1
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Sofer S, Vershinin Z, Mashni L, Zalk R, Shahar A, Eichler J, Grossman-Haham I. Perturbed N-glycosylation of Halobacterium salinarum archaellum filaments leads to filament bundling and compromised cell motility. Nat Commun 2024; 15:5841. [PMID: 38992036 PMCID: PMC11239922 DOI: 10.1038/s41467-024-50277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024] Open
Abstract
The swimming device of archaea-the archaellum-presents asparagine (N)-linked glycans. While N-glycosylation serves numerous roles in archaea, including enabling their survival in extreme environments, how this post-translational modification contributes to cell motility remains under-explored. Here, we report the cryo-EM structure of archaellum filaments from the haloarchaeon Halobacterium salinarum, where archaellins, the building blocks of the archaellum, are N-glycosylated, and the N-glycosylation pathway is well-resolved. We further determined structures of archaellum filaments from two N-glycosylation mutant strains that generate truncated glycans and analyzed their motility. While cells from the parent strain exhibited unidirectional motility, the N-glycosylation mutant strain cells swam in ever-changing directions within a limited area. Although these mutant strain cells presented archaellum filaments that were highly similar in architecture to those of the parent strain, N-linked glycan truncation greatly affected interactions between archaellum filaments, leading to dramatic clustering of both isolated and cell-attached filaments. We propose that the N-linked tetrasaccharides decorating archaellins act as physical spacers that minimize the archaellum filament aggregation that limits cell motility.
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Affiliation(s)
- Shahar Sofer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Zlata Vershinin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Leen Mashni
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ran Zalk
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anat Shahar
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Iris Grossman-Haham
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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2
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Liu J, Eastep GN, Cvirkaite-Krupovic V, Rich-New ST, Kreutzberger MAB, Egelman EH, Krupovic M, Wang F. Two distinct archaeal type IV pili structures formed by proteins with identical sequence. Nat Commun 2024; 15:5049. [PMID: 38877064 PMCID: PMC11178852 DOI: 10.1038/s41467-024-45062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/10/2024] [Indexed: 06/16/2024] Open
Abstract
Type IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from small pilin proteins, can be many microns long and serve diverse functions, including adhesion, biofilm formation, motility, and intercellular communication. Here, we determine atomic structures of two distinct adhesive T4P from Saccharolobus islandicus via cryo-electron microscopy (cryo-EM). Unexpectedly, both pili were assembled from the same pilin polypeptide but under different growth conditions. One filament, denoted mono-pilus, conforms to canonical archaeal T4P structures where all subunits are equivalent, whereas in the other filament, the tri-pilus, the same polypeptide exists in three different conformations. The three conformations in the tri-pilus are very different from the single conformation found in the mono-pilus, and involve different orientations of the outer immunoglobulin-like domains, mediated by a very flexible linker. Remarkably, the outer domains rotate nearly 180° between the mono- and tri-pilus conformations. Both forms of pili require the same ATPase and TadC-like membrane pore for assembly, indicating that the same secretion system can produce structurally very different filaments. Our results show that the structures of archaeal T4P appear to be less constrained and rigid than those of the homologous archaeal flagellar filaments that serve as helical propellers.
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Affiliation(s)
- Junfeng Liu
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Gunnar N Eastep
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Shane T Rich-New
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France.
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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3
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Gaines MC, Sivabalasarma S, Isupov MN, Haque RU, McLaren M, Hanus C, Gold VAM, Albers SV, Daum B. CryoEM reveals the structure of an archaeal pilus involved in twitching motility. Nat Commun 2024; 15:5050. [PMID: 38877033 PMCID: PMC11178815 DOI: 10.1038/s41467-024-45831-w] [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: 08/08/2023] [Accepted: 02/02/2024] [Indexed: 06/16/2024] Open
Abstract
Amongst the major types of archaeal filaments, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). Within Sulfolobales, member species encode for three types of T4P, namely the archaellum, the UV-inducible pilus system (Ups) and the archaeal adhesive pilus (Aap). Whereas the archaellum functions primarily in swimming motility, and the Ups in UV-induced cell aggregation and DNA-exchange, the Aap plays an important role in adhesion and twitching motility. Here, we present a cryoEM structure of the Aap of the archaeal model organism Sulfolobus acidocaldarius. We identify the component subunit as AapB and find that while its structure follows the canonical T4P blueprint, it adopts three distinct conformations within the pilus. The tri-conformer Aap structure that we describe challenges our current understanding of pilus structure and sheds new light on the principles of twitching motility.
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Affiliation(s)
- Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Shamphavi Sivabalasarma
- Institute of Biology, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Risat Ul Haque
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK
| | - Sonja-Verena Albers
- Institute of Biology, Molecular Biology of Archaea, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBBS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, UK.
- Department of Biosciences, Faculty of Health and Life Sciences, Exeter, UK.
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4
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Gaisin VA, van Wolferen M, Albers SV, Pilhofer M. Distinct life cycle stages of an ectosymbiotic DPANN archaeon. THE ISME JOURNAL 2024; 18:wrae076. [PMID: 38691426 PMCID: PMC11104419 DOI: 10.1093/ismejo/wrae076] [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: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell-cell interactions remains largely unknown. We applied live-cell imaging and cryo-electron tomography to the DPANN archaeon Nanobdella aerobiophila and its host, revealing two distinct life cycle stages. Free cells possess archaella and are motile. Ectobiotic cells are intimately linked with the host through an elaborate attachment organelle. Our data suggest that free cells may actively seek a new host, while the ectobiotic state is adapted to mediate intricate interaction with the host.
