1
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Mills J, Gebhard LJ, Schubotz F, Shevchenko A, Speth DR, Liao Y, Duggin IG, Marchfelder A, Erdmann S. Extracellular vesicle formation in Euryarchaeota is driven by a small GTPase. Proc Natl Acad Sci U S A 2024; 121:e2311321121. [PMID: 38408251 DOI: 10.1073/pnas.2311321121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/14/2024] [Indexed: 02/28/2024] Open
Abstract
Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms interact with their extracellular world. EVs are able to traffic a diverse array of molecules across different species and even domains, facilitating numerous functions. In this study, we investigate EV production in Euryarchaeota, using the model organism Haloferax volcanii. We uncover that EVs enclose RNA, with specific transcripts preferentially enriched, including those with regulatory potential, and conclude that EVs can act as an RNA communication system between haloarchaea. We demonstrate the key role of an EV-associated small GTPase for EV formation in H. volcanii that is also present across other diverse evolutionary branches of Archaea. We propose the name, ArvA, for the identified family of archaeal vesiculating GTPases. Additionally, we show that two genes in the same operon with arvA (arvB and arvC) are also involved in EV formation. Both, arvB and arvC, are closely associated with arvA in the majority of other archaea encoding ArvA. Our work demonstrates that small GTPases involved in membrane deformation and vesiculation, ubiquitous in Eukaryotes, are also present in Archaea and are widely distributed across diverse archaeal phyla.
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Affiliation(s)
- Joshua Mills
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - L Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen 28359, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Daan R Speth
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Yan Liao
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Iain G Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | | | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
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2
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Nußbaum P, Kureisaite-Ciziene D, Bellini D, van der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nat Microbiol 2024; 9:698-711. [PMID: 38443575 DOI: 10.1038/s41564-024-01600-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 01/08/2024] [Indexed: 03/07/2024]
Abstract
Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea.
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Affiliation(s)
- Phillip Nußbaum
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Chris van der Does
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marko Kojic
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Najwa Taib
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anna Yeates
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Maxime Tourte
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Martin Loose
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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3
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Barillà D. Finding pieces in the archaeal cell division puzzle. Nat Microbiol 2024; 9:591-592. [PMID: 38443573 DOI: 10.1038/s41564-024-01621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Affiliation(s)
- Daniela Barillà
- Department of Biology, University of York, York, UK.
- York Biomedical Research Institute, University of York, York, UK.
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4
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Zhao S, Makarova KS, Zheng W, Zhan L, Wan Q, Liu Y, Gong H, Krupovic M, Lutkenhaus J, Chen X, Koonin EV, Du S. Widespread photosynthesis reaction centre barrel proteins are necessary for haloarchaeal cell division. Nat Microbiol 2024; 9:712-726. [PMID: 38443574 DOI: 10.1038/s41564-024-01615-y] [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: 03/28/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024]
Abstract
Cell division is fundamental to all cellular life. Most archaea depend on either the prokaryotic tubulin homologue FtsZ or the endosomal sorting complex required for transport for division but neither system has been robustly characterized. Here, we show that three of the four photosynthesis reaction centre barrel domain proteins of Haloferax volcanii (renamed cell division proteins B1/2/3 (CdpB1/2/3)) play important roles in cell division. CdpB1 interacts directly with the FtsZ membrane anchor SepF and is essential for cell division, whereas deletion of cdpB2 and cdpB3 causes a major and a minor division defect, respectively. Orthologues of CdpB proteins are also involved in cell division in other haloarchaea, indicating a conserved function of these proteins. Phylogenetic analysis shows that photosynthetic reaction centre barrel proteins are widely distributed among archaea and appear to be central to cell division in most if not all archaea.
