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Article ; Online: Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids

Joon-Hwa Lee / Masato Katahira

International Journal of Molecular Sciences, Vol 23, Iss 5836, p

2022 Volume 5836

Abstract: Nucleic acids have essential roles in all biological processes related to genetic information, such as replication, transcription, translation, repair, and recombination [.] ...

Abstract	Nucleic acids have essential roles in all biological processes related to genetic information, such as replication, transcription, translation, repair, and recombination [.]
Keywords	n/a ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Observation of nucleic acids inside living human cells by in-cell NMR spectroscopy

Yudai Yamaoki / Takashi Nagata / Tomoki Sakamoto / Masato Katahira

Biophysics and Physicobiology, Vol

2020 Volume 17

Abstract: The intracellular environment is highly crowded with biomacromolecules such as proteins and nucleic acids. Under such conditions, the structural and biophysical features of nucleic acids have been thought to be different from those in vitro. To obtain ... ...

Abstract	The intracellular environment is highly crowded with biomacromolecules such as proteins and nucleic acids. Under such conditions, the structural and biophysical features of nucleic acids have been thought to be different from those in vitro. To obtain high-resolution structural information on nucleic acids in living cells, the in-cell NMR method is a unique tool. Following the first in-cell NMR measurement of nucleic acids in 2009, several interesting insights were obtained using Xenopus laevis oocytes. However, the in-cell NMR spectrum of nucleic acids in living human cells was not reported until two years ago due to the technical challenges of delivering exogenous nucleic acids. We reported the first in-cell NMR spectra of nucleic acids in living human cells in 2018, where we applied a pore-forming toxic protein, streptolysin O. The in-cell NMR measurements demonstrated that the hairpin structures of nucleic acids can be detected in living human cells. In this review article, we summarize our recent work and discuss the future prospects of the in-cell NMR technique for nucleic acids.
Keywords	dna ; rna ; intracellular structure ; streptolysin o (slo) ; solution nmr ; Biology (General) ; QH301-705.5 ; Physiology ; QP1-981 ; Physics ; QC1-999
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	The Biophysical Society of Japan
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Non-coding RNA suppresses FUS aggregation caused by mechanistic shear stress on pipetting in a sequence-dependent manner

Nesreen Hamad / Ryoma Yoneda / Masatomo So / Riki Kurokawa / Takashi Nagata / Masato Katahira

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS ...

Abstract	Abstract Fused in sarcoma/translocated in liposarcoma (FUS/TLS) is a multitasking RNA/DNA binding protein. FUS aggregation is implicated in various neurodegenerative diseases. RNA was suggested to modulate phase transition of FUS. Here, we found that FUS transforms into the amorphous aggregation state as an instant response to the shear stress caused by usual pipetting even at a low FUS concentration, 100 nM. It was revealed that non-coding RNA can suppress the transformation of FUS into aggregates. The suppressive effect of RNA on FUS aggregation is sequence-dependent. These results suggested that the non-coding RNA could be a prospective suppressor of FUS aggregation caused by mechanistic stress in cells. Our finding might pave the way for more research on the role of RNAs as aggregation inhibitors, which could facilitate the development of therapies for neurodegenerative diseases.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Direct evidence for α ether linkage between lignin and carbohydrates in wood cell walls

Hiroshi Nishimura / Akihiro Kamiya / Takashi Nagata / Masato Katahira / Takashi Watanabe

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 11

Abstract: Abstract Cross-linking between lignin and polysaccharide in plant cell-wall determines physical, chemical, and biological features of lignocellulosic biomass. Since Erdmann’s first report in 1866, numerous studies have suggested the presence of a bond ... ...

Abstract	Abstract Cross-linking between lignin and polysaccharide in plant cell-wall determines physical, chemical, and biological features of lignocellulosic biomass. Since Erdmann’s first report in 1866, numerous studies have suggested the presence of a bond between hemicelluloses and lignin; however, no clear evidence for this interaction has been reported. We describe the first direct proof of covalent bonding between plant cell-wall polysaccharides and lignin. Nuclear magnetic resonance spectroscopy was used to observe the long-range correlations through an α-ether bond between lignin and the primary hydroxyl group of a mannose residue in glucomannan. Complete signal assignment of the cognate structural units was also achieved. Thus, we identified lignin–carbohydrate bonds by complete connectivity analysis from the phenylpropane unit to the carbohydrate moiety.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-04-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigation of the Interaction of Human Origin Recognition Complex Subunit 1 with G-Quadruplex DNAs of Human c-myc Promoter and Telomere Regions

