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Shtratnikova VY, Sсhelkunov MI, Fokina VV, Bragin EY, Shutov AA, Donova MV. Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac-2033D to phytosterol and cortisone 21-acetate. BMC Biotechnol 2021; 21:7. [PMID: 33441120 PMCID: PMC7807495 DOI: 10.1186/s12896-021-00668-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq. RESULTS Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N. simplex. Unlike phytosterol, cortisone 21-acetate does not provide induction of the genes with predicted KstR and KstR2 sites. Superior 3-ketosteroid-Δ1-dehydrogenase activity of N. simplex VKM Ac-2033D is due to the kstDs redundancy in the genome, with the highest expression level of the gene KR76_27125 orthologous to kstD2, in response to cortisone 21-acetate. The substrate spectrum of N. simplex 3-ketosteroid-Δ1-dehydrogenase was expanded in this study with progesterone and its 17α-hydroxylated and 11α,17α-dihydroxylated derivatives, that effectively were 1(2)-dehydrogenated in vivo by the whole cells of the N. simplex VKM Ac-2033D. CONCLUSION The results contribute to the knowledge of biocatalytic features and diversity of steroid modification capabilities of actinobacteria, defining targets for further bioengineering manipulations with the purpose of expansion of their biotechnological applications.
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Affiliation(s)
- Victoria Yu Shtratnikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, h. 1, b. 40, Moscow, Russian Federation 119991
| | - Mikhail I. Sсhelkunov
- Skolkovo Institute of Science and Technology, Nobelya str., 3, Moscow, Russian Federation 121205
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per., h. 19, b. 1, Moscow, Russian Federation 127994
| | - Victoria V. Fokina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
| | - Eugeny Y. Bragin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
| | - Andrey A. Shutov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
| | - Marina V. Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, pr. Nauki, 5, Pushchino, Moscow Region, Russian Federation 142290
- Pharmins, Ltd., R&D, Institutskaya str, 4, Pushchino, Moscow Region, Russian Federation 142290
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Zheng XF, Liu XQ, Peng SY, Zhou Q, Xu B, Yuan H, Tang GL. Characterization of the Rifamycin-Degrading Monooxygenase From Rifamycin Producers Implicating Its Involvement in Saliniketal Biosynthesis. Front Microbiol 2020; 11:971. [PMID: 32582048 PMCID: PMC7283461 DOI: 10.3389/fmicb.2020.00971] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/22/2020] [Indexed: 01/18/2023] Open
Abstract
Rifamycin derivatives, such as rifampicin, have potent antibiotic activity and have long been used in the clinic as mainstay components for the treatment of tuberculosis, leprosy, and AIDS-associated mycobacterial infections. However, the extensive usage of these antibiotics has resulted in the rapid development of bacterial resistance. The resistance mechanisms mainly include mutations of the rifamycin target RNA polymerase of bacteria and enzymatic modifications of rifamycin antibiotics. One modification is the recently characterized rifamycin degradation catalyzed by Rox enzymes, which belong to the widely occurring flavin monooxygenases. Intriguingly, our recent sequence analysis revealed the rifamycin producers also encode Rox homologs that are not yet characterized. In this work, we expanded the study of the Rox-catalyzed rifamycin degradation. We first showed that the Rox proteins from rifamycin producers have the enzymatic rifamycin SV-degrading activity. Then we used the structurally diverse rifamycin compounds rifampicin and 16-demethylrifamycin W to probe the substrate scope and found that they each have a slightly different substrate scope. Finally, we demonstrated that Rox proteins can also catalyze the transformation of 16-demethylsalinisporamycin to 16-demethylsaliniketal A. Since 16-demethylsalinisporamycin and 16-demethylsaliniketal A are the counterpart analogs of salinisporamycin and saliniketal A, our biochemical findings not only uncover a previously uncharacterized self-resistance mechanism in the rifamycin producers, but also bridge the gap between the biosynthesis of the potential antitumor compound saliniketal A.
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Affiliation(s)
- Xiao-Fu Zheng
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Xin-Qiang Liu
- CAS-Key Laboratory of Synthetic Biology, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shu-Ya Peng
- Institute of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Qiang Zhou
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bin Xu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Hua Yuan
- College of Life Sciences, Shanghai Normal University, Shanghai, China.,State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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