Search Results (52)

Phytochrome-interacting factors (PIFs) are key transcriptional regulators of phytochrome signalling that coordinate photomorphogenesis and photosynthesis under different environmental conditions. PIFs play an important role in this regulation and act mainly as negative regulators of photomorphogenesis, but under high-intensity light (HIL), their functions can also include adaptive roles. We investigated the contribution of individual PIFs to the adaptation of the photosynthetic apparatus in wild-type A. thaliana and pif4, pif5, pif4pif5, and pif1pif3pif4pif5 mutants exposed to HIL for 0, 16, 32, or 48 h. Chlorophyll fluorescence parameters (Y(II), F_v/F_m, NPQ), net photosynthesis (Pn), transpiration rates, stomatal conductance (g_S), pigment contents and the expression of key genes were evaluated. The response of plants to HIL varied depending on the duration of exposure. After 16 h of irradiation, the greatest reductions in Pn and g_S were observed in the pif4pif5 and pif1pif3pif4pif5 mutants, whereas after 48 h, the decreases were most pronounced in the pif4, pif5, and pif4pif5 mutants. After 16 h of HIL exposure, the absence of pif4 and pif5 did not substantially alter the chlorophyll fluorescence parameters. However, after 48 h, both Y(II) and Fv/Fm were lower in these mutants than in the wild type, indicating changes in PSII functional status rather than direct reductions in photochemical quantum efficiency. At 16 h, chlorophyll levels were the highest in pif5 and WT, whereas anthocyanin and UV-absorbing pigment (UAP) levels were the highest in pif4, pif5 and WT. After 48 h, the highest levels of any pigments were detected in the WT and the pif1pif3pif4pif5 mutant. These results suggest that the accumulation of anthocyanins and UAPs under HIL is likely associated with the regulation of transcription factors, such as PIFs, de-etiolated 1 (DET1), constitutive photomorphogenic 1 (COP1), and elongated hypocotyl 5 (HY5). During prolonged HIL exposure, the absence of PIF4 and PIF5 has a critical impact on photosynthesis and the accumulation of photosynthetic pigments, whereas the simultaneous loss of PIF1, PIF3, PIF4, and PIF5 is less detrimental. This finding likely indicates opposite roles of PIF1 and PIF3 in the above-described processes, on the one hand, and PIF4 and PIF5, on the other hand, under HIL conditions. Full article

Plants, as sessile organisms, rely on sophisticated gene regulatory networks (GRNs) to adapt to dynamic environmental conditions. Among the central components of these networks are the interconnected pathways of light signaling and circadian rhythms, which together optimize growth, development, and stress resilience. While light and circadian pathways have been extensively investigated independently, their integrative coordination in mediating climate change adaptation responses remains a critical knowledge gap. Light perception via photoreceptors initiates transcriptional reprogramming, while the circadian clock generates endogenous rhythms that anticipate daily and seasonal changes. This review explores the molecular integration of light and circadian signaling, emphasizing how their crosstalk fine-tunes GRNs to balance resource allocation, photomorphogenesis, and stress adaptation. We highlight recent advances in systems biology tools, e.g., single-cell omics, CRISPR screens that unravel spatiotemporal regulation of shared hubs like phytochrome-interacting factors (PIFs), ELONGATED HYPOCOTYL 5 (HY5), and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). Here, we synthesize mechanistic insights across model and crop species to bridge fundamental molecular crosstalk with actionable strategies for enhancing cropresilience. Moreover, we have tried to discuss agricultural implications in engineering light–clock interactions for the enhancement in crop productivity under climate change scenarios. Through synthesizing mechanistic insights and translational applications, this work will help underscore the potential for manipulating light–circadian networks to promote sustainability in agriculture. Full article

