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

Kohler, Christian; Lourenço, Rogério F; Avelar, Gabriela M; Gomes, Suely L

doi:10.1186/1471-2180-12-210

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

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

					Microarray^f	qRT-PCR^g
Gene number^a	Length^b	TM^c	Domain^d	Putative identification^e	Δ*sigF* Cr/ WT Cr	WT Cr/ WT no stress	ΔsigF Cr/Δ*sigF* no stress	Δ*sigF* 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 σ^F	NC	1.577	0.265	−1.312
CC3253	179		Sigma70_r2 Sigma70_r4	ECF sigma factor σ^F	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

^a according to CMR (“Comprehensive Microbial Resource”) annotation of genome of CB15 strain.
^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.
^c corresponding to the number of possible transmembrane (TM) helices in the mature protein. The number was determined by TMHMM tool.
^d according to a re-analysis of the deduced protein sequences by using Pfam and SMART tools to search for conserved domains.
^e sequences were compared with protein databases using Blastp.
^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.
^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.

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ISSN: 1471-2180

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