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Palacios PA, Philips J, Bentien A, Kofoed MVW. Relevance of extracellular electron uptake mechanisms for electromethanogenesis applications. Biotechnol Adv 2024; 73:108369. [PMID: 38685440 DOI: 10.1016/j.biotechadv.2024.108369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/21/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Electromethanogenesis has emerged as a biological branch of Power-to-X technologies that implements methanogenic microorganisms, as an alternative to chemical Power-to-X, to convert electrical power from renewable sources, and CO2 into methane. Unlike biomethanation processes where CO2 is converted via exogenously added hydrogen, electromethanogenesis occurs in a bioelectrochemical set-up that combines electrodes and microorganisms. Thereby, mixed, or pure methanogenic cultures catalyze the reduction of CO2 to methane via reducing equivalents supplied by a cathode. Recent advances in electromethanogenesis have been driven by interdisciplinary research at the intersection of microbiology, electrochemistry, and engineering. Integrating the knowledge acquired from these areas is essential to address the specific challenges presented by this relatively young biotechnology, which include electron transfer limitations, low energy and product efficiencies, and reactor design to enable upscaling. This review approaches electromethanogenesis from a multidisciplinary perspective, putting emphasis on the extracellular electron uptake mechanisms that methanogens use to obtain energy from cathodes, since understanding these mechanisms is key to optimize the electrochemical conditions for the development of these systems. This work summarizes the direct and indirect extracellular electron uptake mechanisms that have been elucidated to date in methanogens, along with the ones that remain unsolved. As the study of microbial corrosion, a similar bioelectrochemical process with Fe0 as electron source, has contributed to elucidate different mechanisms on how methanogens use solid electron donors, insights from both fields, biocorrosion and electromethanogenesis, are combined. Based on the repertoire of mechanisms and their potential to convert CO2 to methane, we conclude that for future applications, electromethanogenesis should focus on the indirect mechanism with H2 as intermediary. By summarizing and linking the general aspects and challenges of this process, we hope that this review serves as a guide for researchers working on electromethanogenesis in different areas of expertise to overcome the current limitations and continue with the optimization of this promising interdisciplinary technology.
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Affiliation(s)
- Paola Andrea Palacios
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8200 Aarhus, Denmark.
| | - Jo Philips
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8200 Aarhus, Denmark
| | - Anders Bentien
- Department of Biological and Chemical Engineering, Aarhus University, Aabogade 40, Aarhus N, 8200 Aarhus, Denmark
| | - Michael Vedel Wegener Kofoed
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8200 Aarhus, Denmark
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2
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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 haloarchaeal 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] [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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3
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Baker BA, Gutiérrez-Preciado A, Rodríguez Del Río Á, McCarthy CGP, López-García P, Huerta-Cepas J, Susko E, Roger AJ, Eme L, Moreira D. Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments. Nat Microbiol 2024; 9:964-975. [PMID: 38519541 DOI: 10.1038/s41564-024-01647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/20/2024] [Indexed: 03/25/2024]
Abstract
Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.
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Affiliation(s)
- Brittany A Baker
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Charley G P McCarthy
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Edward Susko
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
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4
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Stöckl R, Nißl L, Reichelt R, Rachel R, Grohmann D, Grünberger F. The transcriptional regulator EarA and intergenic terminator sequences modulate archaellation in Pyrococcus furiosus. Front Microbiol 2023; 14:1241399. [PMID: 38029142 PMCID: PMC10665913 DOI: 10.3389/fmicb.2023.1241399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The regulation of archaellation, the formation of archaeal-specific cell appendages called archaella, is crucial for the motility, adhesion, and survival of archaeal organisms. Although the heavily archaellated and highly motile Pyrococcus furiosus is a key model organism for understanding the production and function of archaella in Euryarchaea, the transcriptional regulation of archaellum assembly is so far unknown. Here we show that the transcription factor EarA is the master regulator of the archaellum (arl) operon transcription, which is further modulated by intergenic transcription termination signals. EarA deletion or overexpression strains demonstrate that EarA is essential for archaellation in P. furiosus and governs the degree of archaellation. Providing a single-molecule update on the transcriptional landscape of the arl operon in P. furiosus, we identify sequence motifs for EarA binding upstream of the arl operon and intergenic terminator sequences as critical elements for fine-tuning the expression of the multicistronic arl cluster. Furthermore, transcriptome re-analysis across different Thermococcales species demonstrated a heterogeneous production of major archaellins, suggesting a more diverse composition of archaella than previously recognized. Overall, our study provides novel insights into the transcriptional regulation of archaellation and highlights the essential role of EarA in Pyrococcus furiosus. These findings advance our understanding of the mechanisms governing archaellation and have implications for the functional diversity of archaella.
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Affiliation(s)
- Richard Stöckl
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Laura Nißl
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
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5
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Fritz-Laylin LK, Titus MA. The evolution and diversity of actin-dependent cell migration. Mol Biol Cell 2023; 34:pe6. [PMID: 37906436 PMCID: PMC10846614 DOI: 10.1091/mbc.e22-08-0358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 11/02/2023] Open
Abstract
Many eukaryotic cells, including animal cells and unicellular amoebae, use dynamic-actin networks to crawl across solid surfaces. Recent discoveries of actin-dependent crawling in additional lineages have sparked interest in understanding how and when this type of motility evolved. Tracing the evolution of cell crawling requires understanding the molecular mechanisms underlying motility. Here we outline what is known about the diversity and evolution of the molecular mechanisms that drive cell motility, with a focus on actin-dependent crawling. Classic studies and recent work have revealed a surprising number of distinct mechanical modes of actin-dependent crawling used by different cell types and species to navigate different environments. The overlap in actin network regulators driving multiple types of actin-dependent crawling, along with cortical-actin networks that support the plasma membrane in these cells, suggest that actin motility and cortical actin networks might have a common evolutionary origin. The rapid development of additional evolutionarily diverse model systems, advanced imaging technologies, and CRISPR-based genetic tools, is opening the door to testing these and other new ideas about the evolution of actin-dependent cell crawling.
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Affiliation(s)
| | - Margaret A. Titus
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
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Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol 2023; 14:1219779. [PMID: 37649629 PMCID: PMC10465181 DOI: 10.3389/fmicb.2023.1219779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.
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Affiliation(s)
- Beverly K. Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Kiel University, Kiel, Germany
| | - Öykü Z. Mete
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Erin M. Eggleston
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
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7
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Recalde A, González-Madrid G, Acevedo-López J, Jerez CA. Sessile Lifestyle Offers Protection against Copper Stress in Saccharolobus solfataricus. Microorganisms 2023; 11:1421. [PMID: 37374923 DOI: 10.3390/microorganisms11061421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Some archaea from the genus Sulfolobus are important for bioleaching of copper, where metal resistant microorganisms are required. Biofilm generation is one of the ways microorganisms cope with some stimuli in nature, including heavy metals. The response to external factors, particularly in the biofilm form of life, is still underexplored in archaea. To explore how model thermoacidophilic archaeon Saccharolobus solfataricus faces copper stress during this lifestyle, changes in biofilms were studied using crystal violet staining, confocal fluorescence microscopy, and qPCR approaches. It was found that biofilm formation reached a maximum at 0.5 mM Cu, before starting to decrease at higher metal concentrations. The morphology of biofilms at 0.5 mM Cu was observed to be different, displaying lower thickness, different sugar patterns, and higher amounts of cells compared to standard growing conditions. Furthermore, copA, which is responsive to intracellular Cu concentration, was downregulated in biofilm cells when compared with planktonic cells exposed to the same metal concentration. The latest results suggests that cells in biofilms are less exposed to Cu than those in planktonic culture. In a PolyP-deficient strain, Cu was not able to induce biofilm formation at 0.5 mM. In summary, the findings reported here suggest that the biofilm form of life confers S. solfataricus advantages to face stress caused by Cu.Biofilm formation remains a relatively unexplored topic in archaeal research. Therefore, this knowledge in model organisms such as S. solfataricus, and how they use it to face stress, could be of great importance to engineer organisms with improved capabilities to be applied in biotechnological processes, such as bioleaching of metals.
