Genome Sequence of Bacillus endophyticus and Analysis of Its Companion Mechanism in the Ketogulonigenium vulgare-Bacillus Strain Consortium
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{"title"=>"Genome sequence of Bacillus endophyticus and analysis of its companion mechanism in the Ketogulonigenium vulgare-Bacillus strain consortium", "type"=>"journal", "authors"=>[{"first_name"=>"Nan", "last_name"=>"Jia", "scopus_author_id"=>"56857234400"}, {"first_name"=>"Jin", "last_name"=>"Du", "scopus_author_id"=>"36491314600"}, {"first_name"=>"Ming Zhu", "last_name"=>"Ding", "scopus_author_id"=>"25647398800"}, {"first_name"=>"Feng", "last_name"=>"Gao", "scopus_author_id"=>"56431760600"}, {"first_name"=>"Ying Jin", "last_name"=>"Yuan", "scopus_author_id"=>"7402709347"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"606057345", "doi"=>"10.1371/journal.pone.0135104", "sgr"=>"84941979078", "pmid"=>"26248285", "scopus"=>"2-s2.0-84941979078"}, "id"=>"4276e05a-cd5c-30ab-881f-efcf84d7004c", "abstract"=>"Bacillus strains have been widely used as the companion strain of Ketogulonigenium vulgare in the process of vitamin C fermentation. Different Bacillus strains generate different effects on the growth of K. vulgare and ultimately influence the productivity. First, we identified that Bacillus endophyticus Hbe603 was an appropriate strain to cooperate with K. vulgare and the product conversion rate exceeded 90% in industrial vitamin C fermentation. Here, we report the genome sequencing of the B. endophyticus Hbe603 industrial companion strain and speculate its possible advantage in the consortium. The circular chromosome of B. endophyticus Hbe603 has a size of 4.87 Mb with GC content of 36.64% and has the highest similarity with that of Bacillus megaterium among all the bacteria with complete genomes. By comparing the distribution of COGs with that of Bacillus thuringiensis, Bacillus cereus and B. megaterium, B. endophyticus has less genes related to cell envelope biogenesis and signal transduction mechanisms, and more genes related to carbohydrate transport and metabolism, energy production and conversion, as well as lipid transport and metabolism. Genome-based functional studies revealed the specific capability of B. endophyticus in sporulation, transcription regulation, environmental resistance, membrane transportation, extracellular proteins and nutrients synthesis, which would be beneficial for K. vulgare. In particular, B. endophyticus lacks the Rap-Phr signal cascade system and, in part, spore coat related proteins. In addition, it has specific pathways for vitamin B12 synthesis and sorbitol metabolism. The genome analysis of the industrial B. endophyticus will help us understand its cooperative mechanism in the K. vulgare-Bacillus strain consortium to improve the fermentation of vitamin C.", "link"=>"http://www.mendeley.com/research/genome-sequence-bacillus-endophyticus-analysis-companion-mechanism-ketogulonigenium-vulgarebacillus", "reader_count"=>9, "reader_count_by_academic_status"=>{"Researcher"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Other"=>1, "Professor"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Other"=>1, "Professor"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>6, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2204580"], "description"=>"<p>Predicted sigma factors in <i>B</i>. <i>endophyticus</i> Hbe603.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505088, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.t002", "stats"=>{"downloads"=>7, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_sigma_factors_in_B_endophyticus_Hbe603_/1505088", "title"=>"Predicted sigma factors in <i>B</i>. <i>endophyticus</i> Hbe603.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204578"], "description"=>"<p>The red dashed line represents the defected pathways in <i>K</i>. <i>vulgare</i>.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505086, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.g006", "stats"=>{"downloads"=>0, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_interaction_and_communication_between_K_vulgare_Y25_and_B_endophyticus_Hbe603_at_a_genome_wide_scale_/1505086", "title"=>"Schematic representation of the interaction and communication between <i>K</i>. <i>vulgare</i> Y25 and <i>B</i>. <i>endophyticus</i> Hbe603 at a genome-wide scale.