Camellia’s ornamental value is constrained by its natural winter–spring flowering period. Although the discovery of Camellia azalea provides important germplasm resources for developing cultivars with year-round flowering, the molecular mechanisms underlying flowering time variation remain unclear. Here, we investigated three germplasms with distinct flowering patterns: winter–spring flowering Camellia japonica ‘Tieke Baozhu’, summer–autumn flowering Camellia azalea, and their hybrid Camellia ‘Lingnan Yuanbao’ inheriting the latter’s flowering traits. Integrated transcriptomic and metabolomic analyses revealed that differentially expressed genes (DEGs) and metabolites (DAMs) were mainly enriched in the pathways related to photoperiod regulation, plant hormone synthesis and signal transduction and flavonoid synthesis. The transcription factor (TF) analysis revealed that the bHLH and MYB TF families were significantly differentially expressed in different Camellia germplasm, suggesting their potential involvement in the regulation of flowering time through the plant hormone signal transduction and photoperiod pathway. Meanwhile, photoperiod regulation related genes, including Cryptochrome circadian regulator (CRY), Timing of CAB expression 1 (TOC1), and phytochrome interacting factor 3 (PIF3), showed significant expression differences, further confirming the photoperiod pathway’s crucial regulatory function. In terms of plant hormone levels, there were significant differences in the levels of gibberellin (GA), abscisic acid (ABA), and jasmonic acid (JA) among Camellia germplasm. The differential expression characteristics of DELLA (Asp-Glu-Leu-Leu-Ala) proteins indicated that the GA signal transduction pathway was one of the key factors regulating flowering time in Camellia. Additionally, metabolomics analyses showed significant differences in flavonoid metabolite content among Camellia germplasm, which was significantly correlated with the different developmental stages of the buds. Our findings provide a theoretical basis for the molecular breeding of everblooming Camellia cultivars, advancing the understanding of flowering regulation mechanism in ornamental species. Full article

Anthocyanins are key metabolites that determine red pigmentation in pear skin (Pyrus spp.) and their biosynthesis is controlled by multiple transcription factors. Although phytochrome-interacting factors (PIFs) of the bHLH family have been shown to regulate anthocyanin biosynthesis in Arabidopsis thaliana, their genome-wide identification and regulatory mechanisms in pear (Pyrus spp.) anthocyanin synthesis remain unclear. Here, we characterized PIFs family in pear, identifying eight PbPIF proteins. Promoter cis-elements and expression patterns analysis suggested that PbPIF3a and PbPIF4 might be involved in anthocyanin biosynthesis. Subcellular localization confirmed nuclear enrichment of PbPIF3a and PbPIF4. Functional studies demonstrated that overexpression of PbPIF3a and PbPIF4 significantly suppressed anthocyanin accumulation in fruit skins, downregulating key biosynthetic genes such as PbDFR and PbUFGT. In contrast, the silencing of related genes led to an enhancement of anthocyanin accumulation. Dual-luciferase reporter assays and yeast one-hybrid assays confirmed that PbPIF3a directly bound to the promoters of PbDFR and PbUFGT and repressed their transcriptional activation, while PbPIF4 specifically inhibited the activity of the PbDFR promoter. Taken together, we demonstrated that PbPIF3a and PbPIF4 negatively regulated pear fruit coloration by directly repressing the transcriptional activity of key anthocyanin biosynthesis genes, providing novel insights into PIF-mediated regulation of anthocyanin biosynthesis. Full article

Hypocotyl length is closely related to quality in seedlings and is an important component of plant height vital for plant-type breeding in cucumber. However, the underlying molecular mechanisms of hypocotyl elongation are poorly understood. In this study, the endogenous hormone content of indole acetic acid (IAA) and gibberellin (GA₃) showed an increase in the long hypocotyl Csphyb (phytochrome B) mutant AM274M compared with its wild-type AM274W. An RNA-sequencing analysis identified 1130 differentially expressed genes (DEGs), of which 476 and 654 were up- and downregulated in the mutant AM274M, respectively. A KEGG enrichment analysis exhibited that these DEGs were mainly enriched in the plant hormone signal transduction pathway. The expression levels of the pivotal genes CsGA20ox-2, in the gibberellin biosynthesis pathway, and CsYUCCA8, in the auxin biosynthesis pathway, were notably elevated in the hypocotyl of the mutant AM274M, in contrast to the wild-type AM274W. Additionally, GUS staining and a dual-luciferase reporter assay corroborated that the phytochrome-interacting factors CsPIF3/4 can bind to the E(G)-box motifs present in the promoters of the CsGA20ox-2 and CsYUCCA8 genes, thereby modulating their expression and subsequently influencing hypocotyl elongation. Consequently, this research offers profound insights into the regulation of hypocotyl elongation by auxin and gibberellin in response to light signals and establishes a crucial theoretical groundwork for cultivating robust cucumber seedlings in agricultural practice. Full article

