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Gewtaisong J, Chukeatirote E, Ahn J. Characterization of Bacillus subtilis bacteriophage BasuTN3 isolated from Thua Nao, a thai fermented soybean food product. Food Sci Biotechnol 2023; 32:203-208. [PMID: 36647518 PMCID: PMC9839916 DOI: 10.1007/s10068-022-01188-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/22/2022] [Accepted: 10/11/2022] [Indexed: 01/19/2023] Open
Abstract
The infection of bacteriophage is of great concern in food industry as this can result in complete fermentation failure. In this study, a virulent bacteriophage, named BasuTN3, was isolated from Thua Nao, a Thai fermented soybean. The stability of BasuTN3 was evaluated under various ranges of temperature, pH, chloroform, UV, and disinfectants. The results showed that the isolated BasuTN3 appeared to be specific to its bacterial host, which was identified as Bacillus subtilis strain TN3 based on the 16 S rRNA gene sequence analysis. Under TEM, the BasuTN3 belonged to the family Myoviridae. The isolated BasuTN3 could withstand wide temperature ranges (4-45 °C) and pH conditions (5-11). The BasuTN3 was susceptible to chloroform, UV, and commonly used disinfectants. The results obtained expand the knowledge of the Bacillus bacteriophage diversity in the fermented soybean products and provide useful information for the bacteriophage and its bacterial starter cultures.
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Affiliation(s)
| | | | - Juhee Ahn
- Department of Biomedical Science, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341 Republic of Korea
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2
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Itaya M, Sato M, Watanabe S, Kataoka M. Effective plasmid delivery to a plasmid-free Bacillus natto strain by a conjugational transfer system. J Biochem 2022; 172:313-319. [PMID: 36047835 DOI: 10.1093/jb/mvac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
In this study, a Bacillus natto strain named NEST141 was constructed. The strain carries no plasmids and is an authentic proline auxotroph-a feature that confers effective selection conditions for plasmids transferred from a donor, such as B. subtilis 168, via a pLS20-based conjugational transfer system. We have provided a standard effective protocol for the delivery of plasmids larger than 50 kilobase pairs. These results indicate that the B. natto NEST141 strain can become a standard model, like B. subtilis 168, for extensive genetic engineering with diverse applications.
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Affiliation(s)
- Mitsuhiro Itaya
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano-shi, Nagano 380-8553, Japan.,Institute for Advanced Biosciences, Keio University, Nipponkoku, Tsuruoka, Yamagata 997-0017, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Tsuruoka, Yamagata 997-0017, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masakazu Kataoka
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano-shi, Nagano 380-8553, Japan
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Hou Q, Kolodkin-Gal I. Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome. FEMS Microbiol Ecol 2021; 96:5872479. [PMID: 32672816 DOI: 10.1093/femsec/fiaa142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.
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Affiliation(s)
- Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Schönbichler A, Díaz-Moreno SM, Srivastava V, McKee LS. Exploring the Potential for Fungal Antagonism and Cell Wall Attack by Bacillus subtilis natto. Front Microbiol 2020; 11:521. [PMID: 32296406 PMCID: PMC7136451 DOI: 10.3389/fmicb.2020.00521] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
To develop more ecologically sustainable agricultural practices requires that we reduce our reliance on synthetic chemical pesticides for crop protection. This will likely involve optimized biocontrol approaches - the use of beneficial soil microbes to attack potential plant pathogens to protect plants from diseases. Many bacterial species, including strains of Bacillus subtilis, have been explored for their biocontrol properties, as they can control the growth of harmful fungi, often by disrupting the fungal cell wall. A strain that is not often considered for this particular application is Bacillus subtilis natto, primarily known for fermenting soybeans via cell wall degradation in the Japanese probiotic dish "natto." Because deconstruction of the fungal cell wall is considered an important biocontrol trait, we were motivated to explore the possible anti-fungal properties of the B. subtilis natto strain. We show that B. subtilis natto can use complex fungal material as a carbon source for growth, and can effectively deconstruct fungal cell walls. We found degradation of fungal cell wall proteins, and showed that growth on a mix of peptides was very strong. We also found that intact fungal cell walls can induce the secretion of chitinases and proteases. Surprisingly, we could show that chitin, the bulk component of the fungal cell wall, does not permit successful growth of the natto strain or induce the secretion of chitinolytic enzymes, although these were produced during exposure to proteins or to complex fungal material. We have further shown that protease secretion is likely a constitutively enabled mechanism for nutrient scavenging by B. subtilis natto, as well as a potent tool for the degradation of fungal cell walls. Overall, our data highlight B. subtilis natto as a promising candidate for biocontrol products, with relevant behaviors that can be optimized by altering growth conditions. Whereas it is common for bacterial biocontrol products to be supplied with chitin or chitosan as a priming polysaccharide, our data indicate that this is not a useful approach with this particular bacterium, which should instead be supplied with either glucose or attenuated fungal material.
