Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1
Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis...
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| creator | Luan, Hemi Meng, Nan Fu, Jin Chen, Xiaomin Xu, Xun Feng, Qiang Jiang, Hui Dai, Jun Yuan, Xune Lu, Yanping Roberts, Alexandra A Luo, Xiao Chen, Maoshan Xu, Shengtao Li, Jun Hamilton, Chris J Fang, Chengxiang Wang, Jun |
| description | Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans. |
| doi_str_mv | 10.1371/journal.pone.0085649 |
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Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0085649</identifier><identifier>PMID: 24465634</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Antioxidants ; Antioxidants (Nutrients) ; Antioxidants - metabolism ; Antisense RNA ; Apoptosis ; Bacilli ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biology ; Biosynthesis ; Carotenoids ; Chemistry ; Deinococcus - genetics ; Deinococcus - metabolism ; Deinococcus - radiation effects ; Deinococcus radiodurans ; Deoxyribonucleic acid ; DNA ; DNA damage ; DNA Repair ; E coli ; Escherichia coli ; Gene expression ; Gene Expression Regulation, Bacterial - radiation effects ; Gene sequencing ; Genes ; Genomes ; Genomics ; Ionizing radiation ; Irradiation ; Life sciences ; Metabolic Networks and Pathways - genetics ; Metabolism ; Metabolites ; Metabolomics ; Oxidative stress ; Pharmacy ; Phytoene synthase ; Pigments ; Principal Component Analysis ; Proteins ; Proteomics ; Radiation ; Radiation therapy ; Radiation Tolerance ; Recovery ; Repair ; Research parks ; Ribonucleic acid ; RNA ; RNA sequencing ; RNA, Bacterial - genetics ; RNA, Bacterial - metabolism ; Sequence Analysis, RNA ; Transcriptome ; Tricarboxylic acid cycle</subject><ispartof>PloS one, 2014-01, Vol.9 (1), p.e85649</ispartof><rights>COPYRIGHT 2014 Public Library of Science</rights><rights>2014 Luan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.</description><subject>Antioxidants</subject><subject>Antioxidants (Nutrients)</subject><subject>Antioxidants - metabolism</subject><subject>Antisense RNA</subject><subject>Apoptosis</subject><subject>Bacilli</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biology</subject><subject>Biosynthesis</subject><subject>Carotenoids</subject><subject>Chemistry</subject><subject>Deinococcus - genetics</subject><subject>Deinococcus - metabolism</subject><subject>Deinococcus - radiation effects</subject><subject>Deinococcus radiodurans</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA damage</subject><subject>DNA Repair</subject><subject>E coli</subject><subject>Escherichia coli</subject><subject>Gene 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environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24465634</pmid><doi>10.1371/journal.pone.0085649</doi><tpages>e85649</tpages><oa>free_for_read</oa></addata></record> |
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| recordid | cdi_plos_journals_1491323516 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Antioxidants Antioxidants (Nutrients) Antioxidants - metabolism Antisense RNA Apoptosis Bacilli Bacterial Proteins - genetics Bacterial Proteins - metabolism Biology Biosynthesis Carotenoids Chemistry Deinococcus - genetics Deinococcus - metabolism Deinococcus - radiation effects Deinococcus radiodurans Deoxyribonucleic acid DNA DNA damage DNA Repair E coli Escherichia coli Gene expression Gene Expression Regulation, Bacterial - radiation effects Gene sequencing Genes Genomes Genomics Ionizing radiation Irradiation Life sciences Metabolic Networks and Pathways - genetics Metabolism Metabolites Metabolomics Oxidative stress Pharmacy Phytoene synthase Pigments Principal Component Analysis Proteins Proteomics Radiation Radiation therapy Radiation Tolerance Recovery Repair Research parks Ribonucleic acid RNA RNA sequencing RNA, Bacterial - genetics RNA, Bacterial - metabolism Sequence Analysis, RNA Transcriptome Tricarboxylic acid cycle |
| title | Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1 |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-06T06%3A09%3A14IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-wide%20transcriptome%20and%20antioxidant%20analyses%20on%20gamma-irradiated%20phases%20of%20deinococcus%20radiodurans%20R1&rft.jtitle=PloS%20one&rft.au=Luan,%20Hemi&rft.date=2014-01-23&rft.volume=9&rft.issue=1&rft.spage=e85649&rft.pages=e85649-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0085649&rft_dat=%3Cgale_plos_%3EA478850914%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1491323516&rft_id=info:pmid/24465634&rft_galeid=A478850914&rft_doaj_id=oai_doaj_org_article_7adf7af89a504862a37ae28f8c05c4db&rfr_iscdi=true |