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Structure and transcriptional control of five phase-variable capsular polysaccharide (CPS) operons (PVR7, PVR8, PVR9, PVR11, PVR12) in B. intestinalis APC919/174. a Host transcriptional response in a B. intestinalis APC919/174-ΦcrAss001 serial broth co-culture (24-120h in vitro persistence) experiment, analyzed using RNAseq (values are log 2 fold gene transcript expression change relative to the un-infected control from two independent experimental runs); clone-8T, phage-resistant derivative of the parental strain; clone-8W, spontaneous phage-sensitive revertant clone; only genes with significantly changed expression ( p < 0.01 in DESeq2, n = 826) are shown; genes, associated with phase-variable genomic regions (PVR) are marked with color bars on top; b structure of phase variable operons, encoding five different CPS; protein sequence homologies (tBLASTx) between gene products are shown as colored parallelograms; two-sided arrows and ON/OFF labels mark positions of invertible promoters; c consensus sequence of the regions flanking invertible promoters (ON orientation) in CPS biosynthesis loci; approximate transcription start was identified though analysis of RNAseq data; stacked area charts show RNAseq read coverage of regions adjacent to the promoter in four CPS loci; d , e fraction of <t>concordantly-aligned</t> <t>Illumina</t> read pairs supporting orientation of invertible promoters in ON direction; WT, wild type strain; clones 8T, PhR1-9, phage-resistant derivatives; 8W, phage-sensitive revertant; P18d/P23d, samples in e were taken from the long-term in vitro persistence experiment (also see Additional file : Fig. S3 for similar data on the long term in vivo persistence)
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Structure and transcriptional control of five phase-variable capsular polysaccharide (CPS) operons (PVR7, PVR8, PVR9, PVR11, PVR12) in B. intestinalis APC919/174. a Host transcriptional response in a B. intestinalis APC919/174-ΦcrAss001 serial broth co-culture (24-120h in vitro persistence) experiment, analyzed using RNAseq (values are log 2 fold gene transcript expression change relative to the un-infected control from two independent experimental runs); clone-8T, phage-resistant derivative of the parental strain; clone-8W, spontaneous phage-sensitive revertant clone; only genes with significantly changed expression ( p < 0.01 in DESeq2, n = 826) are shown; genes, associated with phase-variable genomic regions (PVR) are marked with color bars on top; b structure of phase variable operons, encoding five different CPS; protein sequence homologies (tBLASTx) between gene products are shown as colored parallelograms; two-sided arrows and ON/OFF labels mark positions of invertible promoters; c consensus sequence of the regions flanking invertible promoters (ON orientation) in CPS biosynthesis loci; approximate transcription start was identified though analysis of RNAseq data; stacked area charts show RNAseq read coverage of regions adjacent to the promoter in four CPS loci; d , e fraction of <t>concordantly-aligned</t> <t>Illumina</t> read pairs supporting orientation of invertible promoters in ON direction; WT, wild type strain; clones 8T, PhR1-9, phage-resistant derivatives; 8W, phage-sensitive revertant; P18d/P23d, samples in e were taken from the long-term in vitro persistence experiment (also see Additional file : Fig. S3 for similar data on the long term in vivo persistence)
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Structure and transcriptional control of five phase-variable capsular polysaccharide (CPS) operons (PVR7, PVR8, PVR9, PVR11, PVR12) in B. intestinalis APC919/174. a Host transcriptional response in a B. intestinalis APC919/174-ΦcrAss001 serial broth co-culture (24-120h in vitro persistence) experiment, analyzed using RNAseq (values are log 2 fold gene transcript expression change relative to the un-infected control from two independent experimental runs); clone-8T, phage-resistant derivative of the parental strain; clone-8W, spontaneous phage-sensitive revertant clone; only genes with significantly changed expression ( p < 0.01 in DESeq2, n = 826) are shown; genes, associated with phase-variable genomic regions (PVR) are marked with color bars on top; b structure of phase variable operons, encoding five different CPS; protein sequence homologies (tBLASTx) between gene products are shown as colored parallelograms; two-sided arrows and ON/OFF labels mark positions of invertible promoters; c consensus sequence of the regions flanking invertible promoters (ON orientation) in CPS biosynthesis loci; approximate transcription start was identified though analysis of RNAseq data; stacked area charts show RNAseq read coverage of regions adjacent to the promoter in four CPS loci; d , e fraction of concordantly-aligned Illumina read pairs supporting orientation of invertible promoters in ON direction; WT, wild type strain; clones 8T, PhR1-9, phage-resistant derivatives; 8W, phage-sensitive revertant; P18d/P23d, samples in e were taken from the long-term in vitro persistence experiment (also see Additional file : Fig. S3 for similar data on the long term in vivo persistence)

Journal: BMC Biology

Article Title: Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

doi: 10.1186/s12915-021-01084-3

Figure Lengend Snippet: Structure and transcriptional control of five phase-variable capsular polysaccharide (CPS) operons (PVR7, PVR8, PVR9, PVR11, PVR12) in B. intestinalis APC919/174. a Host transcriptional response in a B. intestinalis APC919/174-ΦcrAss001 serial broth co-culture (24-120h in vitro persistence) experiment, analyzed using RNAseq (values are log 2 fold gene transcript expression change relative to the un-infected control from two independent experimental runs); clone-8T, phage-resistant derivative of the parental strain; clone-8W, spontaneous phage-sensitive revertant clone; only genes with significantly changed expression ( p < 0.01 in DESeq2, n = 826) are shown; genes, associated with phase-variable genomic regions (PVR) are marked with color bars on top; b structure of phase variable operons, encoding five different CPS; protein sequence homologies (tBLASTx) between gene products are shown as colored parallelograms; two-sided arrows and ON/OFF labels mark positions of invertible promoters; c consensus sequence of the regions flanking invertible promoters (ON orientation) in CPS biosynthesis loci; approximate transcription start was identified though analysis of RNAseq data; stacked area charts show RNAseq read coverage of regions adjacent to the promoter in four CPS loci; d , e fraction of concordantly-aligned Illumina read pairs supporting orientation of invertible promoters in ON direction; WT, wild type strain; clones 8T, PhR1-9, phage-resistant derivatives; 8W, phage-sensitive revertant; P18d/P23d, samples in e were taken from the long-term in vitro persistence experiment (also see Additional file : Fig. S3 for similar data on the long term in vivo persistence)

Article Snippet: For detection of PVR promoter inversions and variant analysis in the in vitro co-culture and mouse colonization experiments (Figs. d-e, b) paired Illumina reads were mapped to the assembled APC919/174 as a reference.

Techniques: Co-Culture Assay, In Vitro, Expressing, Infection, Sequencing, Clone Assay, In Vivo