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Affiliation(s)
- Anna Schönbichler
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Sara M Díaz-Moreno
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lauren Sara McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Center, Stockholm, Sweden
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Itaya M, Nagasaku M, Shimada T, Ohtani N, Shiwa Y, Yoshikawa H, Kaneko S, Tomita M, Sato M. Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids. FEMS Microbiol Lett 2019; 366:5307882. [PMID: 30726909 DOI: 10.1093/femsle/fnz032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis (natto) is generally regarded as a safe bacterium and used as a host for the production of several materials. However, genetic engineering of B. subtilis (natto) is not well established because of poor DNA delivery methods and the lack of a standard strain for the aim. Here, we developed a genetic delivery tool in B. subtilis (natto) using the pLS20 conjugational plasmid (65 kbp). Transmission of pLS20 from B. subtilis 168 to wild-type B. subtilis (natto) did not occur via established mating protocols. We isolated B. subtilis (natto) mutants showing dramatically increased recipient activity. Whole-genome sequence analyses revealed three common alterations: mutations in the restriction endonuclease gene and in the methyl-accepting chemotaxis protein gene, and a 43-kbp deletion at the genome replication termination locus. A representative strain named NEST116 was generated as the first B. subtilis (natto) strain suitable for exploring pLS20-based genetic engineering.
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Affiliation(s)
- Mitsuhiro Itaya
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Mayumi Nagasaku
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Tomoe Shimada
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Naoto Ohtani
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shinya Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
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Salina EA, Nesterov MA, Frenkel Z, Kiseleva AA, Timonova EM, Magni F, Vrána J, Šafář J, Šimková H, Doležel J, Korol A, Sergeeva EM. Features of the organization of bread wheat chromosome 5BS based on physical mapping. BMC Genomics 2018; 19:80. [PMID: 29504906 PMCID: PMC5836826 DOI: 10.1186/s12864-018-4470-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The IWGSC strategy for construction of the reference sequence of the bread wheat genome is based on first obtaining physical maps of the individual chromosomes. Our aim is to develop and use the physical map for analysis of the organization of the short arm of wheat chromosome 5B (5BS) which bears a number of agronomically important genes, including genes conferring resistance to fungal diseases. RESULTS A physical map of the 5BS arm (290 Mbp) was constructed using restriction fingerprinting and LTC software for contig assembly of 43,776 BAC clones. The resulting physical map covered ~ 99% of the 5BS chromosome arm (111 scaffolds, N50 = 3.078 Mb). SSR, ISBP and zipper markers were employed for anchoring the BAC clones, and from these 722 novel markers were developed based on previously obtained data from partial sequencing of 5BS. The markers were mapped using a set of Chinese Spring (CS) deletion lines, and F2 and RICL populations from a cross of CS and CS-5B dicoccoides. Three approaches have been used for anchoring BAC contigs on the 5BS chromosome, including clone-by-clone screening of BACs, GenomeZipper analysis, and comparison of BAC-fingerprints with in silico fingerprinting of 5B pseudomolecules of T. dicoccoides. These approaches allowed us to reach a high level of BAC contig anchoring: 96% of 5BS BAC contigs were located on 5BS. An interesting pattern was revealed in the distribution of contigs along the chromosome. Short contigs (200-999 kb) containing markers for the regions interrupted by tandem repeats, were mainly localized to the 5BS subtelomeric block; whereas the distribution of larger 1000-3500 kb contigs along the chromosome better correlated with the distribution of the regions syntenic to rice, Brachypodium, and sorghum, as detected by the Zipper approach. CONCLUSION The high fingerprinting quality, LTC software and large number of BAC clones selected by the informative markers in screening of the 43,776 clones allowed us to significantly increase the BAC scaffold length when compared with the published physical maps for other wheat chromosomes. The genetic and bioinformatics resources developed in this study provide new possibilities for exploring chromosome organization and for breeding applications.
