JAPANESE SITEMAP
@Actinomycetes such as Streptomyces genus, Actinoplanes genus and so on, are Gram-positive filamentous bacteria that are well-known for producing a vast array of bioactive compounds, including more than 70% of commercially important antibiotics. The antibiotic production by these organisms is regulated by a variety of physiological and nutritional conditions and is coordinated with processes of morphological differentiation. However, although the commercial importance of antibiotics has led to many years of research, the overall regulatory pathway governing antibiotic production remains obscure.
Elucidation of regulatory and biosynthetic pathway at molecular level provides clues to make a high-producer strain and create novel compounds by genetic engineering. The purpose of this study is to isolate useful actinomycetes strains that produce new bioactive compounds and to know the biosynthetic mechanisms.




  • Deciphering regulatory networks for secondary metabolism in streptomycetes
  • Discovery of novel compounds by awakening the cryptic secondary metabolism in actinomycetes
  • Screening natural products of endophytic and marine actinomycetes
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*Dian Anggraini SUROTO Researcher Indonesia
*Shizuka KAWAKAMI Technical Assistant
*Ivy Grace Umadhay PAIT PhD student (E) Philippines
*Nguyen Bich THAO PhD student (E) Vietnam
*Nindya Resha PRAMESTI Master student (E) Indonesia
*Shohei UEDA PhD student
*Kouhei OGURA Master student
*Takuya WAKAMATSU Master student
*Takuya YOSHIOKA Master student
*Hiroki NODA Master student
*Dai HAMAMOTO Master student
*Yukinori IKEJIRI Master student
*Ryo TAKAHASHI Master student
*Mayuko HIROTA Master student
*Eemaan MEMON Undergaraduate Pakistan
*Natsuki IKEHATA Undergaraduate
*Takayuki UENO Undergaraduate
*Yuri NISHIMOTO Undergaraduate
*Nozomi MATSUSHIMA Undergaraduate
*Masahisa YAMADA Undergaraduate
July 2017
(E): Biotechnology Global Human Resource Development Program @ @
@ @ @
Past Group Members (non-Japanese)
*Suandi Pratama SULTAN PhD student (2016) Indonesia
*Poungsombat PHORNPHATCHARANAN Master student (UNESCO school)(2016) Thailand
*Yohanes Novi KURNIAWAN PhD student (2015) Indonesia
*Neng Tanty SOFYANA Master student (2015) Indonesia
*Nutthanit THUMRONGSIRI Master student (UNESCO school) (2015) Thailand
*Ratama Daduang PhD student (2015) Thailand
*Fitria NINGSIH PhD student (2014) Indonesia
*Mario Rovani HENDRIYANTO Master student (2013) Indonesia
*Aiyada AROONSRI PhD studnet (2012) Thailand
*Dr. Dana ULANOVA JSPS Postdoctoral Fellow (2011) Russia
*Farah Wahidah ROSLAN Master student (2011) Malaysia
*Floris van EERDEN Frontier Lab student (2010) Netherland
*Jirawas SORNKOM Frontier Lab student (2010) Thailand
*Yong Jik LEE PhD student (2010) Korea
*Pauline Angelic ROXAS Frontier Lab student (2009) Philippine
*Jirayut EUABIRASETR Frontier Lab student (2008) Thailand
*Akkaraphol SRICHAISUPAKIT Frontier Lab student (2008) Thailand
*Anna BUJKO OUSSEP student (2007) Poland
*Apichaya ANEKSAMPANT Exchange student (2007) Thailand
*Su Jin KANG Master student (2007) Korea
*Nai Hua HSIAO Exchange student (2007) Taiwan (Netherland)
*Nattika PULSAWAT PhD student (2007) Thailand
*Jelger LYCKLAMA Exchange student (2006) Netherland
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Recent publications (2003-2017)
Presentation of international conference (2003-2010)
*: Citation Index (March 2015)
Kitani S, Ueguchi T, Igarashi Y, Leetanasaksakul K, Thamchaipenet A, and Nihira T. (*0)
Rakicidin F, a new antibacterial cyclic depsipeptide from a marine sponge-derived Streptomyces sp.
