain, a preadaptation for the subsequent emergence of the vent creatures from their microchamber cradles. Differences between bacteria and archaea suggests cellularization evolved at least twice. Later, the bacterial development of oxidative phosphorylation and the archaeal development of proteins to stabilize its DNA laid the foundation for the merger that led to the formation of eukaryotic cells.
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Affiliation(s)
- Clifford F. Brunk
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, USA
| | - Charles R. Marshall
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA 94720-4780, USA
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21
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Arahal DR, Bull CT, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Ventosa A, Young P, Göker M. Judicial Opinion 129. Int J Syst Evol Microbiol 2024; 74. [PMID: 38376502 DOI: 10.1099/ijsem.0.006064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, QLD 4072, Australia
| | - Svetlana N Dedysh
- Research Center of Biotechnology RAS, Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Charles T Parker
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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22
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Harish A. Protein structures unravel the signatures and patterns of deep time evolution. QRB Discov 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gambelli L, McLaren M, Conners R, Sanders K, Gaines MC, Clark L, Gold VAM, Kattnig D, Sikora M, Hanus C, Isupov MN, Daum B. Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 2024; 13:e84617. [PMID: 38251732 PMCID: PMC10903991 DOI: 10.7554/elife.84617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 01/23/2024] Open
Abstract
Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lewis Clark
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniel Kattnig
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Frankfurt, Germany
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
- GHU Psychiatrie et Neurosciences de Paris, Paris, France
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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24
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Müller MC, Lemaire ON, Kurth JM, Welte CU, Wagner T. Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Commun Biol 2024; 7:111. [PMID: 38243071 PMCID: PMC10799026 DOI: 10.1038/s42003-023-05726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024] Open
Abstract
Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.
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Affiliation(s)
- Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Olivier N Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Microcosm Earth Center, Philipps-University Marburg and Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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25
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Willard DJ, Manesh MJH, Bing RG, Kelly RM. Complete genome sequence for the thermoacidophilic archaeon Sulfuracidifex (f . Sulfolobus) metallicus DSM 6482. Microbiol Resour Announc 2024; 13:e0098123. [PMID: 38054707 PMCID: PMC10793343 DOI: 10.1128/mra.00981-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/08/2023] [Indexed: 12/07/2023] Open
Abstract
Reported here is the complete genome sequence (2,191,724 bp) for the thermoacidophilic archaeon Sulfuracidifex (f. Sulfolobus) metallicus DSM 6482 (Topt 65°C, pHopt 2.0). This obligately chemolithoautotrophic microorganism is a prolific metal and sulfur oxidizer and has application in metal bioleaching operations. A multi-assembly reconciliation approach enabled closure of the genome.
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Affiliation(s)
- Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Mohamad J. H. Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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26
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Crump BC, Bowen JL. The Microbial Ecology of Estuarine Ecosystems. Ann Rev Mar Sci 2024; 16:335-360. [PMID: 37418833 DOI: 10.1146/annurev-marine-022123-101845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.
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Affiliation(s)
- Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA;
| | - Jennifer L Bowen
- Marine Science Center, Department of Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, USA;
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27
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Manners SH, Carere CR, Dhami MK, Dobson RCJ, Stott MB. Draft genome sequence of Thermococcus waiotapuensis WT1 T, a thermophilic sulfur-dependent archaeon from the order Thermococcales. Microbiol Resour Announc 2024; 13:e0081523. [PMID: 38095867 DOI: 10.1128/mra.00815-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Thermococcus waiotapuensis WT1T is a thermophilic, peptide, and amino acid-fermenting archaeon from the order Thermococcales. It was isolated from Waiotapu, Aotearoa-New Zealand, and has a genome size of 1.80 Mbp. The genome contains 2,000 total genes, of which 1,913 encode proteins and 46 encode tRNA.