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Affiliation(s)
- Elena A Salina
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
| | - Mikhail A Nesterov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Antonina A Kiseleva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina M Timonova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Ekaterina M Sergeeva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Kamada M, Hase S, Fujii K, Miyake M, Sato K, Kimura K, Sakakibara Y. Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods. PLoS One 2015; 10:e0141369. [PMID: 26505996 PMCID: PMC4624242 DOI: 10.1371/journal.pone.0141369] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/06/2015] [Indexed: 12/22/2022] Open
Abstract
Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. subtilis strains and its relationship with the productivity of extracellular poly-γ-glutamic acid (γPGA), we sequenced the whole genome of eight B. subtilis stains isolated from non-salted fermented soybean foods in Southeast Asia. Assembled nucleotide sequences were compared with those of a natto (fermented soybean food) starter strain B. subtilis BEST195 and the laboratory standard strain B. subtilis 168 that is incapable of γPGA production. Detected variants were investigated in terms of insertion sequences, biotin synthesis, production of subtilisin NAT, and regulatory genes for γPGA synthesis, which were related to fermentation process. Comparing genome sequences, we found that the strains that produce γPGA have a deletion in a protein that constitutes the flagellar basal body, and this deletion was not found in the non-producing strains. We further identified diversity in variants of the bio operon, which is responsible for the biotin auxotrophism of the natto starter strains. Phylogenetic analysis using multilocus sequencing typing revealed that the B. subtilis strains isolated from the non-salted fermented soybeans were not clustered together, while the natto-fermenting strains were tightly clustered; this analysis also suggested that the strain isolated from "Tua Nao" of Thailand traces a different evolutionary process from other strains.
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Affiliation(s)
- Mayumi Kamada
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kazushi Fujii
- Department of Biological Sciences, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masato Miyake
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Keitarou Kimura
- Division of Applied Microbiology, National Food Research Institute, 2-1-12 12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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Kamada M, Hase S, Sato K, Toyoda A, Fujiyama A, Sakakibara Y. Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads. PLoS One 2014; 9:e109999. [PMID: 25329997 PMCID: PMC4199626 DOI: 10.1371/journal.pone.0109999] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 09/04/2014] [Indexed: 01/24/2023] Open
Abstract
De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.
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Affiliation(s)
- Mayumi Kamada
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Sumitaka Hase
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Kengo Sato
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan
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Abstract
Sporulation by Bacillus subtilis is a cell density-dependent response to nutrient deprivation. Central to the decision of entering sporulation is a phosphorelay, through which sensor kinases promote phosphorylation of Spo0A. The phosphorelay integrates both positive and negative signals, ensuring that sporulation, a time- and energy-consuming process that may bring an ecological cost, is only triggered should other adaptations fail. Here we report that a gastrointestinal isolate of B. subtilis sporulates with high efficiency during growth, bypassing the cell density, nutritional, and other signals that normally make sporulation a post-exponential-phase response. Sporulation during growth occurs because Spo0A is more active per cell and in a higher fraction of the population than in a laboratory strain. This in turn, is primarily caused by the absence from the gut strain of the genes rapE and rapK, coding for two aspartyl phosphatases that negatively modulate the flow of phosphoryl groups to Spo0A. We show, in line with recent results, that activation of Spo0A through the phosphorelay is the limiting step for sporulation initiation in the gut strain. Our results further suggest that the phosphorelay is tuned to favor sporulation during growth in gastrointestinal B. subtilis isolates, presumably as a form of survival and/or propagation in the gut environment.
