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Thongchol J, Yu Z, Harb L, Lin Y, Koch M, Theodore M, Narsaria U, Shaevitz J, Gitai Z, Wu Y, Zhang J, Zeng L. Removal of Pseudomonas type IV pili by a small RNA virus. Science 2024; 384:eadl0635. [PMID: 38574145 PMCID: PMC11126211 DOI: 10.1126/science.adl0635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa. The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.
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Affiliation(s)
- Jirapat Thongchol
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Zihao Yu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Laith Harb
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yiruo Lin
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Matthias Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew Theodore
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Utkarsh Narsaria
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Joshua Shaevitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, NY 10461, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
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2
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Meng R, Xing Z, Chang JY, Yu Z, Thongchol J, Xiao W, Wang Y, Chamakura K, Zeng Z, Wang F, Young R, Zeng L, Zhang J. Structural basis of Acinetobacter type IV pili targeting by an RNA virus. Nat Commun 2024; 15:2746. [PMID: 38553443 PMCID: PMC10980823 DOI: 10.1038/s41467-024-47119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. Single-stranded RNA bacteriophages target the bacterial retractile pili, including type IV. Our study delves into the interaction between Acinetobacter phage AP205 and type IV pili. Using cryo-electron microscopy, we solve structures of the AP205 virion with an asymmetric dimer of maturation proteins, the native Acinetobacter type IV pili bearing a distinct post-translational pilin cleavage, and the pili-bound AP205 showing its maturation proteins adapted to pilin modifications, allowing each phage to bind to one or two pili. Leveraging these results, we develop a 20-kilodalton AP205-derived protein scaffold targeting type IV pili in situ, with potential for research and diagnostics.
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Affiliation(s)
- Ran Meng
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Yale University, New Haven, CT, 06520, USA
| | - Zhongliang Xing
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jeng-Yih Chang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- UMass Chan Medical School, Worcester, MA, 01655, USA
| | - Zihao Yu
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jirapat Thongchol
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Wen Xiao
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Yuhang Wang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Karthik Chamakura
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Armata Pharmaceuticals, Inc., Marina del Rey, CA, 90292, USA
| | - Zhiqi Zeng
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Ry Young
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Lanying Zeng
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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Kishida K, Li YG, Ogawa-Kishida N, Khara P, Al Mamun AAM, Bosserman RE, Christie PJ. Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines. PLoS Genet 2024; 20:e1011088. [PMID: 38437248 PMCID: PMC10939261 DOI: 10.1371/journal.pgen.1011088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/14/2024] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
Bacterial type IV secretion systems (T4SSs) are a versatile family of macromolecular translocators, collectively able to recruit diverse DNA and protein substrates and deliver them to a wide range of cell types. Presently, there is little understanding of how T4SSs recognize substrate repertoires and form productive contacts with specific target cells. Although T4SSs are composed of a number of conserved subunits and adopt certain conserved structural features, they also display considerable compositional and structural diversity. Here, we explored the structural bases underlying the functional versatility of T4SSs through systematic deletion and subunit swapping between two conjugation systems encoded by the distantly-related IncF plasmids, pED208 and F. We identified several regions of intrinsic flexibility among the encoded T4SSs, as evidenced by partial or complete functionality of chimeric machines. Swapping of VirD4-like TraD type IV coupling proteins (T4CPs) yielded functional chimeras, indicative of relaxed specificity at the substrate-TraD and TraD-T4SS interfaces. Through mutational analyses, we further delineated domains of the TraD T4CPs contributing to recruitment of cognate vs heterologous DNA substrates. Remarkably, swaps of components comprising the outer membrane core complexes, a few F-specific subunits, or the TraA pilins supported DNA transfer in the absence of detectable pilus production. Among sequenced enterobacterial species in the NCBI database, we identified many strains that harbor two or more F-like plasmids and many F plasmids lacking one or more T4SS components required for self-transfer. We confirmed that host cells carrying co-resident, non-selftransmissible variants of pED208 and F elaborate chimeric T4SSs, as evidenced by transmission of both plasmids. We propose that T4SS plasticity enables the facile assembly of functional chimeras, and this intrinsic flexibility at the structural level can account for functional diversification of this superfamily over evolutionary time and, on a more immediate time-scale, to proliferation of transfer-defective MGEs in nature.
