Insights into the radiation and oxidative stress mechanisms in genus Deinococcus
Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococc...
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Veröffentlicht in: | Computational biology and chemistry 2024-10, Vol.112, p.108161, Article 108161 |
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creator | Singhvi, Nirjara Talwar, Chandni Nagar, Shekhar Verma, Helianthous Kaur, Jasvinder Mahato, Nitish Kumar Ahmad, Nabeel Mondal, Krishnendu Gupta, Vipin Lal, Rup |
description | Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.
[Display omitted]
•This study delves into the intricate mechanisms that underlie radiation resistance within the Deinococcus genus.•The research involves an extensive examination of 82 Deinococcus species genomes, both complete and near-complete, to dissect the distribution and significance of radiation-resistance associated proteins.•The presence or absence of radiation-resistance associated proteins within various species, has broadened our understanding of how these mechanisms have evolved.•protein-protein interactions has identified key interactions central to radiation response, providing functional aspects of these proteins. |
doi_str_mv | 10.1016/j.compbiolchem.2024.108161 |
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[Display omitted]
•This study delves into the intricate mechanisms that underlie radiation resistance within the Deinococcus genus.•The research involves an extensive examination of 82 Deinococcus species genomes, both complete and near-complete, to dissect the distribution and significance of radiation-resistance associated proteins.•The presence or absence of radiation-resistance associated proteins within various species, has broadened our understanding of how these mechanisms have evolved.•protein-protein interactions has identified key interactions central to radiation response, providing functional aspects of these proteins.</description><identifier>ISSN: 1476-9271</identifier><identifier>ISSN: 1476-928X</identifier><identifier>EISSN: 1476-928X</identifier><identifier>DOI: 10.1016/j.compbiolchem.2024.108161</identifier><identifier>PMID: 39116702</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Deinococcus ; Extremophile ; Network analysis ; Protein-protein interaction ; Radiation-resistance</subject><ispartof>Computational biology and chemistry, 2024-10, Vol.112, p.108161, Article 108161</ispartof><rights>2024 Elsevier Ltd</rights><rights>Copyright © 2024 Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c253t-2491b5eb1fb6de4b6d072f1277280f7a00939ea8a98750a872164ffe81cf0a4a3</cites><orcidid>0000-0002-7455-4423</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.compbiolchem.2024.108161$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39116702$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Singhvi, Nirjara</creatorcontrib><creatorcontrib>Talwar, Chandni</creatorcontrib><creatorcontrib>Nagar, Shekhar</creatorcontrib><creatorcontrib>Verma, Helianthous</creatorcontrib><creatorcontrib>Kaur, Jasvinder</creatorcontrib><creatorcontrib>Mahato, Nitish Kumar</creatorcontrib><creatorcontrib>Ahmad, Nabeel</creatorcontrib><creatorcontrib>Mondal, Krishnendu</creatorcontrib><creatorcontrib>Gupta, Vipin</creatorcontrib><creatorcontrib>Lal, Rup</creatorcontrib><title>Insights into the radiation and oxidative stress mechanisms in genus Deinococcus</title><title>Computational biology and chemistry</title><addtitle>Comput Biol Chem</addtitle><description>Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.