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Affiliation(s)
- Alejandra Recalde
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, 8330111 Santiago, Chile
- Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, 79104 Freiburg, Germany
| | - Gabriela González-Madrid
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, 8330111 Santiago, Chile
| | - José Acevedo-López
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, 8330111 Santiago, Chile
| | - Carlos A Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, 8330111 Santiago, Chile
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8
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Rao A, de Kok NAW, Driessen AJM. Membrane Adaptations and Cellular Responses of Sulfolobus acidocaldarius to the Allylamine Terbinafine. Int J Mol Sci 2023; 24:ijms24087328. [PMID: 37108491 PMCID: PMC10138448 DOI: 10.3390/ijms24087328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Cellular membranes are essential for compartmentalization, maintenance of permeability, and fluidity in all three domains of life. Archaea belong to the third domain of life and have a distinct phospholipid composition. Membrane lipids of archaea are ether-linked molecules, specifically bilayer-forming dialkyl glycerol diethers (DGDs) and monolayer-forming glycerol dialkyl glycerol tetraethers (GDGTs). The antifungal allylamine terbinafine has been proposed as an inhibitor of GDGT biosynthesis in archaea based on radiolabel incorporation studies. The exact target(s) and mechanism of action of terbinafine in archaea remain elusive. Sulfolobus acidocaldarius is a strictly aerobic crenarchaeon thriving in a thermoacidophilic environment, and its membrane is dominated by GDGTs. Here, we comprehensively analyzed the lipidome and transcriptome of S. acidocaldarius in the presence of terbinafine. Depletion of GDGTs and the accompanying accumulation of DGDs upon treatment with terbinafine were growth phase-dependent. Additionally, a major shift in the saturation of caldariellaquinones was observed, which resulted in the accumulation of unsaturated molecules. Transcriptomic data indicated that terbinafine has a multitude of effects, including significant differential expression of genes in the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization. Combined, these findings suggest that the response of S. acidocaldarius to terbinafine inhibition involves respiratory stress and the differential expression of genes involved in isoprenoid biosynthesis and saturation.
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Affiliation(s)
- Alka Rao
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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Sivabalasarma S, de Sousa Machado JN, Albers SV, Jarrell KF. Archaella Isolation. Methods Mol Biol 2023; 2646:183-195. [PMID: 36842116 DOI: 10.1007/978-1-0716-3060-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Swimming archaea are propelled by a filamentous structure called the archaellum. The first step for the structural characterization of this filament is its isolation. Here we provide various methods that allow for the isolation of archaella filaments from well-studied archaeal model organisms. Archaella filaments have been successfully extracted from organisms belonging to different archaeal phyla, e.g., euryarchaeal methanogens such as Methanococcus voltae, and crenarchaeal hyperthermoacidophiles like Sulfolobus acidocaldarius. The filament isolation protocols that we provide in this chapter follow one of two strategies: either the filaments are sheared or extracted from whole cells by detergent extraction, prior to further final purification by centrifugation methods.
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Affiliation(s)
- Shamphavi Sivabalasarma
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - João N de Sousa Machado
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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10
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Archaea as a Model System for Molecular Biology and Biotechnology. Biomolecules 2023; 13:biom13010114. [PMID: 36671499 PMCID: PMC9855744 DOI: 10.3390/biom13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
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11
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Dubay MM, Acres J, Riekeles M, Nadeau JL. Recent advances in experimental design and data analysis to characterize prokaryotic motility. J Microbiol Methods 2023; 204:106658. [PMID: 36529156 DOI: 10.1016/j.mimet.2022.106658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying run distances and speeds, turn angles and behavior by surfaces or cell-cell interactions) remains a challenging task. A qualitative and quantitative understanding of bacterial motility is needed to bridge the gap between experimentation, omics analysis, and bacterial motility theory. In this review, we discuss the strengths and limitations of how phase contrast microscopy, fluorescence microscopy, and digital holographic microscopy have been used to quantify bacterial motility. Approaches to automated software analysis, including cell recognition, tracking, and track analysis, are also discussed with a view to providing a guide for experimenters to setting up the appropriate imaging and analysis system for their needs.
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Affiliation(s)
- Megan Marie Dubay
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Jacqueline Acres
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Max Riekeles
- Astrobiology Group, Center of Astronomy and Astrophysics, Technical University Berlin, Hardenbergstraße 36A, 10623 Berlin, Germany
| | - Jay L Nadeau
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America.
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12
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Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in Halobacterium salinarum. Microorganisms 2022; 10:microorganisms10122442. [PMID: 36557695 PMCID: PMC9786353 DOI: 10.3390/microorganisms10122442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Halobacterium salinarum NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, we compared a low salt (2.6 M NaCl) stress condition with 4.3 M of NaCl and found 283 differentially expressed loci. The more commonly found classes of genes were: ABC-type transporters and transcription factors. Similarities, and most importantly, differences between our findings and previously published datasets in similar experimental conditions are discussed. We validated three important biological processes differentially expressed: gas vesicles production (due to down-regulation of gvpA1b, gvpC1b, gvpN1b, and gvpO1b); archaellum formation (due to down-regulation of arlI, arlB1, arlB2, and arlB3); and glycerol metabolism (due to up-regulation of glpA1, glpB, and glpC). Direct comparison between transcriptomics and proteomics showed 58% agreement between mRNA and protein level changes, pointing to post-transcriptional regulation candidates. From those genes, we highlight rpl15e, encoding for the 50S ribosomal protein L15e, for which we hypothesize an ionic strength-dependent conformational change that guides post-transcriptional processing of its mRNA and, thus, possible salt-dependent regulation of the translation machinery.
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13
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van Wolferen M, Pulschen AA, Baum B, Gribaldo S, Albers SV. The cell biology of archaea. Nat Microbiol 2022; 7:1744-1755. [PMID: 36253512 PMCID: PMC7613921 DOI: 10.1038/s41564-022-01215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Buzz Baum
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institute Pasteur, Paris, France.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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14
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Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea. Appl Environ Microbiol 2022; 88:e0157422. [DOI: 10.1128/aem.01574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood.
