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Article ; Online: Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT3.

Liu, Jun / Yashiro, Yuka / Sakaguchi, Yuriko / Suzuki, Tsutomu / Tomita, Kozo

2024

Abstract: Mycobacterium tuberculosis transfer RNA (tRNA) terminal nucleotidyltransferase toxin, MenT3, incorporates nucleotides at the 3'-CCA end of tRNAs, blocking their aminoacylation and inhibiting protein synthesis. Here, we show that MenT3 most effectively ... ...

Abstract	Mycobacterium tuberculosis transfer RNA (tRNA) terminal nucleotidyltransferase toxin, MenT3, incorporates nucleotides at the 3'-CCA end of tRNAs, blocking their aminoacylation and inhibiting protein synthesis. Here, we show that MenT3 most effectively adds CMPs to the 3'-CCA end of tRNA. The crystal structure of MenT3 in complex with CTP reveals a CTP-specific nucleotide-binding pocket. The 4-NH2 and the N3 and O2 atoms of cytosine in CTP form hydrogen bonds with the main-chain carbonyl oxygen of P120 and the side chain of R238, respectively. MenT3 expression in Escherichia coli selectively reduces the levels of seryl-tRNASers, indicating specific inactivation of tRNASers by MenT3. Consistently, MenT3 incorporates CMPs into tRNASer most efficiently, among the tested E. coli tRNA species. The longer variable loop unique to class II tRNASers is crucial for efficient CMP incorporation into tRNASer by MenT3. Replacing the variable loop of E. coli tRNAAla with the longer variable loop of M. tuberculosis tRNASer enables MenT3 to incorporate CMPs into the chimeric tRNAAla. The N-terminal positively charged region of MenT3 is required for CMP incorporation into tRNASer. A docking model of tRNA onto MenT3 suggests that an interaction between the N-terminal region and the longer variable loop of tRNASer facilitates tRNA substrate selection.
Language	English
Publishing date	2024-03-15
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/gkae177
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Article ; Online: Frequent occurrence of mutations in nsp3 and nsp4 of SARS-CoV-2, presumably caused by the inhaled asthma drug ciclesonide.

Doi, Akihiro / Tomita, Yuriko / Okura, Hiyori / Matsuyama, Shutoku

PNAS nexus

2022 Volume 1, Issue 4, Page(s) pgac197

Abstract: Mutations in nonstructural protein 3 (nsp3) and nsp4 of SARS-CoV-2, presumably induced by the asthma drug ciclesonide (which also has anti-SARS-CoV-2 activity), were counted 5,851 cases in the GISAID EpiCoV genome database. Sporadic occurrence of mutants ...

Abstract	Mutations in nonstructural protein 3 (nsp3) and nsp4 of SARS-CoV-2, presumably induced by the asthma drug ciclesonide (which also has anti-SARS-CoV-2 activity), were counted 5,851 cases in the GISAID EpiCoV genome database. Sporadic occurrence of mutants not linked to each other in the phylogenetic tree were identified at least 88 times; of which, 58 had one or more descendants in the same branch. Five of these had spread to more than 100 cases, and one had expanded to 4,748 cases, suggesting the mutations are frequent, selected in individual patients, and transmitted to form clusters of cases. Clinical trials of ciclesonide as a treatment for COVID-19 are the presumed cause of the frequent occurrence of mutations between 2020 June and 2021 November. In addition, because ciclesonide is a common treatment for asthma, it can drive mutations in asthmatics suffering from COVID-19. Ciclesonide-resistant mutations, which have unpredictable effects in humans, are likely to continue to emerge because SARS-CoV-2 remains prevalent globally.
Language	English
Publishing date	2022-09-20
Publishing country	England
Document type	Journal Article
ISSN	2752-6542
ISSN (online)	2752-6542
DOI	10.1093/pnasnexus/pgac197
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Article ; Online: The anti-influenza virus drug favipiravir has little effect on replication of SARS-CoV-2 in cultured cells.

Tomita, Yuriko / Takeda, Makoto / Matsuyama, Shutoku

Antimicrobial agents and chemotherapy

2021 Volume 65, Issue 5

Abstract: Favipiravir (T-705, commercial name Avigan), a drug developed to treat influenza virus infection, has been used in some countries as an oral treatment for COVID-19; however, its clinical efficacy in this context is controversial.…. ...

