1
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Hashimi A, Tocheva EI. Cell envelope diversity and evolution across the bacterial tree of life. Nat Microbiol 2024:10.1038/s41564-024-01812-9. [PMID: 39294462 DOI: 10.1038/s41564-024-01812-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 08/16/2024] [Indexed: 09/20/2024]
Abstract
The bacterial cell envelope is a complex multilayered structure conserved across all bacterial phyla. It is categorized into two main types based on the number of membranes surrounding the cell. Monoderm bacteria are enclosed by a single membrane, whereas diderm cells are distinguished by the presence of a second, outer membrane (OM). An ancient divide in the bacterial domain has resulted in two major clades: the Gracilicutes, consisting strictly of diderm phyla; and the Terrabacteria, encompassing monoderm and diderm species with diverse cell envelope architectures. Recent structural and phylogenetic advancements have improved our understanding of the diversity and evolution of the OM across the bacterial tree of life. Here we discuss cell envelope variability within major bacterial phyla and focus on conserved features found in diderm lineages. Characterizing the mechanisms of OM biogenesis and the evolutionary gains and losses of the OM provides insights into the primordial cell and the last universal common ancestor from which all living organisms subsequently evolved.
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Affiliation(s)
- Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada.
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2
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Caffrey BJ, Pedrazo-Tardajos A, Liberti E, Gaunt B, Kim JS, Kirkland AI. Liquid Phase Electron Microscopy of Bacterial Ultrastructure. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2402871. [PMID: 39239997 DOI: 10.1002/smll.202402871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/05/2024] [Indexed: 09/07/2024]
Abstract
Recent advances in liquid phase scanning transmission electron microscopy (LP-STEM) have enabled the study of dynamic biological processes at nanometer resolutions, paving the way for live-cell imaging using electron microscopy. However, this technique is often hampered by the inherent thickness of whole cell samples and damage from electron beam irradiation. These restrictions degrade image quality and resolution, impeding biological interpretation. Using graphene encapsulation, scanning transmission electron microscopy (STEM), and energy-dispersive X-ray (EDX) spectroscopy to mitigate these issues provides unprecedented levels of intracellular detail in aqueous specimens. This study demonstrates the potential of LP-STEM to examine and identify internal cellular structures in thick biological samples. Specifically, it highlights the use of LP-STEM to investigate the radiation resistant, gram-positive bacterium, Deinococcus radiodurans using various imaging techniques.
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Affiliation(s)
- Brian J Caffrey
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
| | - Adrián Pedrazo-Tardajos
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
| | - Emanuela Liberti
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
| | - Benjamin Gaunt
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
- Nuffield Department of Women's & Reproductive Health, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Judy S Kim
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Angus I Kirkland
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 OQX, UK
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
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3
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Beaud Benyahia B, Taib N, Beloin C, Gribaldo S. Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution. Nat Rev Microbiol 2024:10.1038/s41579-024-01088-0. [PMID: 39198708 DOI: 10.1038/s41579-024-01088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 09/01/2024]
Abstract
The bacterial envelope is one of the oldest and most essential cellular components and has been traditionally divided into Gram-positive (monoderm) and Gram-negative (diderm). Recent landmark studies have challenged a major paradigm in microbiology by inferring that the last bacterial common ancestor had a diderm envelope and that the outer membrane (OM) was lost repeatedly in evolution to give rise to monoderms. Intriguingly, OM losses appear to have occurred exclusively in the Terrabacteria, one of the two major clades of bacteria. In this Review, we present current knowledge about the Terrabacteria. We describe their diversity and phylogeny and then highlight the vast phenotypic diversity of the Terrabacteria cell envelopes, which display large deviations from the textbook examples of diderms and monoderms, challenging the classical Gram-positive-Gram-negative divide. We highlight the striking differences in the systems involved in OM biogenesis in Terrabacteria with respect to the classical diderm experimental models and how they provide novel insights into the diversity and biogenesis of the bacterial cell envelope. We also discuss the potential evolutionary steps that might have led to the multiple losses of the OM and speculate on how the very first OM might have emerged before the last bacterial common ancestor.
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Affiliation(s)
- Basile Beaud Benyahia
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - 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
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France.
