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Article ; Online: Structural similarity of tailed phages and pathogenic bacterial secretion systems.

Kanamaru, Shuji

Proceedings of the National Academy of Sciences of the United States of America

2009 Volume 106, Issue 11, Page(s) 4067–4068

MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Bacteriophage T4/chemistry ; Bacteriophage lambda/chemistry ; Caudovirales/chemistry ; Gram-Negative Bacteria/pathogenicity ; Membrane Transport Proteins/metabolism ; Membrane Transport Proteins/physiology ; Protein Conformation ; Structural Homology, Protein ; Viral Proteins/chemistry
Chemical Substances	Bacterial Proteins ; Membrane Transport Proteins ; Viral Proteins
Language	English
Publishing date	2009-03-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0901205106
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Article ; Online: Cell-free protein crystallization for nanocrystal structure determination.

Abe, Satoshi / Tanaka, Junko / Kojima, Mariko / Kanamaru, Shuji / Hirata, Kunio / Yamashita, Keitaro / Kobayashi, Ayako / Ueno, Takafumi

Scientific reports

2022 Volume 12, Issue 1, Page(s) 16031

Abstract: In-cell protein crystallization (ICPC) has been investigated as a technique to support the advancement of structural biology because it does not require protein purification and a complicated crystallization process. However, only a few protein ... ...

Abstract	In-cell protein crystallization (ICPC) has been investigated as a technique to support the advancement of structural biology because it does not require protein purification and a complicated crystallization process. However, only a few protein structures have been reported because these crystals formed incidentally in living cells and are insufficient in size and quality for structure analysis. Here, we have developed a cell-free protein crystallization (CFPC) method, which involves direct protein crystallization using cell-free protein synthesis. We have succeeded in crystallization and structure determination of nano-sized polyhedra crystal (PhC) at a high resolution of 1.80 Å. Furthermore, nanocrystals were synthesized at a reaction scale of only 20 μL using the dialysis method, enabling structural analysis at a resolution of 1.95 Å. To further demonstrate the potential of CFPC, we attempted to determine the structure of crystalline inclusion protein A (CipA), whose structure had not yet been determined. We added chemical reagents as a twinning inhibitor to the CFPC solution, which enabled us to determine the structure of CipA at 2.11 Å resolution. This technology greatly expands the high-throughput structure determination method of unstable, low-yield, fusion, and substrate-biding proteins that have been difficult to analyze with conventional methods.
MeSH term(s)	Crystallization/methods ; Crystallography, X-Ray ; Indoles ; Nanoparticles ; Propionates ; Proteins/chemistry
Chemical Substances	Indoles ; Propionates ; Proteins ; 3-(2-carboxyindol-3-yl)propionic acid (31529-28-9)
Language	English
Publishing date	2022-10-03
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/s41598-022-19681-9
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Article ; Online: Structure and Function of the T4 Spackle Protein Gp61.3.

Kanamaru, Shuji / Uchida, Kazuya / Nemoto, Mai / Fraser, Alec / Arisaka, Fumio / Leiman, Petr G

Viruses

2020 Volume 12, Issue 10

Abstract: The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity- ...

Abstract	The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity-
MeSH term(s)	Bacteriophage T4/enzymology ; Bacteriophage T4/genetics ; Crystallography, X-Ray ; Escherichia coli/virology ; Genome, Viral/genetics ; Muramidase/antagonists & inhibitors ; Protein Conformation ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	Viral Proteins ; spackle protein, bacteriophage T4 ; Muramidase (EC 3.2.1.17)
Language	English
Publishing date	2020-09-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12101070
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Article: Structure and Function of the T4 Spackle Protein Gp61.3

Kanamaru, Shuji / Uchida, Kazuya / Nemoto, Mai / Fraser, Alec / Arisaka, Fumio / Leiman, Petr G

Viruses. 2020 Sept. 24, v. 12, no. 10

2020

Abstract: The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity—e and 5. Gene e encodes the well-known T4 lysozyme (commonly called T4L) that functions to break the peptidoglycan layer late in the infection cycle, which is ... ...

