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. 2020 Jul 10;7:127. doi: 10.3389/fmolb.2020.00127

Figure 2.

Figure 2

Structural properties of CsrA proteins and their interaction with RNA sequence/structural motifs. (A) Primary sequence alignment of CsrA polypeptides from selected eubacterial species: Gsulf, Geobacter sulfurreducens; Pprot, Pseudomonas protegens; Ecoli, Escherichia coli; Vchol, Vibrio cholerae; Bsubt, Bacillus subtilis; Hpylo, Helicobacter pylori; Tmari, Thermotoga maritima; Cbotu, Clostridium botulinum. The degree of residue conservation is indicated below each position of the alignment, as follows: an (*) indicates positions with a fully conserved residue; a (:) indicates conservation between amino acid groups of strongly similar biochemical properties; a (.) indicates conservation between groups of weakly similar properties. The residue shaded in gray (R) corresponds to the conserved arginine (R44 in E. coli CsrA) that is essential for the RNA-binding activity of CsrA proteins (Heeb et al., 2006; Schubert et al., 2007). The core region comprises the prototypical portion of the molecule that defines the CsrA fold, namely the β1β2β3β4β5H1 arrangement; the C-terminal extension is highly variable among different taxa. (B) Secondary structure properties the E. coli CsrA polypeptide. The data was generated with the Protein feature view tool of the RCSB PDB server www.rcsb.org (Berman et al., 2000). (C) The graph shows the length distribution of CsrA homologs within different eubacterial classes. For each group the average length (nr. of residues) ± standard deviation is indicated. (D) Ribbon diagram of the solution quaternary structure of the E. coli CsrA dimeric protein (PDB 1Y00). (E) Predicted charge distribution along the surface of the dimeric P. protegens RsmE protein (PDB 2JPP). (F) Consensus sequence/structural motif preferentially bound by E. coli CsrA in vivo, as detected following CLIP-Seq (adapted from Potts et al., 2019). R = G or A, Y = C or U. (G) Predicted secondary structure of the 14-mer encompassing the Shine-Dalgarno sequence (underlined nucleotides) of the hcnA 5′-UTR from P. protegens strain CHA0, an experimentally validated target for the CsrA homolog protein RsmE (Lapouge et al., 2007; Schubert et al., 2007). The arrowheads point to the nucleotides contacted by specific RsmE residues in the complex shown in (H) (Schubert et al., 2007). (H) Ribbon diagram of the NMR solution structure of the RsmE–hcnA 5′-UTR complex (PDB 2JPP). Each RNA binding site of the dimeric RsmE protein is interacting with one of two identical synthetic 20-mers containing the sequence-structural motif shown in (G).