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

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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509574/
https://www.ncbi.nlm.nih.gov/pubmed/26125937
http://dx.doi.org/10.1371/journal.pone.0130902
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author 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
author_facet 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
author_sort Zhang, Yuanhao
collection PubMed
description 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.
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spelling pubmed-45095742015-07-24 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 PLoS One Research Article 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. Public Library of Science 2015-06-30 /pmc/articles/PMC4509574/ /pubmed/26125937 http://dx.doi.org/10.1371/journal.pone.0130902 Text en © 2015 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
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
Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
title Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
title_full Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
title_fullStr Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
title_full_unstemmed Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
title_short Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis
title_sort identification of candidate adherent-invasive e. coli signature transcripts by genomic/transcriptomic analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509574/
https://www.ncbi.nlm.nih.gov/pubmed/26125937
http://dx.doi.org/10.1371/journal.pone.0130902
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