1
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He L, Miguel-Romero L, Patkowski JB, Alqurainy N, Rocha EPC, Costa TRD, Fillol-Salom A, Penadés JR. Tail assembly interference is a common strategy in bacterial antiviral defenses. Nat Commun 2024; 15:7539. [PMID: 39215040 PMCID: PMC11364771 DOI: 10.1038/s41467-024-51915-4] [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: 02/02/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Many bacterial immune systems recognize phage structural components to activate antiviral responses, without inhibiting the function of the phage component. These systems can be encoded in specific chromosomal loci, known as defense islands, and in mobile genetic elements such as prophages and phage-inducible chromosomal islands (PICIs). Here, we identify a family of bacterial immune systems, named Tai (for 'tail assembly inhibition'), that is prevalent in PICIs, prophages and P4-like phage satellites. Tai systems protect their bacterial host population from other phages by blocking the tail assembly step, leading to the release of tailless phages incapable of infecting new hosts. To prevent autoimmunity, some Tai-positive phages have an associated counter-defense mechanism that is expressed during the phage lytic cycle and allows for tail formation. Interestingly, the Tai defense and counter-defense genes are organized in a non-contiguous operon, enabling their coordinated expression.
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Affiliation(s)
- Lingchen He
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Laura Miguel-Romero
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nasser Alqurainy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences & King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Tiago R D Costa
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Alfred Fillol-Salom
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
- School of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca, Spain.
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2
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Hobbs SJ, Nomburg J, Doudna JA, Kranzusch PJ. Animal and bacterial viruses share conserved mechanisms of immune evasion. Cell 2024:S0092-8674(24)00889-4. [PMID: 39197447 DOI: 10.1016/j.cell.2024.07.057] [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: 04/29/2024] [Revised: 07/05/2024] [Accepted: 07/30/2024] [Indexed: 09/01/2024]
Abstract
Animal and bacterial cells sense and defend against viral infections using evolutionarily conserved antiviral signaling pathways. Here, we show that viruses overcome host signaling using mechanisms of immune evasion that are directly shared across the eukaryotic and prokaryotic kingdoms of life. Structures of animal poxvirus proteins that inhibit host cGAS-STING signaling demonstrate architectural and catalytic active-site homology shared with bacteriophage Acb1 proteins, which inactivate CBASS anti-phage defense. In bacteria, phage Acb1 proteins are viral enzymes that degrade host cyclic nucleotide immune signals. Structural comparisons of poxvirus protein-2'3'-cGAMP and phage Acb1-3'3'-cGAMP complexes reveal a universal mechanism of host nucleotide immune signal degradation and explain kingdom-specific additions that enable viral adaptation. Chimeric bacteriophages confirm that animal poxvirus proteins are sufficient to evade immune signaling in bacteria. Our findings identify a mechanism of immune evasion conserved between animal and bacterial viruses and define shared rules that explain host-virus interactions across multiple kingdoms of life.
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Affiliation(s)
- Samuel J Hobbs
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jason Nomburg
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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3
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Tang S, Conte V, Zhang DJ, Žedaveinytė R, Lampe GD, Wiegand T, Tang LC, Wang M, Walker MWG, George JT, Berchowitz LE, Jovanovic M, Sternberg SH. De novo gene synthesis by an antiviral reverse transcriptase. Science 2024:eadq0876. [PMID: 39116258 DOI: 10.1126/science.adq0876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024]
Abstract
Defense-associated reverse transcriptase (DRT) systems perform DNA synthesis to protect bacteria against viral infection, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems encode an unprecedented immune pathway that involves de novo gene synthesis via rolling circle reverse transcription of a non-coding RNA (ncRNA). Programmed template jumping on the ncRNA generates a concatemeric cDNA, which becomes double-stranded upon viral infection. Remarkably, this DNA product constitutes a protein-coding, nearly endless ORF (neo) gene whose expression leads to potent cell growth arrest, thereby restricting the viral infection. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.
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Affiliation(s)
- Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Valentin Conte
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Dennis J Zhang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Rimantė Žedaveinytė
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Lauren C Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Megan Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jerrin Thomas George
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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4
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Ledvina HE, Whiteley AT. Conservation and similarity of bacterial and eukaryotic innate immunity. Nat Rev Microbiol 2024; 22:420-434. [PMID: 38418927 DOI: 10.1038/s41579-024-01017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Pathogens are ubiquitous and a constant threat to their hosts, which has led to the evolution of sophisticated immune systems in bacteria, archaea and eukaryotes. Bacterial immune systems encode an astoundingly large array of antiviral (antiphage) systems, and recent investigations have identified unexpected similarities between the immune systems of bacteria and animals. In this Review, we discuss advances in our understanding of the bacterial innate immune system and highlight the components, strategies and pathogen restriction mechanisms conserved between bacteria and eukaryotes. We summarize evidence for the hypothesis that components of the human immune system originated in bacteria, where they first evolved to defend against phages. Further, we discuss shared mechanisms that pathogens use to overcome host immune pathways and unexpected similarities between bacterial immune systems and interbacterial antagonism. Understanding the shared evolutionary path of immune components across domains of life and the successful strategies that organisms have arrived at to restrict their pathogens will enable future development of therapeutics that activate the human immune system for the precise treatment of disease.
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Affiliation(s)
- Hannah E Ledvina
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Aaron T Whiteley
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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5
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Hu WF, Yang JY, Wang JJ, Yuan SF, Yue XJ, Zhang Z, Zhang YQ, Meng JY, Li YZ. Characteristics and immune functions of the endogenous CRISPR-Cas systems in myxobacteria. mSystems 2024; 9:e0121023. [PMID: 38747603 PMCID: PMC11237760 DOI: 10.1128/msystems.01210-23] [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] [Received: 11/13/2023] [Accepted: 04/15/2024] [Indexed: 06/19/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The cas genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in Myxococcus xanthus DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery. IMPORTANCE Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials. Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in myxobacteria but also their potential applications.
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Affiliation(s)
- Wei-Feng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jiang-Yu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Fei Yuan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ya-Qi Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jun-Yan Meng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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6
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Beamud B, Benz F, Bikard D. Going viral: The role of mobile genetic elements in bacterial immunity. Cell Host Microbe 2024; 32:804-819. [PMID: 38870898 DOI: 10.1016/j.chom.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Bacteriophages and other mobile genetic elements (MGEs) pose a significant threat to bacteria, subjecting them to constant attacks. In response, bacteria have evolved a sophisticated immune system that employs diverse defensive strategies and mechanisms. Remarkably, a growing body of evidence suggests that most of these defenses are encoded by MGEs themselves. This realization challenges our traditional understanding of bacterial immunity and raises intriguing questions about the evolutionary forces at play. Our review provides a comprehensive overview of the latest findings on the main families of MGEs and the defense systems they encode. We also highlight how a vast diversity of defense systems remains to be discovered and their mechanism of mobility understood. Altogether, the composition and distribution of defense systems in bacterial genomes only makes sense in the light of the ecological and evolutionary interactions of a complex network of MGEs.
