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. 2011 Dec 16;40(8):3623–3640. doi: 10.1093/nar/gkr1156

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — (A) Genomic context of the sdsR gene in various Enterobacteria. Synteny analysis of the sdsR/sraC genes in various enterobacterial species revealed partial conservation of the locus. In all cases sdsR is positioned downstream of yebY or homologues; the flanking gene at the 3′-end is variable. Distances to flanking genes are indicated in bp. STM: Salmonella typhimurium; STY: Salmonella typhi; CKO: Citrobacter koseri; ECO: Escherichia coli; SFL: Shigella flexneri; ENT: Enterobacter; CTU: Cronobacter turicensis; KPN: Klebsiella pneumoniae; SPR: Serratia proteamaculans; YPE: Yersinia pestis; YEN: Yersinia enterolitica; DDA: Dickeya dadantii; PAN: Pantoea ananatis; SGL: Sodalis glossinidius; EPY: Erwinia pyrifoliae; PLU: Photorhabdus luminescens; XNE: Xenorhabdus nematophila. (B) Expression levels of SdsR and SraC sRNAs in Salmonella, E. coli and Shigella. Northern blot analysis of total RNA isolated from wild-type Salmonella (JVS-1574), E. coli (JVS-5105) and Shigella (JVS-0012) cells grown to OD₆₀₀ of 0.5, 1.0, 2.0 and 3 h after cells had reached an OD₆₀₀ of 2.0. SdsR and SraC sRNAs were detected by radio-labelled oligo probes directed against the conserved sRNA sequences. 5S rRNA levels were determined to confirm equal loading. (C) SdsR copy number over growth. SdsR levels at various timepoints (OD₆₀₀ of 0.5, 1.0, 2.0 and 2, 3, 4 or 6 h after cells had reached an OD₆₀₀ of 2.0) in wild-type Salmonella were compared by northern blotting to signals of in vitro transcribed SdsR in indicated amounts. SdsR was detected using a riboprobe; probing for 5S RNA confirmed equal loading. Expression of RpoS at different growth stages was determined by western blotting. Detection of ribosomal protein S1 was used as loading control.