In crops, nitrogen directly determines productivity and biomass. However, the improvement of nitrogen utilization efficiency (NUE) is still a major challenge in modern agriculture. Here, we report the characterization of are1, a genetic suppressor of a rice fd-gogat mutant defective in nitrogen assimilation. ARE1 is a highly conserved gene, encoding a chloroplast-localized protein. Loss-of-function mutations in ARE1 cause delayed senescence and result in 10–20% grain yield increases, hence enhance NUE under nitrogen-limiting conditions. Analysis of a panel of 2155 rice varieties reveals that 18% indica and 48% aus accessions carry small insertions in the ARE1 promoter, which result in a reduction in ARE1 expression and an increase in grain yield under nitrogen-limiting conditions. We propose that ARE1 is a key mediator of NUE and represents a promising target for breeding high-yield cultivars under nitrogen-limiting condition.

Most of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements—the presence of acidic amino acids and the absence of positively charged amino acids in certain positions—to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM method allows for in silico high fidelity prediction of AIMs in AIM-containing proteins (ACPs) on a genome-wide scale in various organisms. Furthermore, by using hfAIM to identify putative AIMs in the Arabidopsis proteome, we illustrate a potential contribution of selective autophagy to various biological processes. More specifically, we identified 9 peroxisomal PEX proteins that contain hfAIM motifs, among which AtPEX1, AtPEX6 and AtPEX10 possess evolutionary-conserved AIMs. Bimolecular fluorescence complementation (BiFC) results verified that AtPEX6 and AtPEX10 indeed interact with Atg8 in planta. In addition, we show that mutations occurring within or nearby hfAIMs in PEX1, PEX6 and PEX10 caused defects in the growth and development of various organisms. Taken together, the above results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy. The hfAIM system is a web tool that can be accessed at link: http://bioinformatics.psb.ugent.be/hfAIM/.

An actin nucleation protein affects rice panicle development as well as root growth.

Leaf morphology, particularly in crop, is one of the most important agronomic traits because it influences the yield through the manipulation of photosynthetic capacity and transpiration. To understand the regulatory mechanism of leaf morphogenesis, an Oryza sativa dominant mutant, rolled and erect leaf 1 (rel1) has been characterized. This mutant has a predominant rolled leaf, increased leaf angle, and reduced plant height phenotype that results in a reduction in grain yield. Electron microscope observations indicated that the leaf incurvations of rel1 dominant mutants result from the alteration of the size and number of bulliform cells. Molecular cloning revealed that the rel1 dominant mutant phenotype is caused by the activation of the REL1 gene, which encodes a novel unknown protein, despite its high degree of conservation among monocot plants. Moreover, the downregulation of the REL1 gene in the rel1 dominant mutant restored the phenotype of this dominant mutant. Alternatively, overexpression of REL1 in wild-type plants induced a phenotype similar to that of the dominant rel1 mutant, indicating that REL1 plays a positive role in leaf rolling and bending. Consistent with the observed rel1 phenotype, the REL1 gene was predominantly expressed in the meristem of various tissues during plant growth and development. Nevertheless, the responsiveness of both rel1 dominant mutants and REL1-overexpressing plants to exogenous brassinosteroid (BR) was reduced. Moreover, transcript levels of BR response genes in the rel1 dominant mutants and REL1-overexpressing lines were significantly altered. Additionally, seven REL1-interacting proteins were also identified from a yeast two-hybrid screen. Taken together, these findings suggest that REL1 regulates leaf morphology, particularly in leaf rolling and bending, through the coordination of BR signalling transduction.