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Affiliation(s)
- Kouhei Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Natsumi Ogawa-Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Abu Amar M. Al Mamun
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Rachel E. Bosserman
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, Texas, United States of America
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Zhang X, Wan H, Jin M, Huang L, Zhang X. Environmental viromes reveal global virosphere of deep-sea sediment RNA viruses. J Adv Res 2024; 56:87-102. [PMID: 37054879 PMCID: PMC10834809 DOI: 10.1016/j.jare.2023.04.003] [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: 11/20/2022] [Revised: 01/30/2023] [Accepted: 04/08/2023] [Indexed: 04/15/2023] Open
Abstract
INTRODUCTION Viruses are the most abundant and diverse life forms on the earth. Both DNA viruses and RNA viruses play important roles in marine ecosystems via regulating biogeochemical cycles. OBJECTIVES However, the virome of marine RNA viruses has been rarely explored so far. In this study, therefore, the environmental viromes of deep-sea sediment RNA viruses were characterized on a global scale to reveal the global virosphere of deep-sea RNA viruses. METHODS The viral particles were purified from each of 133 deep-sea sediment samples and then characterized based on metagenomes of RNA viruses. RESULTS In this study, we established the global virome dataset of deep-sea RNA viruses purified from 133 sediment samples that were collected from typical deep-sea ecosystems of three oceans. A total of 85,059 viral operational taxonomic units (vOTUs) were identified, of which only 1.72% were hitherto known, indicating that the deep-sea sediment is a repository of novel RNA viruses. These vOTUs were classified into 20 viral families, including prokaryotic (7.09%) and eukaryotic (65.81%) RNA viruses. Furthermore, 1,463 deep-sea RNA viruses with complete genomes were obtained. The differentiation of RNA viral communities was driven by the deep-sea ecosystems as opposed to geographical region. Specifically, the virus-encoded metabolic genes took great effects on the differentiation of RNA viral communities by mediating the energy metabolism in the deep-sea ecosystems. CONCLUSIONS Therefore, our findings indicate that the deep sea is a vast reservoir of novel RNA viruses for the first time, and the differentiation of RNA viral communities is driven by the deep-sea ecosystems through energy metabolism.
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Affiliation(s)
- Xinyi Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Haitao Wan
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Min Jin
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, People's Republic of China
| | - Liquan Huang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao) and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou 310058, People's Republic of China.
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5
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Li XT, Peng SY, Feng SM, Bao TY, Li SZ, Li SY. Recent Progress in Phage-Based Nanoplatforms for Tumor Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307111. [PMID: 37806755 DOI: 10.1002/smll.202307111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Nanodrug delivery systems have demonstrated a great potential for tumor therapy with the development of nanotechnology. Nonetheless, traditional drug delivery systems are faced with issues such as complex synthetic procedures, low reproducibility, nonspecific distribution, impenetrability of biological barrier, systemic toxicity, etc. In recent years, phage-based nanoplatforms have attracted increasing attention in tumor treatment for their regular structure, fantastic carrying property, high transduction efficiency and biosafety. Notably, therapeutic or targeting peptides can be expressed on the surface of the phages through phage display technology, enabling the phage vectors to possess multifunctions. As a result, the drug delivery efficiency on tumor will be vastly improved, thereby enhancing the therapeutic efficacy while reducing the side effects on normal tissues. Moreover, phages can overcome the hindrance of biofilm barrier to elicit antitumor effects, which exhibit great advantages compared with traditional synthetic drug delivery systems. Herein, this review not only summarizes the structure and biology of the phages, but also presents their potential as prominent nanoplatforms against tumor in different pathways to inspire the development of effective nanomedicine.