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Complete nucleotide sequence of Bacillus subtilis (natto) bacteriophage PM1, a phage associated with disruption of food production. Virus Genes 2013; 46:524-34. [PMID: 23315235 DOI: 10.1007/s11262-013-0876-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/04/2013] [Indexed: 12/14/2022]
Abstract
"Natto", considered a traditional food, is made by fermenting boiled soybeans with Bacillus subtilis (natto), which is a natto-producing strain related to B. subtilis. The production of natto is disrupted by phage infections of B. subtilis (natto); hence, it is necessary to control phage infections. PM1, a phage of B. subtilis (natto), was isolated during interrupted natto production in a factory. In a previous study, PM1 was classified morphologically into the family Siphoviridae, and its genome, comprising approximately 50 kbp of linear double-stranded DNA, was assumed to be circularly permuted. In the present study, the complete nucleotide sequence of the PM1 genomic DNA of 50,861 bp (41.3 %G+C) was determined, and 86 open reading frames (ORFs) were deduced. Forty-one ORFs of PM1 shared similarities with proteins deduced from the genome of phages reported so far. Twenty-three ORFs of PM1 were associated with functions related to the phage multiplication process of gene control, DNA replication/modification, DNA packaging, morphogenesis, and cell lysis. Bacillus subtilis (natto) produces a capsular polypeptide of glutamate with a γ-linkage (called poly-γ-glutamate), which appears to serve as a physical barrier to phage adsorption. One ORF of PM1 had similarity with a poly-γ-glutamate hydrolase, which is assumed to degrade the capsular barrier to allow phage progenies to infect encapsulated host cells. The genome analysis of PM1 revealed the characteristics of the phage that are consistent as Bacillus subtilis (natto)-infecting phage.
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Synergistic effects of probiotic Leuconostoc mesenteroides and Bacillus subtilis in malted ragi (Eleucine corocana) food for antagonistic activity against V. cholerae and other beneficial properties. Journal of Food Science and Technology 2012; 51:3072-82. [PMID: 26396299 DOI: 10.1007/s13197-012-0834-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/21/2012] [Accepted: 08/23/2012] [Indexed: 10/27/2022]
Abstract
Finger millet (Elucine corocana), locally known as ragi, and probiotics have been recognized for their health benefits. In the present work we describe novel probiotic ragi malt (functional food) that has been prepared using ragi and probiotic Leuconostoc mesenteroides (Lm) and Bacillus subtilis natto (Bs), alone and in combination, for antagonistic activity against Vibrio cholerae (Vc). In vitro studies using pure cultures showed that each probiotic strain (Lm or Bs) was able to inhibit the planktonic growth of Vc as well as its ability to make biofilms and adhere to extracellular matrix proteins (fibronectin, Fn) that may function in vivo as initial ports of entrance of the pathogen. Interestingly, the combination of both probiotic strains (Lm plus Bs) produced the strongest activity against the Vc. When both cultures were used together in the ragi malt the antimicrobial activity against Vc was enhanced due to synergistic effect of both probiotic strains. The inclusion of both probiotic strains in the functional food produced higher amounts of beneficial fatty acids like linoleic and linolenic acid and increased the mineral content (iron and zinc). The viability and activity of Lm and Bs against Vc was further enhanced with the use of adjuvants like ascorbic acid, tryptone, cysteine hydrochloride and casein hydrolysate in the ragi malt. In sum, the intake of probiotic ragi malt supplemented with Lm and Bs may provide nutrition, energy, compounds of therapeutic importance and antagonistic activity against Vc to a large extent to the consumer.
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Surface display of recombinant protein on the cell surface of Bacillus subtilis by the CotB anchor protein. World J Microbiol Biotechnol 2010. [PMCID: PMC7088572 DOI: 10.1007/s11274-010-0490-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We developed a novel surface display system based on the CotB anchoring motif in order to express foreign protein on the surface of vegetative Bacillus subtilis cells. CotB is a protein in the B. subtilis spore coat. In this system, three repeats of the immunodominant ovalbumin T-cell epitope (OVA323–339) were linked with the cholera toxin B subunit (CTB) to construct a fusion protein, CTB-OVA epi, which was then fused to the C-terminal of the CotB protein so that CTB-OVA epi was expressed in vegetatively-growing B. subtilis. The expression and localization of the CTB-OVA epi protein was confirmed by western blotting, immunofluorescence microscopy, and flow cytometry. The results indicated that a CotB-based surface display system was successfully used to express the CTB-OVA epi protein on the surface of vegetative B. subtilis cells.
