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Article ; Online: Cloning, expression, and characterization of Baeyer-Villiger monooxygenases from eukaryotic Exophiala jeanselmei strain KUFI-6N.

Yamamoto, Taisei / Kobayashi, Kento / Hasegawa, Yoshie / Iwaki, Hiroaki

Bioscience, biotechnology, and biochemistry

2021 Volume 85, Issue 7, Page(s) 1675–1685

Abstract: The fungus Exophiala jeanselmei strain KUFI-6N produces a unique cycloalkanone monooxygenase (ExCAMO) that displays an uncommon substrate spectrum of Baeyer-Villiger oxidation of 4-10-membered ring ketones. In this study, we aimed to identify and ... ...

Abstract	The fungus Exophiala jeanselmei strain KUFI-6N produces a unique cycloalkanone monooxygenase (ExCAMO) that displays an uncommon substrate spectrum of Baeyer-Villiger oxidation of 4-10-membered ring ketones. In this study, we aimed to identify and sequence the gene encoding ExCAMO from KUFI-6N and overexpress the gene in Escherichia coli. We found that the primary structure of ExCAMO is most closely related to the cycloalkanone monooxygenase from Cylindrocarpon radicicola ATCC 11011, with 54.2% amino acid identity. ExCAMO was functionally expressed in E. coli and its substrate spectrum and kinetic parameters were investigated. Substrate profiling indicated that ExCAMO is unusual among known Baeyer-Villiger monooxygenases owing to its ability to accept a variety of substrates, including C4-C12 membered ring ketones. ExCAMO has high affinity and catalytic efficiency toward cycloalkanones, the highest being toward cyclohexanone. Five other genes encoding Baeyer-Villiger monooxygenases were also cloned and expressed in E. coli.
MeSH term(s)	Cloning, Molecular ; Enzyme Stability ; Escherichia coli/genetics ; Exophiala/enzymology ; Kinetics ; Mixed Function Oxygenases/chemistry ; Mixed Function Oxygenases/genetics ; Mixed Function Oxygenases/metabolism ; Molecular Weight ; Substrate Specificity ; Temperature
Chemical Substances	Mixed Function Oxygenases (EC 1.-)
Language	English
Publishing date	2021-05-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1106450-x
ISSN	1347-6947 ; 0916-8451
ISSN (online)	1347-6947
ISSN	0916-8451
DOI	10.1093/bbb/zbab079
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Article ; Online: Identification and characterization of a novel class of self-sufficient cytochrome P450 hydroxylase involved in cyclohexanecarboxylate degradation in Paraburkholderia terrae strain KU-64.

Yamamoto, Taisei / Hasegawa, Yoshie / Iwaki, Hiroaki

Bioscience, biotechnology, and biochemistry

2021 Volume 86, Issue 2, Page(s) 199–208

Abstract: Cytochrome P450 monooxygenases play important roles in metabolism. Here, we report the identification and biochemical characterization of P450CHC, a novel self-sufficient cytochrome P450, from cyclohexanecarboxylate-degrading Paraburkholderia terrae KU- ... ...

Abstract	Cytochrome P450 monooxygenases play important roles in metabolism. Here, we report the identification and biochemical characterization of P450CHC, a novel self-sufficient cytochrome P450, from cyclohexanecarboxylate-degrading Paraburkholderia terrae KU-64. P450CHC was found to comprise a [2Fe-2S] ferredoxin domain, NAD(P)H-dependent FAD-containing reductase domain, FCD domain, and cytochrome P450 domain (in that order from the N terminus). Reverse transcription-polymerase chain reaction results indicated that the P450CHC-encoding chcA gene was inducible by cyclohexanecarboxylate. chcA overexpression in Escherichia coli and recombinant protein purification enabled functional characterization of P450CHC as a catalytically self-sufficient cytochrome P450 that hydroxylates cyclohexanecarboxylate. Kinetic analysis indicated that P450CHC largely preferred NADH (Km = 0.011 m m) over NADPH (Km = 0.21 m m). The Kd, Km, and kcat values for cyclohexanecarboxylate were 0.083 m m, 0.084 m m, and 15.9 s-1, respectively. The genetic and biochemical analyses indicated that the physiological role of P450CHC is initial hydroxylation in the cyclohexanecarboxylate degradation pathway.
MeSH term(s)	Burkholderiaceae
Language	English
Publishing date	2021-12-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1106450-x
ISSN	1347-6947 ; 0916-8451
ISSN (online)	1347-6947
ISSN	0916-8451
DOI	10.1093/bbb/zbab199
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Article ; Online: Complete Genome Sequence of Mameliella alba Strain KU6B, a Cyclohexylamine-Utilizing Marine Bacterium.

