Applied Molecular Microbiology Research Group


Publications (since 2015)


  • Kato S, Takashino M, Igarashi K, Kitagawa W. (2020) Isolation and genomic characterization of a proteobacterial methanotroph requiring lanthanides. Microbe Environ 35(1):ME19128. DIO=10.1264/jsme2.ME19128
  • Kato S, Terashima M, Yama A, Sato M, Kitagawa W, Kawasaki K, Kamagata Y. (2020) Improved Isolation of Uncultured Anaerobic Bacteria using Medium Prepared with Separate Sterilization of Agar and Phosphate. Microbe Environ 35(1):ME19060. DIO=10.1264/jsme2.ME19060
  • Yamamoto S, Kitagawa W, Nakano M, Asakura H, Iwabuchi E, Sone T, Asano K. (2020) Plasmid sequences of four large plasmids carrying antimicrobial resistance genes in Escherichia coli strains isolated from beef cattle in Japan. Microbiol Resour Announc 9(20). DOI=10.1128/MRA.00219-20
  • Umeno A, Sakashita M, Sugino S, Murotomi K, Okuzawa T, Morita N, Tomii K, Tsuchiya Y, Yamasaki K, Horie M, Takahara K, Yoshida Y. Comprehensive analysis of PPARg agonist activities of stereo-, regio-, and enantio-isomers of hydroxyoctadecadienoic acids. BIosci Rep, DOI=10.1042/BSR20193767.
  • Akiyama K, Fujisawa K, Kondo H, Netsu Y, Nishikawa K, Takata Y, Nakamura, Y, Kino Y, Ayukawa S, Yamamura M, Hayashi N, Tagawa Y, Nakashima N. (2020) MazF activation causes ACA sequence-independent and selective alterations in RNA levels in Escherichia coli. Arch Microbiol 202(1):105-114. DOI=10.1042/BSR20193767 
  • Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H. (2020) Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine. Sci Rep 10:3021. DOI=10.1038/s41598-020-59775-w
  • Usuki S, Yasutake Y, Tamura N, Tamura T, Tanji K, Saitoh T, Murai Y, Mikami D, Yuyama K, Monde K, Mukai K, Igarashi Y. (2020) Nrp1 is activated by konjac ceramide binding-induced structural rigidification of the a1a2 domain. Cells 9(2):517. DOI=10.3390/cells9020517
  • Mie Y, Yasutake Y, Takayama H, Tamura T. (2020) Electrochemically boosted cytochrome P450 reaction that efficiently produces 25-hydroxyvitamin D3. J Catal 384:30-36. DOI=10.1016/j.jcat.2020.02.012
  • Kan E, Katsuyama Y, Maruyama JI, Tamano K, Koyama Y, Ohnishi Y. (2020) Efficient heterologous production of atrochrysone carboxylic acid-related polyketides in an Aspergillus oryzae host with enhanced malonyl-coenzyme A supply. J Gen Appl Microbiol (in press).
  • Chintagavongse N, Yoneda T, Ming-Hsuan C, Hayakawa T, Wakamatsu JI, Tamano K, Kumura H. (2020) Attempt at the adjunctive use of solid-state culture products and its freeze-dried powder from Aspergillus sojae for semihard cheese. J Sci Food Agric (in press)
  • 2019

