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Zuke JD, Burton BM. From isotopically labeled DNA to fluorescently labeled dynamic pili: building a mechanistic model of DNA transport to the cytoplasmic membrane. Microbiol Mol Biol Rev 2024; 88:e0012523. [PMID: 38466096 PMCID: PMC10966944 DOI: 10.1128/mmbr.00125-23] [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] [Indexed: 03/12/2024] Open
Abstract
SUMMARYNatural competence, the physiological state wherein bacteria produce proteins that mediate extracellular DNA transport into the cytosol and the subsequent recombination of DNA into the genome, is conserved across the bacterial domain. DNA must successfully translocate across formidable permeability barriers during import, including the cell membrane(s) and the cell wall, that are normally impermeable to large DNA polymers. This review will examine the mechanisms underlying DNA transport from the extracellular space to the cytoplasmic membrane. First, the challenges inherent to DNA movement through the cell periphery will be discussed to provide context for DNA transport during natural competence. The following sections will trace the development of a comprehensive model for DNA translocation to the cytoplasmic membrane, highlighting the crucial studies performed over the last century that have contributed to building contemporary DNA import models. Finally, this review will conclude by reflecting on what is still unknown about the process and the possible solutions to overcome these limitations.
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Affiliation(s)
- Jason D. Zuke
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Briana M. Burton
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
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2
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Little JI, Singh PK, Zhao J, Dunn S, Matz H, Donnenberg MS. Type IV pili of Enterobacteriaceae species. EcoSal Plus 2024:eesp00032023. [PMID: 38294234 DOI: 10.1128/ecosalplus.esp-0003-2023] [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: 04/03/2023] [Accepted: 12/01/2023] [Indexed: 02/01/2024]
Abstract
Type IV pili (T4Ps) are surface filaments widely distributed among bacteria and archaea. T4Ps are involved in many cellular functions and contribute to virulence in some species of bacteria. Due to the diversity of T4Ps, different properties have been observed for homologous proteins that make up T4Ps in various organisms. In this review, we highlight the essential components of T4Ps, their functions, and similarities to related systems. We emphasize the unique T4Ps of enteric pathogens within the Enterobacteriaceae family, which includes pathogenic strains of Escherichia coli and Salmonella. These include the bundle-forming pilus (BFP) of enteropathogenic E. coli (EPEC), longus (Lng) and colonization factor III (CFA/III) of enterotoxigenic E. coli (ETEC), T4P of Salmonella enterica serovar Typhi, Colonization Factor Citrobacter (CFC) of Citrobacter rodentium, T4P of Yersinia pseudotuberculosis, a ubiquitous T4P that was characterized in enterohemorrhagic E. coli (EHEC), and the R64 plasmid thin pilus. Finally, we highlight areas for further study.
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Affiliation(s)
- Janay I Little
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Pradip K Singh
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jinlei Zhao
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shakeera Dunn
- Internal Medicine Residency, Bayhealth Medical Center, Dover, Delaware, USA
| | - Hanover Matz
- Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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Ashikur Rahman M, Akter S, Ashrafudoulla M, Anamul Hasan Chowdhury M, Uddin Mahamud AGMS, Hong Park S, Ha SD. Insights into the mechanisms and key factors influencing biofilm formation by Aeromonas hydrophila in the food industry: A comprehensive review and bibliometric analysis. Food Res Int 2024; 175:113671. [PMID: 38129021 DOI: 10.1016/j.foodres.2023.113671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023]
Abstract
Biofilm formation by Aeromonas hydrophila in the food industry poses significant challenges to food safety and quality. Therefore, this comprehensive review aimed to provide insights into the mechanisms and key factors influencing A. hydrophila biofilm formation. It explores the molecular processes involved in initial attachment, microcolony formation, and biofilm maturation; moreover, it concurrently examines the impact of intrinsic factors, including quorum sensing, cyclic-di-GMP, the efflux pump, and antibiotic resistance, as well as environmental conditions, such as temperature, nutrient availability, and osmotic pressure, on biofilm architecture and resilience. Furthermore, the article highlights the potential of bibliometric analysis as a promising method for conceptualizing the research landscape of and identifying knowledge gaps in A. hydrophila biofilm research. The findings underscore the requirement for focused interventions that prevent biofilm development and raise food sector safety. The consolidation of current information and incorporation of bibliometric analysis enhances existing understanding of A. hydrophila biofilm formation and offers insights for future research and control strategies within a food industry context.
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Affiliation(s)
- Md Ashikur Rahman
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea; Bangladesh Fisheries Research Institute, Bangladesh
| | - Shirin Akter
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea; Department of Fisheries and Marine Bioscience, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Ashrafudoulla
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea
| | | | | | - Si Hong Park
- Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Sang-Do Ha
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea.
