LONG HYPOCOTYL IN FAR-RED 1 mediates a trade-off between growth and defence under shade in Arabidopsis

Abstract

Plants respond to vegetative shade with developmental and physiological changes that is collectively known as shade avoidance syndrome (SAS). Although LONG HYPOCOTYL IN FAR-RED 1 (HFR1) is known to be a negative regulator of SAS by forming heterodimers with other basic helix-loop-helix (bHLH) transcription factors to inhibit them, its function in genome-wide transcriptional regulation is not fully elucidated. Here, we performed RNA-sequencing analyses of hfr1-5 and HFR1 overexpression line (HFR1(ΔN)-OE) to comprehensively identify HFR1-regulated genes at different time points of shade treatment. We found that HFR1 mediates the trade-off between shade-induced growth and shade-repressed defense, by regulating the expression of relevant genes in shade. Genes involved in promoting growth, such as for auxin biosynthesis, transport, signaling and response were induced by shade but suppressed by HFR1 at both short and long durations of shade. Likewise, most ethylene-related genes were shade-induced and HFR1-repressed. On the other hand, shade suppressed defense-related genes while HFR1 induced their expression, especially under long duration of shade treatment. We demonstrated that HFR1 confers increased resistance to bacterial infection under shade.

Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses

“…The shade and the invasion of insects or microbes usually jointly affect plant survival, therefore, plants need to balance the interactions between shade avoidance and defense responses to achieve a better survival [128,129]. PIFs have been revealed to be involved in this interaction by modulating resource allocation to coordinate plant defense and development [130,131]. It is reported that when shaded plants are challenged with pathogens or herbivores, growth is prioritized over defense responses [130][131][132][133].…”

“…PIFs have been revealed to be involved in this interaction by modulating resource allocation to coordinate plant defense and development [130,131]. It is reported that when shaded plants are challenged with pathogens or herbivores, growth is prioritized over defense responses [130][131][132][133]. Specifically, under the concurrence of pest infestation and shading, PIF4 suppresses the JA signaling pathway by repressing the transcription of Myelocytomatosis (MYC), the master regulator in the pathway [130].…”

Discovery of a second‐site nia2 mutation in the background of multiple ArabidopsisPIF‐related mutants containing the pif3‐3 allele

“…pifq and pqp6p7 ) have been widely used to study PIF functions (e.g. Jiang et al ., 2020 ; Bernula et al ., 2021 ; Yoo et al ., 2021 ; Piskurewicz et al ., 2023 ; Sng et al ., 2023 ). The identification of the hidden nia2‐2 mutation revealed here might render it worthwhile re‐examining the alternative interpretation that some of the reported mutant phenotypes were due to the deficiency in N metabolism and/or NO production, especially for any studies investigating the crosstalk between the PIF and NO signalling pathways (Lozano‐Juste & León, 2011 ; Bai et al ., 2014 ).…”