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15
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Gu W, Müller AL, Deutzmann JS, Williamson JR, Spormann AM. Growth rate-dependent coordination of catabolism and anabolism in the archaeon Methanococcus maripaludis under phosphate limitation. THE ISME JOURNAL 2022; 16:2313-2319. [PMID: 35780255 PMCID: PMC9478154 DOI: 10.1038/s41396-022-01278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Catabolic and anabolic processes are finely coordinated in microorganisms to provide optimized fitness under varying environmental conditions. Understanding this coordination and the resulting physiological traits reveals fundamental strategies of microbial acclimation. Here, we characterized the system-level physiology of Methanococcus maripaludis, a niche-specialized methanogenic archaeon, at different dilution rates ranging from 0.09 to 0.003 h-1 in chemostat experiments under phosphate (i.e., anabolic) limitation. Phosphate was supplied as the limiting nutrient, while formate was supplied in excess as the catabolic substrate and carbon source. We observed a decoupling of catabolism and anabolism resulting in lower biomass yield relative to catabolically limited cells at the same dilution rates. In addition, the mass abundance of several coarse-grained proteome sectors (i.e., combined abundance of proteins grouped based on their function) exhibited a linear relationship with growth rate, mostly ribosomes and their biogenesis. Accordingly, cellular RNA content also correlated with growth rate. Although the methanogenesis proteome sector was invariant, the metabolic capacity for methanogenesis, measured as methane production rates immediately after transfer to batch culture, correlated with growth rate suggesting translationally independent regulation that allows cells to only increase catabolic activity under growth-permissible conditions. These observations are in stark contrast to the physiology of M. maripaludis under formate (i.e., catabolic) limitation, where cells keep an invariant proteome including ribosomal content and a high methanogenesis capacity across a wide range of growth rates. Our findings reveal that M. maripaludis employs fundamentally different strategies to coordinate global physiology during anabolic phosphate and catabolic formate limitation.
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Affiliation(s)
- Wenyu Gu
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Albert L Müller
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Jörg S Deutzmann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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16
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Benito Merino D, Zehnle H, Teske A, Wegener G. Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane. Front Microbiol 2022; 13:988871. [PMID: 36212815 PMCID: PMC9539880 DOI: 10.3389/fmicb.2022.988871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/15/2022] [Indexed: 01/03/2023] Open
Abstract
In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate-methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.
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Affiliation(s)
- David Benito Merino
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Hanna Zehnle
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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17
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Structural insights into the mechanism of archaellar rotational switching. Nat Commun 2022; 13:2857. [PMID: 35606361 PMCID: PMC9126983 DOI: 10.1038/s41467-022-30358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Signal transduction via phosphorylated CheY towards the flagellum and the archaellum involves a conserved mechanism of CheY phosphorylation and subsequent conformational changes within CheY. This mechanism is conserved among bacteria and archaea, despite substantial differences in the composition and architecture of archaellum and flagellum, respectively. Phosphorylated CheY has higher affinity towards the bacterial C-ring and its binding leads to conformational changes in the flagellar motor and subsequent rotational switching of the flagellum. In archaea, the adaptor protein CheF resides at the cytoplasmic face of the archaeal C-ring formed by the proteins ArlCDE and interacts with phosphorylated CheY. While the mechanism of CheY binding to the C-ring is well-studied in bacteria, the role of CheF in archaea remains enigmatic and mechanistic insights are absent. Here, we have determined the atomic structures of CheF alone and in complex with activated CheY by X-ray crystallography. CheF forms an elongated dimer with a twisted architecture. We show that CheY binds to the C-terminal tail domain of CheF leading to slight conformational changes within CheF. Our structural, biochemical and genetic analyses reveal the mechanistic basis for CheY binding to CheF and allow us to propose a model for rotational switching of the archaellum. Signal transduction via phosphorylated CheY is conserved in bacteria and archaea. In this study, the authors employ structural biochemistry combined with cell biology to delineate the mechanism of CheY recognition by the adaptor protein CheF.
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18
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Nuno de Sousa Machado J, Albers SV, Daum B. Towards Elucidating the Rotary Mechanism of the Archaellum Machinery. Front Microbiol 2022; 13:848597. [PMID: 35387068 PMCID: PMC8978795 DOI: 10.3389/fmicb.2022.848597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Motile archaea swim by means of a molecular machine called the archaellum. This structure consists of a filament attached to a membrane-embedded motor. The archaellum is found exclusively in members of the archaeal domain, but the core of its motor shares homology with the motor of type IV pili (T4P). Here, we provide an overview of the different components of the archaellum machinery and hypothetical models to explain how rotary motion of the filament is powered by the archaellum motor.
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Affiliation(s)
- João Nuno de Sousa Machado
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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19
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Glodowska M, Welte CU, Kurth JM. Metabolic potential of anaerobic methane oxidizing archaea for a broad spectrum of electron acceptors. Adv Microb Physiol 2022; 80:157-201. [PMID: 35489791 DOI: 10.1016/bs.ampbs.2022.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Methane (CH4) is a potent greenhouse gas significantly contributing to the climate warming we are currently facing. Microorganisms play an important role in the global CH4 cycle that is controlled by the balance between anaerobic production via methanogenesis and CH4 removal via methanotrophic oxidation. Research in recent decades advanced our understanding of CH4 oxidation, which until 1976 was believed to be a strictly aerobic process. Anaerobic oxidation of methane (AOM) coupled to sulfate reduction is now known to be an important sink of CH4 in marine ecosystems. Furthermore, in 2006 it was discovered that anaerobic CH4 oxidation can also be coupled to nitrate reduction (N-DAMO), demonstrating that AOM may be much more versatile than previously thought and linked to other electron acceptors. In consequence, an increasing number of studies in recent years showed or suggested that alternative electron acceptors can be used in the AOM process including FeIII, MnIV, AsV, CrVI, SeVI, SbV, VV, and BrV. In addition, humic substances as well as biochar and perchlorate (ClO4-) were suggested to mediate AOM. Anaerobic methanotrophic archaea, the so-called ANME archaea, are key players in the AOM process, yet we are still lacking deeper understanding of their metabolism, electron acceptor preferences and their interaction with other microbial community members. It is still not clear whether ANME archaea can oxidize CH4 and reduce metallic electron acceptors independently or via electron transfer to syntrophic partners, interspecies electron transfer, nanowires or conductive pili. Therefore, the aim of this review is to summarize and discuss the current state of knowledge about ANME archaea, focusing on their physiology, metabolic flexibility and potential to use various electron acceptors.
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Affiliation(s)
- Martyna Glodowska
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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20
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Gambelli L, Isupov MN, Conners R, McLaren M, Bellack A, Gold V, Rachel R, Daum B. An archaellum filament composed of two alternating subunits. Nat Commun 2022; 13:710. [PMID: 35132062 PMCID: PMC8821640 DOI: 10.1038/s41467-022-28337-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
Abstract
Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament’s flexibility. The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Annett Bellack
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Vicki Gold
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Reinhard Rachel
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK. .,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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21
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Zhang X, Yuan Z, Hu S. Anaerobic oxidation of methane mediated by microbial extracellular respiration. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:790-804. [PMID: 34523810 DOI: 10.1111/1758-2229.13008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic oxidation of methane (AOM) can be microbially mediated by the reduction of different terminal electron acceptors. AOM coupled to reduction of sulfate, manganese/iron oxides, humic substances, selenate, arsenic and other artificial extracellular electron acceptors are recognized as processes associated with microbial extracellular respiration. In these processes, methane-oxidizing archaea transfer electrons to external electron acceptors or to interdependent microbial species, which are mechanistically dependent on versatile extracellular electron transfer (EET) pathways. This review compiles recent progress in the research of electromicrobiology of AOM based on the catalogue of different electron acceptors. Naturally distributed and artificially constructed EET-mediated AOM is summarized, with the discussion of their environmental importance and application potentials. The diversity of responsible microorganisms involved in EET-mediated AOM is discussed with both methane-oxidizing archaea and their putative bacterial partners. More importantly, the review highlights progress and deficiencies in our understanding of EET pathways in EET-mediated AOM, raising open research questions for future research.
