SHORT HYPOCOTYL IN WHITE LIGHT1, a serine-arginine-aspartate-rich protein in Arabidopsis, acts as a negative regulator of photomorphogenic growth

Genome-wide association study uncovers key genomic regions governing agro-morphological and quality traits in Indian mustard [Brassica juncea (L.) Czern. and Coss.]

In Indian mustard, improving agro-morphological and quality traits through conventional methods are both cumbersome and resource-intensive. Marker-aided breeding presents a promising solution to these challenges. Hence, the present research aimed to identify genomic regions governing agro-morphological and quality traits using genome-wide association studies (GWAS). The GWAS panel comprised 142 diverse genotypes of Indian mustard were evaluated for 20 different agro-morphological and quality traits, revealing significant difference among genotypes. Subsequently, the GWAS panel genotyped using the Brassica 90K SNP array (Illumina). Structure and diversity analysis grouped the GWAS panel into 3 sub-populations or groups, and LD decay of 1.05 Mb was confirmed through genotypic analysis. GWAS using the BLINK model revealed a total of 49 marker-trait associations (MTAs), in which 28 and 21 MTAs were observed during rabi 2020-21 and rabi 2021-22 for various agro-morphological and quality traits, respectively. Amongst them, twelve MTAs demonstrated stable associations with the studied traits, including days to 50% flowering (DF), days to 100% flower termination (DFT), days to maturity (DM), plant height (PH), main shoot length (MSL), siliqua length (SL), seeds per siliqua (SPS), oil content (OC), and glucosinolates content (Glu) in both years. Moreover, in silico analysis of nearby regions of these stable SNPs revealed their association with 31 candidate genes known to be involved in various molecular, physiological, and biochemical pathways relevant to the studied traits. These genes can be further characterized and deciphered for more precise utilization in breeding programs in the future.

The concerted function of a novel class of transcription factors, ZBFs, in light, jasmonate, and abscisic acid signaling pathways

Several classes of transcription factors have been investigated in light signaling pathways that bind to the light-responsive elements (LREs) present in the promoters of light regulatory genes for transcriptional regulation. Some of these transcription factors have been shown to bind to numerous promoters through genome-wide ChIP-on-chip (ChIP-chip) studies. Furthermore, through the integration of ChIP-seq and RNA-seq techniques, it has been demonstrated that a transcription factor modifies the expression of numerous genes with which it interacts. However, the mode of action of these transcription factors and their dependency on other regulators in the pathway has just started to be unraveled. In this review, we focus on a particular class of transcription factors, ZBFs (Z-box-binding factors), and their associated partners within the same or other classes of transcription factors and regulatory proteins during photomorphogenesis. Moreover, we have further made an attempt to summarize the crosstalk of these transcription factors with jasmonic acid-, abscisic acid-, and salicylic acid-mediated defense signaling pathways. This review offers an in-depth insight into the manner in which ZBFs and their interactors reshape cellular functions and plant behavior. The underlying principles not only contribute to a comprehensive understanding but also establish a framework for analyzing the interplay between early developmental events and hormone signaling, a regulation orchestrated by the ZBF family.

The homeostasis of AtMYB4 is maintained by ARA4, HY5, and CAM7 during Arabidopsis seedling development

Calmodulin7 (CAM7) is a key transcription factor of Arabidopsis seedling development. CAM7 works together with HY5 bZIP protein to promote photomorphogenesis at various wavelengths of light. In this study, we show that AtMYB4, identified from a yeast two-hybrid screen, physically interacts with CAM7 and works as a positive regulator of photomorphogenesis at various wavelengths of light. CAM7 and HY5 directly bind to the promoter of AtMYB4 to promote its expression for photomorphogenic growth. On the other hand, ARA4, identified from the same yeast two-hybrid screen, works as a negative regulator of photomorphogenic growth specifically in white light. The double mutant analysis reveals that the altered hypocotyl elongation of atmyb4 and ara4 is either partly or completely suppressed by additional loss of function of CAM7. Furthermore, ARA4 genetically interacts with AtMYB4 in an antagonistic manner to suppress the elongated hypocotyl phenotype of atmyb4. The transactivation studies reveal that while CAM7 activates the promoter of AtMYB4 in association with HY5, ARA4 negatively regulates AtMYB4 expression. Taken together, these results demonstrate that working as a negative regulator of photomorphogenesis, ARA4 plays a balancing act on CAM7 and HY5-mediated regulation of AtMYB4.