Abstract	The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity—e and 5. Gene e encodes the well-known T4 lysozyme (commonly called T4L) that functions to break the peptidoglycan layer late in the infection cycle, which is required for liberating newly assembled phage progeny. Gene product 5 (gp5) is the tail-associated lysozyme, a component of the phage particle. It forms a spike at the tip of the tail tube and functions to pierce the outer membrane of the Escherichia coli host cell after the phage has attached to the cell surface. Gp5 contains a T4L-like lysozyme domain that locally digests the peptidoglycan layer upon infection. The T4 Spackle protein (encoded by gene 61.3) has been thought to play a role in the inhibition of gp5 lysozyme activity and, as a consequence, in making cells infected by bacteriophage T4 resistant to later infection by T4 and closely related phages. Here we show that (1) gp61.3 is secreted into the periplasm where its N-terminal periplasm-targeting peptide is cleaved off; (2) gp61.3 forms a 1:1 complex with the lysozyme domain of gp5 (gp5Lys); (3) gp61.3 selectively inhibits the activity of gp5, but not that of T4L; (4) overexpression of gp5 causes cell lysis. We also report a crystal structure of the gp61.3-gp5Lys complex that demonstrates that unlike other known lysozyme inhibitors, gp61.3 does not interact with the active site cleft. Instead, it forms a “wall” that blocks access of an extended polysaccharide substrate to the cleft and, possibly, locks the enzyme in an “open-jaw”-like conformation making catalysis impossible.
Keywords	Escherichia coli ; active sites ; bacteriophages ; catalytic activity ; crystal structure ; enzyme activity ; enzyme inhibitors ; genes ; lysozyme ; peptides ; peptidoglycans ; progeny ; proteins ; viral morphology
Language	English
Dates of publication	2020-0924
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v12101070
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Heterogeneous IgE reactivities to Staphylococcus pseudintermedius strains in dogs with atopic dermatitis, and the identification of DM13-domain-containing protein as a bacterial IgE-reactive molecule.

Takemura-Uchiyama, Iyo / Tsurui, Hiroki / Shimakura, Hidekatsu / Nasukawa, Tadahiro / Imanishi, Ichiro / Uchiyama, Jumpei / Fukuyama, Tomoki / Sakamoto, Shuji / Morisawa, Keiko / Fujimura, Masato / Murakami, Hironobu / Kanamaru, Shuji / Kurokawa, Kenji / Kawamoto, Keiko / Iyori, Keita / Sakaguchi, Masahiro

FEMS microbiology letters

2022 Volume 369, Issue 1

Abstract: Staphylococcus pseudintermedius is one of the major pathogens causing canine skin infection. In canine atopic dermatitis (AD), heterogeneous strains of S. pseudintermedius reside on the affected skin site. Because an increase in specific IgE to this ... ...

Abstract	Staphylococcus pseudintermedius is one of the major pathogens causing canine skin infection. In canine atopic dermatitis (AD), heterogeneous strains of S. pseudintermedius reside on the affected skin site. Because an increase in specific IgE to this bacterium has been reported, S. pseudintermedius is likely to exacerbate the severity of canine AD. In this study, the IgE reactivities to various S. pseudintermedius strains and the IgE-reactive molecules of S. pseudintermedius were investigated. First, examining the IgE reactivities to eight strains of S. pseudintermedius using 141 sera of AD dogs, strain variation of S. pseudintermedius showed 10-63% of the IgE reactivities. This is different from the expected result based on the concept of Staphylococcus aureus clonality in AD patients. Moreover, according to the western blot analysis, there were more than four proteins reactive to IgE. Subsequently, the analysis of the common IgE-reactive protein at ∼15 kDa confirmed that the DM13-domain-containing protein was reactive in AD dogs, which is not coincident with any S. aureus IgE-reactive molecules. Considering these, S. pseudintermedius is likely to exacerbate AD severity in dogs, slightly different from the case of S. aureus in human AD.
MeSH term(s)	Animals ; Dermatitis, Atopic/microbiology ; Dermatitis, Atopic/veterinary ; Dogs ; Humans ; Immunoglobulin E/metabolism ; Staphylococcus/genetics ; Staphylococcus aureus/genetics
Chemical Substances	Immunoglobulin E (37341-29-0)
Language	English
Publishing date	2022-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1093/femsle/fnac019
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Article: Structural similarity of tailed phages and pathogenic bacterial secretion systems

Kanamaru, Shuji

Proceedings of the National Academy of Sciences of the United States of America. 2009 Mar. 17, v. 106, no. 11

2009

Language	English
Dates of publication	2009-0317
Size	p. 4067-4068.
Publishing place	National Academy of Sciences
Document type	Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Rapid and sensitive SARS-CoV-2 detection using a homogeneous fluorescent immunosensor Quenchbody with crowding agents.

Zhu, Bo / Nosaka, Nobuyuki / Kanamaru, Shuji / Dong, Jinhua / Dai, Yancen / Inoue, Akihito / Yang, Yinghui / Kobayashi, Kaori / Kitaguchi, Tetsuya / Iwasaki, Hiroshi / Koike, Ryuji / Wakabayashi, Kenji / Ueda, Hiroshi

The Analyst

2022 Volume 147, Issue 22, Page(s) 4971–4979

Abstract: Antigen tests for SARS-CoV-2 are widely used by the public during the ongoing COVID-19 pandemic, which demonstrates the societal impact of homogeneous immunosensor-related technologies. In this study, we used the PM Q-probe and Quenchbody technologies to ...

