Kyushu University Academic Staff Educational and Research Activities Database
List of Reports
Jiro Nakayama Last modified date:2023.11.27

Professor / Division of Systems Bioengineering / Department of Bioscience and Biotechnology / Faculty of Agriculture

1. Phatthanaphong Therdtatha, Akari Shinoda, Jiro Nakayama, Crisis of the Asian gut: associations among diet, microbiota, and metabolic diseases, Bioscience of microbiota, food and health, 10.12938/bmfh.2021-085, 41(3), 83-93, 2022.04.
2. Mugihito Oshiro, Takeshi Zendo, Jiro Nakayama , Diversity and dynamics of sourdough lactic acid bacteriota created by a slow food fermentation system, Journal of Bioscience and Bioengineering,, 131(4), 333-340, 2021.04, Sourdough is a naturally fermented dough that is used worldwide to produce a variety of baked foods. Various lactic acid bacteria (LAB), which can determine the quality of sourdough baked foods by producing metabolites, have been found in the sourdough ecosystem. However, spontaneous fermentation of sourdough leads to unpredictable growth of various micro-organisms, which result in unstable product quality. From an ecological perspective, many researchers have recently studied sourdough LAB diversity, particularly the elucidation of LAB community interactions and the dynamic mechanisms during the fermentation process, in response to requests for the control and design of a desired sourdough microbial community. This article reviews recent advances in the study of sourdough LAB diversity and its dynamics in association with unique characteristics of the fermentation system; it also discusses future perspectives for better understanding of the complex sourdough microbial ecosystem, which can be attained efficiently by both in vitro and in situ experimental approaches.
3. The association between dietary habit and gut microbiota and lifestyle diseases in Asia.
4. 麹に含まれるグリコシルセラミドの健康効果.
5. Masaru Tanaka, Jiro Nakayama, Development of the gut microbiota in infancy and its impact on health in later life
, Allergology International, 66, 515-522, 2017.07.
6. Jiro Nakayama, Heping Zhang, Yuan Kun Lee, Asian gut microbiome, Science Bulletin, 10.1016/j.scib.2017.04.001, 62(12), 816-817, 2017.06.
7. Juma Kisuse, Jiro Nakayama, 16S rRNA Metagenomics of Asian Gut Microbiota, Understanding Host-Microbiome Interactions - An Omics Approach, 10.1007/978-981-10-5050-3, 1, 71-81, 2017.01.
8. Jiro Nakayama, Ravindra Pal Singh, Quorum quenching strategy targeting Gram-positive pathogenic bacteria, Advances in Microbiology and Infectious Diseases and Public Health, 910, 109-130, 2016.05.
9. Jiro Nakayama, Pyrosequence-based 16S rRNA profiling of gastro-intestinal microbiota, Bioscience & Microflora, 29(2), 83-96, 2010.04.
10. 性的領域への関心が低い男性人格に関する検討.
11. AVSS時にヒト男性の人格が影響をおよぼす視覚関心領域に関する検討.
12. 視線追跡装置と人格評価による性的関心度に対する性差解析.
13. Jun Ichi Nagao, Yuji Aso, Kouki Shioya, Jiro Nakayama, Kenji Sonomoto, Lantibiotic engineering
Molecular characterization and exploitation of lantibiotic-synthesizing enzymes for peptide engineering
, Journal of Molecular Microbiology and Biotechnology, 10.1159/000104749, 13(4),235-242, 2007.09, Lanthionine-containing peptide antibiotics called lantibiotics are produced by a large number of Gram-positive bacteria. Nukacin ISK-1 produced by Staphylococcus warneri ISK-1 is type-A(II) lantibiotic. Ribosomally synthesized nukacin ISK-1 prepeptide (NukA) consists of an N-terminal leader peptide followed by a C-terminal propeptide moiety that undergoes several post-translational modification events including unusual amino acid formation by the modification enzyme NukM, cleavage of leader peptide and export by the dual functional ABC transporter NukT, finally yielding a biologically active peptide. Unusual amino acids in lantibiotics contribute to biological activity and also structural stability against proteases. Thus, lantibiotic-synthesizing enzymes have a high potentiality for peptide engineering by introduction of unusual amino acids into desired peptides with altering biological and physicochemical properties, e.g., activity and stability, termed lantibiotic engineering. We report the establishment of a heterologous expression of nukacin ISK-1 biosynthetic gene cluster by the nisin-controlled expression system and discuss our recent progress in understanding of the biosynthetic enzymes for nukacin ISK-1 such as localization, molecular interaction in biophysical and biochemical aspects. Substrate specificity of the lantibiotic-synthesizing enzymes was evaluated by complementation of the biosynthetic enzymes (LctM and LctT) of closely related lantibiotic lacticin 481 for nukacin ISK-1 biosynthesis. We further explored a rapid and powerful tool for introduction of unusual amino acids by co-expression of hexa-histidine-tagged NukA and NukM in Escherichia coli..