Regulation of alternative splicing by retrograde and light signals converges to control chloroplast proteins

Retrograde signals sent by chloroplasts control transcription in the nucleus. These signals antagonistically converge with light signals to coordinate the expression of genes involved in chloroplast functioning and seedling development. Although significant advances have been made in understanding the molecular interplay between light and retrograde signals at the transcriptional level, little is known about their interconnection at the post-transcriptional level. By using different publicly available datasets, this study addresses the influence of retrograde signaling on alternative splicing and defines the molecular and biological functions of this regulation. These analyses revealed that alternative splicing mimics transcriptional responses triggered by retrograde signals at different levels. First, both molecular processes similarly depend on the chloroplast-localized pentatricopeptide-repeat protein GUN1 to modulate the nuclear transcriptome. Secondly, as described for transcriptional regulation, alternative splicing coupled with the nonsense-mediated decay pathway effectively downregulates expression of chloroplast proteins in response to retrograde signals. Finally, light signals were found to antagonistically control retrograde signaling-regulated splicing isoforms, which consequently generates opposite splicing outcomes that likely contribute to the opposite roles these signals play in controlling chloroplast functioning and seedling development.

MKKK20 works as an upstream triple-kinase of MKK3-MPK6-MYC2 module in Arabidopsis seedling development

The mitogen-activated protein kinase (MAPK) cascade is involved in several signal transduction processes in eukaryotes. Here, we report a mechanistic function of MAP kinase kinase kinase 20 (MKKK20) in light signal transduction pathways. We show that MKKK20 acts as a negative regulator of photomorphogenic growth at various wavelengths of light. MKKK20 not only regulates the expression of light signaling pathway regulatory genes but also gets regulated by the same pathway genes. The atmyc2 mkkk20 double mutant analysis shows that MYC2 works downstream to MKKK20 in the regulation of photomorphogenic growth. MYC2 directly binds to the promoter of MKKK20 to modulate its expression. The protein-protein interaction study indicates that MKKK20 physically interacts with MYC2, and this interaction likely suppresses the MYC2-mediated promotion of MKKK20 expression. Further, the protein phosphorylation studies demonstrate that MKKK20 works as the upstream kinase of MKK3-MPK6-MYC2 module in photomorphogenesis.

Signaling events for photomorphogenic root development

A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.

Functional interrelation of MYC2 and HY5 plays an important role in Arabidopsis seedling development

Arabidopsis MYC2 bHLH transcription factor plays a negative regulatory role in blue light (BL)-mediated seedling development. HY5 bZIP protein works as a positive regulator of multiple wavelengths of light and promotes photomorphogenesis. Both MYC2 and HY5, belonging to two different classes of transcription factors, are the integrators of multiple signaling pathways. However, the functional interrelations of these two transcription factors in seedling development remain unknown. Additionally, whereas HY5-mediated regulation of gene expression has been investigated in detail, the transcriptional regulation of HY5 itself is yet to be understood. Here, we show that HY5 and MYC2 work in an antagonistic manner in Arabidopsis seedling development. Our results reveal that HY5 expression is negatively regulated by MYC2 predominantly in BL, and at various stages of development. On the other hand, HY5 negatively regulates the expression of MYC2 at various wavelengths of light. In vitro and in vivo DNA-protein interaction studies suggest that MYC2 binds to the E-box cis-acting element of HY5 promoter. Collectively, this study demonstrates a coordinated regulation of MYC2 and HY5 in blue-light-mediated Arabidopsis seedling development.

COP1 regulates the stability of CAM7 to promote photomorphogenic growth

The unique member of the calmodulin gene family, Calmodulin7 (CAM7), plays a crucial role as transcriptional regulator to promote Arabidopsis seedling development. CAM7 regulates the expression of HY5, which is intimately involved in the promotion of photomorphogenic growth and light-regulated gene expression. COP1 ubiquitin ligase suppresses photomorphogenesis by degrading multiple photomorphogenesis promoting factors including HY5 in darkness. Genetic interaction studies, in this report, reveal that CAM7 and COP1 co-ordinately work to promote photomorphogenic growth and light-regulated gene expression at lower intensity of light. CAM7 physically interacts with COP1 in the nucleus. Further, in vivo study suggests that CAM7 and COP1 interaction is light intensity dependent. We have also shown that functional COP1 is required for optimum accumulation of CAM7 at lower fluences of light. Taken together, this study demonstrates the coordinated function of CAM7 and COP1 in Arabidopsis seedling development.

