Wednesday, 11 June 2014

Is there any example of study on amino acid sites under positive selection (dN/dS) that have been tested in vitro (confirmatory or not)?

(This post is more a open question than a direct answer).


Is there any example of study on amino acid sites under positive selection (dN/dS) that have been tested in vitro (confirmatory or not)?

By dN/dS, I mean any amino acid sites in any species that have been detected with CodeML, either the site models (M2a, M8), or the branch-site model. Or any other similar methods that aim to identify sites that could favour adaptation during evolutionary course.

By in vitro, I mean that these sites has been mutated in vitro and tested to see if they provide a different phenotype, or if the targeted protein exhibits different biochemical properties.


===>   I have the impression that there are plenty of studies that identifies such amino acids under positive selection in a large-scale manner, i.e.:

More genes underwent positive selection in chimpanzee evolution than in human evolution
http://www.pnas.org/content/104/18/7489.full

Patterns of Positive Selection in Six Mammalian Genomes
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000144

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
http://genome.cshlp.org/content/18/9/1393.short

Patterns of Positive Selection in Seven Ant Genomes
http://mbe.oxfordjournals.org/content/early/2014/05/06/molbev.msu141.abstract



===> There are many studies that analyse these sites in silico by mapping them on the 3D structures, i.e.:

Patterns of Positive Selection in Six Mammalian Genomes
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000144

Adaptive Divergence of Ancient Gene Duplicates in the Avian MHC Class II β
http://mbe.oxfordjournals.org/content/27/10/2360

Evolution of Genes Involved in Gamete Interaction: Evidence for Positive Selection, Duplications and Losses in Vertebrates
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044548


===> A few of them identifies the effect on the protein stability, i.e.:

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002929

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO
http://www.pnas.org/content/111/6/2223.long


===> But I have difficulties to find studies that actually tested these sites in vitro. I found these ones:

Adaptive evolution of multicolored fluorescent proteins in reef-building corals.
http://link.springer.com/article/10.1007%2Fs00239-005-0129-9

Structural and Functional Evolution of Positively Selected Sites in Pine Glutathione S-Transferase Enzyme Family
http://www.jbc.org/content/288/34/24441.full


But I am wondering if there are many other similar studies?


Thank you for your help!

1 comment:

  1. http://www.pnas.org/content/early/2008/09/02/0802426105.full.pdf

    The paper shows that dN/dS ratio could be misleading.

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