engleski

Evaluation of intergene distances across bacterial species

This poster will present an extensive study of correlation of intergene region lengths to Gene Ontology (GO) assignments in prokaryotic genomes. Our intention is to assess the dependence of intergene region length of the genes in a particular GO category on the role of that GO category in the prokaryotic life cycle. Out of 624 prokaryotic complete genome sequences present at the NCBI FTP site (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria) in November 2007, 461 were selected. The selection was made in order to have exactly one representative of each species, and in that way – most importantly – to remove redundancies, and as a side benefit, to be more computationally efficient. Organisms we kept in the analysis are representatives of each species group contained in the original list. Prokaryotic organisms in general have short intergene regions, compared to many eukaryotes. This means that during evolution the prokaryotic cell was under strong selective pressures for growth rate and doubling time, and was particular about having extra DNA devoted to regulatory regions, as it takes approx. 50 milliseconds and two ATP molecules to transcribe one nucleotide. Combined with the extra cost of regulatory proteins, it would be expected that the minimal promoter is the only regulatory mechanism constitutively expressed genes (operons) would need. Basic metabolism and cell maintenance are pathways anticipated to be present in this group. On the other hand, genes that are expressed in specific environmental conditions (for example alternative carbon source use, heat or cold shock, lower pH or higher osmotic pressure) or at specific cell cycle stages (for example DNA replication/recombination initiation and regulation) require stringent expression control and as such need longer regulatory regions preceding them. In light of this expectation we present the results in an intuitive chart that distributes the Gene Ontology categories in a 3D space by using a semantic similarity metric between GO categories (simRel, Schlicker et al. BMC Bioinformatics 2006, 7:302), alongside the enrichment of the GO category in long or short intergene regions. To assess enrichment of particular Gene Ontology categories in genes having long intergene regions, we have calculated intergene region lengths and made a statistical analysis of their distribution over GO. This was done by first making a list of non-coding region lengths present upstream of each gene. Secondly, for a respective organism, a normalization of this value was done by dividing by the average intergene length in a particular genome element (prokaryote’ s chromosome or plasmid). Lastly, the genes were divided into two groups, depending on their intergene region (IGR) length being above average (long IGR, approx. 33% of genes) and below average (short IGR, approx. 67% of genes). This list was analyzed by using a number of Fisher’ s exact tests for correlation between two categorical variables – first, short or long IGR ; and second, member or non-member of a GO category. We used a permutation-based algorithm to correct the statistical significance estimates for multiple testing (Manly, Randomization, Bootstrap and Monte Carlo Methods in Biology, 3rd ed., 2007). The result is a table showing only significantly enriched Gene Ontology categories in long or short IGR genes. The poster will present a visualization of these results in an intuitive and interpretable manner. There are two aspects in our analysis: one is viewing the Gene Ontology categories that are enriched in long IGR genes (we suggest that these are the genes under rigid transcriptional control, in need of long regulatory regions), and the other is focusing on those enriched in short IGR genes (genes we suspect are constitutively expressed, and therefore do not need to be regulated). We have found here that the genes with long IGRs are assigned to GO categories responsible for functions such as citrate transport, carbon utilization, cell morphogenesis, DNA topoisomerase (ATP-hydrolyzing) activity, glutamate synthase activity, light-harvesting complex and excinuclease repair complex. The short IGR gene group contains members whose functions are designated to lipoprotein and fatty acid biosynthetic process, ion transport, protein refolding, cellular respiration, sensory perception of chemical stimulus, cofactor, RNA and lipid binding, tRNA adenylyltransferase activity, 1-phosphofructokinase activity, genes coding for small and large ribosomal subunits, and proton-transporting ATP synthase complex. In themselves these observations are quite intuitive, but, to our knowledge, no systematic examination of prokaryotic intergene regions with regard to GO annotations has been done previously. We present Gene Ontology categories that are either enriched or depleted in long intergene regions, and show a pool of GOs where constitutively expressed genes are found. We also intend to extend the research beyond this poster presentation to include comparisons of IGR lengths between groups of bacteria living in different habitats. It is tempting to hypothesize that in these long intergene regions a motif conserved for a particular GO function is present. This would reduce the prokaryote’ s cost of regulation by having a small pool of proteins that enable the transcription of the whole Gene Ontology category. One known example would be the cAMP receptor protein (CRP) that regulates transcription of over 100 genes in E. coli via a specific 22 bp motif (Brown and Callan, PNAS 2004, 101/8: 2404-9). Most notably – examining the generality level of the GO categories in question – would be worth looking into.

intergene region; prokaryote; Gene Ontology

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