Silencing, Positive Selection and Parallel Evolution: Busy History of Primate Cytochromes c

Denis Pierron,Lawrence I Grossman,Roberto Romero,Derek E Wildman,Monica Uddin,Margit Heiske,Zack Papper,Juan C Opazo,Morris Goodman,Gopi Chand,Art F Y Poon

doi:10.1371/journal.pone.0026269

Abstract

Cytochrome c (cyt c) participates in two crucial cellular processes, energy production and apoptosis, and unsurprisingly is a highly conserved protein. However, previous studies have reported for the primate lineage (i) loss of the paralogous testis isoform, (ii) an acceleration and then a deceleration of the amino acid replacement rate of the cyt c somatic isoform, and (iii) atypical biochemical behavior of human cyt c. To gain insight into the cause of these major evolutionary events, we have retraced the history of cyt c loci among primates. For testis cyt c, all primate sequences examined carry the same nonsense mutation, which suggests that silencing occurred before the primates diversified. For somatic cyt c, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses yielded the same tree topology. The evolutionary analyses show that a fast accumulation of non-synonymous mutations (suggesting positive selection) occurred specifically on the anthropoid lineage root and then continued in parallel on the early catarrhini and platyrrhini stems. Analysis of evolutionary changes using the 3D structure suggests they are focused on the respiratory chain rather than on apoptosis or other cyt c functions. In agreement with previous biochemical studies, our results suggest that silencing of the cyt c testis isoform could be linked with the decrease of primate reproduction rate. Finally, the evolution of cyt c in the two sister anthropoid groups leads us to propose that somatic cyt c evolution may be related both to COX evolution and to the convergent brain and body mass enlargement in these two anthropoid clades.

Highlights

Cytochrome c, a protein with 104 amino acids, contains at least five known functions: a) transfer of electrons from complex III to complex IV in the electron transport chain, b) initiation of apoptosis by forming a complex with Apaf-1 to activate caspase-9, c) acting as a cardiolipin oxygenase at an earlier step in promoting apoptosis, d) acting as an electron donor to p66Shc to mediate mitochondrial apoptosis, and e) acting as an electron acceptor in the translocation of mitochondrial intermembrane space proteins with disulfide bonds [1].Both this functional density and the central role of these functions for life help to explain why cyt c evolves slowly [2,3] among eukaryotes
The two most studied eutherian somatic cyt cs, mouse and cow, share 97.2% amino acid identity. Despite this overall sequence conservation, human cyt c presents several atypical properties compared to other related mammals: (i) human has only a single cyt c gene ubiquitously expressed in all tissues whereas mouse has one testis isoform and one somatic isoform [4]; (ii) human and mouse somatic cyt c sequences exhibit 9 amino acid differences (93.4% identity) due to a relatively fast amino acid replacement rate during human descent from the LCA of Primates [5]; and (iii) biochemical analyses have pointed to a higher affinity of human cyt c with electron transport chain complexes [6,7] and a pKa value for the alkaline transition higher than those for horse and yeast [8]
Phylogenetic relationships among primates estimated from cytochrome c divergence Using maximum likelihood, maximum parsimony, and Bayesian approaches on the cyt c somatic gene sequence (CYCS, GeneBank Accession numbers: JF919224-JF919284), we estimated phylogenetic relationships among 56 primate and 4 non-primate species

Summary

Introduction

Cytochrome c (cyt c), a protein with 104 amino acids, contains at least five known functions: a) transfer of electrons from complex III to complex IV in the electron transport chain, b) initiation of apoptosis by forming a complex with Apaf-1 to activate caspase-9, c) acting as a cardiolipin oxygenase at an earlier step in promoting apoptosis, d) acting as an electron donor to p66Shc to mediate mitochondrial apoptosis, and e) acting as an electron acceptor in the translocation of mitochondrial intermembrane space proteins with disulfide bonds [1].Both this functional density and the central role of these functions for life help to explain why cyt c evolves slowly [2,3] among eukaryotes. Cytochrome c (cyt c), a protein with 104 amino acids, contains at least five known functions: a) transfer of electrons from complex III to complex IV in the electron transport chain, b) initiation of apoptosis by forming a complex with Apaf-1 to activate caspase-9, c) acting as a cardiolipin oxygenase at an earlier step in promoting apoptosis, d) acting as an electron donor to p66Shc to mediate mitochondrial apoptosis, and e) acting as an electron acceptor in the translocation of mitochondrial intermembrane space proteins with disulfide bonds [1]. We have investigated here whether the atypical properties of human somatic cyt c are due to (i) the silencing of cyt c testis isoform, (ii) coevolution with cytochrome c oxidase, or (iii) a co-evolutionary step involving both silencing of cyt c testis isoform and evolution of cytochrome c oxidase

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Conclusion