Purpose: The underlying molecular mechanism for Salmonella’s growth and survival in acidic environment inside raw tomato was investigated using RNA-seq approach.
Methods: mRNAs of Salmonella Newport strains grown to mid-log phase in hand-expressed tomato juices from different tomato varieties (round and Roma) and those in tryptic soy broth (TSB) at pH 7.0 and pH 4.1 were extracted and subjected to RNA-seq. Three biological replicates of RNA-seq from each sample were used to identify the differences among the transcriptomes (average 5 million 151-bp reads per sample). After mapping the paired-end reads to the 4,912 unique features within the closed annotated Salmonella Newport reference genome (CP001113), the R packages DESeq2 and EdgeR were used to identify genes with significantly different expression levels (P ≤ 0.05).
Results: Growth curves showed that Salmonella Newport strains grew much better in tomato juices (pH 3.8 - 4.0) than in TSB at pH 4.0, where Salmonella Newport strains survived poorly at pH below 4.0. Although the transcriptional profile of Salmonella Newport was not affected by tomato varieties (round versus Roma tomatoes), a principle component analysis showed that distinct transcriptional profiles existed between Salmonella growth in tomato juice and in TSB with pH 4.1. Different from response to growth medium, sigma 28 and its regulated operons as well as glp operon in Salmonella Newport were suppressed in responding to acidic environment in tomato.
Significance: Results here presented a global view of Salmonella Newport acid adaptation in tomato, which will guide further research efforts to control the unique challenge of Salmonella Newport contamination of raw tomato.