Flexible growth and immune responses in rice: Plants that are fighting microbial pathogens often divert resources that could be used for growth into the immune response. For crops, this translates into lower yield when plant immunity is activated. Wang et al. show that, in rice, reversible phosphorylation of a key transcription factor allows the plant to defend against fungal attack when needed but then, within days, reallocate resources back to growth (see the Perspective by Greene and Dong). Thus, both pathogen defense and crop yield can be sustained. Science , this issue p. 1026 ; see also p. 976

Crops are exposed to attacks by various pathogens that cause substantial yield losses and severely threaten food security. To cope with pathogenic infection, crops have elaborated strategies to enhance resistance against pathogens. In addition to the role of protein-coding genes as key regulators in plant immunity, accumulating evidence has demonstrated the importance of non-coding RNAs (ncRNAs) in the plant immune response. Here, we summarize the roles and molecular mechanisms of endogenous ncRNAs, especially microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), in plant immunity. We discuss the coordination between miRNAs and small interfering RNAs (siRNAs), between lncRNAs and miRNAs or siRNAs, and between circRNAs and miRNAs in the regulation of plant immune responses. We also address the role of cross-kingdom mobile small RNAs in plant–pathogen interactions. These insights improve our understanding of the mechanisms by which ncRNAs regulate plant immunity and can promote the development of better approaches for breeding disease-resistant crops.

Hydrogen peroxide (H₂O₂) is a ubiquitous signal regulating many biological processes, including innate immunity, in all eukaryotes. However, it remains largely unknown that how transcription factors directly sense H₂O₂ in eukaryotes. Here, we report that rice basic/helix-loop-helix transcription factor bHLH25 directly senses H₂O₂ to confer resistance to multiple diseases caused by fungi or bacteria. Upon pathogen attack, rice plants increase the production of H₂O₂, which directly oxidizes bHLH25 at methionine 256 in the nucleus. Oxidized bHLH25 represses miR397b expression to activate lignin biosynthesis for plant cell wall reinforcement, preventing pathogens from penetrating plant cells. Lignin biosynthesis consumes H₂O₂ causing accumulation of non-oxidized bHLH25. Non-oxidized bHLH25 switches to promote the expression of Copalyl Diphosphate Synthase 2 (CPS2), which increases phytoalexin biosynthesis to inhibit expansion of pathogens that escape into plants. This oxidization/non-oxidation status change of bHLH25 allows plants to maintain H₂O₂, lignin and phytoalexin at optimized levels to effectively fight against pathogens and prevents these three molecules from over-accumulation that harms plants. Thus, our discovery reveals a novel mechanism by which a single protein promotes two independent defense pathways against pathogens. Importantly, the bHLH25 orthologues from available plant genomes all contain a conserved M256-like methionine suggesting the broad existence of this mechanism in the plant kingdom. Moreover, this Met-oxidation mechanism may also be employed by other eukaryotic transcription factors to sense H₂O₂ to change functions.

Global warming impacts crop production and increases crop disease. It is commonly known that heat stress (HS) caused by extreme high temperature induces HS responses but suppresses disease resistance in plants. However, the molecular basis of this trade-off remains largely unknown. Here, we report that OsHsfA4d shows strongest induction upon HS and pathogen infection among Heat Shock Factors (HSFs) in rice. The transcription factor OsHSFA4d enhances thermotolerance by binding to the heat shock element (HSE) in the promoter of HSP101 to activate its expression. OsHSFA4d also binds to the HSE in the first intron of Cellulose synthase-like F6 (CslF6) to promote its expression for suppressing PAMP-triggered ROS bursts and pathogenesis-related gene expression, inhibiting disease resistance. OsCDPK24 and OsCDPK28 interact with OsHSFA4d to form a complex that phosphorylates serine 146 (S146) of OsHSFA4d, thereby enhancing its DNA binding ability. HS induces the kinase activity of OsCDPK24/28 to increase the phosphorylation level of OsHSFA4d. Importantly, residues similar to S146 are conserved in OsHSFA4d orthologues across plant species, suggesting that such phosphorylation modules are widely employed to regulate abiotic and biotic stress responses in the plant kingdom.

Black and red rice are rich in both anthocyanin and proanthocyanin content, which belong to a large class of flavonoids derived from a group of phenolic secondary metabolites. However, the molecular pathways and mechanisms underlying the flavonoid biosynthetic pathway are far from clear. Therefore, this study was undertaken to gain insight into physiological factors that are involved in the flavonoid biosynthetic pathway in rice cultivars with red, black, and white colors. RNA sequencing of caryopsis and isobaric tags for relative and absolute quantification (iTRAQ) analyses have generated a nearly complete catalog of mRNA and expressed proteins in different colored rice cultivars. A total of 31,700 genes were identified, of which 3417, 329, and 227 genes were found specific for red, white, and black rice, respectively. A total of 13,996 unique peptides corresponding to 3916 proteins were detected in the proteomes of black, white, and red rice. Coexpression network analyses of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) among the different rice cultivars showed significant differences in photosynthesis and flavonoid biosynthesis pathways. Based on a differential enrichment analysis, 32 genes involved in the flavonoid biosynthesis pathway were detected, out of which only CHI, F3H, ANS, and FLS were detected by iTRAQ. Taken together, the results point to differences in flavonoid biosynthesis pathways among different colored rice cultivars, which may reflect differences in physiological functions. The differences in contents and types of flavonoids among the different colored rice cultivars are related to changes in base sequences of Os06G0162500, Os09G0455500, Os09G0455500, and Os10G0536400. Current findings expand and deepen our understanding of flavonoid biosynthesis and concurrently provides potential candidate genes for improving the nutritional qualities of rice.