Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli

Detalhes bibliográficos
Autor(a) principal: Dash, Suchintak
Data de Publicação: 2022
Outros Autores: Palma, Cristina S. D., Baptista, Ines S. C., Almeida, Bilena L. B., Bahrudeen, Mohamed N. M., Chauhan, Vatsala, Jagadeesan, Rahul, Ribeiro, André S.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/148592
Resumo: Jane and Aatos Erkko Foundation [10-10524-38 to A.S.R.]; Suomalainen Tiedeakatemia (to C.S.D.P.); Finnish Cultural Foundation [00200193 and 00212591 to I.S.C.B., 50201300 to S.D., 00210818 to C.S.D.P.]; EDUFI Fellowship [TM19-11105 to S.D. and TM-21-11655 to R.J.]; Tampere University Graduate Program (to V.C., M.N.M.B., B.L.B.A.); the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding for open access charge: Tampere University [to C.S.D.P. and S.D.].
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spelling Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coliGeneticsJane and Aatos Erkko Foundation [10-10524-38 to A.S.R.]; Suomalainen Tiedeakatemia (to C.S.D.P.); Finnish Cultural Foundation [00200193 and 00212591 to I.S.C.B., 50201300 to S.D., 00210818 to C.S.D.P.]; EDUFI Fellowship [TM19-11105 to S.D. and TM-21-11655 to R.J.]; Tampere University Graduate Program (to V.C., M.N.M.B., B.L.B.A.); the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding for open access charge: Tampere University [to C.S.D.P. and S.D.].Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers’ variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli’s short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.CTS - Centro de Tecnologia e SistemasUNINOVA-Instituto de Desenvolvimento de Novas TecnologiasRUNDash, SuchintakPalma, Cristina S. D.Baptista, Ines S. C.Almeida, Bilena L. B.Bahrudeen, Mohamed N. M.Chauhan, VatsalaJagadeesan, RahulRibeiro, André S.2023-02-02T22:20:33Z2022-08-262022-08-26T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article17application/pdfhttp://hdl.handle.net/10362/148592eng0305-1048PURE: 51491289https://doi.org/10.1093/nar/gkac643info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:30:15Zoai:run.unl.pt:10362/148592Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:53:25.870793Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
title Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
spellingShingle Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
Dash, Suchintak
Genetics
title_short Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
title_full Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
title_fullStr Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
title_full_unstemmed Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
title_sort Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli
author Dash, Suchintak
author_facet Dash, Suchintak
Palma, Cristina S. D.
Baptista, Ines S. C.
Almeida, Bilena L. B.
Bahrudeen, Mohamed N. M.
Chauhan, Vatsala
Jagadeesan, Rahul
Ribeiro, André S.
author_role author
author2 Palma, Cristina S. D.
Baptista, Ines S. C.
Almeida, Bilena L. B.
Bahrudeen, Mohamed N. M.
Chauhan, Vatsala
Jagadeesan, Rahul
Ribeiro, André S.
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv CTS - Centro de Tecnologia e Sistemas
UNINOVA-Instituto de Desenvolvimento de Novas Tecnologias
RUN
dc.contributor.author.fl_str_mv Dash, Suchintak
Palma, Cristina S. D.
Baptista, Ines S. C.
Almeida, Bilena L. B.
Bahrudeen, Mohamed N. M.
Chauhan, Vatsala
Jagadeesan, Rahul
Ribeiro, André S.
dc.subject.por.fl_str_mv Genetics
topic Genetics
description Jane and Aatos Erkko Foundation [10-10524-38 to A.S.R.]; Suomalainen Tiedeakatemia (to C.S.D.P.); Finnish Cultural Foundation [00200193 and 00212591 to I.S.C.B., 50201300 to S.D., 00210818 to C.S.D.P.]; EDUFI Fellowship [TM19-11105 to S.D. and TM-21-11655 to R.J.]; Tampere University Graduate Program (to V.C., M.N.M.B., B.L.B.A.); the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funding for open access charge: Tampere University [to C.S.D.P. and S.D.].
publishDate 2022
dc.date.none.fl_str_mv 2022-08-26
2022-08-26T00:00:00Z
2023-02-02T22:20:33Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/148592
url http://hdl.handle.net/10362/148592
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 0305-1048
PURE: 51491289
https://doi.org/10.1093/nar/gkac643
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 17
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instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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