Limits...
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.


Comparing the Codon Adaptation Index of predicted transcription factor-coding genes and other genes across prokaryotic genomes. This curve shows that TF-coding genes in approx. 94% of the genomes tested had lower average CAI than other genes, thus suggesting that TF-coding genes tend to be more horizontally transferred than other genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Comparing the Codon Adaptation Index of predicted transcription factor-coding genes and other genes across prokaryotic genomes. This curve shows that TF-coding genes in approx. 94% of the genomes tested had lower average CAI than other genes, thus suggesting that TF-coding genes tend to be more horizontally transferred than other genes.

Mentions: Previous work has suggested that at least half of the TF-coding genes of E. coli come from horizontal gene transfer (HGT) events [4]. This might be one of the reasons why associations brought about via TFs evolve quickly (another reason might be that operators, the sites in DNA where TFs bind, have low information contents, meaning that they can easily evolve [30]). To further test for the possibility of TF-coding genes coming from HGT across prokaryotes we calculated the Codon Adaptation Index (CAI) for all the genes of the genomes under analysis. We found that the CAI of TF-coding genes tends to be lower than that of non-TF-coding genes in 809 of the 857 (94%) of the genomes containing at least 80 predicted TFs (Figure 3). Furthermore, t-tests showed significant differences between the CAIs of non-TFs and TFs in 691 of the 857 genomes (80%), out of which 676 (98%) had a positive statistical difference (p ≤ 0.05; see Additional files 1 and 2). Our results are also in agreement with previous work showing that genes predicted to have been horizontally transferred are enriched in genes encoding for proteins with DNA-binding functions [31].Figure 3


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

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

Comparing the Codon Adaptation Index of predicted transcription factor-coding genes and other genes across prokaryotic genomes. This curve shows that TF-coding genes in approx. 94% of the genomes tested had lower average CAI than other genes, thus suggesting that TF-coding genes tend to be more horizontally transferred than other genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Comparing the Codon Adaptation Index of predicted transcription factor-coding genes and other genes across prokaryotic genomes. This curve shows that TF-coding genes in approx. 94% of the genomes tested had lower average CAI than other genes, thus suggesting that TF-coding genes tend to be more horizontally transferred than other genes.
Mentions: Previous work has suggested that at least half of the TF-coding genes of E. coli come from horizontal gene transfer (HGT) events [4]. This might be one of the reasons why associations brought about via TFs evolve quickly (another reason might be that operators, the sites in DNA where TFs bind, have low information contents, meaning that they can easily evolve [30]). To further test for the possibility of TF-coding genes coming from HGT across prokaryotes we calculated the Codon Adaptation Index (CAI) for all the genes of the genomes under analysis. We found that the CAI of TF-coding genes tends to be lower than that of non-TF-coding genes in 809 of the 857 (94%) of the genomes containing at least 80 predicted TFs (Figure 3). Furthermore, t-tests showed significant differences between the CAIs of non-TFs and TFs in 691 of the 857 genomes (80%), out of which 676 (98%) had a positive statistical difference (p ≤ 0.05; see Additional files 1 and 2). Our results are also in agreement with previous work showing that genes predicted to have been horizontally transferred are enriched in genes encoding for proteins with DNA-binding functions [31].Figure 3

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.