Independent Recruitment of Duplicated β-Subunit-Coding NAD-ME Genes Aided the Evolution of C4 Photosynthesis in Cleomaceae

TRONCONI, MARCOS A.; HUDIG, MEIKE; SCHRANZ, ERIC; MAURINO, VERONICA GRACIELA

Frontiers in Plant Science

Frontiers Media S.A.

Año: 2020 vol. 11

1664-462X

In different lineages of C4 plants, the release of CO2 by decarboxylation of a C4 acidnear rubisco is catalyzed by NADP-malic enzyme (ME) or NAD-ME, and the facultativeuse of phosphoenolpyruvate carboxykinase. The co-option of gene lineages during theevolution of C4-NADP-ME has been thoroughly investigated, whereas that of C4-NADMEhas received less attention. In this work, we aimed at elucidating the mechanism ofrecruitment of NAD-ME for its function in the C4 pathway by focusing on the eudicotfamily Cleomaceae. We identified a duplication of NAD-ME in vascular plants thatgenerated the two paralogs lineages: a- and b-NAD-ME. Both gene lineages wereretained across seed plants, and their fixation was likely driven by a degenerativeprocess of sub-functionalization, which resulted in a NAD-ME operating primarily asa heteromer of a- and b-subunits. We found most angiosperm genomes maintain a 1:1b-NAD-ME/a-NAD-ME (b/a) relative gene dosage, but with some notable exceptionsmainly due to additional duplications of b-NAD-ME subunits. For example, a significantlyhigh proportion of species with C4-NAD-ME-type photosynthesis have a non-1:1 ratioof b/a. In the Brassicales, we found C4 species with a 2:1 ratio due to a b-NAD-MEduplication (b1 and b2); this was also observed in the C3 Tarenaya hassleriana andBrassica crops. In the independently evolved C4 species, Gynandropsis gynandra andCleome angustifolia, all three genes were affected by C4 evolution with a- and b1-NAD-ME driven by adaptive selection. In particular, the b1-NAD-MEs possess manydifferentially substituted amino acids compared with other species and the b2-NAD-MEsof the same species. Five of these amino acids are identically substituted in b1-NAD-MEof G. gynandra and C. angustifolia, two of them were identified as positively selected.Using synteny analysis, we established that b-NAD-ME duplications were derived fromancient polyploidy events and that a-NAD-ME is in a unique syntenic context in bothCleomaceae and Brassicaceae. We discuss our hypotheses for the evolution of NADMEand its recruitment for C4 photosynthesis. We propose that gene duplications provided the basis for the recruitment of NAD-ME in C4 Cleomaceae and that allmembers of the NAD-ME gene family have been adapted to fit the C4-biochemistry.Also, one of the b-NAD-ME gene copies was independently co-opted for its function inthe C4 pathway.