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Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.

Schaefke B, Wang TY, Wang CY, Li WH - Genome Biol Evol (2015)

Bottom Line: We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions.Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains).We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains).

View Article: PubMed Central - PubMed

Affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan National Yang-Ming University, Taipei, Taiwan Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.

No MeSH data available.


Related in: MedlinePlus

ML tree used for the reconstruction of ancestral sequences. (a) The branch lengths were drawn according to scale. The x axis indicates the number of nucleotide substitutions per nucleotide site. (b) Tree topology only. Branch labels indicate bootstrap values.
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evv138-F1: ML tree used for the reconstruction of ancestral sequences. (a) The branch lengths were drawn according to scale. The x axis indicates the number of nucleotide substitutions per nucleotide site. (b) Tree topology only. Branch labels indicate bootstrap values.

Mentions: We used the MUSCLE (MUltiple Sequence Comparison by Log-Expectation) tool (Edgar 2004) to align promoter sequences, ORFs, and CDSs. A maximum-likelihood (ML) tree (fig. 1) for the concatenated aligned ORFs and promoter sequences was constructed using PhyML (Guindon et al. 2009, 2010; Criscuolo 2011). For each internal node of the phylogenetic tree, a likelihood-based reconstruction of the ancestral promoter sequences (Yang et al. 1995; Koshi and Goldstein 1996) was obtained using the BASEML program in the PAML package (Yang 1997, 2007). The tree topology was fixed, the branch lengths estimated by PhyML were used as the initial values, and alignment gaps and ambiguous letters were removed for the ancestral sequence reconstruction, using the general time-reversible nucleotide substitution model (BASEML parameters: cleandata = 1, fix_blength = 1, model = 7). The removal of alignment gaps and ambiguous nucleotides limits our analysis to nucleotide substitutions between the different strains (and excludes insertions and deletions). After removal of regions overlapping with neighboring proximal promoters and of nonalignable sequences, the average length of proximal promoters was 163.1 bp (median: 168 bp) and that of distal promoters was 142 bp (median: 146 bp).Fig. 1.—


Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.

Schaefke B, Wang TY, Wang CY, Li WH - Genome Biol Evol (2015)

ML tree used for the reconstruction of ancestral sequences. (a) The branch lengths were drawn according to scale. The x axis indicates the number of nucleotide substitutions per nucleotide site. (b) Tree topology only. Branch labels indicate bootstrap values.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4558856&req=5

evv138-F1: ML tree used for the reconstruction of ancestral sequences. (a) The branch lengths were drawn according to scale. The x axis indicates the number of nucleotide substitutions per nucleotide site. (b) Tree topology only. Branch labels indicate bootstrap values.
Mentions: We used the MUSCLE (MUltiple Sequence Comparison by Log-Expectation) tool (Edgar 2004) to align promoter sequences, ORFs, and CDSs. A maximum-likelihood (ML) tree (fig. 1) for the concatenated aligned ORFs and promoter sequences was constructed using PhyML (Guindon et al. 2009, 2010; Criscuolo 2011). For each internal node of the phylogenetic tree, a likelihood-based reconstruction of the ancestral promoter sequences (Yang et al. 1995; Koshi and Goldstein 1996) was obtained using the BASEML program in the PAML package (Yang 1997, 2007). The tree topology was fixed, the branch lengths estimated by PhyML were used as the initial values, and alignment gaps and ambiguous letters were removed for the ancestral sequence reconstruction, using the general time-reversible nucleotide substitution model (BASEML parameters: cleandata = 1, fix_blength = 1, model = 7). The removal of alignment gaps and ambiguous nucleotides limits our analysis to nucleotide substitutions between the different strains (and excludes insertions and deletions). After removal of regions overlapping with neighboring proximal promoters and of nonalignable sequences, the average length of proximal promoters was 163.1 bp (median: 168 bp) and that of distal promoters was 142 bp (median: 146 bp).Fig. 1.—

Bottom Line: We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions.Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains).We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains).

View Article: PubMed Central - PubMed

Affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan National Yang-Ming University, Taipei, Taiwan Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.

No MeSH data available.


Related in: MedlinePlus