  • ​​​​​​Yasutake Y, Hattori SI, Tamura N, Matsuda K, Kohgo S, Maeda K, Mitsuya H. (2019) Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4ʹ-modified nucleoside RT inhibitors. Biochem Biophys Res Commun 509(4):943-948. 
  • Tamano K, Kuninaga M, Kojima N, Umemura M, Machida M, Koike H. (2019) Use of the kojA promoter, involved in kojic acid biosynthesis, for polyketide production in Aspergillus oryzae: implications for long-term production. BMC Biotechnol 19(1):70.
  • Tamano K, Cox RS 3rd, Tsuge K, Miura A, Itoh A, Ishii J, Tamura T, Kondo A, Machida M. (2019) Heterologous production of free dihomo-γ-linolenic acid by Aspergillus oryzae and its extracellular release via surfactant supplementation. J Biosci Bioeng 127(4):451-457.
  • Saito Y, Kitagawa W, Kumagai T, Tajima N, Nishimiya Y, Tamano K, Yasutake Y, Tamura T, Kameda T. (2019) Developing a codon optimization method for improved expression of recombinant proteins in actinobacteria. Sci Rep 9:8338.
  • Mie Y, Yasutake Y, Ikegami M, Tamura T. (2019) Anodized gold surface enables mediator-free and low-overpotential electrochemical oxidation of NADH: A facile method for the development of an NAD+-dependent enzyme biosensor. Sensor Actuat B-Chem 288:512-518.
  • Yoshida K, Konishi K, Magana-Mora A, Rougny A, Yasutake Y, Muramatsu S, Murata S, Kumagai T, Aburatani S, Sakasegawa S, Tamura T. (2019) Production of recombinant extracellular cholesterol esterase using consistently active promoters in Burkholderia stabilis. Biosci Biotechnol Biochem 83(10):1974-1984.
  • Kan E, Katsuyama Y, Maruyama JI, Tamano K, Koyama Y, Ohnishi Y. (2019) Production of the plant polyketide curcumin in Aspergillus oryzae: strengthening malonyl-CoA supply for yield improvement. Biosci Biotechnol Biochem 83(7):1372-1381.
  • Itoh H, Miura A, Takeda I, Matsui M, Tamano K, Machida M, Shibata T. (2019) Search for transcription factors affecting productivity of the polyketide FR901512 in filamentous fungal sp. No. 14919 and identification of Drf1, a novel negative regulator of the biosynthetic gene cluster. Biosci Biotechnol Biochem 83(6):1163-1170.
  • Kato S, Wada K, Kitagawa W, Mayumi D, Ikarashi M, Sone T, Asano K, Kamagata Y. (2019) Conductive iron oxides promote methanogenic acetate degradation by microbial communities in a high-temperature petroleum reservoir. Microbe Environ 34(1):95-98.
  • Yoshida K, Kitagawa W, Ishiya K, Mitani Y, Nakashima N, Aburatani S, Tamura T. (2019) Genome sequence of Rhodococcus erythropolis type strain JCM 3201. Microbiol Resour Announc 8(14):e01730-18.
  • Haga, S, Yimin, Yamaki H, Jin S, Sogon T, Morita N, Ozaki M. (2019) Extracts of bilberry (Vaccinium myrtillus L.) fruits improve liver steatosis and injury in mice by preventing lipid accumulation and cell death. Biosci Biotechnol Biochem 83(11): 2110-2120.
  • Makino M, Sahara T, Morita N, Ueno H. (2019) Carboxypeptidase Y activity and maintenance is modulated by a large helical structure. FEBS Open Bio 9(7): 1337-1343.
  • Kato S, Tobe H, Matsubara H, Sawada M, Sasaki Y, Fukiya S, Morita N, Yokota A. (2019) The membrane phospholipid cardiolipin plays a pivotal role in bile acid adaptation by Lactobacillus gasseri JCM1131T. Biochim Biophys Acta 1864(3): 403-412.
  • 2018

  • Usuki S, Tamura N, Yuyama K, Tamura T, Mukai K, Igarashi Y. (2018) Konjac ceramide (kCer) regulates NGF-induced neurite outgrowth via the Sema3A signaling pathway. J Oleo Sci 67(1):77-86.
  • Usuki S, Tamura N, Yuyama K, Tamura T, Mukai K, Igarashi Y. (2018) Characterization of konjac ceramide (kCer) binding to Sema3A receptor Nrp1. J Oleo Sci 67(1):87-94.
  • Yasutake Y, Hattori S, Hayashi H, Matsuda K, Tamura N, Kohgo S, Maeda K, Mitsuya H. (2018) HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir. Sci Rep 8:1624.
  • Itoh H, Miura A, Matsui M, Arazoe T, Nishida K, Kumagai T, Arita M, Tamano K, Machida M, Shibata T. (2018) Knockout of the SREBP system increases production of the polyketide FR901512 in filamentous fungal sp. No. 14919 and lovastatin in Aspergillus terreus ATCC20542. Appl Microbiol Biotechnol 102(3):1393-1405.
  • Nakashima N, Tamura T. (2018) Whole-Genome Sequence of Acetobacter orientalis Strain FAN1, Isolated from Caucasian Yogurt. Genome Announc 6(13):e00201-18.
  • Kato S, Yamagishi A, Daimon S, Kawasaki K, Tamaki H, Kitagawa W, Abe A, Tanaka M, Sone T, Asano K, Kamagata Y. (2018) Isolation of previously uncultured slow-growing bacteria by using a simple modification in the preparation of agar media. Appl Environ Microbiol 84(19):e00807-18.
  • Kitagawa W, Mitsuhashi S, Hata M, Tamura T. (2018) Identification of a novel bacteriocin-like protein and structural gene from Rhodococcus erythropolis JCM 2895, using suppression-subtractive hybridization. J Antibiot (Tokyo), 71(10):872-879.
  • Yoshida K, Yasutake Y, Tamura T. (2018) Complete genome sequence of an efficient vitamin D3-hydroxylating bacterium, Pseudonocardia autotrophica NBRC 12743. Microbiol Resourc Announc 7(12): e01105-18.
  • Yamamoto R, Minami H, Matsusaki H, Sakashita M, Morita N, Nishimiya O, Tsutsumi N, Hosokawa M, Itabashi Y, Matsui T, Ura K. (2018) Consumption of the edible sea urchin Mesocentrotus nudus attenuates body weight gain and hepatic lipid accumulation in mice. J Func Foods 47: 40-47.
  • Haga S, Kanno H, Ozawa T, Morita N, Asano M, Ozaki M. (2018) Detection of necroptosis in ligand-mediated and hypoxia-induced injury of hepatocytes using a novel optic probe detecting receptor-interacting protein (RIP)1/RIP3 binding. ncol Res 26(3): 503-513.
  • Haga S, Ozawa T, Morita N, Asano M, Jin S, Yimin, Ozaki M. (2019) A photo-activatable Akt probe - A new tool to study Akt-dependent physio-pathology of cancer cells. Oncol Res 26(3): 467-472.
  • 2017

