Genome-wide inference of regulatory networks in Streptomyces coelicolor View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-10-18

AUTHORS

Marlene Castro-Melchor, Salim Charaniya, George Karypis, Eriko Takano, Wei-Shou Hu

ABSTRACT

BACKGROUND: The onset of antibiotics production in Streptomyces species is co-ordinated with differentiation events. An understanding of the genetic circuits that regulate these coupled biological phenomena is essential to discover and engineer the pharmacologically important natural products made by these species. The availability of genomic tools and access to a large warehouse of transcriptome data for the model organism, Streptomyces coelicolor, provides incentive to decipher the intricacies of the regulatory cascades and develop biologically meaningful hypotheses. RESULTS: In this study, more than 500 samples of genome-wide temporal transcriptome data, comprising wild-type and more than 25 regulatory gene mutants of Streptomyces coelicolor probed across multiple stress and medium conditions, were investigated. Information based on transcript and functional similarity was used to update a previously-predicted whole-genome operon map and further applied to predict transcriptional networks constituting modules enriched in diverse functions such as secondary metabolism, and sigma factor. The predicted network displays a scale-free architecture with a small-world property observed in many biological networks. The networks were further investigated to identify functionally-relevant modules that exhibit functional coherence and a consensus motif in the promoter elements indicative of DNA-binding elements. CONCLUSIONS: Despite the enormous experimental as well as computational challenges, a systems approach for integrating diverse genome-scale datasets to elucidate complex regulatory networks is beginning to emerge. We present an integrated analysis of transcriptome data and genomic features to refine a whole-genome operon map and to construct regulatory networks at the cistron level in Streptomyces coelicolor. The functionally-relevant modules identified in this study pose as potential targets for further studies and verification. More... »

PAGES

578-578

References to SciGraph publications

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  • 2008-01-29. Genome-wide transcriptome analysis reveals that a pleiotropic antibiotic regulator, AfsS, modulates nutritional stress response in Streptomyces coelicolor A3(2) in BMC GENOMICS
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  • 2000-10. The large-scale organization of metabolic networks in NATURE
  • 2007-01-26. Identification of functional modules using network topology and high-throughput data in BMC SYSTEMS BIOLOGY
  • 2008-02-12. Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor in BMC GENOMICS
  • 2004-11-26. GOToolBox: functional analysis of gene datasets based on Gene Ontology in GENOME BIOLOGY
  • 2005-03-20. Reverse engineering of regulatory networks in human B cells in NATURE GENETICS
  • 2007-07-10. Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans in BMC GENOMICS
  • 2007-05-22. GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products in BMC BIOINFORMATICS
  • 2006-03-20. ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context in BMC BIOINFORMATICS
  • 2010-03-25. TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach in BMC BIOINFORMATICS
  • 2001-10. Negative regulation of the heat shock response in Streptomyces in ARCHIVES OF MICROBIOLOGY
  • 2009-01-12. On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information in EURASIP JOURNAL ON BIOINFORMATICS AND SYSTEMS BIOLOGY
  • 2006-06-27. Reverse engineering cellular networks in NATURE PROTOCOLS
  • 2010-01-06. The dynamic architecture of the metabolic switch in Streptomyces coelicolor in BMC GENOMICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-11-578

    DOI

    http://dx.doi.org/10.1186/1471-2164-11-578

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1052178900

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20955611


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    35 schema:description BACKGROUND: The onset of antibiotics production in Streptomyces species is co-ordinated with differentiation events. An understanding of the genetic circuits that regulate these coupled biological phenomena is essential to discover and engineer the pharmacologically important natural products made by these species. The availability of genomic tools and access to a large warehouse of transcriptome data for the model organism, Streptomyces coelicolor, provides incentive to decipher the intricacies of the regulatory cascades and develop biologically meaningful hypotheses. RESULTS: In this study, more than 500 samples of genome-wide temporal transcriptome data, comprising wild-type and more than 25 regulatory gene mutants of Streptomyces coelicolor probed across multiple stress and medium conditions, were investigated. Information based on transcript and functional similarity was used to update a previously-predicted whole-genome operon map and further applied to predict transcriptional networks constituting modules enriched in diverse functions such as secondary metabolism, and sigma factor. The predicted network displays a scale-free architecture with a small-world property observed in many biological networks. The networks were further investigated to identify functionally-relevant modules that exhibit functional coherence and a consensus motif in the promoter elements indicative of DNA-binding elements. CONCLUSIONS: Despite the enormous experimental as well as computational challenges, a systems approach for integrating diverse genome-scale datasets to elucidate complex regulatory networks is beginning to emerge. We present an integrated analysis of transcriptome data and genomic features to refine a whole-genome operon map and to construct regulatory networks at the cistron level in Streptomyces coelicolor. The functionally-relevant modules identified in this study pose as potential targets for further studies and verification.
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