Abstract	Favipiravir (T-705, commercial name Avigan), a drug developed to treat influenza virus infection, has been used in some countries as an oral treatment for COVID-19; however, its clinical efficacy in this context is controversial.….
Language	English
Publishing date	2021-03-01
Publishing country	United States
Document type	Letter
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.00020-21
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Zs.A 809: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Book ; Online: Fast and Examination-agnostic Reciprocal Recommendation in Matching Markets

Tomita, Yoji / Togashi, Riku / Hashizume, Yuriko / Ohsaka, Naoto

2023

Abstract: In matching markets such as job posting and online dating platforms, the recommender system plays a critical role in the success of the platform. Unlike standard recommender systems that suggest items to users, reciprocal recommender systems (RRSs) that ... ...

Abstract	In matching markets such as job posting and online dating platforms, the recommender system plays a critical role in the success of the platform. Unlike standard recommender systems that suggest items to users, reciprocal recommender systems (RRSs) that suggest other users must take into account the mutual interests of users. In addition, ensuring that recommendation opportunities do not disproportionately favor popular users is essential for the total number of matches and for fairness among users. Existing recommendation methods in matching markets, however, face computational challenges on large-scale platforms and depend on specific examination functions in the position-based model (PBM). In this paper, we introduce the reciprocal recommendation method based on the matching with transferable utility (TU matching) model in the context of ranking recommendations in matching markets and propose a fast and examination-model-free algorithm. Furthermore, we evaluate our approach on experiments with synthetic data and real-world data from an online dating platform in Japan. Our method performs better than or as well as existing methods in terms of the total number of matches and works well even in a large-scale dataset for which one existing method does not work.
Keywords	Computer Science - Information Retrieval
Subject code	005
Publishing date	2023-06-15
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Reliability and validity of the Japanese version of the Infant Breastfeeding Assessment Tool.

Tomita, Aya / Tahara-Sasagawa, Emi / Yonezawa, Kaori / Usui, Yuriko / Haruna, Megumi

Midwifery

2023 Volume 121, Page(s) 103670

Abstract: Objective: To translate the Infant Breastfeeding Assessment Tool (IBFAT) into Japanese and confirm the reliability and validity of the Japanese version of IBFAT.: Design: The methodological study examining the reliability and validity of the Japanese ...

Abstract	Objective: To translate the Infant Breastfeeding Assessment Tool (IBFAT) into Japanese and confirm the reliability and validity of the Japanese version of IBFAT. Design: The methodological study examining the reliability and validity of the Japanese version of the IBFAT. Setting: A maternity hospital in Tokyo. Participants: Ten mother-newborn pairs were recruited for the reliability analysis. 101 mother-newborn pairs were recruited for the validity analysis. Measurements and findings: Reliability was verified by video recording and direct observation. The observers are one researcher, and 11 evaluators consisting of midwives and nurses. Amongst the 11 evaluators, six evaluators directly observed breastfeeding behaviours and five evaluators observed breastfeeding behaviours through video viewing. Regarding the inter-rater agreement, the intraclass correlation (ICC) between the researcher and six direct evaluators was 0.985 (95% confidence interval [CI]: 0.941-0.996) and that amongst five video viewing evaluators was 0.827 (95% CI: 0.647-0.945). In the intra-rater agreement, the lowest ICC amongst all those investigating IBFAT scores was 0.810 (95% CI: 0.433-0.948). In concurrent validity, the correlation coefficients between the IBFAT and Breastfeeding behaviour Assessment (BBA) scores on the first day after birth and the fourth or fifth day after birth (at discharge) were 0.66 (p < 0.001) and 0.40 (p < 0.001), respectively. In predictive validity, the medians and interquartile ranges (IQRs) of IBFAT scores at discharge were 11.0 (IQR: 11.0-12.0) and 11.0 (IQR: 11.0-12.0) for the breast and mixed milk groups at one-month check-up, respectively. While both median values were the same, the Mann-Whitney U test showed a significant difference. Key conclusions: The Japanese version of the IBFAT is valid and reliable for measuring feeding behaviour amongst newborns in the first week of life. Implications for practice: The Japanese version of the IBFAT can be available both in a clinical setting and in research to help support breastfeeding.
MeSH term(s)	Female ; Humans ; Infant, Newborn ; Pregnancy ; Breast Feeding ; Feeding Behavior ; Mothers ; Reproducibility of Results ; Japan
Language	English
Publishing date	2023-03-26
Publishing country	Scotland
Document type	Journal Article
ZDB-ID	1036567-9
ISSN	1532-3099 ; 0266-6138
ISSN (online)	1532-3099
ISSN	0266-6138
DOI	10.1016/j.midw.2023.103670
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Article: Detection of the ORF1 Gene Is an Indicator of the Possible Isolation of Severe Acute Respiratory Syndrome Coronavirus 2.