Yamamoto, Taisei / Liu, Yaxuan / Hasegawa, Yoshie / Iwaki, Hiroaki

Microbiology resource announcements

2020 Volume 9, Issue 19

Abstract: Here, we report the complete genome sequence ... ...

Abstract	Here, we report the complete genome sequence of
Language	English
Publishing date	2020-05-07
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00273-20
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Article ; Online: Identification and characterization of a chc gene cluster responsible for the aromatization pathway of cyclohexanecarboxylate degradation in Sinomonas cyclohexanicum ATCC 51369.

Yamamoto, Taisei / Hasegawa, Yoshie / Lau, Peter C K / Iwaki, Hiroaki

Journal of bioscience and bioengineering

2021 Volume 132, Issue 6, Page(s) 621–629

Abstract: Cyclohexanecarboxylate (CHCA) is formed by oxidative microbial degradation of n-alkylcycloparaffins and anaerobic degradation of benzoate, and also known to be a synthetic intermediate or the starter unit of biosynthesis of cellular constituents and ... ...

Abstract	Cyclohexanecarboxylate (CHCA) is formed by oxidative microbial degradation of n-alkylcycloparaffins and anaerobic degradation of benzoate, and also known to be a synthetic intermediate or the starter unit of biosynthesis of cellular constituents and secondary metabolites. Although two degradation pathways have been proposed, genetic information has been limited to the β-oxidation-like pathway. In this study, we identified a gene cluster, designated chcC1XTC2B1B2RAaAbAc, that is responsible for the CHCA aromatization pathway in Sinomonas (formerly Corynebacterium) cyclohexanicum strain ATCC 51369. Reverse transcription-PCR analysis indicated that the chc gene cluster is inducible by CHCA and that it consists of two transcriptional units, chcC1XTC2B1B2R and chcAaAbAc. Overexpression of the various genes in Escherichia coli, and purification of the recombinant proteins led to the functional characterization of ChcAaAbAc as subunits of a cytochrome P450 system responsible for CHCA hydroxylation; ChcB1 and ChcB2 as trans-4-hydroxyCHCA and cis-4-hydroxyCHCA dehydrogenases, respectively; ChcC1 was identified as a 4-oxoCHCA desaturase containing a covalently bound FAD; and ChcC2 was identified as a 4-oxocyclohexenecarboxylate desaturase. The binding constant of ChcAa for CHCA was found to be 0.37 mM. Kinetic parameters established for ChcB1 indicated that it has a high catalytic efficiency towards 4-oxoCHCA compared to trans- or cis-4-hydroxyCHCA. The K
MeSH term(s)	Bacterial Outer Membrane Proteins ; Base Sequence ; Benzoates ; Escherichia coli/genetics ; Escherichia coli Proteins ; Genes, Bacterial ; Multigene Family
Chemical Substances	Bacterial Outer Membrane Proteins ; Benzoates ; Escherichia coli Proteins ; traN protein, E coli (147416-08-8)
Language	English
Publishing date	2021-09-25
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1465387-4
ISSN	1347-4421 ; 1389-1723
ISSN (online)	1347-4421
ISSN	1389-1723
DOI	10.1016/j.jbiosc.2021.08.013
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Article ; Online: Cloning of two gene clusters involved in the catabolism of 2,4-dinitrophenol by Paraburkholderia sp. strain KU-46 and characterization of the initial DnpAB enzymes and a two-component monooxygenases DnpC1C2.

Liu, Yaxuan / Yamamoto, Taisei / Kohaya, Nozomi / Yamamoto, Kota / Okano, Kenji / Sumiyoshi, Takaaki / Hasegawa, Yoshie / Lau, Peter C K / Iwaki, Hiroaki

Journal of bioscience and bioengineering

2023 Volume 136, Issue 3, Page(s) 223–231

Abstract: Little is currently known about the metabolism of the industrial pollutant 2,4-dinitrophenol (DNP), particularly among gram-negative bacteria. In this study, we identified two non-contiguous genetic loci spanning 22 kb of Paraburkholderia (formerly ... ...

