Analysis of gene expression in operons of Streptomyces coelicolor

Laing, Emma; Mersinias, Vassilis; Smith, Colin P.; Hubbard, Simon J.

doi:10.1186/gb-2006-7-6-r46

Cited by 35 publications

(15 citation statements)

References 54 publications

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“…This was achieved by combining two RNA sequencing approaches, one that identifies and ‘differentiates’ sites of transcription initiation and endonucleolytic cleavage (dRNA-seq) and another that provides a ‘global’ view of transcript abundance and the boundaries of transcription (gRNA-seq) (Lin et al ., 2013 ). We also conducted a parallel analysis of Escherichia coli , which has been used as a reference for studying Streptomyces gene regulation (Taguchi et al ., 1990 ; Messer and Zakrzewska-Czerwinska, 2002 ; Bralley et al ., 2006 ; Laing et al ., 2006 ; Gatewood and Jones, 2010 ), as well as being an important model, most recently in the development of systems-level understanding (Schwille and Diez, 2009 ; De Smet and Marchal, 2010 ; Hyduke and Palsson, 2010 ; Zhang et al ., 2010 ; Porter et al ., 2011 ). The inclusion of E. coli provided insight over and above that obtained by many groups via extensive study using traditional gene-specific methods such as northern blotting and primer extension (Kime et al ., 2008 ).…”

Section: Introductionmentioning

confidence: 99%

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

Hasan

Lin

et al. 2014

Molecular Microbiology

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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.

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Section: Introductionmentioning

confidence: 99%

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

Hasan

Lin

et al. 2014

Molecular Microbiology

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“…The relationships between IGA and various computationally derived characteristics of gene promoters, including binding site counts, quality, and locations were determined by correlation and regression analysis. For each operon, only the IGA of the first gene was included in the statistical analysis, since unequal levels of expression among genes of the same operon are common, likely because of putative internal promoters or because of alternative regulatory mechanisms controlling gene expression within operons 48. In the following sections we give a brief description of the experimental studies used to characterize CRP/ArcA IGA.…”

Section: Methodsmentioning

confidence: 99%

Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA

Leuze

Karpinets

Syed

et al. 2012

Gene�Regul Syst Bio

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Bacterial gene regulation involves transcription factors (TF) that bind to DNA recognition sequences in operon promoters. These recognition sequences, many of which are palindromic, are known as regulatory elements or transcription factor binding sites (TFBS). Some TFs are global regulators that can modulate the expression of hundreds of genes. In this study we examine global regulator half-sites, where a half-site, which we shall call a binding motif (BM), is one half of a palindromic TFBS. We explore the hypothesis that the number of BMs plays an important role in transcriptional regulation, examining empirical data from transcriptional profiling of the CRP and ArcA regulons. We compare the power of BM counts and of full TFBS characteristics to predict induced transcriptional activity. We find that CRP BM counts have a nonlinear effect on CRP-dependent transcriptional activity and predict this activity better than full TFBS quality or location.

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“…However, it has been demonstrated that genes within an operon do not conform to the simple notion that they have equal levels of expression (43). Several studies revealed the existence of the internal promoters and read-through terminators in bacterial operons (43,44). These additional promoters are often located downstream of the first gene so that only part of the operon is transcribed from the internal promoter.…”

Section: Discussionmentioning

confidence: 99%

“…The regulatory mechanism controlling the transcription of the AcrAB-OprM genes after clarithromycin treatment is indistinct at this point and needs further investigation. However, it has been demonstrated that genes within an operon do not conform to the simple notion that they have equal levels of expression (43). Several studies revealed the existence of the internal promoters and read-through terminators in bacterial operons (43,44).…”

Section: Discussionmentioning

confidence: 99%

Moraxella catarrhalis AcrAB-OprM Efflux Pump Contributes to Antimicrobial Resistance and Is Enhanced during Cold Shock Response

Spaniol

Bernhard

Aebi

2015

Antimicrob Agents Chemother

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bMoraxella catarrhalis is a common pathogen of the human respiratory tract. Multidrug efflux pumps play a major role in antibiotic resistance and virulence in many Gram-negative organisms. In the present study, the role of the AcrAB-OprM efflux pump in antibiotic resistance was investigated by constructing mutants that lack the acrA, acrB, and oprM genes in M. catarrhalis strain O35E. We observed a moderate (1.5-fold) decrease in the MICs of amoxicillin and cefotaxime and a marked (4.7-fold) decrease in the MICs of clarithromycin for acrA, acrB, and oprM mutants in comparison with the wild-type O35E strain. Exposure of the M. catarrhalis strains O35E and 300 to amoxicillin triggered an increased transcription of all AcrAB-OprM pump genes, and exposure of strains O35E, 300, and 415 to clarithromycin enhanced the expression of acrA and oprM mRNA. Inactivation of the AcrAB-OprM efflux pump genes demonstrated a decreased ability to invade epithelial cells compared to the parental strain, suggesting that acrA, acrB, and oprM are required for efficient invasion of human pharyngeal epithelial cells. Cold shock increases the expression of AcrAB-OprM efflux pump genes in all three M. catarrhalis strains tested. Increased expression of AcrAB-OprM pump genes after cold shock leads to a lower accumulation of Hoechst 33342 (H33342), a substrate of AcrABOprM efflux pumps, indicating that cold shock results in increased efflux activity. In conclusion, the AcrAB-OprM efflux pump appears to play a role in the antibiotic resistance and virulence of M. catarrhalis and is involved in the cold shock response. Moraxella catarrhalis colonizes the mucosal surface of the human nasopharynx and is a major cause of acute otitis media in children and of exacerbations of chronic obstructive pulmonary disease in adults (1-4). The proportion of cases of acute otitis media caused by M. catarrhalis varies between 5% and 20%, with recent studies showing a relative increase in M. catarrhalis-caused otitis media since the introduction of routine infant immunization with the pneumococcal conjugate vaccine (2, 4-6). Furthermore, clinical studies revealed that the prevalence of pharyngeal colonization and respiratory tract infections caused by M. catarrhalis displays seasonal variation and increases in winter (7-10). The human nasopharyngeal flora is recurrently exposed to rapid downshifts of environmental temperature. Breathing cold air (e.g., Ϫ1°C at 10 to 20 liters/min) reduces the nasopharyngeal temperature from 34°C at room temperature to about 26°C within several minutes and for extended periods (11). Such rapid variation of temperature induces adaptive events in the residential upper respiratory tract flora that may contribute to the transition from asymptomatic colonization to infection. Our previous in vitro studies demonstrated that a 26°C cold shock upregulates the expression of important virulence traits, such as adherence to epithelial cells, iron acquisition, complement resistance, and immune evasion (12)(13)(14).Adaptive resistance also...

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Analysis of gene expression in operons of Streptomyces coelicolor

Cited by 35 publications

References 54 publications

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

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

Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA

Moraxella catarrhalis AcrAB-OprM Efflux Pump Contributes to Antimicrobial Resistance and Is Enhanced during Cold Shock Response

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