Biomedical subjects

Lise Petersen

Publications and source records attributed to Lise Petersen.

3 recordsLinked to original sources

PubMed2006

Novel overlapping coding sequences in Chlamydia trachomatis.

Chlamydia trachomatis is the aetiological agent of trachoma and sexually transmitted infections. The C. trachomatis genome sequence revealed an organism adapted to the intracellular habitat with a high coding ratio and a small genome consisting of 1.042-kilobase (kb) with 895 annotated protein coding genes. Here, we repredict the protein-coding genes of the C. trachomatis genome using the gene-finder EasyGene that was trained specifically for C. trachomatis, and compare it with the primary C. trachomatis annotation. Our work predicts 15 genes not listed in the primary annotation and 853 that are in agreement with the primary annotation. Forty two genes from the primary annotation are not predicted by EasyGene. The majority of these genes are listed as hypothetical in the primary annotation. The 15 novel predicted genes all overlap with genes on the complementary strand. We find homologues of several of the novel genes in C. trachomatis Serovar A and Chlamydia muridarum. Several of the genes have typical gene-like and protein-like features. Furthermore, we confirm transcriptional activity from 10 of the putative genes. The combined evidence suggests that at least seven of the 15 are protein coding genes. The data suggest the presence of overlapping active genes in C. trachomatis.

Chlamydia trachomatis↗

PubMed2006

Numerical analysis of DNA microarray data of Campylobacter jejuni strains correlated with survival, cytolethal distending toxin and haemolysin analyses.

Molecular epidemiological studies of the enteric pathogen Campylobacter jejuni have suggested that not all animal isolates are equally pathogenic to humans. We examined the use of numerical analysis of whole-genomotype data as a potential tool for evaluating C. jejuni virulence potential. Whole-genome microarray analysis was used to determine the gene-level complementarity of 12 Danish strains to the pathogenic, genome-sequenced strain NCTC 11168. Cytolethal distending toxin (CDT) and haemolysin activities, and survival characteristics under aerobic conditions at room temperature were also determined. Among the strains examined, 439 genes were polymorphic. Numerical analysis of these data by use of the squared Euclidean distance coefficient and Ward's clustering method clearly delineated strains into two clusters. CDT and haemolysin activities of cluster 1 strains were not statistically significantly different from cluster 2 strains. However, viability during aerobic incubation of cluster 1 strains was statistically significantly lower than corresponding estimates of cluster 2 strains. The number of missing or highly divergent genes in cluster 1 strains with respect to NCTC 11168 was also statistically significantly greater compared with those of cluster 2 strains. Sixty-seven genes present in NCTC 11168 were characteristically missing or divergent among cluster 1 strains. Of these, 53 genes were localised within 11 major gene clusters, of which eight were associated with surface structures and included flagellar, lipo-oligosaccharide, and membrane transport proteins. Our data indicate a correlation between C. jejuni genomic content, particularly in surface-coding regions, and its capacity for environmental survival, and may help explain why certain serotypes are more commonly reported in human disease.

Animals↗

PubMed2003

RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.

We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a very strong periodic variation in the AT-content and semi-conserved T-stretches, with a period of 10-11 nucleotides. The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended -10 promoter. We predicted a total of 764 presumed RpoD promoters in the C.jejuni genome, of which 654 were located upstream of annotated genes. A similar promoter was identified in Helicobacter pylori, a close phylogenetic relative of Campylobacter, but not in Escherichia coli, Vibrio cholerae, or six other Proteobacterial genomes, or in Staphylococcus aureus. We used upstream regions of high confidence genes as training data (n=529, for the C.jejuni genome). We found it necessary to limit the training set to genes that are preceded by an intergenic region of >100bp or by a gene oriented in the opposite direction to be able to identify a conserved sequence motif, and ended up with a training set of 175 genes. This leads to the conclusion that the remaining genes (354) are more rarely preceded by a (RpoD) promoter, and consequently that operon structure may be more widespread in C.jejuni than has been assumed by others. Structural predictions of the regions upstream of the TATA-box indicates a region of highly curved DNA, and we assume that this facilitates the wrapping of the DNA around the RNA polymerase holoenzyme, and offsets the absence of a conserved -35 binding motif.

Bacterial Proteins↗