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Affiliation(s)
- Shan Zhao
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wenchao Zheng
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Le Zhan
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qianqian Wan
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yafei Liu
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Han Gong
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Shishen Du
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
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5
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Patro M, Duggin IG, Albers SV, Ithurbide S. "Influence of plasmids, selection markers and auxotrophic mutations on Haloferax volcanii cell shape plasticity". Front Microbiol 2023; 14:1270665. [PMID: 37840741 PMCID: PMC10570808 DOI: 10.3389/fmicb.2023.1270665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Haloferax volcanii and other Haloarchaea can be pleomorphic, adopting different shapes, which vary with growth stages. Several studies have shown that H. volcanii cell shape is sensitive to various external factors including growth media and physical environment. In addition, several studies have noticed that the presence of a recombinant plasmid in the cells is also a factor impacting H. volcanii cell shape, notably by favoring the development of rods in early stages of growth. Here we investigated the reasons for this phenomenon by first studying the impact of auxotrophic mutations on cell shape in strains that are commonly used as genetic backgrounds for selection during strain engineering (namely: H26, H53, H77, H98, and H729) and secondly, by studying the effect of the presence of different plasmids containing selection markers on the cell shape of these strains. Our study showed that most of these auxotrophic strains have variation in cell shape parameters including length, aspect ratio, area and circularity and that the plasmid presence is impacting these parameters too. Our results indicated that ΔhdrB strains and hdrB selection markers have the most influence on H. volcanii cell shape, in addition to the sole presence of a plasmid. Finally, we discuss limitations in studying cell shape in H. volcanii and make recommendations based on our results for improving reproducibility of such studies.
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Affiliation(s)
- Megha Patro
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Iain G. Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Solenne Ithurbide
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
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6
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Cooper A, Makkay AM, Papke RT. Archaeal Tubulin-like Proteins Modify Cell Shape in Haloferax volcanii during Early Biofilm Development. Genes (Basel) 2023; 14:1861. [PMID: 37895209 PMCID: PMC10606840 DOI: 10.3390/genes14101861] [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: 08/01/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Tubulin, an extensively studied self-assembling protein, forms filaments in eukaryotic cells that affect cell shape, among other functions. The model archaeon Haloferax volcanii uses two tubulin-like proteins (FtsZ1/FtsZ2) for cell division, similar to bacteria, but has an additional six related tubulins called CetZ. One of them, CetZ1, was shown to play a role in cell shape. Typically, discoid and rod shapes are observed in planktonic growth, but under biofilm formation conditions (i.e., attached to a substratum), H. volcanii can grow filamentously. Here, we show that the deletion mutants of all eight tubulin-like genes significantly impacted morphology when cells were allowed to form a biofilm. ΔftsZ1, ΔcetZ2, and ΔcetZ4-6 created longer, less round cells than the parental and a higher percentage of filaments. ΔcetZ1 and ΔcetZ3 were significantly rounder than the parental, and ΔftsZ2 generated larger, flat, amorphic cells. The results show all tubulin homologs affect morphology at most timepoints, which therefore suggests these genes indeed have a function.
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Affiliation(s)
| | | | - R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA; (A.C.); (A.M.M.)
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7
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Rados T, Andre K, Cerletti M, Bisson A. A sweet new set of inducible and constitutive promoters in Haloferax volcanii. Front Microbiol 2023; 14:1204876. [PMID: 37637112 PMCID: PMC10448506 DOI: 10.3389/fmicb.2023.1204876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Inducible promoters are one of cellular and molecular biology's most important technical tools. The ability to deplete, replete, and overexpress genes on demand is the foundation of most functional studies. Here, we developed and characterized a new xylose-responsive promoter (Pxyl), the second inducible promoter system for the model haloarcheon Haloferax volcanii. Generating RNA-seq datasets from cultures in the presence of four historically used inducers (arabinose, xylose, maltose, and IPTG), we mapped upregulated genomic regions primarily repressed in the absence of the above inducers. We found a highly upregulated promoter that controls the expression of the xacEA (HVO_B0027-28) operon in the pHV3 chromosome. To characterize this promoter region, we cloned msfGFP (monomeric superfold green fluorescent protein) under the control of two upstream regions into a modified pTA962 vector: the first 250 bp (P250) and the whole 750 bp intergenic fragments (P750). The P250 sequence drove the expression of msfGFP constitutively, and its expression did not respond to the presence or absence of xylose. However, the P750 promoter showed not only to be repressed in the absence of xylose but also expressed higher levels of msfGFP than the previously described inducible promoter PtnaA in the presence of the inducer. Finally, we validated the inducible Pxyl promoter by reproducing morphological phenotypes already described in the literature. By overexpressing the tubulin-like FtsZ1 and FtsZ2, we observed similar but slightly more pronounced morphological defects than the tryptophan-inducible promoter PtnaA. FtsZ1 overexpression created larger, deformed cells, whereas cells overexpressing FtsZ2 were smaller but mostly retained their shape. In summary, this work contributes a new xylose-inducible promoter that could be used simultaneously with the well-established PtnaA in functional studies in H. volcanii in the future.
