The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)
Yujin Jeong,Ji-Nu Kim,Min Woo Kim,Giselda Bucca,Suhyung Cho,Yeo Joon Yoon,Byung-Gee Kim,Jung-Hye Roe,Sun Chang Kim,Colin P. Smith,Byung-Kwan Cho +10 more
TLDR
Nucleotide resolution genome-scale measurements of the transcriptome and translatome of Streptomyces coelicolor, the model antibiotic-producing actinomycete, are integrated and it is revealed that the translation efficiency of secondary metabolic genes is negatively correlated with transcription and that several key antibiotic regulatory genes are translationally induced at transition growth phase.Abstract:
Individual Streptomyces species have the genetic potential to produce a diverse array of natural products of commercial, medical and veterinary interest. However, these products are often not detectable under laboratory culture conditions. To harness their full biosynthetic potential, it is important to develop a detailed understanding of the regulatory networks that orchestrate their metabolism. Here we integrate nucleotide resolution genome-scale measurements of the transcriptome and translatome of Streptomyces coelicolor, the model antibiotic-producing actinomycete. Our systematic study determines 3,570 transcription start sites and identifies 230 small RNAs and a considerable proportion (∼21%) of leaderless mRNAs; this enables deduction of genome-wide promoter architecture. Ribosome profiling reveals that the translation efficiency of secondary metabolic genes is negatively correlated with transcription and that several key antibiotic regulatory genes are translationally induced at transition growth phase. These findings might facilitate the design of new approaches to antibiotic discovery and development.read more
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Recent advances in understanding streptomyces
TL;DR: This review integrates around 100 papers in sections dealing with evolution, ecology, pathogenicity, growth and development, stress responses and secondary metabolism, gene expression, and technical advances of Streptomyces, which are the richest known source of antibiotics.
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Towards systems metabolic engineering in Pichia pastoris
TL;DR: The methylotrophic yeast Pichia pastoris is firmly established as a host for the production of recombinant proteins, frequently outperforming other heterologous hosts, and recent efforts to establish yeast peroxisomes for compartmentalized metabolite synthesis appear to fit ideally with the well-studied high capacity peroxISomal machinery of P. pastoris.
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Adaptive laboratory evolution of a genome-reduced Escherichia coli
Donghui Choe,Jun Hyoung Lee,Minseob Yoo,Soonkyu Hwang,Bong Hyun Sung,Suhyung Cho,Bernhard O. Palsson,Sun Chang Kim,Byung-Kwan Cho +8 more
TL;DR: Adaptive laboratory evolution is deployed to re-optimise growth performance and show transcriptome and translatome-wide remodeling of the organism that orchestrate metabolism and growth.
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Synthetic biology and metabolic engineering of actinomycetes for natural product discovery.
TL;DR: New advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.
Journal ArticleDOI
Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms.
E Palazzotto,Tilmann Weber +1 more
TL;DR: This review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new antibiotics.
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Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
Stephen D. Bentley,Keith F. Chater,Ana Cerdeño-Tárraga,Gregory L. Challis,Gregory L. Challis,Nicholas R. Thomson,Keith D. James,David Harris,Michael A. Quail,H. M. Kieser,D. Harper,Alex Bateman,Steve D.M. Brown,Govind Chandra,Carton W. Chen,Mark O. Collins,Ann Cronin,Andrew G. Fraser,Arlette Goble,J. Hidalgo,T. Hornsby,S. Howarth,Chih-Hung Huang,Tobias Kieser,L. Larke,Lee Murphy,Karen Oliver,Susan O'Neil,Ester Rabbinowitsch,Marie-Adèle Rajandream,Kim Rutherford,Simon Rutter,Kathy Seeger,David L. Saunders,Sarah Sharp,R. Squares,S. Squares,K. Taylor,T. Warren,Andreas Wietzorrek,John Woodward,Bart Barrell,Julian Parkhill,David A. Hopwood +43 more
TL;DR: The 8,667,507 base pair linear chromosome of Streptomyces coelicolor is reported, containing the largest number of genes so far discovered in a bacterium.
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Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
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