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.

琥珀酸（succinate）是三羧酸循环（tricarboxylic acid cycle）中的中间代谢产物。作为一种二羧酸（dicarboxylic acid），琥珀酸极少被用作微生物培养的单一碳源。因此，本研究为解析以琥珀酸为唯一碳源的恶臭假单胞菌（Pseudomonas putida）KT2440的RNA测序转录组（RNA-seq transcriptome）提供了独特契机，该数据集的ArrayExpress数据库登录号为E-GEOD-46491。
本研究通过对70万条测序读段（reads）进行分析，所获得的转录组图谱显示，非核糖体肽合成基因与外膜蛋白的表达占据主导地位。鉴于RNA提取自指数生长中期的菌体细胞，非核糖体肽合成酶的表达特征尤为引人关注。
总计筛选得到的高表达基因包括：非核糖体肽合成酶pvdL、鞭毛蛋白fliC、依赖TonB的外膜铁载假单胞菌素转运蛋白fpvA、推定表面黏附蛋白、非核糖体肽合成酶pvdD、非核糖体肽合成酶pvdJ、L-鸟氨酸5-单加氧酶pvdA、分子伴侣GroEL、groL、非核糖体肽合成酶pvdI、双功能琥珀酰辅酶A合成酶亚基sucC、2类延胡索酸水合酶fumC-1，以及琥珀酰辅酶A合成酶α亚基sucD。
sucC与sucD的高表达表明，恶臭假单胞菌KT2440的部分基因组对琥珀酸具有响应敏感性，进而暗示存在尚未被阐明的琥珀酸调控子（succinate regulon）。
本研究希望通过将本次获得的RNA测序转录组数据，与以其他碳源存活的恶臭假单胞菌KT2440的转录组数据开展深入对比分析，以更全面地阐明与琥珀酸分解代谢相关的差异基因表达模式。