Transcriptomic analysis of the stationary phase response regulator SpdR in Caulobacter crescentus

BMC Microbiology

Table 1 Genes differentially expressed in the ΔspdR mutant relative to the wild type strain

Gene^a	Fold change^b	Putative function^c
Downregulated
CC0035	0.229	Small subunit ribosomal protein S15
CC0247	0.163	Two-component system, response regulator SpdR
CC0260	0.483	Ribonucleoside-diphosphate reductase beta chain
CC0445	0.366	GntR family transcriptional regulator NagR
CC0446	0.231	TonB-dependent receptor NagA
CC0482	0.327	5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase
CC0517	0.289	Protein of unknown function
CC0583	0.380	Succinylarginine dihydrolase
CC0653	0.331	CarD_CdnL_TRCF family transcriptional regulator
CC0679	0.380	Abi-domain protein
CC0731	0.340	Protein of unknown function
CC0873	0.385	Toxin ParE1 from a toxin-antitoxin system
CC1005	0.354	Protein of unknown function
CC1247	0.317	Small subunit ribosomal protein S10/NusE
CC1363	0.456	Membrane-bound proton translocating pyrophosphatase
CC1387	0.344	Cold-shock protein CspD
CC1745	0.291	RNA-binding protein Hfq
CC1746	0.312	GTP-binding protein HflX
CC1991	0.470	Preprotein translocase subunit SecD
CC2912	0.350	Quinolinate synthetase
CC3164	0.389	Cro/CI family transcriptional regulator
CC3205	0.456	Transcription antitermination protein NusG
CC3268	0.455	Protein of unknown function
CC3270	0.394	Cro/CI family transcriptional regulator
Upregulated
CC2114	2.331	Methyltransferase of unknown specificity
CC2234	2.924	Protein of unknown function
CC3404	2.740	Protein of unknown function
CC3654	29.412	Protein of unknown function
CC3655	17.857	Malate dehydrogenase

^aAccording to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database for the C. crescentus CB15 genome
^bValues are the ∆spdR/WT ratio determined by microarray hybridization of RNA samples isolated from cells at the stationary growth phase (24 h after dilution of culture to OD₆₀₀ = 0.1). Genes with M value of < 0.5 or > 2.0 were assumed as differentially expressed between strains analyzed. Results shown are the average of four independent biological experiments
^cAccording to a reanalysis of the deduced protein sequences by using Pfam [61] and BLASTP [62] to search for conserved domains and proteins with predicted function, respectively

ISSN: 1471-2180