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Affiliation(s)
- Beatriz Beamud
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
| | - Fabienne Benz
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
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7
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Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JJG. Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Nature 2024; 630:484-492. [PMID: 38811729 DOI: 10.1038/s41586-024-07486-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/29/2024] [Indexed: 05/31/2024]
Abstract
The CRISPR system is an adaptive immune system found in prokaryotes that defends host cells against the invasion of foreign DNA1. As part of the ongoing struggle between phages and the bacterial immune system, the CRISPR system has evolved into various types, each with distinct functionalities2. Type II Cas9 is the most extensively studied of these systems and has diverse subtypes. It remains uncertain whether members of this family can evolve additional mechanisms to counter viral invasions3,4. Here we identify 2,062 complete Cas9 loci, predict the structures of their associated proteins and reveal three structural growth trajectories for type II-C Cas9. We found that novel associated genes (NAGs) tended to be present within the loci of larger II-C Cas9s. Further investigation revealed that CbCas9 from Chryseobacterium species contains a novel β-REC2 domain, and forms a heterotetrameric complex with an NAG-encoded CRISPR-Cas-system-promoting (pro-CRISPR) protein of II-C Cas9 (PcrIIC1). The CbCas9-PcrIIC1 complex exhibits enhanced DNA binding and cleavage activity, broader compatibility for protospacer adjacent motif sequences, increased tolerance for mismatches and improved anti-phage immunity, compared with stand-alone CbCas9. Overall, our work sheds light on the diversity and 'growth evolutionary' trajectories of II-C Cas9 proteins at the structural level, and identifies many NAGs-such as PcrIIC1, which serves as a pro-CRISPR factor to enhance CRISPR-mediated immunity.
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Affiliation(s)
- Shouyue Zhang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ao Sun
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing-Mei Qian
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuo Lin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenjing Xing
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yun Yang
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Han-Zhou Zhu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin-Yi Zhou
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Shuo Guo
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Liu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yu Meng
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shu-Lin Jin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Song
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Cheng-Ping Li
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhaofu Li
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuai Jin
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Caixia Gao
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunlai Chen
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Yang Bai
- State Key Laboratory of Plant Genomics, CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China.
| | - Jun-Jie Gogo Liu
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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8
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Wang Y, Dagan T. The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages. Nat Commun 2024; 15:4555. [PMID: 38811529 PMCID: PMC11137137 DOI: 10.1038/s41467-024-48352-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is often facilitated by mobile genetic elements that copy or translocate ARGs between DNA molecules. The agglomeration of mobile elements in plasmids generates resistance islands comprising multiple ARGs. However, whether the emergence of resistance islands is restricted to specific MDR plasmid lineages remains understudied. Here we show that the agglomeration of ARGs in resistance islands is biased towards specific large plasmid lineages. Analyzing 6784 plasmids in 2441 Escherichia, Salmonella, and Klebsiella isolates, we quantify that 84% of the ARGs in MDR plasmids are found in resistance islands. We furthermore observe rapid evolution of ARG combinations in resistance islands. Most regions identified as resistance islands are shared among closely related plasmids but rarely among distantly related plasmids. Our results suggest the presence of barriers for the dissemination of ARGs between plasmid lineages, which are related to plasmid genetic properties, host range and the plasmid evolutionary history. The agglomeration of ARGs in plasmids is attributed to the workings of mobile genetic elements that operate within the framework of existing plasmid lineages.
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Affiliation(s)
- Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany.
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9
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Otero-Olarra JE, Díaz-Cárdenas G, Aguilera-Arreola MG, Curiel-Quesada E, Pérez-Valdespino A. Aeromonas trota Is Highly Refractory to Acquire Exogenous Genetic Material. Microorganisms 2024; 12:1091. [PMID: 38930473 PMCID: PMC11206119 DOI: 10.3390/microorganisms12061091] [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: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Aeromonas trota is sensitive to most antibiotics and the sole species of this genus susceptible to ampicillin. This susceptibility profile could be related to its inability to acquire exogenous DNA. In this study, A. trota isolates were analyzed to establish their capacity to incorporate foreign DNA. Fourteen strains were identified as A. trota by multilocus phylogenetic analysis (MLPA). Minimal inhibitory concentrations of antibiotics (MIC) were assessed, confirming the susceptibility to most antibiotics tested. To explore their capacity to be transformed, A. trota strains were used as recipients in different horizontal transfer assays. Results showed that around fifty percent of A. trota strains were able to incorporate pBAMD1-2 and pBBR1MCS-3 plasmids after conjugal transfer. In all instances, conjugation frequencies were very low. Interestingly, several isoforms of plasmid pBBR1MCS-3 were observed in transconjugants. Strains could not receive pAr-32, a native plasmid from A. salmonicida. A. trota strains were unable to receive DNA by means of electroporation, natural transformation or vesiduction. These results confirm that A. trota species are extremely refractory to horizontal gene transfer, which could be associated to plasmid instability resulting from oligomerization or to the presence of defense systems against exogenous genetic material in their genomes. To explain the poor results of horizontal gene transfer (HGT), selected genomes were sequenced and analyzed, revealing the presence of defense systems, which could prevent the stable incorporation of exogenous DNA in A. trota.
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Affiliation(s)
- Jorge Erick Otero-Olarra
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
| | - Gilda Díaz-Cárdenas
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
| | - Ma Guadalupe Aguilera-Arreola
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico;
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.E.O.-O.); (G.D.-C.)
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10
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Pfeifer E, Rocha EPC. Phage-plasmids promote recombination and emergence of phages and plasmids. Nat Commun 2024; 15:1545. [PMID: 38378896 PMCID: PMC10879196 DOI: 10.1038/s41467-024-45757-3] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
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Affiliation(s)
- Eugen Pfeifer
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
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11
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Banchi E, Corre E, Del Negro P, Celussi M, Malfatti F. Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:126-142. [PMID: 38433960 PMCID: PMC10902248 DOI: 10.1007/s42995-023-00192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00192-z.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Erwan Corre
- FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), Sorbonne Université CNRS, 29680 Roscoff, France
| | - Paola Del Negro
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Francesca Malfatti
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
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12
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Oggenfuss U, Badet T, Croll D. A systematic screen for co-option of transposable elements across the fungal kingdom. Mob DNA 2024; 15:2. [PMID: 38245743 PMCID: PMC10799480 DOI: 10.1186/s13100-024-00312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived from Academ, Kolobok or Helitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of putative host-TE fusions and facilitates systematic investigations of candidate fusion proteins.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Department of Microbiology and Immunology, University of Minnesota, Medical School, Minneapolis, Minnesota, United States of America
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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13
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Lucia-Sanz A, Peng S, Leung CY(J, Gupta A, Meyer JR, Weitz JS. Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574707. [PMID: 38260415 PMCID: PMC10802490 DOI: 10.1101/2024.01.08.574707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary -and largely uncharacterized- genetics of adsorption, injection, and cell take-over. Here we present a machine learning (ML) approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions amongst 51 Escherichia coli strains and 45 phage λ strains that coevolved in laboratory conditions for 37 days. Leveraging multiple inference strategies and without a priori knowledge of driver mutations, this framework predicts both who infects whom and the quantitative levels of infections across a suite of 2,295 potential interactions. The most effective ML approach inferred interaction phenotypes from independent contributions from phage and bacteria mutations, predicting phage host range with 86% mean classification accuracy while reducing the relative error in the estimated strength of the infection phenotype by 40%. Further, transparent feature selection in the predictive model revealed 18 of 176 phage λ and 6 of 18 E. coli mutations that have a significant influence on the outcome of phage-bacteria interactions, corroborating sites previously known to affect phage λ infections, as well as identifying mutations in genes of unknown function not previously shown to influence bacterial resistance. While the genetic variation studied was limited to a focal, coevolved phage-bacteria system, the method's success at recapitulating strain-level infection outcomes provides a path forward towards developing strategies for inferring interactions in non-model systems, including those of therapeutic significance.