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Affiliation(s)
- Sarah H Manners
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Carlo R Carere
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
- Department of Chemical and Process Engineering, Te Tari Pūhanga Tukanga Matū, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research , Lincoln, New Zealand
| | - Renwick C J Dobson
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora School of Biological Sciences, Te Whare Wānanga o Waitaha University of Canterbury , Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha, University of Canterbury , Christchurch, New Zealand
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28
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Ding L, Chen H, Wang M, Wang P. Shrub expansion raises both aboveground and underground multifunctionality on a subtropical plateau grassland: coupling multitrophic community assembly to multifunctionality and functional trade-off. Front Microbiol 2024; 14:1339125. [PMID: 38274762 PMCID: PMC10808678 DOI: 10.3389/fmicb.2023.1339125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Shrubs have expanded into grasslands globally. However, the relative importance of aboveground and underground diversity and the relative importance of underground community assembly and diversity in shaping multifunctionality and functional trade-offs over shrub expansion remains unknown. Methods In this study, aboveground and underground multitrophic communities (abundant and rare archaea, bacteria, fungi, nematodes, and protists) and 208 aboveground and underground ecosystem properties or indicators were measured at three stages (Grass, Mosaic, Shrub) of shrub expansion on the Guizhou subtropical plateau grassland to study multifunctionality and functional trade-offs. Results The results showed that shrub expansion significantly enhanced aboveground, underground, and entire ecosystem multifunctionality. The functional trade-off intensities of the aboveground, underground, and entire ecosystems showed significant V-shaped changes with shrub expansion. Shrub expansion improved plant species richness and changed the assembly process and species richness of soil abundant and rare subcommunities. Plant species diversity had a greater impact on multifunctionality than soil microbial diversity by more than 16%. The effect of plant species diversity on functional trade-offs was only one-fifth of the effect of soil microbial diversity. The soil microbial species richness did not affect multifunctionality, however, the assembly process of soil microbial communities did. Rather than the assembly process of soil microbial communities, the soil microbial species richness affected functional trade-offs. Discussion Our study is the first to couple multitrophic community assemblies to multifunctionality and functional trade-offs. Our results would boost the understanding of the role of aboveground and underground diversity in multifunctionality and functional trade-offs.
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Affiliation(s)
- Leilei Ding
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Hong Chen
- Guizhou Songbaishan Reservoir Management Office, Guiyang, Guizhou, China
| | - Mengya Wang
- College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Puchang Wang
- School of Life Science, Guizhou Normal University, Guiyang, Guizhou, China
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29
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Basta T, Crozat E, Grainge I. Editorial: Chromosome architecture and DNA topology in prokaryotes. Front Microbiol 2024; 14:1355036. [PMID: 38274756 PMCID: PMC10808810 DOI: 10.3389/fmicb.2023.1355036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Affiliation(s)
- Tamara Basta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Estelle Crozat
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Ian Grainge
- School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
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30
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Lynes MM, Jay ZJ, Kohtz AJ, Hatzenpichler R. Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring. ISME J 2024; 18:wrae026. [PMID: 38452205 PMCID: PMC10945360 DOI: 10.1093/ismejo/wrae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/09/2024] [Accepted: 02/08/2024] [Indexed: 03/09/2024]
Abstract
Over the past decade, environmental metagenomics and polymerase chain reaction-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic Euryarchaeota that have long been considered to live non-methanogenic lifestyles. Here, we enriched Candidatus Methanoglobus hypatiae, a methanogen affiliated with the family Archaeoglobaceae, from a hot spring in Yellowstone National Park. The enrichment is sediment-free, grows at 64-70°C and a pH of 7.8, and produces methane from mono-, di-, and tri-methylamine. Ca. M. hypatiae is represented by a 1.62 Mb metagenome-assembled genome with an estimated completeness of 100% and accounts for up to 67% of cells in the culture according to fluorescence in situ hybridization. Via genome-resolved metatranscriptomics and stable isotope tracing, we demonstrate that Ca. M. hypatiae expresses methylotrophic methanogenesis and energy-conserving pathways for reducing monomethylamine to methane. The detection of Archaeoglobi populations related to Ca. M. hypatiae in 36 geochemically diverse geothermal sites within Yellowstone National Park, as revealed through the examination of previously published gene amplicon datasets, implies a previously underestimated contribution to anaerobic carbon cycling in extreme ecosystems.