14. 視線追跡装置を用いたヒト男性の性的興味とMMPIによる人格評価との関連性.
15. Jun ichi Nagao, Sikder M. Asaduzzaman, Yuji Aso, Ken ichi Okuda, Jiro Nakayama, Kenji Sonomoto, Lantibiotics
Insight and foresight for new paradigm
, Journal of Bioscience and Bioengineering, 10.1263/jbb.102.139, 102(3),139-149, 2006.09, Lantibiotics are a unique type of antimicrobial peptide produced by a large number of gram-positive bacteria that contain unusual amino acids, such as lanthionine and dehydrated amino acids. Ribosomally synthesized lantibiotic prepeptide consists of an N-terminal leader peptide followed by a C-terminal propeptide moiety that undergoes several post-translational modification events to yield a biologically active lantibiotic. Research on lantibiotics has drawn much attention in recent years and has undergone extensive progress as a step forward to the next paradigm. Unusual amino acids in lantibiotics solely contribute to their biological activity and also enhance their structural stability. Thus, enzymes involved in lantibiotic biosynthesis would have a high potential for peptide engineering by introducing unusual amino acids into desired peptides, which may establish a universal approach to advance the structural design of novel peptides, termed lantibiotic engineering. In this review, we focus on recent development with contemporary innovations and perspective of lantibiotic research..
16. Identification and production of a bacteriocin from Enterococcus mundtii QU 2 isolated from soybean
Aims: Identification of the bacteriocin produced by Enterococcus mundtii QU 2 newly isolated from soybean and fermentative production of the bacteriocin. Methods and Results: The bacteriocin produced by Ent. mundtii QU 2 inhibited the growth of various indicator strains, including Enterococcus, Lactobacillus, Leuconostoc, Pediococcus and Listeria. The bacteriocin activity was stable at wide pH range and against heat treatment, but completely abolished by proteolytic enzymes. The bacteriocin was purified from the culture supernatant by the three-step chromatographic procedure. Mass spectrometry, amino acid sequencing and DNA sequencing revealed that the bacteriocin was similar to class IIa bacteriocins produced by other Ent. mundtii strains. The bacteriocin production decreased in the absence of glucose, nitrogen sources, or Tween 80 in MRS medium. Additionally, it was strongly suppressed by addition of Ca2+(CaCO3or CaCl2). In pH-controlled fermentations, the highest bacteriocin production was achieved at pH 6.0 whereas the highest cell growth was obtained at pH 7.0. Conclusions: Ent. mundtii QU 2 produced a class IIa bacteriocin. Some growth factors (e.g. Ca2+and pH) influenced the bacteriocin production. Significance and Impact of the Study: A new soybean isolate, Ent. mundtii QU 2 was found to be a class IIa bacteriocin producer. Factors influencing the bacteriocin production described herein are valuable for applications of the bacteriocins from Ent. mundtii strains. © 2005 The Society for Applied Microbiology..
17. J Nagao, Y Harada, K Shloya, Y Aso, T Zendo, J Nakayama, K Sonomoto, Lanthionine introduction into nukacin ISK-1 prepeptide by co-expression. with modification enzyme NAM in Escherichia coli, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 10.1016/j.bbrc.2005.08.125, Vol.336, No.2, pp.507-513, 2005.10, We demonstrated lanthionine introduction into hexa-histidine-tagged (His-tagged) nukacin ISK-1 prepeptide NukA by modification enzyme NukM in Escherichia coli. Co-expression of nukA and nukM, purification of the resulting His-tagged prepeptide by affinity chromatography, and subsequent mass spectrometry analysis showed that the prepeptide was converted into a postulated peptide with decrease in mass of 72 Da which resulted from dehydration of four amino acids. Characterization of the resultant prepeptide indicated the presence of unusual amino acids, such as dehydrated amino acid, lanthionine or 3-methyllanthionine, in its C-terminal propeptide moiety. The modified prepeptide encompassing the leader peptide attached to the post-translation ally modified propeptide moiety was readily obtained by one-step purification. Our findings will thus be a powerful tool for introducing unusual amino acids aimed at peptide engineering and also helpful to provide new insight for further understanding of lanthionine-forming enzymes for lantibiotics. (c) 2005 Elsevier Inc. All rights reserved..