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Affiliation(s)
- Adriana Lucia-Sanz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | | | - Animesh Gupta
- Department of Physics, University of California San Diego, La Jolla, California, USA
| | - Justin R. Meyer
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| | - Joshua S. Weitz
- Department of Biology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
- Institut d’Biologie, École Normale Supérieure, Paris, France
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14
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Schmitz M, Querques I. DNA on the move: mechanisms, functions and applications of transposable elements. FEBS Open Bio 2024; 14:13-22. [PMID: 38041553 PMCID: PMC10761935 DOI: 10.1002/2211-5463.13743] [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: 03/27/2023] [Revised: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023] Open
Abstract
Transposons are mobile genetic elements that have invaded all domains of life by moving between and within their host genomes. Due to their mobility (or transposition), transposons facilitate horizontal gene transfer in bacteria and foster the evolution of new molecular functions in prokaryotes and eukaryotes. As transposition can lead to detrimental genomic rearrangements, organisms have evolved a multitude of molecular strategies to control transposons, including genome defense mechanisms provided by CRISPR-Cas systems. Apart from their biological impacts on genomes, DNA transposons have been leveraged as efficient gene insertion vectors in basic research, transgenesis and gene therapy. However, the close to random insertion profile of transposon-based tools limits their programmability and safety. Despite recent advances brought by the development of CRISPR-associated genome editing nucleases, a strategy for efficient insertion of large, multi-kilobase transgenes at user-defined genomic sites is currently challenging. The discovery and experimental characterization of bacterial CRISPR-associated transposons (CASTs) led to the attractive hypothesis that these systems could be repurposed as programmable, site-specific gene integration technologies. Here, we provide a broad overview of the molecular mechanisms underpinning DNA transposition and of its biological and technological impact. The second focus of the article is to describe recent mechanistic and functional analyses of CAST transposition. Finally, current challenges and desired future advances of CAST-based genome engineering applications are briefly discussed.
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Affiliation(s)
| | - Irma Querques
- Department of BiochemistryUniversity of ZurichSwitzerland
- Max Perutz Labs, Vienna Biocenter Campus (VBC)Austria
- Department of Structural and Computational Biology, Center for Molecular BiologyUniversity of ViennaAustria
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15
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Rousset F. Innate immunity: the bacterial connection. Trends Immunol 2023; 44:945-953. [PMID: 37919213 DOI: 10.1016/j.it.2023.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/07/2023] [Accepted: 10/07/2023] [Indexed: 11/04/2023]
Abstract
Pathogens have fueled the diversification of intracellular defense strategies that collectively define cell-autonomous innate immunity. In bacteria, innate immunity is manifested by a broad arsenal of defense systems that provide protection against bacterial viruses, called phages. The complexity of the bacterial immune repertoire has only been realized recently and is now suggesting that innate immunity has commonalities across the tree of life: many components of eukaryotic innate immunity are found in bacteria where they protect against phages, including the cGAS-STING pathway, gasdermins, and viperins. Here, I summarize recent findings on the conservation of innate immune pathways between prokaryotes and eukaryotes and hypothesize that bacterial defense mechanisms can catalyze the discovery of novel molecular players of eukaryotic innate immunity.
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Affiliation(s)
- François Rousset
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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16
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Koonin EV, Krupovic M. New faces of prokaryotic mobile genetic elements: guide RNAs link transposition with host defense mechanisms. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 36:100473. [PMID: 37779558 PMCID: PMC10538440 DOI: 10.1016/j.coisb.2023.100473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Most life forms harbor multiple, diverse mobile genetic elements (MGE) that widely differ in their rates and mechanisms of mobility. Recent findings on two classes of MGE in prokaryotes revealed a novel mechanism, RNA-guided transposition, where a transposon-encoded guide RNA directs the transposase to a unique site in the host genome. Tn7-like transposons, on multiple occasions, recruited CRISPR systems that lost the capacity to cleave target DNA and instead mediate RNA-guided transposition via CRISPR RNA. Conversely, the abundant transposon-associated, RNA-guided nucleases IscB and TnpB that appear to promote proliferation of IS200/IS605 and IS607 transposons were the likely evolutionary ancestors of type II and type V CRISPR systems, respectively. Thus, RNA-guided target recognition is a major biological phenomenon that connects MGE with host defense mechanisms. More RNA-guided defensive and MGE-associated functionalities are likely to be discovered.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015 Paris
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17
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Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol 2023; 14:1264877. [PMID: 37886057 PMCID: PMC10598620 DOI: 10.3389/fmicb.2023.1264877] [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: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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18
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Meers C, Le HC, Pesari SR, Hoffmann FT, Walker MWG, Gezelle J, Tang S, Sternberg SH. Transposon-encoded nucleases use guide RNAs to promote their selfish spread. Nature 2023; 622:863-871. [PMID: 37758954 DOI: 10.1038/s41586-023-06597-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Insertion sequences are compact and pervasive transposable elements found in bacteria, which encode only the genes necessary for their mobilization and maintenance1. IS200- and IS605-family transposons undergo 'peel-and-paste' transposition catalysed by a TnpA transposase2, but they also encode diverse, TnpB- and IscB-family proteins that are evolutionarily related to the CRISPR-associated effectors Cas12 and Cas9, respectively3,4. Recent studies have demonstrated that TnpB and IscB function as RNA-guided DNA endonucleases5,6, but the broader biological role of this activity has remained enigmatic. Here we show that TnpB and IscB are essential to prevent permanent transposon loss as a consequence of the TnpA transposition mechanism. We selected a family of related insertion sequences from Geobacillus stearothermophilus that encode several TnpB and IscB orthologues, and showed that a single TnpA transposase was broadly active for transposon mobilization. The donor joints formed upon religation of transposon-flanking sequences were efficiently targeted for cleavage by RNA-guided TnpB and IscB nucleases, and co-expression of TnpB and TnpA led to substantially greater transposon retention relative to conditions in which TnpA was expressed alone. Notably, TnpA and TnpB also stimulated recombination frequencies, surpassing rates observed with TnpB alone. Collectively, this study reveals that RNA-guided DNA cleavage arose as a primal biochemical activity to bias the selfish inheritance and spread of transposable elements, which was later co-opted during the evolution of CRISPR-Cas adaptive immunity for antiviral defence.
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Affiliation(s)
- Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Hoang C Le
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sanjana R Pesari
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Biochemistry and Molecular Biophysics Program, University of California, San Diego, CA, USA
| | - Florian T Hoffmann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jeanine Gezelle
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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19
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Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol 2023; 21:686-700. [PMID: 37460672 DOI: 10.1038/s41579-023-00934-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/14/2023]
Abstract
Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.
