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Article ; Online: Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes.

Numata, Tomoyuki

Bioscience, biotechnology, and biochemistry

2015 Volume 79, Issue 3, Page(s) 347–353

Abstract: Bacteria and archaea have 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, at the first (wobble) position of the anticodon of the AUA codon-specific tRNA(Ile). These lysine- or agmatine-conjugated cytidine ... ...

Abstract	Bacteria and archaea have 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, at the first (wobble) position of the anticodon of the AUA codon-specific tRNA(Ile). These lysine- or agmatine-conjugated cytidine derivatives are crucial for the precise decoding of the genetic code. L is synthesized by tRNA(Ile)-lysidine synthetase (TilS), which uses l-lysine and ATP as substrates. Agm(2)C formation is catalyzed by tRNA(Ile)-agm(2)C synthetase (TiaS), which uses agmatine and ATP for the reaction. Despite the fact that TilS and TiaS synthesize structurally similar cytidine derivatives, these enzymes belong to non-related protein families. Therefore, these enzymes modify the wobble cytidine by distinct catalytic mechanisms, in which TilS activates the C2 carbon of the wobble cytidine by adenylation, while TiaS activates it by phosphorylation. In contrast, TilS and TiaS share similar tRNA recognition mechanisms, in which the enzymes recognize the tRNA acceptor stem to discriminate tRNA(Ile) and tRNA(Met).
MeSH term(s)	Archaea/genetics ; Archaea/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Codon/genetics ; Cytidine/analogs & derivatives ; Cytidine/metabolism ; Lysine/analogs & derivatives ; Lysine/metabolism ; Pyrimidine Nucleosides/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/genetics
Chemical Substances	Codon ; Pyrimidine Nucleosides ; agmatidine ; Cytidine (5CSZ8459RP) ; RNA, Transfer (9014-25-9) ; lysidine (987F50E3PE) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2015
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1106450-x
ISSN	1347-6947 ; 0916-8451
ISSN (online)	1347-6947
ISSN	0916-8451
DOI	10.1080/09168451.2014.975185
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Article ; Online: Structure, mechanism, and phylogeny of LysM-chitinase conjugates specifically found in fern plants.

Kitaoku, Yoshihito / Taira, Toki / Numata, Tomoyuki / Ohnuma, Takayuki / Fukamizo, Tamo

Plant science : an international journal of experimental plant biology

2022 Volume 321, Page(s) 111310

Abstract: A unique GH18 chitinase containing two N-terminal lysin motifs (PrLysM1 and PrLysM2) was first found in fern, Pteris ryukyuensis (Onaga and Taira, Glycobiology, 18, 414-423, 2008). This type of LysM-chitinase conjugates is not usually found in plants but ...

Abstract	A unique GH18 chitinase containing two N-terminal lysin motifs (PrLysM1 and PrLysM2) was first found in fern, Pteris ryukyuensis (Onaga and Taira, Glycobiology, 18, 414-423, 2008). This type of LysM-chitinase conjugates is not usually found in plants but in fungi. Here, we produced a similar GH18 chitinase with one N-terminal LysM module (EaLysM) from the fern, Equisetum arvense (EaChiA, Inamine et al., Biosci. Biotechnol. Biochem., 79, 1296-1304, 2015), using an Escherichia coli expression system and characterized for its structure and mechanism of action. The crystal structure of EaLysM exhibited an almost identical fold (βααβ) to that of PrLysM2. From isothermal titration calorimetry and nuclear magnetic resonance, the binding mode and affinities of EaLysM for chitooligosaccharides (GlcNAc)
MeSH term(s)	Chitin/chemistry ; Chitin/metabolism ; Chitinases/genetics ; Chitinases/metabolism ; Ferns/genetics ; Ferns/metabolism ; Phylogeny
Chemical Substances	Chitin (1398-61-4) ; Chitinases (EC 3.2.1.14)
Language	English
Publishing date	2022-05-06
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2022.111310
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Article: [Molecular basis for tRNA(Ile) agmatinylation essential for AUA codon decoding].

