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Indeed, DNA-binding domains are often highly conserved across species and, in many cases, appear to be under stronger evolutionary constraints than other regions of the protein (Hirsch and Aggarwal 1995; Luscombe and Thornton 2002; Rorick and Wagner 2010).
This indicated that the younger bZIP proteins may be under stronger evolutionary constraints than older proteins, but supported the notion that the legume bZIP gene family is essential for the regulation of cellular processes.
Although robust purifying selection was encountered in most of the analyses, the secretory protein genes were found to be under stronger evolutionary selection pressure than non-secretary protein genes in symbiotic and pathogenic strains.
These studies and others (Barbosa-Morais et al., 2012; Brawand et al., 2011) suggest that regulation in other somatic tissues evolves similarly, though embryonic tissues and their enhancers may be under stronger evolutionary constraint (Faure et al., 2012; He et al., 2011; Nord et al., 2013).
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This conclusion is in line with the expectation that contact residues are in general much more likely to be under strong evolutionary constraint compared with noncontact residues.
Cis-regulatory elements can be predicted by sequence conservation analysis, as tight clusters of functional TFBSs can be under strong evolutionary constraint [ 4- 7].
On the other hand, the likely enrichment of recent positive selections at the subcentral positions can be explained: Genes with protein products of very high centrality could be under strong evolutionary constraints and hence accommodate fewer selective events, whereas genes at the periphery may not contribute strongly enough to phenotypic effects for selection due to their network locations.
This can be rationalized by noting that the sequences of the start and stop-codons are under stronger evolutionary constraints.
An investigation of the three-dimensional structures of about 100 yeast proteins indicated that buried residues – which are located on a stable interaction surface between protein units – are under stronger evolutionary constraints than solvent exposed sites [24], even after excluding the effect of expression level.
Analysis of derived allele frequency data indicates that sites in stems are under stronger evolutionary constraint than sites in loops/bulges.
Analyses of the variant sequences that exist in human populations demonstrate that sites in stems of the predicted secondary structures are under stronger evolutionary constraint than sites on loops/bulges, which are still more constrained than non-conserved sequences.
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