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20
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Ma J, Zhao H, Mo S, Li J, Ma X, Tang Y, Li H, Liu Z. Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii. Microb Genom 2023; 9:001107. [PMID: 37754275 PMCID: PMC10569733 DOI: 10.1099/mgen.0.001107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacteraemia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii. In this study, we analysed the pan-genome of 233 A. veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii. Single molecule real-time sequencing was applied to identify the motif methylated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.
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Affiliation(s)
- Jiayue Ma
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Honghao Zhao
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Shuangyi Mo
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Xiang Ma
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Yanqiong Tang
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Hong Li
- School of Life Sciences, Hainan University, Haikou, PR China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou, PR China
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21
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Shmakov SA, Barth ZK, Makarova KS, Wolf Y, Brover V, Peters J, Koonin E. Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems. Nucleic Acids Res 2023; 51:8150-8168. [PMID: 37283088 PMCID: PMC10450183 DOI: 10.1093/nar/gkad495] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
CRISPR-cas loci typically contain CRISPR arrays with unique spacers separating direct repeats. Spacers along with portions of adjacent repeats are transcribed and processed into CRISPR(cr) RNAs that target complementary sequences (protospacers) in mobile genetic elements, resulting in cleavage of the target DNA or RNA. Additional, standalone repeats in some CRISPR-cas loci produce distinct cr-like RNAs implicated in regulatory or other functions. We developed a computational pipeline to systematically predict crRNA-like elements by scanning for standalone repeat sequences that are conserved in closely related CRISPR-cas loci. Numerous crRNA-like elements were detected in diverse CRISPR-Cas systems, mostly, of type I, but also subtype V-A. Standalone repeats often form mini-arrays containing two repeat-like sequence separated by a spacer that is partially complementary to promoter regions of cas genes, in particular cas8, or cargo genes located within CRISPR-Cas loci, such as toxins-antitoxins. We show experimentally that a mini-array from a type I-F1 CRISPR-Cas system functions as a regulatory guide. We also identified mini-arrays in bacteriophages that could abrogate CRISPR immunity by inhibiting effector expression. Thus, recruitment of CRISPR effectors for regulatory functions via spacers with partial complementarity to the target is a common feature of diverse CRISPR-Cas systems.
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Affiliation(s)
- Sergey A Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Zachary K Barth
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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22
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Singh M, Kondrashkina AM, Widmann TJ, Cortes JL, Bansal V, Wang J, Römer C, Garcia-Canadas M, Garcia-Perez JL, Hurst LD, Izsvák Z. A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass. PLoS Biol 2023; 21:e3002162. [PMID: 37339119 DOI: 10.1371/journal.pbio.3002162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/12/2023] [Indexed: 06/22/2023] Open
Abstract
There remains much that we do not understand about the earliest stages of human development. On a gross level, there is evidence for apoptosis, but the nature of the affected cell types is unknown. Perhaps most importantly, the inner cell mass (ICM), from which the foetus is derived and hence of interest in reproductive health and regenerative medicine, has proven hard to define. Here, we provide a multi-method analysis of the early human embryo to resolve these issues. Single-cell analysis (on multiple independent datasets), supported by embryo visualisation, uncovers a common previously uncharacterised class of cells lacking commitment markers that segregates after embryonic gene activation (EGA) and shortly after undergo apoptosis. The discovery of this cell type allows us to clearly define their viable ontogenetic sisters, these being the cells of the ICM. While ICM is characterised by the activity of an Old non-transposing endogenous retrovirus (HERVH) that acts to suppress Young transposable elements, the new cell type, by contrast, expresses transpositionally competent Young elements and DNA-damage response genes. As the Young elements are RetroElements and the cells are excluded from the developmental process, we dub these REject cells. With these and ICM being characterised by differential mobile element activities, the human embryo may be a "selection arena" in which one group of cells selectively die, while other less damaged cells persist.
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Affiliation(s)
- Manvendra Singh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
- Max Planck Institute of Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | | | - Thomas J Widmann
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jose L Cortes
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Vikas Bansal
- German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Jichang Wang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Christine Römer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Marta Garcia-Canadas
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jose L Garcia-Perez
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
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23
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Petrovic Fabijan A, Iredell J, Danis-Wlodarczyk K, Kebriaei R, Abedon ST. Translating phage therapy into the clinic: Recent accomplishments but continuing challenges. PLoS Biol 2023; 21:e3002119. [PMID: 37220114 PMCID: PMC10204993 DOI: 10.1371/journal.pbio.3002119] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Phage therapy is a medical form of biological control of bacterial infections, one that uses naturally occurring viruses, called bacteriophages or phages, as antibacterial agents. Pioneered over 100 years ago, phage therapy nonetheless is currently experiencing a resurgence in interest, with growing numbers of clinical case studies being published. This renewed enthusiasm is due in large part to phage therapy holding promise for providing safe and effective cures for bacterial infections that traditional antibiotics acting alone have been unable to clear. This Essay introduces basic phage biology, provides an outline of the long history of phage therapy, highlights some advantages of using phages as antibacterial agents, and provides an overview of recent phage therapy clinical successes. Although phage therapy has clear clinical potential, it faces biological, regulatory, and economic challenges to its further implementation and more mainstream acceptance.
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Affiliation(s)
- Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Western Sydney Local Health District, Westmead, New South Wales, Australia
| | - Katarzyna Danis-Wlodarczyk
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Razieh Kebriaei
- P3 Research Laboratory, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, United States of America
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24
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Crespo-Bellido A, Duffy S. The how of counter-defense: viral evolution to combat host immunity. Curr Opin Microbiol 2023; 74:102320. [PMID: 37075547 DOI: 10.1016/j.mib.2023.102320] [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: 01/07/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Viruses are locked in an evolutionary arms race with their hosts. What ultimately determines viral evolvability, or capacity for adaptive evolution, is their ability to efficiently explore and expand sequence space while under the selective regime imposed by their ecology, which includes innate and adaptive host defenses. Viral genomes have significantly higher evolutionary rates than their host counterparts and should have advantages relative to their slower-evolving hosts. However, functional constraints on virus evolutionary landscapes along with the modularity and mutational tolerance of host defense proteins may help offset the advantage conferred to viruses by high evolutionary rates. Additionally, cellular life forms from all domains of life possess many highly complex defense mechanisms that act as hurdles to viral replication. Consequently, viruses constantly probe sequence space through mutation and genetic exchange and are under pressure to optimize diverse counter-defense strategies.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.
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25
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Hochhauser D, Millman A, Sorek R. The defense island repertoire of the Escherichia coli pan-genome. PLoS Genet 2023; 19:e1010694. [PMID: 37023146 PMCID: PMC10121019 DOI: 10.1371/journal.pgen.1010694] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/21/2023] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
It has become clear in recent years that anti-phage defense systems cluster non-randomly within bacterial genomes in so-called "defense islands". Despite serving as a valuable tool for the discovery of novel defense systems, the nature and distribution of defense islands themselves remain poorly understood. In this study, we comprehensively mapped the defense system repertoire of >1,300 strains of Escherichia coli, the most widely studied organism for phage-bacteria interactions. We found that defense systems are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, which preferentially integrate at several dozens of dedicated hotspots in the E. coli genome. Each mobile genetic element type has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.7 hotspots occupied by defense system-containing mobile elements, with some strains possessing up to eight defensively occupied hotspots. Defense systems frequently co-localize with other systems on the same mobile genetic element, in agreement with the observed defense island phenomenon. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements, explaining why the immune repertoire varies substantially between different strains of the same species.