J Antibiot (Tokyo). 2017 [PubMed]
Suroto DA, Kitani S, Miyamoto KT, Sakihama Y, Arai M, Ikeda H, and Nihira T. (*0)
Activation of cryptic phthoxazolin A production in Streptomyces avermitilis by the disruption of autoregulator-receptor homologue AvaR3.
J Biosci Bioeng. 2017 [PubMed]
Thao NB, Kitani S, Nitta H, Tomioka T, and Nihira T. (*0)
Discovering potential Streptomyces hormone producers by using disruptants of essential biosynthetic genes as indicator strains.
J Antibiot (Tokyo). 2017 [PubMed]
Pait IGU, Kitani S, Kurniawan YN, Maeda A, Iwai T, Ikeda H, and Nihira T. (*0)
Identification and characterization of lbpA, an indigoidine biosynthetic gene in the -butyrolactone signaling system of Streptomyces lavendulae FRI-5.
J Biosci Bioeng. 2017 [PubMed]
Sultan SP, Kitani S, Miyamoto KT, Iguchi H, Atago T, Ikeda H, and Nihira T. (*0)
Characterization of AvaR1, a butenolide-autoregulator receptor for biosynthesis of a Streptomyces hormone in Streptomyces avermitilis.
Appl Microbiol Biotechnol. 121:372-9. 2016 [PubMed]
Kurniawan YN, Kitani S, Iida A, Maeda A, Nijeholt JLA, Lee YJ, and Nihira T. (*0)
Regulation of production of the blue pigment indigoidine by the pseudo -butyrolactone receptor FarR2 in Streptomyces lavendulae FRI-5.
J Biosci Bioeng. 121:372-9. 2016 [PubMed]
Kitani S.
Deciphering regulatory mechanisms for antibiotic production by Streptomyces hormones.
Actinomycetologica. 29:10-7. 2015 [Publisher site]
Intra B, Euanorasetr J, Nihira T, Panbangred W. (*0)
Characterization of a -butyrolactone synthetase gene homologue (stcA) involved in bafilomycin production and aerial mycelium formation in Streptomyces sp. SBI034.
Appl Microbiol Biotechnol. 2015 [PubMed]
Daduang R, Kitani S, Hashimoto J, Thamchaipenet A, Igarashi Y, Shin-ya K, Ikeda H, and Nihira T. (*0)
Characterization of the biosynthetic gene cluster for maklamicin, a spirotetronate-class antibiotic of the endophytic Micromonospora sp. NBRC 110955.
Microbiological Res. 180:30-9. 2015 [PubMed]
Daduang R, Kitani S, Sudoh Y, Pait IGU, Thamchaipenet A, Ikeda H, Igarashi Y, and NihiraT. (*0)
29-Deoxymaklamicin, a new maklamicin analogue produced by a genetically engineered strain of Micromonospora sp. NBRC 110955.
J Biosci Bioeng. 120:608-13. 2015 [PubMed]
Kurniawan YN, Kitani S, Maeda A, and Nihira T. (*1)
Differential contributions of two SARP family regulatory genes to indigoidine biosynthesis in Streptomyces lavendulae FRI-5.
Appl Microbiol Biotechnol. 98:9713-21. 2014 [PubMed]
Choi SU and and Nihira T. (*0)
Characterization of intergeneric conjugation and attB site for molecular genetic studies of Streptomyces scabies ATCC 23962.
J Pure Appl Microbio. 8:1783-9. 2014 [Publisher site]
Yu L, Oikawa T, Kitani S, Nihira T, Bayanmunkh B, Panbangred W, and Igarashi Y. (*0)
Jomthonic acids B and C, two new modified amino acids from Streptomyces sp.