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Affiliation(s)
- Vasil A Gaisin
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
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5
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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6
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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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7
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Liu J, Eastep GN, Cvirkaite-Krupovic V, Rich-New ST, Kreutzberger MAB, Egelman EH, Krupovic M, Wang F. Two dramatically distinct archaeal type IV pili structures formed by the same pilin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.07.552285. [PMID: 37609343 PMCID: PMC10441282 DOI: 10.1101/2023.08.07.552285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Type IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from relatively small pilin proteins, can be many microns long and serve diverse functions, including adhesion, biofilm formation, motility, and intercellular communication. Using cryo-electron microscopy (cryo-EM), we determined atomic structures of two dramatically different T4P from Saccharolobus islandicus REY15A. Unexpectedly, both pili were assembled from the same pilin protein but under different growth conditions. One filament, denoted mono-pilus, conforms to canonical archaeal T4P structures where all subunits are equivalent, whereas in the other filament, the tri-pilus, the same protein exists in three different conformations. The three conformations involve different orientations of the outer immunoglobulin (Ig)-like domains, mediated by a very flexible linker, and all three of these conformations are very different from the single conformation found in the mono-pilus. Remarkably, the outer domains rotate nearly 180° between the mono- and tri-pilus conformations, formally similar to what has been shown for outer domains in bacterial flagellar filaments, despite lack of homology between bacterial flagella and archaeal T4P. Interestingly, both forms of pili require the same ATPase and TadC-like membrane pore for assembly, indicating that the same secretion system can produce structurally very different filaments. However, the expression of the ATPase and TadC genes was significantly different under the conditions yielding mono- and tri-pili. While archaeal T4P are homologs of archaeal flagellar filaments, our results show that in contrast to the rigid supercoil that the flagellar filaments must adopt to serve as helical propellers, archaeal T4P are likely to have fewer constraints on their structure and enjoy more internal degrees of freedom.
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8
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Kreutzberger MAB, Cvirkaite-Krupovic V, Liu Y, Baquero DP, Liu J, Sonani RR, Calladine CR, Wang F, Krupovic M, Egelman EH. The evolution of archaeal flagellar filaments. Proc Natl Acad Sci U S A 2023; 120:e2304256120. [PMID: 37399404 PMCID: PMC10334743 DOI: 10.1073/pnas.2304256120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/08/2023] [Indexed: 07/05/2023] Open
Abstract
Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from Pyrobaculum calidifontis with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
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Affiliation(s)
- Mark A. B. Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | | | - Ying Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Diana P. Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Junfeng Liu
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Ravi R. Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | - Chris R. Calladine
- Department of Engineering, University of Cambridge, CambridgeCB2 1PZ, United Kingdom
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris75015, France
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
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9
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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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Gambelli L, Isupov M, Daum B. Escaping the symmetry trap in helical reconstruction. Faraday Discuss 2022; 240:303-311. [PMID: 35929538 PMCID: PMC9642006 DOI: 10.1039/d2fd00051b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Helical reconstruction is the method of choice for obtaining 3D structures of filaments from electron cryo-microscopy (cryoEM) projections. This approach relies on applying helical symmetry parameters deduced from Fourier-Bessel or real space analysis, such as sub-tomogram averaging. While helical reconstruction continues to provide invaluable structural insights into filaments, its inherent dependence on imposing a pre-defined helical symmetry can also introduce bias. The applied helical symmetry produces structures that are infinitely straight along the filament's axis and can average out biologically important heterogeneities. Here, we describe a simple workflow aimed at overcoming these drawbacks in order to provide truer representations of filamentous structures.
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Affiliation(s)
- Lavinia Gambelli
- College of Engineering, Mathematics and Physical Sciences, University of ExeterExeterEX4 4QFUK,Living Systems Institute, University of ExeterExeterEX4 4QDUK
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of ExeterExeterEX4 4QDUK
| | - Bertram Daum
- Living Systems Institute, University of ExeterExeterEX4 4QDUK,College of Life and Environmental Sciences, University of ExeterExeterEX4 4QDUK
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11
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Abstract
Flagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli, Pyrococcus furiosus, and Chlamydomonas reinhardtii. Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature yield flagellar costs for another ~200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole-cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum.
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Affiliation(s)
- Paul E Schavemaker
- Biodesign Center for Mechanisms of Evolution, Arizona State UniversityTempeUnited States
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State UniversityTempeUnited States
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12
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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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13
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Ortega D, Beeby M. How Did the Archaellum Get Its Rotation? Front Microbiol 2022; 12:803720. [PMID: 35558523 PMCID: PMC9087265 DOI: 10.3389/fmicb.2021.803720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
How new functions evolve fascinates many evolutionary biologists. Particularly captivating is the evolution of rotation in molecular machines, as it evokes familiar machines that we have made ourselves. The archaellum, an archaeal analog of the bacterial flagellum, is one of the simplest rotary motors. It features a long helical propeller attached to a cell envelope-embedded rotary motor. Satisfyingly, the archaellum is one of many members of the large type IV filament superfamily, which includes pili, secretion systems, and adhesins, relationships that promise clues as to how the rotating archaellum evolved from a non-rotary ancestor. Nevertheless, determining exactly how the archaellum got its rotation remains frustratingly elusive. Here we review what is known about how the archaellum got its rotation, what clues exist, and what more is needed to address this question.