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Affiliation(s)
- Xiao-Tong Li
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Shu-Yi Peng
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Shao-Mei Feng
- Department of Anesthesiology, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, P. R. China
| | - Ting-Yu Bao
- Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Sheng-Zhang Li
- Department of Clinical Medicine, the Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Shi-Ying Li
- Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, P. R. China
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6
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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7
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Christie PJ. Illuminating type IV secretion-mediated DNA trafficking through long filaments. Proc Natl Acad Sci U S A 2023; 120:e2318508120. [PMID: 38019843 PMCID: PMC10722965 DOI: 10.1073/pnas.2318508120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Affiliation(s)
- Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030
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8
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Kishida K, Li YG, Ogawa-Kishida N, Khara P, Al Mamun AAM, Bosserman RE, Christie PJ. Chimeric systems composed of swapped Tra subunits between distantly-related F plasmids reveal striking plasticity among type IV secretion machines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570194. [PMID: 38106057 PMCID: PMC10723329 DOI: 10.1101/2023.12.05.570194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bacterial type IV secretion systems (T4SSs) are a versatile family of macromolecular translocators, collectively able to recruit diverse DNA and protein substrates and deliver them to a wide range of cell types. Presently, there is little understanding of how T4SSs recognize substrate repertoires and form productive contacts with specific target cells. Although T4SSs are composed of a number of conserved subunits and adopt certain conserved structural features, they also display considerable compositional and structural diversity. Here, we explored the structural bases underlying the functional versatility of T4SSs through systematic deletion and subunit swapping between two conjugation systems encoded by the distantly-related IncF plasmids, pED208 and F. We identified several regions of intrinsic flexibility among the encoded T4SSs, as evidenced by partial or complete functionality of chimeric machines. Swapping of VirD4-like TraD type IV coupling proteins (T4CPs) yielded functional chimeras, indicative of relaxed specificity at the substrate - TraD and TraD - T4SS interfaces. Through mutational analyses, we further delineated domains of the TraD T4CPs contributing to recruitment of cognate vs heterologous DNA substrates. Remarkably, swaps of components comprising the outer membrane core complexes, a few F-specific subunits, or the TraA pilins supported DNA transfer in the absence of detectable pilus production. Among sequenced enterobacterial species in the NCBI database, we identified many strains that harbor two or more F-like plasmids and many F plasmids lacking one or more T4SS components required for self-transfer. We confirmed that host cells carrying co-resident, non-selftransmissible variants of pED208 and F elaborate chimeric T4SSs, as evidenced by transmission of both plasmids. We propose that T4SS plasticity enables the facile assembly of functional chimeras, and this intrinsic flexibility at the structural level can account for functional diversification of this superfamily over evolutionary time and, on a more immediate time-scale, to proliferation of transfer-defective MGEs in nature.
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Affiliation(s)
- Kouhei Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Yang Grace Li
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Natsumi Ogawa-Kishida
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Abu Amar M Al Mamun
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Rachel E. Bosserman
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, 6431 Fannin St, Houston, Texas 77030, United States of America
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Nguyen HM, Watanabe S, Sharmin S, Kawaguchi T, Tan XE, Wannigama DL, Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses. Int J Mol Sci 2023; 24:17029. [PMID: 38069353 PMCID: PMC10707117 DOI: 10.3390/ijms242317029] [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: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.
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Affiliation(s)
- Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Sultana Sharmin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Yamagata, Japan;
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
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10
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Goldlust K, Ducret A, Halte M, Dedieu-Berne A, Erhardt M, Lesterlin C. The F pilus serves as a conduit for the DNA during conjugation between physically distant bacteria. Proc Natl Acad Sci U S A 2023; 120:e2310842120. [PMID: 37963249 PMCID: PMC10666033 DOI: 10.1073/pnas.2310842120] [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: 06/28/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
Horizontal transfer of F-like plasmids by bacterial conjugation is responsible for disseminating antibiotic resistance and virulence determinants among pathogenic Enterobacteriaceae species, a growing health concern worldwide. Central to this process is the conjugative F pilus, a long extracellular filamentous polymer that extends from the surface of plasmid donor cells, allowing it to probe the environment and make contact with the recipient cell. It is well established that the F pilus can retract to bring mating pair cells in tight contact before DNA transfer. However, whether DNA transfer can occur through the extended pilus has been a subject of active debate. In this study, we use live-cell microscopy to show that while most transfer events occur between cells in direct contact, the F pilus can indeed serve as a conduit for the DNA during transfer between physically distant cells. Our findings enable us to propose a unique model for conjugation that revises our understanding of the DNA transfer mechanism and the dissemination of drug resistance and virulence genes within complex bacterial communities.
