Comments on: ‘Friendly’ genes are more likely to be passed around http://blogs.discovermagazine.com/notrocketscience/2010/12/13/friendly-genes-are-more-likely-to-be-passed-around/ Mon, 26 Nov 2012 12:00:51 +0000 hourly 1 http://wordpress.org/?v=3.4.2 By: Dan Gaston http://blogs.discovermagazine.com/notrocketscience/2010/12/13/friendly-genes-are-more-likely-to-be-passed-around/#comment-10105 Dan Gaston Tue, 14 Dec 2010 14:16:08 +0000 http://blogs.discovermagazine.com/notrocketscience/?p=3278#comment-10105 Although I haven't had a chance to read the paper yet, since it is not available until later in the week, I ahd a few brief thoughts on this issue after discussing with a colleague. One is the claim that transfered proteins with high connectivity are unlikely to "fit" well with their xenologous counterparts after a transfer event even if they are at the 90% identity level. When talking about protein-protein interactions, global sequence divergence is not going to be an appropriate measure, that 10% sequence divergence may be located entirely within surface loops that are uninvolved, even allosterically, in the protein-protein interaction. It will be primarily the sequence (and structural) conservation in the binding sites that will be important. I have worked with proteins involved in large protein complexes that are hugely divergent that still function well in complementation studies for instance, because the proper interaction sites where mostly conserved. Which is my second point/question. These more recent HGT events, what sort of evolutionary distance were they transfered over? Within strain or within Phylum transfers of proteins with high connectivity seem much more likely to me than HGT events of highly connected proteins over large evolutionary distances in the tree. For those interested Cohen, Gophna, and Pupko have an article out concerning gene family acquisition by HGT out in MBE Advance Access <a href="http://mbe.oxfordjournals.org/content/early/2010/12/13/molbev.msq333.abstract?etoc" target="new" rel="nofollow">here</a> Although I haven’t had a chance to read the paper yet, since it is not available until later in the week, I ahd a few brief thoughts on this issue after discussing with a colleague. One is the claim that transfered proteins with high connectivity are unlikely to “fit” well with their xenologous counterparts after a transfer event even if they are at the 90% identity level. When talking about protein-protein interactions, global sequence divergence is not going to be an appropriate measure, that 10% sequence divergence may be located entirely within surface loops that are uninvolved, even allosterically, in the protein-protein interaction. It will be primarily the sequence (and structural) conservation in the binding sites that will be important. I have worked with proteins involved in large protein complexes that are hugely divergent that still function well in complementation studies for instance, because the proper interaction sites where mostly conserved.

Which is my second point/question. These more recent HGT events, what sort of evolutionary distance were they transfered over? Within strain or within Phylum transfers of proteins with high connectivity seem much more likely to me than HGT events of highly connected proteins over large evolutionary distances in the tree.

For those interested Cohen, Gophna, and Pupko have an article out concerning gene family acquisition by HGT out in MBE Advance Access here

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