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A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

Romero, DA, Hasan, AH, Lin, Y-F, Kime, L, Ruiz-Larrabeiti, O, Urem, M, Bucca, G, Mamanova, L, Laing, EE, van Wezel, GP, Smith, CP, Kaberdin, VR and McDowall, KJ (2014) A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing MOLECULAR MICROBIOLOGY, 94 (5). pp. 963-987.

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Abstract

Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post-genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. This was achieved by combining RNA-sequencing approaches suited to the analysis of GC-rich organisms. Escherichia coli was analysed in parallel to validate the methodology and allow comparison. Previously, sites of RNA processing and degradation had not been mapped on a transcriptome-wide scale for E. coli. Through examples, we show the value of our approach and data sets. This includes the identification of new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor and the identification of host-encoded leaderless mRNA and rRNA processing associated with the generation of specialized ribosomes in E. coli. New regulatory small RNAs were identified for both organisms. Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Biosciences and Medicine > Department of Microbial and Cellular Sciences
Authors :
AuthorsEmailORCID
Romero, DAUNSPECIFIEDUNSPECIFIED
Hasan, AHUNSPECIFIEDUNSPECIFIED
Lin, Y-FUNSPECIFIEDUNSPECIFIED
Kime, LUNSPECIFIEDUNSPECIFIED
Ruiz-Larrabeiti, OUNSPECIFIEDUNSPECIFIED
Urem, MUNSPECIFIEDUNSPECIFIED
Bucca, GUNSPECIFIEDUNSPECIFIED
Mamanova, LUNSPECIFIEDUNSPECIFIED
Laing, EEUNSPECIFIEDUNSPECIFIED
van Wezel, GPUNSPECIFIEDUNSPECIFIED
Smith, CPUNSPECIFIEDUNSPECIFIED
Kaberdin, VRUNSPECIFIEDUNSPECIFIED
McDowall, KJUNSPECIFIEDUNSPECIFIED
Date : 1 December 2014
Identification Number : 10.1111/mmi.12810
Uncontrolled Keywords : Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, Microbiology, 16S RIBOSOMAL-RNA, SMALL NONCODING RNAS, GENOME-WIDE IDENTIFICATION, LEADERLESS MESSENGER-RNAS, PHASE-DEPENDENT CONTROL, IN-VIVO, POLYNUCLEOTIDE PHOSPHORYLASE, ANTIBIOTIC PRODUCTION, PROMOTER SEQUENCES, TRANSLATION INITIATION
Related URLs :
Additional Information : © 2014 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Depositing User : Symplectic Elements
Date Deposited : 01 Dec 2015 18:02
Last Modified : 01 Dec 2015 18:02
URI: http://epubs.surrey.ac.uk/id/eprint/809059

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