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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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2
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Mun SY, Lee W, Lee SY, Chang JY, Chang HC. Pediococcus inopinatus with a well-developed CRISPR-Cas system dominates in long-term fermented kimchi, Mukeunji. Food Microbiol 2024; 117:104385. [PMID: 37919000 DOI: 10.1016/j.fm.2023.104385] [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: 06/26/2023] [Revised: 08/16/2023] [Accepted: 09/12/2023] [Indexed: 11/04/2023]
Abstract
Kimchi is produced through a low-temperature fermentation without pre-sterilization, resulting in a heterogeneous microbial community. As fermentation progresses, dominant lactic acid bacteria (LAB) species emerge and undergo a transition process. In this study, LAB were isolated from Mukeunji, a long-term fermented kimchi that is in the final stage of kimchi fermentation process. It was confirmed, through culture-dependent and independent analysis, as well as metagenome analysis, that Pediococcus inopinatus are generally dominant in long-term fermented kimchi. Comparative analysis of the de novo assembled whole genome of P. inopinatus with other kimchi LAB revealed that this species has a well-developed clustered regularly interspaced short palindromic repeats (CRISPR) system. The CRISPR system of P. inopinatus has an additional copy of the csa3 gene, a transcription factor for cas genes. Indeed, this species not only highly expresses cas1 and cas2, which induce spacer acquisition, but also has many diverse spacers that are actively expressed. These findings indicate that the well-developed CRISPR-Cas system is enabling P. inopinatus to dominate in long-fermented kimchi. Overall, this study revealed that LAB with a robust defense system dominate in the final stage of kimchi fermentation and presented a model for the succession mechanism of kimchi LAB.
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Affiliation(s)
- So Yeong Mun
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea; Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea
| | - Wooje Lee
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea
| | - Soo-Young Lee
- Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea
| | - Ji Yoon Chang
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea
| | - Hae Choon Chang
- Research and Development Division, World Institute of Kimchi, 86 Kimchi-ro, Nam-gu, Gwangju, 61755, South Korea; Department of Food and Nutrition, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju, 61452, South Korea.
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3
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López-Rojo A, Jackson SA, Bernal-Bernal D, Galbis-Martínez M, Fineran PC, Elías-Arnanz M. Genome sequences of Mx1, the first Myxococcus phage isolated, and Mx4, a generalized transducing myxophage. Microbiol Resour Announc 2023; 12:e0090423. [PMID: 38009928 PMCID: PMC10720576 DOI: 10.1128/mra.00904-23] [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: 09/28/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Myxococcus xanthus is the best-studied member of the phylum Myxococcota, but the bacteriophages infecting it and their characterization remain limited. Here, we present complete genomes of Mx1, the first Myxococcus phage isolated, and of an Mx4 derivative widely used for generalized transduction, both unclassified Caudoviricetes with long, contractile tails.
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Affiliation(s)
- Alfonso López-Rojo
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
| | - Simon A. Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Diego Bernal-Bernal
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
| | - Marisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad asociada al IQFR-CSIC), Universidad de Murcia, Murcia, Spain
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4
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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5
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Pérez-Castaño R, Bastida-Martínez E, Fernández Zapata J, Polanco MDC, Galbis-Martínez ML, Iniesta AA, Fontes M, Padmanabhan S, Elías-Arnanz M. Coenzyme B 12 -dependent and independent photoregulation of carotenogenesis across Myxococcales. Environ Microbiol 2022; 24:1865-1886. [PMID: 35005822 PMCID: PMC9304148 DOI: 10.1111/1462-2920.15895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/28/2022]
Abstract
