RNA-seq transcriptome of Pseudomonas putida KT2440 subsisting on succinate as sole carbon source

Succinate is an intermediate in the tricarboxylic acid cycle. A dicarboxylic acid, succinate is seldom used as a carbon source for cultivating microorganisms. Thus, this work presents a unique opportunity to analyse the RNA-seq transcriptome of Pseudomonas putida KT2440 (ArrayExpress accession number: E-GEOD-46491) fed with succinate as sole carbon source. Through profiling 0.7 million reads, the transcriptome image gathered suggests a predominance of non-ribosomal peptide synthesis genes and outer membrane proteins. Expression of non-ribosomal peptide synthetase is particularly interesting given that RNA was extracted from cells in the mid-exponential phase. In total, highly expressed genes were: non-ribosomal peptide synthetase pvdL, flagellin fliC, TonB-dependent outer membrane ferripyoverdine fpvA, putative surface adhesion protein, non-ribosomal peptide synthetase pvdD, non-ribosomal peptide synthetase pvdJ, L-ornithine 5-monooxygenase pvdA, chaperonin GroEL, groL, non-ribosomal peptide synthetase pvdI, bifunctional succinyl-CoA synthetase subunit sucC, class 2 fumarate hydratase fumC-1, and succinyl-CoA synthetase subunit alpha sucD. High expression levels of sucC and sucD illustrated that part of the genome of P. putida KT2440 was sensitive to succinate and responded to its presence; thereby, implying the existence of a succinate regulon that remains to be deciphered. Hopefully, deeper analysis of the presented RNA-seq transcriptome with those of P. putida KT2440 subsisting on other carbon substrates would illuminate a more comprehensive picture of the differential gene expression pattern associated with succinate catabolism.