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Affiliation(s)
- Kelly Goldlust
- Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, Inserm, UMR5086, Lyon69007, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, Inserm, UMR5086, Lyon69007, France
| | - Manuel Halte
- Institute for Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin10115, Germany
| | - Annick Dedieu-Berne
- Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, Inserm, UMR5086, Lyon69007, France
| | - Marc Erhardt
- Institute for Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin10115, Germany
- Max Planck Unit for the Science of Pathogens, Berlin10117, Germany
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, Inserm, UMR5086, Lyon69007, France
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11
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Farafonov VS, Stich M, Nerukh DA. Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome. J Chem Theory Comput 2023; 19:7924-7933. [PMID: 37856311 DOI: 10.1021/acs.jctc.3c00846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
For the first time, a complete all-atom molecular dynamics (MD) model of a virus, bacteriophage MS2, in its entirety, including a protein outer shell, native genomic RNA with necessary divalent ions, and surrounding explicit aqueous solution with ions at physiological concentration, was built. The model is based on an experimentally measured cryo-EM structure, which was substantially augmented by reconstructing missing or low-resolution parts of the measured density (where the atomistic structure cannot be fit unambiguously). The model was tested by a quarter of a microsecond MD run, and various biophysical characteristics are obtained and analyzed. The developed methodology of building the model can be used for reconstructing other large biomolecular structures when experimental data are fragmented and/or of varying resolution, while the model itself can be used for studying the biology of MS2, including the dynamics of its interaction with the host bacteria.
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Affiliation(s)
- Vladimir S Farafonov
- Department of Physical Chemistry, V. N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
| | - Michael Stich
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
- Área de Matemática Aplicada, Departamento de Matemática Aplicada, Ciencia e Ingeniería de Materiales y Tecnología Electrónica, Universidad Rey Juan Carlos, C. Tulipán s/n, Móstoles, Madrid 28933, Spain
| | - Dmitry A Nerukh
- Department of Mathematics, Aston University, Birmingham B4 7ET, U.K
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12
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Thongchol J, Lill Z, Hoover Z, Zhang J. Recent Advances in Structural Studies of Single-Stranded RNA Bacteriophages. Viruses 2023; 15:1985. [PMID: 37896763 PMCID: PMC10610835 DOI: 10.3390/v15101985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Positive-sense single-stranded RNA (ssRNA) bacteriophages (phages) were first isolated six decades ago. Since then, extensive research has been conducted on these ssRNA phages, particularly those infecting E. coli. With small genomes of typically 3-4 kb that usually encode four essential proteins, ssRNA phages employ a straightforward infectious cycle involving host adsorption, genome entry, genome replication, phage assembly, and host lysis. Recent advancements in metagenomics and transcriptomics have led to the identification of ~65,000 sequences from ssRNA phages, expanding our understanding of their prevalence and potential hosts. This review article illuminates significant investigations into ssRNA phages, with a focal point on their structural aspects, providing insights into the various stages of their infectious cycle.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; (J.T.); (Z.L.); (Z.H.)
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13
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Laguna-Castro M, Rodríguez-Moreno A, Llorente E, Lázaro E. The balance between fitness advantages and costs drives adaptation of bacteriophage Qβ to changes in host density at different temperatures. Front Microbiol 2023; 14:1197085. [PMID: 37303783 PMCID: PMC10248866 DOI: 10.3389/fmicb.2023.1197085] [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: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Host density is one of the main factors affecting the infective capacity of viruses. When host density is low, it is more difficult for the virus to find a susceptible cell, which increases its probability of being damaged by the physicochemical agents of the environment. Nevertheless, viruses can adapt to variations in host density through different strategies that depend on the particular characteristics of the life cycle of each virus. In a previous work, using the bacteriophage Qβ as an experimental model, we found that when bacterial density was lower than optimal the virus increased its capacity to penetrate into the bacteria through a mutation in the minor capsid protein (A1) that is not described to interact with the cell receptor. Results Here we show that the adaptive pathway followed by Qβ in the face of similar variations in host density depends on environmental temperature. When the value for this parameter is lower than optimal (30°C), the mutation selected is the same as at the optimal temperature (37°C). However, when temperature increases to 43°C, the mutation selected is located in a different protein (A2), which is involved both in the interaction with the cell receptor and in the process of viral progeny release. The new mutation increases the entry of the phage into the bacteria at the three temperatures assayed. However, it also considerably increases the latent period at 30 and 37°C, which is probably the reason why it is not selected at these temperatures. Conclusion The conclusion is that the adaptive strategies followed by bacteriophage Qβ, and probably other viruses, in the face of variations in host density depend not only on their advantages at this selective pressure, but also on the fitness costs that particular mutations may present in function of the rest of environmental parameters that influence viral replication and stability.
