Journal: Frontiers in Microbiology

Article Title: Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

doi: 10.3389/fmicb.2018.00307

Figure Lengend Snippet: Genome statistics of B. licheniformis DW2.

Article Snippet: The DW2 strain used in this study was provided by China Center for Type Culture Collection (CCTCC), whose number was CCTCC M2011344.

Techniques:

Journal: Frontiers in Microbiology

Article Title: Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

doi: 10.3389/fmicb.2018.00307

Figure Lengend Snippet: General genome features of the four B. licheniformis strains.

Article Snippet: The DW2 strain used in this study was provided by China Center for Type Culture Collection (CCTCC), whose number was CCTCC M2011344.

Techniques: Sequencing

Journal: Frontiers in Microbiology

Article Title: Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

doi: 10.3389/fmicb.2018.00307

Figure Lengend Snippet: Comparative genomics of four B. licheniformis strains and other genomic features of B. licheniformis DW2. (A) Multiple genomic alignments of four B. licheniformis strains. (B) Distribution of 6mA motifs in B. licheniformis DW2 genome. (C) The operon acoABCL associated with acetoin catabolism in B. licheniformis DW2. (D) The stage V sporulation protein in B. licheniformis DW2.

Article Snippet: The DW2 strain used in this study was provided by China Center for Type Culture Collection (CCTCC), whose number was CCTCC M2011344.

Techniques:

Journal: Frontiers in Microbiology

Article Title: Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

doi: 10.3389/fmicb.2018.00307

Figure Lengend Snippet: Gene expression of wild B. licheniformis DW2 and AbrB-knockout strains. (A) The correlation of three biological replicates in three time points of wild and AbrB-knockout strains. (B) The AbrB gene was knocked out and not expressed in AbrB-knockout strain. (C) The number of expressed genes in three different time points of wild and AbrB-knockout strains. (D) The different gene expression pattern between wild and AbrB-knockout strains.

Article Snippet: The DW2 strain used in this study was provided by China Center for Type Culture Collection (CCTCC), whose number was CCTCC M2011344.

Techniques: Gene Expression, Knock-Out

Journal: Frontiers in Microbiology

Article Title: Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2

doi: 10.3389/fmicb.2018.00307

Figure Lengend Snippet: Functional enrichment of DEGs and different expression of bacitracin biosynthesis related genes. (A) The functional categories of DEGs in three different time points of wild type and AbrB-knockout strains. (B) The top 20 significantly enriched pathways of DEGs in three time points. (C) The cluster of bacitracin biosynthesis related genes in B. licheniformis DW2. (D) The different expression of bacitracin biosynthesis related genes bacA, bacB, bacC and bacT between wild and AbrB-knockout strains.

Article Snippet: The DW2 strain used in this study was provided by China Center for Type Culture Collection (CCTCC), whose number was CCTCC M2011344.

Techniques: Functional Assay, Expressing, Knock-Out

Journal: Applied and Environmental Microbiology

Article Title: Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis

doi: 10.1128/AEM.00262-18

Figure Lengend Snippet: AbrB negatively regulates pulcherriminic acid biosynthesis by binding to the promoter of yvmC-cypX. (A) Effects of abrB deletion (DW2 ΔabrB) and overexpression (DW2/pHY-abrB) on pulcherriminic acid production. (B) Gene transcription variations in abrB deletion and overexpression strains. The transcription levels of genes in DW2 were set to 1. (C) Binding of the AbrB protein to the promoter regions of yvmC and yvnA. Gel shifts of the labeled 91-bp P1-yvmC and P1-yvnA probes by the AbrB protein are shown. The concentrations of AbrB in lanes 1 to 8 were 0, 1, 2, 5, 0, 1, 2, and 5 ng/μl, respectively. Twenty nanograms of the P1-yvmC (lanes 1 to 4) or P1-yvnA (lanes 5 to 8) probe was added to each lane. The nonspecific competitor poly(dI-dC) was added to the EMSA binding buffer. (D) Expression-level comparisons of PyvmC-amyL and PyvnA-amyL transcriptional fusions. The amyL gene on the chromosome was deleted in DW2 and DW2 ΔabrB for the construction of DW2 ΔamyL and DW2 ΔabrB Δamy, respectively. pHY-PyvmC-amyL was then transformed into DW2 ΔamyL and DW2 ΔabrB ΔamyL to construct DW2 ΔamyL/pHY-PyvmC-amyL and DW2 ΔabrB ΔamyL/pHY-PyvmC-amyL. pHY-PyvnA-amyL was transformed into DW2 ΔamyL and DW2 ΔabrB ΔamyL to construct DW2 ΔamyL/pHY-PyvnA-amyL and DW2 ΔabrB ΔamyL/pHY-PyvnA-amyL.

Article Snippet: DW2 , Wild type (CCTCC M2011344) , CCTCC.

Techniques: Binding Assay, Over Expression, Labeling, Expressing, Transformation Assay, Construct

Journal: Applied and Environmental Microbiology

Article Title: Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis

doi: 10.1128/AEM.00262-18

Figure Lengend Snippet: YvmB represses pulcherriminic acid biosynthesis by binding to the promoter of yvmC-cypX. (A) Effects of yvmB deletion (DW2 ΔyvmB) and overexpression (DW2/pHY-yvmB) on pulcherriminic acid production. (B) Gene transcription variations in yvmB deletion and overexpression strains. (C) Binding of the YvmB protein to the promoter regions of yvmC and yvmA. Gel shifts of the labeled P2-yvmC (87 bp) and P1-yvmA (91 bp) probes by the YvmB protein are shown. The concentrations of YvmB in lanes 1 to 8 were 0, 1, 2, 5, 0, 1, 2, and 5 ng/μl, respectively. Twenty nanograms of the P2-yvmC (lanes 1 to 4) or P1-yvmA (lanes 5 to 8) probe was added to each lane. The nonspecific competitor poly(dI-dC) was added to the EMSA binding buffer. (D) Expression-level comparisons of PyvmC-amyL and PyvmA-amyL transcriptional fusions. The amyL gene on the chromosome was deleted in DW2 ΔyvmB for the construction of DW2 ΔyvmB ΔamyL. pHY-PyvmC-amyL was transformed into DW2 ΔamyL and DW2 ΔyvmB ΔamyL to construct DW2 ΔamyL/pHY-PyvmC-amyL and DW2 ΔyvmB ΔamyL/pHY-PyvmC-amyL. pHY-PyvmA-amyL was transformed into DW2 ΔamyL and DW2 ΔyvmB ΔamyL to construct DW2 ΔamyL/pHY-PyvmA-amyL and DW2 ΔyvmB ΔamyL/pHY-PyvmA-amyL.

Article Snippet: DW2 , Wild type (CCTCC M2011344) , CCTCC.

Techniques: Binding Assay, Over Expression, Labeling, Expressing, Transformation Assay, Construct

Journal: Applied and Environmental Microbiology

Article Title: Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis

doi: 10.1128/AEM.00262-18

Figure Lengend Snippet: Influence of YvnA on pulcherriminic acid biosynthesis. (A) Effects of yvnA on pulcherriminic acid production. The DW2 ΔyvnA ΔyvmB strain was set as a control to exclude the effects of yvmB. DW2/pHY-yvnA and DW2 ΔyvnA ΔyvmB/pHY-yvnA did not produce pulcherriminic acid (data not shown). (B) Effects of yvnA deletion and overexpression on gene transcription. (C) Binding of the YvnA protein to the promoter regions of yvmC and yvmB. Gel shifts of the labeled P2-yvmC (87 bp) and P2-yvmB (87 bp) probes by the YvnA protein are shown. The concentrations of YvnA in lanes 1 to 8 were 0, 1, 2, 5, 0, 1, 2, and 5 ng/μl, respectively. Twenty nanograms of the P2-yvmC (lanes 1 to 4) or P2-yvmB (lanes 5 to 8) probe was added to each lane. The nonspecific competitor poly(dI-dC) was added to the EMSA binding buffer. (D) Expression-level comparisons of PyvmC-amyL and PyvmB-amyL transcriptional fusions. The amyL gene on the chromosome was deleted in DW2 ΔyvmB and DW2 ΔyvmB ΔyvnA for the construction of DW2 ΔyvmB ΔamyL and DW2 ΔyvmB ΔyvnA ΔamyL, respectively. pHY-PyvmC-amyL was transformed into DW2 ΔyvmB ΔamyL and DW2 ΔyvmB ΔyvnA ΔamyL to construct DW2 ΔyvmB ΔamyL/pHY-PyvmC-amyL and DW2 ΔyvmB ΔyvnA ΔamyL/pHY-PyvmC-amyL, respectively. pHY-PyvmB-amyL was transformed into DW2 ΔyvmB ΔamyL and DW2 ΔyvmB ΔyvnA ΔamyL to construct DW2 ΔyvmB ΔamyL/pHY-PyvmB-amyL and DW2 ΔyvmB ΔyvnA ΔamyL/pHY-PyvmB-amyL, respectively.

Article Snippet: DW2 , Wild type (CCTCC M2011344) , CCTCC.

Techniques: Control, Over Expression, Binding Assay, Labeling, Expressing, Transformation Assay, Construct

Journal: Applied and Environmental Microbiology

Article Title: Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis

doi: 10.1128/AEM.00262-18

Figure Lengend Snippet: YvmA is required for secretion of pulcherriminic acid. (A) Effects of yvmA deletion (DW2 ΔyvmA) and overexpression (DW2/pHY-yvmA) on pulcherriminic acid production. (B) Gene transcription variations in yvmA deletion and overexpression strains. The transcription levels of genes in DW2 were set to 1. (C) Effects of yvmA deletion (DW2 ΔyvmA) and overexpression (DW2/pHY-yvmA) on intracellular accumulation of pulcherriminic acid.

Article Snippet: DW2 , Wild type (CCTCC M2011344) , CCTCC.

Techniques: Over Expression

Journal: Applied and Environmental Microbiology

Article Title: Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis

doi: 10.1128/AEM.00262-18

Figure Lengend Snippet: Formation of pigmented halo and inhibition zone around F. oxysporum on PDA plates

Article Snippet: DW2 , Wild type (CCTCC M2011344) , CCTCC.

Techniques: Inhibition

Journal: Applied and Environmental Microbiology

Article Title: Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis

doi: 10.1128/AEM.00262-18

Figure Lengend Snippet: Effects of FeCl3 concentration on transcription of genes. The relative transcription levels of the genes in DW2 (A), DW2 ΔyvnA (B), and DW2 ΔyvnA ΔyvmB (C) in media containing 0, 5, and 20 mg/liter FeCl3 are shown. The transcription levels of genes in DW2 in the medium contain 0 mg/liter FeCl3 were set to 1.

Article Snippet: DW2 , Wild type (CCTCC M2011344) , CCTCC.

Techniques: Concentration Assay

Journal: Applied and Environmental Microbiology

Article Title: Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis

doi: 10.1128/AEM.00262-18

Figure Lengend Snippet: Bacterial strains and plasmids used for this study

Article Snippet: DW2 , Wild type (CCTCC M2011344) , CCTCC.

Techniques: Plasmid Preparation, Knock-Out, Expressing