Afaf Eladl / Yudai Yamaoki / Shoko Hoshina / Haruka Horinouchi / Keiko Kondo / Shou Waga / Takashi Nagata / Masato Katahira

International Journal of Molecular Sciences, Vol 22, Iss 3481, p

2021 Volume 3481

Abstract: Origin recognition complex (ORC) binds to replication origins in eukaryotic DNAs and plays an important role in replication. Although yeast ORC is known to sequence-specifically bind to a replication origin, how human ORC recognizes a replication origin ... ...

Abstract	Origin recognition complex (ORC) binds to replication origins in eukaryotic DNAs and plays an important role in replication. Although yeast ORC is known to sequence-specifically bind to a replication origin, how human ORC recognizes a replication origin remains unknown. Previous genome-wide studies revealed that guanine (G)-rich sequences, potentially forming G-quadruplex (G4) structures, are present in most replication origins in human cells. We previously suggested that the region comprising residues 413–511 of human ORC subunit 1, hORC1 413–511 , binds preferentially to G-rich DNAs, which form a G4 structure in the absence of hORC1 413–511 . Here, we investigated the interaction of hORC1 413-511 with various G-rich DNAs derived from human c-myc promoter and telomere regions. Fluorescence anisotropy revealed that hORC1 413–511 binds preferentially to DNAs that have G4 structures over ones having double-stranded structures. Importantly, circular dichroism (CD) and nuclear magnetic resonance (NMR) showed that those G-rich DNAs retain the G4 structures even after binding with hORC1 413–511 . NMR chemical shift perturbation analyses revealed that the external G-tetrad planes of the G4 structures are the primary binding sites for hORC1 413–511 . The present study suggests that human ORC1 may recognize replication origins through the G4 structure.
Keywords	origin recognition complex ; G-quadruplex ; DNA replication ; replication origin ; NMR ; structure ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	572 ; 333
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: NMR Analysis on Molecular Interaction of Lignin with Amino Acid Residues of Carbohydrate-Binding Module from Trichoderma reesei Cel7A

Yuki Tokunaga / Takashi Nagata / Takashi Suetomi / Satoshi Oshiro / Keiko Kondo / Masato Katahira / Takashi Watanabe

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 12

Abstract: Abstract Lignocellulosic biomass is anticipated to serve as a platform for green chemicals and fuels. Nonproductive binding of lignin to cellulolytic enzymes should be avoided for conversion of lignocellulose through enzymatic saccharification. Although ... ...

Abstract	Abstract Lignocellulosic biomass is anticipated to serve as a platform for green chemicals and fuels. Nonproductive binding of lignin to cellulolytic enzymes should be avoided for conversion of lignocellulose through enzymatic saccharification. Although carbohydrate-binding modules (CBMs) of cellulolytic enzymes strongly bind to lignin, the adsorption mechanism at molecular level is still unclear. Here, we report NMR-based analyses of binding sites on CBM1 of cellobiohydrolase I (Cel7A) from a hyper-cellulase-producing fungus, Trichoderma reesei, with cellohexaose and lignins from Japanese cedar (C-MWL) and Eucalyptus globulus (E-MWL). A method was established to obtain properly folded TrCBM1. Only TrCBM1 that was expressed in freshly transformed E. coli had intact conformation. Chemical shift perturbation analyses revealed that TrCBM1 adsorbed cellohexaose in highly specific manner via two subsites, flat plane surface and cleft, which were located on the opposite side of the protein surface. Importantly, MWLs were adsorbed at multiple binding sites, including the subsites, having higher affinity than cellohexaose. G6 and Q7 were involved in lignin binding on the flat plane surface of TrCBM1, while cellohexaose preferentially interacted with N29 and Q34. TrCBM1 used much larger surface area to bind with C-MWL than E-MWL, indicating the mechanisms of adsorption toward hardwood and softwood lignins are different.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-02-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Catalytic analysis of APOBEC3G involving real-time NMR spectroscopy reveals nucleic acid determinants for deamination.