Light-induced carotenogenesis in Myxococcus xanthus is controlled by the B12 -based CarH repressor and photoreceptor, and by a separate intricate pathway involving singlet oxygen, the B12 -independent CarH paralog CarA and various other proteins, some eukaryotic-like. Whether other myxobacteria conserve these pathways and undergo photoregulated carotenogenesis is unknown. Here, comparative analyses across 27 Myxococcales genomes identified carotenogenic genes, albeit arranged differently, with carH often in their genomic vicinity, in all three Myxococcales suborders. However, CarA and its associated factors were found exclusively in suborder Cystobacterineae, with carA-carH invariably in tandem in a syntenic carotenogenic operon, except for Cystobacter/Melittangium, which lack CarA but retain all other factors. We experimentally show B12 -mediated photoregulated carotenogenesis in representative myxobacteria, and a remarkably plastic CarH operator design and DNA binding across Myxococcales. Unlike the two characterized CarH from other phyla, which are tetrameric, Cystobacter CarH (the first myxobacterial homolog amenable to analysis in vitro) is a dimer that combines direct CarH-like B12 -based photoregulation with CarA-like DNA-binding and inhibition by an antirepressor. This study provides new molecular insights into B12 -dependent photoreceptors. It further establishes the B12 -dependent pathway for photoregulated carotenogenesis as broadly prevalent across myxobacteria and its evolution, exclusively in one suborder, into a parallel complex B12 -independent circuit. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Jesús Fernández Zapata
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - María Del Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - María Luisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Antonio A Iniesta
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
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6
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Hu WF, Niu L, Yue XJ, Zhu LL, Hu W, Li YZ, Wu C. Characterization of Constitutive Promoters for the Elicitation of Secondary Metabolites in Myxobacteria. ACS Synth Biol 2021; 10:2904-2909. [PMID: 34757714 DOI: 10.1021/acssynbio.1c00444] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genome mining has revealed that myxobacteria contain a myriad of cryptic biosynthetic gene clusters (BGCs). Here, we report the characterization of a panel of myxobacterial promoters with variable strength that are applicable in the engineering of BGCs in myxobacteria. The screened strongest constitutive promoter was used to efficiently enhance the expression of two complex BGCs governing the biosynthesis of myxochromide and DKxanthene in the model myxobacterium Myxococcus xanthus DK1622. We also showcased the combination of promoter engineering and MS2-based spectral networking as an effective strategy to shed light on the previously overlooked chemistry in the family of myxochromide-type lipopeptides. The enriched promoter library substantially expanded the synthetic biology toolkit available for myxobacteria.
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Affiliation(s)
- Wei-Feng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Luo Niu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Le-Le Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
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7
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Complete Genome Sequence of Myxococcus Phage Mx4. Microbiol Resour Announc 2021; 10:e0095321. [PMID: 34672703 PMCID: PMC8530038 DOI: 10.1128/mra.00953-21] [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] [Indexed: 11/20/2022] Open
Abstract
Myxococcus xanthus is a bacterial model in microbial developmental biology and social evolution. Here, I present the 57.0-kb circular genomic sequence of the wild-type Myxococcus phage Mx4, with a GC content of 70.1%. Annotation predicted 97 protein-coding genes. Head-neck-tail protein classification assigns Mx4 to the tailed, Mu-like members of the family Myoviridae of group type 1 (cluster 8).
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8
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Lucas-Elío P, Molina-Quintero LR, Xu H, Sánchez-Amat A. A histidine kinase and a response regulator provide phage resistance to Marinomonas mediterranea via CRISPR-Cas regulation. Sci Rep 2021; 11:20564. [PMID: 34663886 PMCID: PMC8523701 DOI: 10.1038/s41598-021-99740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022] Open
Abstract
CRISPR-Cas systems are used by many prokaryotes to defend against invading genetic elements. In many cases, more than one CRISPR-Cas system co-exist in the same cell. Marinomonas mediterranea MMB-1 possesses two CRISPR-Cas systems, of type I-F and III-B respectively, which collaborate in phage resistance raising questions on how their expression is regulated. This study shows that the expression of both systems is controlled by the histidine kinase PpoS and a response regulator, PpoR, identified and cloned in this study. These proteins show similarity to the global regulators BarA/UvrY. In addition, homologues to the sRNAs CsrB and CsrC and the gene coding for the post-transcriptional repressor CsrA have been also identified indicating the conservation of the elements of the BarA/UvrY regulatory cascade in M. mediterranea. RNA-Seq analyses have revealed that all these genetics elements are regulated by PpoS/R supporting their participation in the regulatory cascade. The regulation by PpoS and PpoR of the CRISPR-Cas systems plays a role in phage defense since mutants in these proteins show an increase in phage sensitivity.
