Akira Hirata and Bunzo Mikami : Structural insight into sugar-binding modes of microbial ß-amylase, Biochemical and Biophysical Research Communications, Vol.733, No.12, 150695, 2024.
Shu Fujita, Yuzuru Sugio, Takuya Kawamura, Ryota Yagamai, Natsuhisa Oka, Akira Hirata, Takashi Yokogawa and Hiroyuki Hori : ArcS from Thermococcus kodakarensis transfers L-lysine to preQ0 nucleoside derivatives as minimum substrate RNAs., The Journal of Biological Chemistry, Vol.300, No.8, 107505, 2024.
(要約)
Archaeosine (G) is an archaea-specific tRNA modification synthesized via multiple steps. In the first step, archaeosine tRNA guanine transglucosylase (ArcTGT) exchanges the G15 base in tRNA with 7-cyano-7-deazaguanine (preQ). In Euryarchaea, preQ15 in tRNA is further modified by archaeosine synthase (ArcS). Thermococcus kodakarensis ArcS catalyzes a lysine-transfer reaction to produce preQ-lysine (preQ-Lys) as an intermediate. The resulting preQ-Lys15 in tRNA is converted to G15 by a radical S-adenosyl-L-methionine enzyme for archaeosine formation (RaSEA), which forms a complex with ArcS. Here, we focus on the substrate tRNA recognition mechanism of ArcS. Kinetic parameters of ArcS for lysine and tRNA-preQ were determined using a purified enzyme. RNA fragments containing preQ were prepared from Saccharomyces cerevisiae tRNA-preQ15. ArcS transferred C-labeled lysine to RNA fragments. Furthermore, ArcS transferred lysine to preQ nucleoside and preQ nucleoside 5'-monophosphate. Thus, the L-shaped structure and the sequence of tRNA are not essential for the lysine-transfer reaction by ArcS. However, the presence of D-arm structure accelerates the lysine-transfer reaction. Because ArcTGT from thermophilic archaea recognizes the common D-arm structure, we expected the combination of T. kodakarensis ArcTGT and ArcS and RaSEA complex would result in the formation of preQ-Lys15 in all tRNAs. This hypothesis was confirmed using 46 T. kodakarensis tRNA transcripts and three Haloferax volcanii tRNA transcripts. In addition, ArcTGT did not exchange the preQ-Lys15 in tRNA with guanine or preQ base, showing that formation of tRNA-preQ-Lys by ArcS plays a role in preventing the reverse reaction in G biosynthesis.
Yoh Kohno, Asako Ito, Aya Okamoto, Ryota Yamagami, Akira Hirata and Hiroyuki Hori : Escherichia coli tRNA (Gm18) methyltransferase (TrmH) requires the correct localization of its methylation site (G18) in the D-loop for efficient methylation., The Journal of Biochemistry, Vol.175, No.1, 43-56, 2024.
(要約)
TrmH is a eubacterial tRNA methyltransferase responsible for formation of 2'-O-methylguaosine at position 18 (Gm18) in tRNA. In Escherichia coli cells, only 14 tRNA species possess the Gm18 modification. To investigate the substrate tRNA selection mechanism of E. coli TrmH, we performed biochemical and structural studies. Escherichia coli TrmH requires a high concentration of substrate tRNA for efficient methylation. Experiments using native tRNA SerCGA purified from a trmH gene disruptant strain showed that modified nucleosides do not affect the methylation. A gel mobility-shift assay reveals that TrmH captures tRNAs without distinguishing between relatively good and very poor substrates. Methylation assays using wild-type and mutant tRNA transcripts revealed that the location of G18 in the D-loop is very important for efficient methylation by E. coli TrmH. In the case of tRNASer, tRNATyrand tRNALeu, the D-loop structure formed by interaction with the long variable region is important. For tRNAGln, the short distance between G18 and A14 is important. Thus, our biochemical study explains all Gm18 modification patterns in E. coli tRNAs. The crystal structure of E. coli TrmH has also been solved, and the tRNA binding mode of E. coli TrmH is discussed based on the structure.
Yu Nishida, Shiho Ohmori, Risa Kakizono, Kunpei Kawai, Miyu Namba, Kazuki Okada, Ryota Yamagami, Akira Hirata and Hiroyuki Hori : Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine- N2-) Methyltransferase (Trm11-Trm112 Complex), International Journal of Molecular Sciences, Vol.23, No.7, 2022.
(要約)
class I tRNAs and elucidates the Trm11-Trm112 binding sites.
Yancheng Liu, Yuko Takagi, Milyadi Sugijanto, Kieu My Duong Nguyen, Akira Hirata, Hiroyuki Hori and C. Kiong Ho : Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing, Frontiers in Molecular Biosciences, Vol.9, No.8, 811548, 2022.
(要約)
RNA ligases play important roles in repairing and circularizing RNAs post-transcriptionally. In this study, we generated an allelic knockout of ATP-dependent RNA ligase (Rnl) in the hyperthermophilic archaeon to identify its biological targets. A comparative analysis of circular RNA reveals that the Rnl-knockout strain represses circularization of C/D box sRNAs without affecting the circularization of tRNA and rRNA processing intermediates. Recombinant archaeal Rnl could circularize C/D box sRNAs with a mutation in the conserved C/D box sequence element but not when the terminal stem structures were disrupted, suggesting that proximity of the two ends could be critical for intramolecular ligation. Furthermore, accumulates aberrant RNA fragments derived from ribosomal RNA in the absence of Rnl. These results suggest that Rnl is responsible for C/D box sRNA circularization and may also play a role in ribosomal RNA processing.
T Yokogawa, Y Nomura, A Yasuda, H Ogino, K Hiura, S Nakada, N Oka, K Ando, T Kawamura, Akira Hirata, H Hori and S Ohno : Identification of a radical SAM enzyme involved in the synthesis of archaeosine, Nature Chemical Biology, Vol.15, No.12, 1148-1155, 2019.
(要約)
Archaeosine (G), 7-formamidino-7-deazaguanosine, is an archaea-specific modified nucleoside found at the 15th position of tRNAs. In Euryarchaeota, 7-cyano-7-deazaguanine (preQ)-containing tRNA (qN-tRNA), synthesized by archaeal tRNA-guanine transglycosylase (ArcTGT), has been believed to be converted to G-containing tRNA (G-tRNA) by the paralog of ArcTGT, ArcS. However, we found that several euryarchaeal ArcSs have lysine transfer activity to qN-tRNA to form qkN-tRNA, which has a preQ lysine adduct as a base. Through comparative genomics and biochemical experiments, we found that ArcS forms a robust complex with a radical S-adenosylmethionine (SAM) enzyme named RaSEA. The ArcS-RaSEA complex anaerobically converted qN-tRNA to G-tRNA in the presence of SAM and lysine via qkN-tRNA. We propose that ArcS and RaSEA should be considered an archaeosine synthase α-subunit (lysine transferase) and β-subunit (qkN-tRNA lyase), respectively.
Akira Hirata, Keisuke Okada, Kazuaki Yoshii, Hiroyuki Shiraishi, Shinya Saijo, Kento Yonezawa, Nobutaka Shimizu and Hiroyuki Hori : Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition., Nucleic Acids Research, Vol.47, No.20, 10942-10955, 2019.
(要約)
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.
Akira Hirata, Takeo Suzuki, Tomoko Nagano, Daijiro Fujii, Mizuki Okamoto, Manaka Sora, Todd M. Lowe, Tamotsu Kanai, Haruyuki Atomi, Tsutomu Suzuki and H Hori : Distinct Modified Nucleosides in tRNATrp from the Hyperthermophilic Archaeon Thermococcus kodakarensis and Requirement of tRNA m2G10/m22G10 Methyltransferase (Archaeal Trm11) for Survival at High Temperatures, Journal of Bacteriology, Vol.201, No.21, 2019.