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Affiliation(s)
- Xueqin Zhang
- Advanced Water Management Centre, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, Brisbane, Qld, 4072, Australia
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22
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Makarova KS, Wolf YI, Karamycheva S, Koonin EV. A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains. Front Microbiol 2021; 12:721392. [PMID: 34489912 PMCID: PMC8416519 DOI: 10.3389/fmicb.2021.721392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Molecular mechanisms involved in biological conflicts and self vs nonself recognition in archaea remain poorly characterized. We apply phylogenomic analysis to identify a hypervariable gene module that is widespread among Thermococcales. These loci consist of an upstream gene coding for a large protein containing several immunoglobulin (Ig) domains and unique combinations of downstream genes, some of which also contain Ig domains. In the large Ig domain containing protein, the C-terminal Ig domain sequence is hypervariable, apparently, as a result of recombination between genes from different Thermococcales. To reflect the hypervariability, we denote this gene module VARTIG (VARiable Thermococcales IG). The overall organization of the VARTIG modules is similar to the organization of Polymorphic Toxin Systems (PTS). Archaeal genomes outside Thermococcales encode a variety of Ig domain proteins, but no counterparts to VARTIG and no Ig domains with comparable levels of variability. The specific functions of VARTIG remain unknown but the identified features of this system imply three testable hypotheses: (i) involvement in inter-microbial conflicts analogous to PTS, (ii) role in innate immunity analogous to the vertebrate complement system, and (iii) function in self vs nonself discrimination analogous to the vertebrate Major Histocompatibility Complex. The latter two hypotheses seem to be of particular interest given the apparent analogy to the vertebrate immunity.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, United States
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, United States
| | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, United States
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, United States
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23
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Li YX, Rao YZ, Qi YL, Qu YN, Chen YT, Jiao JY, Shu WS, Jiang H, Hedlund BP, Hua ZS, Li WJ. Deciphering Symbiotic Interactions of " Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks. mSystems 2021; 6:e0060621. [PMID: 34313464 PMCID: PMC8407114 DOI: 10.1128/msystems.00606-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022] Open
Abstract
"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.
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Affiliation(s)
- Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Ya-Ting Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People’s Republic of China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People’s Republic of China
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, People’s Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People’s Republic of China
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24
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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Slobodkina G, Allioux M, Merkel A, Cambon-Bonavita MA, Alain K, Jebbar M, Slobodkin A. Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus. Front Microbiol 2021; 12:679245. [PMID: 34335500 PMCID: PMC8322695 DOI: 10.3389/fmicb.2021.679245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022] Open
Abstract
Hyperthermophilic archaea of the genus Archaeoglobus are the subject of many fundamental and biotechnological researches. Despite their significance, the class Archaeoglobi is currently represented by only eight species obtained as axenic cultures and taxonomically characterized. Here, we report the isolation and characterization of a new species of Archaeoglobus from a deep-sea hydrothermal vent (Mid-Atlantic Ridge, TAG) for which the name Archaeoglobus neptunius sp. nov. is proposed. The type strain is SE56T (=DSM 110954T = VKM B-3474T). The cells of the novel isolate are motile irregular cocci growing at 50–85°C, pH 5.5–7.5, and NaCl concentrations of 1.5–4.5% (w/v). Strain SE56T grows lithoautotrophically with H2 as an electron donor, sulfite or thiosulfate as an electron acceptor, and CO2/HCO3− as a carbon source. It is also capable of chemoorganotrophic growth by reduction of sulfate, sulfite, or thiosulfate. The genome of the new isolate consists of a 2,115,826 bp chromosome with an overall G + C content of 46.0 mol%. The whole-genome annotation confirms the key metabolic features of the novel isolate demonstrated experimentally. Genome contains a complete set of genes involved in CO2 fixation via reductive acetyl-CoA pathway, gluconeogenesis, hydrogen and fatty acids oxidation, sulfate reduction, and flagellar motility. The phylogenomic reconstruction based on 122 conserved single-copy archaeal proteins supported by average nucleotide identity (ANI), average amino acid identity (AAI), and alignment fraction (AF) values, indicates a polyphyletic origin of the species currently included into the genus Archaeoglobus, warranting its reclassification.
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Affiliation(s)
- Galina Slobodkina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maxime Allioux
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marie-Anne Cambon-Bonavita
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Mohamed Jebbar
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, Plouzané, France
| | - Alexander Slobodkin
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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26
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers SV. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerization and interaction with ArlI, the motor ATPase of the archaellum. Mol Microbiol 2021; 116:943-956. [PMID: 34219289 DOI: 10.1111/mmi.14781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Since autophosphorylation and dephosphorylation of KaiC are central properties for the function of KaiC, we asked whether autophosphorylation is also a property of ArlH proteins. We observed that both ArlH from the euryarchaeon Pyrococcus furiosus (PfArlH) and from the crenarchaeon Sulfolobus acidocaldarius (SaArlH) have autophosphorylation activity. Using a combination of single-molecule fluorescence measurements and biochemical assays, we show that autophosphorylation of ArlH is closely linked to its oligomeric state when bound to hexameric ArlI. These experiments also strongly suggest that ArlH is a hexamer in its ArlI-bound state. Mutagenesis of the putative catalytic residue (Glu-57 in SaArlH) in ArlH results in a reduced autophosphorylation activity and abolished archaellation and motility in S. acidocaldarius, indicating that optimum phosphorylation activity of ArlH is essential for archaellation and motility.
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Affiliation(s)
- J Nuno de Sousa Machado
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Leonie Vollmar
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Julia Schimpf
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Rashmi Kumariya
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Counts JA, Willard DJ, Kelly RM. Life in hot acid: a genome-based reassessment of the archaeal order Sulfolobales. Environ Microbiol 2021; 23:3568-3584. [PMID: 32776389 PMCID: PMC10560490 DOI: 10.1111/1462-2920.15189] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 01/07/2023]
Abstract
The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re-organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.
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Affiliation(s)
- James A. Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
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28
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Grognot M, Taute KM. More than propellers: how flagella shape bacterial motility behaviors. Curr Opin Microbiol 2021; 61:73-81. [PMID: 33845324 DOI: 10.1016/j.mib.2021.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/05/2021] [Accepted: 02/14/2021] [Indexed: 12/22/2022]
Abstract
Bacteria use a wide variety of flagellar architectures to navigate their environment. While the iconic run-tumble motility strategy of the peritrichously flagellated Escherichia coli has been well studied, recent work has revealed a variety of new motility behaviors that can be achieved with different flagellar architectures, such as single, bundled, or opposing polar flagella. The recent discovery of various flagellar gymnastics such as flicking and flagellar wrapping is increasingly shifting the view from flagella as passive propellers to versatile appendages that can be used in a wide range of conformations. Here, we review recent observations of how flagella shape motility behaviors and summarize the nascent structure-function map linking flagellation and behavior.
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Affiliation(s)
- Marianne Grognot
- Rowland Institute at Harvard, 100 Edwin H Land Blvd, Cambridge, MA 02142, USA
| | - Katja M Taute
- Rowland Institute at Harvard, 100 Edwin H Land Blvd, Cambridge, MA 02142, USA.
