title: Transcriptional regulators of GntR family in Streptomyces coelicolor A3(2): analysis in silico and in vivo of YtrA subfamily.
abstract: Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family. All 56 GntR proteins of M145 strain were classified into FadR, HutC, MocR, YtrA, and DevA subfamilies according to their secondary structure. We then checked for the presence of GntR orthologs in six other sequenced Streptomyces and one Kitasatospora genomes, revealing that 12 GntRs were conserved in all analyzed strains. Genomic analysis of the less studied YtrA type regulators revealed 160 sequences present in 88 members of Coriobacteridae, Rubrobacteridae, and Actinobacteridae subclasses. These proteins form seven dense clusters on the consensus phylogenetic tree and their genes are usually co-located with the genes for transport proteins. Probable operator sites were identified for orthologous groups of Sco0823 and Sco3812 proteins. All S. coelicolor YtrA-like regulatory genes (SCO0823, SCO1728, SCO3812) were analyzed at transcriptional level, knocked out, and introduced on moderate copy number plasmid in M145 strain. Also, gene SCO0824, a part of putative SCO0823 operon, was studied. Results of these experiments are discussed here.
authors.affiliation: Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine.
authors.forename: O
authors.initials: O
authors.lastname: Tsypik
authors.affiliation: Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine.
authors.forename: O
authors.initials: O
authors.lastname: Yushchuk
authors.affiliation: Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine.
authors.forename: N
authors.initials: N
authors.lastname: Zaburannyi
authors.affiliation: Department of Biology, Lund University, Lund, 22362, Sweden.
authors.forename: K
authors.initials: K
authors.lastname: Flärdh
authors.affiliation: Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
authors.forename: S
authors.initials: S
authors.lastname: Walker
authors.affiliation: Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine.
authors.forename: V
authors.initials: V
authors.lastname: Fedorenko
authors.affiliation: Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Hrushevskoho st. 4, Lviv, 79005, Ukraine. b.ostash@lnu.edu.ua.|Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. b.ostash@lnu.edu.ua.
authors.forename: B
authors.identifier: http://orcid.org/0000-0001-5904-5957
authors.initials: B
authors.lastname: Ostash
mesh_terms: D000900:Anti-Bacterial Agents / Q000096:biosynthesis; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial; D055786:Gene Knockout Techniques; D016680:Genome, Bacterial; D005966:Glucuronidase / Q000378:metabolism; D005810:Multigene Family; D016366:Open Reading Frames; D010641:Phenotype; D010802:Phylogeny; D048372:Streptomyces coelicolor / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D005966:Glucuronidase