(要約)
tRNA mG10/mG10 methyltransferase (archaeal Trm11) methylates the 2-amino group in guanosine at position 10 in tRNA and forms ,-dimethylguanosine (mG10) via -methylguanosine (mG10). We determined the complete sequence of tRNA, one of the substrate tRNAs for archaeal Trm11 from , a hyperthermophilic archaeon. Liquid chromatography/mass spectrometry following enzymatic digestion of tRNA identified 15 types of modified nucleoside at 21 positions. Several modifications were found at novel positions in tRNA, including 2'--methylcytidine at position 6, 2-thiocytidine at position 17, 2'--methyluridine at position 20, 5,2'--dimethylcytidine at position 32, and 2'--methylguanosine at position 42. Furthermore, methylwyosine was found at position 37 in this tRNA, although 1-methylguanosine is generally found at this location in tRNA from other archaea. We constructed (Δ) and some gene disruptant strains and compared their tRNA with that of the wild-type strain, which confirmed the absence of mG10 and other corresponding modifications, respectively. The lack of 2-methylguanosine (mG) at position 67 in the double disruptant strain suggested that this methylation is mediated by Trm14, which was previously identified as an mG6 methyltransferase. The Δ strain grew poorly at 95°C, indicating that archaeal Trm11 is required for survival at high temperatures. The mG10 modification might have effects on stabilization of tRNA and/or correct folding of tRNA at the high temperatures. Collectively, these results provide new clues to the function of modifications and the substrate specificities of modification enzymes in archaeal tRNA, enabling us to propose a strategy for tRNA stabilization of this archaeon at high temperatures. is a hyperthermophilic archaeon that can grow at 60 to 100°C. The sequence of tRNA from this archaeon was determined by liquid chromatography/mass spectrometry. Fifteen types of modified nucleoside were observed at 21 positions, including 5 modifications at novel positions; in addition, methylwyosine at position 37 was newly observed in an archaeal tRNA The construction of (Δ) and other gene disruptant strains confirmed the enzymes responsible for modifications in this tRNA. The lack of 2-methylguanosine (mG) at position 67 in the double disruptant strain suggested that this position is methylated by Trm14, which was previously identified as an mG6 methyltransferase. The Δ strain grew poorly at 95°C, indicating that archaeal Trm11 is required for survival at high temperatures.
Ayano Kaneta, Kosuke Fujishima, Wataru Morikazu, Hiroyuki Hori and Akira Hirata : The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity., Nucleic Acids Research, Vol.46, No.4, 1958-1972, 2018.
(要約)
Four different types (α4, α'2, (αβ)2 and ϵ2) of RNA-splicing endonucleases (EndAs) for RNA processing are known to exist in the Archaea. Only the (αβ)2 and ϵ2 types can cleave non-canonical introns in precursor (pre)-tRNA. Both enzyme types possess an insert associated with a specific loop, allowing broad substrate specificity in the catalytic α units. Here, the hyperthermophilic euryarchaeon Methanopyrus kandleri (MKA) was predicted to harbor an (αβ)2-type EndA lacking the specific loop. To characterize MKA EndA enzymatic activity, we constructed a fusion protein derived from MKA α and β subunits (fMKA EndA). In vitro assessment demonstrated complete removal of the canonical bulge-helix-bulge (BHB) intron structure from MKA pre-tRNAAsn. However, removal of the relaxed BHB structure in MKA pre-tRNAGlu was inefficient compared to crenarchaeal (αβ)2 EndA, and the ability to process the relaxed intron within mini-helix RNA was not detected. fMKA EndA X-ray structure revealed a shape similar to that of other EndA types, with no specific loop. Mapping of EndA types and their specific loops and the tRNA gene diversity among various Archaea suggest that MKA EndA is evolutionarily related to other (αβ)2-type EndAs found in the Thaumarchaeota, Crenarchaeota and Aigarchaeota but uniquely represents constrained substrate specificity.
Hirotaka Sugino, Takanori Usui, Tomohiro Shimada, Masahiro Nakano, Hiroshi Ogasawara, Akira Ishihama and Akira Hirata : A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation., FEBS Letters, Vol.591, No.13, 2019-2031, 2017.
(要約)
RcdA is a regulator of curlin subunit gene D, the master regulator of biofilm formation in Escherichia coli. Here, we determined the X-ray structure of RcdA at 2.55 Å resolution. RcdA consists of an N-terminal DNA-binding domain (DBD) containing a helix-turn-helix (HTH) motif and a C-terminal dimerization domain, and forms a homodimer in crystals. A computational docking model of the RcdA-DNA complex allowed prediction of the candidate residues responsible for DNA binding. Our structure-guided mutagenesis, in combination with gel shift assay, atomic force microscopic observation, and reporter assay, indicate that R32 in α2 of the HTH motif plays an essential role in the recognition and binding of target DNA while T46 in α3 influences the mode of oligomerization. These results provide insights into the DNA-binding mode of RcdA.
H Putra, H Yasuhara, N Kinoshita and Akira Hirata : Optimization of Enzyme-Mediated Calcite Precipitation as a Soil-Improvement Technique: The Effect of Aragonite and Gypsum on the Mechanical Properties of Treated Sand, Crystals, Vol.7, No.2, 59, 2017.
H Putra, H Yasuhara, N Kinoshita and Akira Hirata : Application of magnesium to improve uniform distribution of precipitated minerals in 1-m column specimens, Geomechanics and Engineering, Vol.12, No.5, 803-813, 2017.
Akira Hirata, Seiji Nishiyama, Toshihiro Tamura, Ayano Yamauchi and Hiroyuki Hori : Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules., Nucleic Acids Research, Vol.44, No.13, 6377-6390, 2016.
(要約)
N(2)-methylguanosine is one of the most universal modified nucleosides required for proper function in transfer RNA (tRNA) molecules. In archaeal tRNA species, a specific S-adenosyl-L-methionine (SAM)-dependent tRNA methyltransferase (MTase), aTrm11, catalyzes formation of N(2)-methylguanosine and N(2),N(2)-dimethylguanosine at position 10. Here, we report the first X-ray crystal structures of aTrm11 from Thermococcus kodakarensis (Tko), of the apo-form, and of its complex with SAM. The structures show that TkoTrm11 consists of three domains: an N-terminal ferredoxinlike domain (NFLD), THUMP domain and Rossmann-fold MTase (RFM) domain. A linker region connects the THUMP-NFLD and RFM domains. One SAM molecule is bound in the pocket of the RFM domain, suggesting that TkoTrm11 uses a catalytic mechanism similar to that of other tRNA MTases containing an RFM domain. Furthermore, the conformation of NFLD and THUMP domains in TkoTrm11 resembles that of other tRNA-modifying enzymes specifically recognizing the tRNA acceptor stem. Our docking model of TkoTrm11-SAM in complex with tRNA, combined with biochemical analyses and pre-existing evidence, provides insights into the substrate tRNA recognition mechanism: The THUMP domain recognizes a 3'-ACCA end, and the linker region and RFM domain recognize the T-stem, acceptor stem and V-loop of tRNA, thereby causing TkoTrm11 to specifically identify its methylation site.
Ryota Yamagami, Chie Tomikawa, Naoki Shigi, Ai Kazayama, Shin-Ichi Asai, Hiroyuki Takuma, Akira Hirata, Dominique Fourmy, Haruichi Asahara, Kimitsuna Watanabe, Satoko Yoshizawa and Hiroyuki Hori : Folate-/FAD-dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures., Genes to Cells, Vol.21, No.7, 740-754, 2016.