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Affiliation(s)
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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14
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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: 8] [Impact Index Per Article: 4.0] [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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15
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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: 17] [Impact Index Per Article: 8.5] [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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16
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Umrekar TR, Winterborn YB, Sivabalasarma S, Brantl J, Albers SV, Beeby M. Evolution of Archaellum Rotation Involved Invention of a Stator Complex by Duplicating and Modifying a Core Component. Front Microbiol 2021; 12:773386. [PMID: 34912317 PMCID: PMC8667602 DOI: 10.3389/fmicb.2021.773386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 11/14/2022] Open
Abstract
Novelty in biology can arise from opportunistic repurposing of nascent characteristics of existing features. Understanding how this process happens at the molecular scale, however, suffers from a lack of case studies. The evolutionary emergence of rotary motors is a particularly clear example of evolution of a new function. The simplest of rotary motors is the archaellum, a molecular motor that spins a helical propeller for archaeal motility analogous to the bacterial flagellum. Curiously, emergence of archaellar rotation may have pivoted on the simple duplication and repurposing of a pre-existing component to produce a stator complex that anchors to the cell superstructure to enable productive rotation of the rotor component. This putative stator complex is composed of ArlF and ArlG, gene duplications of the filament component ArlB, providing an opportunity to study how gene duplication and neofunctionalization contributed to the radical innovation of rotary function. Toward understanding how this happened, we used electron cryomicroscopy to determine the structure of isolated ArlG filaments, the major component of the stator complex. Using a hybrid modeling approach incorporating structure prediction and validation, we show that ArlG filaments are open helices distinct to the closed helical filaments of ArlB. Curiously, further analysis reveals that ArlG retains a subset of the inter-protomer interactions of homologous ArlB, resulting in a superficially different assembly that nevertheless reflects the common ancestry of the two structures. This relatively simple mechanism to change quaternary structure was likely associated with the evolutionary neofunctionalization of the archaellar stator complex, and we speculate that the relative deformable elasticity of an open helix may facilitate elastic energy storage during the transmission of the discrete bursts of energy released by ATP hydrolysis to continuous archaellar rotation, allowing the inherent properties of a duplicated ArlB to be co-opted to fulfill a new role. Furthermore, agreement of diverse experimental evidence in our work supports recent claims to the power of new structure prediction techniques.
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Affiliation(s)
- Trishant R. Umrekar
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - 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
| | - Julian Brantl
- Molecular Biology of Archaea, Faculty of Biology, Institute of Biology II, 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
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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17
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Ehsan M, Wang H, Cecchetti C, Mortensen JS, Du Y, Hariharan P, Nygaard A, Lee HJ, Ghani L, Guan L, Loland CJ, Byrne B, Kobilka BK, Chae PS. Maltose-bis(hydroxymethyl)phenol (MBPs) and Maltose-tris(hydroxymethyl)phenol (MTPs) Amphiphiles for Membrane Protein Stability. ACS Chem Biol 2021; 16:1779-1790. [PMID: 34445864 DOI: 10.1021/acschembio.1c00578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Membrane protein structures provide a fundamental understanding of their molecular actions and are of importance for drug development. Detergents are widely used to solubilize, stabilize, and crystallize membrane proteins, but membrane proteins solubilized in conventional detergents are prone to denaturation and aggregation. Thus, developing novel detergents with enhanced efficacy for protein stabilization remains important. We report herein the design and synthesis of a class of phenol-derived maltoside detergents. Using two different linkers, we prepared two sets of new detergents, designated maltose-bis(hydroxymethyl)phenol (MBPs) and maltose-tris(hydroxymethyl)phenol (MTPs). The evaluation of these detergents with three transporters and two G-protein coupled receptors allowed us to identify a couple of new detergents (MBP-C9 and MTP-C12) that consistently conferred enhanced stability to all tested proteins compared to a gold standard detergent (DDM). Furthermore, the data analysis based on the detergent structures provides key detergent features responsible for membrane protein stabilization that together will facilitate the future design of novel detergents.
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Affiliation(s)
- Muhammad Ehsan
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jonas S. Mortensen
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Yang Du
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Andreas Nygaard
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ho Jin Lee
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Lubna Ghani
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, California 94305, United States
| | - Pil Seok Chae
- Department of Bionano Engineering, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 155-88, South Korea
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18
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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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19
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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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20
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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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21
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Clarkson SM, Haja DK, Adams MWW. The hyperthermophilic archaeon Pyrococcus furiosus utilizes environmental iron sulfide cluster complexes as an iron source. Extremophiles 2021; 25:249-256. [PMID: 33779854 DOI: 10.1007/s00792-021-01224-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/10/2021] [Indexed: 11/27/2022]
Abstract
Iron is an essential nutrient for almost all known organisms, but in aerobic, neutral pH environments, it is present primarily as precipitated oxyhydroxide minerals. In contrast, in anaerobic environments, iron can exist in its ferrous form (Fe2+) and remain soluble. In sulfide-rich, anaerobic environments, Fe2+ and sulfide react to form iron sulfide cluster complexes of the form FexSx (FeSaq), which further condense to form the mineral mackinawite, which itself is partly soluble. However, the ability of microorganisms to utilize iron sulfide as an iron source is not known. Here, we show that the anaerobic, hyperthermophilic archaeon Pyrococcus furiosus can directly assimilate the iron in dissolved iron sulfide cluster complexes (FeSaq) without further dissolution to Fe2+. Growth is only inhibited in the presence of a Fe2+-specific chelator. The FeSaq that is utilized can be formed either by reaction of chelated Fe2+ with sulfide or dissolved from mackinawite. Pyrococcus furiosus can utilize FeSaq larger than 3.5 kDa, or Fe40S40, and may actively aid in the dissolution of mackinawite to the assimilated FeSaq. A model for iron sulfide assimilation from an insoluble mineral is proposed.
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Affiliation(s)
- Sonya M Clarkson
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Bldg, Athens, GA, 30602-7229, USA
- Conagen Inc, Bedford, MA, 01730, USA
| | - Dominik K Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Bldg, Athens, GA, 30602-7229, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Bldg, Athens, GA, 30602-7229, USA.