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Affiliation(s)
- Dina Hochhauser
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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26
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Sasnauskas G, Tamulaitiene G, Druteika G, Carabias A, Silanskas A, Kazlauskas D, Venclovas Č, Montoya G, Karvelis T, Siksnys V. TnpB structure reveals minimal functional core of Cas12 nuclease family. Nature 2023; 616:384-389. [PMID: 37020015 DOI: 10.1038/s41586-023-05826-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 04/07/2023]
Abstract
The widespread TnpB proteins of IS200/IS605 transposon family have recently emerged as the smallest RNA-guided nucleases capable of targeted genome editing in eukaryotic cells1,2. Bioinformatic analysis identified TnpB proteins as the likely predecessors of Cas12 nucleases3-5, which along with Cas9 are widely used for targeted genome manipulation. Whereas Cas12 family nucleases are well characterized both biochemically and structurally6, the molecular mechanism of TnpB remains unknown. Here we present the cryogenic-electron microscopy structures of the Deinococcus radiodurans TnpB-reRNA (right-end transposon element-derived RNA) complex in DNA-bound and -free forms. The structures reveal the basic architecture of TnpB nuclease and the molecular mechanism for DNA target recognition and cleavage that is supported by biochemical experiments. Collectively, these results demonstrate that TnpB represents the minimal structural and functional core of the Cas12 protein family and provide a framework for developing TnpB-based genome editing tools.
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Affiliation(s)
- Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gytis Druteika
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Arturo Carabias
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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27
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Makarova KS, Wolf YI, Koonin EV. In Silico Approaches for Prediction of Anti-CRISPR Proteins. J Mol Biol 2023; 435:168036. [PMID: 36868398 PMCID: PMC10073340 DOI: 10.1016/j.jmb.2023.168036] [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: 10/26/2022] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023]
Abstract
Numerous viruses infecting bacteria and archaea encode CRISPR-Cas system inhibitors, known as anti-CRISPR proteins (Acr). The Acrs typically are highly specific for particular CRISPR variants, resulting in remarkable sequence and structural diversity and complicating accurate prediction and identification of Acrs. In addition to their intrinsic interest for understanding the coevolution of defense and counter-defense systems in prokaryotes, Acrs could be natural, potent on-off switches for CRISPR-based biotechnological tools, so their discovery, characterization and application are of major importance. Here we discuss the computational approaches for Acr prediction. Due to the enormous diversity and likely multiple origins of the Acrs, sequence similarity searches are of limited use. However, multiple features of protein and gene organization have been successfully harnessed to this end including small protein size and distinct amino acid compositions of the Acrs, association of acr genes in virus genomes with genes encoding helix-turn-helix proteins that regulate Acr expression (Acr-associated proteins, Aca), and presence of self-targeting CRISPR spacers in bacterial and archaeal genomes containing Acr-encoding proviruses. Productive approaches for Acr prediction also involve genome comparison of closely related viruses, of which one is resistant and the other one is sensitive to a particular CRISPR variant, and "guilt by association" whereby genes adjacent to a homolog of a known Aca are identified as candidate Acrs. The distinctive features of Acrs are employed for Acr prediction both by developing dedicated search algorithms and through machine learning. New approaches will be needed to identify novel types of Acrs that are likely to exist.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
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28
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Meers C, Le H, Pesari SR, Hoffmann FT, Walker MW, Gezelle J, Sternberg SH. Transposon-encoded nucleases use guide RNAs to selfishly bias their inheritance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532601. [PMID: 36993599 PMCID: PMC10055086 DOI: 10.1101/2023.03.14.532601] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Insertion sequences (IS) are compact and pervasive transposable elements found in bacteria, which encode only the genes necessary for their mobilization and maintenance. IS 200 /IS 605 elements undergo 'peel-and-paste' transposition catalyzed by a TnpA transposase, but intriguingly, they also encode diverse, TnpB- and IscB-family proteins that are evolutionarily related to the CRISPR-associated effectors Cas12 and Cas9, respectively. Recent studies demonstrated that TnpB-family enzymes function as RNA-guided DNA endonucleases, but the broader biological role of this activity has remained enigmatic. Here we show that TnpB/IscB are essential to prevent permanent transposon loss as a consequence of the TnpA transposition mechanism. We selected a family of related IS elements from Geobacillus stearothermophilus that encode diverse TnpB/IscB orthologs, and showed that a single TnpA transposase was active for transposon excision. The donor joints formed upon religation of IS-flanking sequences were efficiently targeted for cleavage by RNA-guided TnpB/IscB nucleases, and co-expression of TnpB together with TnpA led to significantly greater transposon retention, relative to conditions in which TnpA was expressed alone. Remarkably, TnpA and TnpB/IscB recognize the same AT-rich transposon-adjacent motif (TAM) during transposon excision and RNA-guided DNA cleavage, respectively, revealing a striking convergence in the evolution of DNA sequence specificity between collaborating transposase and nuclease proteins. Collectively, our study reveals that RNA-guided DNA cleavage is a primal biochemical activity that arose to bias the selfish inheritance and spread of transposable elements, which was later co-opted during the evolution of CRISPR-Cas adaptive immunity for antiviral defense.
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Affiliation(s)
- Chance Meers
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Hoang Le
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Sanjana R. Pesari
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Florian T. Hoffmann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Matt W.G. Walker
- Department of Biological Sciences, Columbia University, New York, NY
| | - Jeanine Gezelle
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
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29
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [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: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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30
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Botelho J, Tüffers L, Fuss J, Buchholz F, Utpatel C, Klockgether J, Niemann S, Tümmler B, Schulenburg H. Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa. EBioMedicine 2023; 90:104532. [PMID: 36958270 PMCID: PMC10053402 DOI: 10.1016/j.ebiom.2023.104532] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named A, B, and C). Here, we assessed phylogroup-specific evolutionary dynamics across available and also new P. aeruginosa genomes. METHODS In this genomic analysis, we first generated new genome assemblies for 18 strains of the major P. aeruginosa clone type (mPact) panel, comprising a phylogenetically diverse collection of clinical and environmental isolates for this species. Thereafter, we combined these new genomes with 1991 publicly available P. aeruginosa genomes for a phylogenomic and comparative analysis. We specifically explored to what extent antimicrobial resistance (AMR) genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and "masked" (RGP-free) genomes, and to what extent this variation differs among the phylogroups. FINDINGS We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, inter- and intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events. Finally, we provide here the mPact panel of diverse P. aeruginosa strains that may serve as a valuable reference for functional analyses. INTERPRETATION Altogether, our results highlight distinct pangenome characteristics of the P. aeruginosa phylogroups, which are possibly influenced by variation in the abundance of CRISPR-Cas systems and are shaped by the differential distribution of other defence systems and AMR genes. FUNDING German Science Foundation, Max-Planck Society, Leibniz ScienceCampus Evolutionary Medicine of the Lung, BMBF program Medical Infection Genomics, Kiel Life Science Postdoc Award.
