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  1. Article ; Online: ALS-linked TDP-43 mutations interfere with the recruitment of RNA recognition motifs to G-quadruplex RNA.

    Ishiguro, Akira / Ishihama, Akira

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 5982

    Abstract: TDP-43 is a major pathological protein in sporadic and familial amyotrophic lateral sclerosis (ALS) and mediates mRNA fate. TDP-43 dysfunction leads to causes progressive degeneration of motor neurons, the details of which remain elusive. Elucidation of ... ...

    Abstract TDP-43 is a major pathological protein in sporadic and familial amyotrophic lateral sclerosis (ALS) and mediates mRNA fate. TDP-43 dysfunction leads to causes progressive degeneration of motor neurons, the details of which remain elusive. Elucidation of the molecular mechanisms of RNA binding could enhance our understanding of this devastating disease. We observed the involvement of the glycine-rich (GR) region of TDP-43 in the initial recognition and binding of G-quadruplex (G4)-RNA in conjunction with its RNA recognition motifs (RRM). We performed a molecular dissection of these intramolecular RNA-binding modules in this study. We confirmed that the ALS-linked mutations in the GR region lead to alteration in the G4 structure. In contrast, amino acid substitutions in the GR region alter the protein structure but do not void the interaction with G4-RNA. Based on these observations, we concluded that the structural distortion of G4 caused by these mutations interferes with RRM recruitment and leads to TDP-43 dysfunction. This intramolecular organization between RRM and GR regions modulates the overall G4-binding properties.
    MeSH term(s) Humans ; Amyotrophic Lateral Sclerosis/metabolism ; DNA-Binding Proteins/metabolism ; Mutation ; RNA/genetics ; RNA/metabolism ; RNA Recognition Motif/genetics
    Chemical Substances DNA-Binding Proteins ; RNA (63231-63-0) ; TARDBP protein, human
    Language English
    Publishing date 2023-04-12
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-33172-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Essential Roles and Risks of G-Quadruplex Regulation: Recognition Targets of ALS-Linked TDP-43 and FUS.

    Ishiguro, Akira / Ishihama, Akira

    Frontiers in molecular biosciences

    2022  Volume 9, Page(s) 957502

    Abstract: A non-canonical DNA/RNA structure, G-quadruplex (G4), is a unique structure formed by two or more guanine quartets, which associate through Hoogsteen hydrogen bonding leading to form a square planar arrangement. A set of RNA-binding proteins specifically ...

    Abstract A non-canonical DNA/RNA structure, G-quadruplex (G4), is a unique structure formed by two or more guanine quartets, which associate through Hoogsteen hydrogen bonding leading to form a square planar arrangement. A set of RNA-binding proteins specifically recognize G4 structures and play certain unique physiological roles. These G4-binding proteins form ribonucleoprotein (RNP) through a physicochemical phenomenon called liquid-liquid phase separation (LLPS). G4-containing RNP granules are identified in both prokaryotes and eukaryotes, but extensive studies have been performed in eukaryotes. We have been involved in analyses of the roles of G4-containing RNAs recognized by two G4-RNA-binding proteins, TDP-43 and FUS, which both are the amyotrophic lateral sclerosis (ALS) causative gene products. These RNA-binding proteins play the essential roles in both G4 recognition and LLPS, but they also carry the risk of agglutination. The biological significance of G4-binding proteins is controlled through unique 3D structure of G4, of which the risk of conformational stability is influenced by environmental conditions such as monovalent metals and guanine oxidation.
    Language English
    Publishing date 2022-07-11
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2022.957502
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Metal-Responsive Transcription Factors Co-Regulate Anti-Sigma Factor (Rsd) and Ribosome Dimerization Factor Expression.

    Yoshida, Hideji / Shimada, Tomohiro / Ishihama, Akira

    International journal of molecular sciences

    2023  Volume 24, Issue 5

    Abstract: Bacteria exposed to stress survive by regulating the expression of several genes at the transcriptional and translational levels. For instance, ... ...

    Abstract Bacteria exposed to stress survive by regulating the expression of several genes at the transcriptional and translational levels. For instance, in
    MeSH term(s) Escherichia coli/metabolism ; Ribosomal Proteins/metabolism ; Escherichia coli Proteins/metabolism ; Dimerization ; Transcription Factors/metabolism ; Sigma Factor/metabolism ; Ribosomes/metabolism ; Bacterial Proteins/metabolism
    Chemical Substances Ribosomal Proteins ; Escherichia coli Proteins ; Transcription Factors ; Sigma Factor ; Bacterial Proteins
    Language English
    Publishing date 2023-03-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24054717
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  4. Article ; Online: Building a complete image of genome regulation in the model organism Escherichia coli.

    Ishihama, Akira

    The Journal of general and applied microbiology

    2017  Volume 63, Issue 6, Page(s) 311–324

    Abstract: The model organism, Escherichia coli, contains a total of more than 4,500 genes, but the total number of RNA polymerase (RNAP) core enzyme or the transcriptase is only about 2,000 molecules per genome. The regulatory targets of RNAP are, however, ... ...

