Journal: Microbial Biotechnology

Article Title: Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella

doi: 10.1111/1751-7915.70312

Figure Lengend Snippet: The opvAB operon in the genus Salmonella . (a) Delimitation of the opvAB ‐containing DNA fragment acquired by horizontal gene transfer (HGT). Analysis of GC content of opvAB and neighbouring regions. The sequence of Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14028 was analysed using SnapGene software. Diagram of GC content of the sequence located between opvA and yeiW genes. GC content suggests the boundary of the operon is located 220 nucleotides upstream of the opvA gene. The promoter‐proximal boundary of the HGT fragment is located 220 nucleotides upstream of opvA ATG. The diagram depicts the ribosome binding site, RBS (green), the −35 and −10 promoter modules (blue), the four GATCs (red) found in the upstream activating sequence (UAS) and the four OxyR binding sites, OBS A OBS B OBS C and OBS D (purple). (b) Assortment of the 992‐nucleotide sequence containing the opvAB operon in 5530 Salmonella genomes available in the NCBI database, classified by species and subspecies. Number of opvAB positive genomes among the sequences available at the NCBI database. A total of 824 genomes were annotated as S. enterica without subspecies‐level classification; among them, 344 contained the opvAB operon sequence. (c) Inter‐subspecies mutational landscape of the opvAB key regulatory elements across Salmonella enterica genomes classified by subspecies. Analysis includes mutations in the −35 and −10 promoter boxes, four GATC sites and four OxyR binding sites. Among the analysed genomes, 1710 correspond to subsp. enterica , 14 to subsp. arizonae , 20 to subsp. diarizonae and 18 to subsp. salamae . The reference sequence from strain ATCC 14028 is displayed below the heatmap. Each row represents a genome, and each column corresponds to a nucleotide position. OBS motifs are annotated following established consensus sequences, while invariant positions are shown in uppercase, degenerate positions (i.e., variable nucleotides) are shown in lowercase (Storz et al. ; Toledano et al. ). Nucleotide changes are represented by colours as follows: Substitutions (blue), insertions (green), deletions (red) and conserved positions (white).

Article Snippet: Unless otherwise noted, Salmonella enterica strains belong to serovar Typhimurium and are derived from the mouse‐virulent strain ATCC 14028.

Techniques: Sequencing, Software, Binding Assay

Journal: Microbial Biotechnology

Article Title: Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella

doi: 10.1111/1751-7915.70312

Figure Lengend Snippet: Intra‐subspecies mutational distribution in the regulatory region of the opvAB operon in Salmonella enterica subsp. enterica . (a) Localisation and distribution of mutations within the 220 nucleotides upstream of the opvA start codon, across S. enterica subsp. enterica genomes carrying between 1 and 8 mutations. Each row represents a genome, and each column corresponds to a nucleotide position. The nucleotide sequence of the ATCC 14028 strain used as reference is shown below the heatmap, with key regulatory elements such as GATC sites, OxyR binding sites (OBSs) and the −35 and −10 promoter boxes highlighted in colours. Nucleotides corresponding to conserved positions in the OBS consensus sequence are highlighted in green. Mutations are categorised as deletions (red), insertions (green) and substitutions (blue), while conserved nucleotides are represented in white. (b) Localisation and distribution of mutations within the regulatory region of opvAB in eight Salmonella strains collected in poultry farms. Each row represents one strain, and each column corresponds to a nucleotide position. The nucleotide sequence of the ATCC 14028 strain used as reference is shown below the heatmap, with key regulatory elements such as GATC sites, OxyR binding sites (OBSs) and the −35 and −10 promoter boxes highlighted in colours. Nucleotides corresponding to conserved positions in the OBS consensus sequence are highlighted in green. Mutations are categorised as deletions (red), insertions (green) and substitutions (blue), while conserved nucleotides are represented in white.

Article Snippet: Unless otherwise noted, Salmonella enterica strains belong to serovar Typhimurium and are derived from the mouse‐virulent strain ATCC 14028.

Techniques: Sequencing, Binding Assay

Journal: Microbial Biotechnology

Article Title: Structured Promoter Variability in Epigenetically Regulated Operons Contributes to Surface Adaptation in Salmonella

doi: 10.1111/1751-7915.70312

Figure Lengend Snippet: Intra‐subspecies mutational distribution in the regulatory region of the gtrABC operon in Salmonella enterica subsp. enterica . Localisation and distribution of mutations within the 220 nucleotides upstream of the gtrA start codon across S. enterica subsp. enterica genomes carrying between 1 and 8 mutations. Each row represents a genome, and each column corresponds to a nucleotide position. The nucleotide sequence of the ATCC 14028 strain used as reference is shown below the heatmap, with key regulatory elements such as GATC sites, OxyR binding sites (OBSs) and the −35 and −10 promoter boxes highlighted in colours (Broadbent et al. ). Nucleotides corresponding to conserved positions in the OBS consensus sequence are highlighted in green. Mutations are categorised as deletions (red), insertions (green) and substitutions (blue), while conserved nucleotides are represented in white.

Article Snippet: Unless otherwise noted, Salmonella enterica strains belong to serovar Typhimurium and are derived from the mouse‐virulent strain ATCC 14028.

Techniques: Sequencing, Binding Assay