Keisuke Kamba / Takashi Nagata / Masato Katahira

PLoS ONE, Vol 10, Iss 4, p e

2015 Volume 0124142

Abstract: APOBEC3G (A3G) is a single-stranded DNA-specific cytidine deaminase that preferentially converts cytidine to uridine at the third position of triplet cytosine (CCC) hotspots. A3G restricts the infectivity of viruses, such as HIV-1, by targeting CCC ... ...

Abstract	APOBEC3G (A3G) is a single-stranded DNA-specific cytidine deaminase that preferentially converts cytidine to uridine at the third position of triplet cytosine (CCC) hotspots. A3G restricts the infectivity of viruses, such as HIV-1, by targeting CCC hotspots scattered through minus DNA strands, reverse-transcribed from genomic RNA. Previously, we developed a real-time NMR method and elucidated the origin of the 3'→5' polarity of deamination of DNA by the C-terminal domain of A3G (CD2), which is a phenomenon by which a hotspot located closer to the 5'-end is deaminated more effectively than one less close to the 5'-end, through quantitative analysis involving nonspecific binding to and sliding along DNA. In the present study we applied the real-time NMR method to analyze the catalytic activity of CD2 toward DNA oligonucleotides containing a nucleotide analog at a single or multiple positions. Analyses revealed the importance of the sugar and base moieties throughout the consecutive 5 nucleotides, the CCC hotspot being positioned at the center. It was also shown that the sugar or base moieties of the nucleotides outside this 5 nucleotide recognition sequence are also relevant as to CD2's activity. Analyses involving DNA oligonucleotides having two CCC hotspots linked by a long sequence of either deoxyribonucleotides, ribonucleotides or abasic deoxyribonucleotides suggested that the phosphate backbone is required for CD2 to slide along the DNA strand and to exert the 3'→5' polarity. Examination of the effects of different salt concentrations on the 3'→5' polarity indicated that the higher the salt concentration, the less prominent the 3'→5' polarity. This is most likely the result of alleviation of sliding due to a decrease in the affinity of CD2 with the phosphate backbone at high salt concentrations. We also investigated the reactivity of substrates containing 5-methylcytidine (5mC) or 5-hydroxymethylcytidine, and found that A3G exhibited low activity toward 5mC.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Classification of fungal glucuronoyl esterases (FGEs) and characterization of two new FGEs from Ceriporiopsis subvermispora and Pleurotus eryngii

Lin, Meng-I / Akiho Hiyama / Keiko Kondo / Takashi Nagata / Masato Katahira

Applied microbiology and biotechnology. 2018 Nov., v. 102, no. 22

2018

Abstract: Fungal glucuronoyl esterases (FGEs) catalyze cleavage of the ester bond connecting a lignin alcohol to the xylan-bound 4-O-methyl-D-glucuronic acid of glucuronoxylans. Thus, FGEs are capable of degrading lignin-carbohydrate complexes and have potential ... ...

Abstract	Fungal glucuronoyl esterases (FGEs) catalyze cleavage of the ester bond connecting a lignin alcohol to the xylan-bound 4-O-methyl-D-glucuronic acid of glucuronoxylans. Thus, FGEs are capable of degrading lignin-carbohydrate complexes and have potential for biotechnological applications toward woody biomass utilization. Therefore, identification and characterization of new FGEs are of critical importance. Firstly, in this study, we built a phylogenetic tree from almost 400 putative FGEs obtained on BLAST analysis and defined six main clades. In the phylogenetic tree, all the putative FGEs of ascomycetes cluster in clades I to IV, and most of the putative FGEs of basidiomycetes (B-FGEs) cluster in clades V to VI. Interestingly, several B-FGEs were found to cluster in clade II; most FGEs of clade II were found to have higher theoretical isoelectric points than those in the other five clades. To gain an insight into the putative FGEs in the clades that have not been characterized yet, we chose the FGEs of Ceriporiopsis subvermispora (CsGE) and Pleurotus eryngii (PeGE), which belong to clades V and II, respectively. The catalytic domains of both CsGE and PeGE were successfully expressed using Pichia pastoris, and then purified. Benzyl glucuronic acid was used as a substrate to confirm the activities of the CsGE and PeGE, and the hydrolyzed product, glucuronic acid, was quantified spectrophotometrically. Both CsGE and PeGE clearly exhibited the esterase activity. Additionally, we demonstrated that PeGE exhibits high tolerance toward several denaturing agents, which may make it a potentially more applicable enzyme.
Keywords	Ceriporiopsis subvermispora ; Pichia pastoris ; Pleurotus eryngii ; active sites ; alcohols ; biomass ; enzyme activity ; esterases ; fungi ; glucuronic acid ; hydrolysis ; isoelectric point ; lignin ; phylogeny
Language	English
Dates of publication	2018-11
Size	p. 9635-9645.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-018-9318-5
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA

Ryo Iwaoka / Takashi Nagata / Kengo Tsuda / Takao Imai / Hideyuki Okano / Naohiro Kobayashi / Masato Katahira

Molecules, Vol 22, Iss 7, p

2017 Volume 1207

Abstract: Musashi-1 (Msi1) controls the maintenance of stem cells and tumorigenesis through binding to its target mRNAs and subsequent translational regulation. Msi1 has two RNA-binding domains (RBDs), RBD1 and RBD2, which recognize r(GUAG) and r(UAG), ... ...

Abstract	Musashi-1 (Msi1) controls the maintenance of stem cells and tumorigenesis through binding to its target mRNAs and subsequent translational regulation. Msi1 has two RNA-binding domains (RBDs), RBD1 and RBD2, which recognize r(GUAG) and r(UAG), respectively. These minimal recognition sequences are connected by variable linkers in the Msi1 target mRNAs, however, the molecular mechanism by which Msi1 recognizes its targets is not yet understood. We previously determined the solution structure of the Msi1 RBD1:r(GUAGU) complex. Here, we determined the first structure of the RBD2:r(GUAGU) complex. The structure revealed that the central trinucleotide, r(UAG), is specifically recognized by the intermolecular hydrogen-bonding and aromatic stacking interactions. Importantly, the C-terminal region, which is disordered in the free form, took a certain conformation, resembling a helix. The observation of chemical shift perturbation and intermolecular NOEs, together with increases in the heteronuclear steady-state {1H}-15N NOE values on complex formation, indicated the involvement of the C-terminal region in RNA binding. On the basis of the two complex structures, we built a structural model of consecutive RBDs with r(UAGGUAG) containing both minimal recognition sequences, which resulted in no steric hindrance. The model suggests recognition of variable lengths (n) of the linker up to n = 50 may be possible.
Keywords	RNA-binding protein ; Msi1 ; solution structure determination ; protein-RNA complex ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2017-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Plastic roles of phenylalanine and tyrosine residues of TLS/FUS in complex formation with the G-quadruplexes of telomeric DNA and TERRA

Keiko Kondo / Tsukasa Mashima / Takanori Oyoshi / Ryota Yagi / Riki Kurokawa / Naohiro Kobayashi / Takashi Nagata / Masato Katahira

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 11

Abstract: Abstract The length of a telomere is regulated via elongation and shortening processes. Telomeric DNA and telomeric repeat-containing RNA (TERRA), which both contain G-rich repeated sequences, form G-quadruplex structures. Previously, translocated in ... ...

Abstract	Abstract The length of a telomere is regulated via elongation and shortening processes. Telomeric DNA and telomeric repeat-containing RNA (TERRA), which both contain G-rich repeated sequences, form G-quadruplex structures. Previously, translocated in liposarcoma (TLS) protein, also known as fused in sarcoma (FUS) protein, was found to form a ternary complex with the G-quadruplex structures of telomeric DNA and TERRA. We then showed that the third RGG motif of TLS, the RGG3 domain, is responsible for the complex formation. However, the structural basis for their binding remains obscure. Here, NMR-based binding assaying revealed the interactions in the binary and ternary complexes of RGG3 with telomeric DNA or/and TERRA. In the ternary complex, tyrosine bound exclusively to TERRA, while phenylalanine bound exclusively to telomeric DNA. Thus, tyrosine and phenylalanine each play a central role in the recognition of TERRA and telomeric DNA, respectively. Surprisingly in the binary complexes, RGG3 used both tyrosine and phenylalanine residues to bind to either TERRA or telomeric DNA. We propose that the plastic roles of tyrosine and phenylalanine are important for RGG3 to efficiently form the ternary complex, and thereby regulate the telomere shortening.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2018-02-01T00:00:00Z
Publisher	Nature Publishing Group
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Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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