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29
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Jarrell KF, Albers SV, Machado JNDS. A comprehensive history of motility and Archaellation in Archaea. FEMS MICROBES 2021; 2:xtab002. [PMID: 37334237 PMCID: PMC10117864 DOI: 10.1093/femsmc/xtab002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/18/2021] [Indexed: 08/24/2023] Open
Abstract
Each of the three Domains of life, Eukarya, Bacteria and Archaea, have swimming structures that were all originally called flagella, despite the fact that none were evolutionarily related to either of the other two. Surprisingly, this was true even in the two prokaryotic Domains of Bacteria and Archaea. Beginning in the 1980s, evidence gradually accumulated that convincingly demonstrated that the motility organelle in Archaea was unrelated to that found in Bacteria, but surprisingly shared significant similarities to type IV pili. This information culminated in the proposal, in 2012, that the 'archaeal flagellum' be assigned a new name, the archaellum. In this review, we provide a historical overview on archaella and motility research in Archaea, beginning with the first simple observations of motile extreme halophilic archaea a century ago up to state-of-the-art cryo-tomography of the archaellum motor complex and filament observed today. In addition to structural and biochemical data which revealed the archaellum to be a type IV pilus-like structure repurposed as a rotating nanomachine (Beeby et al. 2020), we also review the initial discoveries and subsequent advances using a wide variety of approaches to reveal: complex regulatory events that lead to the assembly of the archaellum filaments (archaellation); the roles of the various archaellum proteins; key post-translational modifications of the archaellum structural subunits; evolutionary relationships; functions of archaella other than motility and the biotechnological potential of this fascinating structure. The progress made in understanding the structure and assembly of the archaellum is highlighted by comparing early models to what is known today.
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Affiliation(s)
- Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Sonja-Verena Albers
- Institute for Biology II- Microbiology, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, Freiburg 79104, Germany
| | - J Nuno de Sousa Machado
- Institute for Biology II- Microbiology, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, Freiburg 79104, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany
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30
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Gao K, Lu Y. Putative Extracellular Electron Transfer in Methanogenic Archaea. Front Microbiol 2021; 12:611739. [PMID: 33828536 PMCID: PMC8019784 DOI: 10.3389/fmicb.2021.611739] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/03/2021] [Indexed: 11/14/2022] Open
Abstract
It has been suggested that a few methanogens are capable of extracellular electron transfers. For instance, Methanosarcina barkeri can directly capture electrons from the coexisting microbial cells of other species. Methanothrix harundinacea and Methanosarcina horonobensis retrieve electrons from Geobacter metallireducens via direct interspecies electron transfer (DIET). Recently, Methanobacterium, designated strain YSL, has been found to grow via DIET in the co-culture with Geobacter metallireducens. Methanosarcina acetivorans can perform anaerobic methane oxidation and respiratory growth relying on Fe(III) reduction through the extracellular electron transfer. Methanosarcina mazei is capable of electromethanogenesis under the conditions where electron-transfer mediators like H2 or formate are limited. The membrane-bound multiheme c-type cytochromes (MHC) and electrically-conductive cellular appendages have been assumed to mediate the extracellular electron transfer in bacteria like Geobacter and Shewanella species. These molecules or structures are rare but have been recently identified in a few methanogens. Here, we review the current state of knowledge for the putative extracellular electron transfers in methanogens and highlight the opportunities and challenges for future research.
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Affiliation(s)
- Kailin Gao
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
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31
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers S. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerisation and interaction with ArlI, the motor ATPase of the archaellum.. [DOI: 10.1101/2021.03.19.436134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Similar to KaiC, ArlH exhibits autophosphorylation activity, which was observed for both ArlH of the euryarchaeonPyrococcus furiosus (PfArlH)and the crenarchaeonSulfolobus acidocaldarius(SaArlH). Using a combination of single molecule fluorescence measurements and biochemical assays, it is shown that autophosphorylation of ArlH is closely linked to the oligomeric state of ArlH bound to ArlI. These experiments also strongly suggest that ArlH is a hexamer in its functional ArlI bound state. Mutagenesis of the putative catalytic residue Glu-57 inSaArlH results in a reduced autophosphorylation activity and abolished archaellation and motility, suggesting that optimum phosphorylation activity of ArlH is essential for both archaellation and motility.
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32
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Abstract
All living cells interact dynamically with a constantly changing world. Eukaryotes, in particular, evolved radically new ways to sense and react to their environment. These advances enabled new and more complex forms of cellular behaviour in eukaryotes, including directional movement, active feeding, mating, and responses to predation. But what are the key events and innovations during eukaryogenesis that made all of this possible? Here we describe the ancestral repertoire of eukaryotic excitability and discuss five major cellular innovations that enabled its evolutionary origin. The innovations include a vastly expanded repertoire of ion channels, the emergence of cilia and pseudopodia, endomembranes as intracellular capacitors, a flexible plasma membrane and the relocation of chemiosmotic ATP synthesis to mitochondria, which liberated the plasma membrane for more complex electrical signalling involved in sensing and reacting. We conjecture that together with an increase in cell size, these new forms of excitability greatly amplified the degrees of freedom associated with cellular responses, allowing eukaryotes to vastly outperform prokaryotes in terms of both speed and accuracy. This comprehensive new perspective on the evolution of excitability enriches our view of eukaryogenesis and emphasizes behaviour and sensing as major contributors to the success of eukaryotes. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.
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Affiliation(s)
- Kirsty Y. Wan
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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33
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Knüppel R, Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax TEF, Albers SV, Oeffinger M, Ferreira-Cerca S. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucleic Acids Res 2021; 49:1662-1687. [PMID: 33434266 PMCID: PMC7897474 DOI: 10.1093/nar/gkaa1268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are intricate molecular machines ensuring proper protein synthesis in every cell. Ribosome biogenesis is a complex process which has been intensively analyzed in bacteria and eukaryotes. In contrast, our understanding of the in vivo archaeal ribosome biogenesis pathway remains less characterized. Here, we have analyzed the in vivo role of the almost universally conserved ribosomal RNA dimethyltransferase KsgA/Dim1 homolog in archaea. Our study reveals that KsgA/Dim1-dependent 16S rRNA dimethylation is dispensable for the cellular growth of phylogenetically distant archaea. However, proteomics and functional analyses suggest that archaeal KsgA/Dim1 and its rRNA modification activity (i) influence the expression of a subset of proteins and (ii) contribute to archaeal cellular fitness and adaptation. In addition, our study reveals an unexpected KsgA/Dim1-dependent variability of rRNA modifications within the archaeal phylum. Combining structure-based functional studies across evolutionary divergent organisms, we provide evidence on how rRNA structure sequence variability (re-)shapes the KsgA/Dim1-dependent rRNA modification status. Finally, our results suggest an uncoupling between the KsgA/Dim1-dependent rRNA modification completion and its release from the nascent small ribosomal subunit. Collectively, our study provides additional understandings into principles of molecular functional adaptation, and further evolutionary and mechanistic insights into an almost universally conserved step of ribosome synthesis.
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Affiliation(s)
- Robert Knüppel
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Christian Trahan
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Michael Kern
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Alexander Wagner
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Felix Grünberger
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- Chair of Microbiology – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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34
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Tittes C, Schwarzer S, Pfeiffer F, Dyall-Smith M, Rodriguez-Franco M, Oksanen HM, Quax TEF. Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1. Front Microbiol 2021; 12:625599. [PMID: 33664716 PMCID: PMC7921747 DOI: 10.3389/fmicb.2021.625599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/28/2021] [Indexed: 01/14/2023] Open
Abstract
Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus–host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Haloferax volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures, and cell shape. Its genome sequence showed that LR2-5 is a new strain of Haloferax gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus–host studies in euryarchaea.