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4
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Delgado KN, Caimano MJ, Orbe IC, Vicente CF, La Vake CJ, Grassmann AA, Moody MA, Radolf JD, Hawley KL. Immunodominant extracellular loops of Treponema pallidum FadL outer membrane proteins elicit antibodies with opsonic and growth-inhibitory activities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605823. [PMID: 39131275 PMCID: PMC11312542 DOI: 10.1101/2024.07.30.605823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The global resurgence of syphilis has created a potent stimulus for vaccine development. To identify potentially protective antibodies (Abs) against Treponema pallidum (TPA), we used Pyrococcus furiosus thioredoxin (PfTrx) to display extracellular loops (ECLs) from three TPA outer membrane protein families (outer membrane factors for efflux pumps, eight-stranded β-barrels, and FadLs) to assess their reactivity with immune rabbit serum (IRS). Five ECLs from the FadL orthologs TP0856, TP0858 and TP0865 were immunodominant. Rabbits and mice immunized with these five PfTrx constructs produced ECL-specific Abs that promoted opsonophagocytosis of TPA by rabbit peritoneal and murine bone marrow-derived macrophages at levels comparable to IRS and mouse syphilitic serum. ECL-specific rabbit and mouse Abs also impaired viability, motility, and cellular attachment of spirochetes during in vitro cultivation. The results support the use of ECL-based vaccines and suggest that ECL-specific Abs promote spirochete clearance via Fc receptor-independent as well as Fc receptor-dependent mechanisms.
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Affiliation(s)
- Kristina N Delgado
- Department of Medicine, UConn Health, Farmington, Connecticut, United States
| | - Melissa J Caimano
- Department of Medicine, UConn Health, Farmington, Connecticut, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Department of Research, Connecticut Children's Research Institute, Hartford, CT, United States
| | - Isabel C Orbe
- Department of Pediatrics, UConn Health, Farmington, CT, United States
| | - Crystal F Vicente
- Department of Pediatrics, UConn Health, Farmington, CT, United States
| | - Carson J La Vake
- Department of Pediatrics, UConn Health, Farmington, CT, United States
| | - André A Grassmann
- Department of Medicine, UConn Health, Farmington, Connecticut, United States
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Justin D Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Department of Research, Connecticut Children's Research Institute, Hartford, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, United States
| | - Kelly L Hawley
- Department of Medicine, UConn Health, Farmington, Connecticut, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Research, Connecticut Children's Research Institute, Hartford, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children's, Hartford, CT, United States
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5
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Jeong S, Singh H, Jung JH, Jung KW, Ryu S, Lim S. Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains. Front Microbiol 2024; 15:1410024. [PMID: 38962131 PMCID: PMC11219805 DOI: 10.3389/fmicb.2024.1410024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024] Open
Abstract
The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/β hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.
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Affiliation(s)
- Soyoung Jeong
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, India
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Kwang-Woo Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sangyong Lim
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, Republic of Korea
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6
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von Kügelgen A, Cassidy CK, van Dorst S, Pagani LL, Batters C, Ford Z, Löwe J, Alva V, Stansfeld PJ, Bharat TAM. Membraneless channels sieve cations in ammonia-oxidizing marine archaea. Nature 2024; 630:230-236. [PMID: 38811725 PMCID: PMC11153153 DOI: 10.1038/s41586-024-07462-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - C Keith Cassidy
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lennart L Pagani
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christopher Batters
- Protein and Nucleic Acid Chemistry Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Zephyr Ford
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
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7
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Farci D, Piano D. Spatial arrangement and density variations in the cell envelope of Deinococcus radiodurans. Can J Microbiol 2024; 70:190-198. [PMID: 38525892 DOI: 10.1139/cjm-2023-0163] [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: 03/26/2024]
Abstract
The cell envelope of the poly-extremophile bacterium Deinococcus radiodurans is renowned for its highly organized structure and unique functional characteristics. In this bacterium, a precise regularity characterizes not just the S-layer, but it also extends to the underlying cell envelope layers, resulting in a dense and tightly arranged configuration. This regularity is attributed to a minimum of three protein complexes located at the outer membrane level. Together, they constitute a recurring structural unit that extends across the cell envelope, effectively tiling the entirety of the cell body. Nevertheless, a comprehensive grasp of the vacant spaces within each layer and their functional roles remains limited. In this study, we delve into these aspects by integrating the state of the art with structural calculations. This approach provides crucial evidence supporting an evolutive pressure intricately linked to surface phenomena depending on the environmental conditions.