Shirato, Kazuya / Kakizaki, Masatoshi / Tomita, Yuriko / Kawase, Miyuki / Takeda, Makoto

Pathogens (Basel, Switzerland)

2022 Volume 11, Issue 3

Abstract: In the ongoing coronavirus diseases 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), real-time RT-PCR based diagnostic assays have been used for the detection of infection, but the positive signal of real- ... ...

Abstract	In the ongoing coronavirus diseases 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), real-time RT-PCR based diagnostic assays have been used for the detection of infection, but the positive signal of real-time RT-PCR does not necessarily indicate the infectivity of the patient. Due to the unique replication system of the coronavirus, primer/probe sets targeted nucleocapsid (N) and spike (S) protein detect the abundantly synthesized subgenomic RNAs as well as the virus genome, possibly making the assay unsuitable for estimation of the infectivity of the specimen, although it has an advantage for the diagnostic tests. In this study, the primer/probe set targeting the open reading frame 1a (ORF1a) gene was developed to specifically detect viral genomic RNA. Then the relation between the ORF1a signal and infectivity of the clinical specimens was validated by virus isolation using VeroE6 cells, which constitutively express transmembrane protease, serine 2, (VeroE6/TMPRSS2). The analytical sensitivity of developed ORF1a set was similar to that of previously developed N and S sets. Nevertheless, in the assay of the clinical specimen, detection rate of the ORF1a gene was lower than that of the N and S genes. These data indicated that clinical specimens contain a significant amount of subgenomic RNAs. However, as expected, the isolation-succeeded specimen always showed an RT-PCR-positive signal for the ORF1a gene, suggesting ORF1a detection in combination with N and S sets could be a more rational indicator for the possible infectivity of the clinical specimens.
Language	English
Publishing date	2022-02-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11030302
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Article ; Online: Mechanistic insights into tRNA cleavage by a contact-dependent growth inhibitor protein and translation factors.

Wang, Jing / Yashiro, Yuka / Sakaguchi, Yuriko / Suzuki, Tsutomu / Tomita, Kozo

Nucleic acids research

2022 Volume 50, Issue 8, Page(s) 4713–4731

Abstract: Contact-dependent growth inhibition is a mechanism of interbacterial competition mediated by delivery of the C-terminal toxin domain of CdiA protein (CdiA-CT) into neighboring bacteria. The CdiA-CT of enterohemorrhagic Escherichia coli EC869 (CdiA- ... ...

Abstract	Contact-dependent growth inhibition is a mechanism of interbacterial competition mediated by delivery of the C-terminal toxin domain of CdiA protein (CdiA-CT) into neighboring bacteria. The CdiA-CT of enterohemorrhagic Escherichia coli EC869 (CdiA-CTEC869) cleaves the 3'-acceptor regions of specific tRNAs in a reaction that requires the translation factors Tu/Ts and GTP. Here, we show that CdiA-CTEC869 has an intrinsic ability to recognize a specific sequence in substrate tRNAs, and Tu:Ts complex promotes tRNA cleavage by CdiA-CTEC869. Uncharged and aminoacylated tRNAs (aa-tRNAs) were cleaved by CdiA-CTEC869 to the same extent in the presence of Tu/Ts, and the CdiA-CTEC869:Tu:Ts:tRNA(aa-tRNA) complex formed in the presence of GTP. CdiA-CTEC869 interacts with domain II of Tu, thereby preventing the 3'-moiety of tRNA to bind to Tu as in canonical Tu:GTP:aa-tRNA complexes. Superimposition of the Tu:GTP:aa-tRNA structure onto the CdiA-CTEC869:Tu structure suggests that the 3'-portion of tRNA relocates into the CdiA-CTEC869 active site, located on the opposite side to the CdiA-CTEC869 :Tu interface, for tRNA cleavage. Thus, CdiA-CTEC869 is recruited to Tu:GTP:Ts, and CdiA-CT:Tu:GTP:Ts recognizes substrate tRNAs and cleaves them. Tu:GTP:Ts serves as a reaction scaffold that increases the affinity of CdiA-CTEC869 for substrate tRNAs and induces a structural change of tRNAs for efficient cleavage by CdiA-CTEC869.
MeSH term(s)	Enterohemorrhagic Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Growth Inhibitors ; Guanosine Triphosphate/metabolism ; Membrane Proteins/metabolism ; Peptide Elongation Factor Tu/metabolism ; RNA, Transfer/metabolism ; RNA, Transfer, Amino Acyl
Chemical Substances	CdiA protein, E coli ; Escherichia coli Proteins ; Growth Inhibitors ; Membrane Proteins ; RNA, Transfer, Amino Acyl ; Guanosine Triphosphate (86-01-1) ; RNA, Transfer (9014-25-9) ; Peptide Elongation Factor Tu (EC 3.6.1.-)
Language	English
Publishing date	2022-04-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
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/gkac228
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Article ; Online: Detection of the ORF1 Gene Is an Indicator of the Possible Isolation of Severe Acute Respiratory Syndrome Coronavirus 2