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Affiliation(s)
- João Botelho
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
| | - Leif Tüffers
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Florian Buchholz
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Hinrich Schulenburg
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
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31
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Sather LM, Zamani M, Muhammed Z, Kearsley JVS, Fisher GT, Jones KM, Finan TM. A broadly distributed predicted helicase/nuclease confers phage resistance via abortive infection. Cell Host Microbe 2023; 31:343-355.e5. [PMID: 36893733 DOI: 10.1016/j.chom.2023.01.010] [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: 08/31/2022] [Revised: 11/16/2022] [Accepted: 01/11/2023] [Indexed: 03/11/2023]
Abstract
There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
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Affiliation(s)
- Leah M Sather
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Maryam Zamani
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Zahed Muhammed
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Jason V S Kearsley
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Gabrielle T Fisher
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Kathryn M Jones
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Turlough M Finan
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada.
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32
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Weltzer ML, Wall D. Social Diversification Driven by Mobile Genetic Elements. Genes (Basel) 2023; 14:648. [PMID: 36980919 PMCID: PMC10047993 DOI: 10.3390/genes14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.
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Affiliation(s)
- Michael L Weltzer
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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33
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Shmakov SA, Barth ZK, Makarova KS, Wolf YI, Brover V, Peters JE, Koonin EV. Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.03.530964. [PMID: 37090614 PMCID: PMC10120712 DOI: 10.1101/2023.03.03.530964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
CRISPR- cas loci typically contain CRISPR arrays with unique spacers separating direct repeats. Spacers along with portions of adjacent repeats are transcribed and processed into CRISPR(cr) RNAs that target complementary sequences (protospacers) in mobile genetic elements, resulting in cleavage of the target DNA or RNA. Additional, standalone repeats in some CRISPR- cas loci produce distinct cr-like RNAs implicated in regulatory or other functions. We developed a computational pipeline to systematically predict crRNA-like elements by scanning for standalone repeat sequences that are conserved in closely related CRISPR- cas loci. Numerous crRNA-like elements were detected in diverse CRISPR-Cas systems, mostly, of type I, but also subtype V-A. Standalone repeats often form mini-arrays containing two repeat-like sequence separated by a spacer that is partially complementary to promoter regions of cas genes, in particular cas8 , or cargo genes located within CRISPR-Cas loci, such as toxins-antitoxins. We show experimentally that a mini-array from a type I-F1 CRISPR-Cas system functions as a regulatory guide. We also identified mini-arrays in bacteriophages that could abrogate CRISPR immunity by inhibiting effector expression. Thus, recruitment of CRISPR effectors for regulatory functions via spacers with partial complementarity to the target is a common feature of diverse CRISPR-Cas systems.
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Affiliation(s)
- Sergey A. Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Zachary K. Barth
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Joseph E. Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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34
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Sun YH, Cui H, Song C, Shen JT, Zhuo X, Wang RH, Yu X, Ndamba R, Mu Q, Gu H, Wang D, Murthy GG, Li P, Liang F, Liu L, Tao Q, Wang Y, Orlowski S, Xu Q, Zhou H, Jagne J, Gokcumen O, Anthony N, Zhao X, Li XZ. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. Nat Commun 2023; 14:812. [PMID: 36781861 PMCID: PMC9925758 DOI: 10.1038/s41467-023-36354-x] [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: 07/14/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.
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Affiliation(s)
- Yu H Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hongxiao Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chi Song
- College of Public Health, Division of Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiafei Teng Shen
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, 322000, China
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ruoqiao Huiyi Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rudo Ndamba
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Qian Mu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hanwen Gu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Duolin Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gayathri Guru Murthy
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Pidong Li
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Fan Liang
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Lei Liu
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Qing Tao
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Sara Orlowski
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Qi Xu
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Jarra Jagne
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, NY, 14850, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Nick Anthony
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada.
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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35
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Beltran LC, Cvirkaite-Krupovic V, Miller J, Wang F, Kreutzberger MAB, Patkowski JB, Costa TRD, Schouten S, Levental I, Conticello VP, Egelman EH, Krupovic M. Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery. Nat Commun 2023; 14:666. [PMID: 36750723 PMCID: PMC9905601 DOI: 10.1038/s41467-023-36349-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/27/2023] [Indexed: 02/09/2023] Open
Abstract
Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.
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Affiliation(s)
- Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA
| | | | - Jessalyn Miller
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama Birmingham, Birmingham, AL, 35233, USA
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA
| | - Jonasz B Patkowski
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, UK
| | - Stefan Schouten
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, The Netherlands
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, 22903, USA
| | | | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015, Paris, France.
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36
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Abedon ST. Ecology and Evolutionary Biology of Hindering Phage Therapy: The Phage Tolerance vs. Phage Resistance of Bacterial Biofilms. Antibiotics (Basel) 2023; 12:245. [PMID: 36830158 PMCID: PMC9952518 DOI: 10.3390/antibiotics12020245] [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: 12/31/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
As with antibiotics, we can differentiate various acquired mechanisms of bacteria-mediated inhibition of the action of bacterial viruses (phages or bacteriophages) into ones of tolerance vs. resistance. These also, respectively, may be distinguished as physiological insensitivities (or protections) vs. resistance mutations, phenotypic resistance vs. genotypic resistance, temporary vs. more permanent mechanisms, and ecologically vs. also near-term evolutionarily motivated functions. These phenomena can result from multiple distinct molecular mechanisms, many of which for bacterial tolerance of phages are associated with bacterial biofilms (as is also the case for the bacterial tolerance of antibiotics). The resulting inhibitions are relevant from an applied perspective because of their potential to thwart phage-based treatments of bacterial infections, i.e., phage therapies, as well as their potential to interfere more generally with approaches to the phage-based biological control of bacterial biofilms. In other words, given the generally low toxicity of properly chosen therapeutic phages, it is a combination of phage tolerance and phage resistance, as displayed by targeted bacteria, that seems to represent the greatest impediments to phage therapy's success. Here I explore general concepts of bacterial tolerance of vs. bacterial resistance to phages, particularly as they may be considered in association with bacterial biofilms.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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37
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Alqurainy N, Miguel-Romero L, Moura de Sousa J, Chen J, Rocha EPC, Fillol-Salom A, Penadés JR. A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature. Cell Host Microbe 2023; 31:69-82.e5. [PMID: 36596306 DOI: 10.1016/j.chom.2022.12.001] [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: 05/19/2022] [Revised: 10/06/2022] [Accepted: 12/01/2022] [Indexed: 01/03/2023]
Abstract
Phage satellites are genetic elements that couple their life cycle to that of helper phages they parasitize, interfering with phage packaging through the production of small capsids, where only satellites are packaged. So far, in all analyzed systems, the satellite-sized capsids are composed of phage proteins. Here, we report that a family of phage-inducible chromosomal islands (PICIs), a type of satellites, encodes all the proteins required for both the production of small-sized capsids and the exclusive packaging of the PICIs into these capsids. Therefore, this new family, named capsid-forming PICIs (cf-PICIs), only requires phage tails to generate PICI particles. Remarkably, the representative cf-PICIs are produced with no cost from their helper phages, suggesting that the relationship between these elements is not parasitic. Finally, our phylogenomic studies indicate that cf-PICIs are present both in gram-positive and gram-negative bacteria and have evolved at least three times independently to spread in nature.
