Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS), Japan Science and Technology
Ribosomal RNAs (rRNAs) contain various modifications that play critical roles in ribosome assembly and function. Here, we discovered two stereoselective methylations of the rRNA backbone in the peptidyl-transferase center (PTC) of the 50S subunit of Escherichia coli cultured under anaerobic conditions. Methylation occurs at carbon 5'(S) of ribose moieties of dihydrouridine at position 2449 (D 5S m2449) and 2'-O-metylcytidine at position 2498 (Cm 5S m2498). We identified the rlmX gene, encoding a cobalamin-dependent radical S-adenosylmethionine (SAM) methyltransferase responsible for these methylations. Intriguingly, D 5S m2449, Cm 5S m2498, and 5-hydroxycytidine (ho 5 C2501) in the PTC were elevated under anaerobic growth conditions. A double knockout strain lacking rlmX and rlhA (responsible for ho 5 C2501) impaired anaerobic growth. Biochemical studies showed that these rRNA modifications stimulate protein synthesis. The cryoelectron microscopy (cryo-EM) structure of the ribosome indicated that these hypoxia-induced modifications stabilize the P-site and the PTC. These findings demonstrate that ribosomes are activated by hypoxia-induced modifications to enhance translational capability and thereby survival, under anaerobic conditions.
Organizational Affiliation:
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; RIKEN Center for Biosystems Dynamics Research, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama 230-0045, Japan.
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Institute of Molecular and Cell Biology, University of Tartu, Riia street 23B, Tartu 51010, Estonia.
RIKEN Center for Biosystems Dynamics Research, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan; The Advanced Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.
RIKEN Center for Biosystems Dynamics Research, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama 230-0045, Japan.
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. Electronic address: ts@chembio.t.u-tokyo.ac.jp.
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