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Affiliation(s)
- Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, 30100, Murcia, Spain
| | | | - Hengyi Xu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Antonio Sánchez-Amat
- Department of Genetics and Microbiology, University of Murcia, 30100, Murcia, Spain.
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9
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Light-Triggered Carotenogenesis in Myxococcus xanthus: New Paradigms in Photosensory Signaling, Transduction and Gene Regulation. Microorganisms 2021; 9:microorganisms9051067. [PMID: 34063365 PMCID: PMC8156234 DOI: 10.3390/microorganisms9051067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Myxobacteria are Gram-negative δ-proteobacteria found predominantly in terrestrial habitats and often brightly colored due to the biosynthesis of carotenoids. Carotenoids are lipophilic isoprenoid pigments that protect cells from damage and death by quenching highly reactive and toxic oxidative species, like singlet oxygen, generated upon growth under light. The model myxobacterium Myxococcus xanthus turns from yellow in the dark to red upon exposure to light because of the photoinduction of carotenoid biosynthesis. How light is sensed and transduced to bring about regulated carotenogenesis in order to combat photooxidative stress has been extensively investigated in M. xanthus using genetic, biochemical and high-resolution structural methods. These studies have unearthed new paradigms in bacterial light sensing, signal transduction and gene regulation, and have led to the discovery of prototypical members of widely distributed protein families with novel functions. Major advances have been made over the last decade in elucidating the molecular mechanisms underlying the light-dependent signaling and regulation of the transcriptional response leading to carotenogenesis in M. xanthus. This review aims to provide an up-to-date overview of these findings and their significance.
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10
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Smith LM, Jackson SA, Malone LM, Ussher JE, Gardner PP, Fineran PC. The Rcs stress response inversely controls surface and CRISPR-Cas adaptive immunity to discriminate plasmids and phages. Nat Microbiol 2021; 6:162-172. [PMID: 33398095 DOI: 10.1038/s41564-020-00822-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022]
Abstract
Bacteria harbour multiple innate defences and adaptive CRISPR-Cas systems that provide immunity against bacteriophages and mobile genetic elements. Although some bacteria modulate defences in response to population density, stress and metabolic state, a lack of high-throughput methods to systematically reveal regulators has hampered efforts to understand when and how immune strategies are deployed. We developed a robust approach called SorTn-seq, which combines saturation transposon mutagenesis, fluorescence-activated cell sorting and deep sequencing to characterize regulatory networks controlling CRISPR-Cas immunity in Serratia sp. ATCC 39006. We applied our technology to assess csm gene expression for ~300,000 mutants and uncovered multiple pathways regulating type III-A CRISPR-Cas expression. Mutation of igaA or mdoG activated the Rcs outer-membrane stress response, eliciting cell-surface-based innate immunity against diverse phages via the transcriptional regulators RcsB and RcsA. Activation of this Rcs phosphorelay concomitantly attenuated adaptive immunity by three distinct type I and III CRISPR-Cas systems. Rcs-mediated repression of CRISPR-Cas defence enabled increased acquisition and retention of plasmids. Dual downregulation of cell-surface receptors and adaptive immunity in response to stress by the Rcs pathway enables protection from phage infection without preventing the uptake of plasmids that may harbour beneficial traits.
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Affiliation(s)
- Leah M Smith
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Lucia M Malone
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Paul P Gardner
- Genetics Otago, University of Otago, Dunedin, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. .,Genetics Otago, University of Otago, Dunedin, New Zealand. .,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand.