    Abstract The model organism, Escherichia coli, contains a total of more than 4,500 genes, but the total number of RNA polymerase (RNAP) core enzyme or the transcriptase is only about 2,000 molecules per genome. The regulatory targets of RNAP are, however, modulated by changing its promoter selectivity through two-steps of protein-protein interplay with 7 species of the sigma factor in the first step, and then 300 species of the transcription factor (TF) in the second step. Scientists working in the field of prokaryotic transcription in Japan have made considerable contributions to the elucidation of genetic frameworks and regulatory modes of the genome transcription in E. coli K-12. This review summarizes the findings by this group, first focusing on three sigma factors, the stationary-phase sigma RpoS, the heat-shock sigma RpoH, and the flagellar-chemotaxis sigma RpoF, as examples. It also presents an overview of the current state of the systematic research being carried out to identify the regulatory functions of all TFs from a single and the same bacterium E. coli K-12, using the genomic SELEX and PS-TF screening systems. All these studies have been undertaken with the aim of understanding the genome regulation in E. coli K-12 as a whole.
    MeSH term(s) DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Models, Genetic ; Promoter Regions, Genetic ; Protein Binding ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Escherichia coli Proteins ; Transcription Factors ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2017-09-12
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 218355-9
    ISSN 1349-8037 ; 0022-1260
    ISSN (online) 1349-8037
    ISSN 0022-1260
    DOI 10.2323/jgam.2017.01.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators.

    Ishihama, Akira / Shimada, Tomohiro

    FEMS microbiology reviews

    2021  Volume 45, Issue 6

    Abstract: Transcriptional regulation for genome expression determines growth and adaptation of single-cell bacteria that are directly exposed to environment. The transcriptional apparatus in Escherichia coli K-12 is composed of RNA polymerase core enzyme and two ... ...

    Abstract Transcriptional regulation for genome expression determines growth and adaptation of single-cell bacteria that are directly exposed to environment. The transcriptional apparatus in Escherichia coli K-12 is composed of RNA polymerase core enzyme and two groups of its regulatory proteins, seven species of promoter-recognition subunit sigma and about 300 species of transcription factors. The identification of regulatory targets for all these regulatory proteins is critical toward understanding the genome regulation as a whole. For this purpose, we performed a systematic search in vitro of the whole set of binding sites for each factor by gSELEX system. This review summarizes the accumulated knowledge of regulatory targets for more than 150 TFs from E. coli K-12. Overall TFs could be classified into four families: nucleoid-associated bifunctional TFs; global regulators; local regulators; and single-target regulators, in which the regulatory functions remain uncharacterized for the nucleoid-associated TFs. Here we overview the regulatory targets of two nucleoid-associated TFs, H-NS and its paralog StpA, both together playing the silencing role of a set of non-essential genes. Participation of LeuO and other global regulators have been indicated for the anti-silencing. Finally, we propose the hierarchy of TF network as a key framework of the bacterial genome regulation.
    MeSH term(s) Escherichia coli K12/genetics ; Escherichia coli K12/metabolism ; Escherichia coli Proteins/genetics ; Fimbriae Proteins ; Gene Expression Regulation, Bacterial ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Escherichia coli Proteins ; FimG protein, E coli ; Transcription Factors ; Fimbriae Proteins (147680-16-8)
    Language English
    Publishing date 2021-06-29
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 283740-7
    ISSN 1574-6976 ; 0168-6445
    ISSN (online) 1574-6976
    ISSN 0168-6445
    DOI 10.1093/femsre/fuab032
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Genomic SELEX Reveals Pervasive Role of the Flagella Master Regulator FlhDC in Carbon Metabolism.

    Takada, Hiraku / Kijima, Kaede / Ishiguro, Akira / Ishihama, Akira / Shimada, Tomohiro

    International journal of molecular sciences

    2023  Volume 24, Issue 4

    Abstract: Flagella are vital bacterial organs that allow microorganisms to move to favorable environments. However, their construction and operation consume a large amount of energy. The master regulator FlhDC mediates all flagellum-forming genes ... ...

    Abstract Flagella are vital bacterial organs that allow microorganisms to move to favorable environments. However, their construction and operation consume a large amount of energy. The master regulator FlhDC mediates all flagellum-forming genes in
    MeSH term(s) Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Bacterial Proteins/metabolism ; Trans-Activators/metabolism ; Genomics ; Flagella/metabolism ; Sugars/metabolism ; Gene Expression Regulation, Bacterial
    Chemical Substances Escherichia coli Proteins ; Bacterial Proteins ; Trans-Activators ; Sugars
    Language English
    Publishing date 2023-02-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24043696
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Apoplastic Expression of CARD1-ecto Domain in

    Ishihama, Nobuaki / Laohavisit, Anuphon / Takizawa, Kaori / Shirasu, Ken

    Bio-protocol

    2022  Volume 12, Issue 8, Page(s) e4387

    Abstract: The protein expression and purification process is an essential initial step for biochemical analysis of a protein of interest. Traditionally, heterologous protein expression systems (such ... ...