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Affiliation(s)
- Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, Thermal Biology Institute, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
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31
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Cisek AA, Szymańska E, Wierzbicka-Rucińska A, Aleksandrzak-Piekarczyk T, Cukrowska B. Methanogenic Archaea in the Pediatric Inflammatory Bowel Disease in Relation to Disease Type and Activity. Int J Mol Sci 2024; 25:673. [PMID: 38203843 PMCID: PMC10779203 DOI: 10.3390/ijms25010673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The inflammatory bowel disease (IBD) is associated with gut microbiota dysbiosis; however, studies on methanogens-especially those focused on children-are extremely limited. The aim of this study was to determine the abundance of total methanogenic archaea and their three subgroups: Methanobrevibacter (Mb.) smithii, Methanosphaera (Ms.) stadtmanae, and Methanomassiliicoccales, in the feces of children with both active and inactive Crohn's disease (CD) and ulcerative colitis (UC). The results of a quantitative real-time PCR were cross-referenced with the disease type (CD vs. UC) and activity assessed with the use of Pediatric Crohn's Disease Activity Index (PCDAI) and Pediatric Ulcerative Colitis Activity Index (PUCAI) indices, and fecal calprotectin (FCP) concentration, and compared with controls. There was a significant decrease in the number of total methanogens in CD and UC compared to controls. The prevalence of total methanogens was also lower in UC compared to controls. Furthermore, patients from the inactive UC group were colonized by a lower number of Mb. smithii, and demonstrated the most pronounced positive correlation between the number of Ms. stadtmanae and the FCP concentration. Our results demonstrate that gut methanogens are related to the type and activity of pediatric IBD.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Edyta Szymańska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | - Aldona Wierzbicka-Rucińska
- Department of Biochemistry, Radioimmunology and Experimental Medicine, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
| | | | - Bożena Cukrowska
- Department of Pathomorphology, The Children’s Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland;
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32
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Abdul Halim MF, Fonseca DR, Niehaus TD, Costa KC. Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis. J Biol Chem 2024; 300:105550. [PMID: 38072055 PMCID: PMC10805699 DOI: 10.1016/j.jbc.2023.105550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/02/2024] Open
Abstract
Methanogens are essential for the complete remineralization of organic matter in anoxic environments. Most cultured methanogens are hydrogenotrophic, using H2 as an electron donor to reduce CO2 to CH4, but in the absence of H2 many can also use formate. Formate dehydrogenase (Fdh) is essential for formate oxidation, where it transfers electrons for the reduction of coenzyme F420 or to a flavin-based electron bifurcating reaction catalyzed by heterodisulfide reductase (Hdr), the terminal reaction of methanogenesis. Furthermore, methanogens that use formate encode at least two isoforms of Fdh in their genomes, but how these different isoforms participate in methanogenesis is unknown. Using Methanococcus maripaludis, we undertook a biochemical characterization of both Fdh isoforms involved in methanogenesis. Both Fdh1 and Fdh2 interacted with Hdr to catalyze the flavin-based electron bifurcating reaction, and both reduced F420 at similar rates. F420 reduction preceded flavin-based electron bifurcation activity for both enzymes. In a Δfdh1 mutant background, a suppressor mutation was required for Fdh2 activity. Genome sequencing revealed that this mutation resulted in the loss of a specific molybdopterin transferase (moeA), allowing for Fdh2-dependent growth, and the metal content of the proteins suggested that isoforms are dependent on either molybdenum or tungsten for activity. These data suggest that both isoforms of Fdh are functionally redundant, but their activities in vivo may be limited by gene regulation or metal availability under different growth conditions. Together these results expand our understanding of formate oxidation and the role of Fdh in methanogenesis.
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Affiliation(s)
- Mohd Farid Abdul Halim
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Dallas R Fonseca
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Thomas D Niehaus
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Kyle C Costa
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA.