  • Kasuga K, Sasaki A, Matsuo T, Yamamoto C, Minato Y, Kuwahara N, Fujii C, Kobayashi M, Agematsu H, Tamura T, Komatsu M, Ishikawa J, Ikeda H, Kojima I. (2017) Heterologous production of kasugamycin, an aminoglycoside antibiotic from Streptomyces kasugaensis, in Streptomyces lividans and Rhodococcus erythropolis L-88 by constitutive expression of the biosynthetic gene cluster. Appl Microbiol Biotechnol 101(10):4259-4268.
  • Yasutake Y, Kameda T, Tamura T. (2017) Structural insights into the mechanism of the drastic changes in enzymatic activity of the cytochrome P450 vitamin D3 hydroxylase (CYP107BR1) caused by a mutation distant from the active site. Acta Crystallogr Sect F 73(5):266-275.
  • Konishi K, Kumagai T, Sakasegawa S, Tamura T. (2017) Complete genome sequence of Burkuhorderia stabilis FERMP-21014. Genome Announcements 5(29):e00636-17.
  • Yasutake Y, Kusada H, Ebuchi T, Hanada S, Kamagata Y, Tamura T, Kimura N. (2017) Bifuncrional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides. Sci Rep 7:8946.
  • Mohd Yusoff MZ, Akita H, Hassan MA, Fujimoto S, Yoshida M, Nakashima N, Hoshino T. (2017) Production of acetoin from hydrothermally pretreated oil mesocarp fiber using metabolically engineered Escherichia coli in a bioreactor system. Bioresour Technol 245(Pt A):1040-1048.
  • Akita H, Kimura ZI, Yusoff MZM, Nakashima N, Hoshino T. (2017) Identification and characterization of Burkholderia multivorans CCA53. BMC Res Notes 10(1):249.
  • Akita H, Nakashima N, Hoshino T. (2017) Production of d-lactate using a pyruvate-producing Escherichia coli strain. Biosci Biotechnol Biochem 81(7):1452-1455.
  • Tamano K, Miura A, Koike H, Kamisaka Y, Umeura M, Machida M. (2017) High-efficiency extracellular release of free fatty acids from Aspergillus oryzae using non-ionic surfactants. J Biotechnol 248:9-14.
  • Matsui M, Yokoyama T, Nemoto K, Kumagai T, Tamano K, Machida M, Shibata T. (2017) Further enhancement of FR901469 productivity by co-overexpression of cpcA, a cross-pathway control gene, and frbF in fungal sp. No. 11243. J Biosci Bioeng 124(1):8-14.
  • Kato S, Kanata Y, Kitagawa W, Sone T, Asano K, Kamagata Y. (2017) Restoration of the growth of Escherichia coli under K+-deficient conditions by Cs+ incorporation via the K+ transporter Kup. Sci Rep 7:1965.
  • Matsui M, Yokoyama T, Nemoto K, Kumagai T, Terai G, Tamano K, Machida M, Shibata T. (2017) Identification of a putative FR901469 biosynthesis gene cluster in fungal sp. No. 11243 and enhancement of the productivity by overexpressing the transcription factor gene frbF. J Biosci Bioeng. 123(2):147-153.
  • Adachi T, Sahara T, Okuyama H, Morita N. (2017) Glass bead-based genetic transformation: An efficient method for transformation of thraustochytrid microorganisms. J Oleo Sci 66(7): 791-795.
  • 2016