(要約)
TrmFO is a N(5) , N(10) -methylenetetrahydrofolate (CH2 THF)-/FAD-dependent tRNA methyltransferase, which synthesizes 5-methyluridine at position 54 (m(5) U54) in tRNA. Thermus thermophilus is an extreme-thermophilic eubacterium, which grows in a wide range of temperatures (50-83 °C). In T. thermophilus, modified nucleosides in tRNA and modification enzymes form a network, in which one modification regulates the degrees of other modifications and controls the flexibility of tRNA. To clarify the role of m(5) U54 and TrmFO in the network, we constructed the trmFO gene disruptant (∆trmFO) strain of T. thermophilus. Although this strain did not show any growth retardation at 70 °C, it showed a slow-growth phenotype at 50 °C. Nucleoside analysis showed increase in 2'-O-methylguanosine at position 18 and decrease in N(1) -methyladenosine at position 58 in the tRNA mixture from the ∆trmFO strain at 50 °C. These in vivo results were reproduced by in vitro experiments with purified enzymes. Thus, we concluded that the m(5) U54 modification have effects on the other modifications in tRNA through the network at 50 °C. (35) S incorporations into proteins showed that the protein synthesis activity of ∆trmFO strain was inferior to the wild-type strain at 50 °C, suggesting that the growth delay at 50 °C was caused by the inferior protein synthesis activity.
Takuya Kawamura, Akira Hirata, Satoshi Ohno, Yuichiro Nomura, Tomoko Nagano, Nobukazu Nameki, Takashi Yokogawa and Hiroyuki Hori : Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon., Nucleic Acids Research, Vol.44, No.4, 1894-1908, 2015.
(要約)
Archaeosine (G(+)), which is found only at position 15 in many archaeal tRNA, is formed by two steps, the replacement of the guanine base with preQ0 by archaeosine tRNA-guanine transglycosylase (ArcTGT) and the subsequent modification of preQ0 to G(+) by archaeosine synthase. However, tRNA(Leu) from Thermoplasma acidophilum, a thermo-acidophilic archaeon, exceptionally has two G(+)13 and G(+)15 modifications. In this study, we focused on the biosynthesis mechanism of G(+)13 and G(+)15 modifications in this tRNA(Leu). Purified ArcTGT from Pyrococcus horikoshii, for which the tRNA recognition mechanism and structure were previously characterized, exchanged only the G15 base in a tRNA(Leu) transcript with (14)C-guanine. In contrast, T. acidophilum cell extract exchanged both G13 and G15 bases. Because T. acidophilum ArcTGT could not be expressed as a soluble protein in Escherichia coli, we employed an expression system using another thermophilic archaeon, Thermococcus kodakarensis. The arcTGT gene in T. kodakarensis was disrupted, complemented with the T. acidophilum arcTGT gene, and tRNA(Leu) variants were expressed. Mass spectrometry analysis of purified tRNA(Leu) variants revealed the modifications of G(+)13 and G(+)15 in the wild-type tRNA(Leu). Thus, T. acidophilum ArcTGT has a multisite specificity and is responsible for the formation of both G(+)13 and G(+)15 modifications.
Hiroaki Kusuba, Takeshi Yoshida, Eri Iwasaki, Takako Awai, Ai Kazayama, Akira Hirata, Chie Tomikawa, Ryota Yamagami and Hiroyuki Hori : In vitro dihydrouridine formation by tRNA dihydrouridine synthase from Thermus thermophilus, an extreme-thermophilic eubacterium, The Journal of Biochemistry, Vol.158, No.6, 513-521, 2015.
(要約)
Dihydrouridine (D) is formed by tRNA dihydrouridine synthases (Dus). In mesophiles, multiple Dus enzymes bring about D modifications at several positions in tRNA. The extreme-thermophilic eubacterium Thermus thermophilus, in contrast, has only one dus gene in its genome and only two D modifications (D20 and D20a) in tRNA have been identified. Until now, an in vitro assay system for eubacterial Dus has not been reported. In this study, therefore, we constructed an in vitro assay system using purified Dus. Recombinant T. thermophilus Dus lacking bound tRNA was successfully purified. The in vitro assay revealed that no other factors in living cells were required for D formation. A dus gene disruptant (Δdus) strain of T. thermophilus verified that the two D20 and D20a modifications in tRNA were derived from one Dus protein. The Δdus strain did not show growth retardation at any temperature. The assay system showed that Dus modified tRNA(Phe) transcript at 60°C, demonstrating that other modifications in tRNA are not essential for Dus activity. However, a comparison of the formation of D in native tRNA(Phe) purified from the Δdus strain and tRNA(Phe) transcript revealed that other tRNA modifications are required for D formation at high temperatures.
Hiroyuki Takuma, Natsumi Ushio, Masayuki Minoji, Ai Kazayama, Naoki Shigi, Akira Hirata, Chie Tomikawa, Anna Ochi and Hiroyuki Hori : Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI)., The Journal of Biological Chemistry, Vol.290, No.9, 5912-5925, 2015.
(要約)
TrmI generates N(1)-methyladenosine at position 58 (m(1)A58) in tRNA. The Thermus thermophilus tRNA(Phe) transcript was methylated efficiently by T. thermophilus TrmI, whereas the yeast tRNA(Phe) transcript was poorly methylated. Fourteen chimeric tRNA transcripts derived from these two tRNAs revealed that TrmI recognized the combination of aminoacyl stem, variable region, and T-loop. This was confirmed by 10 deletion tRNA variants: TrmI methylated transcripts containing the aminoacyl stem, variable region, and T-arm. The requirement for the T-stem itself was confirmed by disrupting the T-stem. Disrupting the interaction between T- and D-arms accelerated the methylation, suggesting that this disruption is included in part of the reaction. Experiments with 17 point mutant transcripts elucidated the positive sequence determinants C56, purine 57, A58, and U60. Replacing A58 with inosine and 2-aminopurine completely abrogated methylation, demonstrating that the 6-amino group in A58 is recognized by TrmI. T. thermophilus tRNAGGU(Thr)GGU(Thr) contains C60 instead of U60. The tRNAGGU(Thr) transcript was poorly methylated by TrmI, and replacing C60 with U increased the methylation, consistent with the point mutation experiments. A gel shift assay revealed that tRNAGGU(Thr) had a low affinity for TrmI than tRNA(Phe). Furthermore, analysis of tRNAGGU(Thr) purified from the trmI gene disruptant strain revealed that the other modifications in tRNA accelerated the formation of m(1)A58 by TrmI. Moreover, nucleoside analysis of tRNAGGU(Thr) from the wild-type strain indicated that less than 50% of tRNAGG(Thr) contained m(1)A58. Thus, the results from the in vitro experiments were confirmed by the in vivo methylation patterns.
Sung-Hoon Jun, Akira Hirata, Tamotsu Kanai, Thomas J. Santangelo, Tadayuki Imanaka and Katsuhiko S. Murakami : The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration., Nature Communications, Vol.5, 5132, 2014.
(要約)
The archaeal transcription apparatus is closely related to the eukaryotic RNA polymerase II (Pol II) system. Archaeal RNA polymerase (RNAP) and Pol II evolved from a common ancestral structure and the euryarchaeal RNAP is the simplest member of the extant archaeal-eukaryotic RNAP family. Here we report the first crystal structure of euryarchaeal RNAP from Thermococcus kodakarensis (Tko). This structure reveals that the clamp domain is able to swing away from the main body of RNAP in the presence of the Rpo4/Rpo7 stalk by coordinated movements of these domains. More detailed structure-function analysis of yeast Pol II and Tko RNAP identifies structural additions to Pol II that correspond to the binding sites of Pol II-specific general transcription factors including TFIIF, TFIIH and Mediator. Such comparisons provide a framework for dissecting interactions between RNAP and these factors during formation of the pre-initiation complex.
Anna Ochi, Koki Makabe, Ryota Yamagami, Akira Hirata, Reiko Sakaguchi, Ya-Ming Hou, Kazunori Watanabe, Osamu Nureki, Kunihiro Kuwajima and Hiroyuki Hori : The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process., The Journal of Biological Chemistry, Vol.288, No.35, 25562-25574, 2013.
(要約)
A conserved guanosine at position 18 (G18) in the D-loop of tRNAs is often modified to 2'-O-methylguanosine (Gm). Formation of Gm18 in eubacterial tRNA is catalyzed by tRNA (Gm18) methyltransferase (TrmH). TrmH enzymes can be divided into two types based on their substrate tRNA specificity. Type I TrmH, including Thermus thermophilus TrmH, can modify all tRNA species, whereas type II TrmH, for example Escherichia coli TrmH, modifies only a subset of tRNA species. Our previous crystal study showed that T. thermophilus TrmH is a class IV S-adenosyl-l-methionine-dependent methyltransferase, which maintains a topological knot structure in the catalytic domain. Because TrmH enzymes have short stretches at the N and C termini instead of a clear RNA binding domain, these stretches are believed to be involved in tRNA recognition. In this study, we demonstrate by site-directed mutagenesis that both N- and C-terminal regions function in tRNA binding. However, in vitro and in vivo chimera protein studies, in which four chimeric proteins of type I and II TrmHs were used, demonstrated that the catalytic domain discriminates substrate tRNAs from nonsubstrate tRNAs. Thus, the N- and C-terminal regions do not function in the substrate tRNA discrimination process. Pre-steady state analysis of complex formation between mutant TrmH proteins and tRNA by stopped-flow fluorescence measurement revealed that the C-terminal region works in the initial binding process, in which nonsubstrate tRNA is not excluded, and that structural movement of the motif 2 region of the catalytic domain in an induced-fit process is involved in substrate tRNA discrimination.
Ryota Yamagami, Koki Yamashita, Hiroshi Nishimasu, Chie Tomikawa, Anna Ochi, Chikako Iwashita, Akira Hirata, Ryuichiro Ishitani, Osamu Nureki and Hiroyuki Hori : The tRNA recognition mechanism of folate/FAD-dependent tRNA methyltransferase (TrmFO)., The Journal of Biological Chemistry, Vol.287, No.51, 42480-42494, 2012.
(要約)
The conserved U54 in tRNA is often modified to 5-methyluridine (m(5)U) and forms a reverse Hoogsteen base pair with A58 that stabilizes the L-shaped tRNA structure. In Gram-positive and some Gram-negative eubacteria, m(5)U54 is produced by folate/FAD-dependent tRNA (m(5)U54) methyltransferase (TrmFO). TrmFO utilizes N(5),N(10)-methylenetetrahydrofolate (CH(2)THF) as a methyl donor. We previously reported an in vitro TrmFO assay system, in which unstable [(14)C]CH(2)THF was supplied from [(14)C]serine and tetrahydrofolate by serine hydroxymethyltransferase. In the current study, we have improved the TrmFO assay system by optimization of enzyme and substrate concentrations and introduction of a filter assay system. Using this assay, we have focused on the tRNA recognition mechanism of TrmFO. 42 tRNA mutant variants were prepared, and experiments with truncated tRNA and microhelix RNAs revealed that the minimum requirement of TrmFO exists in the T-arm structure. The positive determinants for TrmFO were found to be the U54U55C56 sequence and G53-C61 base pair. The gel mobility shift assay and fluorescence quenching showed that the affinity of TrmFO for tRNA in the initial binding process is weak. The inhibition experiments showed that the methylated tRNA is released before the structural change process. Furthermore, we found that A38 prevents incorrect methylation of U32 in the anticodon loop. Moreover, the m(1)A58 modification clearly accelerates the TrmFO reaction, suggesting a synergistic effect of the m(5)U54, m(1)A58, and s(2)U54 modifications on m(5)s(2)U54 formation in Thermus thermophilus cells. The docking model of TrmFO and the T-arm showed that the G53-C61 base pair is not able to directly contact the enzyme.
Akira Hirata, Kosuke Fujishima, Ryota Yamagami, Takuya Kawamura, Jillian F. Banfield, Akio Kanai and Hiroyuki Hori : X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity., Nucleic Acids Research, Vol.40, No.20, 10554-10566, 2012.
(要約)
Cleavage of introns from precursor transfer RNAs (tRNAs) by tRNA splicing endonuclease (EndA) is essential for tRNA maturation in Archaea and Eukarya. In the past, archaeal EndAs were classified into three types (α'2, α4 and α2β2) according to subunit composition. Recently, we have identified a fourth type of archaeal EndA from an uncultivated archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2, which is deeply branched within Euryarchaea. The ARMAN-2 EndA forms an ϵ2 homodimer and has broad substrate specificity like the α2β2 type EndAs found in Crenarchaea and Nanoarchaea. However, the precise architecture of ARMAN-2 EndA was unknown. Here, we report the crystal structure of the ϵ2 homodimer of ARMAN-2 EndA. The structure reveals that the ϵ protomer is separated into three novel units (αN, α and βC) fused by two distinct linkers, although the overall structure of ARMAN-2 EndA is similar to those of the other three types of archaeal EndAs. Structural comparison and mutational analyses reveal that an ARMAN-2 type-specific loop (ASL) is involved in the broad substrate specificity and that K161 in the ASL functions as the RNA recognition site. These findings suggest that the broad substrate specificities of ϵ2 and α2β2 EndAs were separately acquired through different evolutionary processes.
Lessner H. Faith, Jennings E. Matthew, Akira Hirata, Duin C. Eduardus and Lessner J. Daniel : Subunit D of RNA Polymerase from Methanosarcina acetivorans Contains Two Oxygen-labile [4Fe-4S] Clusters IMPLICATIONS FOR OXIDANT-DEPENDENT REGULATION OF TRANSCRIPTION, The Journal of Biological Chemistry, Vol.287, No.22, 18510-18523, 2012.
(要約)
Subunit D of multisubunit RNA polymerase from many species of archaea is predicted to bind one to two iron-sulfur (Fe-S) clusters, the function of which is unknown. A survey of encoded subunit D in the genomes of sequenced archaea revealed six distinct groups based on the number of complete or partial [4Fe-4S] cluster motifs within domain 3. Only subunit D from strictly anaerobic archaea, including all members of the Methanosarcinales, are predicted to bind two [4Fe-4S] clusters. We report herein the purification and characterization of Methanosarcina acetivorans subunit D in complex with subunit L. Expression of subunit D and subunit L in Escherichia coli resulted in the purification of a D-L heterodimer with only partial [4Fe-4S] cluster content. Reconstitution in vitro with iron and sulfide revealed that the M. acetivorans D-L heterodimer is capable of binding two redox-active [4Fe-4S] clusters. M. acetivorans subunit D deleted of domain 3 (DΔD3) was still capable of co-purifying with subunit L but was devoid of [4Fe-4S] clusters. Affinity purification of subunit D or subunit DΔD3 from M. acetivorans resulted in the co-purification of endogenous subunit L with each tagged subunit D. Overall, these results suggest that domain 3 of subunit D is required for [4Fe-4S] cluster binding, but the [4Fe-4S] clusters and domain 3 are not required for the formation of the D-L heterodimer. However, exposure of two [4Fe-4S] cluster-containing D-L heterodimer to oxygen resulted in loss of the [4Fe-4S] clusters and subsequent protein aggregation, indicating that the [4Fe-4S] clusters influence the stability of the D-L heterodimer and therefore have the potential to regulate the assembly and/or activity of RNA polymerase in an oxidant-dependent manner.