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14
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Ch'ng ACW, Konthur Z, Lim TS. Magnetic Nanoparticle-Based Semi-automated Panning for High-Throughput Antibody Selection. Methods Mol Biol 2023; 2702:291-313. [PMID: 37679626 DOI: 10.1007/978-1-0716-3381-6_15] [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: 09/09/2023]
Abstract
Bio-panning is a common process involved in recombinant antibody selection against defined targets. The biopanning process aims to isolate specific antibodies against an antigen via affinity selection from a phage display library. In general, antigens are immobilized on solid surfaces such as polystyrene plastic, magnetic beads, and nitrocellulose. For high-throughput selection, semi-automated panning selection allows simultaneous panning against multiple target antigens adapting automated particle processing systems such as the KingFisher Flex. The system setup allows for minimal human intervention for pre- and post-panning steps such as antigen immobilization, phage rescue, and amplification. In addition, the platform is also adaptable to perform polyclonal and monoclonal ELISA for the evaluation process. This chapter will detail the protocols involved from the selection stage until the monoclonal ELISA evaluation with important notes attached at the end of this chapter for optimization and troubleshooting purposes.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Reseach in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Zoltán Konthur
- Department of Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany
| | - Theam Soon Lim
- Institute for Reseach in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
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15
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Chandler-Bostock R, Bingham RJ, Clark S, Scott AJP, Wroblewski E, Barker A, White SJ, Dykeman EC, Mata CP, Bohon J, Farquhar E, Twarock R, Stockley PG. Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection. J Mol Biol 2022; 434:167797. [PMID: 35998704 DOI: 10.1016/j.jmb.2022.167797] [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: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Many single-stranded, positive-sense RNA viruses regulate assembly of their infectious virions by forming multiple, cognate coat protein (CP)-genome contacts at sites termed Packaging Signals (PSs). We have determined the secondary structures of the bacteriophage MS2 ssRNA genome (gRNA) frozen in defined states using constraints from X-ray synchrotron footprinting (XRF). Comparison of the footprints from phage and transcript confirms the presence of multiple PSs in contact with CP dimers in the former. This is also true for a virus-like particle (VLP) assembled around the gRNA in vitro in the absence of the single-copy Maturation Protein (MP) found in phage. Since PS folds are present at many sites across gRNA transcripts, it appears that this genome has evolved to facilitate this mechanism of assembly regulation. There are striking differences between the gRNA-CP contacts seen in phage and the VLP, suggesting that the latter are inappropriate surrogates for aspects of phage structure/function. Roughly 50% of potential PS sites in the gRNA are not in contact with the protein shell of phage. However, many of these sit adjacent to, albeit not in contact with, PS-binding sites on CP dimers. We hypothesize that these act as PSs transiently during assembly but subsequently dissociate. Combining the XRF data with PS locations from an asymmetric cryo-EM reconstruction suggests that the genome positions of such dissociations are non-random and may facilitate infection. The loss of many PS-CP interactions towards the 3' end of the gRNA would allow this part of the genome to transit more easily through the narrow basal body of the pilus extruding machinery. This is the known first step in phage infection. In addition, each PS-CP dissociation event leaves the protein partner trapped in a non-lowest free-energy conformation. This destabilizes the protein shell which must disassemble during infection, further facilitating this stage of the life-cycle.
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Affiliation(s)
| | - Richard J Bingham
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Sam Clark
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Andrew J P Scott
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Emma Wroblewski
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Amy Barker
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Eric C Dykeman
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Carlos P Mata
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jen Bohon
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Erik Farquhar
- CWRU Center for Synchrotron Biosciences, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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16
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Vodolazkaya N, Nikolskaya M, Laguta A, Farafonov V, Balklava Z, Stich M, Mchedlov-Petrossyan N, Nerukh D. Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface. J Phys Chem B 2022; 126:8166-8176. [PMID: 36198175 DOI: 10.1021/acs.jpcb.2c04491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
MS2 bacteriophage is often used as a model for evaluating pathogenic viruses' behavior in aqueous solution. However, the questions of the virus surface's hydrophilic/hydrophobic balance, the charge distribution, and the binding mechanism are open. Using the dynamic light scattering method and laser Doppler electrophoresis, the hydrodynamic diameter and the ζ-potential of the virus particles were measured at their concentration of 5 × 1011 particles per mL and ionic strength 0.03 M. The values were found to be 30 nm and -29 or -34 mV (by Smoluchowski or Ohshima approximations), respectively. The MS2 bacteriophage surface was also investigated using a series of acid-base indicator dyes of various charge type, size, and structure. Their spectral and acid-base properties (pKa) are very sensitive to the microenvironment in aqueous solution, including containing nanoparticles. The electrostatic potential of the surface Ψ was estimated using the common formula: Ψ = 59 × (pKai - pKa) in mV at 25 °C. The Ψ values were -50 and +10 mV, respectively, which indicate the "mosaic" way of the charge distribution on the surface. These data are in good agreement with the obtained ζ-potential values and provide even more information about the virus surface. It was found that the surface of the MS2 virus is hydrophilic in solution in contrast to the commonly accepted hypothesis of the hydrophobicity of virus particles. No hydrophobic interactions between various molecular probes and the capsid were observed.