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Affiliation(s)
- Theopi Rados
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Katherine Andre
- Department of Biology, Brandeis University, Waltham, MA, United States
| | - Micaela Cerletti
- Department of Biology, Brandeis University, Waltham, MA, United States
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Alex Bisson
- Department of Biology, Brandeis University, Waltham, MA, United States
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8
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Yao H, Li G, Xiong X, Jin F, Li S, Xie X, Zhong D, Zhang R, Meng F, Yin Y, Jiao X. LygA retention on the surface of Listeria monocytogenes via its interaction with wall teichoic acid modulates bacterial homeostasis and virulence. PLoS Pathog 2023; 19:e1011482. [PMID: 37379353 DOI: 10.1371/journal.ppat.1011482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/13/2023] [Indexed: 06/30/2023] Open
Abstract
Wall teichoic acid (WTA) is the abundant cell wall-associated glycopolymer in Gram-positive bacteria, playing crucial roles in surface proteins retention, bacterial homeostasis, and virulence. Hypervirulent serovar (SV) 4h Listeria monocytogenes is a newly designated serotype with only galactosylated (Gal) type II WTA. Although the surface association of some proteins relies on the WTA glycosylation, the nature and function of the noncovalent interactions between cell wall-associated proteins and WTA are less known. In this study, we found Gal-WTA plays a key role in modulating the novel glycine-tryptophan (GW) domain-containing autolysin protein LygA through direct interactions. An SV 4h strain deficient in WTA galactosylation (XYSNΔgalT) showed a dramatic reduction of LygA on the cell surface, significantly decreasing the autolytic activity, impairing the bacterial colonization in colon and brain. Notably, we demonstrated LygA binds to Gal-WTA with high affinity through the GW domain and that the extent of binding increases with the number of GW domains. Moreover, we confirmed the direct Gal-dependent binding of the GW protein Auto from the type I WTA strain, which has no interaction with l-rhamnosylated WTA, indicating that the complexity of both WTA and GW proteins can affect the coordination patterns. Altogether, our findings suggest that both the glycosylation patterns of WTA and a fixed numbers of GW domains are closely associated with the retention of LygA on the cell surface, which facilitates L. monocytogenes infection by promoting bacteria colonization in intestine and brain.
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Affiliation(s)
- Hao Yao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Guo Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Xianglian Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Fanxin Jin
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Sirui Li
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Xinyu Xie
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Dan Zhong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Renling Zhang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Fanzeng Meng
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Yuelan Yin
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
| | - Xin'an Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Yangzhou, Jiangsu Province, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou, Jiangsu Province, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou, Jiangsu Province, China
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9
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Gebhard LJ, Duggin IG, Erdmann S. Improving the genetic system for Halorubrum lacusprofundi to allow in-frame deletions. Front Microbiol 2023; 14:1095621. [PMID: 37065119 PMCID: PMC10102395 DOI: 10.3389/fmicb.2023.1095621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Halorubrum lacusprofundi is a cold-adapted halophilic archaeon isolated from Deep Lake, Antarctica. Hrr. lacusprofundi is commonly used to study adaptation to cold environments and thereby a potential source for biotechnological products. Additionally, in contrast to other haloarchaeal model organisms, Hrr. lacusprofundi is also susceptible to a range of different viruses and virus-like elements, making it a great model to study virus-host interactions in a cold-adapted organism. A genetic system has previously been reported for Hrr. lacusprofundi; however, it does not allow in-frame deletions and multiple gene knockouts. Here, we report the successful generation of uracil auxotrophic (pyrE2) mutants of two strains of Hrr. lacusprofundi. Subsequently, we attempted to generate knockout mutants using the auxotrophic marker for selection. However, surprisingly, only the combination of the auxotrophic marker and antibiotic selection allowed the timely and clean in-frame deletion of a target gene. Finally, we show that vectors established for the model organism Haloferax volcanii are deployable for genetic manipulation of Hrr. lacusprofundi, allowing the use of the portfolio of genetic tools available for H. volcanii in Hrr. lacusprofundi.
