Comparative Transcriptome Analysis Reveals Different Molecular Mechanisms of Bacillus coagulans 2-6 Response to Sodium Lactate and Calcium Lactate during Lactic Acid Production
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{"title"=>"Comparative transcriptome analysis reveals different molecular mechanisms of Bacillus coagulans 2-6 response to sodium lactate and calcium lactate during lactic acid production", "type"=>"journal", "authors"=>[{"first_name"=>"Jiayang", "last_name"=>"Qin", "scopus_author_id"=>"13104606300"}, {"first_name"=>"Xiuwen", "last_name"=>"Wang", "scopus_author_id"=>"36646943300"}, {"first_name"=>"Landong", "last_name"=>"Wang", "scopus_author_id"=>"56423814200"}, {"first_name"=>"Beibei", "last_name"=>"Zhu", "scopus_author_id"=>"56647307800"}, {"first_name"=>"Xiaohua", "last_name"=>"Zhang", "scopus_author_id"=>"56966794100"}, {"first_name"=>"Qingshou", "last_name"=>"Yao", "scopus_author_id"=>"56647457200"}, {"first_name"=>"Ping", "last_name"=>"Xu", "scopus_author_id"=>"55457651200"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84929460833", "pmid"=>"25875592", "doi"=>"10.1371/journal.pone.0124316", "pui"=>"604107217", "issn"=>"19326203", "scopus"=>"2-s2.0-84929460833"}, "id"=>"e8a8dfcb-c662-3877-8950-49435e0f674d", "abstract"=>"Lactate production is enhanced by adding calcium carbonate or sodium hydroxide during fermentation. However, Bacillus coagulans 2-6 can produce more than 180 g/L L-lactic acid when calcium lactate is accumulated, but less than 120 g/L L-lactic acid when sodium lactate is formed. The molecular mechanisms by which B. coagulans responds to calcium lactate and sodium lactate remain unclear. In this study, comparative transcriptomic methods based on high-throughput RNA sequencing were applied to study gene expression changes in B. coagulans 2-6 cultured in non-stress, sodium lactate stress and calcium lactate stress conditions. Gene expression profiling identified 712 and 1213 significantly regulated genes in response to calcium lactate stress and sodium lactate stress, respectively. Gene ontology assignments of the differentially expressed genes were performed. KEGG pathway enrichment analysis revealed that 'ATP-binding cassette transporters' were significantly affected by calcium lactate stress, and 'amino sugar and nucleotide sugar metabolism' was significantly affected by sodium lactate stress. It was also found that lactate fermentation was less affected by calcium lactate stress than by sodium lactate stress. Sodium lactate stress had negative effect on the expression of 'glycolysis/gluconeogenesis' genes but positive effect on the expression of 'citrate cycle (TCA cycle)' genes. However, calcium lactate stress had positive influence on the expression of 'glycolysis/gluconeogenesis' genes and had minor influence on 'citrate cycle (TCA cycle)' genes. Thus, our findings offer new insights into the responses of B. coagulans to different lactate stresses. Notably, our RNA-seq dataset constitute a robust database for investigating the functions of genes induced by lactate stress in the future and identify potential targets for genetic engineering to further improve L-lactic acid production by B. coagulans.", "link"=>"http://www.mendeley.com/research/comparative-transcriptome-analysis-reveals-different-molecular-mechanisms-bacillus-coagulans-26-resp-1", "reader_count"=>8, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Ph. D. Student"=>4, "Other"=>1}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Ph. D. Student"=>4, "Other"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>6}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Thailand"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2022030"], "description"=>"<p>Significantly upregulated genes involved in ‘glycolysis/gluconeogenesis’ under sodium lactate stress.</p>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380745, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124316.t006", "stats"=>{"downloads"=>5, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_upregulated_genes_involved_in_8216_glycolysis_gluconeogenesis_8217_under_sodium_lactate_stress_/1380745", "title"=>"Significantly upregulated genes involved in ‘glycolysis/gluconeogenesis’ under sodium lactate stress.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-15 03:17:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2022028"], "description"=>"<p>Significantly upregulated genes involved in ‘amino sugar and nucleotide sugar metabolism’ under sodium lactate stress.