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22
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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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23
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Nußbaum P, Ithurbide S, Walsh JC, Patro M, Delpech F, Rodriguez-Franco M, Curmi PMG, Duggin IG, Quax TEF, Albers SV. An Oscillating MinD Protein Determines the Cellular Positioning of the Motility Machinery in Archaea. Curr Biol 2020; 30:4956-4972.e4. [PMID: 33125862 DOI: 10.1016/j.cub.2020.09.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/28/2020] [Accepted: 09/23/2020] [Indexed: 01/14/2023]
Abstract
MinD proteins are well studied in rod-shaped bacteria such as E. coli, where they display self-organized pole-to-pole oscillations that are important for correct positioning of the Z-ring at mid-cell for cell division. Archaea also encode proteins belonging to the MinD family, but their functions are unknown. MinD homologous proteins were found to be widespread in Euryarchaeota and form a sister group to the bacterial MinD family, distinct from the ParA and other related ATPase families. We aimed to identify the function of four archaeal MinD proteins in the model archaeon Haloferax volcanii. Deletion of the minD genes did not cause cell division or size defects, and the Z-ring was still correctly positioned. Instead, one of the deletions (ΔminD4) reduced swimming motility and hampered the correct formation of motility machinery at the cell poles. In ΔminD4 cells, there is reduced formation of the motility structure and chemosensory arrays, which are essential for signal transduction. In bacteria, several members of the ParA family can position the motility structure and chemosensory arrays via binding to a landmark protein, and consequently these proteins do not oscillate along the cell axis. However, GFP-MinD4 displayed pole-to-pole oscillation and formed polar patches or foci in H. volcanii. The MinD4 membrane-targeting sequence (MTS), homologous to the bacterial MinD MTS, was essential for the oscillation. Surprisingly, mutant MinD4 proteins failed to form polar patches. Thus, MinD4 from H. volcanii combines traits of different bacterial ParA/MinD proteins.
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Affiliation(s)
- Phillip Nußbaum
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Solenne Ithurbide
- The ithree institute, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - James C Walsh
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, NSW 2052, Australia
| | - Megha Patro
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Floriane Delpech
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Marta Rodriguez-Franco
- Cell Biology, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Paul M G Curmi
- School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Iain G Duggin
- The ithree institute, University of Technology, Sydney, Ultimo, NSW 2007, Australia.
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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24
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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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25
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The structures of two archaeal type IV pili illuminate evolutionary relationships. Nat Commun 2020; 11:3424. [PMID: 32647180 PMCID: PMC7347861 DOI: 10.1038/s41467-020-17268-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
We have determined the cryo-electron microscopic (cryo-EM) structures of two archaeal type IV pili (T4P), from Pyrobaculum arsenaticum and Saccharolobus solfataricus, at 3.8 Å and 3.4 Å resolution, respectively. This triples the number of high resolution archaeal T4P structures, and allows us to pinpoint the evolutionary divergence of bacterial T4P, archaeal T4P and archaeal flagellar filaments. We suggest that extensive glycosylation previously observed in T4P of Sulfolobus islandicus is a response to an acidic environment, as at even higher temperatures in a neutral environment much less glycosylation is present for Pyrobaculum than for Sulfolobus and Saccharolobus pili. Consequently, the Pyrobaculum filaments do not display the remarkable stability of the Sulfolobus filaments in vitro. We identify the Saccharolobus and Pyrobaculum T4P as host receptors recognized by rudivirus SSRV1 and tristromavirus PFV2, respectively. Our results illuminate the evolutionary relationships among bacterial and archaeal T4P filaments and provide insights into archaeal virus-host interactions. Archaeal type IV pili (T4P) mediate adhesion to surfaces and are receptors for hyperthermophilic archaeal viruses. Here, the authors present the cryo-EM structures of two archaeal T4P from Pyrobaculum arsenaticum and Saccharolobus solfataricus and discuss evolutionary relationships between bacterial T4P, archaeal T4P and archaeal flagellar filaments.
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26
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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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27
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Neuhaus A, Selvaraj M, Salzer R, Langer JD, Kruse K, Kirchner L, Sanders K, Daum B, Averhoff B, Gold VAM. Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium. Nat Commun 2020; 11:2231. [PMID: 32376942 PMCID: PMC7203116 DOI: 10.1038/s41467-020-15650-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus ('wide' and 'narrow'), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility.
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Affiliation(s)
- Alexander Neuhaus
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Muniyandi Selvaraj
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Laboratory of Structural Biology, Helsinki Institute of Life Science, 00014 University of Helsinki, Helsinki, Finland
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
- Structural Studies Division, Medical Research Council-Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Max-von-Laue Str. 4, 60438, Frankfurt am Main, Germany
| | - Kerstin Kruse
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Lennart Kirchner
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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28
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Pyatibratov MG, Syutkin AS, Quax TEF, Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV. Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum. Microbiologyopen 2020; 9:e1047. [PMID: 32352651 PMCID: PMC7349177 DOI: 10.1002/mbo3.1047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/23/2020] [Accepted: 03/28/2020] [Indexed: 12/24/2022] Open
Abstract
Halophilic archaea from the genus Halorubrum possess two extraordinarily diverged archaellin genes, flaB1 and flaB2. To clarify roles for each archaellin, we compared two natural Halorubrum lacusprofundi strains: One of them contains both archaellin genes, and the other has the flaB2 gene only. Both strains synthesize functional archaella; however, the strain, where both archaellins are present, is more motile. In addition, we expressed these archaellins in a Haloferax volcanii strain from which the endogenous archaellin genes were deleted. Three Hfx. volcanii strains expressing Hrr. lacusprofundi archaellins produced functional filaments consisting of only one (FlaB1 or FlaB2) or both (FlaB1/FlaB2) archaellins. All three strains were motile, although there were profound differences in the efficiency of motility. Both native and recombinant FlaB1/FlaB2 filaments have greater thermal stability and resistance to low salinity stress than single‐component filaments. Functional supercoiled Hrr. lacusprofundi archaella can be composed of either single archaellin: FlaB2 or FlaB1; however, the two divergent archaellin subunits provide additional stabilization to the archaellum structure and thus adaptation to a wider range of external conditions. Comparative genomic analysis suggests that the described combination of divergent archaellins is not restricted to Hrr. lacusprofundi, but is occurring also in organisms from other haloarchaeal genera.
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Affiliation(s)
- Mikhail G Pyatibratov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey S Syutkin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Tatjana N Melnik
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Pushchino Branch, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,State Research Center for Applied Microbiology & Biotechnology, Obolensk, Moscow Region, Russia
| | - Sergei N Beznosov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anna V Galeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oleg V Fedorov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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29
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Effect of changes at the conserved + 3 position of mature archaellins on in vitro cleavage by the pre-archaellin peptidase FlaK of Methanococcus maripaludis. Arch Microbiol 2020; 202:1669-1675. [PMID: 32285165 DOI: 10.1007/s00203-020-01873-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/28/2020] [Accepted: 04/01/2020] [Indexed: 10/24/2022]
Abstract
Archaea swim using archaella that are domain-specific rotary type IV pilus-like appendages. The structural components of the archaellum filament are archaellins, initially made as preproteins with type IV pilin-like signal peptides which are removed by signal peptidases that are homologues of prepilin peptidases that remove signal peptides from type IV pilins. N-terminal sequences of archaellins, including the signal peptide cleavage site, are conserved and various positions have been previously shown to be critical for signal peptide removal. Archaellins have an absolute conservation of glycine at the + 3 position from the signal peptide cleavage site. To investigate its role in signal peptide cleavage, I used archaellin variants in which the + 3 glycine was mutated to all other possibilities in in vitro cleavage reactions. Cleavage was observed with ten different amino acids at the + 3 position, indicating that the observed glycine conservation is not required for this essential processing step.
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30
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Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient. Proc Natl Acad Sci U S A 2020; 117:8941-8947. [PMID: 32241888 PMCID: PMC7183148 DOI: 10.1073/pnas.1916935117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In order to understand the evolution of complex biological machines like the bacterial flagellar motor, it is crucial to know what each component does and when it arose. Here, we show that a subcomplex of the motor thought to act as a bushing for the spinning motor likely also serves another function—it plugs the hole in the outer membrane left when the flagellum disassembles. Moreover, this component and function is ancient, since it appears in diverse phyla without evidence of recent gene transfer. The bacterial flagellum is an amazing nanomachine. Understanding how such complex structures arose is crucial to our understanding of cellular evolution. We and others recently reported that in several Gammaproteobacterial species, a relic subcomplex comprising the decorated P and L rings persists in the outer membrane after flagellum disassembly. Imaging nine additional species with cryo-electron tomography, here, we show that this subcomplex persists after flagellum disassembly in other phyla as well. Bioinformatic analyses fail to show evidence of any recent horizontal transfers of the P- and L-ring genes, suggesting that this subcomplex and its persistence is an ancient and conserved feature of the flagellar motor. We hypothesize that one function of the P and L rings is to seal the outer membrane after motor disassembly.
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31
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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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32
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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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33
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The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility. Nat Microbiol 2019; 5:216-225. [PMID: 31844299 DOI: 10.1038/s41564-019-0622-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 10/23/2019] [Indexed: 11/08/2022]
Abstract
Motility structures are vital in all three domains of life. In Archaea, motility is mediated by the archaellum, a rotating type IV pilus-like structure that is a unique nanomachine for swimming motility in nature. Whereas periplasmic FlaF binds the surface layer (S-layer), the structure, assembly and roles of other periplasmic components remain enigmatic, limiting our knowledge of the archaellum's functional interactions. Here, we find that the periplasmic protein FlaG and the association with its paralogue FlaF are essential for archaellation and motility. Therefore, we determine the crystal structure of Sulfolobus acidocaldarius soluble FlaG (sFlaG), which reveals a β-sandwich fold resembling the S-layer-interacting FlaF soluble domain (sFlaF). Furthermore, we solve the sFlaG2-sFlaF2 co-crystal structure, define its heterotetrameric complex in solution by small-angle X-ray scattering and find that mutations that disrupt the complex abolish motility. Interestingly, the sFlaF and sFlaG of Pyrococcus furiosus form a globular complex, whereas sFlaG alone forms a filament, indicating that FlaF can regulate FlaG filament assembly. Strikingly, Sulfolobus cells that lack the S-layer component bound by FlaF assemble archaella but cannot swim. These collective results support a model where a FlaG filament capped by a FlaG-FlaF complex anchors the archaellum to the S-layer to allow motility.
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34
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Architecture and modular assembly of Sulfolobus S-layers revealed by electron cryotomography. Proc Natl Acad Sci U S A 2019; 116:25278-25286. [PMID: 31767763 PMCID: PMC6911244 DOI: 10.1073/pnas.1911262116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Many bacteria and most archaea are enveloped in S-layers, protective lattices of proteins that are among the most abundant on earth. S-layers define both the cell’s shape and periplasmic space, and play essential roles in cell division, adhesion, biofilm formation, protection against harsh environments and phages, and comprise important virulence factors in pathogenic bacteria. Despite their importance, structural information about archaeal S-layers is sparse. Here, we describe in situ structural data on archaeal S-layers by cutting-edge electron cryotomography. Our results shed light on the function and evolution of archaeal cell walls and thus our understanding of microbial life. They will also inform approaches in nanobiotechnology aiming to engineer S-layers for a vast array of applications. Surface protein layers (S-layers) often form the only structural component of the archaeal cell wall and are therefore important for cell survival. S-layers have a plethora of cellular functions including maintenance of cell shape, osmotic, and mechanical stability, the formation of a semipermeable protective barrier around the cell, and cell–cell interaction, as well as surface adhesion. Despite the central importance of S-layers for archaeal life, their 3-dimensional (3D) architecture is still poorly understood. Here we present detailed 3D electron cryomicroscopy maps of archaeal S-layers from 3 different Sulfolobus strains. We were able to pinpoint the positions and determine the structure of the 2 subunits SlaA and SlaB. We also present a model describing the assembly of the mature S-layer.
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35
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McCallum M, Benlekbir S, Nguyen S, Tammam S, Rubinstein JL, Burrows LL, Howell PL. Multiple conformations facilitate PilT function in the type IV pilus. Nat Commun 2019; 10:5198. [PMID: 31729381 PMCID: PMC6858323 DOI: 10.1038/s41467-019-13070-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Type IV pilus-like systems are protein complexes that polymerize pilin fibres. They are critical for virulence in many bacterial pathogens. Pilin polymerization and depolymerization are powered by motor ATPases of the PilT/VirB11-like family. This family is thought to operate with C2 symmetry; however, most of these ATPases crystallize with either C3 or C6 symmetric conformations. The relevance of these conformations is unclear. Here, we determine the X-ray structures of PilT in four unique conformations and use these structures to classify the conformation of available PilT/VirB11-like family member structures. Single particle electron cryomicroscopy (cryoEM) structures of PilT reveal condition-dependent preferences for C2, C3, and C6 conformations. The physiologic importance of these conformations is validated by coevolution analysis and functional studies of point mutants, identifying a rare gain-of-function mutation that favours the C2 conformation. With these data, we propose a comprehensive model of PilT function with broad implications for PilT/VirB11-like family members.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Samir Benlekbir
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Sheryl Nguyen
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Stephanie Tammam
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - John L Rubinstein
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1l7, Canada.
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - P Lynne Howell
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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36
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Abstract
Cells from all three domains of life on Earth utilize motile macromolecular devices that protrude from the cell surface to generate forces that allow them to swim through fluid media. Research carried out on archaea during the past decade or so has led to the recognition that, despite their common function, the motility devices of the three domains display fundamental differences in their properties and ancestry, reflecting a striking example of convergent evolution. Thus, the flagella of bacteria and the archaella of archaea employ rotary filaments that assemble from distinct subunits that do not share a common ancestor and generate torque using energy derived from distinct fuel sources, namely chemiosmotic ion gradients and FlaI motor-catalyzed ATP hydrolysis, respectively. The cilia of eukaryotes, however, assemble via kinesin-2-driven intraflagellar transport and utilize microtubules and ATP-hydrolyzing dynein motors to beat in a variety of waveforms via a sliding filament mechanism. Here, with reference to current structural and mechanistic information about these organelles, we briefly compare the evolutionary origins, assembly and tactic motility of archaella, flagella and cilia.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Jonathan M Scholey
- Department of Molecular and Cell Biology, University of California @ Davis, CA 95616, USA.
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37
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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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38
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Otegui MS, Pennington JG. Electron tomography in plant cell biology. Microscopy (Oxf) 2019; 68:69-79. [PMID: 30452668 DOI: 10.1093/jmicro/dfy133] [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: 08/30/2018] [Revised: 10/15/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Electron tomography (ET) approaches are based on the imaging of a biological specimen at different tilt angles by transmission electron microscopy (TEM). ET can be applied to both plastic-embedded and frozen samples. Technological advancements in TEM, direct electron detection, automated image collection, and imaging processing algorithms allow for 2-7-nm scale axial resolution in tomographic reconstructions of cells and organelles. In this review, we discussed the application of ET in plant cell biology and new opportunities for imaging plant cells by cryo-ET and other 3D electron microscopy approaches.
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Affiliation(s)
- Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison WI, USA.,Laboratory of Molecular and Cellular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison WI, USA.,Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison WI, USA
| | - Jannice G Pennington
- Institute for Molecular Virology, University of Wisconsin-Madison, 1525 Linden Drive, Madison WI, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, USA
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39
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Grünberger F, Reichelt R, Bunk B, Spröer C, Overmann J, Rachel R, Grohmann D, Hausner W. Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of the Pyrococcus furiosus DSM 3638 Genome and Provide Insights Into Archaeal Antisense Transcription. Front Microbiol 2019; 10:1603. [PMID: 31354685 PMCID: PMC6640164 DOI: 10.3389/fmicb.2019.01603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/26/2019] [Indexed: 01/07/2023] Open
Abstract
Pyrococcus furiosus DSM 3638 is a model organism for hyperthermophilic archaea with an optimal growth temperature near 100°C. The genome was sequenced about 18 years ago. However, some publications suggest that in contrast to other Pyrococcus species, the genome of P. furiosus DSM 3638 is prone to genomic rearrangements. Therefore, we re-sequenced the genome using third generation sequencing techniques. The new de novo assembled genome is 1,889,914 bp in size and exhibits high sequence identity to the published sequence. However, two major deviations were detected: (1) The genome is 18,342 bp smaller than the NCBI reference genome due to a recently described deletion. (2) The region between PF0349 and PF0388 is inverted most likely due an assembly problem for the original sequence. In addition, numerous minor variations, ranging from single nucleotide exchanges, deletions or insertions were identified. The total number of insertion sequence (IS) elements is also reduced from 30 to 24 in the new sequence. Re-sequencing of a 2-year-old “lab culture” using Nanopore sequencing confirmed the overall stability of the P. furiosus DSM 3638 genome even under normal lab conditions without taking any special care. To improve genome annotation, the updated DNA sequence was combined with an RNA sequencing approach. Here, RNAs from eight different growth conditions were pooled to increase the number of detected transcripts. Furthermore, a differential RNA-Seq approach was employed for the identification of transcription start sites (TSSs). In total, 2515 TSSs were detected and classified into 834 primary (pTSS), 797 antisense (aTSS), 739 internal and 145 secondary TSSs. Our analysis of the upstream regions revealed a well conserved archaeal promoter structure. Interrogation of the distances between pTSSs and aTSSs revealed a significant number of antisense transcripts, which are a result of bidirectional transcription from the same TATA box. This mechanism of antisense transcript production could be further confirmed by in vitro transcription experiments. We assume that bidirectional transcription gives rise to non-functional antisense RNAs and that this is a widespread phenomenon in archaea due to the architecture of the TATA element and the symmetric structure of the TATA-binding protein.
