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Article ; Online: ThermusQ: Toward the cell simulation platform for Thermus thermophilus.

Hijikata, Atsushi / Oshima, Tairo / Yura, Kei / Bessho, Yoshitaka

The Journal of general and applied microbiology

2023 Volume 69, Issue 2, Page(s) 59–67

Abstract: ThermusQ is a website (https://www.thermusq.net/) that aims to gather all the molecular information on Thermus thermophilus and to provide a platform to easily access the whole view of the bacterium. ThermusQ comprises the genome sequences of 22 strains ... ...

Abstract	ThermusQ is a website (https://www.thermusq.net/) that aims to gather all the molecular information on Thermus thermophilus and to provide a platform to easily access the whole view of the bacterium. ThermusQ comprises the genome sequences of 22 strains from T. thermophilus and T. oshimai strains, plus the sequences of known Thermus phages. ThermusQ also contains information and map diagrams of pathways unique to Thermus strains. The website provides tools to retrieve sequence data in different ways. By gathering the whole data of T. thermophilus strains, the strainspecific characteristics was found. This bird's-eye view of the whole data will lead the research community to identify missing important data and the integration will provide a platform to conduct future biochemical simulations of the bacterium.
MeSH term(s)	Thermus thermophilus/genetics ; Thermus/genetics ; Thermus/metabolism
Language	English
Publishing date	2023-09-20
Publishing country	Japan
Document type	Journal Article
ZDB-ID	218355-9
ISSN	1349-8037 ; 0022-1260
ISSN (online)	1349-8037
ISSN	0022-1260
DOI	10.2323/jgam.2023.07.001
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Article ; Online: Whole genome analyses for c-type cytochromes associated with respiratory chains in the extreme thermophile, Thermus thermophilus.

Hon-Nami, Koyu / Hijikata, Atsushi / Yura, Kei / Bessho, Yoshitaka

The Journal of general and applied microbiology

2023 Volume 69, Issue 2, Page(s) 68–78

Abstract: In thermophilic microorganisms, c-type cytochrome (cyt) proteins mainly function in the respiratory chain as electron carriers. Genome analyses at the beginning of this century revealed a variety of genes harboring the heme c motif. Here, we describe the ...

Abstract	In thermophilic microorganisms, c-type cytochrome (cyt) proteins mainly function in the respiratory chain as electron carriers. Genome analyses at the beginning of this century revealed a variety of genes harboring the heme c motif. Here, we describe the results of surveying genes with the heme c motif, CxxCH, in a genome database comprising four strains of Thermus thermophilus, including strain HB8, and the confirmation of 19 c-type cytochromes among 27 selected genes. We analyzed the 19 genes, including the expression of four, by a bioinformatics approach to elucidate their individual attributes. One of the approaches included an analysis based on the secondary structure alignment pattern between the heme c motif and the 6th ligand. The predicted structures revealed many cyt c domains with fewer β-strands, such as mitochondrial cyt c, in addition to the β-strand unique to Thermus inserted in cyt c domains, as in T. thermophilus cyt c
MeSH term(s)	Thermus thermophilus/genetics ; Thermus thermophilus/metabolism ; Electron Transport ; Cytochromes/metabolism ; Thermus/metabolism ; Electron Transport Complex IV/genetics ; Electron Transport Complex IV/chemistry ; Electron Transport Complex IV/metabolism
Chemical Substances	Cytochromes ; Electron Transport Complex IV (EC 1.9.3.1)
Language	English
Publishing date	2023-06-30
Publishing country	Japan
Document type	Journal Article
ZDB-ID	218355-9
ISSN	1349-8037 ; 0022-1260
ISSN (online)	1349-8037
ISSN	0022-1260
DOI	10.2323/jgam.2023.06.005
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Article ; Online: Changes in the hydrophobic network of the FliG

Nishikino, Tatsuro / Hijikata, Atsushi / Kojima, Seiji / Shirai, Tsuyoshi / Kainosho, Masatsune / Homma, Michio / Miyanoiri, Yohei

iScience

2023 Volume 26, Issue 8, Page(s) 107320

Abstract: The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational ... ...

Abstract	The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational direction, the detailed molecular mechanism was not elucidated. Here, we studied the structural changes in the FliG fragment containing the middle and C-terminal regions, named FliG
Language	English
Publishing date	2023-07-11
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107320
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Article: Cellular response of

Miyauchi, Hiroki / Ishikawa, Tomoharu / Hirakawa, Yutaro / Sudou, Ayumu / Okada, Katsuhiko / Hijikata, Atsushi / Sato, Norihiro / Tsuzuki, Mikio / Fujiwara, Shoko

Frontiers in plant science

2023 Volume 14, Page(s) 1175080

Abstract: Attached culture allows high biomass productivity and is a promising biomass cultivating system because neither a huge facility area nor a large volume of culture medium are needed. This study investigates photosynthetic and transcriptomic behaviors ... ...