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Affiliation(s)
- L. Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Iain G. Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
- *Correspondence: Susanne Erdmann,
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10
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Zhao S, Makarova KS, Zheng W, Liu Y, Zhan L, Wan Q, Gong H, Krupovic M, Lutkenhaus J, Chen X, Koonin EV, Du S. Widespread PRC barrel proteins play critical roles in archaeal cell division. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534520. [PMID: 37090588 PMCID: PMC10120694 DOI: 10.1101/2023.03.28.534520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Cell division is fundamental to all cellular life. Most of the archaea employ one of two alternative division machineries, one centered around the prokaryotic tubulin homolog FtsZ and the other around the endosomal sorting complex required for transport (ESCRT). However, neither of these mechanisms has been thoroughly characterized in archaea. Here, we show that three of the four PRC (Photosynthetic Reaction Center) barrel domain proteins of Haloferax volcanii (renamed Cell division proteins B1/2/3 (CdpB1/2/3)), play important roles in division. CdpB1 interacts directly with the FtsZ membrane anchor SepF and is essential for division, whereas deletion of cdpB2 and cdpB3 causes a major and a minor division defect, respectively. Orthologs of CdpB proteins are also involved in cell division in other haloarchaea. Phylogenetic analysis shows that PRC barrel proteins are widely distributed among archaea, including the highly conserved CdvA protein of the crenarchaeal ESCRT-based division system. Thus, diverse PRC barrel proteins appear to be central to cell division in most if not all archaea. Further study of these proteins is expected to elucidate the division mechanisms in archaea and their evolution.
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Affiliation(s)
- Shan Zhao
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Wenchao Zheng
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yafei Liu
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Le Zhan
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Qianqian Wan
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Han Gong
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, France
| | - Joe Lutkenhaus
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Shishen Du
- Department of Microbiology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
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11
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The archaeal Cdv cell division system. Trends Microbiol 2023; 31:601-615. [PMID: 36658033 DOI: 10.1016/j.tim.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 12/09/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023]
Abstract
The Cdv system is the protein machinery that performs cell division and other membrane-deforming processes in a subset of archaea. Evolutionarily, the system is closely related to the eukaryotic ESCRT machinery, with which it shares many structural and functional similarities. Since its first description 15 years ago, the understanding of the Cdv system progressed rather slowly, but recent discoveries sparked renewed interest and insights. The emerging physical picture appears to be that CdvA acts as a membrane anchor, CdvB as a scaffold that localizes division to the mid-cell position, CdvB1 and CvdB2 as the actual constriction machinery, and CdvC as the ATPase that detaches Cdv proteins from the membrane. This paper provides a comprehensive overview of the research done on Cdv and explains how this relatively understudied machinery acts to perform its cell-division function. Understanding of the Cdv system helps to better grasp the biophysics and evolution of archaea, and furthermore provides new opportunities for the bottom-up building of a divisome for synthetic cells.
