Structural basis for ribosome protein S1 interaction with RNA in trans-translation of Mycobacterium tuberculosis

Yi Fan; Yazhuang Dai; Meijing Hou; Huilin Wang; Hongwei Yao; Chenyun Guo; Donghai Lin; Xinli Liao

doi:10.1016/j.bbrc.2017.04.048

Structural basis for ribosome protein S1 interaction with RNA in trans-translation of Mycobacterium tuberculosis

Biochem Biophys Res Commun. 2017 May 27;487(2):268-273. doi: 10.1016/j.bbrc.2017.04.048. Epub 2017 Apr 12.

Authors

Yi Fan¹, Yazhuang Dai², Meijing Hou¹, Huilin Wang¹, Hongwei Yao¹, Chenyun Guo¹, Donghai Lin³, Xinli Liao⁴

Affiliations

¹ Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
² School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China.
³ Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China. Electronic address: dhlin@xmu.edu.cn.
⁴ Key Laboratory of Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China. Electronic address: xlliao@xmu.edu.cn.

PMID: 28412369
DOI: 10.1016/j.bbrc.2017.04.048

Abstract

Ribosomal protein S1 (RpsA), the largest 30S protein in ribosome, plays a significant role in translation and trans-translation. In Mycobacterium tuberculosis, the C-terminus of RpsA is known as tuberculosis drug target of pyrazinoic acid, which inhibits the interaction between MtRpsA and tmRNA in trans-translation. However, the molecular mechanism underlying the interaction of MtRpsA with tmRNA remains unknown. We herein analyzed the interaction of the C-terminal domain of MtRpsA with three RNA fragments poly(A), sMLD and pre-sMLD. NMR titration analysis revealed that the RNA binding sites on MtRpsA^CTD are mainly located in the β2, β3 and β5 strands and the adjacent L3 loop of the S1 domain. Fluorescence experiments determined the MtRpsA^CTD binding to RNAs are in the micromolar affinity range. Sequence analysis also revealed conserved residues in the mapped RNA binding region. Residues L304, V305, G308, F310, H322, I323, R357 and I358 were verified to be the key residues influencing the interaction between MtRpsA^CTD and pre-sMLD. Molecular docking further confirmed that the poly(A)-like sequence and sMLD of tmRNA are all involved in the protein-RNA interaction, through charged interaction and hydrogen bonds. The results will be beneficial for designing new anti-tuberculosis drugs.

Keywords: Anti-tuberculosis; MtRpsA; NMR; Protein-RNA interaction; Trans-translation; tmRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Models, Chemical
Molecular Docking Simulation*
Mycobacterium tuberculosis / metabolism*
Protein Binding
Protein Biosynthesis / physiology
Protein Conformation
RNA, Bacterial / chemistry*
RNA, Bacterial / metabolism*
RNA, Bacterial / ultrastructure
Ribosomal Proteins / chemistry*
Ribosomal Proteins / metabolism*
Ribosomal Proteins / ultrastructure
Structure-Activity Relationship

Substances

RNA, Bacterial
Ribosomal Proteins
ribosomal protein S1
tmRNA