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Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A. Structure-based insights into recognition and regulation of SAM-sensing riboswitches. SCIENCE CHINA. LIFE SCIENCES 2023; 66:31-50. [PMID: 36459353 DOI: 10.1007/s11427-022-2188-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/17/2022] [Indexed: 12/03/2022]
Abstract
Riboswitches are highly conserved RNA elements that located in the 5'-UTR of mRNAs, which undergo real-time structure conformational change to achieve the regulation of downstream gene expression by sensing their cognate ligands. S-adenosylmethionine (SAM) is a ubiquitous methyl donor for transmethylation reactions in all living organisms. SAM riboswitch is one of the most abundant riboswitches that bind to SAM with high affinity and selectivity, serving as regulatory modules in multiple metabolic pathways. To date, seven SAM-specific riboswitch classes that belong to four families, one SAM/SAH riboswitch and one SAH riboswitch have been identified. Each SAM riboswitch family has a well-organized tertiary core scaffold to support their unique ligand-specific binding pocket. In this review, we summarize the current research progress on the distribution, structure, ligand recognition and gene regulation mechanism of these SAM-related riboswitch families, and further discuss their evolutionary prospects and potential applications.
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Affiliation(s)
- Luqian Zheng
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.,The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Qianqian Song
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xin Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chunyan Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hongcheng Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Aiming Ren
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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Dixit B, Prakash A, Kumar P, Gogoi P, Kumar M. The core Cas1 protein of CRISPR-Cas I-B in Leptospira shows metal-tunable nuclease activity. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100059. [PMID: 34841349 PMCID: PMC8610301 DOI: 10.1016/j.crmicr.2021.100059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/26/2022] Open
Abstract
Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 is the causative agent of leptospirosis in animals and humans. This organism carries a functional cas1 gene classified under CRISPR-Cas I-B. In this study, using various nuclease assays and bioinformatics analysis, we report that the recombinant Cas1 (LinCas1) possesses metal-ion dependent DNase activity, which is inhibited upon substitution or chelation of metal-ion and/or interaction with recombinant Cas2 (LinCas2) of L. interrogans. Model of LinCas1 structure shows a shorter N-terminal domain unlike other Cas1 orthologs reported to date. The C-terminal domain of LinCas1 contains conserved divalent-metal binding residues (Glu108, His176, and Glu191) and the mutation of these residues leads to abolition in DNase activity. Immunoassay using anti-LinCas2 demonstrates that LinCas1 interacts with LinCas2 and attains a saturation point. Moreover, the nuclease activity of the LinCas1-Cas2 mixture on ds-DNA displayed a reduction in activity compared to the pure core LinCas proteins under in vitro condition. The DNase activity for LinCas1 is consistent with a role for this protein in the recognition/cleavage of foreign DNA and integration of foreign DNA as spacer into the CRISPR array.
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Affiliation(s)
- Bhuvan Dixit
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Aman Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Pankaj Kumar
- Division of Livestock and Fisheries Management, ICAR Research Complex for Eastern Region, Patna, Bihar 800014, India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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Xue Y, Chen R, Qu L, Cao X. Noncoding RNA: from dark matter to bright star. SCIENCE CHINA-LIFE SCIENCES 2020; 63:463-468. [DOI: 10.1007/s11427-020-1676-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Indexed: 12/16/2022]
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