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12
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Brown HJ, Duggin IG. Diversity and Potential Multifunctionality of Archaeal CetZ Tubulin-like Cytoskeletal Proteins. Biomolecules 2023; 13:biom13010134. [PMID: 36671519 PMCID: PMC9856176 DOI: 10.3390/biom13010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Tubulin superfamily (TSF) proteins are widespread, and are known for their multifaceted roles as cytoskeletal proteins underpinning many basic cellular functions, including morphogenesis, division, and motility. In eukaryotes, tubulin assembles into microtubules, a major component of the dynamic cytoskeletal network of fibres, whereas the bacterial homolog FtsZ assembles the division ring at midcell. The functions of the lesser-known archaeal TSF proteins are beginning to be identified and show surprising diversity, including homologs of tubulin and FtsZ as well as a third archaea-specific family, CetZ, implicated in the regulation of cell shape and possibly other unknown functions. In this study, we define sequence and structural characteristics of the CetZ family and CetZ1 and CetZ2 subfamilies, identify CetZ groups and diversity amongst archaea, and identify potential functional relationships through analysis of the genomic neighbourhoods of cetZ genes. We identified at least three subfamilies of orthologous CetZ proteins in the archaeal class Halobacteria, including CetZ1 and CetZ2 as well as a novel uncharacterized subfamily. CetZ1 and CetZ2 were correlated to one another as well as to cell shape and motility phenotypes across diverse Halobacteria. Among other known CetZ clusters in orders Archaeoglobales, Methanomicrobiales, Methanosarcinales, and Thermococcales, an additional uncharacterized group from Archaeoglobales and Methanomicrobiales is affiliated strongly with Halobacteria CetZs, suggesting that they originated via horizontal transfer. Subgroups of Halobacteria CetZ2 and Thermococcales CetZ genes were found adjacent to different type IV pili regulons, suggesting potential utilization of CetZs by type IV systems. More broadly conserved cetZ gene neighbourhoods include nucleotide and cofactor biosynthesis (e.g., F420) and predicted cell surface sugar epimerase genes. These findings imply that CetZ subfamilies are involved in multiple functions linked to the cell surface, biosynthesis, and motility.
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13
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van Wolferen M, Pulschen AA, Baum B, Gribaldo S, Albers SV. The cell biology of archaea. Nat Microbiol 2022; 7:1744-1755. [PMID: 36253512 PMCID: PMC7613921 DOI: 10.1038/s41564-022-01215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Buzz Baum
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institute Pasteur, Paris, France.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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14
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Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. Proc Natl Acad Sci U S A 2022; 119:e2205037119. [PMID: 35994644 PMCID: PMC9436352 DOI: 10.1073/pnas.2205037119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are important ecological, biogeochemical, and evolutionary drivers in every environment. Upon infection, they often cause the lysis of the host cell. However, some viruses exhibit alternative life cycles, such as chronic infections without cell lysis. The nature and the impact of chronic infections in prokaryotic host organisms remains largely unknown. Here, we characterize a novel haloarchaeal virus, Haloferax volcanii pleomorphic virus 1 (HFPV-1), which is currently the only virus infecting the model haloarchaeon Haloferax volcanii DS2, and demonstrate that HFPV-1 and H. volcanii are a great model system to study virus-host interactions in archaea. HFPV-1 is a pleomorphic virus that causes a chronic infection with continuous release of virus particles, but host and virus coexist without cell lysis or the appearance of resistant cells. Despite an only minor impact of the infection on host growth, we uncovered an extensive remodeling of the transcriptional program of the host (up to 1,049 differentially expressed genes). These changes are highlighted by a down-regulation of two endogenous provirus regions in the host genome, and we show that HFPV-1 infection is strongly influenced by a cross-talk between HFPV-1 and one of the proviruses mediated by a superinfection-like exclusion mechanism. Furthermore, HFPV-1 has a surprisingly wide host range among haloarchaea, and purified virus DNA can cause an infection after transformation into the host, making HFPV-1 a candidate for being developed into a genetic tool for a range of so far inaccessible haloarchaea.