18. MHJ Sturme, J Nakayama, D Molenaar, Y Murakami, R Kunugi, T Fujii, EE Vaughan, M Kleerebezem, WM de Vos, An agr-like two-component regulatory system in Lactobacillus plantarum is involved in production of a novel cyclic peptide and regulation of adherence, JOURNAL OF BACTERIOLOGY, 10.1128/JB.187.15.5224-5235.2005, Vol.187, No.15, pp.5224-5235, 2005.08, We have analyzed a locus on the annotated Lactobacillus plantarum WCFS1 genome that showed homology to the staphylococcal agr quorum-sensing system and designated it lam for Lactobacillus agr-like module. Production of the lamBDCA transcript was shown to be growth phase dependent. Analysis of a response regulator-defective mutant (Delta lamA) in an adherence assay showed that lam regulates adherence of L. plantarum to a glass surface. Global transcription analysis of the wild-type and Delta lamA strains in early, mid-, and late log phase of growth was performed using a clone-based microarray. Remarkably, only a small set of genes showed significant differences in transcription profiles between the wild-type and lamA mutant strains. The microarray analysis confirmed that lamBDCA is autoregulatory and showed that lamA is involved in regulation of expression of genes encoding surface polysaccharides, cell membrane proteins, and sugar utilization proteins. The lamBD genes encoding the putative autoinducing peptide precursor (LamD) and its processing protein (LamB) were overexpressed using the nisin-controlled expression system, and culture supernatants were analyzed by liquid chromatography/mass spectrometry (LC/MS) to identify overproduced Lam-derived peptides. In this way, a cyclic thiolactone pentapeptide that possesses a ring structure similar to those of autoinducing peptides of the staphylococcal agr system was identified. The peptide was designated LamD558, and its sequence (CVGIW) matched the annotated precursor peptide sequence. Time course analysis of wild-type culture supernatants by LC/MS indicated that LamD558 production was increased markedly from mid-log to late log growth phase. This is the first example of an agr-like system in nonpathogenic bacteria that encodes a cyclic thiolactone autoinducing peptide and is involved in regulation of adherence..
19. Y Aso, T Sashihara, J Nagao, Y Kanemasa, H Koga, T Hashimoto, T Higuchi, A Adachi, H Nomiyama, A Ishizaki, J Nakayama, K Sonomoto, Characterization of a gene cluster of Staphylococcus warneri ISK-1 encoding the biosynthesis of and immunity to the lantibiotic, nukacin ISK-1, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 10.1271/bbb.68.1663, Vol.68, No.8, pp.1663-1671, 2004.08, We characterized a gene cluster in a plasmid designated pPI-1 of Staphylococcus warneri ISK-1 encoding the biosynthesis of and immunity to the lacticin-481 type lantibiotic, nukacin ISK-1. The DNA sequence suggested that the nukacin ISK-1 gene cluster consists of at least six genes, nukA (a structural gene), -M, -T, -F, -E, -G, and two open reading frames, ORF1 and ORF7. NukM and NukT were predicted to be involved in post-translational modification and secretion of nukacin ISK-1 respectively. NukF, -E, and -G were predicted to form a membrane complex which contributes to self-protection from nukacin ISK-1. Transcriptional analyses revealed that nukM through ORF7 comprises an operon, and that ORF1 is transcribed independently from downstream of nukA. The transcriptional levels of the nukA and nukM genes were enhanced by osmotic stress. The expression level of the nukA transcript was scarcely enhanced by nukacin ISK-1, suggesting that expression is not under the control of the autoregulatory circuit..
20. Analysis of the Composition of the Intestinal Flora : Analysis of Intestinal Bacterial Community by DGGE/TGGE.
21. S Sugimoto, J Nakayama, D Fukuda, S Sonezaki, M Watanabe, A Tosukhowong, K Sonomoto, Effect of heterologous expression of molecular chaperone DnaK from Tetragenococcus halophilus on salinity adaptation of Escherichia coli, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, Vol.96, No.2, pp.129-133, 2003.08, Molecular chaperone DnaK of halophilic Tetragenococcus halophilus JCM5888 was characterized under salinity conditions both in vitro and in vivo. The dnaK gene was cloned into an expression vector And transformed into Escherichia coli. The DnaK protein obtained from the recombinant E. coli showed a significantly higher refolding activity of denatured lactate dehydrogenase than that from non-halophilic Lactococcus lactis under NaCl concentrations higher than I M. E. coli without the overexpression of DnaK exhibited a growth profile with a prolonged lag phase and suppressed maximum cell density in Luria-Bertani medium containing 5% (0.86 M) NaCl. On the contrary, the overexpression of T halophilus DnaK greatly shortened this prolonged lag phase with no effect on maximum growth, while that of L. lactis DnaK decreased maximum growth. The amount of protein aggregates was increased by salt stress in the E. coli cells, while this aggregation was greatly suppressed by the overexpression of T halophilus DnaK. These results suggest that heterologous overexpression of T halophilus DnaK, via its chaperone activity, promotes salinity adaptation of E. coli..