[Display omitted]
•This study delves into the intricate mechanisms that underlie radiation resistance within the Deinococcus genus.•The research involves an extensive examination of 82 Deinococcus species genomes, both complete and near-complete, to dissect the distribution and significance of radiation-resistance associated proteins.•The presence or absence of radiation-resistance associated proteins within various species, has broadened our understanding of how these mechanisms have evolved.•protein-protein interactions has identified key interactions central to radiation response, providing functional aspects of these proteins.</description><subject>Deinococcus</subject><subject>Extremophile</subject><subject>Network analysis</subject><subject>Protein-protein interaction</subject><subject>Radiation-resistance</subject><issn>1476-9271</issn><issn>1476-928X</issn><issn>1476-928X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNqNkE1PwzAMhiMEYmPwF1DEicuGk3ZNyw2NTwkJDiBxi9LU3TKtyYhbBP-eThuIIxd_yO9ryw9jZwImAkR2sZzY0KxLF1Z2gc1Egkz7QS4ysceGIlXZuJD52_5vrcSAHREtAWQCMD1kg6QQIlMgh-z5wZObL1rizreBtwvk0VTOtC54bnzFw6er-u4DObURiXiDdmG8o2Zj4XP0HfFrdD7YYG1Hx-ygNivCk10esdfbm5fZ_fjx6e5hdvU4tnKatGOZFqKcYinqMqsw7QMoWQuplMyhVgagSAo0uSlyNQWTKymytK4xF7YGk5pkxM63e9cxvHdIrW4cWVytjMfQkU6ggCJNM5H10sut1MZAFLHW6-gaE7-0AL0hqpf6L1G9Iaq3RHvz6e5OVzZY_Vp_EPaC660A-28_HEZN1qG3WLmIttVVcP-58w06aI65</recordid><startdate>20241001</startdate><enddate>20241001</enddate><creator>Singhvi, Nirjara</creator><creator>Talwar, Chandni</creator><creator>Nagar, Shekhar</creator><creator>Verma, Helianthous</creator><creator>Kaur, Jasvinder</creator><creator>Mahato, Nitish Kumar</creator><creator>Ahmad, Nabeel</creator><creator>Mondal, Krishnendu</creator><creator>Gupta, Vipin</creator><creator>Lal, Rup</creator><general>Elsevier Ltd</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-7455-4423</orcidid></search><sort><creationdate>20241001</creationdate><title>Insights into the radiation and oxidative stress mechanisms in genus Deinococcus</title><author>Singhvi, Nirjara ; Talwar, Chandni ; Nagar, Shekhar ; Verma, Helianthous ; Kaur, Jasvinder ; Mahato, Nitish Kumar ; Ahmad, Nabeel ; Mondal, Krishnendu ; Gupta, Vipin ; Lal, Rup</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c253t-2491b5eb1fb6de4b6d072f1277280f7a00939ea8a98750a872164ffe81cf0a4a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Deinococcus</topic><topic>Extremophile</topic><topic>Network analysis</topic><topic>Protein-protein interaction</topic><topic>Radiation-resistance</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Singhvi, Nirjara</creatorcontrib><creatorcontrib>Talwar, Chandni</creatorcontrib><creatorcontrib>Nagar, Shekhar</creatorcontrib><creatorcontrib>Verma, Helianthous</creatorcontrib><creatorcontrib>Kaur, Jasvinder</creatorcontrib><creatorcontrib>Mahato, Nitish Kumar</creatorcontrib><creatorcontrib>Ahmad, Nabeel</creatorcontrib><creatorcontrib>Mondal, Krishnendu</creatorcontrib><creatorcontrib>Gupta, Vipin</creatorcontrib><creatorcontrib>Lal, Rup</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Computational biology and chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Singhvi, Nirjara</au><au>Talwar, Chandni</au><au>Nagar, Shekhar</au><au>Verma, Helianthous</au><au>Kaur, Jasvinder</au><au>Mahato, Nitish Kumar</au><au>Ahmad, Nabeel</au><au>Mondal, Krishnendu</au><au>Gupta, Vipin</au><au>Lal, Rup</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Insights into the radiation and oxidative stress mechanisms in genus Deinococcus</atitle><jtitle>Computational biology and chemistry</jtitle><addtitle>Comput Biol Chem</addtitle><date>2024-10-01</date><risdate>2024</risdate><volume>112</volume><spage>108161</spage><pages>108161-</pages><artnum>108161</artnum><issn>1476-9271</issn><issn>1476-928X</issn><eissn>1476-928X</eissn><abstract>Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.
[Display omitted]
•This study delves into the intricate mechanisms that underlie radiation resistance within the Deinococcus genus.•The research involves an extensive examination of 82 Deinococcus species genomes, both complete and near-complete, to dissect the distribution and significance of radiation-resistance associated proteins.•The presence or absence of radiation-resistance associated proteins within various species, has broadened our understanding of how these mechanisms have evolved.•protein-protein interactions has identified key interactions central to radiation response, providing functional aspects of these proteins.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>39116702</pmid><doi>10.1016/j.compbiolchem.2024.108161</doi><orcidid>https://orcid.org/0000-0002-7455-4423</orcidid></addata></record> |
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subjects | Deinococcus Extremophile Network analysis Protein-protein interaction Radiation-resistance |
title | Insights into the radiation and oxidative stress mechanisms in genus Deinococcus |
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