Numata, Tomoyuki

Seikagaku. The Journal of Japanese Biochemical Society

2012 Volume 84, Issue 12, Page(s) 1004–1008

MeSH term(s)	Animals ; Codon/chemistry ; Codon/genetics ; Codon/metabolism ; Cytidine/analogs & derivatives ; Cytidine/chemistry ; Cytidine/metabolism ; Isoleucine/genetics ; Isoleucine/metabolism ; Protein Biosynthesis/physiology ; RNA, Transfer, Ile/chemistry ; RNA, Transfer, Ile/genetics ; RNA, Transfer, Ile/metabolism
Chemical Substances	Codon ; RNA, Transfer, Ile ; agmatidine ; Isoleucine (04Y7590D77) ; Cytidine (5CSZ8459RP)
Language	Japanese
Publishing date	2012-12
Publishing country	Japan
Document type	Journal Article ; Review
ZDB-ID	282319-6
ISSN	0037-1017
ISSN	0037-1017
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Article: Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes

Numata, Tomoyuki

Bioscience, biotechnology, and biochemistry. 2015 Mar. 4, v. 79, no. 3

2015

Abstract: Bacteria and archaea have 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm²C or agmatidine), respectively, at the first (wobble) position of the anticodon of the AUA codon-specific tRNAᴵˡᵉ. These lysine- or agmatine-conjugated cytidine ... ...

Abstract	Bacteria and archaea have 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm²C or agmatidine), respectively, at the first (wobble) position of the anticodon of the AUA codon-specific tRNAᴵˡᵉ. These lysine- or agmatine-conjugated cytidine derivatives are crucial for the precise decoding of the genetic code. L is synthesized by tRNAᴵˡᵉ-lysidine synthetase (TilS), which uses l-lysine and ATP as substrates. Agm²C formation is catalyzed by tRNAᴵˡᵉ-agm²C synthetase (TiaS), which uses agmatine and ATP for the reaction. Despite the fact that TilS and TiaS synthesize structurally similar cytidine derivatives, these enzymes belong to non-related protein families. Therefore, these enzymes modify the wobble cytidine by distinct catalytic mechanisms, in which TilS activates the C2 carbon of the wobble cytidine by adenylation, while TiaS activates it by phosphorylation. In contrast, TilS and TiaS share similar tRNA recognition mechanisms, in which the enzymes recognize the tRNA acceptor stem to discriminate tRNAᴵˡᵉ and tRNAᴹᵉᵗ.
Keywords	Archaea ; agmatine ; biotechnology ; carbon ; cytidine ; genetic code ; lysine ; phosphorylation ; prokaryotic cells
Language	English
Dates of publication	2015-0304
Size	p. 347-353.
Publishing place	Taylor & Francis
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1106450-x
ISSN	1347-6947 ; 0916-8451
ISSN (online)	1347-6947
ISSN	0916-8451
DOI	10.1080/09168451.2014.975185
Database	NAL-Catalogue (AGRICOLA)

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Article: Structure, mechanism, and phylogeny of LysM-chitinase conjugates specifically found in fern plants

Kitaoku, Yoshihito / Taira, Toki / Numata, Tomoyuki / Ohnuma, Takayuki / Fukamizo, Tamo

Plant science. 2022 Aug., v. 321

2022

Abstract: A unique GH18 chitinase containing two N-terminal lysin motifs (PrLysM1 and PrLysM2) was first found in fern, Pteris ryukyuensis (Onaga and Taira, Glycobiology, 18, 414–423, 2008). This type of LysM-chitinase conjugates is not usually found in plants but ...

