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item Meinersmann, Richard - Rick

Submitted to: Genome Letters
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2003
Publication Date: 9/1/2003
Citation: Meinersmann, R.J., Wassenaar, T.M. 2003. Patterns in the interviewing sequences of camypylobacter jejuni. Genome Letters. 2(1/2):28-33.

Interpretive Summary: Campylobacter jejuni is the leading bacterial cause of diarrheal disease in humans. The organism is highly variable, which makes it difficult to track in outbreaks and may give it advantages in establishing infections. This study was designed to look at the DNA sequence of the genome of C. jejuni to see if there are patterns that indicate rules that will limit the variability of the organism. Specifically, we looked at how genes were organized with relationship to neighboring genes. It was found that many more genes than were expected overlap by a short distance and this was related to the use of the genetic code TGA. It was also found that genes had special organizational features that correlated with how the gene was expressed and how much was expressed. Knowledge of the rules of organization will help us identify parts of the genome that may be less variable and, therefore, better targets for intervention or for use in assays to track types

Technical Abstract: With the release of the genomic sequence of Campylobacter jejuni NCTC 11168 (Parkhill et al., Nature 403:665-668, 2000) 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. The length distribution of IVSs was analyzed in relation to flanking start and stop codons. A relation between IVS length distribution to following genes with a predicted high expression was also investigated. The length of the IVSs had a bimodal distribution; the larger mode was at -4 bp, i.e. overlapping with the preceding gene by 4 bp, and a second broader mode was found between 80 and 100 bp. 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. There was no detectable difference in the distribution of IVS lengths proceeding ATG, TTG or GTG start codons. Genes that coded in the same direction (tail-to-head) or toward each other (tail-to-tail) were far more likely to be overlapping (IVS < 1) than genes that coded in divergent directions (head-to-head). The distributions of IVS lengths >1 for tail-to-head gene pairs and tail-to-tail gene pairs were similar to each other. 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 starts overlapping the preceding gene were in a single operon composed of several ribosomal proteins. This study shows that there are nonrandom patterns in the gene distribution of C. jejuni that may be related to the function of the genes.