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 <i>Pseudomonas putida</i> 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 <i>pvdL</i>, flagellin <i>fliC</i>, TonB-dependent outer membrane ferripyoverdine <i>fpvA</i>, putative surface adhesion protein, non-ribosomal peptide synthetase <i>pvdD</i>, non-ribosomal peptide synthetase <i>pvdJ</i>, L-ornithine 5-monooxygenase <i>pvdA</i>, chaperonin GroEL, <i>groL</i>, non-ribosomal peptide synthetase <i>pvdI</i>, bifunctional succinyl-CoA synthetase subunit <i>sucC</i>, class 2 fumarate hydratase <i>fumC-1</i>, and succinyl-CoA synthetase subunit alpha <i>sucD</i>. High expression levels of <i>sucC </i>and <i>sucD </i>illustrated that part of the genome of <i>P. putida</i> 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 <i>P. putida</i> KT2440 subsisting on other carbon substrates would illuminate a more comprehensive picture of the differential gene expression pattern associated with succinate catabolism.<br><br>