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13
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Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, Itaya M, Sakakibara Y. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics 2010; 11:243. [PMID: 20398357 PMCID: PMC2867830 DOI: 10.1186/1471-2164-11-243] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 04/16/2010] [Indexed: 11/21/2022] Open
Abstract
Background Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated B. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, B. subtilis natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length. Results We applied a comparative genome assembly method, which combines de novo assembly and reference guided assembly, to one of the B. subtilis natto strains. We successfully assembled 28 scaffolds and managed to avoid substantial fragmentation. Completion of the assembly through long PCR experiments resulted in one connected scaffold for B. subtilis natto. Based on the assembled genome sequence, our orthologous gene analysis between natto BEST195 and Marburg 168 revealed that 82.4% of 4375 predicted genes in BEST195 are one-to-one orthologous to genes in 168, with two genes in-paralog, 3.2% are deleted in 168, 14.3% are inserted in BEST195, and 5.9% of genes present in 168 are deleted in BEST195. The natto genome contains the same alleles in the promoter region of degQ and the coding region of swrAA as the wild strain, RO-FF-1. These are specific for γ-PGA production ability, which is related to natto production. Further, the B. subtilis natto strain completely lacked a polyketide synthesis operon, disrupted the plipastatin production operon, and possesses previously unidentified transposases. Conclusions The determination of the whole genome sequence of Bacillus subtilis natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that B. subtilis natto harbors but B. subtilis 168 lacks. Multiple genome-level comparisons among five closely related Bacillus species were also carried out. The determined genome sequence of B. subtilis natto and gene annotations are available from the Natto genome browser http://natto-genome.org/.
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Affiliation(s)
- Yukari Nishito
- Department of Biosciences and Informatics, Keio University, Hiyoshi, Kohoku-ku, Yokohama, Japan
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14
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Umene K, Oohashi S, Yamanaka F, Shiraishi A. Molecular characterization of the genome of Bacillus subtilis (natto) bacteriophage PM1, a phage associated with disruption of food production. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0086-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Development of natto with germination-defective mutants of Bacillus subtilis (natto). Appl Microbiol Biotechnol 2009; 82:741-8. [PMID: 19205688 DOI: 10.1007/s00253-009-1894-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 01/14/2009] [Accepted: 01/22/2009] [Indexed: 10/21/2022]
Abstract
The effects of cortex-lysis related genes with the pdaA, sleB, and cwlD mutations of Bacillus subtilis (natto) NAFM5 on sporulation and germination were investigated. Single or double mutations did not prevent normal sporulation, but did affect germination. Germination was severely inhibited by the double mutation of sleB and cwlD. The quality of natto made with the sleB cwlD double mutant was tested, and the amounts of glutamic acid and ammonia were very similar to those in the wild type. The possibility of industrial development of natto containing a reduced number of viable spores is presented.
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16
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Takahashi K, Sekine Y, Chibazakura T, Yoshikawa H. Development of an intermolecular transposition assay system in Bacillus subtilis 168 using IS4Bsu1 from Bacillus subtilis (natto). Microbiology (Reading) 2007; 153:2553-2559. [PMID: 17660419 DOI: 10.1099/mic.0.2007/007104-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most of the spontaneous poly-gamma-glutamate (gamma-PGA)-deficient mutants of Bacillus subtilis (natto) appear to have resulted from the insertion of IS4Bsu1 exclusively into the comP gene. However, complete genomic analysis of B. subtilis 168, a close relative of B. subtilis (natto), revealed no IS4Bsu1 insertion. Preliminary experiments using a transformable 'natto' strain indicated that the frequency of transposition of IS4Bsu1 was exceptionally high under competence-developing conditions. On the other hand, such high-frequency transposition was not observed when cells were grown in a rich medium, such as LB medium, suggesting that there must be suitable environmental conditions that give rise to the transposition of IS4Bsu1. To assess the behaviour of IS4Bsu1 and explore any host factors playing roles in IS transposition, an intermolecular transposition assay system was constructed using a modified IS4Bsu1 element in B. subtilis 168. Here, the details of the intermolecular transposition assay system are given, and the increase in transposition frequency observed under high-temperature and competence-inducing conditions is described.
