Detecting changes in the functional constraints of paralogous genes

We describe a new procedure to determine whether regional alterations in th e evolutionary constraints imposed on paralogous proteins have occurred. We used as models the A and B (alternatively called alpha and beta) subunits of V/F/A-ATPases, originated by a gene duplication more than 3 billion year s ago. Changes associated to three major splits (eubacteria versus Archaea- eukaryotes; Archaea versus eukaryotes; and among free-living bacteria and s ymbiotic mitochondria) were studied. Only in the first case, when we compar ed eubacterial or mitochondrial F-ATPases versus eukaryotic vacuolar V-ATPa ses or archaeal A-ATPases, constraint changes were observed. Modifications in the degree of regional constraining were not detected for the other two types of comparisons (V-ATPases versus A-ATPases and within F-ATPases, resp ectively). When the rates of evolution of the two subunits were compared, i t was found that F-ATPases regulatory subunits evolved faster than catalyti c subunits, but the opposite was true for A- and V-ATPases. Our results sug gest that, even for universal and essential proteins, selective constraints may be occasionally altered. On the other hand, in some cases no changes w ere detected after Periods of more than 2.2 billion years.