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15
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Zhang C, Liu W, Deng J, Ma S, Chang Z, Yang J. Structural Insights into the Interaction between Bacillus subtilis SepF Assembly and FtsZ by Solid-State NMR Spectroscopy. J Phys Chem B 2022; 126:5219-5230. [PMID: 35799411 DOI: 10.1021/acs.jpcb.2c02810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many species of Gram-positive bacteria, SepF participated in the membrane tethering of FtsZ Z-ring during bacteria division. However, atomic-level details of interaction between SepF and FtsZ in an assembled state are lacking. Here, by combining solid-state NMR (SSNMR) with biochemical analyses, the interaction of Bacillus subtilis SepF and the C-terminal domain (CTD) of FtsZ was investigated. We obtained near complete chemical shift assignments of SepF and determined the structural model of the SepF monomer. Interaction with FtsZ-CTD caused further packing of SepF rings, and SSNMR experiments revealed the affected residues locating at α1, α2, β3, and β4 of SepF. Solution NMR experiments of dimeric SepF constructed by point mutation strategy proved a prerequisite role of α-α interface formation in SepF for FtsZ binding. Overall, our results provide structural insights into the mechanisms of SepF-FtsZ interaction for better understanding the function of SepF in bacteria.
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Affiliation(s)
- Chang Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.,National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Wenjing Liu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Shaojie Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.,National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jun Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.,National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
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16
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Ithurbide S, Gribaldo S, Albers SV, Pende N. Spotlight on FtsZ-based cell division in Archaea. Trends Microbiol 2022; 30:665-678. [PMID: 35246355 DOI: 10.1016/j.tim.2022.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota. In this review we highlight recent findings in this emerging field of research. We present current knowledge of the cell division machinery of halophiles which relies on two FtsZ proteins, and we compare it with that of methanobacteria, which relies on only one FtsZ. Finally, we discuss how these differences relate to the distinct cell envelopes of these two archaeal model systems.
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Affiliation(s)
- Solenne Ithurbide
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
| | - Nika Pende
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France
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17
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van Wolferen M, Albers SV. Progress and Challenges in Archaeal Cell Biology. Methods Mol Biol 2022; 2522:365-371. [PMID: 36125763 DOI: 10.1007/978-1-0716-2445-6_24] [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: 06/15/2023]
Abstract
Over the past decades there has been a growing interest in the domain of archaea. In this chapter we highlight the recent advances that have been made in studying the cell biology of archaea. We particularly focus on methods for genetic manipulation and imaging of different archaeal species and discuss the technical limitations at the often-extreme growth conditions. Several ongoing developments will help us overcoming these limitations, thereby facilitating future studies in the existing field of archaeal cell biology.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.
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18
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Pradhan P, Margolin W, Beuria TK. Targeting the Achilles Heel of FtsZ: The Interdomain Cleft. Front Microbiol 2021; 12:732796. [PMID: 34566937 PMCID: PMC8456036 DOI: 10.3389/fmicb.2021.732796] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/16/2021] [Indexed: 02/03/2023] Open
Abstract
Widespread antimicrobial resistance among bacterial pathogens is a serious threat to public health. Thus, identification of new targets and development of new antibacterial agents are urgently needed. Although cell division is a major driver of bacterial colonization and pathogenesis, its targeting with antibacterial compounds is still in its infancy. FtsZ, a bacterial cytoskeletal homolog of eukaryotic tubulin, plays a highly conserved and foundational role in cell division and has been the primary focus of research on small molecule cell division inhibitors. FtsZ contains two drug-binding pockets: the GTP binding site situated at the interface between polymeric subunits, and the inter-domain cleft (IDC), located between the N-terminal and C-terminal segments of the core globular domain of FtsZ. The majority of anti-FtsZ molecules bind to the IDC. Compounds that bind instead to the GTP binding site are much less useful as potential antimicrobial therapeutics because they are often cytotoxic to mammalian cells, due to the high sequence similarity between the GTP binding sites of FtsZ and tubulin. Fortunately, the IDC has much less sequence and structural similarity with tubulin, making it a better potential target for drugs that are less toxic to humans. Over the last decade, a large number of natural and synthetic IDC inhibitors have been identified. Here we outline the molecular structure of IDC in detail and discuss how it has become a crucial target for broad spectrum and species-specific antibacterial agents. We also outline the drugs that bind to the IDC and their modes of action.
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Affiliation(s)
- Pinkilata Pradhan
- Institute of Life Sciences, Nalco Square, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, United States
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