J Antibiot (Tokyo). 67:345-7. 2014 [PubMed]
Ulanova D, Kitani S, Fukusaki E, and Nihira T. (*1)
SdrA, a new DeoR family regulator involved in Streptomyces avermitilis morphological development and antibiotic production.
Appl Environ Microbiol. 79:7916-21. 2013 [PubMed]
Kitani S, Tomio A, Srichaisupakit A, Daduang R, Intra B, Panbangred W, Oku N, Igarashi Y, Nihira T. (*0)
Sarmentosamide, a novel hexadienamide from Thai soil actinomycetes.
Nat Prod Res. 27:226-31. 2013 [PubMed]
Aroonsri A, Kitani S, Hashimoto J, Kosone I, Izumikawa M, Komatsu M, Fujita N, Takahashi Y, Shin-ya K, Ikeda H, and Nihira T. (*2)
Pleiotropic control of secondary metabolism and morphological development by KsbC, a butyrolactone-autoregulator receptor homologue in Kitasatospora setae.
Appl Environ Microbiol. 78:8015-24. 2012 [PubMed]
Igarashi Y, Yu L, Ikeda M, Oikawa T, Kitani S, Nihira T, Bayanmunkh B, Panbangred W. (*2)
Jomthonic acid A, a modified amino acid from a soil-derived Streptomyces.
J Nat Prod. 75:986-90. 2012 [PubMed]
Aroonsri A, Kitani S, Ikeda H, and Nihira T. (*2)
Kitasetaline, a novel -carboline alkaloid from Kitasatospora setae NBRC 14216T.
J Biosci Bioeng. 114:56-8. 2012 [PubMed]
Igarashi Y, Tanaka Y, Ikeda M, Oikawa T, Kitani S, Nihira T, Mongkol P, Janhom M, and Panbangred W. (*2)
Prajinamide, a new modified peptide from a soil-derived Streptomyces.
J Antibiot (Tokyo). 65:157-9. 2012 [PubMed]
Uchida M, Takamatsu S, Arima S, Miyamoto KT, Kitani S, Nihira T, Ikeda H, and Nagamitsu T. (*2)
Total synthesis and absolute configuration of avenolide, extracellular factor in Streptomyces avermitilis.
J Antibiot (Tokyo). 64:781-87.2011 [PubMed]
Kitani S, Miyamoto KT, Takamatsu S, Herawati E, Iguchi H, Nishitomi K, Uchida M, Nagamitsu T, Omura S, Ikeda H, and Nihira T. (*23)
Avenolide, a Streptomyces hormone controlling antibiotic production in Streptomyces avermitilis.
Proc Natl Acad Sci U S A. 108:16410-5.2011 [PubMed]
Ningsih F, Kitani S, Fukushima E, and Nihira T. (*4)
VisG is essential for biosynthesis of virginiamycin S, a streptogramin type B antibiotic, as a provider of the nonproteinogenic amino acid phenylglycine.
Microbiology 157:3213-20.2011 [PubMed]
Miyamoto KT, Kitani S, Komatsu M, Ikeda H, and Nihira T. (*10)
The autoregulator-receptor homologue AvaR3 plays a regulatory role in antibiotic production, mycelial aggregation and colony development of Streptomyces avermitilis.
Microbiology 157:2257-65.2011 [PubMed]
Kitani S, Yamauchi T, Fukushima E, Lee CK, Ningsih F, Kinoshita H, and Nihira T. (*0)
Characterization of varM encoding type II ABC transporter in Streptomyces virginiae, a virginiamycin M1 producer.