</p>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380743, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124316.t004", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_upregulated_genes_involved_in_8216_amino_sugar_and_nucleotide_sugar_metabolism_8217_under_sodium_lactate_stress_/1380743", "title"=>"Significantly upregulated genes involved in ‘amino sugar and nucleotide sugar metabolism’ under sodium lactate stress.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-15 03:17:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2022029"], "description"=>"<p>Significantly regulated genes involved in ‘amino sugar and nucleotide sugar metabolism’ under calcium lactate stress.</p>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380744, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124316.t005", "stats"=>{"downloads"=>7, "page_views"=>69, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_regulated_genes_involved_in_8216_amino_sugar_and_nucleotide_sugar_metabolism_8217_under_calcium_lactate_stress_/1380744", "title"=>"Significantly regulated genes involved in ‘amino sugar and nucleotide sugar metabolism’ under calcium lactate stress.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-15 03:17:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2022024"], "description"=>"<p>NA vs GY refers to the comparison between sodium lactate stressed (NA) and untreated (GY) groups. CA vs GY refers to the comparison between calcium lactate stressed (CA) and GY groups. NA vs CA refers to the comparison between NA and CA groups. Numbers in each section of the figure indicate the numbers of differently expressed genes in the indicated comparison.</p>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380739, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124316.g002", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_expressed_genes_that_are_unique_or_shared_among_three_groups_of_GY_NA_and_CA_/1380739", "title"=>"Differentially expressed genes that are unique or shared among three groups of GY, NA and CA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-15 03:17:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2022035", "https://ndownloader.figshare.com/files/2022036", "https://ndownloader.figshare.com/files/2022037", "https://ndownloader.figshare.com/files/2022038", "https://ndownloader.figshare.com/files/2022039", "https://ndownloader.figshare.com/files/2022040", "https://ndownloader.figshare.com/files/2022041", "https://ndownloader.figshare.com/files/2022042", "https://ndownloader.figshare.com/files/2022043", "https://ndownloader.figshare.com/files/2022044", "https://ndownloader.figshare.com/files/2022045"], "description"=>"<div><p>Lactate production is enhanced by adding calcium carbonate or sodium hydroxide during fermentation. However, <i>Bacillus coagulans</i> 2-6 can produce more than 180 g/L L-lactic acid when calcium lactate is accumulated, but less than 120 g/L L-lactic acid when sodium lactate is formed. The molecular mechanisms by which <i>B</i>. <i>coagulans</i> responds to calcium lactate and sodium lactate remain unclear. In this study, comparative transcriptomic methods based on high-throughput RNA sequencing were applied to study gene expression changes in <i>B</i>. <i>coagulans</i> 2-6 cultured in non-stress, sodium lactate stress and calcium lactate stress conditions. Gene expression profiling identified 712 and 1213 significantly regulated genes in response to calcium lactate stress and sodium lactate stress, respectively. Gene ontology assignments of the differentially expressed genes were performed. KEGG pathway enrichment analysis revealed that ‘ATP-binding cassette transporters’ were significantly affected by calcium lactate stress, and ‘amino sugar and nucleotide sugar metabolism’ was significantly affected by sodium lactate stress. It was also found that lactate fermentation was less affected by calcium lactate stress than by sodium lactate stress. Sodium lactate stress had negative effect on the expression of ‘glycolysis/gluconeogenesis’ genes but positive effect on the expression of ‘citrate cycle (TCA cycle)’ genes. However, calcium lactate stress had positive influence on the expression of ‘glycolysis/gluconeogenesis’ genes and had minor influence on ‘citrate cycle (TCA cycle)’ genes. Thus, our findings offer new insights into the responses of <i>B</i>. <i>coagulans</i> to different lactate stresses. Notably, our RNA-seq dataset constitute a robust database for investigating the functions of genes induced by lactate stress in the future and identify potential targets for genetic engineering to further improve L-lactic acid production by <i>B</i>. <i>coagulans</i>.