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Table 1 Expression analysis of σ F -dependent genes upon dichromate stress

From: Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress

      Microarrayf qRT-PCRg
Gene numbera Lengthb TMc Domaind Putative identificatione ΔsigF Cr/ WT Cr WT Cr/ WT no stress ΔsigF Cr/ΔsigF no stress ΔsigF Cr/WT Cr
CC2748 313   Oxidored_molyb sulfite oxidase subunit YedY −2.097 4.654 2.500 −2.154
CC2905 261   DUF2063 protein of unknown function −1.299 2.164 −0.481 −2.645
CC2906 289   DUF692 protein of unknown function −2.917 3.358 0.967 −2.392
CC2907 105 1 DUF2282 predicted integral membrane protein −2.386 NA NA NA
CC3252 214 6 DUF1109 negative regulator of σF NC 1.577 0.265 −1.312
CC3253 179   Sigma70_r2 Sigma70_r4 ECF sigma factor σF NC NA NA NA
CC3254 93 1 DUF2282 predicted integral membrane protein −4.904 NA NA NA
CC3255 280   DUF692 protein of unknown function −4.783 4.697 −1.123 −5.820
CC3256 254   DUF2063 protein of unknown function −3.311 NA NA NA
CC3257 150 2 DoxX protein of DoxX family −2.644 2.473 −2.879 −5.352
  1. a according to CMR (“Comprehensive Microbial Resource”) annotation of genome of CB15 strain.
  2. b referring to the number of amino acid of the deduced protein sequence. Protein length is according to CMR annotation or prediction from our analysis.
  3. c corresponding to the number of possible transmembrane (TM) helices in the mature protein. The number was determined by TMHMM tool.
  4. d according to a re-analysis of the deduced protein sequences by using Pfam and SMART tools to search for conserved domains.
  5. e sequences were compared with protein databases using Blastp.
  6. f microarray hybridization of RNA samples isolated from exponential phase cells exposed to 55 μM potassium dichromate (K2Cr2O7, denoted as Cr) for 30 min. Genes with M value of < −1.0 or > 1.0 were assumed as differentially expressed between strains analyzed. Values are the log2 ratio as mentioned. Results shown are the average of three independent biological experiments. WT and ΔsigF refer to the parental strain NA1000 and sigF deletion mutant, respectively. NC refers to no significant change in gene expression.
  7. g quantitative RT-PCR experiments performed with total RNA extracted from exponentially growing cells immediately before (no stress condition) and following exposure during 30 min to 55 μM potassium dichromate (K2Cr2O7, denoted as Cr). Results were normalized using gene CC0088 as the endogenous control, which was constitutively expressed under the conditions analyzed. Values are the log2 ratio as mentioned. Data are mean values of two independent experiments. WT and ΔsigF refer to the parental strain NA1000 and sigF deletion mutant, respectively. NA corresponds to genes not analyzed in qRT-PCR experiments.