Actinomycetologica 24:51-57. 2010 [Publisher site]
Ichikawa N, Oguchi A, Ikeda H, Ishikawa J, Kitani S, Watanabe Y, Nakamura S, Katano Y, Kishi E, Sasagawa M, Ankai A, Fukui S, Hashimoto Y, Kamata S, Otoguro M, Tanikawa S, Nihira T, Horinouchi S, Ohnishi Y, Hayakawa M, Kuzuyama T, Arisawa A, Nomoto F, Miura H, Takahashi Y, and Fujita N. (*21)
Genome sequence of Kitasatospora setae NBRC 14216T; an evolutionary snapshot of the family Streptomycetaceae.
DNA Res. 17:393-406.2010 [PubMed]
Igarashi Y, Shimasaki R, Miyanaga S, Oku N, Onaka H, Sakurai H, Saiki I, Kitani S, Nihira T, Panbangred W, and Wimonsiravude W. (*8)
Rakicidin D, an inhibitor of tumor cell invasion from marine-derived Streptomyces sp.
J Antibiot (Tokyo). 63:563-5. 2010 [PubMed]
Yoon YH, Kawai F, Sugiyama K, Park SY, Nihira T, Choi SU, and Hwang YI. (*0)
Crystallization and preliminary crystallographic studies of the butyrolactone autoregulator receptor protein (BarA) from Streptomyces virginiae.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 66:662-4. 2010 [PubMed]
Kitani S, Doi M, Shimizu T, Maeda A, and Nihira T. (*8)
Control of secondary metabolism by farX, which is involved in the -butyrolactone biosynthesis of Streptomyces lavendulae FRI-5.
Arch Microbiol. 192:211-20. 2010 [PubMed]
Lee YJ, Kitani S, and Nihira T. (*8)
Null mutation analysis of an afsA-family gene, barX, that is involved in biosynthesis of the -butyrolactone autoregulator in Streptomyces virginiae.
Microbiology 156:206-210. 2010 [PubMed]
Hsiao NH, Nakayama S, Merlo ME, Vries MD, Bunet R, Kitani S, Nihira T, and Takano E. (*19)
Analysis of two additional signaling molecules in Streptomyces coelicolor and the development of a novel butyrolactone-specific reporter system.
Chem Biol. 16:1-10. 2009 [PubMed]
Pulsawat N, Kitani S, Fukushima E, and Nihira T. (*8)
Hierarchical control of virginiamycin production in Streptomyces virginiae by three pathway-specific regulators: VmsS, VmsT, and VmsR.
Microbiology 155:1250-59. 2009 [PubMed]
Kitani S, Ikeda H, Sakamoto T, Noguchi S, and Nihira T. (*31)
Characterization of a regulatory gene, aveR, for the biosynthesis of avermectin in Streptomyces avermitilis.
Appl Microbiol Biotechnol. 82:1089-96. 2009 [PubMed]
Kitani S, Iida A, Izumi T, Maeda A, Yamada Y, and Nihira T. (*13)
Identification of genes involved in the butyrolactone autoregulator cascade that modulates secondary metabolism in Streptomyces lavendulae FRI-5.
Gene 425:9-16. 2008. [PubMed]
Aroonsri A, Kitani S, Choi SU, and Nihira T. (*1)
Isolation and characterization of bamA genes, homologues of the -butyrolactone autoregulator-receptor gene in Amycolatopsis mediterranei, a rifamycin producer.
Biotechnol Lett. 30:2019-24. 2008. [PubMed]
Kitani S, Hoshika M, and Nihira T. (*5)
Disruption of sscR encoding a -butyrolactone autoregulator receptor in Streptomyces scabies NBRC12914 affects production of secondary metabolites
Folia Microbiol. 53:115-24. 2008. [PubMed]
Lee YJ, Kitani S, Kinoshita H, and Nihira T. (*5)
Identification by gene disruption analysis of barS2, a gene for biosynthesis of a -butyrolactone autoregulator in Streptomyces virginiae
Arch Microbiol. 189:367-74. 2008. [PubMed]
Pulsawat N, Kitani S, Kinoshita H, Lee CK, and Nihira T. (*7)
Identification of the bkdAB gene cluster, a plausible source of the starter-unit for virginiamycin M production in Streptomyces virginiae.