Kazuya Shirato / Masatoshi Kakizaki / Yuriko Tomita / Miyuki Kawase / Makoto Takeda

Pathogens, Vol 11, Iss 302, p

2022 Volume 302

Abstract	In the ongoing coronavirus diseases 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), real-time RT-PCR based diagnostic assays have been used for the detection of infection, but the positive signal of real-time RT-PCR does not necessarily indicate the infectivity of the patient. Due to the unique replication system of the coronavirus, primer/probe sets targeted nucleocapsid (N) and spike (S) protein detect the abundantly synthesized subgenomic RNAs as well as the virus genome, possibly making the assay unsuitable for estimation of the infectivity of the specimen, although it has an advantage for the diagnostic tests. In this study, the primer/probe set targeting the open reading frame 1a (ORF1a) gene was developed to specifically detect viral genomic RNA. Then the relation between the ORF1a signal and infectivity of the clinical specimens was validated by virus isolation using VeroE6 cells, which constitutively express transmembrane protease, serine 2, (VeroE6/TMPRSS2). The analytical sensitivity of developed ORF1a set was similar to that of previously developed N and S sets. Nevertheless, in the assay of the clinical specimen, detection rate of the ORF1a gene was lower than that of the N and S genes. These data indicated that clinical specimens contain a significant amount of subgenomic RNAs. However, as expected, the isolation-succeeded specimen always showed an RT-PCR-positive signal for the ORF1a gene, suggesting ORF1a detection in combination with N and S sets could be a more rational indicator for the possible infectivity of the clinical specimens.
Keywords	coronavirus diseases 19 (COVID-19) ; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ; real-time RT-PCR ; virus isolation ; ORF1a ; Medicine ; R
Subject code	610
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular basis of glycyl-tRNA

Yashiro, Yuka / Zhang, Chuqiao / Sakaguchi, Yuriko / Suzuki, Tsutomu / Tomita, Kozo

Cell reports

2021 Volume 37, Issue 12, Page(s) 110130

Abstract: Bacterial toxin-antitoxin modules contribute to the stress adaptation, persistence, and dormancy of bacteria for survival under environmental stresses and are involved in bacterial pathogenesis. In Salmonella Typhimurium, the Gcn5-related N- ... ...

Abstract	Bacterial toxin-antitoxin modules contribute to the stress adaptation, persistence, and dormancy of bacteria for survival under environmental stresses and are involved in bacterial pathogenesis. In Salmonella Typhimurium, the Gcn5-related N-acetyltransferase toxin TacT reportedly acetylates the α-amino groups of the aminoacyl moieties of several aminoacyl-tRNAs, inhibits protein synthesis, and promotes persister formation during the infection of macrophages. Here, we show that TacT exclusively acetylates Gly-tRNA
Language	English
Publishing date	2021-12-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.110130
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Article ; Online: Mechanism of aminoacyl-tRNA acetylation by an aminoacyl-tRNA acetyltransferase AtaT from enterohemorrhagic E. coli

Yuka Yashiro / Yuriko Sakaguchi / Tsutomu Suzuki / Kozo Tomita

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 12

Abstract: AtaT is a type-II toxin from enterohemorrhagic E. coli, reported to acetylate the aminoacyl-moiety of initiator Met-tRNAfMet, thus inhibiting translation initiation. Biochemical analysis suggests that AtaT has a broader specificity for aminoacyl-tRNAs ... ...

Abstract	AtaT is a type-II toxin from enterohemorrhagic E. coli, reported to acetylate the aminoacyl-moiety of initiator Met-tRNAfMet, thus inhibiting translation initiation. Biochemical analysis suggests that AtaT has a broader specificity for aminoacyl-tRNAs and inhibits global translation. Structure of AtaT in complex with acetylated Met-tRNAfMet offers insight into the substrate selection by the enzyme.
Keywords	Science ; Q
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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