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Langlois GA, Rueckert S. In memoriam: Thomas Cavalier-Smith (1942-2021). J Eukaryot Microbiol 2024; 71:e13013. [PMID: 38059499 DOI: 10.1111/jeu.13013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 12/08/2023]
Abstract
Thomas Cavalier-Smith, born in London, U.K., on October 21, 1942, was a Professor of Evolutionary Biology in the Department of Zoology at the University of Oxford at the time of his death on March 19, 2021. Credited with at least 235 research works and over 20,000 citations, Cavalier-Smith was a well-known and widely respected scientist who took a bold and detailed approach to understanding major transitions in evolution, including the role of endosymbiosis. He was noted for his willingness to question theories and constantly accumulate and evaluate data, motivated by science for the sake of science. This paper reviews Thomas Cavalier-Smith's major accomplishments, examines his theoretical approaches, and provides highlights from the "Tree of Life Symposium" sponsored by the International Society of Protistologists (ISOP) and the International Society of Evolutionary Protistology (ISEP) on June 21, 2021, to celebrate Tom's life and work.
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Affiliation(s)
- Gaytha A Langlois
- Marine Microbial Research Laboratory, Bryant University, Smithfield, Rhode Island, USA
| | - Sonja Rueckert
- Department of Eukaryotic Microbiology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
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Badel C, Bell SD. Chromosome architecture in an archaeal species naturally lacking structural maintenance of chromosomes proteins. Nat Microbiol 2024; 9:263-273. [PMID: 38110698 PMCID: PMC10769869 DOI: 10.1038/s41564-023-01540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/20/2023]
Abstract
Proteins in the structural maintenance of chromosomes (SMC) superfamily play key roles in chromosome organization and are ubiquitous across all domains of life. However, SMC proteins are notably absent in the Desulfurococcales of phylum Crenarchaeota. Intrigued by this observation, we performed chromosome conformation capture experiments in the model Desulfurococcales species Aeropyrum pernix. As in other archaea, we observe chromosomal interaction domains across the chromosome. The boundaries between chromosomal interaction domains show a dependence on transcription and translation for their definition. Importantly, however, we reveal an additional higher-order, bipartite organization of the chromosome-with a small high-gene-expression and self-interacting domain that is defined by transcriptional activity and loop structures. Viewing these data in the context of the distribution of SMC superfamily proteins in the Crenarchaeota, we suggest that the organization of the Aeropyrum genome represents an evolutionary antecedent of the compartmentalized architecture observed in the Sulfolobus lineage.
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Affiliation(s)
- Catherine Badel
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA.
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, Strasbourg, France.
| | - Stephen D Bell
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA.
- Biology Department, Indiana University, Bloomington, IN, USA.
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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 Commun 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Caffrey PJ, Eckenroth BE, Burkhart BW, Zatopek KM, McClung CM, Santangelo TJ, Doublié S, Gardner AF. Thermococcus kodakarensis TK0353 is a novel AP lyase with a new fold. J Biol Chem 2024; 300:105503. [PMID: 38013090 PMCID: PMC10731606 DOI: 10.1016/j.jbc.2023.105503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 11/02/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023] Open
Abstract
Hyperthermophilic organisms thrive in extreme environments prone to high levels of DNA damage. Growth at high temperature stimulates DNA base hydrolysis resulting in apurinic/apyrimidinic (AP) sites that destabilize the genome. Organisms across all domains have evolved enzymes to recognize and repair AP sites to maintain genome stability. The hyperthermophilic archaeon Thermococcus kodakarensis encodes several enzymes to repair AP site damage including the essential AP endonuclease TK endonuclease IV. Recently, using functional genomic screening, we discovered a new family of AP lyases typified by TK0353. Here, using biochemistry, structural analysis, and genetic deletion, we have characterized the TK0353 structure and function. TK0353 lacks glycosylase activity on a variety of damaged bases and is therefore either a monofunctional AP lyase or may be a glycosylase-lyase on a yet unidentified substrate. The crystal structure of TK0353 revealed a novel fold, which does not resemble other known DNA repair enzymes. The TK0353 gene is not essential for T. kodakarensis viability presumably because of redundant base excision repair enzymes involved in AP site processing. In summary, TK0353 is a novel AP lyase unique to hyperthermophiles that provides redundant repair activity necessary for genome maintenance.