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204575"], "description"=>"<p>The information presented here corresponds to the original annotation. Alterations could occur due to possible updates. The information is in accordance to the genome information provided in the corresponding NCBI .gbk files. COG designations are described as follows: C, Energy production and conversion; D, Cell division and chromosome partitioning; E, Amino acid transport and metabolism; F, Nucleotide transport and metabolism; G, Carbohydrate transport and metabolism; H, Coenzyme metabolism; I, Lipid metabolism; J, Translation, ribosomal structure and biogenesis; K, Transcription; L, DNA replication, recombination, and repair; M, Cell envelope biogenesis, outer membrane; N, Cell motility and secretion; O, Posttranslational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; Q, Secondary metabolite biosynthesis, transport and catabolism; R, General function prediction only; S, Function unknown; T, Signal transduction mechanisms; U, Intracellular trafficking and secretion; V, Defense mechanisms.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505083, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.g003", "stats"=>{"downloads"=>0, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_COG_analysis_of_B_endophyticus_Hbe603_with_other_Bacillus_species_/1505083", "title"=>"COG analysis of <i>B</i>. <i>endophyticus</i> Hbe603 with other <i>Bacillus</i> species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204566"], "description"=>"<p>Circles from the outside to the inside show the positions of protein-coding genes (blue), tRNA genes (red) and rRNA genes (pink) on the positive (circle 1), and negative (circle 2) strands. Circles 3–5 show the positions of BLAST hits detected through blastx comparisons of <i>B</i>. <i>endophyticus</i> Hbe603 against <i>B</i>. <i>megaterium</i> QM B1551 (circle 3), <i>B</i>. <i>megaterium</i> DSM 319 (circle 4) and <i>B</i>. <i>megaterium</i> WSH-002 (circle 5). The height of the shading in the BLAST results rings is proportional to the percentage of identity of the hit. Circles 6 and 7 show plots of GC content and GC skew plotted as the deviation from the average for the entire sequence.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505076, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.g001", "stats"=>{"downloads"=>0, "page_views"=>51, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_genome_visualization_of_B_endophyticus_Hbe603_/1505076", "title"=>"Circular genome visualization of <i>B</i>. <i>endophyticus</i> Hbe603.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204582", "https://ndownloader.figshare.com/files/2204583", "https://ndownloader.figshare.com/files/2204584", "https://ndownloader.figshare.com/files/2204585", "https://ndownloader.figshare.com/files/2204586"], "description"=>"<div><p><i>Bacillus</i> strains have been widely used as the companion strain of <i>Ketogulonigenium vulgare</i> in the process of vitamin C fermentation. Different <i>Bacillus</i> strains generate different effects on the growth of <i>K</i>. <i>vulgare</i> and ultimately influence the productivity. First, we identified that <i>Bacillus endophyticus</i> Hbe603 was an appropriate strain to cooperate with <i>K</i>. <i>vulgare</i> and the product conversion rate exceeded 90% in industrial vitamin C fermentation. Here, we report the genome sequencing of the <i>B</i>. <i>endophyticus</i> Hbe603 industrial companion strain and speculate its possible advantage in the consortium. The circular chromosome of <i>B</i>. <i>endophyticus</i> Hbe603 has a size of 4.87 Mb with GC content of 36.64% and has the highest similarity with that of <i>Bacillus megaterium</i> among all the bacteria with complete genomes. By comparing the distribution of COGs with that of <i>Bacillus thuringiensis</i>, <i>Bacillus cereus</i> and <i>B</i>. <i>megaterium</i>, <i>B</i>. <i>endophyticus</i> has less genes related to cell envelope biogenesis and signal transduction mechanisms, and more genes related to carbohydrate transport and metabolism, energy production and conversion, as well as lipid transport and metabolism. Genome-based functional studies revealed the specific capability of <i>B</i>. <i>endophyticus</i> in sporulation, transcription regulation, environmental resistance, membrane transportation, extracellular proteins and nutrients synthesis, which would be beneficial for <i>K</i>. <i>vulgare</i>. In particular, <i>B</i>. <i>endophyticus</i> lacks the Rap-Phr signal cascade system and, in part, spore coat related proteins. In addition, it has specific pathways for vitamin B12 synthesis and sorbitol metabolism. The genome analysis of the industrial <i>B</i>. <i>endophyticus</i> will help us understand its cooperative mechanism in the <i>K</i>. <i>vulgare</i>-<i>Bacillus</i> strain consortium to improve the fermentation of vitamin C.