Complete Genome Sequence of  Streptomyces lavendulae  subsp.  lavendulae  CCM 3239 (Formerly “ Streptomyces aureofaciens  CCM 3239”), a Producer of the Angucycline-Type Antibiotic Auricin

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ABSTRACT

Streptomyces lavendulae subsp. lavendulae CCM 3239 produces the angucycline antibiotic auricin and was thought to be the type strain of Streptomyces aureofaciens. We report the complete genome sequence of this strain, which consists of a linear chromosome and the linear plasmid pSA3239, and demonstrate it to be S. lavendulae subsp. lavendulae.

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antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

Kai Blin, Thomas Wolf, Marc Chevrette … (2017)

Abstract Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the ‘antibiotics and secondary metabolite analysis shell—antiSMASH’ has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.

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Recent advances in understanding Streptomyces

Keith F Chater (2016)

About 2,500 papers dated 2014–2016 were recovered by searching the PubMed database for Streptomyces, which are the richest known source of antibiotics. This review integrates around 100 of these papers in sections dealing with evolution, ecology, pathogenicity, growth and development, stress responses and secondary metabolism, gene expression, and technical advances. Genomic approaches have greatly accelerated progress. For example, it has been definitively shown that interspecies recombination of conserved genes has occurred during evolution, in addition to exchanges of some of the tens of thousands of non-conserved accessory genes. The closeness of the association of Streptomyces with plants, fungi, and insects has become clear and is reflected in the importance of regulators of cellulose and chitin utilisation in overall Streptomyces biology. Interestingly, endogenous cellulose-like glycans are also proving important in hyphal growth and in the clumping that affects industrial fermentations. Nucleotide secondary messengers, including cyclic di-GMP, have been shown to provide key input into developmental processes such as germination and reproductive growth, while late morphological changes during sporulation involve control by phosphorylation. The discovery that nitric oxide is produced endogenously puts a new face on speculative models in which regulatory Wbl proteins (peculiar to actinobacteria) respond to nitric oxide produced in stressful physiological transitions. Some dramatic insights have come from a new model system for Streptomyces developmental biology, Streptomyces venezuelae, including molecular evidence of very close interplay in each of two pairs of regulatory proteins. An extra dimension has been added to the many complexities of the regulation of secondary metabolism by findings of regulatory crosstalk within and between pathways, and even between species, mediated by end products. Among many outcomes from the application of chromosome immunoprecipitation sequencing (ChIP-seq) analysis and other methods based on “next-generation sequencing” has been the finding that 21% of Streptomyces mRNA species lack leader sequences and conventional ribosome binding sites. Further technical advances now emerging should lead to continued acceleration of knowledge, and more effective exploitation, of these astonishing and critically important organisms.

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Four genes in Streptomyces aureofaciens containing a domain characteristic of principal sigma factors

Jan Kormanec, Marian Farkasovsky, Laura Potúčková (1992)

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Journal

Journal ID (nlm-ta): Genome Announc

Journal ID (iso-abbrev): Genome Announc

Journal ID (hwp): ga

Journal ID (pmc): ga

Journal ID (publisher-id): GA

Title: Genome Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2169-8287

Publication date (Electronic): 1 March 2018

Publication date Collection: March 2018

Volume: 6

Issue: 9

Electronic Location Identifier: e00103-18

Affiliations

[a ]Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany

[b ]Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia

Author notes

Address correspondence to Christian Rückert, christian.rueckert@ 123456cebitec.uni-bielefeld.de .

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Christian Rückert https://orcid.org/0000-0002-9722-4435

Article

Publisher ID: genomeA00103-18

DOI: 10.1128/genomeA.00103-18

PMC ID: 5834325

PubMed ID: 29496832

SO-VID: 1a395224-b0af-44bc-9f84-deab074bf579

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 26 January 2018

Date accepted : 2 February 2018

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Figures: 0, Tables: 0, Equations: 0, References: 12, Pages: 2, Words: 1292

Funding

Funded by: Slovak Research and Development Agency;

Award ID: APVV-15-0410

Award ID: DO7RP-0037-12

Award Recipient : Renata Novakova Award Recipient : Dagmar Homerova Award Recipient : Lubomira Feckova Award Recipient : Bronislava Rezuchova Award Recipient : Erik Mingyar Award Recipient : Dominika Csolleiova Award Recipient : Carmen Bekeova Award Recipient : Beatrica Sevcikova Award Recipient : Jan Kormanec

Funded by: Slovak Academy of Sciences;

Award ID: VEGA grant 2/0002/16

Funded by: Deutsche Forschungsgemeinschaft (DFG), https://doi.org/10.13039/501100001659;

Award ID: Open Access Publication Fund of Bielefeld University

Award Recipient : Tobias Busche Award Recipient : Arwa Al'Dilaimi Award Recipient : Joern Kalinowski Award Recipient : Christian Rückert

Funded by: EC | Seventh Framework Programme (FP7), https://doi.org/10.13039/100011102;

Award ID: STREPSYNTH

Award Recipient : Tobias Busche Award Recipient : Joern Kalinowski Award Recipient : Jan Kormanec Award Recipient : Christian Rückert

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cover-date March 2018

ScienceOpen disciplines: Genetics

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ScienceOpen disciplines: Genetics

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Complete Genome Sequence of Streptomyces lavendulae subsp. lavendulae CCM 3239 (Formerly “ Streptomyces aureofaciens CCM 3239”), a Producer of the Angucycline-Type Antibiotic Auricin

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ABSTRACT

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Genome Integrity

Most cited references 10

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

Recent advances in understanding Streptomyces

Four genes in Streptomyces aureofaciens containing a domain characteristic of principal sigma factors

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