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Affiliation(s)
| | - Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | | | - Thomas J Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
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Medina-Chávez NO, Torres-Cerda A, Chacón JM, Harcombe WR, De la Torre-Zavala S, Travisano M. Disentangling a metabolic cross-feeding in a halophilic archaea-bacteria consortium. Front Microbiol 2023; 14:1276438. [PMID: 38179456 PMCID: PMC10764424 DOI: 10.3389/fmicb.2023.1276438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Abigail Torres-Cerda
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, San Nicolás de los Garza, Mexico
| | - Jeremy M. Chacón
- Minnesota Supercomputing Institute, Minneapolis, MN, United States
| | - William R. Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Susana De la Torre-Zavala
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, San Nicolás de los Garza, Mexico
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
- Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lücking D, Alarcón-Schumacher T, Erdmann S. Distribution and Implications of Halo archaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles. Microorganisms 2023; 12:5. [PMID: 38276173 PMCID: PMC10818511 DOI: 10.3390/microorganisms12010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
Even though viruses and plasmids are both drivers of horizontal gene transfer, they differ fundamentally in their mode of transfer. Virus genomes are enclosed in virus capsids and are not dependent on cell-to-cell contacts for their dissemination. In contrast, the transfer of plasmids most often requires physical contact between cells. However, plasmid pR1SE of Halorubrum lacusprofundi is disseminated between cells, independent of cell-cell contacts, in specialized membrane vesicles that contain plasmid proteins. In this study, we searched for pR1SE-like elements in public databases and a metagenomics dataset from Australian salt lakes and identified 40 additional pR1SE-like elements in hypersaline environments worldwide. Herein, these elements are named apHPVs (archaeal plasmids of haloarchaea potentially transferred in plasmid vesicles). They share two sets of closely related proteins with conserved synteny, strongly indicating an organization into different functional clusters. We find that apHPVs, besides transferring themselves, have the potential to transfer large fragments of DNA between host cells, including virus defense systems. Most interestingly, apHPVs likely play an important role in the evolution of viruses and plasmids in haloarchaea, as they appear to recombine with both of them. This further supports the idea that plasmids and viruses are not distinct but closely related mobile genetic elements.
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Affiliation(s)
| | | | - Susanne Erdmann
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
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40
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Habenicht T, Weidenbach K, Velazquez-Campoy A, Buey RM, Balsera M, Schmitz RA. Small protein mediates inhibition of ammonium transport in Methanosarcina mazei-an ancient mechanism? Microbiol Spectr 2023; 11:e0281123. [PMID: 37909787 PMCID: PMC10714827 DOI: 10.1128/spectrum.02811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Small proteins containing fewer than 70 amino acids, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role of the small protein sP36 in the nitrogen metabolism of M. mazei, which modulates the ammonium transporter AmtB1 according to nitrogen availability. This modulation might represent an ancient archaeal mechanism of AmtB1 inhibition, in contrast to the well-studied uridylylation-dependent regulation in bacteria.
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Affiliation(s)
- Tim Habenicht
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katrin Weidenbach
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigaciones Sanitarias de Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ruben M. Buey
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Monica Balsera
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Spanish National Research Council (IRNASA-CSIC), Salamanca, Spain
| | - Ruth A. Schmitz
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Martinez-Gutierrez CA, Uyeda JC, Aylward FO. A timeline of bacterial and archaeal diversification in the ocean. eLife 2023; 12:RP88268. [PMID: 38059790 DOI: 10.7554/elife.88268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.