Akira Hirata, Tsubasa Kitajima and Hiroyuki Hori : Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop., Nucleic Acids Research, Vol.39, No.21, 9376-9389, 2011.
(要約)
In Crenarchaea, several tRNA genes are predicted to express precursor-tRNAs (pre-tRNAs) with canonical or non-canonical introns at various positions. We initially focused on the tRNA(Thr) species of hyperthermophilic crenarchaeon, Aeropyrum pernix (APE) and found that in the living APE cells three tRNA(Thr) species were transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them were cleaved from standard and non-standard positions. Biochemical studies revealed that the APE splicing endonuclease (APE-EndA) removed both types of introns, including the non-canonical introns, without any nucleotide modification. To clarify the underlying reasons for broad substrate specificity of APE-EndA, we determined the crystal structure of wild-type APE-EndA and subsequently compared its structure with that of Archaeaoglobus fulgidus (AFU)-EndA, which has narrow substrate specificity. Remarkably, structural comparison revealed that APE-EndA possesses a Crenarchaea specific loop (CSL). Introduction of CSL into AFU-EndA enhanced its intron-cleaving activity irrespective of the position or motif of the intron. Thus, our biochemical and crystallographic analyses of the chimera-EndA demonstrated that the CSL is responsible for the broad substrate specificity of APE-EndA. Furthermore, mutagenesis studies revealed that Lys44 in CSL functions as the RNA recognition site.
Takako Awai, Anna Ochi, (名) Ihsanawati, Toru Sengoku, Akira Hirata, Yoshitaka Bessho, Shigeyuki Yokoyama and Hiroyuki Hori : Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure., The Journal of Biological Chemistry, Vol.286, No.40, 35236-35246, 2011.
(要約)
Archaeal and eukaryotic tRNA (N(2),N(2)-guanine)-dimethyltransferase (Trm1) produces N(2),N(2)-dimethylguanine at position 26 in tRNA. In contrast, Trm1 from Aquifex aeolicus, a hyper-thermophilic eubacterium, modifies G27 as well as G26. Here, a gel mobility shift assay revealed that the T-arm in tRNA is the binding site of A. aeolicus Trm1. To address the multisite specificity, we performed an x-ray crystal structure study. The overall structure of A. aeolicus Trm1 is similar to that of archaeal Trm1, although there is a zinc-cysteine cluster in the C-terminal domain of A. aeolicus Trm1. The N-terminal domain is a typical catalytic domain of S-adenosyl-l-methionine-dependent methyltransferases. On the basis of the crystal structure and amino acid sequence alignment, we prepared 30 mutant Trm1 proteins. These mutant proteins clarified residues important for S-adenosyl-l-methionine binding and enabled us to propose a hypothetical reaction mechanism. Furthermore, the tRNA-binding site was also elucidated by methyl transfer assay and gel mobility shift assay. The electrostatic potential surface models of A. aeolicus and archaeal Trm1 proteins demonstrated that the distribution of positive charges differs between the two proteins. We constructed a tRNA-docking model, in which the T-arm structure was placed onto the large area of positive charge, which is the expected tRNA-binding site, of A. aeolicus Trm1. In this model, the target G26 base can be placed near the catalytic pocket; however, the nucleotide at position 27 gains closer access to the pocket. Thus, this docking model introduces a rational explanation of the multisite specificity of A. aeolicus Trm1.
Kazuo Ishida, Takashi Kunibayashi, Chie Tomikawa, Anna Ochi, Tamotsu Kanai, Akira Hirata, Chikako Iwashita and Hiroyuki Hori : Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus., Nucleic Acids Research, Vol.39, No.6, 2304-2318, 2010.
(要約)
Pseudouridine at position 55 (Ψ55) in eubacterial tRNA is produced by TruB. To clarify the role of the Ψ55 modification, we constructed a truB gene disruptant (ΔtruB) strain of Thermus thermophilus which is an extreme-thermophilic eubacterium. Unexpectedly, the ΔtruB strain exhibited severe growth retardation at 50 °C. We assumed that these phenomena might be caused by lack of RNA chaperone activity of TruB, which was previously hypothetically proposed by others. To confirm this idea, we replaced the truB gene in the genome with mutant genes, which express TruB proteins with very weak or no enzymatic activity. However the growth retardation at 50 °C was not rescued by these mutant proteins. Nucleoside analysis revealed that Gm18, m(5)s(2)U54 and m(1)A58 in tRNA from the ΔtruB strain were abnormally increased. An in vitro assay using purified tRNA modification enzymes demonstrated that the Ψ55 modification has a negative effect on Gm18 formation by TrmH. These experimental results show that the Ψ55 modification is required for low-temperature adaptation to control other modified. (35)S-Met incorporation analysis showed that the protein synthesis activity of the ΔtruB strain was inferior to that of the wild-type strain and that the cold-shock proteins were absence in the ΔtruB cells at 50°C.
Hiroshi Nishimasu, Ryuichiro Ishitani, Koki Yamashita, Chikako Iwashita, Akira Hirata, Hiroyuki Hori and Osamu Nureki : Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase., Proceedings of the National Academy of Sciences of the United States of America, Vol.106, No.20, 8180-8185, 2009.
(要約)
tRNAs from all 3 phylogenetic domains have a 5-methyluridine at position 54 (T54) in the T-loop. The methyl group is transferred from S-adenosylmethionine by TrmA methyltransferase in most Gram-negative bacteria and some archaea and eukaryotes, whereas it is transferred from 5,10-methylenetetrahydrofolate (MTHF) by TrmFO, a folate/FAD-dependent methyltransferase, in most Gram-positive bacteria and some Gram-negative bacteria. However, the catalytic mechanism remains unclear, because the crystal structure of TrmFO has not been solved. Here, we report the crystal structures of Thermus thermophilus TrmFO in its free form, tetrahydrofolate (THF)-bound form, and glutathione-bound form at 2.1-, 1.6-, and 1.05-A resolutions, respectively. TrmFO consists of an FAD-binding domain and an insertion domain, which both share structural similarity with those of GidA, an enzyme involved in the 5-carboxymethylaminomethylation of U34 of some tRNAs. However, the overall structures of TrmFO and GidA are basically different because of their distinct domain orientations, which are consistent with their respective functional specificities. In the THF complex, the pteridin ring of THF is sandwiched between the flavin ring of FAD and the imidazole ring of a His residue. This structure provides a snapshot of the folate/FAD-dependent methyl transfer, suggesting that the transferring methylene group of MTHF is located close to the redox-active N5 atom of FAD. Furthermore, we established an in vitro system to measure the methylation activity. Our TrmFO-tRNA docking model, in combination with mutational analyses, suggests a catalytic mechanism, in which the methylene of MTHF is directly transferred onto U54, and then the exocyclic methylene of U54 is reduced by FADH(2).
Akira Hirata, Tamotsu Kanai, Thomas T Santangelo, Momoko Tajiri, kenji Manabe, John N. Reeve, Tadayuki Imanaka and Katsuhiko S. Murakami : Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperaturesensitive, Molecular Microbiology, Vol.70, No.3, 623-633, 2008.