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Affiliation(s)
- Domenica Farci
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
| | - Dario Piano
- Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
- Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy
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8
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Herdman M, Isbilir B, von Kügelgen A, Schulze U, Wainman A, Bharat TAM. Cell cycle dependent coordination of surface layer biogenesis in Caulobacter crescentus. Nat Commun 2024; 15:3355. [PMID: 38637514 PMCID: PMC11026435 DOI: 10.1038/s41467-024-47529-5] [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: 06/23/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Buse Isbilir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alan Wainman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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9
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Modi M, Thambiraja M, Cherukat A, Yennamalli RM, Priyadarshini R. Structure predictions and functional insights into Amidase_3 domain containing N-acetylmuramyl-L-alanine amidases from Deinococcus indicus DR1. BMC Microbiol 2024; 24:101. [PMID: 38532329 DOI: 10.1186/s12866-024-03225-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/15/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND N-acetylmuramyl-L-alanine amidases are cell wall modifying enzymes that cleave the amide bond between the sugar residues and stem peptide in peptidoglycan. Amidases play a vital role in septal cell wall cleavage and help separate daughter cells during cell division. Most amidases are zinc metalloenzymes, and E. coli cells lacking amidases grow as chains with daughter cells attached to each other. In this study, we have characterized two amidase enzymes from Deinococcus indicus DR1. D. indicus DR1 is known for its high arsenic tolerance and unique cell envelope. However, details of their cell wall biogenesis remain largely unexplored. RESULTS We have characterized two amidases Ami1Di and Ami2Di from D. indicus DR1. Both Ami1Di and Ami2Di suppress cell separation defects in E. coli amidase mutants, suggesting that these enzymes are able to cleave septal cell wall. Ami1Di and Ami2Di proteins possess the Amidase_3 catalytic domain with conserved -GHGG- motif and Zn2+ binding sites. Zn2+- binding in Ami1Di is crucial for amidase activity. AlphaFold2 structures of both Ami1Di and Ami2Di were predicted, and Ami1Di was a closer homolog to AmiA of E. coli. CONCLUSION Our results indicate that Ami1Di and Ami2Di enzymes can cleave peptidoglycan, and structural prediction studies revealed insights into the activity and regulation of these enzymes in D. indicus DR1.
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Affiliation(s)
- Malvika Modi
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Menaka Thambiraja
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, 613401, India
| | - Archana Cherukat
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
- Department of Biology, Graduate School of Arts and Sciences, Wake Forest University, 1834 Wake Forest Rd, Winston-Salem, USA
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu, 613401, India
| | - Richa Priyadarshini
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, 201314, India.
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10
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Shi C, Wang L, Xu H, Zhao Y, Tian B, Hua Y. Characterization of a Novel N4-Methylcytosine Restriction-Modification System in Deinococcus radiodurans. Int J Mol Sci 2024; 25:1660. [PMID: 38338939 PMCID: PMC10855626 DOI: 10.3390/ijms25031660] [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: 12/21/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Deinococcus radiodurans is an extremophilic microorganism that possesses a unique DNA damage repair system, conferring a strong resistance to radiation, desiccation, oxidative stress, and chemical damage. Recently, we discovered that D. radiodurans possesses an N4-methylation (m4C) methyltransferase called M.DraR1, which recognizes the 5'-CCGCGG-3' sequence and methylates the second cytosine. Here, we revealed its cognate restriction endonuclease R.DraR1 and recognized that it is the only endonuclease specially for non-4C-methylated 5'-CCGCGG-3' sequence so far. We designated the particular m4C R.DraR1-M.DraR1 as the DraI R-M system. Bioinformatics searches displayed the rarity of the DraI R-M homologous system. Meanwhile, recombination and transformation efficiency experiments demonstrated the important role of the DraI R-M system in response to oxidative stress. In addition, in vitro activity experiments showed that R.DraR1 could exceptionally cleave DNA substrates with a m5C-methlated 5'-CCGCGG-3' sequence instead of its routine activity, suggesting that this particular R-M component possesses a broader substrate choice. Furthermore, an imbalance of the DraI R-M system led to cell death through regulating genes involved in the maintenance of cell survival such as genome stability, transporter, and energy production. Thus, our research revealed a novel m4C R-M system that plays key roles in maintaining cell viability and defending foreign DNA in D. radiodurans.