Abstract	Little is currently known about the metabolism of the industrial pollutant 2,4-dinitrophenol (DNP), particularly among gram-negative bacteria. In this study, we identified two non-contiguous genetic loci spanning 22 kb of Paraburkholderia (formerly Burkholderia) sp. strain KU-46. Additionally, we characterized four key initial genes (dnpA, dnpB, and dnpC1C2) responsible for DNP degradation, providing molecular and biochemical evidence for the degradation of DNP via the formation of 4-nitrophenol (NP), a pathway that is unique among DNP utilizing bacteria. Reverse transcription polymerase chain reaction (PCR) analysis indicated that dnpA, which encodes the initial hydride transferase, and dnpB which encodes a nitrite-eliminating enzyme, were induced by DNP and organized in an operon. Moreover, we purified DnpA and DnpB from recombinant Escherichia coli to demonstrate their effect on the transformation of DNP to NP through the formation of a hydride-Meisenheimer complex of DNP, designated as H
MeSH term(s)	Mixed Function Oxygenases/genetics ; Mixed Function Oxygenases/metabolism ; 2,4-Dinitrophenol/metabolism ; Oxygenases/genetics ; Oxygenases/metabolism ; Cloning, Molecular ; Multigene Family ; Biodegradation, Environmental
Chemical Substances	Mixed Function Oxygenases (EC 1.-) ; 2,4-Dinitrophenol (Q13SKS21MN) ; Oxygenases (EC 1.13.-)
Language	English
Publishing date	2023-06-19
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1465387-4
ISSN	1347-4421 ; 1389-1723
ISSN (online)	1347-4421
ISSN	1389-1723
DOI	10.1016/j.jbiosc.2023.05.013
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Article: Identification and characterization of a chc gene cluster responsible for the aromatization pathway of cyclohexanecarboxylate degradation in Sinomonas cyclohexanicum ATCC 51369

Yamamoto, Taisei / Hasegawa, Yoshie / Lau, Peter C.K. / Iwaki, Hiroaki

The Society for Biotechnology, Japan Journal of bioscience and bioengineering. 2021 Dec., v. 132, no. 6

2021

Abstract	Cyclohexanecarboxylate (CHCA) is formed by oxidative microbial degradation of n-alkylcycloparaffins and anaerobic degradation of benzoate, and also known to be a synthetic intermediate or the starter unit of biosynthesis of cellular constituents and secondary metabolites. Although two degradation pathways have been proposed, genetic information has been limited to the β-oxidation-like pathway. In this study, we identified a gene cluster, designated chcC1XTC2B1B2RAaAbAc, that is responsible for the CHCA aromatization pathway in Sinomonas (formerly Corynebacterium) cyclohexanicum strain ATCC 51369. Reverse transcription-PCR analysis indicated that the chc gene cluster is inducible by CHCA and that it consists of two transcriptional units, chcC1XTC2B1B2R and chcAaAbAc. Overexpression of the various genes in Escherichia coli, and purification of the recombinant proteins led to the functional characterization of ChcAaAbAc as subunits of a cytochrome P450 system responsible for CHCA hydroxylation; ChcB1 and ChcB2 as trans-4-hydroxyCHCA and cis-4-hydroxyCHCA dehydrogenases, respectively; ChcC1 was identified as a 4-oxoCHCA desaturase containing a covalently bound FAD; and ChcC2 was identified as a 4-oxocyclohexenecarboxylate desaturase. The binding constant of ChcAa for CHCA was found to be 0.37 mM. Kinetic parameters established for ChcB1 indicated that it has a high catalytic efficiency towards 4-oxoCHCA compared to trans- or cis-4-hydroxyCHCA. The Kₘ and Kcₐₜ values of ChcC1 for 4-oxoCHCA were 0.39 mM and 44 s⁻¹, respectively. Taken together with previous work on the identification of a pobA gene encoding a 4-hydroxybenzoate hydroxylase, we have now localized the remaining set of genes for the final degradation of protocatechuate before entry into the tricarboxylic acid cycle.
Keywords	4-hydroxybenzoic acid ; Corynebacterium ; Escherichia coli ; aromatization ; biodegradation ; biosynthesis ; catalytic activity ; chemical bonding ; cytochrome P-450 ; hydroxylation ; multigene family ; oxidoreductases ; reverse transcriptase polymerase chain reaction ; secondary metabolites ; transcription (genetics) ; tricarboxylic acid cycle
Language	English
Dates of publication	2021-12
Size	p. 621-629.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1465387-4
ISSN	1347-4421 ; 1389-1723
ISSN (online)	1347-4421
ISSN	1389-1723
DOI	10.1016/j.jbiosc.2021.08.013
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Article ; Online: Complete Genome Sequence of

Yamamoto, Taisei / Hasegawa, Yoshie / Kawahara, Hidehisa / Iwaki, Hiroaki

Microbiology resource announcements

2019 Volume 8, Issue 45

Abstract: ... ...