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11
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Affiliation(s)
- Christine Pourcel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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12
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Abstract
BACKGROUND Development of efficient strategies has always been one of the great perspectives for biotechnologists. During the last decade, genome editing of different organisms has been a fast advancing field and therefore has received a lot of attention from various researchers comprehensively reviewing latest achievements and offering opinions on future directions. This review presents a brief history, basic principles, advantages and disadvantages, as well as various aspects of each genome editing technology including the modes, applications, and challenges that face delivery of gene editing components. MAIN BODY Genetic modification techniques cover a wide range of studies, including the generation of transgenic animals, functional analysis of genes, model development for diseases, or drug development. The delivery of certain proteins such as monoclonal antibodies, enzymes, and growth hormones has been suffering from several obstacles because of their large size. These difficulties encouraged scientists to explore alternative approaches, leading to the progress in gene editing. The distinguished efforts and enormous experimentation have now been able to introduce methodologies that can change the genetic constitution of the living cell. The genome editing strategies have evolved during the last three decades, and nowadays, four types of "programmable" nucleases are available in this field: meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system. Each group has its own characteristics necessary for researchers to select the most suitable method for gene editing tool for a range of applications. Genome engineering/editing technology will revolutionize the creation of precisely manipulated genomes of cells or organisms in order to modify a specific characteristic. Of the potential applications are those in human health and agriculture. Introducing constructs into target cells or organisms is the key step in genome engineering. CONCLUSIONS Despite the success already achieved, the genome editing techniques are still suffering certain difficulties. Challenges must be overcome before the full potential of genome editing can be realized.
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Affiliation(s)
- Ahmad M Khalil
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan.
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13
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Abstract
BACKGROUND Development of efficient strategies has always been one of the great perspectives for biotechnologists. During the last decade, genome editing of different organisms has been a fast advancing field and therefore has received a lot of attention from various researchers comprehensively reviewing latest achievements and offering opinions on future directions. This review presents a brief history, basic principles, advantages and disadvantages, as well as various aspects of each genome editing technology including the modes, applications, and challenges that face delivery of gene editing components. MAIN BODY Genetic modification techniques cover a wide range of studies, including the generation of transgenic animals, functional analysis of genes, model development for diseases, or drug development. The delivery of certain proteins such as monoclonal antibodies, enzymes, and growth hormones has been suffering from several obstacles because of their large size. These difficulties encouraged scientists to explore alternative approaches, leading to the progress in gene editing. The distinguished efforts and enormous experimentation have now been able to introduce methodologies that can change the genetic constitution of the living cell. The genome editing strategies have evolved during the last three decades, and nowadays, four types of "programmable" nucleases are available in this field: meganucleases, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) (CRISPR/Cas-9) system. Each group has its own characteristics necessary for researchers to select the most suitable method for gene editing tool for a range of applications. Genome engineering/editing technology will revolutionize the creation of precisely manipulated genomes of cells or organisms in order to modify a specific characteristic. Of the potential applications are those in human health and agriculture. Introducing constructs into target cells or organisms is the key step in genome engineering. CONCLUSIONS Despite the success already achieved, the genome editing techniques are still suffering certain difficulties. Challenges must be overcome before the full potential of genome editing can be realized.
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Affiliation(s)
- Ahmad M Khalil
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan.
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CdbA is a DNA-binding protein and c-di-GMP receptor important for nucleoid organization and segregation in Myxococcus xanthus. Nat Commun 2020; 11:1791. [PMID: 32286293 PMCID: PMC7156744 DOI: 10.1038/s41467-020-15628-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/19/2020] [Indexed: 01/04/2023] Open
Abstract
Cyclic di-GMP (c-di-GMP) is a second messenger that modulates multiple responses to environmental and cellular signals in bacteria. Here we identify CdbA, a DNA-binding protein of the ribbon-helix-helix family that binds c-di-GMP in Myxococcus xanthus. CdbA is essential for viability, and its depletion causes defects in chromosome organization and segregation leading to a block in cell division. The protein binds to the M. xanthus genome at multiple sites, with moderate sequence specificity; however, its depletion causes only modest changes in transcription. The interactions of CdbA with c-di-GMP and DNA appear to be mutually exclusive and residue substitutions in CdbA regions important for c-di-GMP binding abolish binding to both c-di-GMP and DNA, rendering these protein variants non-functional in vivo. We propose that CdbA acts as a nucleoid-associated protein that contributes to chromosome organization and is modulated by c-di-GMP, thus revealing a link between c-di-GMP signaling and chromosome biology. The second messenger c-di-GMP modulates multiple responses to environmental and cellular signals in bacteria. Here, Skotnicka et al. identify a protein that binds c-di-GMP and contributes to chromosome organization and segregation in Myxococcus xanthus, with DNA-binding activity regulated by c-di-GMP.
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