  • Tamano K, Miura A. (2016) Further increased production of free fatty acids by overexpressing a predicted transketolase gene of the pentose phosphate pathway in Aspergillus oryzae faaA disruptant. Biosci Biotechnol Biochem 80(9):1829-1835.
  • Kato S, Goya E, Tanaka M, Kitagawa W, Kikuchi Y, Asano K, Kamagata Y. (2016) Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion. Sci Rep 6:20041.
  • Usuki S, Tamura N, Sakai A, Tamura T, Mukai K, Igarashi Y. (2016) Chemoenzymatically prepared konjac ceramide inhibits NGF-induced neurite outgrowth by a semaphoring 3A-like action. Biochem Biophys Rep 5:160-167.
  • Akita H, Nakashima N, Hoshino T. (2016) Pyruvate production using engineered Escherichia coli. AMB Express 6(1):94.
  • Akita H, Kimura Z, Yusoff MZ, Nakashima N, Hoshino T. (2016) Draft genome sequence of Burkholderia sp. Strain CCA53, isolated from leaf soil. Genome Announc 4(4):e00630-16.
  • Akita H, Kimura Z, Mohd Yusoff MZ, Nakashima N, Hoshino T. (2016) Isolation and characterization of Burkholderia sp. strain CCA53 exhibiting ligninolytic potential. Springerplus 5:596.
  • Nakamura Y, Yamamoto N, Kino Y, Yamamoto N, Kamei S, Mori H, Kurokawa K, Nakashima N. (2016) Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities. Appl Microbiol Biotechnol 100(16):7263-7279.
  • Morita N, Haga S, Ohmiya Y, Ozaki M. (2016) Long-term ex vivo and in vivo monitoring of tumor progression by using dual luciferases. Anal Biochem 497: 24-26.
  • Yoshida K, Hashimoto M, Hori R, Adachi T, Okuyama H, Orikasa Y, Nagamine T, Shimizu S, Ueno A, Morita N. (2016) Bacterial long-chain polyunsaturated fatty acids: Their biosynthetic genes, functions, and practical use. Marine Drugs 14(5): 94.
  • Okuda T, Morita N. (2016) A very low carbohydrate ketogenic diet increases hepatic glycosphingolipids related to regulation of insulin signaling. J Func Foods 21: 70-74.
  • 2015

  • Tamano K, Bruno KS, Koike H, Ishii T, Miura A, Umemura M, Culley DE, Baker SE, Machida M. (2015) Increased production of free fatty acids in Aspergillus oryzae by disruption of a predicted acyl-CoA synthetase gene. Appl Microbiol Biotechnol. 99(7):3103-3113.
  • Matsumoto Y, Yasutake Y, Takeda Y, Tamura T, Yokota A, Wada M. (2015) Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and of D-erythro-3-hydroxyaspartate. Appl Microbiol Biotechnol 99(17):7137-7150.
  • Nakamura A, Tamura N, Yasutake Y. (2015) Structure of the HIV-1 reverse transcriptase Q151M mutant: insights into the inhibitor resistance of HIV-1 reverse transcriptase and the structure of the nucleotide-binding pocket of Hepatitis B virus polymerase. Acta Crystallogr Sect F 71(11):1384-1390.
  • Puspita ID, Kitagawa W, Kamagata Y, Tanaka M, Nakatsu CH. (2015) Increase in bacterial colony formation from a permafrost ice wedge dosed with a Tomitella biformata recombinant resuscitation-promoting factor protein. Microbes Environ 30(2):151-156.
  • Ohbayashi T, Takeshita K, Kitagawa W, Nikoh N, Koga R, Meng XY, Tago K, Hori T, Hayatsu M, Asano K, Kamagata Y, Lee BK, Fukatsu T, Kikuchi Y. (2015) Insect’s intestinal organ for symbiont sorting. Proc Natl Acad Sci USA 112(37):E5179-E5188.
  • Akita H, Watanabe M, Suzuki T, Nakashima N, Hoshino T. (2015) Molecular cloning and characterization of two YGL039w genes encoding broad specificity NADPH-dependent aldehyde reductases from Kluyveromyces marxianus strain DMB1. FEMS Microbiol Lett 362(16):fnv116.
  • Akita H, Watanabe M, Suzuki T, Nakashima N, Hoshino T. (2015) Characterization of the Kluyveromyces marxianus strain DMB1 YGL157w gene product as a broad specificity NADPH-dependent aldehyde reductase. AMB Express 5:17.
  • Akita H, Nakashima N, Hoshino T. (2015) Bacterial production of isobutanol without expensive reagents. Appl Microbiol Biotechnol 99(2):991-999.
  • Kanno M, Katayama T, Morita N, Tamaki H, Hanada S, Kamagata Y. (2015) Catenisphaera adipatacumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester. Int J Syst Evol Microbiol 65(3): 805-810.

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*About BPRI

Bioproduction Research Institute

AIST Hokkaido
2-17-2-1, Tsukisamu-Higashi,
Toyohira Ward, Sapporo City,
Hokkaido, 062-8517 Japan
AIST Tsukuba Central 6
Central 6,1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan