Nafiseh Davati, Abozar Ghorbani, Elham Ashrafi-Dehkordi, Thomas P Karbanowicz
{"title":"鼠伤寒沙门氏菌的基因网络分析揭示了参与应对低水活性的关键基因的新见解。","authors":"Nafiseh Davati, Abozar Ghorbani, Elham Ashrafi-Dehkordi, Thomas P Karbanowicz","doi":"10.30498/ijb.2023.387696.3640","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>When <i>Salmonella enterica serovar Typhimurium</i>, a foodborne bacterium, is exposed to osmotic stress, cellular adaptations increase virulence severity and cellular survival.</p><p><strong>Objectives: </strong>The aim of the gene network analysis of <i>S. Typhimurium</i> was to provide insights into the various interactions between the genes involved in cellular survival under low water activity (a<sub>w</sub>).</p><p><strong>Materials and methods: </strong>We performed a gene network analysis to identify the gene clusters and hub genes of <i>S. Typhimurium</i> using Cytoscape in three food samples subjected to a<sub>w</sub> stress after 72 hours.</p><p><strong>Results: </strong>The identified hub genes of <i>S. Typhimurium</i> belonged to down-regulated genes and were related to translation, transcription, and ribosome structure in the food samples. The <i>rpsB</i> and <i>Tig</i> were identified as the most important of the hub genes. Enrichment analysis of the hub genes also revealed the importance of translation and cellular protein metabolic processes. Moreover, the biological process associated with organonitrogen metabolism in milk chocolate was identified. According to the KEGG pathway results of gene cluster analysis, cellular responses to stress were associated with RNA polymerase, ribosome, and oxidative phosphorylation. Genes encoding RNA polymerase activity, including <i>rpoA</i>, <i>rpoB</i>, and <i>rpoZ</i>, were also significantly identified in the KEGG pathways. The identified motifs of hub DEGs included EXPREG_00000850, EXPREG_00000b00, EXPREG_000008e0, and EXPREG_00000850.</p><p><strong>Conclusion: </strong>Based on the results of the gene network analysis, the identified hub genes may contribute to adaptation to food compositions and be responsible for the development of low water stress tolerance in <i>Salmonella</i>. Among the food samples, the milk chocolate matrix leads to more adaptation pathways for <i>S. Typhimurium</i> survival, as more hub genes were down-regulated and more motifs were detected. The identified motifs were involved in carbohydrate metabolism, carbohydrate transport, electron transfer, and oxygen transfer.</p>","PeriodicalId":14492,"journal":{"name":"Iranian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":1.6000,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804061/pdf/","citationCount":"0","resultStr":"{\"title\":\"Gene Networks Analysis of <i>Salmonella Typhimurium</i> Reveals New Insights on Key Genes Involved in Response to Low Water Activity.\",\"authors\":\"Nafiseh Davati, Abozar Ghorbani, Elham Ashrafi-Dehkordi, Thomas P Karbanowicz\",\"doi\":\"10.30498/ijb.2023.387696.3640\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>When <i>Salmonella enterica serovar Typhimurium</i>, a foodborne bacterium, is exposed to osmotic stress, cellular adaptations increase virulence severity and cellular survival.</p><p><strong>Objectives: </strong>The aim of the gene network analysis of <i>S. Typhimurium</i> was to provide insights into the various interactions between the genes involved in cellular survival under low water activity (a<sub>w</sub>).</p><p><strong>Materials and methods: </strong>We performed a gene network analysis to identify the gene clusters and hub genes of <i>S. Typhimurium</i> using Cytoscape in three food samples subjected to a<sub>w</sub> stress after 72 hours.</p><p><strong>Results: </strong>The identified hub genes of <i>S. Typhimurium</i> belonged to down-regulated genes and were related to translation, transcription, and ribosome structure in the food samples. The <i>rpsB</i> and <i>Tig</i> were identified as the most important of the hub genes. Enrichment analysis of the hub genes also revealed the importance of translation and cellular protein metabolic processes. Moreover, the biological process associated with organonitrogen metabolism in milk chocolate was identified. According to the KEGG pathway results of gene cluster analysis, cellular responses to stress were associated with RNA polymerase, ribosome, and oxidative phosphorylation. Genes encoding RNA polymerase activity, including <i>rpoA</i>, <i>rpoB</i>, and <i>rpoZ</i>, were also significantly identified in the KEGG pathways. The identified motifs of hub DEGs included EXPREG_00000850, EXPREG_00000b00, EXPREG_000008e0, and EXPREG_00000850.</p><p><strong>Conclusion: </strong>Based on the results of the gene network analysis, the identified hub genes may contribute to adaptation to food compositions and be responsible for the development of low water stress tolerance in <i>Salmonella</i>. Among the food samples, the milk chocolate matrix leads to more adaptation pathways for <i>S. Typhimurium</i> survival, as more hub genes were down-regulated and more motifs were detected. The identified motifs were involved in carbohydrate metabolism, carbohydrate transport, electron transfer, and oxygen transfer.</p>\",\"PeriodicalId\":14492,\"journal\":{\"name\":\"Iranian Journal of Biotechnology\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.6000,\"publicationDate\":\"2023-10-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804061/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Iranian Journal of Biotechnology\",\"FirstCategoryId\":\"5\",\"ListUrlMain\":\"https://doi.org/10.30498/ijb.2023.387696.3640\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Iranian Journal of Biotechnology","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.30498/ijb.2023.387696.3640","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
Gene Networks Analysis of Salmonella Typhimurium Reveals New Insights on Key Genes Involved in Response to Low Water Activity.
Background: When Salmonella enterica serovar Typhimurium, a foodborne bacterium, is exposed to osmotic stress, cellular adaptations increase virulence severity and cellular survival.
Objectives: The aim of the gene network analysis of S. Typhimurium was to provide insights into the various interactions between the genes involved in cellular survival under low water activity (aw).
Materials and methods: We performed a gene network analysis to identify the gene clusters and hub genes of S. Typhimurium using Cytoscape in three food samples subjected to aw stress after 72 hours.
Results: The identified hub genes of S. Typhimurium belonged to down-regulated genes and were related to translation, transcription, and ribosome structure in the food samples. The rpsB and Tig were identified as the most important of the hub genes. Enrichment analysis of the hub genes also revealed the importance of translation and cellular protein metabolic processes. Moreover, the biological process associated with organonitrogen metabolism in milk chocolate was identified. According to the KEGG pathway results of gene cluster analysis, cellular responses to stress were associated with RNA polymerase, ribosome, and oxidative phosphorylation. Genes encoding RNA polymerase activity, including rpoA, rpoB, and rpoZ, were also significantly identified in the KEGG pathways. The identified motifs of hub DEGs included EXPREG_00000850, EXPREG_00000b00, EXPREG_000008e0, and EXPREG_00000850.
Conclusion: Based on the results of the gene network analysis, the identified hub genes may contribute to adaptation to food compositions and be responsible for the development of low water stress tolerance in Salmonella. Among the food samples, the milk chocolate matrix leads to more adaptation pathways for S. Typhimurium survival, as more hub genes were down-regulated and more motifs were detected. The identified motifs were involved in carbohydrate metabolism, carbohydrate transport, electron transfer, and oxygen transfer.
期刊介绍:
Iranian Journal of Biotechnology (IJB) is published quarterly by the National Institute of Genetic Engineering and Biotechnology. IJB publishes original scientific research papers in the broad area of Biotechnology such as, Agriculture, Animal and Marine Sciences, Basic Sciences, Bioinformatics, Biosafety and Bioethics, Environment, Industry and Mining and Medical Sciences.