title: Genome-wide bioinformatics analysis of steroid metabolism-associated genes in Nocardioides simplex VKM Ac-2033D.
abstract: Actinobacteria comprise diverse groups of bacteria capable of full degradation, or modification of different steroid compounds. Steroid catabolism has been characterized best for the representatives of suborder Corynebacterineae, such as Mycobacteria, Rhodococcus and Gordonia, with high content of mycolic acids in the cell envelope, while it is poorly understood for other steroid-transforming actinobacteria, such as representatives of Nocardioides genus belonging to suborder Propionibacterineae. Nocardioides simplex VKM Ac-2033D is an important biotechnological strain which is known for its ability to introduce ∆(1)-double bond in various 1(2)-saturated 3-ketosteroids, and perform convertion of 3β-hydroxy-5-ene steroids to 3-oxo-4-ene steroids, hydrolysis of acetylated steroids, reduction of carbonyl groups at C-17 and C-20 of androstanes and pregnanes, respectively. The strain is also capable of utilizing cholesterol and phytosterol as carbon and energy sources. In this study, a comprehensive bioinformatics genome-wide screening was carried out to predict genes related to steroid metabolism in this organism, their clustering and possible regulation. The predicted operon structure and number of candidate gene copies paralogs have been estimated. Binding sites of steroid catabolism regulators KstR and KstR2 specified for N. simplex VKM Ac-2033D have been calculated de novo. Most of the candidate genes grouped within three main clusters, one of the predicted clusters having no analogs in other actinobacteria studied so far. The results offer a base for further functional studies, expand the understanding of steroid catabolism by actinobacteria, and will contribute to modifying of metabolic pathways in order to generate effective biocatalysts capable of producing valuable bioactive steroids.
authors.affiliation: Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Leninskie Gory, h. 1, b. 73, Moscow, 119991, Russian Federation. vtosha@yandex.ru.
authors.forename: Victoria Y
authors.identifier: http://orcid.org/0000-0002-3118-7977
authors.initials: VY
authors.lastname: Shtratnikova
authors.affiliation: Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, b. 1, Moscow, 127051, Russian Federation.|A.N. Belozersky Research Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskye Gory, h. 1, b. 41, Moscow, 119991, Russian Federation.
authors.forename: Mikhail I
authors.initials: MI
authors.lastname: Schelkunov
authors.affiliation: G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Puschino, Moscow, 142290, Russian Federation.
authors.forename: Victoria V
authors.initials: VV
authors.lastname: Fokina
authors.affiliation: Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Leninskie Gory, h. 1, b. 73, Moscow, 119991, Russian Federation.
authors.forename: Yury A
authors.initials: YA
authors.lastname: Pekov
authors.affiliation: G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Puschino, Moscow, 142290, Russian Federation.
authors.forename: Tanya
authors.initials: T
authors.lastname: Ivashina
authors.affiliation: G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Puschino, Moscow, 142290, Russian Federation.
authors.forename: Marina V
authors.initials: MV
authors.lastname: Donova
mesh_terms: D039903:Actinobacteria / Q000235:genetics* / Q000378:metabolism*; D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial; D015971:Gene Expression Regulation, Enzymologic; D063990:Gene Ontology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study / Q000379:methods; D023281:Genomics; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D056510:Position-Specific Scoring Matrices; D054730:Protein Interaction Domains and Motifs; D013256:Steroids / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D013256:Steroids
keywords: Genome-wide analysis; Nocardioides; Steroid catabolism; Transcriptional repressors KstR and KstR2
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