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Affiliation(s)
- Colin Tittes
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sabine Schwarzer
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mike Dyall-Smith
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
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35
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Huang Q, Lin Z, Wu P, Ni J, Shen Y. Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A. Front Microbiol 2020; 11:586025. [PMID: 33343525 PMCID: PMC7744417 DOI: 10.3389/fmicb.2020.586025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022] Open
Abstract
DNA damage response (DDR) in eukaryotes is largely regulated by protein phosphorylation. In archaea, many proteins are phosphorylated, however, it is unclear how the cells respond to DNA damage through global protein phosphorylation. We previously found that Δrio1, a Rio1 kinase homolog deletion strain of Sulfolobus islandicus REY15A, was sensitive to UV irradiation. In this study, we showed that Δrio1 grew faster than the wild type. Quantitative phosphoproteomic analysis of the wild type and Δrio1, untreated and irradiated with UV irradiation, revealed 562 phosphorylated sites (with a Ser/Thr/Tyr ratio of 65.3%/23.8%/10.9%) of 333 proteins in total. The phosphorylation levels of 35 sites of 30 proteins changed with >1.3-fold in the wild type strain upon UV irradiation. Interestingly, more than half of the UV-induced changes in the wild type did not occur in the Δrio1 strain, which were mainly associated with proteins synthesis and turnover. In addition, a protein kinase and several transcriptional regulators were differentially phosphorylated after UV treatment, and some of the changes were dependent on Rio1. Finally, many proteins involved in various cellular metabolisms exhibited Riol-related and UV-independent phosphorylation changes. Our results suggest that Rio1 is involved in the regulation of protein recycling and signal transduction in response to UV irradiation, and plays regulatory roles in multiple cellular processes in S. islandicus.
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Affiliation(s)
- Qihong Huang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Zijia Lin
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Pengju Wu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Jinfeng Ni
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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36
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Li Z, Rodriguez‐Franco M, Albers S, Quax TEF. The switch complex ArlCDE connects the chemotaxis system and the archaellum. Mol Microbiol 2020; 114:468-479. [PMID: 32416640 PMCID: PMC7534055 DOI: 10.1111/mmi.14527] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
Abstract
Cells require a sensory system and a motility structure to achieve directed movement. Bacteria and archaea possess rotating filamentous motility structures that work in concert with the sensory chemotaxis system. This allows microorganisms to move along chemical gradients. The central response regulator protein CheY can bind to the motor of the motility structure, the flagellum in bacteria, and the archaellum in archaea. Both motility structures have a fundamentally different protein composition and structural organization. Yet, both systems receive input from the chemotaxis system. So far, it was unknown how the signal is transferred from the archaeal CheY to the archaellum motor to initiate motor switching. We applied a fluorescent microscopy approach in the model euryarchaeon Haloferax volcanii and shed light on the sequence order in which signals are transferred from the chemotaxis system to the archaellum. Our findings indicate that the euryarchaeal-specific ArlCDE are part of the archaellum motor and that they directly receive input from the chemotaxis system via the adaptor protein CheF. Hence, ArlCDE are an important feature of the archaellum of euryarchaea, are essential for signal transduction during chemotaxis and represent the archaeal switch complex.
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Affiliation(s)
- Zhengqun Li
- Molecular Biology of Archaea, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | | | - Sonja‐Verena Albers
- Molecular Biology of Archaea, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Tessa E. F. Quax
- Archaeal Virus–Host Interactions, Faculty of BiologyUniversity of FreiburgFreiburgGermany
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37
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Kelly JF, Vinogradov E, Stupak J, Robotham AC, Logan SM, Berezuk A, Khursigara CM, Jarrell KF. Identification of a novel N-linked glycan on the archaellins and S-layer protein of the thermophilic methanogen, Methanothermococcus thermolithotrophicus. J Biol Chem 2020; 295:14618-14629. [PMID: 32817340 DOI: 10.1074/jbc.ra120.012790] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/28/2020] [Indexed: 01/25/2023] Open
Abstract
Motility in archaea is facilitated by a unique structure termed the archaellum. N-Glycosylation of the major structural proteins (archaellins) is important for their subsequent incorporation into the archaellum filament. The identity of some of these N-glycans has been determined, but archaea exhibit extensive variation in their glycans, meaning that further investigations can shed light not only on the specific details of archaellin structure and function, but also on archaeal glycobiology in general. Here we describe the structural characterization of the N-linked glycan modifications on the archaellins and S-layer protein of Methanothermococcus thermolithotrophicus, a methanogen that grows optimally at 65 °C. SDS-PAGE and MS analysis revealed that the sheared archaella are composed principally of two of the four predicted archaellins, FlaB1 and FlaB3, which are modified with a branched, heptameric glycan at all N-linked sequons except for the site closest to the N termini of both proteins. NMR analysis of the purified glycan determined the structure to be α-d-glycero-d-manno-Hep3OMe6OMe-(1-3)-[α-GalNAcA3OMe-(1-2)-]-β-Man-(1-4)-[β-GalA3OMe4OAc6CMe-(1-4)-α-GalA-(1-2)-]-α-GalAN-(1-3)-β-GalNAc-Asn. A detailed investigation by hydrophilic interaction liquid ion chromatography-MS discovered the presence of several, less abundant glycan variants, related to but distinct from the main heptameric glycan. In addition, we confirmed that the S-layer protein is modified with the same heptameric glycan, suggesting a common N-glycosylation pathway. The M. thermolithotrophicus archaellin N-linked glycan is larger and more complex than those previously identified on the archaellins of related mesophilic methanogens, Methanococcus voltae and Methanococcus maripaludis This could indicate that the nature of the glycan modification may have a role to play in maintaining stability at elevated temperatures.
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Affiliation(s)
- John F Kelly
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada.
| | - Evgeny Vinogradov
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Jacek Stupak
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Anna C Robotham
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Susan M Logan
- Human Health Therapeutics Research Centre, National Research Council of Canada, Ottawa, Ontario, Canada
| | - Alison Berezuk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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38
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Miyata M, Robinson RC, Uyeda TQP, Fukumori Y, Fukushima SI, Haruta S, Homma M, Inaba K, Ito M, Kaito C, Kato K, Kenri T, Kinosita Y, Kojima S, Minamino T, Mori H, Nakamura S, Nakane D, Nakayama K, Nishiyama M, Shibata S, Shimabukuro K, Tamakoshi M, Taoka A, Tashiro Y, Tulum I, Wada H, Wakabayashi KI. Tree of motility - A proposed history of motility systems in the tree of life. Genes Cells 2020; 25:6-21. [PMID: 31957229 PMCID: PMC7004002 DOI: 10.1111/gtc.12737] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/27/2022]
Abstract
Motility often plays a decisive role in the survival of species. Five systems of motility have been studied in depth: those propelled by bacterial flagella, eukaryotic actin polymerization and the eukaryotic motor proteins myosin, kinesin and dynein. However, many organisms exhibit surprisingly diverse motilities, and advances in genomics, molecular biology and imaging have showed that those motilities have inherently independent mechanisms. This makes defining the breadth of motility nontrivial, because novel motilities may be driven by unknown mechanisms. Here, we classify the known motilities based on the unique classes of movement‐producing protein architectures. Based on this criterion, the current total of independent motility systems stands at 18 types. In this perspective, we discuss these modes of motility relative to the latest phylogenetic Tree of Life and propose a history of motility. During the ~4 billion years since the emergence of life, motility arose in Bacteria with flagella and pili, and in Archaea with archaella. Newer modes of motility became possible in Eukarya with changes to the cell envelope. Presence or absence of a peptidoglycan layer, the acquisition of robust membrane dynamics, the enlargement of cells and environmental opportunities likely provided the context for the (co)evolution of novel types of motility.