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Affiliation(s)
- Kiwamu Takahashi
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo (St Paul's) University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Taku Chibazakura
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
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18
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Butcher BG, Helmann JD. Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli. Mol Microbiol 2006; 60:765-82. [PMID: 16629676 DOI: 10.1111/j.1365-2958.2006.05131.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus subtilis produces many antibiotics of varying structures and specificity. Here we identify a prominent role for sigma(W), an extracytoplasmic function (ECF) sigma factor, in providing intrinsic resistance to antimicrobial compounds produced by other Bacilli. By using a panel of B. subtilis mutants disrupted for each of the 30 known sigma(W)-dependent operons we identified resistance genes for at least three different antimicrobial compounds. The ydbST and fosB genes contribute to resistance to antimicrobial compound(s) produced by B. amyloliquefaciens FZB42, the yqeZyqfAB operon provides resistance to the SPbeta prophage-encoded bacteriocin sublancin, and the yknWXYZ operon and yfhL provide resistance to the antimicrobial peptide SdpC. YfhL encodes a paralogue of SdpI, a membrane protein that provides immunity to SdpC. In competition experiments, we identify sigma(W) as a key factor in allowing B. subtilis to resist antibiotic killing and encroachment by competing strains. Together with the previous observation that sigma(W) provides inducible resistance against the Streptomyces antibiotic fosfomycin, these studies support the notion that sigma(W) controls an antibiosis regulon important in the microbial ecology of soil bacteria.
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Affiliation(s)
- Bronwyn G Butcher
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
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Itaya M, Tsuge K, Koizumi M, Fujita K. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci U S A 2005; 102:15971-6. [PMID: 16236728 PMCID: PMC1276048 DOI: 10.1073/pnas.0503868102] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cloning the whole 3.5-megabase (Mb) genome of the photosynthetic bacterium Synechocystis PCC6803 into the 4.2-Mb genome of the mesophilic bacterium Bacillus subtilis 168 resulted in a 7.7-Mb composite genome. We succeeded in such unprecedented large-size cloning by progressively assembling and editing contiguous DNA regions that cover the entire Synechocystis genome. The strain containing the two sets of genome grew only in the B. subtilis culture medium where all of the cloning procedures were carried out. The high structural stability of the cloned Synechocystis genome was closely associated with the symmetry of the bacterial genome structure of the DNA replication origin (oriC) and its termination (terC) and the exclusivity of Synechocystis ribosomal RNA operon genes (rrnA and rrnB). Given the significant diversity in genome structure observed upon horizontal DNA transfer in nature, our stable laboratory-generated composite genome raised fundamental questions concerning two complete genomes in one cell. Our megasize DNA cloning method, designated megacloning, may be generally applicable to other genomes or genome loci of free-living organisms.
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Affiliation(s)
- Mitsuhiro Itaya
- Mitsubishi Kagaku Institute of Life Sciences, 11 Minamiooya, Machida-shi, Tokyo 194-8511, Japan.
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20
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Moore CM, Gaballa A, Hui M, Ye RW, Helmann JD. Genetic and physiological responses of Bacillus subtilis to metal ion stress. Mol Microbiol 2005; 57:27-40. [PMID: 15948947 DOI: 10.1111/j.1365-2958.2005.04642.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Metal ion homeostasis is regulated principally by metalloregulatory proteins that control metal ion uptake, storage and efflux genes. We have used transcriptional profiling to survey Bacillus subtilis for genes that are rapidly induced by exposure to high levels of metal ions including Ag(I), Cd(II), Cu(II), Ni(II) and Zn(II) and the metalloid As(V). Many of the genes affected by metal stress were controlled by known metalloregulatory proteins (Fur, MntR, PerR, ArsR and CueR). Additional metal-induced genes are regulated by two newly defined metal-sensing ArsR/SmtB family repressors: CzrA and AseR. CzrA represses the CadA efflux ATPase and the cation diffusion facilitator CzcD and this repression is alleviated by Zn(II), Cd(II), Co(II), Ni(II) and Cu. CadA is the major determinant for Cd(II) resistance, while CzcD protects the cell against elevated levels of Zn(II), Cu, Co(II) and Ni(II). AseR negatively regulates itself and AseA, an As(III) efflux pump which contributes to arsenite resistance in cells lacking a functional ars operon. Our results extend the range of identified effectors for the As(III)-sensor ArsR to include Cd(II) and Ag(I) and for the Cu-sensor CueR to include Ag(I) and, weakly, Cd(II) and Zn(II). In addition to systems dedicated to metal homeostasis, specific metal stresses also strongly induced pathways related to cysteine, histidine and arginine metabolism.
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Affiliation(s)
- Charles M Moore
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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21
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447519 DOI: 10.1002/cfg.420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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