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Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

Zhang, Yuanhao ; Rowehl, Leahana ; Krumsiek, Julia M ; Orner, Erika P ; Shaikh, Nurmohammad ; Tarr, Phillip I ; Sodergren, Erica ; Weinstock, George M ; Boedeker, Edgar C ; Xiong, Xuejian ; Parkinson, John ; Frank, Daniel N ; Li, Ellen ; Gathungu, Grace Chakravortty, Dipshikha

PloS one, 2015-06, Vol.10 (6), p.e0130902-e0130902 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
Autor: Zhang, Yuanhao ; Rowehl, Leahana ; Krumsiek, Julia M ; Orner, Erika P ; Shaikh, Nurmohammad ; Tarr, Phillip I ; Sodergren, Erica ; Weinstock, George M ; Boedeker, Edgar C ; Xiong, Xuejian ; Parkinson, John ; Frank, Daniel N ; Li, Ellen ; Gathungu, Grace
Chakravortty, Dipshikha
Assuntos: Bacteria ; Bacterial Adhesion - genetics ; Biopsy ; Cadmium ; Cell culture ; Cell survival ; Chemotaxis ; Chromosomes ; Comparative analysis ; CRISPR ; Crohn Disease - microbiology ; Disease ; Down-Regulation - genetics ; E coli ; Epithelial cells ; Escherichia coli ; Escherichia coli - genetics ; Escherichia coli Infections - microbiology ; Flagella ; Gastrointestinal diseases ; Gene expression ; Gene sequencing ; Genes ; Genome, Bacterial - genetics ; Genomes ; Genomics ; Genotype & phenotype ; Glucose metabolism ; Glycogen ; Homology ; Humans ; Ileum - microbiology ; Inflammatory bowel disease ; Inflammatory bowel diseases ; Intestinal Mucosa - microbiology ; Intestine ; Laboratories ; Lesions ; Loci ; Macrophages ; Macrophages - microbiology ; Medicine ; Metabolism ; Mucosa ; Nucleotide sequence ; Oxidation ; Oxidation-reduction potential ; Patients ; Pediatrics ; Phenotypes ; Polymerase chain reaction ; Polysaccharides ; Reverse transcription ; Ribonucleic acid ; RNA ; RNA, Bacterial - genetics ; Salmonella ; Sequence Analysis, RNA - methods ; Signal Transduction - genetics ; Stationary phase ; Strains (organisms) ; Transcriptome - genetics ; Up-Regulation - genetics
É parte de: PloS one, 2015-06, Vol.10 (6), p.e0130902-e0130902
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Competing Interests: The authors have declared that no competing interests exist.
Current Address: Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
Conceived and designed the experiments: YZ PT EB JP DF EL GG. Performed the experiments: YZ LR JFK EO NS PT ES GW EB XX JP DF EL GG. Analyzed the data: YZ LR JFK EO NS PT ES GW EB XX JP DF EL GG. Contributed reagents/materials/analysis tools: YZ EO NS PT ES GW EB XX JP DF EL GG. Wrote the paper: YZ LR JFK EO NS PT ES GW EB XX JP DF EL GG.
Descrição: Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn's disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)--CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription quantitative polymerase chain reaction assays for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA samples (p <0.05). These results support a comparative genomic/transcriptomic approach towards identifying candidate AIEC signature transcripts.
Editor: United States: Public Library of Science
Idioma: Inglês

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Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

Zhang, Yuanhao ; Rowehl, Leahana ; Krumsiek, Julia M ; Orner, Erika P ; Shaikh, Nurmohammad ; Tarr, Phillip I ; Sodergren, Erica ; Weinstock, George M ; Boedeker, Edgar C ; Xiong, Xuejian ; Parkinson, John ; Frank, Daniel N ; Li, Ellen ; Gathungu, Grace Chakravortty, Dipshikha

United States: Public Library of Science

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