Abstract	Pseudomonas
Language	English
Publishing date	2019-11-07
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.01204-19
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Article ; Online: A novel piperidine degradation mechanism in a newly isolated piperidine degrader Pseudomonas sp. strain KU43P.

Yamamoto, Taisei / Liu, Yaxuan / Sumiyoshi, Takaaki / Hasegawa, Yoshie / Iwaki, Hiroaki

The Journal of general and applied microbiology

2020 Volume 66, Issue 5, Page(s) 265–272

Abstract: The degradation pathways in microorganisms for piperidine, a secondary amine with various applications, are not yet fully understood, especially in non-Mycobacterium species. In this study, we have identified a piperidine-degrading isolate (KU43P) from a ...

Abstract	The degradation pathways in microorganisms for piperidine, a secondary amine with various applications, are not yet fully understood, especially in non-Mycobacterium species. In this study, we have identified a piperidine-degrading isolate (KU43P) from a soil sample collected in a cultivation field in Osaka, Japan, and characterized its mechanisms of piperidine degradation, thereby furthering current understanding of the process. The genome of isolate KU43P consists of a 5,869,691-bp circular chromosome with 62.67% GC content and with 5,294 predicted protein-coding genes, 77 tRNA genes, and 22 rRNA genes. 16S rRNA gene sequence analysis and average nucleotide identity analysis suggest that the isolate is a novel species of the Pseudomonas putida group in the genus Pseudomonas. The genomic region encoding the piperidine degradation pathway, designated as the pip gene cluster, was identified using transposon mutagenesis and reverse transcription polymerase chain reaction. Deletion analyses of pipA, which encodes a glutamine synthetase (GS)-like protein, and pipBa, which encodes a cytochrome P450 monooxygenase, indicate that pipA and pipBa are involved in piperidine metabolism and suggest that pipA is involved in the first step of the piperidine metabolic pathway. Escherichia coli whole cells overexpressing PipA converted piperidine and glutamate to γ-glutamylpiperidide, and crude cell extract enzyme assays of PipA showed that this reaction requires ATP and Mg
MeSH term(s)	Amide Synthases/genetics ; Amide Synthases/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Cytochrome P-450 Enzyme System/genetics ; Cytochrome P-450 Enzyme System/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Genome, Bacterial/genetics ; Metabolic Networks and Pathways ; Multigene Family ; Mutation ; Phylogeny ; Piperidines/metabolism ; Pseudomonas/classification ; Pseudomonas/genetics ; Pseudomonas/metabolism ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Transcription, Genetic
Chemical Substances	Bacterial Proteins ; Piperidines ; Recombinant Proteins ; piperidine (67I85E138Y) ; Cytochrome P-450 Enzyme System (9035-51-2) ; Amide Synthases (EC 6.3.1.-)
Language	English
Publishing date	2020-07-08
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.2019.11.006
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Article ; Online: HDAC6 inhibition enhances the anti-tumor effect of eribulin through tubulin acetylation in triple-negative breast cancer cells.

Oba, Takaaki / Ono, Mayu / Matoba, Hisanori / Uehara, Takeshi / Hasegawa, Yoshie / Ito, Ken-Ichi

Breast cancer research and treatment

2021 Volume 186, Issue 1, Page(s) 37–51

Abstract: Purpose: Improved prognosis for triple-negative breast cancer (TNBC) has plateaued and the development of novel therapeutic strategies is required. This study aimed to explore the anti-tumor effect of combined eribulin and HDAC inhibitor (vorinostat: ... ...