Phytochrome-interacting factors (PIFs) play a crucial role in regulating plant growth and development. However, studies on soybean PIFs are limited. Here, we identified 22 GmPIF genes from the soybean genome and classified the GmPIF proteins into 13 subfamilies based on amino acid sequence homology, secondary and tertiary structures, protein structure, and conserved motifs. Genome-wide collinearity analysis revealed that fragment duplication events play a dominant role in expanding the GmPIF gene family. Cis-acting element analysis revealed that the GmPIF gene family is involved in light response, hormone response, biotic–abiotic stress response elements, and plant growth and development. Gene expression analysis in different temperature environments showed that the GmPIF family was found to be induced by phytohormone treatments, with a significant increase in the expression level of GmPIF3g. GmPIF3g plays a key role in the regulation of the entire network, and in addition, 30 proteins interacting with the GmPIF3g promoter were identified through the use of a novel biofilm interference technique. This technique showed that the transcription factor Dof (DNA binding with one finger) binds to the GmPIF3g promoter, and Y1H assays indicated that Dof regulates its expression by binding to the PIF promoter. These results provide a theoretical basis for further studies on the regulatory network of GmPIF genes to improve the structure of soybean plants under shade environments, as well as a new method for analyzing regulatory elements that interact with gene promoters. Full article

Phytochrome-interacting factor (PIF) is a subfamily of the basic helix–loop–helix (bHLH) transcription factors (TFs) and plays key roles in plant responses to diverse biotic and abiotic stresses. In this work, a PIF gene named CaPIF7a was cloned and its role in the regulation of pepper’s resistance to Phytophthora capsici infection (PCI) was studied. The cloned CaPIF7a gene has a CDS length of 1383 bp, encodes a hydrophilic protein containing bHLH and APB characteristic domains, and subcellular localization results showed that CaPIF7a was located in the nucleus. Expression analysis showed that CaPIF7a gene has the highest expression level in leaf, and its expression was regulated under PCI and salicylic acid (SA) treatment. Silencing of CaPIF7a in pepper plants by virus-induced gene silencing (VIGS) reduces the resistance of pepper to PCI, with decreased expression of SA-responsive and SA-biosynthesis genes and obviously decreased SA content. DNA affinity purification sequencing (DAP-seq) was employed to identify the potential targets of CaPIF7a, and yeast one-hybrid (Y1H) verified that CaPIF7a could regulate the expression of CaHY5 by binding its promoter. These findings indicated that CaPIF7a might be a key modulator in plant immune response and presented a possible regulatory network of CaPIF7a in PCI. Full article

Plastid retrograde signaling plays a key role in coordinating the expression of plastid genes and photosynthesis-associated nuclear genes (PhANGs). Although plastid retrograde signaling can be substantially compromised by mitochondrial dysfunction, it is not yet clear whether specific mitochondrial factors are required to regulate plastid retrograde signaling. Here, we show that mitochondrial ATP synthase beta-subunit mutants with decreased ATP synthase activity are impaired in plastid retrograde signaling in Arabidopsis thaliana. Transcriptome analysis revealed that the expression levels of PhANGs were significantly higher in the mutants affected in the AT5G08670 gene encoding the mitochondrial ATP synthase beta-subunit, compared to wild-type (WT) seedlings when treated with lincomycin (LIN) or norflurazon (NF). Further studies indicated that the expression of nuclear genes involved in chloroplast and mitochondrial retrograde signaling was affected in the AT5G08670 mutant seedlings treated with LIN. These changes might be linked to the modulation of some transcription factors (TFs), such as LHY (Late Elongated Hypocotyl), PIF (Phytochrome-Interacting Factors), MYB, WRKY, and AP2/ERF (Ethylene Responsive Factors). These findings suggest that the activity of mitochondrial ATP synthase significantly influences plastid retrograde signaling. Full article

Grassland plants that endure livestock grazing exhibit a dwarf phenotype, which can be transmitted to clonal offspring. Yet to date, it remains poorly understood whether such transgenerational dwarf effects alter the plants’ response to shade. Here, we conducted a common garden experiment under sunlight and shade conditions with clonal Leymus chinensis offspring, the parents of which had endured livestock overgrazing (OG) and non-grazing (NG) in the field, respectively. Plant morphological, physiological, and transcriptomic analyses were carried out. The results indicated that NG offspring showed greater shade avoidance than OG offspring. That is, NG offspring exhibited greater plasticity of vegetative height and leaf width, which may be contributed to their greater photosynthetic capacity and gibberellin (GA3) content compared with OG offspring when treated with shade. In addition, RNA-Seq profiling showed that differentially expressed genes in NG offspring were mainly enriched in RNA modification and metabolic processes, which facilitated rapid response to shade. Phytochrome interacting factors (PIFs) promoted downstream shade marker genes in NG offspring by significantly downregulating the expression of PHYC, SPY, and DELLA. Our findings suggest that light conditions should be taken into account to better understand transgenerational dwarf effects induced by livestock grazing on grassland ecosystems. These results provide new insights into the inducible factors of phenotypic variations in grassland plants that experience grazing. Full article