Arch Microbiol. 187:459-66. 2007.[PubMed]
Pulsawat N, Kitani S, and Nihira T. (*38)
Characterization of biosynthetic gene cluster for the production of virginiamycin M, a streptogramin type A antibiotic, in Streptomyces virginiae.
Gene 393:31-42. 2007. [PubMed]
Lee YJ, Yeo SH, Lee IS, Lee SP, Kitani S, Nihira T, and Kim HS. (*1)
Cloning and characterization of a gene encoding the -butyrolactone autoregulator receptor from Saccharopolyspora erythraea.
J Microbiol Biotechnol. 16:77-83. 2006. [PubMed]
Shindo T, Takahashi T, Nihira T, Yamada Y, Kato K, and Shinmyo A. (*1)
Streptomyces-derived induction system for gene expression in cultured plant cells.
J Biosci Bioeng. 102:552-559. 2006. [PubMed]
Lee KM, Lee CK, Choi SU, Park HR, Kitani S, Nihira T, and Hwang YI. (*38)
Cloning and in vivo functional analysis by disruption of a gene encoding the -butyrolactone autoregulator receptor from Streptomyces natalensis.
Arch Microbiol. 184:249-57. 2005. [PubMed]
Takano E, Kinoshita H, Mersinias V, Bucca G, Hotchkiss G, Nihira T, Smith C, Bibb M, Wohlleben W, and Chater K. (*81)
A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor.
Mol Microbiol. 56:465-79. 2005. [PubMed]
Kim HS, Lee YJ, Lee CK, Choi SU, Yeo SH, Hwang YI, Yu TS, Kinoshita H, and Nihira T. (*14)
Cloning and characterization of a gene encoding the -butyrolactone autoregulator eeceptor from Streptomyces clavuligerus.
Arch Microbiol. 182:44-50. 2004. [PubMed]
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Choi SU, Lee CK, Hwang YI, Kinoshita H, and Nihira T. (*20)
Cloning and functional analysis by gene disruption of a gene encoding a -butyrolactone autoregulator receptor from Kitasatospora setae.
J Bacteriol. 186:3423-30. 2004. [PubMed]
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Choi SU, Lee CK, Hwang YI, Kinoshita H, and Nihira T. (*39)
Intergeneric conjugal transfer of plasmid DNA from Escherichia coli to Kitasatospora setae, a bafilomycin B1 producer.
Arch Microbiol. 181:294-98. 2004. [PubMed]
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Matsuno K, Lee CK, and Nihira T. (*33)
Identification by gene deletion analysis of BarB as a negative regulator of the -butyrolactone-autoregulator cascade and controller of an early process of virginiamycin biosynthesis in Streptomyces virginiae.
Arch Microbiol. 181:52-59. 2004. [PubMed]
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Choi SU, Lee CK, Hwang YI, Kinoshita H, and Nihira T. (*19)
-butyrolactone autoregulators and receptor proteins in non-Streptomyces actinomycetes producing commercially important secondary metabolites.
Arch Microbiol. 180:303-7. 2003. [PubMed]
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Matsuura H, Okamoto S, Anamnart S, Wang Q, Zhou ZY, Nihira T, Yamada Y, Kuzuyama T, Seto H, Nakayama J, Suzuki A, Nagasawa H and Sakuda S. (*6)
Nucleotide sequence of genes encoding allosamidin-sensitive and insensitive chitinases produced by allosamidin-producing Streptomyces.
Biosci Biotechnol Biochem. 67:2002-5. 2003. [PubMed]
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Nihira T.
Virginiamycin: Biosynthetic pathway and its regulation, with special emphasis on the genetic aspects and autoregulator-dependent regulation.
In Microbial Secondary Metabolites: Biosynthesis, Genetics and Regulation. pp.99-119. F. Fierro and J. F. Martin, ed. Research Signpost., Leon. 2003.
