1
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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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2
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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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3
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Fields JL, Zhang H, Bellis NF, Petersen HA, Halder SK, Rich-New ST, Wu H, Wang F. Structural diversity and clustering of bacterial flagellar outer domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585621. [PMID: 38562817 PMCID: PMC10983879 DOI: 10.1101/2024.03.18.585621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we elucidate atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyzed all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a previously unexplored cluster, indicating new opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.
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4
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Sonani RR, Palmer LK, Esteves NC, Horton AA, Sebastian AL, Kelly RJ, Wang F, Kreutzberger MAB, Russell WK, Leiman PG, Scharf BE, Egelman EH. An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano. Nat Commun 2024; 15:756. [PMID: 38272938 PMCID: PMC10811340 DOI: 10.1038/s41467-024-44959-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: 01/06/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
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Affiliation(s)
- Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Lee K Palmer
- Mass Spectrometry Facility, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Nathaniel C Esteves
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Abigail A Horton
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rebecca J Kelly
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - William K Russell
- Mass Spectrometry Facility, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA.
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5
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Kavčič L, Kežar A, Koritnik N, Žnidarič MT, Klobučar T, Vičič Ž, Merzel F, Holden E, Benesch JLP, Podobnik M. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Commun Chem 2024; 7:14. [PMID: 38233506 PMCID: PMC10794713 DOI: 10.1038/s42004-024-01100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
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Affiliation(s)
- Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Chemical Sciences', Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Neža Koritnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biomedicine', Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tajda Klobučar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Žiga Vičič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ellie Holden
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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6
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Minamino T, Kinoshita M. Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion. EcoSal Plus 2023; 11:eesp00112023. [PMID: 37260402 PMCID: PMC10729930 DOI: 10.1128/ecosalplus.esp-0011-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/14/2023] [Indexed: 01/28/2024]
Abstract
Many motile bacteria use flagella for locomotion under a variety of environmental conditions. Because bacterial flagella are under the control of sensory signal transduction pathways, each cell is able to autonomously control its flagellum-driven locomotion and move to an environment favorable for survival. The flagellum of Salmonella enterica serovar Typhimurium is a supramolecular assembly consisting of at least three distinct functional parts: a basal body that acts as a bidirectional rotary motor together with multiple force generators, each of which serves as a transmembrane proton channel to couple the proton flow through the channel with torque generation; a filament that functions as a helical propeller that produces propulsion; and a hook that works as a universal joint that transmits the torque produced by the rotary motor to the helical propeller. At the base of the flagellum is a type III secretion system that transports flagellar structural subunits from the cytoplasm to the distal end of the growing flagellar structure, where assembly takes place. In recent years, high-resolution cryo-electron microscopy (cryoEM) image analysis has revealed the overall structure of the flagellum, and this structural information has made it possible to discuss flagellar assembly and function at the atomic level. In this article, we describe what is known about the structure, assembly, and function of Salmonella flagella.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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7
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Sonani RR, Sanchez JC, Baumgardt JK, Kundra S, Wright ER, Craig L, Egelman EH. Tad and toxin-coregulated pilus structures reveal unexpected diversity in bacterial type IV pili. Proc Natl Acad Sci U S A 2023; 120:e2316668120. [PMID: 38011558 PMCID: PMC10710030 DOI: 10.1073/pnas.2316668120] [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: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal domain. Cryo-EM structures have revealed key differences between the bacterial and archaeal T4P in their C-terminal domain structure and in the packing and continuity of α1. This segment forms a continuous α-helix in archaeal T4P but is partially melted in all published bacterial T4P structures due to a conserved helix breaking proline at position 22. The tad (tight adhesion) T4P are found in both bacteria and archaea and are thought to have been acquired by bacteria through horizontal transfer from archaea. Tad pilins are unique among the T4 pilins, being only 40 to 60 residues in length and entirely lacking a C-terminal domain. They also lack the Pro22 found in all high-resolution bacterial T4P structures. We show using cryo-EM that the bacterial tad pilus from Caulobacter crescentus is composed of continuous helical subunits that, like the archaeal pilins, lack the melted portion seen in other bacterial T4P and share the packing arrangement of the archaeal T4P. We further show that a bacterial T4P, the Vibrio cholerae toxin coregulated pilus, which lacks Pro22 but is not in the tad family, has a continuous N-terminal α-helix, yet its α1 s are arranged similar to those in other bacterial T4P. Our results highlight the role of Pro22 in helix melting and support an evolutionary relationship between tad and archaeal T4P.
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Affiliation(s)
- Ravi R. Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
| | - Juan Carlos Sanchez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Joseph K. Baumgardt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Shivani Kundra
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Lisa Craig
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCV5A 1S6, Canada
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA22903
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8
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Cheng Y, Han J, Song M, Zhang S, Cao Q. Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM. Nat Commun 2023; 14:7503. [PMID: 37980359 PMCID: PMC10657474 DOI: 10.1038/s41467-023-43359-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: 08/17/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023] Open
Abstract
Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils.
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Affiliation(s)
- Yijia Cheng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jianting Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Meinai Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shuqin Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China.