Abstract	Purpose: Improved prognosis for triple-negative breast cancer (TNBC) has plateaued and the development of novel therapeutic strategies is required. This study aimed to explore the anti-tumor effect of combined eribulin and HDAC inhibitor (vorinostat: VOR, pan-HDAC inhibitor and ricolinostat: RICO, selective HDAC6 inhibitor) treatment for TNBC. Methods: The effect of eribulin in combination with an HDAC inhibitor was tested in three TNBC cell lines (MDA-MB-231, Hs578T, and MDA-MB-157) and their eribulin-resistant derivatives. The expression of acetylated α-tubulin was analyzed by Western blotting for TNBC cells and immunohistochemical analyses for clinical specimens obtained from breast cancer patients who were treated with eribulin. Results: The simultaneous administration of low concentrations (0.2 μM) of VOR or RICO enhanced the anti-tumor effect of eribulin in MDA-MB-231 and Hs578T cells but not in MDA-MB-157 cells. Meanwhile, pretreatment with 5 μM of VOR or RICO enhanced eribulin sensitivity in all three cell lines. Low concentration of VOR or RICO increased acetylated α-tubulin expression in MDA-MB-231 and Hs578T cells. In contrast, whereas 5 μM of VOR or RICO increased the expression of acetylated α-tubulin in MDA-MB-157 cells, low concentrations did not. Eribulin increased the expression of acetylated α-tubulin in MDA-MB-231 and Hs578T cells but not in MDA-MB-157 cells. These phenomena were also observed in eribulin-resistant cells. Immunohistochemical analyses revealed that the expression of acetylated α-tubulin was increased after eribulin treatment in TNBC. Conclusions: HDAC6 inhibition enhances the anti-tumor effect of eribulin through the acetylation of α-tubulin. This combination therapy could represent a novel therapeutic strategy for TNBC.
MeSH term(s)	Acetylation ; Cell Line, Tumor ; Cell Proliferation ; Furans ; Histone Deacetylase 6/genetics ; Humans ; Ketones ; Triple Negative Breast Neoplasms/drug therapy ; Triple Negative Breast Neoplasms/genetics ; Tubulin/genetics
Chemical Substances	Furans ; Ketones ; Tubulin ; HDAC6 protein, human (EC 3.5.1.98) ; Histone Deacetylase 6 (EC 3.5.1.98) ; eribulin (LR24G6354G)
Language	English
Publishing date	2021-01-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-020-06033-2
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Article ; Online: Usefulness of Fractal Analysis of Kirsch Edge Images for the Tissue Fragment Inner Structure in Breast FNAB.

Yoshioka, Haruhiko / Shimoda, Tsubasa / Oikawa, Sota / Morohashi, Satoko / Hasegawa, Yoshie / Horie, Kayo / Watanabe, Jun

Acta cytologica

2021 Volume 66, Issue 2, Page(s) 149–158

Abstract: Objective: Recent advances in high-precision mammography and ultrasound screening have led to an increase in the detection of early lesions (ductal carcinoma in situ and small cancers) appearing as microcalcified lesions or microcystic images, and there ...

Abstract	Objective: Recent advances in high-precision mammography and ultrasound screening have led to an increase in the detection of early lesions (ductal carcinoma in situ and small cancers) appearing as microcalcified lesions or microcystic images, and there needs to be an improvement in the accuracy of breast fine-needle aspiration biopsy (FNAB) assessing these lesions. The objective of this study was to investigate whether fractal analysis of Kirsch edge images for the tissue fragment inner structure (FKT) is useful in breast FNAB. FKT measures tissue fragment chromasia of hyperchromatic crowded tissue fragments (HCG), tissue fragment shape unevenness, and tissue fragment inner structure complexity. Study Design Materials: Nineteen epithelial tissue fragments of fibroadenoma (FA) from 7 patients and 52 tissue fragments of invasive breast carcinoma of no special type (IBC-NST) (grade 1-2) from 11 patients were assessed. First, tissue fragments were classified into small (smaller than 60 × 102 μm2), medium, and large (100 × 102 μm2 or larger), and the appearance rate of each size was determined. Second, for FKT, the luminance value of tissue fragment chromasia, the unevenness and fractal value, and the tissue fragment inner structure complexity were determined. In statistical analysis, the Steel-Dwass test, nonlinear discriminant analysis, and receiver operating characteristic analysis were performed, setting the significance level at p < 0.05. Results: "Unevenness of the tissue fragment shape," "fractal value of the tissue fragment shape," and "fractal value of the tissue fragment inner structure" were significantly higher in small and large tissue fragments in IBC-NST compared with those in FA. The specificity and sensitivity were the highest (100%) in small tissue fragments in multivariate analysis using 4 variables ("luminance value of tissue fragment chromasia," "unevenness of tissue fragment shape," "fractal value of the tissue fragment shape," and "fractal value of the tissue fragment inner structure"). Conclusion: FKT, which evaluates "tissue fragment darkness," "tissue fragment shape unevenness," and "tissue fragment inner structure complexity" focusing on small tissue fragments of HCG in breast FNAB, is useful as a system that assists cytopathological assessment of breast FNAB.
MeSH term(s)	Biopsy, Fine-Needle/methods ; Breast/diagnostic imaging ; Breast/pathology ; Breast Neoplasms/pathology ; Female ; Fibroadenoma/diagnostic imaging ; Fibroadenoma/pathology ; Fractals ; Humans ; Sensitivity and Specificity
Language	English
Publishing date	2021-10-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	80003-x
ISSN	1938-2650 ; 0001-5547
ISSN (online)	1938-2650
ISSN	0001-5547
DOI	10.1159/000519490
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