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Affiliation(s)
- Natalya Vodolazkaya
- Physical Chemistry Department, V. N. Karazin Kharkiv National University, Svoboda Square 4, Kharkiv, 61022, Ukraine
| | - Marina Nikolskaya
- Physical Chemistry Department, V. N. Karazin Kharkiv National University, Svoboda Square 4, Kharkiv, 61022, Ukraine
| | - Anna Laguta
- Physical Chemistry Department, V. N. Karazin Kharkiv National University, Svoboda Square 4, Kharkiv, 61022, Ukraine
| | - Vladimir Farafonov
- Physical Chemistry Department, V. N. Karazin Kharkiv National University, Svoboda Square 4, Kharkiv, 61022, Ukraine
| | | | - Michael Stich
- Departamento de Matemática Aplicada, Ciencia e Ingeniería de Materiales y Tecnología Electrónica, Universidad Rey Juan Carlos, 28933 Móstoles (Madrid), Spain
| | - Nikolay Mchedlov-Petrossyan
- Physical Chemistry Department, V. N. Karazin Kharkiv National University, Svoboda Square 4, Kharkiv, 61022, Ukraine
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17
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Kishida K, Bosserman RE, Harb L, Khara P, Song L, Hu B, Zeng L, Christie PJ. Contributions of F‐specific Subunits to the F
Plasmid‐Encoded
Type
IV
Secretion System and F pilus. Mol Microbiol 2022; 117:1275-1290. [DOI: 10.1111/mmi.14908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/26/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Kouhei Kishida
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Rachel E. Bosserman
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
- Current address: Department of Medicine, Division of Infectious Diseases Washington School of Medicine St. Louis, MO, 63110
| | - Laith Harb
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX, 77843 USA
- Center for Phage Technology, Texas A&M University College Station TX, 77843 USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Liqiang Song
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Bo Hu
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX, 77843 USA
- Center for Phage Technology, Texas A&M University College Station TX, 77843 USA
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics McGovern Medical School 6431 Fannin St, Houston, Texas 77030
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18
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Liu X, Khara P, Baker ML, Christie PJ, Hu B. Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids. Nat Commun 2022; 13:379. [PMID: 35046412 PMCID: PMC8770708 DOI: 10.1038/s41467-022-28058-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022] Open
Abstract
Bacterial type IV secretion systems (T4SSs) are largely responsible for the proliferation of multi-drug resistance. We solved the structure of the outer-membrane core complex (OMCCF) of a T4SS encoded by a conjugative F plasmid at <3.0 Å resolution by cryoelectron microscopy. The OMCCF consists of a 13-fold symmetrical outer ring complex (ORC) built from 26 copies of TraK and TraV C-terminal domains, and a 17-fold symmetrical central cone (CC) composed of 17 copies of TraB β-barrels. Domains of TraV and TraB also bind the CC and ORC substructures, establishing that these proteins undergo an intraprotein symmetry alteration to accommodate the C13:C17 symmetry mismatch. We present evidence that other pED208-encoded factors stabilize the C13:C17 architecture and define the importance of TraK, TraV and TraB domains to T4SSF function. This work identifies OMCCF structural motifs of proposed importance for structural transitions associated with F plasmid dissemination and F pilus biogenesis.
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Affiliation(s)
- Xiangan Liu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA.
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, TX, 77030, USA.