The phytochrome-interacting factor (PIF) proteins are part of a subfamily of basic helix–loop–helix (bHLH) transcription factors that integrate with phytochromes (PHYs) and are known to play important roles in adaptive changes in plant architecture. However, the characterization and function of PIFs in potatoes are currently poorly understood. In this study, we identified seven PIF members in potatoes and named them StPIF01-1, StPIF01-2, StPIF03, StPIF06-1, StPIF06-2, StPIF07, and StPIF09 based on their location in potato chromosomes. The chromosomal location, gene structures, physicochemical characteristics, phylogenetic tree, and tissue-specific expression of StPIFs were also analyzed. RT-qPCR analysis revealed that the StPIF3 gene was highly induced by shade and may play a crucial regulatory role in potato responses to shade stress. Also, multiple cis-regulatory elements involved in light response were detected in the promoter of the StPIF genes. Subcellular localization analysis indicated that the StPIF3-encoding protein is mainly localized in the nucleus. Transgenic overexpression of StPIF3 in potatoes increased stem length, chlorophyll accumulation, and enhanced shade-avoidance symptoms, whereas the StPIF3-interfering lines had a lower plant height and more chlorophyll accumulation. These findings enhance our comprehension of StPIF gene roles, potentially advancing potato yield and quality research. This study provides detailed information about StPIFs and identifies the function of StPIF3, which is involved in shade-avoidance syndrome. Full article

Plants possess the remarkable ability to sense detrimental environmental stimuli and launch sophisticated signal cascades that culminate in tailored responses to facilitate their survival, and transcription factors (TFs) are closely involved in these processes. Phytochrome interacting factors (PIFs) are among these TFs and belong to the basic helix–loop–helix family. PIFs are initially identified and have now been well established as core regulators of phytochrome-associated pathways in response to the light signal in plants. However, a growing body of evidence has unraveled that PIFs also play a crucial role in adapting plants to various biological and environmental pressures. In this review, we summarize and highlight that PIFs function as a signal hub that integrates multiple environmental cues, including abiotic (i.e., drought, temperature, and salinity) and biotic stresses to optimize plant growth and development. PIFs not only function as transcription factors to reprogram the expression of related genes, but also interact with various factors to adapt plants to harsh environments. This review will contribute to understanding the multifaceted functions of PIFs in response to different stress conditions, which will shed light on efforts to further dissect the novel functions of PIFs, especially in adaption to detrimental environments for a better survival of plants. Full article

Plants monitor day length and memorize changes in temperature signals throughout the day, creating circadian rhythms that support the timely control of physiological and metabolic processes. The DEHYDRATION-RESPONSE ELEMENT-BINDING PROTEIN 1/C-REPEAT BINDING FACTOR (DREB1/CBF) transcription factors are known as master regulators for the acquisition of cold stress tolerance, whereas PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is involved in plant adaptation to heat stress through thermomorphogenesis. Recent studies have shown that circadian clock genes control plant responses to temperature. Temperature-responsive transcriptomes show a diurnal cycle and peak expression levels at specific times of throughout the day. Circadian clock genes play essential roles in allowing plants to maintain homeostasis by accommodating temperature changes within the normal temperature range or by altering protein properties and morphogenesis at the cellular level for plant survival and growth under temperature stress conditions. Recent studies revealed that the central oscillator genes CIRCADIAN CLOCK ASSOCIATED 1/LATE ELONGATED HYPOCOTYL (CCA1/LHY) and PSEUDO-RESPONSE REGULATOR5/7/9 (PRR5/7/9), as well as the EVENING COMPLEX (EC) genes REVEILLE4/REVEILLE8 (REV4/REV8), were involved in the DREB1 pathway of the cold signaling transcription factor and regulated the thermomorphogenesis gene PIF4. Further studies showed that another central oscillator, TIMING OF CAB EXPRESSION 1 (TOC1), and the regulatory protein ZEITLUPE (ZTL) are also involved. These studies led to attempts to utilize circadian clock genes for the acquisition of temperature-stress resistance in crops. In this review, we highlight circadian rhythm regulation and the clock genes involved in plant responses to temperature changes, as well as strategies for plant survival in a rapidly changing global climate. Full article