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Affiliation(s)
- Chenxiang Shi
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
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11
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Bharat TAM, Tocheva EI, Alva V. The cell envelope architecture of Deinococcus: HPI forms the S-layer and SlpA tethers the outer membrane to peptidoglycan. Proc Natl Acad Sci U S A 2023; 120:e2305338120. [PMID: 38085775 PMCID: PMC10743373 DOI: 10.1073/pnas.2305338120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Affiliation(s)
- Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen72076, Germany
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12
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Kawaguchi M, Shimada H, Bessho Y, Nemoto N. Profiling of lipids in Thermus thermophilus HB8 grown under various conditions. J GEN APPL MICROBIOL 2023; 69:79-90. [PMID: 37394432 DOI: 10.2323/jgam.2023.06.006] [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: 07/04/2023]
Abstract
The membrane lipids of Thermus species have unique structures. Only four polar lipid species have so far been identified in Thermus thermophilus HB8; namely, are two phosphoglycolipids and two glycolipids, both of which have three branched fatty acid chains. Other lipid molecules may be present; however, they have not been identified so far. To clarify the whole lipid profile of T. thermophilus HB8, we cultured this organism under four different growth (temperature and/or nutrition) conditions and analyzed the compositions of polar lipids and fatty acids by high-performance thin-layer chromatography (HPTLC) and gas chromatograph-mass spectrometry (GCーMS), respectively. Thirty-one lipid spots were detected on HPTLC plates and profiled in terms of the presence or absence of phosphate, amino, and sugar groups. Then, we allocated ID numbers to all the spots. Comparative analyses of these polar lipids showed that the diversity of lipid molecules increased under high temperature and minimal medium conditions. In particular, aminolipid species increased under high temperature conditions. As for the fatty acid comparison by GC-MS, iso-branched even-numbered carbon atoms, which are unusual in this organism, significantly increased under the minimal medium condition, suggesting that kinds of branched amino acids at the fatty acid terminus varies under different nutrition conditions. In this study, several unidentified lipids were detected, and elucidation of the lipid structures will provide important information on the environmental adaptation of bacteria.
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Affiliation(s)
| | - Haruo Shimada
- BioChromato, Inc
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, Harima Institute
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
| | - Naoki Nemoto
- Faculty of Advanced Engineering, Chiba Institute of Technology
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13
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Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Baslé A, Khalid S, Beloin C, Gribaldo S, van den Berg B. Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes. Nat Commun 2023; 14:7152. [PMID: 37932269 PMCID: PMC10628300 DOI: 10.1038/s41467-023-42601-y] [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: 02/10/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
The outer membrane (OM) in diderm, or Gram-negative, bacteria must be tethered to peptidoglycan for mechanical stability and to maintain cell morphology. Most diderm phyla from the Terrabacteria group have recently been shown to lack well-characterised OM attachment systems, but instead have OmpM, which could represent an ancestral tethering system in bacteria. Here, we have determined the structure of the most abundant OmpM protein from Veillonella parvula (diderm Firmicutes) by single particle cryogenic electron microscopy. We also characterised the channel properties of the transmembrane β-barrel of OmpM and investigated the structure and PG-binding properties of its periplasmic stalk region. Our results show that OM tethering and nutrient acquisition are genetically linked in V. parvula, and probably other diderm Terrabacteria. This dual function of OmpM may have played a role in the loss of the OM in ancestral bacteria and the emergence of monoderm bacterial lineages.
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Affiliation(s)
- Augustinas Silale
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Yiling Zhu
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Jerzy Witwinowski
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Robert E Smith
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Kahlan E Newman
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Satya P Bhamidimarri
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Arnaud Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, Genetics of Biofilms Laboratory, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Bert van den Berg
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK.