22. J Nakayama, ADL Akkermans, WM De Vos, High-throughput PCR screening of genes for three-component regulatory system putatively involved in quorum sensing from low-G + C Gram-positive bacteria, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 10.1271/bbb.67.480, Vol.67, No.3, pp.480-489, 2003.03, Quorum sensing of Gram-positive bacteria is often regulated by three-component regulatory system composed of autoinducing peptide, sensor kinase and response regulator. We used PCR to study a gene cassette encoding this three-component regulatory system. Degenerate primers were designed from consensus amino acid sequences in the HPK10 subfamily, mostly involved in quorum sensing. Products amplified from genomic DNA of Lactobacillus, Enterococcus, and Clostridium species were cloned and sequenced; their deduced amino acid sequences were similar to those of members of the HPK10 subfamily. Complete genes for the putative gene cassette were cloned by inverse PCR from L. paracasei E93490 and L. plantarum WCFS6. Phylogenetic analysis grouped the cloned putative HPKs into the HPK10 subfamily. These results indicated the usefulness of this high-throughput gene screening and suggested that the three-component regulatory gene cassette are widely present..
23. T Horii, H Nagasawa, J Nakayama, Functional analysis of TraA, the sex pheromone receptor encoded by pPD1, in a promoter region essential for the mating response in Enterococcus faecalisi, JOURNAL OF BACTERIOLOGY, 10.1128/JB.22.6343-6350.2002, Vol.184, No.22, pp.6343-6350, 2002.11, Conjugative transfer of a bacteriocin plasmid, pPD1, of Enterococcus faecalis is induced in response to a peptide sex pheromone, cPD1, secreted from plasmid-free recipient cells. cPD1 is taken up by a pPD1 donor cell and binds to an intracellular receptor, TraA. Once a recipient cell acquires pPD1, it starts to produce an inhibitor of cPD1, termed iPD1, which functions as a TraA antagonist and blocks self-induction in donor cells. In this study, we discuss how TraA transduces the signal of cPD1 to the mating response. Gel mobility shift assays indicated that TraA is bound to a traA-ipd intergenic region, which is essential for cPD1 response. DNase I footprinting analysis suggested the presence of one strong (tab1) and two weak (tab2 and tab3) TraA-binding sites in the intergenic region. Primer extension analysis implied that the transcriptional initiation sites of traA and ipd were located in the intergenic region. Northern analysis showed that cPD1 upregulated and downregulated transcription of ipd and traA, respectively. The circular permutation assay showed that TraA bent a DNA fragment corresponding to the tab1 region, and its angle was changed in the presence of cPD1 or iPD1. From these data, we propose a model that TraA changes the conformation of the tab1 region in response to cPD1 and upregulates the transcription of ipd, which may lead to expression of genes required for the mating response..
24. Sturme, M. H. J., M. Kleerebezem, J. Nakayama, A. D. L. Akkermans, E. E. Vaughan and W. M. de Vos, Cell to cell communication by autoinducing peptides in gram-positive bacteria, Antonie van Leeuwenhoek, 10.1023/A:1020522919555, 81, 233-243, 2002.01.
25. SAKUDA Shohei, ONO Makoto, IKEDA Hiroyuki, NAKAMURA Takefumi, INAGAKI Yasuhito, KAWACHI Ryu, NAKAYAMA Jiro, SUZUKI Akinori, ISOGAI Akira, NAGASAWA Hiromichi, Blasticidin A as an Inhibitor of Aflatoxin Production by Aspergillus parasiticus, Journal of antibiotics, 10.7164/antibiotics.53.1265, Vol.53, No.11, pp.1265-1271, 2000.11.
26. Mass spectrometry of refractory body composition - 6. Structual analysis of peptide and protein by mass spectrometry (2) ..
27. Mass spectrometric analysis of slightly volatile body compositions - 5. Structual analysis of peptides and proteins by mass spectrometric analysis. (1)..
28. Bacterial sex pheromone..