High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes
ABSTRACTVirulent genes present in Escherichia coli (E. coli) can cause significant human diseases. These enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) isolates with virulent genes show different expression levels when grown under diverse laboratory conditions. In this research,...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2023-12-01
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| Series: | Gut Microbes |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2023.2228042 |
| _version_ | 1797236648479555584 |
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| author | Rahul Gomes Ashleigh Denison Kroschel Stephanie Day Rick Jansen |
| author_facet | Rahul Gomes Ashleigh Denison Kroschel Stephanie Day Rick Jansen |
| author_sort | Rahul Gomes |
| collection | DOAJ |
| description | ABSTRACTVirulent genes present in Escherichia coli (E. coli) can cause significant human diseases. These enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) isolates with virulent genes show different expression levels when grown under diverse laboratory conditions. In this research, we have performed differential gene expression analysis using publicly available RNA-seq data on three pathogenic E. coli hybrid isolates in an attempt to characterize the variation in gene interactions that are altered by the presence or absence of virulent factors within the genome. Almost 26.7% of the common genes across these strains were found to be differentially expressed. Out of the 88 differentially expressed genes with virulent factors identified from PATRIC, nine were common in all these strains. A combination of Weighted Gene Co-Expression Network Analysis and Gene Ontology Enrichment Analysis reveals significant differences in gene co-expression involving virulent genes common among the three investigated strains. The co-expression pattern is observed to be especially variable among biological pathways involving metabolism-related genes. This suggests a potential difference in resource allocation or energy generation across the three isolates based on genomic variation. |
| first_indexed | 2024-03-11T14:20:18Z |
| format | Article |
| id | doaj.art-5823652578314d6eb1bd8a02b05ec6b7 |
| institution | Directory Open Access Journal |
| issn | 1949-0976 1949-0984 |
| language | English |
| last_indexed | 2024-04-24T17:07:12Z |
| publishDate | 2023-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj.art-5823652578314d6eb1bd8a02b05ec6b72024-03-28T22:38:20ZengTaylor & Francis GroupGut Microbes1949-09761949-09842023-12-0115110.1080/19490976.2023.2228042High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genesRahul Gomes0Ashleigh Denison Kroschel1Stephanie Day2Rick Jansen3Department of Computer Science, University of Wisconsin-Eau Claire, Eau Claire, WI, USADepartment of Computer Science, University of Wisconsin-Eau Claire, Eau Claire, WI, USADepartment of Earth, Environment, and Geospatial Sciences, North Dakota State University, Fargo, ND, USAMasonic Cancer Center, University of Minnesota-Twin Cities, Minneapolis, MN, USAABSTRACTVirulent genes present in Escherichia coli (E. coli) can cause significant human diseases. These enteropathogenic E. coli (EPEC) and enterotoxigenic E. coli (ETEC) isolates with virulent genes show different expression levels when grown under diverse laboratory conditions. In this research, we have performed differential gene expression analysis using publicly available RNA-seq data on three pathogenic E. coli hybrid isolates in an attempt to characterize the variation in gene interactions that are altered by the presence or absence of virulent factors within the genome. Almost 26.7% of the common genes across these strains were found to be differentially expressed. Out of the 88 differentially expressed genes with virulent factors identified from PATRIC, nine were common in all these strains. A combination of Weighted Gene Co-Expression Network Analysis and Gene Ontology Enrichment Analysis reveals significant differences in gene co-expression involving virulent genes common among the three investigated strains. The co-expression pattern is observed to be especially variable among biological pathways involving metabolism-related genes. This suggests a potential difference in resource allocation or energy generation across the three isolates based on genomic variation.https://www.tandfonline.com/doi/10.1080/19490976.2023.2228042E. coliEPECETECWGCNAenrichment analysisdifferential expression |
| spellingShingle | Rahul Gomes Ashleigh Denison Kroschel Stephanie Day Rick Jansen High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes Gut Microbes E. coli EPEC ETEC WGCNA enrichment analysis differential expression |
| title | High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes |
| title_full | High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes |
| title_fullStr | High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes |
| title_full_unstemmed | High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes |
| title_short | High variation across E. coli hybrid isolates identified in metabolism-related biological pathways co-expressed with virulent genes |
| title_sort | high variation across e coli hybrid isolates identified in metabolism related biological pathways co expressed with virulent genes |
| topic | E. coli EPEC ETEC WGCNA enrichment analysis differential expression |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2023.2228042 |
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