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.
Streptomyces Plasmid Transfer Palindromic Sequence M145 Strain Electronic Supplementary Material
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This work was supported by grants M/256-2014 from the State Agency on Science, Innovation and Informatization of Ukraine (to B.O.) and Bg-98f from the Ministry of Education and Science of Ukraine (V.F.). Part of the project was carried out within the frame of the NIH grant R03TW009424 (to S.W. and VF). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Publication was partially based on the research provided by the grant support of the State Fund For Fundamental Research (project № F60/2-2015). O.T. was supported by Visby and DAAD fellowships. We thank Emma Doud (Northwestern University, USA) for editing of our manuscript; Prof. Paul Dyson (Swansea University, UK) is thanked for cosmids from S.coelicolor transposon library.
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