(要約)
All archaeal genomes encode RNA polymerase (RNAP) subunits E and F that share a common ancestry with the eukaryotic RNAP subunits A43 and A14 (Pol I), Rpb7 and Rpb4 (Pol II), and C25 and C17 (Pol III). By gene replacement, we have isolated archaeal mutants of Thermococcus kodakarensis with the subunit F-encoding gene (rpoF) deleted, but we were unable to isolate mutants lacking the subunit E-encoding gene (rpoE). Wild-type T. kodakarensis grows at temperatures ranging from 60 degrees C to 100 degrees C, optimally at 85 degrees C, and the DeltarpoF cells grew at the same rate as wild type at 70 degrees C, but much slower and to lower cell densities at 85 degrees C. The abundance of a chaperonin subunit, CpkB, was much reduced in the DeltarpoF strain growing at 85 degrees C and increased expression of cpkB, rpoF or rpoE integrated at a remote site in the genome, using a nutritionally regulated promoter, improved the growth of DeltarpoF cells. RNAP preparations purified from DeltarpoF cells lacked subunit F and also subunit E and a transcription factor TFE that co-purifies with RNAP from wild-type cells, but in vitro, this mutant RNAP exhibited no discernible differences from wild-type RNAP in promoter-dependent transcription, abortive transcript synthesis, transcript elongation or termination.
Akira Hirata, Brianna J. Klein and Katsuhiko S. Murakami : The X-ray crystal structure of RNA polymerase from Archaea., Nature, Vol.451, No.7180, 851-854, 2008.
(要約)
The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase (RNAP) II counterpart, comprising an RNAPII-like enzyme as well as two general transcription factors, the TATA-binding protein (TBP) and the eukaryotic TFIIB orthologue TFB. It has been widely understood that precise comparisons of cellular RNAP crystal structures could reveal structural elements common to all enzymes and that these insights would be useful in analysing components of each enzyme that enable it to perform domain-specific gene expression. However, the structure of archaeal RNAP has been limited to individual subunits. Here we report the first crystal structure of the archaeal RNAP from Sulfolobus solfataricus at 3.4 A resolution, completing the suite of multi-subunit RNAP structures from all three domains of life. We also report the high-resolution (at 1.76 A) crystal structure of the D/L subcomplex of archaeal RNAP and provide the first experimental evidence of any RNAP possessing an iron-sulphur (Fe-S) cluster, which may play a structural role in a key subunit of RNAP assembly. The striking structural similarity between archaeal RNAP and eukaryotic RNAPII highlights the simpler archaeal RNAP as an ideal model system for dissecting the molecular basis of eukaryotic transcription.
Akira Hirata, Motoyasu Adachi, Shigeru Utsumi and Bunzo Mikami : Engineering of the pH optimum of Bacillus cereus beta-amylase: conversion of the pH optimum from a bacterial type to a higher-plant type., Biochemistry, Vol.43, No.39, 12523-12531, 2004.
(要約)
The optimum pH of Bacillus cereus beta-amylase (BCB, pH 6.7) differs from that of soybean beta-amylase (SBA, pH 5.4) due to the substitution of a few amino acid residues near the catalytic base residue (Glu 380 in SBA and Glu 367 in BCB). To explore the mechanism for controlling the optimum pH of beta-amylase, five mutants of BCB (Y164E, Y164F, Y164H, Y164Q, and Y164Q/T47M/Y164E/T328N) were constructed and characterized with respect to enzymatic properties and X-ray structural crystal analysis. The optimum pH of the four single mutants shifted to 4.2-4.8, approximately 2 pH units and approximately 1 pH unit lower than those of BCB and SBA, respectively, and their k(cat) values decreased to 41-3% of that of the wild-type enzyme. The X-ray crystal analysis of the enzyme-maltose complexes showed that Glu 367 of the wild type is surrounded by two water molecules (W1 and W2) that are not found in SBA. W1 is hydrogen-bonded to both side chains of Glu 367 and Tyr 164. The mutation of Tyr 164 to Glu and Phe resulted in the disruption of the hydrogen bond between Tyr 164 Oeta and W1 and the introduction of two additional water molecules near position 164. In contrast, the triple mutant of BCB with a slightly decreased pH optimum at pH 6.0 has no water molecules (W1 and W2) around Glu 367. These results suggested that a water-mediated hydrogen bond network (Glu 367...W1...Tyr 164...Thr 328) is the primary requisite for the increased pH optimum of wild-type BCB. This strategy is completely different from that of SBA, in which a hydrogen bond network (Glu 380...Thr 340...Glu 178) reduces the optimum pH in a hydrophobic environment.
Akira Hirata, Motoyasu Adachi, Atsushi Sekine, You-Na Kang, Shigeru Utsumi and Bunzo Mikami : Structural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum., The Journal of Biological Chemistry, Vol.279, No.8, 7287-7295, 2003.
(要約)
Comparison of the architecture around the active site of soybean beta-amylase and Bacillus cereus beta-amylase showed that the hydrogen bond networks (Glu380-(Lys295-Met51) and Glu380-Asn340-Glu178) in soybean beta-amylase around the base catalytic residue, Glu380, seem to contribute to the lower pH optimum of soybean beta-amylase. To convert the pH optimum of soybean beta-amylase (pH 5.4) to that of the bacterial type enzyme (pH 6.7), three mutants of soybean beta-amylase, M51T, E178Y, and N340T, were constructed such that the hydrogen bond networks were removed by site-directed mutagenesis. The kinetic analysis showed that the pH optimum of all mutants shifted dramatically to a neutral pH (range, from 5.4 to 6.0-6.6). The Km values of the mutants were almost the same as that of soybean beta-amylase except in the case of M51T, while the Vmax values of all mutants were low compared with that of soybean beta-amylase. The crystal structure analysis of the wild type-maltose and mutant-maltose complexes showed that the direct hydrogen bond between Glu380 and Asn340 was completely disrupted in the mutants M51T, E178Y, and N340T. In the case of M51T, the hydrogen bond between Glu380 and Lys295 was also disrupted. These results indicated that the reduced pKa value of Glu380 is stabilized by the hydrogen bond network and is responsible for the lower pH optimum of soybean beta-amylase compared with that of the bacterial beta-amylase.
HJ Yoon, Akira Hirata, M Adachi, A Sekine, S Utsumi and B Mikami : Structure of the Starch-Binding Domain of Bacillus cereus β-Amylase, Journal of Microbiology and Biotechnology, Vol.9, No.5, 619-623, 1999.
T Kitajima, Akira Hirata and H Hori : Enzymatic and Crystallographic Characterization of Archaeal tRNA Splicing Endonuclease, IEEE: Micro-NanoMechatronics and Human Science, 231-236, 2009.
B Mikami, YN Kang, Akira Hirata and S Utsumi : Distored sugar ring in the active site of β-amylase., Acta Crystallographica Section A Foundations of Crystallography, Vol.60, No.a1, 171, 2004.
Hori Hiroyuki, Akira Hirata, Ueda Takuya, Watanabe Kimitsuna, Tomikawa Chie and Tomita Kozo : Transfer RNA Synthesis and Regulation, Encyclopedia of Life Sciences, Nov. 2021.
Akira Hirata : X-Ray Structure of the tRNA Methyltransferase Complex of Trm7 and Trm734 from Saccharomyces cerevisiae, Photon Factory Highlights 2019, 48-49, Oct. 2020.
Akira Hirata : Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases., Frontiers in Genetics, Vol.10, 103, Feb. 2019.
(要約)
RNA-splicing endonuclease (EndA) cleaves out introns from archaeal and eukaryotic precursor (pre)-tRNA and is essential for tRNA maturation. In archaeal EndA, the molecular mechanisms underlying complex assembly, substrate recognition, and catalysis have been well understood. Recently, certain studies have reported novel findings including the identification of new subunit types in archaeal EndA structures, providing insights into the mechanism underlying broad substrate specificity. Further, metagenomics analyses have enabled the acquisition of numerous DNA sequences of EndAs and intron-containing pre-tRNAs from various species, providing information regarding the co-evolution of substrate specificity of archaeal EndAs and tRNA genetic diversity, and the evolutionary pathway of archaeal and eukaryotic EndAs. Although the complex structure of the heterothermic form of eukaryotic EndAs is unknown, previous reports regarding their functions indicated that mutations in human EndA cause neurological disorders including pontocerebellar hypoplasia and progressive microcephaly, and yeast EndA significantly cleaves mitochondria-localized mRNA encoding cytochrome b mRNA processing 1 (Cpb1) for mRNA maturation. This mini-review summarizes the aforementioned results, discusses their implications, and offers my personal opinion regarding future directions for the analysis of the structure and function of EndAs.
Hiroyuki Hori, Takuya Kawamura, Takako Awai, Anna Ochi, Ryota Yamagami, Chie Tomikawa and Akira Hirata : Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA., Microorganisms, Vol.6, No.4, Oct. 2018.
(要約)
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. , which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
Hori Hiroyuki, Tomikawa Chie, Akira Hirata, Toh Yukimatsu, Tomita Kozo, Ueda Takuya and Watanabe Kimitsuna : Transfer RNA Synthesis and Regulation.'' Encyclopedia in Life Science, Wiley Inter-express, Sep. 2014.
Akira Hirata and Katsuhiko S. Murakami : Archaeal RNA polymerase., Current Opinion in Structural Biology, Vol.19, No.6, 724-731, Oct. 2009.
(要約)
The recently solved X-ray crystal structures of archaeal RNA polymerase (RNAP) allow a structural comparison of the transcription machinery among all three domains of life. Archaeal transcription is very simple and all components, including the structures of general transcription factors and RNAP, are highly conserved in eukaryotes. Therefore, it could be a new model for the dissection of the eukaryotic transcription apparatus. The archaeal RNAP structure also provides a framework for addressing the functional role that Fe-S clusters play within the transcription machinery of archaea and eukaryotes. A comparison between bacterial and archaeal open complex models reveals likely key motifs of archaeal RNAP for DNA unwinding during the open complex formation.
Hori Hiroyuki, Yamagami Ryota, Ishida Kazuo, Takuma Hiroyuki, Kusuba Hiroaki, Akira Hirata, Ochi Anna, Iwashita Chikako and Tomikawa Chie : Regulatory Factors for tRNA modifications in Thermus thermophilus, International Workshop on Neotechnologies for ThermusQ initiative, Oct. 2023.
2.
Akira Hirata, T Suzuki, T Nagano, D Fuji, M Okamoto, M Sora, T M. Lowe, T Kanai, H Atomi, T Suzuki and H Hori : Analysis of distinct modified nucleosides in tRNA from the hyperthermophilic archaeon Thermococcous kodakarensis provides insight into the requirement of specific tRNA modifications and their responsible genes for survival at high temperatures, Thrmophiles2019, Fukuoka, Sep. 2019.
3.
A Kaneta, K Fujishima, W Morikazu, H Hori and Akira Hirata : The RNA-splicing endonuclease from the Euryarchaea Methanopyrus kandleri uniquely represents a heterodimer with constraint range of substrate specificity: Supporting the coevolutionary scenario of protein function and tRNA gene diversity, Extremophiles2018, Italy, Sep. 2018.
4.
Akira Hirata, K Okada, K Yoshii, H Shiraishi, S Saijo, K Yonezawa, N Shimizu and H Hori : Structure of yeast tRNA Nm34 methyltransferase Trm7-Trm734 complex reveals its novel bipartite interaction essential for 2'-O-methylation of N34 in the wobble position of three specific tRNA species, 27th tRNA Conference, Strasbourg, Sep. 2018.
5.
T Kawamura, Akira Hirata, S Ohno, Y Nomura, T Nagano, N Nameki, T Yokogawa and H Hori : Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon, 26th tRNA Conference, korea, Sep. 2016.
6.
Akira Hirata, S Nishiyama, T Tamura, A Yamauchi and H Hori : Structural and functional analyses reveal mechanistic insight into a site specificity of the archaeal tRNA m2G/m22G10 methyltransferase (aTrm11), Extremophiles2016, Kyoto, Sep. 2016.
7.
Akira Hirata, S Nishiyama, T Tamura, A Yamauchi and H Hori : Structural and founctional analyses reveal mechanistic insight into a site specificity of the archaeal tRNA methyltransferase,, RNA2016, Kyoto, Jun. 2016.
8.
H Takuma, N Ushio, M Minoji, A Kazayama, N Shigi, Akira Hirata, C Tomikawa, A Ochi and H Hori : Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI), RNA2016, Kyoto, Jun. 2016.
9.
R Yamagami, C Tomikawa, N Shigi, A Kazayama, S Asai, H Takuma, Akira Hirata, D Fourmy, H Asahara, K Watanabe, S Yoshizawa and H Hori : The folate-dependent tRNA methyltransferase (TrmFO) relates to the adaptation at low-temperature environment and regulates methyl group metabolism in Thermus thermophilus, Thermophiles2015, Chili, Aug. 2015.
10.
T Kawamura, Akira Hirata, S Ohno, Y Nomura, T Nagano, N Nameki, T Yokogawa and H Hori : Multisite-specific archaeosine tRNA-guanine transglycosidase from Thermoplasma acidophilum,, Thermophiles2015, Chili, Aug. 2015.
11.
Akira Hirata, SH Jun, T Kanai, TJ Santangelo, T Imanaka and KS Murakami : X-ray crystal structure of euryarchaeal RNA polymerase (RNAP) from a hyperthermophilic archaeon Thermococcus kodakarensis: Insights into the molecular evolution of the archaeal/eukaryotic RNAP and molecular mechanism underlying the clamp-open state in the pre-initiation complex, Thermophiles2015, Chili, Aug. 2015.
12.
A Ochi, K Makabe, R Yamagami, Akira Hirata, R Sakaguchi, Y-M Hou, K Watanabe, O Nureki, K Kuwajima and H Hori : Topological knot tRNA methyltransferase (TrmH) discriminates substrate tRNA from non-substrate tRNA by a multistep recognition mechanism, 25th tRNA conference, Greek, Sep. 2014.
13.
Akira Hirata, K Fujishima, R Yamagami, T Kawamura, JF Banfiled, A Kanai and H Hori : X-ray crystal structure of the fourth type of tRNA splicing endonuclease from an uncultivated archaeon Candidatus Micrarchaeum acidiphilum (ARMAN-2), Thermophiles2013, Germany, Sep. 2013.
14.
Akira Hirata : Structural and functional diversity of the RNA polymerases from Archaea, CGM seminar, France, Sep. 2012.
15.
Akira Hirata : Structural and functional diversity of the RNA polymerases from Archaea, Invited seminar in University of Paris 5, Paris, Sep. 2012.
16.
R Yamagami, H Yamashita, C Nishimasu, A Tomikawa, A Ochi, C Iwashita, Akira Hirata, R Ishitani, O Nureki and H Hori : Transfer RNA recognition mechanism of Thermus thermophilus folate/FAD-dependent tRNA methyltransferase (TrmFO), Extremohpiles2012, Spain, Sep. 2012.
17.
Akira Hirata, K Fujishima, R Yamagami, T Kawamura, JF Banfiled, A Kanai and H Hori : Structural insight into the evolution and broad substrate specificity of the fourth type of tRNA splicing endonuclease, Extremohpiles2012, Spain, Sep. 2012.
18.
H Takuma, M Minoji, N Ushio, C Tomikawa, Akira Hirata, A Ochi and H Hori : Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI), The 38th international Symposium on Nucleic Acids Chemistry, 北海道, Nov. 2011.
19.
T Awai, A Ochi, T Ihsannawati, S Sengoku, S Kimura, C Tomikawa, T Yokogawa, Akira Hirata, T Bessho, T Suzuki, S Yokoyama and H Hori : Multisite specific tRNA methyltransferase Trm1 from a hyper-thermophilic eubacterium, Aquifex aeolicus, Thermophiles2011, Montana, Sep. 2011.
20.
Akira Hirata, T Kitajima and H Hori : Molecular mechanism for the broad substrate specificity of Crenarchaeal RNA splicing endonuclease, Thermophiles2011 United States, Sep. 2011.
21.
FH Lessner, A Jennings, Akira Hirata, EC Duin and DJ Lessner : Methanosarcina acetivorans RNA polymerase subunit D contains two oxygen-labile [4Fe-4S] clusters which impact the stability of the D/L heterodimer assembly complex, Gordon research conference, Italy, Jul. 2011.
22.
T Nagano, Akira Hirata, Y Ishimaru, A Kanai and H Hori : Structural and functional analyses of archaeal 2´-5´ RNA ligase, Thermophiles2011, Montana, Jul. 2011.
23.
R Yamagami, K Yamashita, C Nishimasu, C Iwashita, Akira Hirata, O Nureki and H Hori : Substrate tRNA recognition mechanism of FAD/folate-dependet tRNA m5U54 methyltransferase TrmFO, 16th Annual Meeting of RNA society, Kyoto, Jun. 2011.
24.
C Tomikawa, K Ishida, T Kunibayashi, A Ochi, T Kanai, Akira Hirata, C Iwashita and H Hori : Regulation of tRNA modification network by pseudouridine 55 in Thermus thermophiles, 16th Annual Meeting of RNA society, Kyoto, Jun. 2011.
25.
A Awai, A Ochi, (名) Ihsanawati, Akira Hirata, Y Bessho, S Yokoyama and H Hori : Transfer RNA recognition mechanism of multi-site specific tRNA methyltransferase (Trm1) from Aquifex aeolicu, 16th Annual Meeting of RNA society, Kyoto, Jun. 2011.
26.
Akira Hirata, T Kitajima and H Hori : A conserved Lys residue in Crenarchaea specific loop determines a broad substrate specificity of Crenarchaeal RNA splicing endonuclease, 16th Annual Meeting of RNA society, Kyoto, Jun. 2011.
27.
M Okuda, T Kitajima, T Shiba, Akira Hirata, DK Inaoka, K Kita, G Kurisu, S Harada, H Hori, YI Watanabe and S Yoshinari : Crystal structure of a splicing endonuclease from Crenarchaeaon Aeropyrum pernix, The 15th Annual meeting of RNA society, United States, Jun. 2010.
28.
H Hori, T Awai, T Toyooka, C Tomikawa, H Okamoto, H Takeda, K Watanabe, A Ochi, Akira Hirata, S Kimura, Y Ikeuchi, T Yokogawa and T Suzuki : Transfer RNA methyltransferase from a Hyperthermophilic Eubacterium, --- Aquifex aeolicus ---, 23th tRNA conference, Portugal, Jan. 2010.
29.
H Nishimasu, R Ishitani, K Yamashita, C Iwashita, Akira Hirata, H Hori and O Nureki : Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase, 23th tRNA conference, Portugal, Jan. 2010.
30.
Akira Hirata, A Ochi, C Tomikawa, T Kitajima, T Kanai and H Hori : Characterization of TrmJ [Transfer RNA (Cm32/Um32) Methyltransferase, 23th tRNA conference, Portugal, Jan. 2010.
31.
T Kitajima, Akira Hirata and H Hori : Enzymatic and Crystallographic Characterization of Archaeal tRNA Splicing Endonuclease, 2009 International Symposium on Micro-NanoMechatronics and Human Science, 231-236, Nagoya, Nov. 2009.
Bunzo Mikami, You-Na Kang, Akira Hirata and Shigeru Utsumi : Distorted Sugar Ring in the Active Site of Soybean β-Amylase, Acta crystallographica. Section A, Foundations of crystallography, Vol.A60, S171, Aug. 2004.
B Mikami, YN Kang, Akira Hirata and S Utsumi : Distored sugar ring in the active site of β-amylase, The 22nd European Crystallography Meeting, Hungary, Aug. 2004.
Sugio Yuzuru, Yamasaki Sota, Ueda Junya, Isogai Ryo, Matsumoto Natsumi, Hayashi Minoru, Yamagami Ryota, 平田 章, Tomikawa Chie, Yokogawa Takashi, Hori Hiroyuki : The third biosynthesis pathway of 4-thiouridine in tRNA, 第25回日本RNA学会年会, 2024年6月.
7.
Fujita Shu, Sugio Yuzuru, Kawamura Takuya, Yamgami Ryota, Oka Natsuhida, 平田 章, Yokogawa Takashi, Hori Hiroyuki : Lysine-transfer reaction by the complex of ArcS and RaSEA for archaeosine biosynthesis in tRNA, 第25回日本RNA学会年会, 2024年6月.
8.
Kawai Kumpei, Norioto Go, Matsuda Teppei, Manaka Sora, Yamagami Ryota, 平田 章, Hori Hiroyuki : Characterization of tRNA methyltransferase Trm14 from a hyper-thermophilic archaeon, Thermococcus kodakarensis, 第46回日本分子生物学会年会, 2023年12月.
9.
Fujita Shu, Sugio Yuzuru, Kawamura Takuya, Yamagami Ryota, Oka Natsuhisa, 平田 章, Yokogawa Takashi, Hori Hiroyuki : ArcS-RaSEA複合体によるLys転移反応の生化学解析, 第46回日本分子生物学会年会, 2023年12月.
Fujita Shu, Sugio Yuzuru, Kawamura Takuya, Yamagami Ryota, Oka Natsuhisa, 平田 章, Yokogawa Takashi, Hori Hiroyuki : Lysine-transfer reaction by the complex of ArcS and RaSEA for archaeosine biosynthesis in tRNA, 第24回日本RNA学会年会, 2023年7月.
Liu Yancheng, Takagi Yuko, Sugijianto Milyadi, Nguyen Doung My Ken, 平田 章, Hori Hiroyuki, Ho Kiong : Archaeal ATP-Dependent RNA Ligase Plays a Role in C/D Box sRNA Circularization and Ribosomal RNA Processing, 第23回日本RNA学会年会, 2022年7月.
17.
Kawai Kumpei, Nishida Yu, Ohomori Shiho, Kakizono Risa, Namba Miyu, Okada Kazuki, Yamagami Ryota, 平田 章, Hori Hiroyuki : Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine-N2-) Methyltransferase (Trm11-Trm112 Complex), 第23回日本RNA学会年会, 2022年7月.
Akira Hirata, K Okada, K Yoshii, H Shiraishi, S Saijo, K Yonezawa, N Simizu and H Hori : Structure of tRNA methyltransferase complex of Trm7 and Trm734 provides insight into its novel bipartite interaction essential for tRNA recognition and 2´-O-methylation at the first position of anticodon in specific tRNAs., 第21回日本RNA学会年会, Jul. 2019.
Y Liu, Y Takagi, Akira Hirata, H Hori, KS Murakami and K Ho : Archaea RNA Ligase is Required for Circularizing Small Non-Coding RNA, 第19回日本RNA学会年会, Jul. 2017.