Research Article: Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD

Date Published: November 2, 2018

Publisher: Public Library of Science

Author(s): Yiyang Jiang, Hailong Yu, Fudong Li, Lin Cheng, Lingru Zhu, Yunyu Shi, Qingguo Gong, Gongyi Zhang.


Methyltransferase RlmCD was previously shown to be responsible for the introduction of C5 methylation at both U747 and U1939 of the 23S ribosomal RNA in Streptococcus pneumoniae. Intriguingly, its structural homologue, RumA, can only catalyze the methylation of U1939, while RlmC is the dedicated enzyme for m5U747 in Escherichia coli. In this study, we describe the structure of RlmCD in complex with its cofactor and the RNA substrate containing U747 at 2.00 Å or U1939 at 3.10 Å. We demonstrate that multiple structural features collaborate to establish the dual enzymatic activities of RlmCD. Of them, the side-chain rearrangement of F145 was observed to be an unusual mechanism through which RlmCD can discriminate between U747- and U1939-containing RNA substrate by switching the intermolecular aromatic stacking between protein and RNA on/off. An in-vitro methyltransferase assay and electrophoretic mobility shift assay were performed to validate these findings. Overall, our complex structures allow for a better understanding of the dual-functional mechanism of RlmCD, suggesting useful implications for the evolution of the RumA-type enzyme and the potential development of antibiotic drugs against S. pneumoniae.

Partial Text

RNA methylation is an abundant post-transcriptional modification occurring in almost all types of RNA molecules from three kingdoms of life. The introduction of methylation into RNAs is conducted by RNA methylation enzymes (methyltransferase, MTase) with diverse catalytic mechanisms [1, 2]. As the key component of protein synthesis machinery in all living organisms, ribosomal RNA (rRNA) is the one of the RNA molecules with most methylation and other types of modifications. For instance, 10 and 14 methylation have already been identified in the 16S and 23S rRNA of E. coli, respectively, with a variety of methylation types including 1-methylguanosine (m1G), 3-methyluridine (m3U), 5-methyluridine (m5U), 5-methylcytidine (m5C) and 2-methyladenosine (m2A) [3, 4]. Although the majority of these methylations is clustered at the functionally important sites of rRNA, such as the peptidyl transferase center (PTC), the nascent peptide exit tunnel (NPET), and the A, P, and E sites of tRNA binding sites, none of them has been shown to be critical for cell survival in prokaryotes [5]. However, recent findings suggest that rRNA modifications may serve as an important source in prompting ribosome heterogeneity related to the certain function of ribosome in response to environmental stress [6]. On the other hand, with the wide use of antibiotic drugs targeting the bacterial ribosome, modulation of rRNA methylation has emerged as a common mechanism of antibiotic resistance or susceptibility [7]. Aberrant methylation (either hypermethylation or loss-of-methylation) serves as an important way to antagonize the function of antibiotics under certain circumstances [8–10].




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