    Abstract The protein expression and purification process is an essential initial step for biochemical analysis of a protein of interest. Traditionally, heterologous protein expression systems (such as
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.4387
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  8. Article: [Foreword].

    Ishihama, Akira

    Seikagaku. The Journal of Japanese Biochemical Society

    2015  Volume 87, Issue 5, Page(s) 499

    MeSH term(s) Biology/education ; Biomedical Research ; Genome ; Humans
    Language Japanese
    Publishing date 2015-10
    Publishing country Japan
    Document type Introductory Journal Article
    ZDB-ID 282319-6
    ISSN 0037-1017
    ISSN 0037-1017
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  9. Article ; Online: Expanded roles of lactate-sensing LldR in transcription regulation of the

    Anzai, Takumi / Kijima, Kaede / Fujimori, Miki / Nakamoto, Soma / Ishihama, Akira / Shimada, Tomohiro

    Microbial genomics

    2023  Volume 9, Issue 5

    Abstract: LldR is a lactate-responsive transcription factor (TF) that transcriptionally regulates ... ...

    Abstract LldR is a lactate-responsive transcription factor (TF) that transcriptionally regulates the
    MeSH term(s) Lactic Acid ; Escherichia coli K12 ; Escherichia coli ; Gene Expression Regulation ; Transcription Factors ; Carbon ; DNA-Binding Proteins ; Escherichia coli Proteins
    Chemical Substances Lactic Acid (33X04XA5AT) ; Transcription Factors ; Carbon (7440-44-0) ; LldR protein, E coli ; DNA-Binding Proteins ; Escherichia coli Proteins
    Language English
    Publishing date 2023-05-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.001015
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  10. Article ; Online: Prognostic impact of the prognostic nutritional index in cases of resected oral squamous cell carcinoma: a retrospective study.

    Abe, Atsushi / Hayashi, Hiroki / Ishihama, Takanori / Furuta, Hiroshi

    BMC oral health

    2021  Volume 21, Issue 1, Page(s) 40

    Abstract: Background: The systemic inflammatory response and nutritional status of patients with malignant tumors are related to postoperative results. We examined the usefulness of the prognostic nutritional index (PNI) as a prognostic tool in patients with oral ...

    Abstract Background: The systemic inflammatory response and nutritional status of patients with malignant tumors are related to postoperative results. We examined the usefulness of the prognostic nutritional index (PNI) as a prognostic tool in patients with oral squamous cell carcinoma who underwent radical surgery.
    Methods: From 2008 to 2019, 102 patients (73 males, 29 females; age, 65.6 ± 9.8 years) who visited our hospital and underwent surgical therapy were included in this study. The endpoint was the total survival period, and the evaluation markers included the lymphocyte count and albumin level in peripheral blood obtained 4 weeks preoperatively, age, sex, alcohol consumption, smoking history, site of the tumor, pathological stage, and surgery status. The PNI was calculated using serum albumin levels and the peripheral blood lymphocyte count. The relationship between the PNI and patient characteristics were analyzed using Fisher's exact test. The Kaplan-Meier method was used to evaluate the survival rate. The survival periods were compared using the log-rank method. We evaluated the prognostic factors for overall survival (OS) and disease-free survival (DFS) in a logistic regression model.
    Results: The tumor sites included the maxilla (n = 12), buccal mucosa (n = 11), mandible (n = 17), floor of the mouth (n = 9), and tongue (n = 53). The number of patients with stage I, II, III, and IV oral cancers was 28 (27.5%), 34 (27.5%), 26 (33.3%), and 14 (13.7%), respectively. During the observation period, 21 patients died of head and neck cancer. The optimal cut-off PNI value was 42.9, according to the receiver operating characteristic analysis. The proportion of patients with a short OS was lower in those with PNI higher than 42.9, and the 5-year OS in patients with PNI higher and lower than the cut-off value was 62.3% and 86.0%, respectively (P = 0.0105).
    Conclusions: The OS of patients with PNI < 42.9 was lower than that of patients with PNI ≥ 42.9. The PNI, which is a preoperative head-to-foot inflammatory marker, can help in estimating the prognosis of oral cancer.
    MeSH term(s) Aged ; Carcinoma, Squamous Cell/surgery ; Female ; Humans ; Male ; Middle Aged ; Mouth Neoplasms/surgery ; Nutrition Assessment ; Nutritional Status ; Prognosis ; Retrospective Studies ; Squamous Cell Carcinoma of Head and Neck
    Language English
    Publishing date 2021-01-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 2091511-1
    ISSN 1472-6831 ; 1472-6831
    ISSN (online) 1472-6831
    ISSN 1472-6831
    DOI 10.1186/s12903-021-01394-6
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