The Mechanism for RNA Recognition by ANTAR Regulators of Gene Expression
Figure 7
Bioinformatic analysis of the ANTAR domain and its two stem-loop RNA substrate.
A) Using a covariance-based search approach (Infernal [28]), we identified additional occurrences of the ANTAR RNA substrate in bacteria that contained eut pathways. The comparative sequence alignment of these RNA sequences is shown in Figure S2 and described in Table S1. A scatter plot is shown for the resulting RNA hits, where each data point represents a different RNA hit. The hit scores for these sequences were plotted for two classes of microorganisms used in this search. Specifically, organisms that are predicted to encode for ANTAR domain proteins (see Table S1) have more RNA hits with higher scores than a control set of organisms that appear to lack any ANTAR domain proteins. Also, these hits were screened using TransTerm for the presence of an intrinsic terminator hairpin located immediately downstream of the P2 helix. Only a subset of the hits satisfied this important criterion. B) A consensus secondary structure was derived from this sequence alignment and is shown herein. C) The covariance-based search approach was then employed against 1902 bacterial genomes to search more broadly for putative ANTAR-based regulatory pathways. Again, a scatter plot is shown for the resulting hits, and for the subsequent screening of these hits for the presence of an overlapping downstream intrinsic terminator hairpin. See also Figures S1, S2 and Tables S1, S2 for more information on the covariance search results.