Convergent evolution of the Hedgehog/Intein fold in protein splicing

The widely used molecular evolutionary clock assumes the divergent evolution of proteins. Convergent evolution has been proposed only for small protein elements but not for an entire protein fold. We investigated the structural basis of the protein splicing mechanism by class 3 inteins, which is distinct from class 1 and 2 inteins. We gathered structural and mechanistic evidence supporting the notion that the Hedgehog/INTein (HINT) superfamily fold, commonly found in protein splicing and related phenomena, could be an example of convergent evolution of an entire protein fold. We propose that the HINT fold is a structural and biochemical solution for trans-peptidyl and trans-esterification reactions.

Simple methods for testing the molecular evolutionary clock hypothesis.

Simple statistical methods for testing the molecular evolutionary clock hypothesis are developed which can be applied to both nucleotide and amino acid sequences. These methods are based on the chi-square test and are applicable even when the pattern of substitution rates is unknown and/or the substitution rate varies among different sites. Furthermore, some of the methods can be applied even when the outgroup is unknown. Using computer simulations, these methods were compared with the likelihood ratio test and the relative rate test. The results indicate that the powers of the present methods are similar to those of the likelihood ratio test and the relative rate test, in spite of the fact that the latter two tests assume that the pattern of substitution rates follows a certain model and that the substitution rate is the same among different sites, while such assumptions are not necessary to apply the present methods. Therefore, the present methods might be useful.

The Study of Plant Phylogeny Using Amino-Acid-Sequences of Ribulose-1,5-Bisphosphate Carboxylase .VI. Some Solanum and Allied Species From Different Continents

The N-terminal 40 amino acid sequences of the small subunit of ribulose bisphosphate carboxylase have been determined for 13 species of Solanum, one other species of Solanaceae and two of Convolvulaceae. From these, and previously published sequences from Solanaceae, a minimal phylogenetic tree is derived. This agrees well with current taxonomy; the first dichotomy in the Solanaceae tree is between the two subfamilies Solanoideae and Cestroideae; within Solanum the subgenera Solanum and Leptostemonum separate dichotomously; within subgenus Leptostemonum the African and Asian species diverge from the Australian. Within the Australian species of subgenus Leptostemonum two most unusual substitutions have been noted. The implications for the hypotheses of a 'molecular evolutionary clock' and of biogeographical dispersal by continental drift are discussed.