E-GEOD-46491 - The glycolytic and gluconeogenic transcriptome of Pseudomonas putida KT2440

Released on 23 July 2013, last updated on 3 May 2014
Pseudomonas putida KT2440
Samples (4)
Protocols (4)
Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida grown in different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on glycolytic (glucose, fructose) and gluconeogenic (succinate or glycerol) substrates revealed that > 20% of the P. putida genome is differentially expressed depending on the ensuing metabolic regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNAP, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the different growth conditions. Furthermore, we found that the two small RNAs crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose. cDNA libraries from Pseudomonas supplemented with different carbon sources (glucose, glycerol, fructose, succinate) were sequenced using HiSeq 2000 to yield 91 paired-end reads. Gene expression values were compared.
Experiment type
RNA-seq of coding RNA 
Juan Carlos Oliveros <geo@ncbi.nlm.nih.gov>, Juan C Oliveros, Juhyun Kim, Rafael Silva-Rocha, Víctor de Lorenzo
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-46491.idf.txt
Sample and data relationshipE-GEOD-46491.sdrf.txt
Processed data (1)E-GEOD-46491.processed.1.zip