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19
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Rocha EPC, Bikard D. Microbial defenses against mobile genetic elements and viruses: Who defends whom from what? PLoS Biol 2022; 20:e3001514. [PMID: 35025885 PMCID: PMC8791490 DOI: 10.1371/journal.pbio.3001514] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
Prokaryotes have numerous mobile genetic elements (MGEs) that mediate horizontal gene transfer (HGT) between cells. These elements can be costly, even deadly, and cells use numerous defense systems to filter, control, or inactivate them. Recent studies have shown that prophages, conjugative elements, their parasites (phage satellites and mobilizable elements), and other poorly described MGEs encode defense systems homologous to those of bacteria. These constitute a significant fraction of the repertoire of cellular defense genes. As components of MGEs, these defense systems have presumably evolved to provide them, not the cell, adaptive functions. While the interests of the host and MGEs are aligned when they face a common threat such as an infection by a virulent phage, defensive functions carried by MGEs might also play more selfish roles to fend off other antagonistic MGEs or to ensure their maintenance in the cell. MGEs are eventually lost from the surviving host genomes by mutational processes and their defense systems can be co-opted when they provide an advantage to the cell. The abundance of defense systems in MGEs thus sheds new light on the role, effect, and fate of the so-called "cellular defense systems," whereby they are not only merely microbial defensive weapons in a 2-partner arms race, but also tools of intragenomic conflict between multiple genetic elements with divergent interests that shape cell fate and gene flow at the population level.
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Affiliation(s)
- Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, Department of Microbiology, Paris, France
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20
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Bier E, Nizet V. Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance. Trends Genet 2021; 37:745-757. [PMID: 33745750 DOI: 10.1016/j.tig.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.
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Affiliation(s)
- Ethan Bier
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA.
| | - Victor Nizet
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA; Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA
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21
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Tittes C, Schwarzer S, Quax TEF. Viral Hijack of Filamentous Surface Structures in Archaea and Bacteria. Viruses 2021; 13:v13020164. [PMID: 33499367 PMCID: PMC7911016 DOI: 10.3390/v13020164] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
The bacterial and archaeal cell surface is decorated with filamentous surface structures that are used for different functions, such as motility, DNA exchange and biofilm formation. Viruses hijack these structures and use them to ride to the cell surface for successful entry. In this review, we describe currently known mechanisms for viral attachment, translocation, and entry via filamentous surface structures. We describe the different mechanisms used to exploit various surface structures bacterial and archaeal viruses. This overview highlights the importance of filamentous structures at the cell surface for entry of prokaryotic viruses.
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22
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Costa TRD, Harb L, Khara P, Zeng L, Hu B, Christie PJ. Type IV secretion systems: Advances in structure, function, and activation. Mol Microbiol 2021; 115:436-452. [PMID: 33326642 DOI: 10.1111/mmi.14670] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022]
Abstract
Bacterial type IV secretion systems (T4SSs) are a functionally diverse translocation superfamily. They consist mainly of two large subfamilies: (i) conjugation systems that mediate interbacterial DNA transfer and (ii) effector translocators that deliver effector macromolecules into prokaryotic or eukaryotic cells. A few other T4SSs export DNA or proteins to the milieu, or import exogenous DNA. The T4SSs are defined by 6 or 12 conserved "core" subunits that respectively elaborate "minimized" systems in Gram-positive or -negative bacteria. However, many "expanded" T4SSs are built from "core" subunits plus numerous others that are system-specific, which presumptively broadens functional capabilities. Recently, there has been exciting progress in defining T4SS assembly pathways and architectures using a combination of fluorescence and cryoelectron microscopy. This review will highlight advances in our knowledge of structure-function relationships for model Gram-negative bacterial T4SSs, including "minimized" systems resembling the Agrobacterium tumefaciens VirB/VirD4 T4SS and "expanded" systems represented by the Helicobacter pylori Cag, Legionella pneumophila Dot/Icm, and F plasmid-encoded Tra T4SSs. Detailed studies of these model systems are generating new insights, some at atomic resolution, to long-standing questions concerning mechanisms of substrate recruitment, T4SS channel architecture, conjugative pilus assembly, and machine adaptations contributing to T4SS functional versatility.
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Affiliation(s)
- Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Laith Harb
- Department of Biochemistry and Biophysics and Center for Phage Technology, Texas A&M University, College Station, TX, USA
| | - Pratick Khara
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics and Center for Phage Technology, Texas A&M University, College Station, TX, USA
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX, USA
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