Abstract	Attached culture allows high biomass productivity and is a promising biomass cultivating system because neither a huge facility area nor a large volume of culture medium are needed. This study investigates photosynthetic and transcriptomic behaviors in
Language	English
Publishing date	2023-06-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2023.1175080
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Article ; Online: Changes in the hydrophobic network of the FliGMC domain induce rotational switching of the flagellar motor

Tatsuro Nishikino / Atsushi Hijikata / Seiji Kojima / Tsuyoshi Shirai / Masatsune Kainosho / Michio Homma / Yohei Miyanoiri

iScience, Vol 26, Iss 8, Pp 107320- (2023)

2023

Abstract: Summary: The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching ... ...

Abstract	Summary: The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational direction, the detailed molecular mechanism was not elucidated. Here, we studied the structural changes in the FliG fragment containing the middle and C-terminal regions, named FliGMC, and the switch-defective FliGMC-G215A, using nuclear magnetic resonance (NMR) and molecular dynamics simulations. NMR analysis revealed multiple conformations of FliGMC, and the exchange process between these conformations was suppressed by the G215A residue substitution. Furthermore, changes in the intradomain orientation of FliG were induced by changes in hydrophobic interaction networks throughout FliG. Our finding applies to FliG in a ring complex in the flagellar basal body, and clarifies the switching mechanism of the flagellar motor.
Keywords	Cell biology ; Specialized functions of cells ; Functional aspects of cell biology ; Science ; Q
Language	English
Publishing date	2023-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Generalized pustular psoriasis that developed in a patient with an NFKB2 variant.

Wada, Shogo / Namiki, Takeshi / Ebata, Aoi / Takeichi, Takuya / Akiyama, Masashi / Yamada, Masafumi / Hijikata, Atsushi / Shimomura, Yutaka / Kanegane, Hirokazu / Okiyama, Naoko

Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG

2023 Volume 22, Issue 1, Page(s) 118–120

MeSH term(s)	Humans ; Acute Disease ; Chronic Disease ; NF-kappa B p52 Subunit ; Psoriasis/diagnosis ; Psoriasis/genetics ; Skin Diseases, Vesiculobullous
Chemical Substances	NF-kappa B p52 Subunit ; NFKB2 protein, human
Language	English
Publishing date	2023-12-20
Publishing country	Germany
Document type	Case Reports ; Letter
ZDB-ID	2093479-8
ISSN	1610-0387 ; 1610-0379
ISSN (online)	1610-0387
ISSN	1610-0379
DOI	10.1111/ddg.15273
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Zs.A 6148: Show issues

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Article ; Online: The complex etiology of autism spectrum disorder due to missense mutations of CHD8.

Shiraishi, Taichi / Katayama, Yuta / Nishiyama, Masaaki / Shoji, Hirotaka / Miyakawa, Tsuyoshi / Mizoo, Taisuke / Matsumoto, Akinobu / Hijikata, Atsushi / Shirai, Tsuyoshi / Mayanagi, Kouta / Nakayama, Keiichi I

Molecular psychiatry

2024

Abstract: CHD8 is an ATP-dependent chromatin-remodeling factor encoded by the most frequently mutated gene in individuals with autism spectrum disorder (ASD). Although many studies have examined the consequences of CHD8 haploinsufficiency in cells and mice, few ... ...

Abstract	CHD8 is an ATP-dependent chromatin-remodeling factor encoded by the most frequently mutated gene in individuals with autism spectrum disorder (ASD). Although many studies have examined the consequences of CHD8 haploinsufficiency in cells and mice, few have focused on missense mutations, the most common type of CHD8 alteration in ASD patients. We here characterized CHD8 missense mutations in ASD patients according to six prediction scores and experimentally examined the effects of such mutations on the biochemical activities of CHD8, neural differentiation of embryonic stem cells, and mouse behavior. Only mutations with high prediction scores gave rise to ASD-like phenotypes in mice, suggesting that not all CHD8 missense mutations detected in ASD patients are directly responsible for the development of ASD. Furthermore, we found that mutations with high scores cause ASD by mechanisms either dependent on or independent of loss of chromatin-remodeling function. Our results thus provide insight into the molecular underpinnings of ASD pathogenesis caused by missense mutations of CHD8.
Language	English
Publishing date	2024-03-05
Publishing country	England
Document type	Journal Article
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-024-02491-y
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Zs.A 4812: Show issues

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Article: A novel variant of NR5A1, p.R350W implicates potential interactions with unknown co-factors or ligands.

