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Nearly all eukaryotes carry DNA transposons of the Robertson’s Mutator ( Mu ) superfamily, a widespread source of genome instability and genetic variation. Despite their pervasive impact on host genomes, much remains unknown about the evolution of these transposons. Transposase recognition of terminal inverted repeats (TIRs) is thought to drive and constrain coevolution of MuDR transposase genes and TIRs. To address the extent of this relationship and its impact, we compared separate phylogenies of TIRs and MuDR gene sequences from Mu elements in the maize genome. Five major clades were identified. As expected, most Mu elements were bound by highly similar TIRs from the same clade (homomorphic type). However, a subset of elements contained dissimilar TIRs derived from divergent clades. These “heteromorphs” typically occurred in multiple copies indicating active transposition in the genome. In addition, analysis of internal sequences showed that exchanges between elements having divergent TIRs produced new mudra and mudrb gene combinations. In several instances, TIR homomorphs had been regenerated within a heteromorph clade with retention of distinctive internal MuDR sequence combinations. Results reveal that recombination between divergent clades facilitates independent evolution of transposase ( mudra ), transposase-binding targets (TIRs), and capacity for insertion ( mudrb ) of active Mu elements. This mechanism would be enhanced by the preference of Mu insertions for recombination-rich regions near the 5′ ends of genes. We suggest that cycles of recombination give rise to alternating homo- and heteromorph forms that enhance the diversity on which selection for Mu fitness can operate. 

SUMMARY Carotenoids perform a broad range of important functions in humans; therefore, carotenoid biofortification of maize (Zea maysL.), one of the most highly produced cereal crops worldwide, would have a global impact on human health.PLASTID TERMINAL OXIDASE(PTOX) genes play an important role in carotenoid metabolism; however, the possible function ofPTOXin carotenoid biosynthesis in maize has not yet been explored. In this study, we characterized the maizePTOXlocus by forward‐ and reverse‐genetic analyses. While most higher plant species possess a single copy of thePTOXgene, maize carries two tandemly duplicated copies. Characterization of mutants revealed that disruption of either copy resulted in a carotenoid‐deficient phenotype. We identified mutations in thePTOXgenes as being causal of the classic maize mutant,albescent1. Remarkably, overexpression ofZmPTOX1significantly improved the content of carotenoids, especially β‐carotene (provitamin A), which was increased by ~threefold, in maize kernels. Overall, our study shows that maizePTOXlocus plays an important role in carotenoid biosynthesis in maize kernels and suggests that fine‐tuning the expression of this gene could improve the nutritional value of cereal grains. 

Significance Statement Narrow odd dwarf ( nod ) and Liguleless narrow ( Lgn ) are pleiotropic maize mutants that severely disrupt growth and development. Here, we share our unexpected discovery that the NOD and LGN proteins physically interact at the plasma membrane. Using a combination of genetics, functional genomics and metabolomics, we then show that nod and Lgn impact overlapping stress–response and developmental patterning pathways in maize. 

SUMMARY Zea mays(maize) makes phytoalexins such as sesquiterpenoid zealexins, to combat invading pathogens. Zealexins are produced from farnesyl diphosphate in microgram per gram fresh weight quantities. As farnesyl diphosphate is also a precursor for many compounds essential for plant growth, the question arises as to howZ. maysproduces high levels of zealexins without negatively affecting vital plant systems. To examine if specific pools of farnesyl diphosphate are made for zealexin synthesis we made CRISPR/Cas9 knockouts of each of the three farnesyl diphosphate synthases (FPS) inZ. maysand examined the resultant impacts on different farnesyl diphosphate‐derived metabolites. We found that FPS3 (GRMZM2G098569) produced most of the farnesyl diphosphate for zealexins, while FPS1 (GRMZM2G168681) made most of the farnesyl diphosphate for the vital respiratory co‐factor ubiquinone. Indeed,fps1mutants had strong developmental phenotypes such as reduced stature and development of chlorosis. The replication and evolution of thefpsgene family inZ. maysenabled it to produce dedicated FPSs for developmentally related ubiquinone production (FPS1) or defense‐related zealexin production (FPS3). This partitioning of farnesyl diphosphate production between growth and defense could contribute to the ability ofZ. maysto produce high levels of phytoalexins without negatively impacting its growth.