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Of the five uncharacterized CRE sites in the H. influenzae genome, several CRE elements (CRE0364, CRE0937 and CRE1181) were located between genes that were oriented in such a way that the CRE sites could control transcription of either, or both operons. However, in three of these, researchers had assigned the CRE element to the genes I didn't feel were probably competence related. So I employed an area of research called comparative genomics to see which genes these three CRE elements probably controlled. I looked for those CRE sites and related genes in the genomic sequences of close relatives of H. influenzae (the family Pasteurellaceae). Here's what I found. Organization and conservation of the CRE0364 region in the family Pasteurellaceae. A. Numbers shown correspond to the HI number in the Rd KW20 annotation unless otherwise indicated and are based upon the closest homolog in the Rd KW20 sequence. Solid colors indicate genes whose location in reference to the CRE element is conserved across the family. Shaded colors indicate genes with partial positional conservation B. Comparison of the putative CRE sequences upstream of the HI0365 homolog in each organism compared to the consensus CRE sequence from Rd KW20 (Cons). Nucleotides in bold share 100% identity with the consensus sequence. C. Degree of identity of proteins homologous to HI0365 and HI0366 in the Pasteurellaceae. Abbreviations used: Hi: H. influenzae Rd KW20; Aa: A. actinomycetemcomitans HK1651; Pm: P. multocida PM70; Hs: H. somnus strains 129PT and 2336; Hd: H. ducreyi 35000HP; Ap: A. pleuropneumoniae serotype 1 str. 4074
Organization and conservation of the CRE0937 region in the family Pasteurellaceae. A. Numbers shown correspond to the HI number in the Rd KW20 annotation unless otherwise indicated and are based upon the closest homolog in the Rd KW20 sequence. Solid colors indicate genes whose location in reference to the CRE element is conserved across the family. Shaded colors indicate genes with partial positional conservation. B. Comparison of the putative CRE sequences upstream of HI0938 in each organism compared to the consensus CRE sequence from Rd KW20 (Cons). Nucleotides in bold share 100% identity with the consensus sequence. C. Degree of identity of proteins homologous to HI0938-HI0942 in the Pasteurellaceae. † and ‡ rpsblast database indicates presence of PulG and PulJ domains respectively. Np indicates homolog not present. See above for abbreviations used, except Mh: M. haemolytica PHL213. Organization and conservation of the CRE1181 region in the family Pasteurellaceae. - A. Numbers shown correspond to the HI number in the Rd KW20 annotation unless otherwise indicated and are based upon the closest homolog in the Rd KW20 sequence. Solid colors indicate genes whose location in reference to the CRE element is conserved across the family. The A. actinomycetemcomitans and H. somnus LigA homologs demonstrated 69% identity (89% similarity) and 71% identity (85% similarity), respectively, to the Rd KW20 LigA sequence. B. Comparison of the putative CRE sequences upstream of the ligA homolog in each organism compared to the consensus CRE sequence from Rd KW20 (Cons). Nucleotides in bold share 100% identity with the consensus sequence. See above for definitions of the abbreviations used.
The results of this comparative genomic analysis indicated by supposition that the three CRE elements I suspected had been wrongly associated was probably right. In other related bacteria, the CRE elements were always found with the genes I felt they were really associated with.
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