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14
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de Groot A, Blanchard L. DNA repair and oxidative stress defense systems in radiation-resistant Deinococcus murrayi. Can J Microbiol 2023; 69:416-431. [PMID: 37552890 DOI: 10.1139/cjm-2023-0074] [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: 08/10/2023]
Abstract
Deinococcus murrayi is a bacterium isolated from hot springs in Portugal, and named after Dr. Robert G.E. Murray in recognition of his research on the genus Deinococcus. Like other Deinococcus species, D. murrayi is extremely resistant to ionizing radiation. Repair of massive DNA damage and limitation of oxidative protein damage are two important factors contributing to the robustness of Deinococcus bacteria. Here, we identify, among others, the DNA repair and oxidative stress defense proteins in D. murrayi, and highlight special features of D. murrayi. For DNA repair, D. murrayi does not contain a standalone uracil-DNA glycosylase (Ung), but it encodes a protein in which Ung is fused to a DNA photolyase domain (PhrB). UvrB and UvrD contain large insertions corresponding to inteins. One of its endonuclease III enzymes lacks a [4Fe-4S] cluster. Deinococcus murrayi possesses a homolog of the error-prone DNA polymerase IV. Concerning oxidative stress defense, D. murrayi encodes a manganese catalase in addition to a heme catalase. Its organic hydroperoxide resistance protein Ohr is atypical because the redox active cysteines are present in a CXXC motif. These and other characteristics of D. murrayi show further diversity among Deinococcus bacteria with respect to resistance-associated mechanisms.
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Affiliation(s)
- Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
| | - Laurence Blanchard
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
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15
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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16
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Sexton D, Hashimi A, Beskrovnaya P, Sibanda L, Huan T, Tocheva E. The cell envelope of Thermotogae suggests a mechanism for outer membrane biogenesis. Proc Natl Acad Sci U S A 2023; 120:e2303275120. [PMID: 37094164 PMCID: PMC10160955 DOI: 10.1073/pnas.2303275120] [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: 03/03/2023] [Accepted: 03/29/2023] [Indexed: 04/26/2023] Open
Abstract
The presence of a cell membrane is one of the major structural components defining life. Recent phylogenomic analyses have supported the hypothesis that the last universal common ancestor (LUCA) was likely a diderm. Yet, the mechanisms that guided outer membrane (OM) biogenesis remain unknown. Thermotogae is an early-branching phylum with a unique OM, the toga. Here, we use cryo-electron tomography to characterize the in situ cell envelope architecture of Thermotoga maritima and show that the toga is made of extended sheaths of β-barrel trimers supporting small (~200 nm) membrane patches. Lipidomic analyses identified the same major lipid species in the inner membrane (IM) and toga, including the rare to bacteria membrane-spanning ether-bound diabolic acids (DAs). Proteomic analyses revealed that the toga was composed of multiple SLH-domain containing Ompα and novel β-barrel proteins, and homology searches detected variable conservations of these proteins across the phylum. These results highlight that, in contrast to the SlpA/OmpM superfamily of proteins, Thermotoga possess a highly diverse bipartite OM-tethering system. We discuss the implications of our findings with respect to other early-branching phyla and propose that a toga-like intermediate may have facilitated monoderm-to-diderm cell envelope transitions.
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Affiliation(s)
- Danielle L. Sexton
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Polina Beskrovnaya
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Lloyd Sibanda
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
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17
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von Kügelgen A, van Dorst S, Yamashita K, Sexton DL, Tocheva EI, Murshudov G, Alva V, Bharat TAM. Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans. Proc Natl Acad Sci U S A 2023; 120:e2215808120. [PMID: 37043530 PMCID: PMC10120038 DOI: 10.1073/pnas.2215808120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/14/2023] [Indexed: 04/13/2023] Open
Abstract
Deinococcus radiodurans is an atypical diderm bacterium with a remarkable ability to tolerate various environmental stresses, due in part to its complex cell envelope encapsulated within a hyperstable surface layer (S-layer). Despite decades of research on this cell envelope, atomic structural details of the S-layer have remained obscure. In this study, we report the electron cryomicroscopy structure of the D. radiodurans S-layer, showing how it is formed by the Hexagonally Packed Intermediate-layer (HPI) protein arranged in a planar hexagonal lattice. The HPI protein forms an array of immunoglobulin-like folds within the S-layer, with each monomer extending into the adjacent hexamer, resulting in a highly interconnected, stable, sheet-like arrangement. Using electron cryotomography and subtomogram averaging from focused ion beam-milled D. radiodurans cells, we have obtained a structure of the cellular S-layer, showing how this HPI S-layer coats native membranes on the surface of cells. Our S-layer structure from the diderm bacterium D. radiodurans shows similarities to immunoglobulin-like domain-containing S-layers from monoderm bacteria and archaea, highlighting common features in cell surface organization across different domains of life, with connotations on the evolution of immunoglobulin-based molecular recognition systems in eukaryotes.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Keitaro Yamashita
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Danielle L. Sexton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Garib Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen72076, Germany
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
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