Evidence for positive selection in the C-terminal domain of the cholesterol metabolism gene PCSK9 based on phylogenetic analysis in 14 primate species

Keyue Ding, Samantha J. McDonough, Iftikhar Jan Kullo

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Background. Cholesterol homeostasis is maintained through finely tuned mechanisms regulating intestinal absorption, hepatic biosynthesis and secretion as well as plasma clearance. Proprotein convertase subtilisin/ kexin type 9 (PCSK9) is a secreted enzyme of the serine protease family that reduces cellular uptake of plasma low-density lipoprotein (LDL) cholesterol by promoting LDL receptor (LDL-R) degradation. Species-specific positive selection has been noted in the LDLR promoter, leading to differential expression of LDLR among primates. Whether PCSK9 experienced significant selective pressure to maintain a functional relationship with its target protein, LDL-R, is unknown. Methodology/Principal Findings. We compiled the sequences of the coding regions of PCSK9 from 14 primate species in the clade of Hominoids, Old World monkeys and New World monkeys. To detect selective pressure at the protein level, the ratios of nonsynonymous/synonymous substitution rate (dN/dS) under different evolutionary models were calculated across the phylogerty of PCSK9. Maximum likelihood analyses of dN/dS ratios for the aligned coding region sequences among 14 primate species indicated that PCSK9 was subject to a strong functional constraint (i.e., purifying selection). However, positive selection was noted in the functional carboxyl-terminal (C-terminal) domain in many branches across the phylogeny, especially in the lineage leading to the orangutan. Furthermore, at least five positively selected amino acids were detected in this lineage using the branch-site model A. In a sliding-window analysis, several dN/dS peaks in the C-terminal domaim in both the human and the orangutan branches were noted. Conclusions. These results suggest that among primates, differential selective pressure has shaped evolutionary patterns in the functional domains of PCSK9, an important regulator of cholesterol homeostasis.

Original languageEnglish (US)
Article numbere1098
JournalPLoS One
Volume2
Issue number10
DOIs
StatePublished - Oct 31 2007

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Proprotein Convertases
Subtilisin
cholesterol metabolism
subtilisin
Metabolism
Primates
Genes
Cholesterol
phylogeny
Pongo
Pongo pygmaeus
genes
low density lipoprotein
homeostasis
Homeostasis
cholesterol
Platyrrhini
Cercopithecidae
Plasmas
Cebidae

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Evidence for positive selection in the C-terminal domain of the cholesterol metabolism gene PCSK9 based on phylogenetic analysis in 14 primate species. / Ding, Keyue; McDonough, Samantha J.; Kullo, Iftikhar Jan.

In: PLoS One, Vol. 2, No. 10, e1098, 31.10.2007.

Research output: Contribution to journalArticle

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AB - Background. Cholesterol homeostasis is maintained through finely tuned mechanisms regulating intestinal absorption, hepatic biosynthesis and secretion as well as plasma clearance. Proprotein convertase subtilisin/ kexin type 9 (PCSK9) is a secreted enzyme of the serine protease family that reduces cellular uptake of plasma low-density lipoprotein (LDL) cholesterol by promoting LDL receptor (LDL-R) degradation. Species-specific positive selection has been noted in the LDLR promoter, leading to differential expression of LDLR among primates. Whether PCSK9 experienced significant selective pressure to maintain a functional relationship with its target protein, LDL-R, is unknown. Methodology/Principal Findings. We compiled the sequences of the coding regions of PCSK9 from 14 primate species in the clade of Hominoids, Old World monkeys and New World monkeys. To detect selective pressure at the protein level, the ratios of nonsynonymous/synonymous substitution rate (dN/dS) under different evolutionary models were calculated across the phylogerty of PCSK9. Maximum likelihood analyses of dN/dS ratios for the aligned coding region sequences among 14 primate species indicated that PCSK9 was subject to a strong functional constraint (i.e., purifying selection). However, positive selection was noted in the functional carboxyl-terminal (C-terminal) domain in many branches across the phylogeny, especially in the lineage leading to the orangutan. Furthermore, at least five positively selected amino acids were detected in this lineage using the branch-site model A. In a sliding-window analysis, several dN/dS peaks in the C-terminal domaim in both the human and the orangutan branches were noted. Conclusions. These results suggest that among primates, differential selective pressure has shaped evolutionary patterns in the functional domains of PCSK9, an important regulator of cholesterol homeostasis.

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