Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB

In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between...

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Published inPLoS genetics Vol. 13; no. 5; p. e1006783
Main Authors Badrinarayanan, Anjana, Le, Tung B. K., Spille, Jan-Hendrik, Cisse, Ibrahim I., Laub, Michael T.
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 10.05.2017
Public Library of Science (PLoS)
Subjects
Assaying
Bacteria
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biodegradation
Biology
Biology and life sciences
Bismuth
Caulobacter
Caulobacter crescentus - genetics
Chromosomes
Couples
Deoxyribonucleic acid
DNA
DNA Breaks, Double-Stranded
DNA damage
DNA helicase
DNA repair
DNA sequencing
Double-strand break repair
E coli
Enzymes
Exodeoxyribonucleases - genetics
Exodeoxyribonucleases - metabolism
Genetic aspects
Genome, Bacterial
Genomes
Genomic Instability
Helicases
Homologous recombination
Homology
Medicine and Health Sciences
Nuclease
Rec A Recombinases - genetics
Rec A Recombinases - metabolism
RecA protein
Research and analysis methods
Studies
Transcription
United States > US
Online AccessGet full text
ISSN1553-7404
1553-7390
1553-7404
DOI10.1371/journal.pgen.1006783

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Abstract In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair-the attenuation of DNA-end processing and the initiation of homology search by RecA-thereby helping to ensure that genomic integrity is maintained during DSB repair.
AbstractList In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair-the attenuation of DNA-end processing and the initiation of homology search by RecA-thereby helping to ensure that genomic integrity is maintained during DSB repair.
In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair-the attenuation of DNA-end processing and the initiation of homology search by RecA-thereby helping to ensure that genomic integrity is maintained during DSB repair.In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400-2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair-the attenuation of DNA-end processing and the initiation of homology search by RecA-thereby helping to ensure that genomic integrity is maintained during DSB repair.
In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro , with translocation speeds between 400–2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus . Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair–the attenuation of DNA-end processing and the initiation of homology search by RecA–thereby helping to ensure that genomic integrity is maintained during DSB repair. Double-strand breaks (DSBs) are a threat to genome integrity and are faithfully repaired via homologous recombination. The initial processing of DSB ends that prepares them for recombination has been well-studied in vitro , but is less well characterized in vivo . We describe a deep sequencing-based assay for assessing the early steps of DSB processing in bacterial cells by the helicase-nuclease complex AddAB. We find that a combination of chi site recognition and RecA loading is required to attenuate AddAB activity. In the absence of RecA, the chromosome is excessively degraded with a concomitant loss in transcription. Our results, along with prior studies, support a model for how chi recognition and RecA together regulate AddAB to maintain genome integrity and facilitate recombination.
Audience Academic
Author Laub, Michael T.
Badrinarayanan, Anjana
Spille, Jan-Hendrik
Le, Tung B. K.
Cisse, Ibrahim I.
AuthorAffiliation 4 Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
5 Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America
3 Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
2 National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bangalore, India
1 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
National Cancer Institute, UNITED STATES
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– name: 5 Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America
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– name: National Cancer Institute, UNITED STATES
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/28489851$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright COPYRIGHT 2017 Public Library of Science
2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: properties of the helicase-nuclease complex AddAB. PLoS Genet 13(5): e1006783. https://doi.org/10.1371/journal.pgen.1006783
2017 Badrinarayanan et al 2017 Badrinarayanan et al
2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: properties of the helicase-nuclease complex AddAB. PLoS Genet 13(5): e1006783. https://doi.org/10.1371/journal.pgen.1006783
Copyright_xml – notice: COPYRIGHT 2017 Public Library of Science
– notice: 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: properties of the helicase-nuclease complex AddAB. PLoS Genet 13(5): e1006783. https://doi.org/10.1371/journal.pgen.1006783
– notice: 2017 Badrinarayanan et al 2017 Badrinarayanan et al
– notice: 2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: properties of the helicase-nuclease complex AddAB. PLoS Genet 13(5): e1006783. https://doi.org/10.1371/journal.pgen.1006783
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Conceptualization: AB MTL.Data curation: AB TBKL JHS.Formal analysis: AB TBKL JHS MTL.Funding acquisition: AB TBKL IIC MTL.Investigation: AB TBKL JHS.Methodology: AB TBKL JHS IIC MTL.Project administration: MTL.Resources: AB TBKL JHS.Software: JHS.Supervision: MTL.Validation: AB TBKL JHS IIC MTL.Visualization: AB TBKL MTL.Writing – original draft: AB MTL.Writing – review & editing: AB TBKL MTL.
The authors have declared that no competing interests exist.
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Snippet In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of...
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StartPage e1006783
SubjectTerms Assaying
Bacteria
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biodegradation
Biology
Biology and life sciences
Bismuth
Caulobacter
Caulobacter crescentus - genetics
Chromosomes
Couples
Deoxyribonucleic acid
DNA
DNA Breaks, Double-Stranded
DNA damage
DNA helicase
DNA repair
DNA sequencing
Double-strand break repair
E coli
Enzymes
Exodeoxyribonucleases - genetics
Exodeoxyribonucleases - metabolism
Genetic aspects
Genome, Bacterial
Genomes
Genomic Instability
Helicases
Homologous recombination
Homology
Medicine and Health Sciences
Nuclease
Rec A Recombinases - genetics
Rec A Recombinases - metabolism
RecA protein
Research and analysis methods
Studies
Transcription
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Title Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB
URI https://www.ncbi.nlm.nih.gov/pubmed/28489851
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https://doaj.org/article/b8f856952ba248c3b28ef217a132f86a
http://dx.doi.org/10.1371/journal.pgen.1006783
Volume 13
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