Gau, Maki / Suga, Ryota / Hijikata, Atsushi / Kashimada, Ayako / Takagi, Masatoshi / Nakagawa, Ryuichi / Takasawa, Kei / Shirai, Tsuyoshi / Kashimada, Kenichi / Morio, Tomohiro

Frontiers in endocrinology

2023 Volume 13, Page(s) 1033074

Abstract: Introduction: NR5A1 and NR5A2 belong to an orphan nuclear receptor group, and approximately 60% of their amino acid sequences are conserved. Transcriptional regulation of NR5A receptors depends on interactions with co-factors or unidentified ligands.: ...

Abstract	Introduction: NR5A1 and NR5A2 belong to an orphan nuclear receptor group, and approximately 60% of their amino acid sequences are conserved. Transcriptional regulation of NR5A receptors depends on interactions with co-factors or unidentified ligands. Purpose and methods: We employed in vitro and in silico analysis for elucidating the pathophysiology of a novel variant in the ligand-binding domain of NR5A1, p.R350W which was identified from a 46,XY patient with atypical genitalia. Results: In the study, [1] reporter assays demonstrated that R350 is essential for NR5A1; [2] 3D model analysis predicted that R350 interacted with endogenous ligands or unknown cofactors rather than stabilizing the structure; [3] R350 is not conserved in NR5A2 but is specifically required for NR5A1; and [4] none of the 22 known missense variants of the ligand binding domain satisfied all the previous conditions [1]-[3], suggesting the unique role of R350 in NR5A1. Conclusion: Our data suggest that NR5A1 has unidentified endogenous ligands or co-activators that selectively potentiate the transcriptional function of NR5A1
MeSH term(s)	Humans ; Mutation ; Ligands ; Disorder of Sex Development, 46,XY ; Mutation, Missense ; Amino Acid Sequence ; Steroidogenic Factor 1/genetics
Chemical Substances	Ligands ; NR5A1 protein, human ; Steroidogenic Factor 1
Language	English
Publishing date	2023-01-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2022.1033074
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Article ; Online: Isolation and genomic analysis of a type IV pili-independent Thermus thermophilus phage, φMN1 from a Japanese hot spring.

Tamakoshi, Masatada / Hijikata, Atsushi / Yura, Kei / Oshima, Kenshiro / Toh, Hidehiro / Mitsuoka, Kaoru / Oshima, Tairo / Bessho, Yoshitaka

The Journal of general and applied microbiology

2023 Volume 69, Issue 2, Page(s) 117–124

Abstract: A Thermus thermophilus lytic phage was isolated from a Japanese hot spring using a type IV pili-deficient strain as an indicator host, and designated as φMN1. Electron microscopic (EM) examination revealed that φMN1 had an icosahedral head and a ... ...

Abstract	A Thermus thermophilus lytic phage was isolated from a Japanese hot spring using a type IV pili-deficient strain as an indicator host, and designated as φMN1. Electron microscopic (EM) examination revealed that φMN1 had an icosahedral head and a contractile tail, suggesting that φMN1 belonged to Myoviridae. An EM analysis focused on φMN1 adsorption to the Thermus host cell showed that the receptor molecules for the phage were uniformly distributed on the outer surface of the cells. The circular double-stranded DNA of φMN1 was 76,659 base pairs in length, and the guanine and cytosine content was 61.8%. It was predicted to contain 99 open reading frames, and its putative distal tail fiber protein, which is essential for non-piliated host cell surface receptor recognition, was dissimilar in terms of sequence and length with its counterpart in the type IV pili-dependent φYS40. A phage proteomic tree revealed that φMN1 and φYS40 are in the same cluster, but many genes had low sequence similarities and some seemed to be derived from both mesophilic and thermophilic organisms. The gene organization suggested that φMN1 evolved from a non-Thermus phage through large-scale recombination events of the genes determining the host specificity, followed by gradual evolution by recombination of both the thermophilic and mesophilic DNAs assimilated by the host Thermus cells. This newly isolated phage will provide evolutionary insights into thermophilic phages.
MeSH term(s)	Bacteriophages/genetics ; Thermus thermophilus/genetics ; Proteomics ; Hot Springs ; Japan ; Open Reading Frames
Language	English
Publishing date	2023-07-07
Publishing country	Japan
Document type	Journal Article
ZDB-ID	218355-9
ISSN	1349-8037 ; 0022-1260
ISSN (online)	1349-8037
ISSN	0022-1260
DOI	10.2323/jgam.2023.06.008
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Article: Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins.

Hijikata, Atsushi / Shionyu, Clara / Nakae, Setsu / Shionyu, Masafumi / Ota, Motonori / Kanaya, Shigehiko / Shirai, Tsuyoshi

Biophysics and physicobiology

2021 Volume 18, Page(s) 226–240

Abstract: More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong ... ...

Abstract	More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of
Language	English
Publishing date	2021-10-05
Publishing country	Japan
Document type	Journal Article
ISSN	2189-4779
ISSN	2189-4779
DOI	10.2142/biophysico.bppb-v18.025
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