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Affiliation(s)
- Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Taro Q P Uyeda
- Department of Physics, Faculty of Science and Technology, Waseda University, Tokyo, Japan
| | - Yoshihiro Fukumori
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Shun-Ichi Fukushima
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Tsuyoshi Kenri
- Laboratory of Mycoplasmas and Haemophilus, Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Katsuya Shimabukuro
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Yamaguchi, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Azuma Taoka
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Isil Tulum
- Department of Botany, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Hirofumi Wada
- Department of Physics, Graduate School of Science and Engineering, Ritsumeikan University, Shiga, Japan
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
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39
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The Cell Membrane of Sulfolobus spp.-Homeoviscous Adaption and Biotechnological Applications. Int J Mol Sci 2020; 21:ijms21113935. [PMID: 32486295 PMCID: PMC7312580 DOI: 10.3390/ijms21113935] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
The microbial cell membrane is affected by physicochemical parameters, such as temperature and pH, but also by the specific growth rate of the host organism. Homeoviscous adaption describes the process of maintaining membrane fluidity and permeability throughout these environmental changes. Archaea, and thereby, Sulfolobus spp. exhibit a unique lipid composition of ether lipids, which are altered in regard to the ratio of diether to tetraether lipids, number of cyclopentane rings and type of head groups, as a coping mechanism against environmental changes. The main biotechnological application of the membrane lipids of Sulfolobus spp. are so called archaeosomes. Archaeosomes are liposomes which are fully or partly generated from archaeal lipids and harbor the potential to be used as drug delivery systems for vaccines, proteins, peptides and nucleic acids. This review summarizes the influence of environmental parameters on the cell membrane of Sulfolobus spp. and the biotechnological applications of their membrane lipids.
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40
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Tourte M, Schaeffer P, Grossi V, Oger PM. Functionalized Membrane Domains: An Ancestral Feature of Archaea? Front Microbiol 2020; 11:526. [PMID: 32296409 PMCID: PMC7137397 DOI: 10.3389/fmicb.2020.00526] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/11/2020] [Indexed: 01/06/2023] Open
Abstract
Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. A novel membrane ultrastructure predicts that monolayer and bilayer domains would be laterally segregated in the hyperthermophilic archaeon Thermococcus barophilus. With very different physico-chemical parameters of the mono- and bilayer, each domain type would thus allow the docking of different membrane proteins and express different biological functions in the membrane. To estimate the ubiquity of this putative membrane ultrastructure in and out of the order Thermococcales, we re-analyzed the core lipid composition of all the Thermococcales type species and collected all the literature data available for isolated archaea. We show that all species of Thermococcales synthesize a mixture of diether bilayer forming and tetraether monolayer forming lipids, in various ratio from 10 to 80% diether in Pyrococcus horikoshii and Thermococcus gorgonarius, respectively. Since the domain formation prediction rests only on the coexistence of di- and tetraether lipids, we show that all Thermococcales have the ability for domain formation, i.e., differential functionalization of their membrane. Extrapolating this view to the whole Archaea domain, we show that almost all archaea also have the ability to synthesize di- and tetraether lipids, which supports the view that functionalized membrane domains may be shared between all Archaea. Hence domain formation and membrane compartmentalization may have predated the separation of the three domains of life and be essential for the cell cycle.
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Affiliation(s)
- Maxime Tourte
- Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France
| | - Philippe Schaeffer
- Université de Strasbourg-CNRS, UMR 7177, Laboratoire de Biogéochimie Moléculaire, Strasbourg, France
| | - Vincent Grossi
- Université de Lyon, ENS Lyon, CNRS, Laboratoire de Géologie de Lyon, UMR 5276, Villeurbanne, France
| | - Phil M. Oger
- Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France
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41
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Beeby M, Ferreira JL, Tripp P, Albers SV, Mitchell DR. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol Rev 2020; 44:253-304. [DOI: 10.1093/femsre/fuaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.
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Affiliation(s)
- Morgan Beeby
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Josie L Ferreira
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Patrick Tripp
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA
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42
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Abstract
The bacterial flagellar motor is driven by an ion flux that is converted to torque by motor-attendant complexes known as stators. The dynamics of stator assembly around the motor in response to external stimuli have been the subject of much recent research, but less is known about the evolutionary origins of stator complexes and how they select for specific ions. Here, we review the latest structural and biochemical data for the stator complexes and compare these with other ion transporters and microbial motors to examine possible evolutionary origins of the stator complex.
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43
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High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles. Appl Environ Microbiol 2019; 85:AEM.01369-19. [PMID: 31420342 DOI: 10.1128/aem.01369-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/11/2019] [Indexed: 11/20/2022] Open
Abstract
Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.
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44
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Paithankar KS, Enderle M, Wirthensohn DC, Miller A, Schlesner M, Pfeiffer F, Rittner A, Grininger M, Oesterhelt D. Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation. Acta Crystallogr F Struct Biol Commun 2019; 75:576-585. [PMID: 31475924 PMCID: PMC6718144 DOI: 10.1107/s2053230x19010896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/04/2019] [Indexed: 12/15/2022] Open
Abstract
Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.
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Affiliation(s)
- Karthik Shivaji Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Mathias Enderle
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - David C. Wirthensohn
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Arthur Miller
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Schlesner
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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45
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Abstract
Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, Microbiology, University of Freiburg, Freiburg, Germany
| | - Alvaro Orell
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Microbiology, University of Freiburg, Freiburg, Germany.
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46
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Schult F, Le TN, Albersmeier A, Rauch B, Blumenkamp P, van der Does C, Goesmann A, Kalinowski J, Albers SV, Siebers B. Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response. Nucleic Acids Res 2019; 46:7179-7192. [PMID: 29982548 PMCID: PMC6101591 DOI: 10.1093/nar/gky527] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/30/2018] [Indexed: 12/19/2022] Open
Abstract
Exposure to UV light can result in severe DNA damage. The alternative general transcription factor (GTF) TFB3 has been proposed to play a key role in the UV stress response in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. Reporter gene assays confirmed that tfb3 is upregulated 90–180 min after UV treatment. In vivo tagging and immunodetection of TFB3 confirmed the induced expression at 90 min. Analysis of a tfb3 insertion mutant showed that genes encoding proteins of the Ups pili and the Ced DNA importer are no longer induced in a tfb3 insertion mutant after UV treatment, which was confirmed by aggregation assays. Thus, TFB3 plays a crucial role in the activation of these genes. Genome wide transcriptome analysis allowed a differentiation between a TFB3-dependent and a TFB3-independent early UV response. The TFB3-dependent UV response is characterized by the early induction of TFB3, followed by TFB3-dependent expression of genes involved in e.g. Ups pili formation and the Ced DNA importer. Many genes were downregulated in the tfb3 insertion mutant confirming the hypothesis that TFB3 acts as an activator of transcription. The TFB3-independent UV response includes the repression of nucleotide metabolism, replication and cell cycle progression in order to allow DNA repair.
