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Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination

In E. coli, double strand breaks (DSBs) are resected and loaded with RecA protein. The genome is then rapidly searched for a sequence that is homologous to the DNA flanking the DSB. Mismatches in homologous partners are rare, suggesting that RecA should rapidly reject mismatched recombination produc...

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Autores principales: Prentiss, Mara, Wang, Dianzhuo, Fu, Jonathan, Prévost, Chantal, Godoy-Carter, Veronica, Kleckner, Nancy, Danilowicz, Claudia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10343044/
https://www.ncbi.nlm.nih.gov/pubmed/37440583
http://dx.doi.org/10.1371/journal.pone.0288611
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author Prentiss, Mara
Wang, Dianzhuo
Fu, Jonathan
Prévost, Chantal
Godoy-Carter, Veronica
Kleckner, Nancy
Danilowicz, Claudia
author_facet Prentiss, Mara
Wang, Dianzhuo
Fu, Jonathan
Prévost, Chantal
Godoy-Carter, Veronica
Kleckner, Nancy
Danilowicz, Claudia
author_sort Prentiss, Mara
collection PubMed
description In E. coli, double strand breaks (DSBs) are resected and loaded with RecA protein. The genome is then rapidly searched for a sequence that is homologous to the DNA flanking the DSB. Mismatches in homologous partners are rare, suggesting that RecA should rapidly reject mismatched recombination products; however, this is not the case. Decades of work have shown that long lasting recombination products can include many mismatches. In this work, we show that in vitro RecA forms readily observable recombination products when 16% of the bases in the product are mismatched. We also consider various theoretical models of mismatch-tolerant homology testing. The models test homology by comparing the sequences of L(test) bases in two single-stranded DNAs (ssDNA) from the same genome. If the two sequences pass the homology test, the pairing between the two ssDNA becomes permanent. Stringency is the fraction of permanent pairings that join ssDNA from the same positions in the genome. We applied the models to both randomly generated genomes and bacterial genomes. For both randomly generated genomes and bacterial genomes, the models show that if no mismatches are accepted stringency is ∼ 99% when L(test) = 14 bp. For randomly generated genomes, stringency decreases with increasing mismatch tolerance, and stringency improves with increasing L(test). In contrast, in bacterial genomes when L(test) ∼ 75 bp, stringency is ∼ 99% for both mismatch-intolerant and mismatch-tolerant homology testing. Furthermore, increasing L(test) does not improve stringency because most incorrect pairings join different copies of repeats. In sum, for bacterial genomes highly mismatch tolerant homology testing of 75 bp provides the same stringency as homology testing that rejects all mismatches and testing more than ∼75 base pairs is not useful. Interestingly, in vivo commitment to recombination typically requires homology testing of ∼ 75 bp, consistent with highly mismatch intolerant testing.
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spelling pubmed-103430442023-07-14 Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination Prentiss, Mara Wang, Dianzhuo Fu, Jonathan Prévost, Chantal Godoy-Carter, Veronica Kleckner, Nancy Danilowicz, Claudia PLoS One Research Article In E. coli, double strand breaks (DSBs) are resected and loaded with RecA protein. The genome is then rapidly searched for a sequence that is homologous to the DNA flanking the DSB. Mismatches in homologous partners are rare, suggesting that RecA should rapidly reject mismatched recombination products; however, this is not the case. Decades of work have shown that long lasting recombination products can include many mismatches. In this work, we show that in vitro RecA forms readily observable recombination products when 16% of the bases in the product are mismatched. We also consider various theoretical models of mismatch-tolerant homology testing. The models test homology by comparing the sequences of L(test) bases in two single-stranded DNAs (ssDNA) from the same genome. If the two sequences pass the homology test, the pairing between the two ssDNA becomes permanent. Stringency is the fraction of permanent pairings that join ssDNA from the same positions in the genome. We applied the models to both randomly generated genomes and bacterial genomes. For both randomly generated genomes and bacterial genomes, the models show that if no mismatches are accepted stringency is ∼ 99% when L(test) = 14 bp. For randomly generated genomes, stringency decreases with increasing mismatch tolerance, and stringency improves with increasing L(test). In contrast, in bacterial genomes when L(test) ∼ 75 bp, stringency is ∼ 99% for both mismatch-intolerant and mismatch-tolerant homology testing. Furthermore, increasing L(test) does not improve stringency because most incorrect pairings join different copies of repeats. In sum, for bacterial genomes highly mismatch tolerant homology testing of 75 bp provides the same stringency as homology testing that rejects all mismatches and testing more than ∼75 base pairs is not useful. Interestingly, in vivo commitment to recombination typically requires homology testing of ∼ 75 bp, consistent with highly mismatch intolerant testing. Public Library of Science 2023-07-13 /pmc/articles/PMC10343044/ /pubmed/37440583 http://dx.doi.org/10.1371/journal.pone.0288611 Text en © 2023 Prentiss et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Prentiss, Mara
Wang, Dianzhuo
Fu, Jonathan
Prévost, Chantal
Godoy-Carter, Veronica
Kleckner, Nancy
Danilowicz, Claudia
Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination
title Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination
title_full Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination
title_fullStr Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination
title_full_unstemmed Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination
title_short Highly mismatch-tolerant homology testing by RecA could explain how homology length affects recombination
title_sort highly mismatch-tolerant homology testing by reca could explain how homology length affects recombination
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10343044/
https://www.ncbi.nlm.nih.gov/pubmed/37440583
http://dx.doi.org/10.1371/journal.pone.0288611
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