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Hirata A, Okada K, Yoshii K, Shiraishi H, Saijo S, Yonezawa K, Shimizu N, Hori H. Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic Acids Res 2020; 47:10942-10955. [PMID: 31586407 PMCID: PMC6847430 DOI: 10.1093/nar/gkz856] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/20/2019] [Accepted: 10/02/2019] [Indexed: 12/18/2022] Open
Abstract
The complex between Trm7 and Trm734 (Trm7–Trm734) from Saccharomyces cerevisiae catalyzes 2′-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7–Trm734 complex. Purified recombinant Trm7–Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7–Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7–Trm734. Small angle X-ray scattering reveals that Trm7–Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7–Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.
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Affiliation(s)
- Akira Hirata
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Keisuke Okada
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Kazuaki Yoshii
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Shiraishi
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Shinya Saijo
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kento Yonezawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
- To whom correspondence should be addressed. Tel: +81 89 927 8548; Fax: +81 89 927 9941;
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Gallagher JEG. Proteins and RNA sequences required for the transition of the t-Utp complex into the SSU processome. FEMS Yeast Res 2019; 19:5184469. [PMID: 30445532 DOI: 10.1093/femsyr/foy120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Ribosomes are synthesized by large ribonucleoprotein complexes cleaving and properly assembling highly structured rRNAs with ribosomal proteins. Transcription and processing of pre-rRNAs are linked by the transcription-Utp sub-complex (t-Utps), a sub-complex of the small subunit (SSU) processome and prompted the investigations for the requirements of t-Utp formation and transition into the SSU processome. The rDNA promoter, the first 44 nucleotides of the 5΄ETS, and active transcription by pol I were sufficient to recruit the t-Utps to the rDNA. Pol5, accessory factor, dissociated as t-Utps matured into the UtpA complex which permitted later recruitment of the UtpB, U3 snoRNP and the Mpp10 complex into the SSU processome. The t-Utp complex associated with short RNAs 121 and 138 nucleotides long transcribed from the 5΄ETS. These transcripts were not present when pol II transcribed the rDNA or in nondividing cells. Depletion of a t-Utp, but not of other SSU processome components led to decreased levels of the short transcripts. However, ectopic expression of the short transcripts slowed the growth of yeast with impaired rDNA transcription. These results provide insight into how transcription of the rRNA primes the assemble of t-Utp complex with the pre-rRNA into the UtpA complex and the later association of SSU processome components.
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Zhao X, Patton JR, Ghosh SK, Fischel-Ghodsian N, Shen L, Spanjaard RA. Pus3p- and Pus1p-Dependent Pseudouridylation of Steroid Receptor RNA Activator Controls a Functional Switch that Regulates Nuclear Receptor Signaling. Mol Endocrinol 2007; 21:686-99. [PMID: 17170069 DOI: 10.1210/me.2006-0414] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Abstract
It was previously shown that mouse Pus1p (mPus1p), a pseudouridine synthase (PUS) known to modify certain transfer RNAs (tRNAs), can also bind with nuclear receptors (NRs) and function as a coactivator through pseudouridylation and likely activation of an RNA coactivator called steroid receptor RNA activator (SRA). Use of cell extract devoid of human Pus1p activity derived from patients with mitochondrial myopathy and sideroblastic anemia, however, still showed SRA-modifying activity suggesting that other PUS(s) can also target this coactivator. Here, we show that related mPus3p, which has a different tRNA specificity than mPus1p, also serves as a NR coactivator. However, in contrast to mPus1p, it does not stimulate sex steroid receptor activity, which is likely due to lack of binding to this class of NRs. As expected from their tRNA activities, in vitro pseudouridylation assays show that mPus3p and mPus1p modify different positions in SRA, although some may be commonly targeted. Interestingly, the order in which these enzymes modify SRA determines the total number of pseudouridines. mPus3p and SRA are mainly cytoplasmic; however, mPus3p and SRA are also localized in distinct nuclear subcompartments. Finally, we identified an in vivo modified position in SRA, U206, which is likely a common target for both mPus1p and mPus3p. When U206 is mutated to A, SRA becomes hyperpseudouridylated in vitro, and it acquires dominant-negative activity in vivo. Thus, Pus1p- and Pus3p-dependent pseudouridylation of SRA is a highly complex posttranscriptional mechanism that controls a coactivator-corepressor switch in SRA with major consequences for NR signaling.
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Affiliation(s)
- Xiansi Zhao
- Department of Otolaryngology and Biochemistry, Cancer Research Center, Boston University School of Medicine, 715 Albany Street R903, Boston, Massachusetts 02118, USA
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Current awareness on yeast. Yeast 2006. [DOI: 10.1002/yea.1316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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