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Savitskaya VY, Strekalovskikh VV, Snyga VG, Monakhova MV, Arutyunyan AM, Dolinnaya NG, Kubareva EA. pilE G-Quadruplex Is Recognized and Preferentially Bound but Not Processed by the MutL Endonuclease from Neisseria gonorrhoeae Mismatch Repair Pathway. Int J Mol Sci 2023; 24:ijms24076167. [PMID: 37047138 PMCID: PMC10094033 DOI: 10.3390/ijms24076167] [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: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
The human pathogen Neisseria gonorrhoeae uses a homologous recombination to undergo antigenic variation and avoid an immune response. The surface protein pilin (PilE) is one of the targets for antigenic variation that can be regulated by N. gonorrhoeae mismatch repair (MMR) and a G-quadruplex (G4) located upstream of the pilE promoter. Using bioinformatics tools, we found a correlation between pilE variability and deletion of DNA regions encoding ngMutS or ngMutL proteins, the main participants in N. gonorrhoeae methyl-independent MMR. To understand whether the G4 structure could affect the ngMutL-mediated regulation of pilin antigenic variation, we designed several synthetic pilE G4-containing oligonucleotides, differing in length, and related DNA duplexes. Using CD measurements and biochemical approaches, we have showed that (i) ngMutL preferentially binds to pilE G4 compared to DNA duplex, although the latter is a cognate substrate for ngMutL endonuclease, (ii) protein binding affinity decreases with shortening of quadruplex-containing and duplex ligands, (iii) the G4 structure inhibits ngMutL-induced DNA nicking and modulates cleavage positions; the enzyme does not cleave DNA within G4, but is able to bypass this noncanonical structure. Thus, pilE G4 may regulate the efficiency of pilin antigenic variation by quadruplex binding to ngMutL and suppression of homologous recombination.
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Affiliation(s)
| | - Vadim V Strekalovskikh
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Viktoriia G Snyga
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mayya V Monakhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alexander M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Nina G Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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Pelicic V. Mechanism of assembly of type 4 filaments: everything you always wanted to know (but were afraid to ask). MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36947586 DOI: 10.1099/mic.0.001311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Type 4 filaments (T4F) are a superfamily of filamentous nanomachines - virtually ubiquitous in prokaryotes and functionally versatile - of which type 4 pili (T4P) are the defining member. T4F are polymers of type 4 pilins, assembled by conserved multi-protein machineries. They have long been an important topic for research because they are key virulence factors in numerous bacterial pathogens. Our poor understanding of the molecular mechanisms of T4F assembly is a serious hindrance to the design of anti-T4F therapeutics. This review attempts to shed light on the fundamental mechanistic principles at play in T4F assembly by focusing on similarities rather than differences between several (mostly bacterial) T4F. This holistic approach, complemented by the revolutionary ability of artificial intelligence to predict protein structures, led to an intriguing mechanistic model of T4F assembly.
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Affiliation(s)
- Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, UMR 7283 CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Marseille, France
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6
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Abstract
Type 4 pili (T4P) are retractable surface appendages found on numerous bacteria and archaea that play essential roles in various microbial functions, including host colonization by pathogens. An ATPase is required for T4P extension, but the mechanism by which chemical energy is transduced to mechanical energy for pilus extension has not been elucidated. Here, we report the cryo-electron microscopy (cryo-EM) structure of the BfpD ATPase from enteropathogenic Escherichia coli (EPEC) in the presence of either ADP or a mixture of ADP and AMP-PNP. Both structures, solved at 3 Å resolution, reveal the typical toroid shape of AAA+ ATPases and unambiguous 6-fold symmetry. This 6-fold symmetry contrasts with the 2-fold symmetry previously reported for other T4P extension ATPase structures, all of which were from thermophiles and solved by crystallography. In the presence of the nucleotide mixture, BfpD bound exclusively AMP-PNP, and this binding resulted in a modest outward expansion in comparison to the structure in the presence of ADP, suggesting a concerted model for hydrolysis. De novo molecular models reveal a partially open configuration of all subunits where the nucleotide binding site may not be optimally positioned for catalysis. ATPase functional studies reveal modest activity similar to that of other extension ATPases, while calculations indicate that this activity is insufficient to power pilus extension. Our results reveal that, despite similarities in primary sequence and tertiary structure, T4P extension ATPases exhibit divergent quaternary configurations. Our data raise new possibilities regarding the mechanism by which T4P extension ATPases power pilus formation. IMPORTANCE Type 4 pili are hairlike surface appendages on many bacteria and archaea that can be extended and retracted with tremendous force. They play a critical role in disease caused by several deadly human pathogens. Pilus extension is made possible by an enzyme that converts chemical energy to mechanical energy. Here, we describe the three-dimensional structure of such an enzyme from a human pathogen in unprecedented detail, which reveals a mechanism of action that has not been seen previously among enzymes that power type 4 pilus extension.
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Gaines MC, Isupov MN, Sivabalasarma S, Haque RU, McLaren M, Mollat CL, Tripp P, Neuhaus A, Gold VAM, Albers SV, Daum B. Electron cryo-microscopy reveals the structure of the archaeal thread filament. Nat Commun 2022; 13:7411. [PMID: 36456543 PMCID: PMC9715654 DOI: 10.1038/s41467-022-34652-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/02/2022] [Indexed: 12/05/2022] Open
Abstract
Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.
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Affiliation(s)
- Matthew C Gaines
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, EX4 4QD, Exeter, UK
| | - Shamphavi Sivabalasarma
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Risat Ul Haque
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Clara L Mollat
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Patrick Tripp
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Alexander Neuhaus
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK
| | - Sonja-Verena Albers
- Institute of Biology II, Molecular Biology of Archaea, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBBS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD, Exeter, UK.
- Department of Biosciences, Faculty of Health and Life Sciences, Stocker Road, EX4 4QD, Exeter, UK.
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