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Affiliation(s)
- Frank Schult
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Thuong N Le
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schaenzlestraße 1, 79104 Freiburg, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CEBITEC), University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Bernadette Rauch
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Patrick Blumenkamp
- Institute for Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Chris van der Does
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schaenzlestraße 1, 79104 Freiburg, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CEBITEC), University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schaenzlestraße 1, 79104 Freiburg, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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47
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Nishizaka T, Masaike T, Nakane D. Insights into the mechanism of ATP-driven rotary motors from direct torque measurement. Biophys Rev 2019; 11:653-657. [PMID: 31321734 DOI: 10.1007/s12551-019-00564-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 06/20/2019] [Indexed: 11/29/2022] Open
Abstract
Motor proteins are molecular machines that convert chemical energy into mechanical work. In addition to existing studies performed on the linear motors found in eukaryotic cells, researchers in biophysics have also focused on rotary motors such as F1-ATPase. Detailed studies on the rotary F1-ATPase motor have correlated all chemical states to specific mechanical events at the single-molecule level. Recent studies showed that there exists another ATP-driven protein motor in life: the rotary machinery that rotates archaeal flagella (archaella). Rotation speed, stepwise movement, and variable directionality of the motor of Halobacterium salinarum were described in previous studies. Here we review recent experimental work discerning the molecular mechanism underlying how the archaellar motor protein FlaI drives rotation by generation of motor torque. In combination, those studies found that rotation slows as the viscous drag of markers increases, but torque remains constant at 160 pN·nm independent of rotation speed. Unexpectedly, the estimated work done in a single rotation is twice the expected energy that would come from hydrolysis of six ATP molecules in the FlaI hexamer. To reconcile the apparent contradiction, a new and general model for the mechanism of ATP-driven rotary motors is discussed.
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Affiliation(s)
- Takayuki Nishizaka
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.
| | - Tomoko Masaike
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda City, Chiba, 278-8510, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
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48
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Iwata S, Kinosita Y, Uchida N, Nakane D, Nishizaka T. Motor torque measurement of Halobacterium salinarum archaellar suggests a general model for ATP-driven rotary motors. Commun Biol 2019; 2:199. [PMID: 31149643 PMCID: PMC6534597 DOI: 10.1038/s42003-019-0422-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
It is unknown how the archaellum-the rotary propeller used by Archaea for motility-works. To further understand the molecular mechanism by which the hexameric ATPase motor protein FlaI drives rotation of the membrane-embedded archaellar motor, we determined motor torque by imposition of various loads on Halobacterium salinarum archaella. Markers of different sizes were attached to single archaella, and their trajectories were quantified using three-dimensional tracking and high-speed recording. We show that rotation slows as the viscous drag of markers increases, but torque remains constant at 160 pN·nm independent of rotation speed. Notably, the estimated work done in a single rotation is twice the expected energy that would come from hydrolysis of six ATP molecules in the hexamer, indicating that more ATP molecules are required for one rotation of archaellum. To reconcile the apparent contradiction, we suggest a new and general model for the mechanism of ATP-driven rotary motors.
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Affiliation(s)
- Seiji Iwata
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Yoshiaki Kinosita
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Nariya Uchida
- Department of Physics, Tohoku University, Sendai, 980-8578 Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
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49
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Hoffmann L, Anders K, Bischof LF, Ye X, Reimann J, Khadouma S, Pham TK, van der Does C, Wright PC, Essen LO, Albers SV. Structure and interactions of the archaeal motility repression module ArnA–ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius. J Biol Chem 2019; 294:7460-7471. [PMID: 30902813 PMCID: PMC6509490 DOI: 10.1074/jbc.ra119.007709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/20/2019] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation-dependent interactions play crucial regulatory roles in all domains of life. Forkhead-associated (FHA) and von Willebrand type A (vWA) domains are involved in several phosphorylation-dependent processes of multiprotein complex assemblies. Although well-studied in eukaryotes and bacteria, the structural and functional contexts of these domains are not yet understood in Archaea. Here, we report the structural base for such an interacting pair of FHA and vWA domain-containing proteins, ArnA and ArnB, in the thermoacidophilic archaeon Sulfolobus acidocaldarius, where they act synergistically and negatively modulate motility. The structure of the FHA domain of ArnA at 1.75 Å resolution revealed that it belongs to the subclass of FHA domains, which recognizes double-pSer/pThr motifs. We also solved the 1.5 Å resolution crystal structure of the ArnB paralog vWA2, disclosing a complex topology comprising the vWA domain, a β-sandwich fold, and a C-terminal helix bundle. We further show that ArnA binds to the C terminus of ArnB, which harbors all the phosphorylation sites identified to date and is important for the function of ArnB in archaellum regulation. We also observed that expression levels of the archaellum components in response to changes in nutrient conditions are independent of changes in ArnA and ArnB levels and that a strong interaction between ArnA and ArnB observed during growth on rich medium sequentially diminishes after nutrient limitation. In summary, our findings unravel the structural features in ArnA and ArnB important for their interaction and functional archaellum expression and reveal how nutrient conditions affect this interaction.
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Affiliation(s)
- Lena Hoffmann
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Katrin Anders
- the Philipps University, Department of Chemistry, 35032 Marburg, Germany
| | - Lisa F Bischof
- From the Institute for Biology II, Molecular Biology of Archaea and
- the Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Xing Ye
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Julia Reimann
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Sunia Khadouma
- From the Institute for Biology II, Molecular Biology of Archaea and
| | - Trong K Pham
- the ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, United Kingdom, and
| | | | - Phillip C Wright
- the Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Lars-Oliver Essen
- the Philipps University, Department of Chemistry, 35032 Marburg, Germany,
- the LOEWE Center for Synthetic Microbiology, 35043 Marburg, Germany
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50
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St John E, Flores GE, Meneghin J, Reysenbach AL. Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:262-270. [PMID: 30768760 DOI: 10.1111/1758-2229.12740] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
Ectosymbiotic Nanoarchaeota live on the surface of diverse archaeal hosts. Despite being broadly distributed in global geothermal systems, only three Nanoarchaeota have been successfully co-cultivated with their hosts, and until now no nanoarchaeotal cultures or genomes have been described from deep-sea hydrothermal vents. We recovered three nanoarchaeotal metagenome-assembled genomes (MAGs) from deep-sea hydrothermal vent sites at the Eastern Lau Spreading Center (M10-121), Guaymas Basin (Gua-46) and the Mid-Cayman Rise (MC-1). Based on average amino acid identity analysis, M10-121 is a novel species in the candidate genus Nanoclepta, while the other two MAGs represent novel genera in the Nanoarchaeota. Like previously sequenced Nanoarchaeota, each MAG encodes at least one split protein-coding gene. The MAGs also contain a mosaic of key nanoarchaeotal features, including CRISPR repeat regions and marker genes for gluconeogenesis and archaeal flagella. MC-1 also encodes the pentose bisphosphate pathway, which may allow the nanoarchaeote to bypass several steps in glycolysis and produce ATP.
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Affiliation(s)
- Emily St John
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Gilberto E Flores
- Department of Biology, California State University, Northridge, CA 91330, USA
| | - Jennifer Meneghin
- Department of Biology, Portland State University, Portland, OR 97201, USA
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