Abstract	A unique GH18 chitinase containing two N-terminal lysin motifs (PrLysM1 and PrLysM2) was first found in fern, Pteris ryukyuensis (Onaga and Taira, Glycobiology, 18, 414–423, 2008). This type of LysM-chitinase conjugates is not usually found in plants but in fungi. Here, we produced a similar GH18 chitinase with one N-terminal LysM module (EaLysM) from the fern, Equisetum arvense (EaChiA, Inamine et al., Biosci. Biotechnol. Biochem., 79, 1296–1304, 2015), using an Escherichia coli expression system and characterized for its structure and mechanism of action. The crystal structure of EaLysM exhibited an almost identical fold (βααβ) to that of PrLysM2. From isothermal titration calorimetry and nuclear magnetic resonance, the binding mode and affinities of EaLysM for chitooligosaccharides (GlcNAc)ₙ (3, 4, 5, and 6) were found to be comparable to those of PrLysM2. The LysM module in EaChiA is likely to bind (GlcNAc)ₙ almost independently through CH-π stacking of a Tyr residue with the pyranose ring. The (GlcNAc)ₙ-binding mode of LysMs in the LysM-chitinase conjugates from fern plants appears to differ from that of plant LysMs acting in chitin- or Nod-signal perception, in which multiple LysMs cooperatively act on (GlcNAc)ₙ. Phylogenetic analysis suggested that LysM-GH18 conjugates of fern plants formed a monophyletic group and had been separated earlier than forming the clade of fungal chitinases with LysMs.
Keywords	Equisetum arvense ; Escherichia coli ; Pteris ; calorimetry ; chitinase ; chitooligosaccharides ; crystal structure ; ferns and fern allies ; fungi ; glycomics ; mechanism of action ; monophyly ; nuclear magnetic resonance spectroscopy ; titration
Language	English
Dates of publication	2022-08
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2022.111310
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Article ; Online: A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region.

Kawamoto, Daiki / Takashima, Tomoya / Fukamizo, Tamo / Numata, Tomoyuki / Ohnuma, Takayuki

Glycobiology

2021 Volume 32, Issue 4, Page(s) 356–364

Abstract: Plant GH19 chitinases have several loop structures, which may define their enzymatic properties. Among these loops, the longest loop, Loop-III, is most frequently conserved in GH19 enzymes. A GH19 chitinase from the moss Bryum coronatum (BcChi-A) has ... ...

Abstract	Plant GH19 chitinases have several loop structures, which may define their enzymatic properties. Among these loops, the longest loop, Loop-III, is most frequently conserved in GH19 enzymes. A GH19 chitinase from the moss Bryum coronatum (BcChi-A) has only one loop structure, Loop-III, which is connected to the catalytically important β-sheet region. Here, we produced and characterized a Loop-III-deleted mutant of BcChi-A (BcChi-A-ΔIII) and found that its stability and chitinase activity were strongly reduced. The deletion of Loop-III also moderately affected the chitooligosaccharide binding ability as well as the binding mode to the substrate-binding groove. The crystal structure of an inactive mutant of BcChi-A-ΔIII was successfully solved, revealing that the remaining polypeptide chain has an almost identical fold to that of the original protein. Loop-III is not necessarily essential for the folding of the enzyme protein. However, closer examination of the crystal structure revealed that the deletion of Loop-III altered the arrangement of the catalytic triad, Glu61, Glu70 and Ser102, and the orientation of the Trp103 side chain, which is important for sugar residue binding. We concluded that Loop-III is not directly involved in the enzymatic activity but assists the enzyme function by stabilizing the conformation of the β-sheet region and the adjacent substrate-binding platform from behind the core-functional regions.
MeSH term(s)	Bryophyta/metabolism ; Bryopsida/metabolism ; Chitin/chemistry ; Chitinases/chemistry ; Protein Conformation, beta-Strand
Chemical Substances	Chitin (1398-61-4) ; Chitinases (EC 3.2.1.14)
Language	English
Publishing date	2021-12-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
DOI	10.1093/glycob/cwab117
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Article ; Online: Characterization of two rice GH18 chitinases belonging to family 8 of plant pathogenesis-related proteins.

