Unlocking the role of novel primary/di-amine oxidases in crop improvement: Tissue specificity leads to specific roles connected to abiotic stress, hormone responses and sensing nitrogen

Genetic improvements of solanaceous crops for quality and stress responsive traits are needed because of the central role vegetables and fruits have in providing nutrients to human diets. Copper amine oxidase (CuAO) encoding genes involved in metabolism of primary/di-amine nitrogenous compounds, play a role in balancing internal nitrogen (N) pools especially when external N supply fluctuates during growth, development and environmental stresses. In the present study, we investigated the occurrence, molecular evolution and possible role(s) of these unknown genes in tomato crops. Multiple genome-wide bioinformatics approaches led to the identification of eight bona fide CuAO genes (SlCuAO1–SlCuAO8) in the tomato genome with gene numbers like those in Arabidopsis and rice indicating their conserved functional relevance with a tandemly duplicated SlCuAO6-SlCuAO7 pair at chr.9. A conserved intron-exon size and phase distribution for SlCuAO2, 3, 4 pairs are similar to a recently identified single duckweed SpCuAO1 orthologue gene indicating its evolutionary conservation. Synteny analysis showed their closest association to Arabidopsis and but not with rice. Transcriptome data indicated that gene expression for about six genes (SlCuAO1, 2, 3, 4, 6, 7) is root specific, fruit specific for SlCuAO5 and flower specific for SlCuAO8 thus indicating amine oxidation is variable across tissues with a prominance in the root tissue. The majority of CuAO genes are negatively regulated by methyl jasmonate. Positive regulation, however, involves CuAO3/8. Transcript analysis of the ethylene-deficient transgenic lines indicated that ethylene is required for activation of SlCuAO4. CuAO4 and CuAO5 exhibited most significant tissues-independent gene expression responses across various nitrogen regimes. Drought, heat and N stress identified CuAO5 as an overlapping highly expressed gene that corroborates with putrescine accumulation for free and conjugated forms with an opposite abundance of bound forms. Taken together our study highlights new insights into the roles of copper amine oxidation genes and identifies CuAO5 as a multiple stress induced gene that can be used in genetic improvement programs for combining heat, drought and nitrogen use efficiency related traits.