Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes

Md Sohanur Rahman; Mst Ara Gulshan; Shigeyoshi Matsumura; Yoshiya Ikawa

doi:10.1080/15257770.2019.1687909

Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes

Nucleosides Nucleotides Nucleic Acids. 2020;39(5):715-729. doi: 10.1080/15257770.2019.1687909. Epub 2020 Feb 10.

Authors

Md Sohanur Rahman^{1

2}, Mst Ara Gulshan^{1

2}, Shigeyoshi Matsumura^{1

2}, Yoshiya Ikawa^{1

2}

Affiliations

¹ Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.
² Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan.

PMID: 32039645
DOI: 10.1080/15257770.2019.1687909

Abstract

The modular structure of bacterial ribonuclease P (RNase P) ribozymes, which recognize tertiary structures of precursor tRNAs (pre-tRNAs) to cleave their 5' leader sequence, can be dissected physically into the two structured domain RNAs (S-domain and C-domain). Separately prepared S-domain RNA and C-domain RNA assemble to form bimolecular forms of RNase P ribozymes. We analyzed the effects of polyethylene glycols (PEGs) on pre-tRNA cleavage catalyzed by bimolecular RNase P ribozymes to examine the effects of molecular crowding on the reaction. PEG molecular crowders significantly enhanced the activities of bimolecular RNase P ribozymes, some of which were hardly active without PEGs.

Keywords: Modular structure; RNA domain; molecular crowding; ribonuclease P; ribozyme; tRNA.

MeSH terms

Bacillus subtilis / enzymology*
Biocatalysis
Escherichia coli / enzymology*
Molecular Structure
Polyethylene Glycols / chemistry
Polyethylene Glycols / metabolism*
RNA, Bacterial / biosynthesis
RNA, Bacterial / chemistry
Ribonuclease P / chemistry
Ribonuclease P / metabolism*

Substances

RNA, Bacterial
Polyethylene Glycols
Ribonuclease P