</p></div>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505090, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0135104.s001", "https://dx.doi.org/10.1371/journal.pone.0135104.s002", "https://dx.doi.org/10.1371/journal.pone.0135104.s003", "https://dx.doi.org/10.1371/journal.pone.0135104.s004", "https://dx.doi.org/10.1371/journal.pone.0135104.s005"], "stats"=>{"downloads"=>23, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Sequence_of_Bacillus_endophyticus_and_Analysis_of_Its_Companion_Mechanism_in_the_Ketogulonigenium_vulgare_Bacillus_Strain_Consortium/1505090", "title"=>"Genome Sequence of <i>Bacillus endophyticus</i> and Analysis of Its Companion Mechanism in the <i>Ketogulonigenium vulgare-Bacillus</i> Strain Consortium", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204577"], "description"=>"<p>Blue bars represent the forward and reverse strands of DNA with CDSs marked as arrows. The scale is marked in base pairs. The red bars represent normal tblastx matches. Inverted matches are colored in blue, and the depth of shading is indicative of the percentage blast match.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505085, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.g005", "stats"=>{"downloads"=>0, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_genes_related_to_vitamin_B12_synthesis_in_B_endophyticus_Hbe603_by_Easyfig_/1505085", "title"=>"Schematic representation of the genes related to vitamin B12 synthesis in <i>B</i>. <i>endophyticus</i> Hbe603 by Easyfig.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204576"], "description"=>"<p>A). Growth curve the <i>B</i>. <i>endophyticus</i> Hbe603 strain grown in seed medium with D-sorbitol (2%). The Y axis represents the average OD<sub>600</sub> of triplicate bacterial cultures at each time point. B). Extracellular concentration of D-sorbitol. Data are averages of three independent experiments.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505084, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.g004", "stats"=>{"downloads"=>0, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Growth_features_of_the_B_endophyticus_Hbe603_strain_/1505084", "title"=>"Growth features of the <i>B</i>. <i>endophyticus</i> Hbe603 strain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204571"], "description"=>"<p>The phylogenetic tree of <i>B</i>. <i>endophyticus</i> Hbe603 was constructed using CVTree with parameters K = 6 and Type = aa. The neighbor-joining tree was constructed using the MEGA5 program based on the CVTree results. Note that <i>Geobacillus kaustophilus</i> HTA426 was included as an outgroup.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505081, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.g002", "stats"=>{"downloads"=>2, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_B_endophyticus_Hbe603_with_other_species_/1505081", "title"=>"Phylogenetic analysis of <i>B</i>. <i>endophyticus</i> Hbe603 with other species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204581"], "description"=>"<p>Predicted genes related to PTS system in <i>B</i>. <i>endophyticus</i> Hbe603.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505089, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.t003", "stats"=>{"downloads"=>3, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_genes_related_to_PTS_system_in_B_endophyticus_Hbe603_/1505089", "title"=>"Predicted genes related to PTS system in <i>B</i>. <i>endophyticus</i> Hbe603.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-08-06 04:19:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2204579"], "description"=>"<p>General features of the genome sequence of <i>B</i>. <i>endophyticus</i> Hbe603 and 2102.</p>", "links"=>[], "tags"=>["companion strain", "vitamin C", "gc", "vitamin B 12 synthesis", "Different Bacillus strains", "vulgare", "cell envelope biogenesis", "cog", "endophyticus Hbe 603", "product conversion rate", "metabolism", "signal transduction mechanisms", "Bacillus endophyticus Hbe 603", "genome"], "article_id"=>1505087, "categories"=>["Biological Sciences"], "users"=>["Nan Jia", "Jin Du", "Ming-Zhu Ding", "Feng Gao", "Ying-Jin Yuan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135104.t001", "stats"=>{"downloads"=>2, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_features_of_the_genome_sequence_of_B_endophyticus_Hbe603_and_2102_/1505087", "title"=>"General features of the genome sequence of <i>B</i>. <i>endophyticus</i> Hbe603 and 2102.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-08-06 04:19:35"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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