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Affiliation(s)
- Nasser Alqurainy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia
| | - Laura Miguel-Romero
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Jorge Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - John Chen
- Department of Microbiology and Immunology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK; Universidad CEU Cardenal Herrera, CEU Universities, Valencia 46115, Spain.
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38
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Botelho J, Cazares A, Schulenburg H. The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements. Nucleic Acids Res 2023; 51:236-252. [PMID: 36610752 PMCID: PMC9841420 DOI: 10.1093/nar/gkac1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023] Open
Abstract
Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance (AMR) genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), across all ESKAPE pathogens. We found that different MGE types are asymmetrically distributed across these pathogens, and that most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and AMR genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we observed that CRISPR spacers found on prophages, ICEs/IMEs, and plasmids have different targeting biases: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IMEs CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.
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Affiliation(s)
- João Botelho
- To whom correspondence should be addressed. Tel: +49 431 880 4143;
| | - Adrian Cazares
- EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Hinrich Schulenburg
- Antibiotic Resistance Evolution Group, Max Planck Institute for Evolutionary Biology, Plön, Germany,Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian Albrechts University, Kiel, Germany
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Mukherjee K, Moroz LL. Transposon-derived transcription factors across metazoans. Front Cell Dev Biol 2023; 11:1113046. [PMID: 36960413 PMCID: PMC10027918 DOI: 10.3389/fcell.2023.1113046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
Transposable elements (TE) could serve as sources of new transcription factors (TFs) in plants and some other model species, but such evidence is lacking for most animal lineages. Here, we discovered multiple independent co-options of TEs to generate 788 TFs across Metazoa, including all early-branching animal lineages. Six of ten superfamilies of DNA transposon-derived conserved TF families (ZBED, CENPB, FHY3, HTH-Psq, THAP, and FLYWCH) were identified across nine phyla encompassing the entire metazoan phylogeny. The most extensive convergent domestication of potentially TE-derived TFs occurred in the hydroid polyps, polychaete worms, cephalopods, oysters, and sea slugs. Phylogenetic reconstructions showed species-specific clustering and lineage-specific expansion; none of the identified TE-derived TFs revealed homologs in their closest neighbors. Together, our study established a framework for categorizing TE-derived TFs and informing the origins of novel genes across phyla.
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Affiliation(s)
- Krishanu Mukherjee
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
- *Correspondence: Leonid L. Moroz, ; Krishanu Mukherjee,
| | - Leonid L. Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
- Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, United States
- *Correspondence: Leonid L. Moroz, ; Krishanu Mukherjee,
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40
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Conrad B, Iseli C, Pirovino M. Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles. PLoS One 2023; 18:e0281661. [PMID: 36972235 PMCID: PMC10042343 DOI: 10.1371/journal.pone.0281661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/29/2023] [Indexed: 03/29/2023] Open
Abstract
All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energy required for survival, and an evolvable, informational polymer-the genome-conferring heredity. Genome replication invariably generates essential and ubiquitous genetic parasites. Here we model the energetic, replicative conditions of LUCA-like organisms and their parasites, as well as adaptive problem solving of host-parasite pairs. We show using an adapted Lotka-Volterra frame-work that three host-parasite pairs-individually a unit of a host and a parasite that is itself parasitized, therefore a nested parasite pair-are sufficient for robust and stable homeostasis, forming a life cycle. This nested parasitism model includes competition and habitat restriction. Its catalytic life cycle efficiently captures, channels and transforms energy, enabling dynamic host survival and adaptation. We propose a Malthusian fitness model for a quasispecies evolving through a host-nested parasite life cycle with two core features, rapid replacement of degenerate parasites and increasing evolutionary stability of host-nested parasite units from one to three pairs.
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Affiliation(s)
| | - Christian Iseli
- Bioinformatics Competence Center, EPFL and Unil, Lausanne, Switzerland
| | - Magnus Pirovino
- OPIRO Consulting Ltd, Triesen, Principality of Liechtenstein
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41
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Salgado O, Guajardo-Leiva S, Moya-Beltrán A, Barbosa C, Ridley C, Tamayo-Leiva J, Quatrini R, Mojica FJM, Díez B. Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities. Front Microbiol 2022; 13:1069452. [DOI: 10.3389/fmicb.2022.1069452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42–80°C, pH 6–9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.
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42
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When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements. Curr Opin Microbiol 2022; 70:102230. [PMID: 36335712 DOI: 10.1016/j.mib.2022.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. We describe two key types of interactions - defense systems and genetic regulation - that allow the partners of the interaction to destroy or control the others. These interactions evolve rapidly by genetic exchanges, including among competing partners. They are sometimes followed by functional diversification. Gene exchanges also facilitate the emergence of cross-talk between elements in the same bacterium. In the end, these processes produce multilayered networks of interactions that shape the outcome of viral infections.
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43
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Eppley JM, Biller SJ, Luo E, Burger A, DeLong EF. Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements. Proc Natl Acad Sci U S A 2022; 119:e2212722119. [PMID: 36256808 PMCID: PMC9618062 DOI: 10.1073/pnas.2212722119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/22/2022] [Indexed: 11/19/2022] Open
Abstract
Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage satellites that were packaged as concatemeric repeats within naturally occurring bacteriophage particles in seawater. These same phage-parasitizing mobile elements were found integrated in the genomes of dominant co-occurring bacterioplankton species. Like known phage satellites, many marine phage satellites encoded genes for integration, DNA replication, phage interference, and capsid assembly. Many also contained distinctive gene suites indicative of unique virus hijacking, phage immunity, and mobilization mechanisms. Marine phage satellite sequences were widespread in local and global oceanic virioplankton populations, reflecting their ubiquity, abundance, and temporal persistence in marine planktonic communities worldwide. Their gene content and putative life cycles suggest they may impact host-cell phage immunity and defense, lateral gene transfer, bacteriophage-induced cell mortality and cellular host and virus productivity. Given that marine phage satellites cannot be distinguished from bona fide viral particles via commonly used microscopic techniques, their predicted numbers (∼3.2 × 1026 in the ocean) may influence current estimates of virus densities, production, and virus-induced mortality. In total, the data suggest that marine phage satellites have potential to significantly impact the ecology and evolution of bacteria and their viruses throughout the oceans. We predict that any habitat that harbors bacteriophage will also harbor similar phage satellites, making them a ubiquitous feature of most microbiomes on Earth.