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Affiliation(s)
| | - Josef C Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, United States
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Vannutelli A, Ouangraoua A, Perreault JP. Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms. Evol Bioinform Online 2023; 19:11769343231212075. [PMID: 38046653 PMCID: PMC10693206 DOI: 10.1177/11769343231212075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
Background G-quadruplexes (G4s) are secondary structures in DNA and RNA that impact various cellular processes, such as transcription, splicing, and translation. Due to their numerous functions, G4s are involved in many diseases, making their study important. Yet, G4s evolution remains largely unknown, due to their low sequence similarity and the poor quality of their sequence alignments across several species. To address this, we designed a strategy that avoids direct G4s alignment to study G4s evolution in the 3 species kingdoms. We also explored the coevolution between RBPs and G4s. Methods We retrieved one-to-one orthologous genes from the Ensembl Compara database and computed groups of one-to-one orthologous genes. For each group, we aligned gene sequences and identified G4 families as groups of overlapping G4s in the alignment. We analyzed these G4 families using Count, a tool to infer feature evolution into a gene or a species tree. Additionally, we utilized these G4 families to predict G4s by homology. To establish a control dataset, we performed mono-, di- and tri-nucleotide shuffling. Results Only a few conserved G4s occur among all living kingdoms. In eukaryotes, G4s exhibit slight conservation among vertebrates, and few are conserved between plants. In archaea and bacteria, at most, only 2 G4s are common. The G4 homology-based prediction increases the number of conserved G4s in common ancestors. The coevolution between RNA-binding proteins and G4s was investigated and revealed a modest impact of RNA-binding proteins evolution on G4 evolution. However, the details of this relationship remain unclear. Conclusion Even if G4 evolution still eludes us, the present study provides key information to compute groups of homologous G4 and to reveal the evolution history of G4 families.
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Affiliation(s)
- Anaïs Vannutelli
- Département de biochimie et de génomique fonctionnelle, faculté de médecine et des sciences de la santé, pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
- Département d’informatique, faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Aïda Ouangraoua
- Département d’informatique, faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Pierre Perreault
- Département de biochimie et de génomique fonctionnelle, faculté de médecine et des sciences de la santé, pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
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Bruto M, Oger PM, Got P, Bernard C, Melayah D, Cloarec LA, Duval C, Escalas A, Duperron S, Guigard L, Leboulanger C, Ader M, Sarazin G, Jézéquel D, Agogué H, Troussellier M, Hugoni M. Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome. Mol Ecol 2023; 32:6824-6838. [PMID: 37901963 DOI: 10.1111/mec.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023]
Abstract
Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co-dominate: a cyanobacterium, Arthrospira fusiformis, and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell-sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non-negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free-living microbiome (i.e. present in the 3-0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free-living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.
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Affiliation(s)
- Maxime Bruto
- VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | - Philippe M Oger
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Patrice Got
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Delphine Melayah
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Lilian A Cloarec
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Charlotte Duval
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Arthur Escalas
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Ludivine Guigard
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | | | - Magali Ader
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon, France
| | - Hélène Agogué
- LIENSs, UMR7266, La Rochelle Université - CNRS, La Rochelle, France
| | | | - Mylène Hugoni
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
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Metze F, Vollmers J, Lenk F, Kaster AK. First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones. Front Microbiol 2023; 14:1241810. [PMID: 38053553 PMCID: PMC10694467 DOI: 10.3389/fmicb.2023.1241810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 10/03/2023] [Indexed: 12/07/2023] Open
Abstract
The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In this study, we present the first shotgun metagenomics study of unamplified DNA from sediment samples from different depths in this stratified environment. Bioinformatic analyses showed a shift from a heterotrophic, Chloroflexota-dominated community above the upper SMTZ to a chemolithoautotrophic Proteobacteria-dominated community below the secondary SMTZ. The reintroduction of sulfate likely enables respiration and boosts active cells that oxidize acetate, iron, and complex carbohydrates to degrade dead biomass in this low-abundance, low-diversity environment. In addition, analyses showed many proteins of unknown function as well as novel metagenome-assembled genomes (MAGs). The study provides new insights into microbial communities in this habitat, enabled by an improved DNA extraction protocol that allows a less biased view of taxonomic composition and metabolic activities, as well as uncovering novel taxa. Our approach presents the first successful attempt at unamplified shotgun sequencing samples from beyond 50 meters below the seafloor and opens new ways for capturing the true diversity and functional potential of deep-sea sediments.