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Affiliation(s)
- Felix Grünberger
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Reinhard Rachel
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
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40
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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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41
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Wang F, Cvirkaite-Krupovic V, Kreutzberger MAB, Su Z, de Oliveira GAP, Osinski T, Sherman N, DiMaio F, Wall JS, Prangishvili D, Krupovic M, Egelman EH. An extensively glycosylated archaeal pilus survives extreme conditions. Nat Microbiol 2019; 4:1401-1410. [PMID: 31110358 PMCID: PMC6656605 DOI: 10.1038/s41564-019-0458-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 04/15/2019] [Indexed: 11/09/2022]
Abstract
Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these extracellular appendages to a very harsh environment. The pili, when removed from cells, resist digestion by trypsin or pepsin, and survive boiling in sodium dodecyl sulfate or 5 M guanidine hydrochloride. We used electron cryo-microscopy to determine the structure of these filaments at 4.1 Å resolution. An atomic model was built by combining the electron density map with bioinformatics without previous knowledge of the pilin sequence-an approach that should prove useful for assemblies where all of the components are not known. The atomic structure of the pilus was unusual, with almost one-third of the residues being either threonine or serine, and with many hydrophobic surface residues. While the map showed extra density consistent with glycosylation for only three residues, mass measurements suggested extensive glycosylation. We propose that this extensive glycosylation renders these filaments soluble and provides the remarkable structural stability. We also show that the overall fold of the archaeal pilin is remarkably similar to that of archaeal flagellin, establishing common evolutionary origins.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | | | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | | | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Nicholas Sherman
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - David Prangishvili
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France
| | - Mart Krupovic
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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42
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Abstract
Archaea are ubiquitous single cellular microorganisms that play important ecological roles in nature. The intracellular organization of archaeal cells is among the unresolved mysteries of archaeal biology. With this work, we show that cells of haloarchaea are polarized. The cellular positioning of proteins involved in chemotaxis and motility is spatially and temporally organized in these cells. This suggests the presence of a specific mechanism responsible for the positioning of macromolecular protein complexes in archaea. Bacteria and archaea exhibit tactical behavior and can move up and down chemical gradients. This tactical behavior relies on a motility structure, which is guided by a chemosensory system. Environmental signals are sensed by membrane-inserted chemosensory receptors that are organized in large ordered arrays. While the cellular positioning of the chemotaxis machinery and that of the flagellum have been studied in detail in bacteria, we have little knowledge about the localization of such macromolecular assemblies in archaea. Although the archaeal motility structure, the archaellum, is fundamentally different from the flagellum, archaea have received the chemosensory machinery from bacteria and have connected this system with the archaellum. Here, we applied a combination of time-lapse imaging and fluorescence and electron microscopy using the model euryarchaeon Haloferax volcanii and found that archaella were specifically present at the cell poles of actively dividing rod-shaped cells. The chemosensory arrays also had a polar preference, but in addition, several smaller arrays moved freely in the lateral membranes. In the stationary phase, rod-shaped cells became round and chemosensory arrays were disassembled. The positioning of archaella and that of chemosensory arrays are not interdependent and likely require an independent form of positioning machinery. This work showed that, in the rod-shaped haloarchaeal cells, the positioning of the archaellum and of the chemosensory arrays is regulated in time and in space. These insights into the cellular organization of H. volcanii suggest the presence of an active mechanism responsible for the positioning of macromolecular protein complexes in archaea.
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43
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Meshcheryakov VA, Shibata S, Schreiber MT, Villar-Briones A, Jarrell KF, Aizawa SI, Wolf M. High-resolution archaellum structure reveals a conserved metal-binding site. EMBO Rep 2019; 20:embr.201846340. [PMID: 30898768 PMCID: PMC6500986 DOI: 10.15252/embr.201846340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 02/16/2019] [Accepted: 02/27/2019] [Indexed: 01/09/2023] Open
Abstract
Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are related to archaeal and bacterial type IV pili. Despite recent advances, our understanding of molecular processes governing archaellum assembly and stability is still incomplete. Here, we determine the structures of Methanococcus archaella by X‐ray crystallography and cryo‐EM. The crystal structure of Methanocaldococcus jannaschii FlaB1 is the first and only crystal structure of any archaellin to date at a resolution of 1.5 Å, which is put into biological context by a cryo‐EM reconstruction from Methanococcus maripaludis archaella at 4 Å resolution created with helical single‐particle analysis. Our results indicate that the archaellum is predominantly composed of FlaB1. We identify N‐linked glycosylation by cryo‐EM and mass spectrometry. The crystal structure reveals a highly conserved metal‐binding site, which is validated by mass spectrometry and electron energy‐loss spectroscopy. We show in vitro that the metal‐binding site, which appears to be a widespread property of archaellin, is required for filament integrity.
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Affiliation(s)
- Vladimir A Meshcheryakov
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Makoto Tokoro Schreiber
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Alejandro Villar-Briones
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
| | - Kenneth F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Kunigami, Okinawa, Japan
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44
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Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
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Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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45
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Syutkin AS, van Wolferen M, Surin AK, Albers SV, Pyatibratov MG, Fedorov OV, Quax TEF. Salt-dependent regulation of archaellins in Haloarcula marismortui. Microbiologyopen 2018; 8:e00718. [PMID: 30270530 PMCID: PMC6528647 DOI: 10.1002/mbo3.718] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/26/2022] Open
Abstract
Microorganisms require a motility structure to move towards optimal growth conditions. The motility structure from archaea, the archaellum, is fundamentally different from its bacterial counterpart, the flagellum, and is assembled in a similar fashion as type IV pili. The archaellum filament consists of thousands of copies of N‐terminally processed archaellin proteins. Several archaea, such as the euryarchaeon Haloarcula marismortui, encode multiple archaellins. Two archaellins of H. marismortui display differential stability under various ionic strengths. This suggests that these proteins behave as ecoparalogs and perform the same function under different environmental conditions. Here, we explored this intriguing system to study the differential regulation of these ecoparalogous archaellins by monitoring their transcription, translation, and assembly into filaments. The salt concentration of the growth medium induced differential expression of the two archaellins. In addition, this analysis indicated that archaellation in H. marismortui is majorly regulated on the level of secretion, by a still unknown mechanism. These findings indicate that in archaea, multiple encoded archaellins are not completely redundant, but in fact can display subtle functional differences, which enable cells to cope with varying environmental conditions.
