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Adams MC, Schiltz C, Sun J, Hosford C, Johnson V, Pan H, Borbat P, Freed J, Thomason L, Court C, Court D, Chappie J. The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins. Nucleic Acids Res 2024; 52:4659-4675. [PMID: 38554102 PMCID: PMC11077077 DOI: 10.1093/nar/gkae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/01/2024] Open
Abstract
RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jing Sun
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Virginia M Johnson
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hao Pan
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Lynn C Thomason
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Carolyn Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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Yang CC, Wang ZY, Cheng CM. Insights into Superinfection Immunity Regulation of Xanthomonas axonopodis Filamentous Bacteriophage cf. Curr Microbiol 2023; 81:42. [PMID: 38112972 DOI: 10.1007/s00284-023-03539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023]
Abstract
Filamentous bacteriophage cf infects Xanthomonas axonopodis pv. citri, a serious plant pathogen which causes citrus canker. To understand the immunity regulation of bacteria infected with bacteriophage cf, we applied DNA shuffling to mutate the cf intergenic region. One of the immunity mutants, cf-m3 (NCBI Taxonomy ID: 3050368) expressed a 106-109 fold greater superinfection ability compared with wild type cf. Nine mutations were identified on the cf-m3 phage, four of which were located within the coding region of an open reading frame (ORF165) for a hypothetical repressor, PT, and five located upstream of the PT coding region. A set of phages with mutations to the predicted PT protein or the upstream coding region were generated. All showed similarly low superinfection efficiency to wild type cf and no superinfection ability on cf lysogens. The results indicate that rather than superinfection inhibition, the PT protein and the un-transcribed cis element function individually as positive regulators of cf superinfection immunity. Greater superinfection ability depends on the simultaneous presence of both elements. This work yields further insight into the possible control of citrus canker disease through phages that overcome host superinfection immunity.
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Affiliation(s)
- Chia-Chin Yang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Zih-Yun Wang
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan
| | - Ching-Ming Cheng
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan.
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Thomason LC, Costantino N, Li X, Court DL. Recombineering: Genetic Engineering in Escherichia coli Using Homologous Recombination. Curr Protoc 2023; 3:e656. [PMID: 36779782 PMCID: PMC10037674 DOI: 10.1002/cpz1.656] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using either PCR products or synthetic double-stranded DNA (dsDNA) or single-stranded DNA as substrates. Multiple linear dsDNA molecules can be assembled into an intact plasmid. The technology of recombineering is possible because bacteriophage-encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to the location of restriction sites and can also be used in combination with CRISPR/Cas targeting systems. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: Making electrocompetent cells and transforming with linear DNA Support Protocol 1: Selection/counter-selections for genome engineering Support Protocol 2: Creating and screening for oligo recombinants by PCR Support Protocol 3: Other methods of screening for unselected recombinants Support Protocol 4: Curing recombineering plasmids containing a temperature-sensitive replication function Support Protocol 5: Removal of the prophage by recombineering Alternate Protocol 1: Using CRISPR/Cas9 as a counter-selection following recombineering Alternate Protocol 2: Assembly of linear dsDNA fragments into functional plasmids Alternate Protocol 3: Retrieval of alleles onto a plasmid by gap repair Alternate Protocol 4: Modifying multicopy plasmids with recombineering Support Protocol 6: Screening for unselected plasmid recombinants Alternate Protocol 5: Recombineering with an intact λ prophage Alternate Protocol 6: Targeting an infecting λ phage with the defective prophage strains.
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Affiliation(s)
- Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Nina Costantino
- formerly with Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Xintian Li
- Armata Pharmaceuticals, 4503 Glencoe Avenue, Marina del Rey, CA 90292
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
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Thomason LC, Court DL. Study of Ren, RexA, and RexB Functions Provides Insight Into the Complex Interaction Between Bacteriophage λ and Its Host, Escherichia coli. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:153-164. [PMID: 36204488 PMCID: PMC9529316 DOI: 10.1089/phage.2022.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The phage λ rexA and rexB genes are expressed from the P RM promoter in λ lysogens along with the cI repressor gene. RexB is also expressed from a second promoter, P LIT, embedded in rexA. The combined expression of rexA and rexB causes Escherichia coli to be more ultraviolet (UV) sensitive. Sensitivity is further increased when RexB levels are reduced by a defect in the P LIT promoter, thus the degree of sensitivity can be modulated by the ratio of RexA/RexB. Expression of the phage λ ren gene rescues this host UV sensitive phenotype; Ren also rescues an aberrant lysis phenotype caused by RexA and RexB. We screened an E. coli two-hybrid library to identify bacterial proteins with which each of these phage proteins physically interact. The results extend previous observations concerning λ Rex exclusion and show the importance of E. coli electron transport and sulfur assimilation pathways for the phage.
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Affiliation(s)
- Lynn C. Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, Maryland, USA
| | - Donald L. Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, Maryland, USA
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Thomason LC, Schiltz CJ, Court C, Hosford CJ, Adams MC, Chappie JS, Court DL. Bacteriophage λ RexA and RexB Functions Assist the Transition from Lysogeny to Lytic Growth. Mol Microbiol 2021; 116:1044-1063. [PMID: 34379857 DOI: 10.1111/mmi.14792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
Abstract
The CI and Cro repressors of bacteriophage λ create a bistable switch between lysogenic and lytic growth. In λ lysogens, CI repressor expressed from the PRM promoter blocks expression of the lytic promoters PL and PR to allow stable maintenance of the lysogenic state. When lysogens are induced, CI repressor is inactivated and Cro repressor is expressed from the lytic PR promoter. Cro repressor blocks PRM transcription and CI repressor synthesis to ensure that the lytic state proceeds. RexA and RexB proteins, like CI, are expressed from the PRM promoter in λ lysogens; RexB is also expressed from a second promoter, PLIT , embedded in rexA. Here we show that RexA binds CI repressor and assists the transition from lysogenic to lytic growth, using both intact lysogens and defective prophages with reporter genes under control of the lytic PL and PR promoters. Once lytic growth begins, if the bistable switch does return to the immune state, RexA expression lessens the probability that it will remain there, thus stabilizing the lytic state and activation of the lytic PL and PR promoters. RexB modulates the effect of RexA and may also help establish phage DNA replication as lytic growth ensues.
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Affiliation(s)
- Lynn C Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, 21702.,RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, 14850.,Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Carolyn Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
| | - Christopher J Hosford
- Department of Molecular Medicine, Cornell University, Ithaca, 14850.,New England Biolabs, Inc, Ipswich, MA, USA
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, 14850
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, 14850
| | - Donald L Court
- RNA Biology Laboratory, National Cancer Institute/Frederick Cancer Research and Development Center, Frederick, 21702
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Benler S, Koonin EV. Phage lysis‐lysogeny switches and programmed cell death: Danse macabre. Bioessays 2020; 42:e2000114. [DOI: 10.1002/bies.202000114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/25/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
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