</p></div>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380750, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0124316.s001", "https://dx.doi.org/10.1371/journal.pone.0124316.s002", "https://dx.doi.org/10.1371/journal.pone.0124316.s003", "https://dx.doi.org/10.1371/journal.pone.0124316.s004", "https://dx.doi.org/10.1371/journal.pone.0124316.s005", "https://dx.doi.org/10.1371/journal.pone.0124316.s006", "https://dx.doi.org/10.1371/journal.pone.0124316.s007", "https://dx.doi.org/10.1371/journal.pone.0124316.s008", "https://dx.doi.org/10.1371/journal.pone.0124316.s009", "https://dx.doi.org/10.1371/journal.pone.0124316.s010", "https://dx.doi.org/10.1371/journal.pone.0124316.s011"], "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_Transcriptome_Analysis_Reveals_Different_Molecular_Mechanisms_of_Bacillus_coagulans_2_6_Response_to_Sodium_Lactate_and_Calcium_Lactate_during_Lactic_Acid_Production/1380750", "title"=>"Comparative Transcriptome Analysis Reveals Different Molecular Mechanisms of <i>Bacillus coagulans</i> 2-6 Response to Sodium Lactate and Calcium Lactate during Lactic Acid Production", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-15 03:17:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2022032"], "description"=>"<p>*Significantly regulated gene under calcium lactate stress, others are significantly regulated genes under sodium lactate stress</p><p>Significantly regulated genes involved in ‘citrate cycle (TCA cycle)’ under lactate stress.</p>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380747, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124316.t008", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_regulated_genes_involved_in_8216_citrate_cycle_TCA_cycle_8217_under_lactate_stress_/1380747", "title"=>"Significantly regulated genes involved in ‘citrate cycle (TCA cycle)’ under lactate stress.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-15 03:17:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/2022031"], "description"=>"<p>Significantly upregulated genes involved in ‘glycolysis/gluconeogenesis’ under calcium lactate stress.</p>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380746, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124316.t007", "stats"=>{"downloads"=>3, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_upregulated_genes_involved_in_8216_glycolysis_gluconeogenesis_8217_under_calcium_lactate_stress_/1380746", "title"=>"Significantly upregulated genes involved in ‘glycolysis/gluconeogenesis’ under calcium lactate stress.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-15 03:17:27"}
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  • {"files"=>["https://ndownloader.figshare.com/files/2022022"], "description"=>"<p>All 2,053 transcripts were assigned to at least one GO term and were grouped into three main GO categories and 43 groups, 19 groups in biological process, 12 in cellular component, and 12 in molecular function. The right-hand Y-axis represents the number of genes in a sub-category. The left-hand Y-axis indicates the percentage of a specific sub-category of genes in each main category.</p>", "links"=>[], "tags"=>["Sodium lactate stress", "KEGG pathway enrichment analysis", "calcium lactate stress", "gene ontology assignments", "tca", "study gene expression changes", "calcium lactate", "coagulan", "Production Lactate production", "sodium lactate", "rna", "Comparative Transcriptome Analysis", "calcium lactate stress conditions", "Different Molecular Mechanisms"], "article_id"=>1380737, "categories"=>["Uncategorised"], "users"=>["Jiayang Qin", "Xiuwen Wang", "Landong Wang", "Beibei Zhu", "Xiaohua Zhang", "Qingshou Yao", "Ping Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0124316.g001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_GO_functional_annotation_of_transcripts_/1380737", "title"=>"Gene Ontology (GO) functional annotation of transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-15 03:17:27"}

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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