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Presentation of international conferences
12. Ueda S, Kitani S, Ikeda H, and Nihira T.
18th International Symposium on the Biology of Actinomycetes
(Jeju, Korea)(May 2017)
Functional characterization of biosynthetic genes for kitasetaline, a -carboline alkaloid, and feneration of new -carboline derivatives
11. Komaki H, Hosoyama A, Ichikawa N, Kimura A, Ichikawa A, Harunari E, Hamada M, Nihira T, Panbagred W, and Igarashi Y.
18th International Symposium on the Biology of Actinomycetes
(Jeju, Korea)(May 2017)
Elucidation of the rakicidin biosynthetic pathway based on genome analysis
10. Kitani S, Kurniawan YN, Maeda A, Doi M, and Nihira T
17th International Symposium on the Biology of Actinomycetes
(Kusadasi, Turkey)(October 2014)
-Butyrolactone autoregulator system of secondary metabolism in Streptomyces lavendulae FRI-5
9. Kitani Miyamoto KT, Takamatsu S, Nagamitsu T, Ikeda H, and Nihira T
16th International Symposium on the Biology of Actinomycetes
(Puerto Vallarta, Mexico)(December 2011)
A novel Streptomyces hormone controlling antibiotic production in Streptomyces avermitilis
8. Miyamoto K, Haruna K, Kitani S, Ikeda H, and Nihira T
15th International Symposium on the Biology of Actinomycetes
(Shanghai, China)(August 2009)
Autoregulator-signalling cascades in Streptomyces avermitilis
Sueharu Horinouchi Prize
7. Kitani S, Pulsawat N, Lee YJ, Fukushima E, Maeda A, Iida A, Doi M, and Nihira T
UK-Japan Workshop 2008: Genomics of Antibiotic-producing Actinomycetes: Implications and Applications (Tokyo, Japan) (October 2008)
Regulatory mechanism of antibiotic production by gamma-butyrolactone autoregulators
6. Miyamoto K, Haruna K, Kitani S, Ikeda H, and Nihira T
UK-Japan Workshop 2008: Genomics of Antibiotic-producing Actinomycetes: Implications and Applications (Tokyo, Japan) (October 2008)
Global regulation of secondary metabolism by autoregulator-signalling cascade in Streptomyces avermitilis
5. Ichikawa et al.
UK-Japan Workshop 2008: Genomics of Antibiotic-producing Actinomycetes: Implications and Applications (Tokyo, Japan) (October 2008)
Complete genome sequence of Kitasatospora setae NBRC 14216T
4. Panbangred W, Tuchinda P, Nilowongse A, Mungsantisuk, Tomio A, Kitani S, Igarashi Y, and Nihira T
The 20th annual meeting and international conference of the Thai society for biotechnology (Maha Sarakham, Thailand) (October 2008)
Study on bacterial antagonist against anthracnose fungi
3. Thamchaipenet A, Kang SJ, Suttiviriya P, Duangmal K, Kitani S, Igarashi Y, and Nihira T
The 20th annual meeting and international conference of the Thai society for biotechnology (Maha Sarakham, Thailand) (October 2008)
Potential bioactive compounds and plant growth promoting agents from endophytic actinomycetes isolated from Thai plants
2. Kitani S, Pulsawat N, and Nihira T
14th International Symposium on the Biology of Actinomycetes (Newcastle upon Tyne, UK) (August 2007)
The genes and enzymes of virginiamycin M biosynthesis in Streptomyces virginiae
1. Miyamoto K, Kitani S, Komatsu M, Ikeda H, and Nihira T
14th International Symposium on the Biology of Actinomycetes (Newcastle upon Tyne, UK) (August 2007)
Identification of gamma-butyrolactone-autoregulator signaling cascade in Streptomyces avermitilis
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Isolation and characterization of nitrogen-fixing bacteria from soil and rhizosphere
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