Tanaka, Jun / Takashima, Tomoya / Abe, Naojiro / Fukamizo, Tamo / Numata, Tomoyuki / Ohnuma, Takayuki

Plant science : an international journal of experimental plant biology

2022 Volume 326, Page(s) 111524

Abstract: Two rice GH18 chitinases, Oschib1 and Oschib2, belonging to family 8 of plant pathogenesis-related proteins (PR proteins) were expressed, purified, and characterized. These enzymes, which have the structural features of class IIIb chitinases, ... ...

Abstract	Two rice GH18 chitinases, Oschib1 and Oschib2, belonging to family 8 of plant pathogenesis-related proteins (PR proteins) were expressed, purified, and characterized. These enzymes, which have the structural features of class IIIb chitinases, preferentially cleaved the second glycosidic linkage from the non-reducing end of substrate chitin oligosaccharides as opposed to rice class IIIa enzymes, OsChib3a and OsChib3b, which mainly cleaved the fourth linkage from the non-reducing end of chitin hexasaccharide [(GlcNAc)
Language	English
Publishing date	2022-10-31
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	742010-9
ISSN	1873-2259 ; 0168-9452
ISSN (online)	1873-2259
ISSN	0168-9452
DOI	10.1016/j.plantsci.2022.111524
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Article ; Online: Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex.

Takeshita, Daijiro / Sato, Momoe / Inanaga, Hideko / Numata, Tomoyuki

Journal of molecular biology

2019 Volume 431, Issue 4, Page(s) 748–763

Abstract: Clustered regularly interspaced short palindromic repeat (CRISPR) loci and CRISPR-associated (Cas) genes encode CRISPR RNAs (crRNA) and Cas proteins, respectively, which play important roles in the adaptive immunity system (CRISPR-Cas system) in ... ...

Abstract	Clustered regularly interspaced short palindromic repeat (CRISPR) loci and CRISPR-associated (Cas) genes encode CRISPR RNAs (crRNA) and Cas proteins, respectively, which play important roles in the adaptive immunity system (CRISPR-Cas system) in prokaryotes. The crRNA and Cas proteins form ribonucleoprotein effector complexes to capture and degrade invading genetic materials with base complementarity to the crRNA guide sequences. The Csm complex, a type III-A effector complex, comprises five Cas proteins (Csm1-Csm5) and a crRNA, which co-transcriptionally degrades invading DNA and RNA. Here we report the crystal structures of the Staphylococcus epidermidis Csm2 (SeCsm2) and Thermoplasma volcanium Csm3 (TvCsm3) at 2.4- and 2.7-Å resolutions, respectively. SeCsm2 adopts a monomeric globular fold by itself, in striking contrast to the previously reported Thermotoga maritima Csm2, which adopted an extended conformation and formed a dimeric structure. We propose that the globular monomeric form is the bona fide structure of Csm2. TvCsm3 forms a filamentous structure in the crystals. The molecular arrangement of TvCsm3 is similar to that of the stacked Cmr4 proteins in the Cmr complex, suggesting the functionally relevant architecture of the present Csm3 structure. We constructed model structures of the Csm complex, which revealed that Csm3 binds the crRNA and periodically deforms the crRNA-target duplex by a similar mechanism to that of Cmr4 in the Cmr complex. The model and mutational analysis suggest that the conserved lysine residue of Csm2 is important for target RNA binding, and Csm2 stabilizes the active structure of the Csm complex to facilitate the reaction.
MeSH term(s)	Amino Acid Sequence ; Bacterial Proteins/genetics ; CRISPR-Associated Proteins/genetics ; CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; RNA, Bacterial/genetics ; Staphylococcus epidermidis/genetics ; Thermotoga maritima/genetics
Chemical Substances	Bacterial Proteins ; CRISPR-Associated Proteins ; RNA, Bacterial
Language	English
Publishing date	2019-01-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2019.01.009
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Article ; Online: Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome.

Oki, Keisuke / Nagata, Mariko / Yamagami, Takeshi / Numata, Tomoyuki / Ishino, Sonoko / Oyama, Takuji / Ishino, Yoshizumi

Nucleic acids research

2021 Volume 50, Issue 7, Page(s) 3601–3615

Abstract: Genomic DNA replication requires replisome assembly. We show here the molecular mechanism by which CMG (GAN-MCM-GINS)-like helicase cooperates with the family D DNA polymerase (PolD) in Thermococcus kodakarensis. The archaeal GINS contains two Gins51 ... ...

Abstract	Genomic DNA replication requires replisome assembly. We show here the molecular mechanism by which CMG (GAN-MCM-GINS)-like helicase cooperates with the family D DNA polymerase (PolD) in Thermococcus kodakarensis. The archaeal GINS contains two Gins51 subunits, the C-terminal domain of which (Gins51C) interacts with GAN. We discovered that Gins51C also interacts with the N-terminal domain of PolD's DP1 subunit (DP1N) to connect two PolDs in GINS. The two replicases in the replisome should be responsible for leading- and lagging-strand synthesis, respectively. Crystal structure analysis of the DP1N-Gins51C-GAN ternary complex was provided to understand the structural basis of the connection between the helicase and DNA polymerase. Site-directed mutagenesis analysis supported the interaction mode obtained from the crystal structure. Furthermore, the assembly of helicase and replicase identified in this study is also conserved in Eukarya. PolD enhances the parental strand unwinding via stimulation of ATPase activity of the CMG-complex. This is the first evidence of the functional connection between replicase and helicase in Archaea. These results suggest that the direct interaction of PolD with CMG-helicase is critical for synchronizing strand unwinding and nascent strand synthesis and possibly provide a functional machinery for the effective progression of the replication fork.
MeSH term(s)	DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA Replication ; DNA-Directed DNA Polymerase/genetics ; Eukaryota/metabolism ; Thermococcus/enzymology ; Thermococcus/metabolism
Chemical Substances	DNA-Directed DNA Polymerase (EC 2.7.7.7) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2021-09-16
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab799
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Article ; Online: GET pathway mediates transfer of mislocalized tail-anchored proteins from mitochondria to the ER.

Matsumoto, Shunsuke / Ono, Suzuka / Shinoda, Saori / Kakuta, Chika / Okada, Satoshi / Ito, Takashi / Numata, Tomoyuki / Endo, Toshiya

The Journal of cell biology

2022 Volume 221, Issue 6

Abstract: Tail-anchored (TA) membrane proteins have a potential risk to be mistargeted to the mitochondrial outer membrane (OM). Such mislocalized TA proteins can be extracted by the mitochondrial AAA-ATPase Msp1 from the OM and transferred to the ER for ER ... ...

Abstract	Tail-anchored (TA) membrane proteins have a potential risk to be mistargeted to the mitochondrial outer membrane (OM). Such mislocalized TA proteins can be extracted by the mitochondrial AAA-ATPase Msp1 from the OM and transferred to the ER for ER protein quality control involving ubiquitination by the ER-resident Doa10 complex. Yet it remains unclear how the extracted TA proteins can move to the ER crossing the aqueous cytosol and whether this transfer to the ER is essential for the clearance of mislocalized TA proteins. Here we show by time-lapse microscopy that mislocalized TA proteins, including an authentic ER-TA protein, indeed move from mitochondria to the ER in a manner strictly dependent on Msp1 expression. The Msp1-dependent mitochondria-to-ER transfer of TA proteins is blocked by defects in the GET system, and this block is not due to impaired Doa10 functions. Thus, the GET pathway facilitates the transfer of mislocalized TA proteins from mitochondria to the ER.
MeSH term(s)	Adenosine Triphosphatases/genetics ; Adenosine Triphosphatases/metabolism ; Endoplasmic Reticulum/metabolism ; Membrane Proteins/metabolism ; Mitochondria/metabolism ; Protein Transport ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Membrane Proteins ; Saccharomyces cerevisiae Proteins ; Adenosine Triphosphatases (EC 3.6.1.-) ; MSP1 protein, S cerevisiae (EC 3.6.1.-)
Language	English
Publishing date	2022-04-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.202104076
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