Plant basic helix-loop-helix (bHLH) transcription factors play pivotal roles in responding to stress, including cold and drought. However, it remains unclear how bHLH family genes respond to these stresses in Kandelia obovata. In this study, we identified 75 bHLH members in K. obovata, classified into 11 subfamilies and unevenly distributed across its 18 chromosomes. Collineation analysis revealed that segmental duplication primarily drove the expansion of KobHLH genes. The KobHLH promoters were enriched with elements associated with light response. Through RNA-seq, we identified several cold/drought-associated KobHLH genes. This correlated with decreased net photosynthetic rates (P_n) in the leaves of cold/drought-treated plants. Weighted gene co-expression network analysis (WGCNA) confirmed that 11 KobHLH genes were closely linked to photoinhibition in photosystem II (PS II). Among them, four Phytochrome Interacting Factors (PIFs) involved in chlorophyll metabolism were significantly down-regulated. Subcellular localization showed that KobHLH52 and KobHLH30 were located in the nucleus. Overall, we have comprehensively analyzed the KobHLH family and identified several members associated with photoinhibition under cold or drought stress, which may be helpfulfor further cold/drought-tolerance enhancement and molecular breeding through genetic engineering in K. obovata. Full article

Growth-regulating factors (GRFs) play an important role in regulating plant organ development, acting primarily as positive regulators of cell proliferation. However, research on the evolutionary history and expression patterns of the moso bamboo GRF family has been limited. In this study, a total of 24 GRFs have been identified in the Moso bamboo genome, and they have been categorized into four subfamilies. Estimation of the divergence time of paralogous gene pairs provided evidence supporting the significant contribution of recent whole-genome duplication events in the expansion of the GRF gene family. Sliding window analysis revealed that coding regions of a few PheGRFs, including the WRC and QLQ domains, may have undergone positive selection, possibly due to the redundant functions of paralogous genes. Coexpression network analysis further revealed the regulatory role of miR396 and various lncRNAs in controlling PheGRF expression. Based on the analysis of tissue-specific expression patterns using transcriptome sequencing, qRT-PCR results, and in situ hybridization, it was observed that most GRFs, particularly PheGRF6a and PheGRF9b, exhibited high levels of accumulation in the moso bamboo shoot. This suggests that the involvement of most PheGRF genes may be crucial for the growth and development of the bamboo shoot. A yeast two-hybrid screening revealed interactions between PheGRF9b and several proteins associated with plant growth and development, including PH02Gene11097.t1 (GIF3), PH02Gene37618.t (Phytochrome B), and PH02Gene01921.t3 (WD40). Based on transcriptome expression analysis, it was observed that a substantial number of PheGRFs exhibited significant variations under cold or drought stress treatments, and most of these genes were found to be downregulated, suggesting their role as abiotic stress-responsive genes. Our findings offer new insights into the GRF family of moso bamboo and provide some experimental evidence to support further gene functional validation research of PheGRF. Full article

The plant architecture of higher plants is regulated through environmental and genetic factors, as well as phytohormones. Phytohormones play a critical role in regulating shoot branching. We determined the branching phenotype of D16 and N99-6, the content of strigolactones, the genetic expression level, and the interaction between auxin and strigolactones. We found that the branching development of the two soybean varieties under shading was significantly slower than that under normal light. The average branch length of N99-6 decreased by 40.9% after shading; however, the branch length of D16 was not significantly affected. Meanwhile, the branch formation rate in D16 was significantly higher than in N99-6. In addition, after shading treatment, the content of strigolactones in D16 and N99-6 axillary buds increased significantly, and the expression of phytochrome genes, PhyA and PhyB, showed opposite changes. However, strigolactone synthesis gene GmMAX4 and signal transduction gene GmMAX2 expression levels of D16 were lower than those of N99-6 after 24 h of shading. In addition, the application of strigolactone inhibitor TIS108 and auxin inhibitor NPA to soybean had no significant effect on the branch phenotype. The expression of the GmMAX2 gene was significantly up-regulated after the external application of the auxin analog, and the expression of auxin transporter gene GmPINI was significantly down-regulated after external application of the strigolactone analog under shade. In this study, we investigated the adverse effect of shade on soybean branching development, which may be due to the interaction of strigolactones with auxins. Full article