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Affiliation(s)
- John M. Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI 96822
| | - Steven J. Biller
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481
| | - Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI 96822
| | - Andrew Burger
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI 96822
| | - Edward F. DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI 96822
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44
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Nguyen MHT, Netter Z, Angermeyer A, Seed KD. A phage weaponizes a satellite recombinase to subvert viral restriction. Nucleic Acids Res 2022; 50:11138-11153. [PMID: 36259649 DOI: 10.1093/nar/gkac845] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/14/2022] [Accepted: 10/10/2022] [Indexed: 11/14/2022] Open
Abstract
Bacteria can acquire mobile genetic elements (MGEs) to combat infection by viruses (phages). Satellite viruses, including the PLEs (phage-inducible chromosomal island-like elements) in epidemic Vibrio cholerae, are MGEs that restrict phage replication to the benefit of their host bacterium. PLEs parasitize the lytic phage ICP1, unleashing multiple mechanisms to restrict phage replication and promote their own spread. In the arms race against PLE, ICP1 uses nucleases, including CRISPR-Cas, to destroy PLE's genome during infection. However, through an unknown CRISPR-independent mechanism, specific ICP1 isolates subvert restriction by PLE. Here, we discover ICP1-encoded Adi that counteracts PLE by exploiting the PLE's large serine recombinase (LSR), which normally mobilizes PLE in response to ICP1 infection. Unlike previously characterized ICP1-encoded anti-PLE mechanisms, Adi is not a nuclease itself but instead appears to modulate the activity of the LSR to promote destructive nuclease activity at the LSR's specific attachment site, attP. The PLE LSR, its catalytic activity, and attP are additionally sufficient to sensitize a PLE encoding a resistant variant of the recombination module to Adi activity. This work highlights a unique type of adaptation arising from inter-genome conflicts, in which the intended activity of a protein can be weaponized to overcome the antagonizing genome.
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Affiliation(s)
- Maria H T Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Zoe Netter
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
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45
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Vassallo CN, Doering CR, Littlehale ML, Teodoro GIC, Laub MT. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat Microbiol 2022; 7:1568-1579. [PMID: 36123438 PMCID: PMC9519451 DOI: 10.1038/s41564-022-01219-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in E. coli, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in E. coli and provide an approach for mapping defence systems in other species.
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Affiliation(s)
| | | | - Megan L Littlehale
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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46
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Choufa C, Tidjani AR, Gauthier A, Harb M, Lao J, Leblond-Bourget N, Vos M, Leblond P, Bontemps C. Prevalence and mobility of integrative and conjugative elements within a Streptomyces natural population. Front Microbiol 2022; 13:970179. [PMID: 36177458 PMCID: PMC9513070 DOI: 10.3389/fmicb.2022.970179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we used in silico and experimental approaches on a set of 11 very closely related strains isolated from a millimeter scale rhizosphere population. Through bioinformatic searches of canonical conjugation proteins, we showed that AICEs are the most frequent integrative conjugative elements, with the central chromosome region being a hotspot for integrative element insertion. Strains exhibited great variation in AICE composition consistent with frequent HGT and/or gene loss. We found that single insertion sites can be home to different elements in different strains (accretion) and conversely, elements belonging to the same family can be found at different insertion sites. A wide variety of cargo genes was present in the AICEs with the potential to mediate strain-specific adaptation (e.g., DNA metabolism and resistance genes to antibiotic and phages). However, a large proportion of AICE cargo genes showed hallmarks of pseudogenization, consistent with deleterious effects of cargo genes on fitness. Pock assays enabled the direct visualization of conjugal AICE transfer and demonstrated the transfer of AICEs between some, but not all, of the isolates. Multiple AICEs were shown to be able to transfer during a single mating event. Although we did not obtain experimental evidence for transfer of the sole chromosomal ICE in this population, genotoxic stress mediated its excision from the chromosome, suggesting its functionality. Our results indicate that AICE-mediated HGT in Streptomyces populations is highly dynamic, with likely impact on strain fitness and the ability to adapt to environmental change.
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Affiliation(s)
| | - Abdoul-Razak Tidjani
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Faculty of Medecine, CNRS, Grenoble INP, CHU Grenoble-Alpes, University Grenoble-Alpes, TIMC (UMR 5525), Grenoble, France
| | | | - Manar Harb
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- INRAE-ONIRIS, Nantes, France
| | - Julie Lao
- INRAE, UR1404 MaIAGE, Jouy-en-Josas, France
| | | | - Michiel Vos
- European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter Medical School, Penryn, United Kingdom
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- *Correspondence: Pierre Leblond,
| | - Cyril Bontemps
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Cyril Bontemps,
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Okazaki Y, Nakano SI, Toyoda A, Tamaki H. Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes. mSystems 2022; 7:e0043322. [PMID: 35938717 PMCID: PMC9426551 DOI: 10.1128/msystems.00433-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022] Open
Abstract
Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.
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Affiliation(s)
- Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Shin-ichi Nakano
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima City, Shizuoka, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
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Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. Proc Natl Acad Sci U S A 2022; 119:e2205037119. [PMID: 35994644 PMCID: PMC9436352 DOI: 10.1073/pnas.2205037119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are important ecological, biogeochemical, and evolutionary drivers in every environment. Upon infection, they often cause the lysis of the host cell. However, some viruses exhibit alternative life cycles, such as chronic infections without cell lysis. The nature and the impact of chronic infections in prokaryotic host organisms remains largely unknown. Here, we characterize a novel haloarchaeal virus, Haloferax volcanii pleomorphic virus 1 (HFPV-1), which is currently the only virus infecting the model haloarchaeon Haloferax volcanii DS2, and demonstrate that HFPV-1 and H. volcanii are a great model system to study virus-host interactions in archaea. HFPV-1 is a pleomorphic virus that causes a chronic infection with continuous release of virus particles, but host and virus coexist without cell lysis or the appearance of resistant cells. Despite an only minor impact of the infection on host growth, we uncovered an extensive remodeling of the transcriptional program of the host (up to 1,049 differentially expressed genes). These changes are highlighted by a down-regulation of two endogenous provirus regions in the host genome, and we show that HFPV-1 infection is strongly influenced by a cross-talk between HFPV-1 and one of the proviruses mediated by a superinfection-like exclusion mechanism. Furthermore, HFPV-1 has a surprisingly wide host range among haloarchaea, and purified virus DNA can cause an infection after transformation into the host, making HFPV-1 a candidate for being developed into a genetic tool for a range of so far inaccessible haloarchaea.
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Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors. Cell 2022; 185:3248-3262.e20. [PMID: 35985290 DOI: 10.1016/j.cell.2022.07.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/08/2022] [Accepted: 07/18/2022] [Indexed: 01/26/2023]
Abstract
Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.
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Dai Z, Wu T, Xu S, Zhou L, Tang W, Hu E, Zhan L, Chen M, Yu G. Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa. Front Microbiol 2022; 13:951774. [PMID: 36051757 PMCID: PMC9424990 DOI: 10.3389/fmicb.2022.951774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas aeruginosa, as one of the bacterial species with ARGs, have not yet been completely demonstrated. In this study, we explored the TA systems from the public genomic sequencing data and genome sequences. A small scale of genomic sequencing data in 281 isolates was selected from the NCBI SRA database, reassembling the genomes of these isolates led to the findings of abundant TA homologs. Furthermore, remapping these identified TA modules on 5,437 genome/draft genomes uncovers a great diversity of TA modules in P. aeruginosa. Moreover, manual inspection revealed several TA systems that were not yet reported in P. aeruginosa including the hok-sok, cptA-cptB, cbeA-cbtA, tomB-hha, and ryeA-sdsR. Additional annotation revealed that a large number of MGEs were closely distributed with TA. Also, 16% of ARGs are located relatively close to TA. Our work confirmed a wealth of TA genes in the unexplored P. aeruginosa pan-genomes, expanded the knowledge on P. aeruginosa, and provided methodological tips on large-scale data mining for future studies. The co-occurrence of MGE, ARG, and TA may indicate a potential interaction in their dissemination.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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