ARS | Publication request: PATTERNS IN THE INTERVENING SEQUENCES OF CAMPYLOBACTER JEJUNI

Submitted to: Campylobacter Helicobacter and Related Organisms International Workshop
Publication Type: Abstract Only
Publication Acceptance Date: June 1, 2001
Publication Date: September 1, 2001
Citation: MEINERSMANN, R.J., WASSENAAR, T. PATTERNS IN THE INTERVENING SEQUENCES OF CAMPYLOBACTER JEJUNI. CAMPYLOBACTER HELICOBACTER AND RELATED ORGANISMS INTERNATIONAL WORKSHOP. 2001.

Technical Abstract: With the release of the genomic sequence of Campylobacter jejuni NCTC 11168 (Parkhill et al., Nature) it was noted that functional operons were uncommon. We hypothesized that patterns found in the intervening sequences (IVS) would yield clues on the basis for genomic organization. This report looks at the lengths of the IVSs. The length of the IVSs had a bimodal distribution; the larger mode was at -4 bp (i.e., overlapping by 4 bp) and a broader mode between 80 and 100 bp. In a pool of 84 predicted highly expressed (PHX) genes the upstream IVS was more likely to be greater than 1 bp; the majority of PHX with overlapping starts were in a single operon composed of several ribosomal proteins. The distribution of the IVS lengths greater than 1 that were upstream of PHX genes was parallel to that seen of the non-PHX genes. Genes ending with the TGA stop codon were far more likely to overlap the following gene. This is significant in light of the presence of a possible seleno-cysteine tRNA (anti-codon = UCA) found in the genomic sequence. Conversely, there was no detectable difference in the distribution of IVS lengths proceeding ATG, TTG or GTG start codons. The IVS between genes that coded in the same direction (tail-to-head) or toward each other (tail-to-tail) were far more likely to be less than 1 than the IVS between genes that coded in divergent directions (head-to-head). The distributions of IVS lengths for tail-to-head gene-pairs and tail-to-tail gene pairs were similar to each other. Thus, study of the lengths of the IVS is sufficient to show that there are nonrandom patterns in the genomic organization of C. jejuni that may be related to the function of the genes.