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Affiliation(s)
- Alexey S Syutkin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Marleen van Wolferen
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Oleg V Fedorov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Tessa E F Quax
- Molecular Biology of Archaea, Faculty of Biology, University of Freiburg, Freiburg, Germany
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46
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Chaudhury P, van der Does C, Albers SV. Characterization of the ATPase FlaI of the motor complex of the Pyrococcus furiosus archaellum and its interactions between the ATP-binding protein FlaH. PeerJ 2018; 6:e4984. [PMID: 29938130 PMCID: PMC6011876 DOI: 10.7717/peerj.4984] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/25/2018] [Indexed: 01/09/2023] Open
Abstract
The archaellum, the rotating motility structure of archaea, is best studied in the crenarchaeon Sulfolobus acidocaldarius. To better understand how assembly and rotation of this structure is driven, two ATP-binding proteins, FlaI and FlaH of the motor complex of the archaellum of the euryarchaeon Pyrococcus furiosus, were overexpressed, purified and studied. Contrary to the FlaI ATPase of S. acidocaldarius, which only forms a hexamer after binding of nucleotides, FlaI of P. furiosus formed a hexamer in a nucleotide independent manner. In this hexamer only 2 of the ATP binding sites were available for binding of the fluorescent ATP-analog MANT-ATP, suggesting a twofold symmetry in the hexamer. P. furiosus FlaI showed a 250-fold higher ATPase activity than S. acidocaldarius FlaI. Interaction studies between the isolated N- and C-terminal domains of FlaI showed interactions between the N- and C-terminal domains and strong interactions between the N-terminal domains not previously observed for ATPases involved in archaellum assembly. These interactions played a role in oligomerization and activity, suggesting a conformational state of the hexamer not observed before. Further interaction studies show that the C-terminal domain of PfFlaI interacts with the nucleotide binding protein FlaH. This interaction stimulates the ATPase activity of FlaI optimally at a 1:1 stoichiometry, suggesting that hexameric PfFlaI interacts with hexameric PfFlaH. These data help to further understand the complex interactions that are required to energize the archaellar motor.
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Affiliation(s)
- Paushali Chaudhury
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Freiburg, Germany
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47
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Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies. Chem Rev 2018; 118:3559-3607. [PMID: 29488756 PMCID: PMC5896743 DOI: 10.1021/acs.chemrev.7b00570] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 12/25/2022]
Abstract
Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents.
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Affiliation(s)
- Christophe Chipot
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - François Dehez
- SRSMC, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire
International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Jason R. Schnell
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | | | - Laurent J. Catoire
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Bruno Miroux
- Laboratory
of Biology and Physico-Chemistry of Membrane Proteins, Institut de Biologie Physico-Chimique (IBPC), UMR
7099 CNRS, Paris 75005, France
- University
Paris Diderot, Paris 75005, France
- PSL
Research University, Paris 75005, France
| | - Edmund R. S. Kunji
- Medical
Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Gianluigi Veglia
- Department
of Biochemistry, Molecular Biology, and Biophysics, and Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy A. Cross
- National
High Magnetic Field Laboratory, Florida
State University, Tallahassee, Florida 32310, United States
| | - Paul Schanda
- Université
Grenoble Alpes, CEA, CNRS, IBS, Grenoble F-38000, France
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Wirth R, Luckner M, Wanner G. Validation of a Hypothesis: Colonization of Black Smokers by Hyperthermophilic Microorganisms. Front Microbiol 2018; 9:524. [PMID: 29619021 PMCID: PMC5871681 DOI: 10.3389/fmicb.2018.00524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/08/2018] [Indexed: 11/22/2022] Open
Abstract
Newly erupted black smokers (hydrothermal vent chimneys) are sterile during their formation, but house hyperthermophilic microorganisms in substantial amounts in later stages. No direct experimental data exist by which mechanisms hyperthermophiles colonize newly erupted black smokers, but a scenario was proposed recently how this might happen. Here we combine high temperature light microscopy with electron microscopy to show that two hyperthermophilic Archaea, namely Pyrococcus furiosus and Methanocaldococcus villosus are able to adhere onto authentic black smoker material (BSM). We especially are able to directly observe the adhesion process via video recordings taken at high temperatures. These data validate the hypothesis that hyperthermophiles are transferred by serendipitous water currents to the outside of newly formed black smokers and react within seconds to the there prevailing high temperatures by very fast movements. They scan the surface of the hydrothermal chimneys via a much slower zigzag seek-movement and adhere via their flagella at a suitable place, building up biofilms.
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Affiliation(s)
- Reinhard Wirth
- Faculty of Biology, Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Manja Luckner
- Department of Biology I, Ludwig-Maximilians-University, Munich, Germany
| | - Gerhard Wanner
- Department of Biology I, Ludwig-Maximilians-University, Munich, Germany
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49
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Direct imaging and computational cryo-electron microscopy of ribbons and nanotubes. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Albers SV, Jarrell KF. The Archaellum: An Update on the Unique Archaeal Motility Structure. Trends Microbiol 2018; 26:351-362. [PMID: 29452953 DOI: 10.1016/j.tim.2018.01.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/08/2018] [Accepted: 01/19/2018] [Indexed: 11/24/2022]
Abstract
Each of the three domains of life exhibits a unique motility structure: while Bacteria use flagella, Eukarya employ cilia, and Archaea swim using archaella. Since the new name for the archaeal motility structure was proposed, in 2012, a significant amount of new data on the regulation of transcription of archaella operons, the structure and function of archaellum subunits, their interactions, and cryo-EM data on in situ archaellum complexes in whole cells have been obtained. These data support the notion that the archaellum is evolutionary and structurally unrelated to the flagellum, but instead is related to archaeal and bacterial type IV pili and emphasize that it is a motility structure unique to the Archaea.
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Affiliation(s)
- Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II - Microbiology, University of Freiburg, 79104 Freiburg, Germany.
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
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