Shtratnikova Victoria Y, Schelkunov Mikhail I, Fokina Victoria V, Pekov Yury A, Ivashina Tanya, Donova Marina V
Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Leninskie Gory, h. 1, b. 73, Moscow, 119991, Russian Federation.
Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per. 19, b. 1, Moscow, 127051, Russian Federation.
Curr Genet. 2016 Aug;62(3):643-56. doi: 10.1007/s00294-016-0568-4. Epub 2016 Feb 1.
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.
放线菌包括能够完全降解或修饰不同甾体化合物的多种细菌。对于棒杆菌亚目（Corynebacterineae）的代表菌株，如细胞壁中含有高含量分枝菌酸的分枝杆菌（Mycobacteria）、红球菌（Rhodococcus）和戈登氏菌（Gordonia），甾体分解代谢的特征最为明确，而对于其他甾体转化放线菌，如丙酸杆菌亚目（Propionibacterineae）的诺卡氏菌属（Nocardioides）的代表菌株，其甾体分解代谢情况却知之甚少。简单诺卡氏菌（Nocardioides simplex）VKM Ac-2033D是一种重要的生物技术菌株，以其在各种1(2)-饱和3-酮甾体中引入∆(1)-双键的能力、将3β-羟基-5-烯甾体转化为3-氧代-4-烯甾体的能力、乙酰化甾体的水解能力、分别还原雄烷和孕烷C-17和C-20位羰基的能力而闻名。该菌株还能够利用胆固醇和植物甾醇作为碳源和能源。在本研究中，进行了全面的全基因组生物信息学筛选，以预测该生物体中与甾体代谢相关的基因、它们的聚类情况以及可能的调控方式。已估计了预测的操纵子结构和候选基因拷贝旁系同源物的数量。从头计算了简单诺卡氏菌VKM Ac-2033D特有的甾体分解代谢调节因子KstR和KstR2的结合位点。大多数候选基因聚集在三个主要簇中，其中一个预测簇在迄今为止研究的其他放线菌中没有类似物。这些结果为进一步的功能研究提供了基础，扩展了对放线菌甾体分解代谢的理解，并将有助于修饰代谢途径，以产生能够生产有价值生物活性甾体的有效生物催化剂。
