The Spot 42 RNA: A regulatory small RNA with roles in the central metabolism

Abstract

The Spot 42 RNA is a 109 nucleotide long (in Escherichia coli) noncoding small regulatory RNA (sRNA) encoded by the spf (spot fourty-two) gene. spf is found in gamma-proteobacteria and the majority of experimental work on Spot 42 RNA has been performed using E. coli, and recently Aliivibrio salmonicida. In the cell Spot 42 RNA plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex. Here we summarize the current knowledge on Spot 42, and present the natural distribution of spf, show family-specific secondary structural features of Spot 42, and link highly conserved structural regions to mRNA target binding.

Keywords: Spot 42; gamma proteobacteria; non-coding RNA; pirin; sRNA; small RNA; spf.

Figure 1.

The natural distribution of spf. spf is restricted to 5 orders of gamma-proteobacteria (shown in bold letters), 4 of which share the same closest common ancestor (indicated by an arrow). The circular phylogenetic tree (made using the iTol web tool) shows all major branches of Bacteria. The gamma-proteobacteria phylogeny in the right panel is based on Gao et al. Here, numbers in parentheses indicate the number of complete genomes that contain spf (first number) and the total number of available complete genomes (second number) in each order. In addition, spf is found in 8 Chromatiales draft genomes (asterisk).

Figure 2.

Secondary structure consensus model of the Spot 42 RNA. The structure model was made by aligning all known spf sequences, and by mapping the consensus sequence onto a secondary structure model of the E. coli Spot 42 (based on Møller et al.¹). The structure consists of a relatively long 5` hairpin, a 9 nt long single-stranded region followed by a second hairpin and a rho-independent terminator. Level of identity is shown using different type of letters in the structure. Uppercase bold letters indicate 80–100 % identity, uppercase regular letters indicate 60–79% identity, and lowercase letters indicate <60% identity. Structural segments with family-specific (i.e., Vibrionaceae, Aeromonadaceae and Shewanellaceae) variations are shown in separate colored boxes. Here, circles indicate U or A insertions (compared to the "consensus"). Gray square around a letter symbolizes aberration from the consensus structure.

Figure 3.

Potential base-pairing between the Spot 42 RNA and experimentally verified mRNA targets from the following genes: (A) galK, (B) pirin, (C) fucI, (D) xylF and sthA, (E) gltA and srlA and (F) nanC, (G) paaK, ascF, caiA and fucP, (H) atoD and puuE and (I) nanT. Fig. 3 is based on data from Møller et al., Hansen et al., Beisel and Storz, and Beisel et al.

Figure 4.

sRNA genes in the intergenic region downstream of polA. The figure shows currently known sRNA genes which have been found in the same intergenic region as spf. The scale bar shows distance in nucleotides. (A) Representative species containing spf are shown. The VSsrna24 sRNA gene is located downstream of spf in V. cholerae and A. salmonicida. Question mark denotes hypothetical protein. (B) Genomic location of the sRNA genes ersA in Pseudomonas aeruginosa, sX13 in Xanthomonas campestris and SMc02857 in Sinorhizobium meliloti.