title: Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae).
abstract: In subfamily Suaedoideae, four independent gains of C4 photosynthesis are proposed, which includes two parallel origins of Kranz anatomy (sections Salsina and Schoberia) and two independent origins of single-cell C4 anatomy (Bienertia and Suaeda aralocaspica). Additional phylogenetic support for this hypothesis was generated from sequence data of the C-terminal portion of the phosphoenolpyruvate carboxylase (PEPC) gene used in C4 photosynthesis (ppc-1) in combination with previous sequence data. ppc-1 sequence was generated for 20 species in Suaedoideae and two outgroup Salsola species that included all types of C4 anatomies as well as two types of C3 anatomies. A branch-site test for positively selected codons was performed using the software package PAML. From labelling of the four branches where C4 is hypothesized to have developed (foreground branches), residue 733 (maize numbering) was identified to be under positive selection with a posterior probability >0.99 and residue 868 at the >0.95 interval using Bayes empirical Bayes (BEB). When labelling all the branches within C4 clades, the branch-site test identified 13 codons to be under selection with a posterior probability >0.95 by BEB; this is discussed considering current information on functional residues. The signature C4 substitution of an alanine for a serine at position 780 in the C-terminal end (which is considered a major determinant of affinity for PEP) was only found in four of the C4 species sampled, while eight of the C4 species and all the C3 species have an alanine residue; indicating that this substitution is not a requirement for C4 function.
authors.affiliation: School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
authors.forename: Josh J
authors.initials: JJ
authors.lastname: Rosnow
authors.affiliation: School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
authors.forename: Gerald E
authors.initials: GE
authors.lastname: Edwards
authors.affiliation: School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA eric_roalson@wsu.edu.
authors.forename: Eric H
authors.initials: EH
authors.lastname: Roalson
mesh_terms: D001483:Base Sequence; D019663:Chenopodiaceae / Q000201:enzymology* / Q000235:genetics; D015233:Models, Statistical; D008961:Models, Structural; D008969:Molecular Sequence Data; D010730:Phosphoenolpyruvate Carboxylase / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D010788:Photosynthesis; D010802:Phylogeny; D018515:Plant Leaves / Q000201:enzymology / Q000235:genetics; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins; D010730:Phosphoenolpyruvate Carboxylase
keywords: Bienertia; C4 photosynthesis; PAML; Suaeda aralocaspica; Suaedoideae.; phosphoenolpyruvate carboxylase; positive selection analysis