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Affiliation(s)
| | | | | | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz, Karlsruhe, Germany
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Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O’Toole PW, Fardeau ML, Ollivier B, Brugère JF. Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov. Microorganisms 2023; 11:2794. [PMID: 38004804 PMCID: PMC10673518 DOI: 10.3390/microorganisms11112794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).
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Affiliation(s)
- Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell, 75015 Paris, France
| | - Khaled Fadhlaoui
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, UMR 6023 CNRS-UCA, Laboratoire Microorganismes: Génome et Environnement LMGE, 63000 Clermont-Ferrand, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Nadia Gaci
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Gérard Pehau-Arnaudet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging, 75015 Paris, France
| | - Prem Prashant Chaudhary
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Nathalie Ballet
- Lesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, France
| | - Monique Alric
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | | | - Marie-Laure Fardeau
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
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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 Halo archaea. 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Protasov E, Nonoh JO, Kästle Silva JM, Mies US, Hervé V, Dietrich C, Lang K, Mikulski L, Platt K, Poehlein A, Köhler-Ramm T, Miambi E, Boga HI, Feldewert C, Ngugi DK, Plarre R, Sillam-Dussès D, Šobotník J, Daniel R, Brune A. Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods. Front Microbiol 2023; 14:1281628. [PMID: 38033561 PMCID: PMC10684969 DOI: 10.3389/fmicb.2023.1281628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.
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Affiliation(s)
- Evgenii Protasov
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - James O. Nonoh
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Joana M. Kästle Silva
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Undine S. Mies
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina Lang
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lena Mikulski
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katja Platt
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Tim Köhler-Ramm
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Edouard Miambi
- Evolutionary Ecology Department, Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), University of Paris-Est Créteil (UPEC), Créteil, France
| | - Hamadi I. Boga
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christopher Feldewert
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David K. Ngugi
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC), UR 4443, Université Sorbonne Paris Nord, Villetaneuse, France
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czechia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Lange-Enyedi NT, Borsodi AK, Németh P, Czuppon G, Kovács I, Leél-Őssy S, Dobosy P, Felföldi T, Demény A, Makk J. Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves. FEMS Microbiol Ecol 2023; 99:fiad161. [PMID: 38066687 DOI: 10.1093/femsec/fiad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/13/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023] Open
Abstract
The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.
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Affiliation(s)
- Nóra Tünde Lange-Enyedi
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Andrea K Borsodi
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
- Institute of Aquatic Ecology, HUN-REN Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary
| | - Péter Németh
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
- Research Institute of Biomolecular and Chemical Engineering, Nanolab, University of Pannonia, Egyetem út 10, H-8200 Veszprém, Hungary
| | - György Czuppon
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
| | - Ivett Kovács
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
| | - Szabolcs Leél-Őssy
- Department of Physical and Applied Geology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Péter Dobosy
- Institute of Aquatic Ecology, HUN-REN Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
- Institute of Aquatic Ecology, HUN-REN Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary
| | - Attila Demény
- Institute for Geological and Geochemical Research, HUN-REN Research Centre for Astronomy and Earth Sciences, Budaörsi út 45, H-1112 Budapest, Hungary
| | - Judit Makk
- Department of Microbiology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
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Javaherdashti R. Editorial: Microbiologically influenced corrosion (MIC): its mechanisms, technological, economic, and environmental impacts. Front Microbiol 2023; 14:1249565. [PMID: 38029075 PMCID: PMC10679745 DOI: 10.3389/fmicb.2023.1249565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
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Sarkar S, Kazarina A, Hansen PM, Ward K, Hargreaves C, Reese N, Ran Q, Kessler W, de Souza LF, Loecke TD, Sarto MVM, Rice CW, Zeglin LH, Sikes BA, Lee ST. Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy. bioRxiv 2023:2023.11.08.566028. [PMID: 37987001 PMCID: PMC10659370 DOI: 10.1101/2023.11.08.566028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. Results We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. Conclusions The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.
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Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Paige M. Hansen
- PMH Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Nicholas Reese
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Willow Kessler
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Ligia F.T. de Souza
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Terry D. Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program, University of Kansas, Lawrence, Kansas, USA
| | | | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Benjamin A. Sikes
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sonny T.M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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