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The loose evolutionary relationships between transcription factors and other gene products across prokaryotes.

del Grande M, Moreno-Hagelsieb G - BMC Res Notes (2014)

Bottom Line: In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes.We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes.The Codon Adaptation Index analyses suggest quick gene exchange and rewiring of transcriptional regulation across prokaryotes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Wilfrid Laurier University, 75 University Ave, W,, N2L 3C5 Waterloo, Ontario, Canada. gmoreno@wlu.ca.

ABSTRACT

Background: Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental information of functional associations in other organisms. We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome. We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available.

Results: We plotted profiles of phylogenetic profiles, p-cubic, to compare the maximally scoring interactions of TFs against those of other genes. In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes. We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes.

Conclusions: The co-occurrence tests suggest that transcriptional regulation evolves quickly in most, if not all, prokaryotes. The Codon Adaptation Index analyses suggest quick gene exchange and rewiring of transcriptional regulation across prokaryotes.

No MeSH data available.


ΔP3 between predicted TF-coding genes and other genes across the prokaryotic genomes analyzed in this study. If the p-cubic curve for genes coding for proteins other than TFs runs above the p-cubic curve for TF-coding genes the ΔP3 will be positive. Thus, a positive ΔP3 indicates less evolutionarily conserved interactions for TF-coding genes. A negative ΔP3 would indicate the opposite. The cumulative proportion shown here indicates that TF-coding genes in approx. 91% of the genomes tested have less conserved interactions than other genes.
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Fig2: ΔP3 between predicted TF-coding genes and other genes across the prokaryotic genomes analyzed in this study. If the p-cubic curve for genes coding for proteins other than TFs runs above the p-cubic curve for TF-coding genes the ΔP3 will be positive. Thus, a positive ΔP3 indicates less evolutionarily conserved interactions for TF-coding genes. A negative ΔP3 would indicate the opposite. The cumulative proportion shown here indicates that TF-coding genes in approx. 91% of the genomes tested have less conserved interactions than other genes.

Mentions: To summarize the results for each of the genomes chosen above, we calculated a difference, ΔP3, between the p-cubic curve for genes other than predicted TFs and the p-cubic for predicted TFs (see Methods). A ΔP3 above zero would indicate that the p-cubic for TF-coding genes shows lower co-occurrence than the p-cubic of other genes, while a ΔP3 below zero would indicate that TF-coding genes have a higher tendency to co-occur, and therefore contain more evolutionarily conserved interactions than other genes. The cumulative curve of ΔP3s shows that genes coding for predicted TFs have less co-occurrence, and therefore proportionally fewer conserved interactions than other genes in 780 of the 857 genomes tested (91%; Figure 2), thus confirming that TF interactions might evolve quickly in most, if not all prokaryotes.Figure 2


The loose evolutionary relationships between transcription factors and other gene products across prokaryotes.

del Grande M, Moreno-Hagelsieb G - BMC Res Notes (2014)

ΔP3 between predicted TF-coding genes and other genes across the prokaryotic genomes analyzed in this study. If the p-cubic curve for genes coding for proteins other than TFs runs above the p-cubic curve for TF-coding genes the ΔP3 will be positive. Thus, a positive ΔP3 indicates less evolutionarily conserved interactions for TF-coding genes. A negative ΔP3 would indicate the opposite. The cumulative proportion shown here indicates that TF-coding genes in approx. 91% of the genomes tested have less conserved interactions than other genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4300776&req=5

Fig2: ΔP3 between predicted TF-coding genes and other genes across the prokaryotic genomes analyzed in this study. If the p-cubic curve for genes coding for proteins other than TFs runs above the p-cubic curve for TF-coding genes the ΔP3 will be positive. Thus, a positive ΔP3 indicates less evolutionarily conserved interactions for TF-coding genes. A negative ΔP3 would indicate the opposite. The cumulative proportion shown here indicates that TF-coding genes in approx. 91% of the genomes tested have less conserved interactions than other genes.
Mentions: To summarize the results for each of the genomes chosen above, we calculated a difference, ΔP3, between the p-cubic curve for genes other than predicted TFs and the p-cubic for predicted TFs (see Methods). A ΔP3 above zero would indicate that the p-cubic for TF-coding genes shows lower co-occurrence than the p-cubic of other genes, while a ΔP3 below zero would indicate that TF-coding genes have a higher tendency to co-occur, and therefore contain more evolutionarily conserved interactions than other genes. The cumulative curve of ΔP3s shows that genes coding for predicted TFs have less co-occurrence, and therefore proportionally fewer conserved interactions than other genes in 780 of the 857 genomes tested (91%; Figure 2), thus confirming that TF interactions might evolve quickly in most, if not all prokaryotes.Figure 2

Bottom Line: In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes.We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes.The Codon Adaptation Index analyses suggest quick gene exchange and rewiring of transcriptional regulation across prokaryotes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Wilfrid Laurier University, 75 University Ave, W,, N2L 3C5 Waterloo, Ontario, Canada. gmoreno@wlu.ca.

ABSTRACT

Background: Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental information of functional associations in other organisms. We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome. We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available.

Results: We plotted profiles of phylogenetic profiles, p-cubic, to compare the maximally scoring interactions of TFs against those of other genes. In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes. We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes.

Conclusions: The co-occurrence tests suggest that transcriptional regulation evolves quickly in most, if not all, prokaryotes. The Codon Adaptation Index analyses suggest quick gene exchange and rewiring of transcriptional regulation across prokaryotes.

No MeSH data available.