Phenotypic similarity of NAD(P)-Malic Enzymes in Tomato: Unveiling Patterns of Convergent and Parallel Evolution

The Solanum lycopersicum (tomato) genome encodes seven malic enzymes (MEs): three cytosolic NADP-ME isoforms (SlNADP-ME1, -2, and -3), two plastidic NADP-ME proteins (SlNADP-ME4a and -4b), and two mitochondrial NAD-dependent subunits (SlNAD-ME1 and -2) of a heteromeric enzyme. Except for SlNADP-ME3, which is almost exclusively expressed in the root, all the genes are active in the major tissues of flowering plants (leaf, stem, flower, and root), with SlNADP-ME2 and -4b transcripts accumulating at relative high levels. During the cell expansion and ripening phases of fruit development, SlNADP-ME3 and -4b expression increased in the pericarp and seeds while SlNADP-ME2 remained at a high level. In green fruit, SlNADP-ME3 and -4b are down-regulated by ethylene, with SlNAD-ME1 and -2 being up-regulated. A correlation between SlNADP-ME4b accumulation and NADP-ME activity was observed from the early immature green to the mature green fruit stages, linking this plastidic isoform to starch and lipid biosynthesis. SlNADP-ME1 and -4a expression increase with temperature, suggesting involvement in defense mechanisms and supported by cis -elements composition in their promoters. Interesting, SlNADP-ME3 biochemical properties and its accumulation in seeds is part of an inherited and long-conserved genetic lineage in Angiosperms including Arabidopsis NADP-ME1, involved in normal seed germination. By analyzing the phylogeny and synteny of SlNAD(P)-ME genes and determining the biochemical properties of the recombinant proteins, we seek functional similarities to Arabidopsis NAD(P)-ME members. Our findings enhance the understanding of malate metabolism in tomatoes, which could inform strategies to improve fruit quality. Additionally, they prompt a re-evaluation of pre-existing notions regarding the functional orthology of enzymes based on phylogenetic relationships.