Abstract	Antigen tests for SARS-CoV-2 are widely used by the public during the ongoing COVID-19 pandemic, which demonstrates the societal impact of homogeneous immunosensor-related technologies. In this study, we used the PM Q-probe and Quenchbody technologies to develop a SARS-CoV-2 nucleocapsid protein (N protein) homogeneous immunosensor based on a human anti-N protein antibody. For the first time, we uncovered the crowding agent's role in improving the performance of the double-labeled Quenchbody, and the possible mechanisms behind this improvement are discussed. The 5% polyethylene glycol 6000 significantly improved both the response speed and sensitivity of SARS-CoV-2 Quenchbodies. The calculated limit of detection for recombinant N protein was 191 pM (9 ng mL
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/diagnosis ; Pandemics ; Biosensing Techniques ; Immunoassay ; Nucleocapsid Proteins
Chemical Substances	Nucleocapsid Proteins
Language	English
Publishing date	2022-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/d2an01051h
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Article: Protein interactions in the assembly of the tail of bacteriophage T4.

Arisaka, Fumio / Kanamaru, Shuji

Biophysical reviews

2013 Volume 5, Issue 2, Page(s) 79–84

Abstract: Protein interactions in the assembly of the baseplate have been investigated. The baseplate of the phage T4 tail consists of a hub and six wedges which surround the former. Both reversible and irreversible interactions were found. Reversible association ... ...

Abstract	Protein interactions in the assembly of the baseplate have been investigated. The baseplate of the phage T4 tail consists of a hub and six wedges which surround the former. Both reversible and irreversible interactions were found. Reversible association includes gp5 and gp27 (gp: gene product) which form a complex in a pH-dependent manner and gp18 polymerization, i.e. the tail sheath formation depends on the ionic strength. These reversible interactions were followed by irreversible or tight binding which pulls the whole association reaction to complete the assembly. The wedge assembly is strictly ordered which means that if one of the seven wedge proteins is missing, the assembly proceeds to that point and the remaining molecules stay non-associated. The strictly sequential assembly pathway is suggested to be materialized by successive conformational change upon binding, which can be shown by proteolytic probe.
Language	English
Publishing date	2013-04-24
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2486483-3
ISSN	1867-2469 ; 1867-2450
ISSN (online)	1867-2469
ISSN	1867-2450
DOI	10.1007/s12551-013-0114-2
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Article ; Online: A conserved Ctp1/CtIP C-terminal peptide stimulates Mre11 endonuclease activity.

Zdravković, Aleksandar / Daley, James M / Dutta, Arijit / Niwa, Tatsuya / Murayama, Yasuto / Kanamaru, Shuji / Ito, Kentaro / Maki, Takahisa / Argunhan, Bilge / Takahashi, Masayuki / Tsubouchi, Hideo / Sung, Patrick / Iwasaki, Hiroshi

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 11

Abstract: The Mre11-Rad50-Nbs1 complex (MRN) is important for repairing DNA double-strand breaks (DSBs) by homologous recombination (HR). The endonuclease activity of MRN is critical for resecting 5'-ended DNA strands at DSB ends, producing 3'-ended single-strand ... ...

Abstract	The Mre11-Rad50-Nbs1 complex (MRN) is important for repairing DNA double-strand breaks (DSBs) by homologous recombination (HR). The endonuclease activity of MRN is critical for resecting 5'-ended DNA strands at DSB ends, producing 3'-ended single-strand DNA, a prerequisite for HR. This endonuclease activity is stimulated by Ctp1, the
MeSH term(s)	Amino Acid Sequence ; Casein Kinase II/metabolism ; Conserved Sequence ; DNA Breaks, Double-Stranded ; DNA-Binding Proteins/metabolism ; Exodeoxyribonucleases/metabolism ; Peptides/metabolism ; Phosphorylation ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/metabolism
Chemical Substances	Ctp1 protein, S pombe ; DNA-Binding Proteins ; Peptides ; Schizosaccharomyces pombe Proteins ; Casein Kinase II (EC 2.7.11.1) ; Exodeoxyribonucleases (EC 3.1.-) ; Mre11 protein, S pombe (EC 3.1.-)
Language	English
Publishing date	2021-04-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2016287118
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Article: Molecular assembly and structure of the bacteriophage T4 tail.

Arisaka, Fumio / Yap, Moh Lan / Kanamaru, Shuji / Rossmann, Michael G

Biophysical reviews

2016 Volume 8, Issue 4, Page(s) 385–396

Abstract: The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to ...

Abstract	The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to the tail sheath that the tailfibers have been adsorbed by a host bacterium. This then triggers the sheath contraction. In order to understand the mechanism of assembly and conformational changes of the baseplate upon infection, we have determined the structure of an in vitro assembled baseplate through the three-dimensional reconstruction of cryo-electron microscopy images to a resolution of 3.8 Å from electron micrographs. The atomic structure was fitted to the baseplate structure before and after sheath contraction in order to elucidate the conformational changes that occur after bacteriophage T4 has attached itself to a cell surface. The structure was also used to investigate the protease digestion of the assembly intermediates and the mutation sites of the tail genes, resulting in a number of phenotypes.
Language	English
Publishing date	2016-11-05
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2486483-3
ISSN	1867-2469 ; 1867-2450
ISSN (online)	1867-2469
ISSN	1867-2450
DOI	10.1007/s12551-016-0230-x
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