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9
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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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10
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [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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11
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Sanchez JC, Montemayor EJ, Ploscariu NT, Parrell D, Baumgardt JK, Yang JE, Sibert B, Cai K, Wright ER. Atomic-level architecture of Caulobacter crescentus flagellar filaments provide evidence for multi-flagellin filament stabilization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548443. [PMID: 37503001 PMCID: PMC10369909 DOI: 10.1101/2023.07.10.548443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Flagella are dynamic, ion-powered machines with assembly pathways that are optimized for efficient flagella production. In bacteria, dozens of genes are coordinated at specific times in the cell lifecycle to generate each component of the flagellum. This is the case for Caulobacter crescentus, but little is known about why this species encodes six different flagellin genes. Furthermore, little is known about the benefits multi-flagellin species possess over single flagellin species, if any, or what molecular properties allow for multi-flagellin filaments to assemble. Here we present an in-depth analysis of several single flagellin filaments from C. crescentus, including an extremely well-resolved structure of a bacterial flagellar filament. We highlight key molecular interactions that differ between each bacterial strain and speculate how these interactions may alleviate or impose helical strain on the overall architecture of the filament. We detail conserved residues within the flagellin subunit that allow for the synthesis of multi-flagellin filaments. We further comment on how these molecular differences impact bacterial motility and highlight how no single flagellin filament achieves wild-type levels of motility, suggesting C. crescentus has evolved to produce a filament optimized for motility comprised of six flagellins. Finally, we highlight an ordered arrangement of glycosylation sites on the surface of the filaments and speculate how these sites may protect the β-hairpin located on the surface exposed domain of the flagellin subunit.
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Affiliation(s)
- Juan C. Sanchez
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
- Biotechnology Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Eric J. Montemayor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Daniel Parrell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI USA
| | - Joseph K. Baumgardt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Cryo-Electron Microscopy Research Center, UW-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
| | - Bryan Sibert
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Cryo-Electron Microscopy Research Center, UW-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
| | - Kai Cai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Cryo-Electron Microscopy Research Center, UW-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
| | - Elizabeth R. Wright
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706
- Biotechnology Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI USA
- Cryo-Electron Microscopy Research Center, UW-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI USA
- Morgridge Institute for Research, UW-Madison, Madison, WI, 53715, USA
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12
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Baquero DP, Cvirkaite-Krupovic V, Hu SS, Fields JL, Liu X, Rensing C, Egelman EH, Krupovic M, Wang F. Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes. Cell 2023; 186:2853-2864.e8. [PMID: 37290436 PMCID: PMC10330847 DOI: 10.1016/j.cell.2023.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/04/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens, recently identified as extracellular cytochrome nanowires (ECNs), have received wide attention due to numerous potential applications. However, whether other organisms employ similar ECNs for electron transfer remains unknown. Here, using cryoelectron microscopy, we describe the atomic structures of two ECNs from two major orders of hyperthermophilic archaea present in deep-sea hydrothermal vents and terrestrial hot springs. Homologs of Archaeoglobus veneficus ECN are widespread among mesophilic methane-oxidizing Methanoperedenaceae, alkane-degrading Syntrophoarchaeales archaea, and in the recently described megaplasmids called Borgs. The ECN protein subunits lack similarities in their folds; however, they share a common heme arrangement, suggesting an evolutionarily optimized heme packing for efficient electron transfer. The detection of ECNs in archaea suggests that filaments containing closely stacked hemes may be a common and widespread mechanism for long-range electron transfer in both prokaryotic domains of life.
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Affiliation(s)
- Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France
| | | | - Shengen Shawn Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Jessie Lynda Fields
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France.
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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13
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Nedeljković M, Kreutzberger MAB, Postel S, Bonsor D, Xing Y, Jacob N, Schuler WJ, Egelman EH, Sundberg EJ. An unbroken network of interactions connecting flagellin domains is required for motility in viscous environments. PLoS Pathog 2023; 19:e1010979. [PMID: 37253071 PMCID: PMC10256154 DOI: 10.1371/journal.ppat.1010979] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/09/2023] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
In its simplest form, bacterial flagellar filaments are composed of flagellin proteins with just two helical inner domains, which together comprise the filament core. Although this minimal filament is sufficient to provide motility in many flagellated bacteria, most bacteria produce flagella composed of flagellin proteins with one or more outer domains arranged in a variety of supramolecular architectures radiating from the inner core. Flagellin outer domains are known to be involved in adhesion, proteolysis and immune evasion but have not been thought to be required for motility. Here we show that in the Pseudomonas aeruginosa PAO1 strain, a bacterium that forms a ridged filament with a dimerization of its flagellin outer domains, motility is categorically dependent on these flagellin outer domains. Moreover, a comprehensive network of intermolecular interactions connecting the inner domains to the outer domains, the outer domains to one another, and the outer domains back to the inner domain filament core, is required for motility. This inter-domain connectivity confers PAO1 flagella with increased stability, essential for its motility in viscous environments. Additionally, we find that such ridged flagellar filaments are not unique to Pseudomonas but are, instead, present throughout diverse bacterial phyla.
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Affiliation(s)
- Marko Nedeljković
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Mark A. B. Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Sandra Postel
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel Bonsor
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Yingying Xing
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Neil Jacob
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - William J. Schuler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Eric J. Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
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14
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Popp PF, Erhardt M. Supercoiled filaments propel them all. Cell 2022; 185:3461-3463. [PMID: 36113424 DOI: 10.1016/j.cell.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 01/26/2023]
Abstract
In this issue of Cell, Kreutzberger and colleagues report the near-atomic-resolution, cryo-EM structures of the supercoiled filaments of both bacterial and archaeal motility machines. Despite the lack of homology, the supercoiled filament structures reveal shared fundamental features of prokaryotic locomotion and represent a prime example of convergent evolution.
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Affiliation(s)
- Philipp F Popp
- Institute for Biology - Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marc Erhardt
- Institute for Biology - Bacterial Physiology, Humboldt-Universität zu Berlin, Berlin, Germany; Max Planck Unit for the Science of Pathogens, Berlin, Germany.
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