Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)

Josh J Rosnow; Gerald E Edwards; Eric H Roalson

doi:10.1093/jxb/eru053

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Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)

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Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)

Josh J Rosnow, Gerald E Edwards and Eric H Roalson

Journal of experimental botany, Vol.65(13), pp.3595-3607

07/2014

DOI: https://doi.org/10.1093/jxb/eru053

Handle:

https://hdl.handle.net/2376/106960

PMCID: PMC4085955

PMID: 24600021

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Abstract

Models, Structural

Chenopodiaceae - genetics

Phosphoenolpyruvate Carboxylase - chemistry

Chenopodiaceae - enzymology

Selection, Genetic

Molecular Sequence Data

Models, Statistical

Phylogeny

Phosphoenolpyruvate Carboxylase - genetics

Sequence Analysis, DNA

Plant Proteins - genetics

Plant Leaves - genetics

Plant Proteins - chemistry

Base Sequence

Phosphoenolpyruvate Carboxylase - metabolism

Plant Proteins - metabolism

Photosynthesis

Plant Leaves - enzymology

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.

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Title: Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)
Creators: Josh J Rosnow - School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
Gerald E Edwards - School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
Eric H Roalson - School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA eric_roalson@wsu.edu
Publication Details: Journal of experimental botany, Vol.65(13), pp.3595-3607
Academic Unit: Biological Sciences, School of
Publisher: England
Identifiers: 99900546974601842
Language: English
Resource Type: Journal article