SHORT HYPOCOTYL1 Encodes a SMARCA3-Like Chromatin Remodeling Factor Regulating Elongation

In Arabidopsis (Arabidopsis thaliana), the UVR8-mediated signaling pathway is employed to attain UVB protection and acclimation to deal with low-dosage UVB (LDUVB)-induced stresses. Here, we identified SHORT HYPOCOTYL1 (SH1) in cucumber (Cucumis sativus), which regulates LDUVB-dependent hypocotyl elongation by modulating the UVR8 signaling pathway. We showed that hypocotyl elongation in cucumbers carrying the recessive sh1 allele was LDUVB insensitive and that Sh1 encoded a human SMARCA3-like chromatin remodeling factor. The allele frequency and distribution pattern at this locus among natural populations supported the wild cucumber origin of sh1 for local adaptation, which was under selection during domestication. The cultivated cucumber carries predominantly the Sh1 allele; the sh1 allele is nearly fixed in the semiwild Xishuangbanna cucumber, and the wild cucumber population is largely at Hardy-Weinberg equilibrium for the two alleles. The SH1 protein sequence was highly conserved among eukaryotic organisms, but its regulation of hypocotyl elongation in cucumber seems to be a novel function. While Sh1 expression was inhibited by LDUVB, its transcript abundance was highly correlated with hypocotyl elongation rate and the expression level of cell-elongation-related genes. Expression profiling of key regulators in the UVR8 signaling pathway revealed significant differential expression of CsHY5 between two near isogenic lines of Sh1 Sh1 and CsHY5 acted antagonistically at transcriptional level. A working model was proposed in which Sh1 regulates LDUVB-dependent hypocotyl elongation in cucumber through changing the chromatin states and thus the accessibility of CsHY5 in the UVR8 signaling pathway to promoters of LDUVB-responsive genes for hypocotyl elongation.

Short Hypocotyl in White Light1 Interacts with Elongated Hypocotyl5 (HY5) and Constitutive Photomorphogenic1 (COP1) and Promotes COP1-Mediated Degradation of HY5 during Arabidopsis Seedling Development

Arabidopsis (Arabidopsis thaliana) Short Hypocotyl in White Light1 (SHW1) encodes a Ser-Arg-Asp-rich protein that acts as a negative regulator of photomorphogenesis. SHW1 and Constitutive Photomorphogenic1 (COP1) genetically interact in an additive manner to suppress photomorphogenesis. Elongated Hypocotyl5 (HY5) is a photomorphogenesis promoting a basic leucine zipper transcription factor that is degraded by COP1 ubiquitin ligase in the darkness. Here, we report the functional interrelation of SHW1 with COP1 and HY5 in Arabidopsis seedling development. The in vitro and in vivo molecular interaction studies show that SHW1 physically interacts with both COP1 and HY5. The genetic studies reveal that SHW1 and HY5 work in an antagonistic manner to regulate photomorphogenic growth. Additional mutation of SHW1 in hy5 mutant background is able to suppress the gravitropic root growth defect of hy5 mutants. This study further reveals that the altered abscisic acid responsiveness of hy5 mutants is modulated by additional loss of SHW1 function. Furthermore, this study shows that SHW1 promotes COP1-mediated degradation of HY5 through enhanced ubiquitylation in the darkness. Collectively, this study highlights a mechanistic view on coordinated regulation of SHW1, COP1, and HY5 in Arabidopsis seedling development.

Citrullus colocynthis NAC transcription factors CcNAC1 and CcNAC2 are involved in light and auxin signaling

Two novel NAC transcription factors from C itrullus colocynthis implicated in light and auxin signaling pathway. NAC transcription factors (NAM, ATAF1, 2, CUC2) have multiple functions in plant growth and development. Two NACs, CcNAC1 and CcNAC2, were recently identified in the highly drought-tolerant cucurbit species, Citrullus colocynthis. This study examines the functional role of these genes under different qualities of light based on the in silico analysis of the CcNAC1 and CcNAC2 promoters that revealed the presence of several light-associated motifs. The impact of both light and auxin on CcNAC1 and CcNAC2 expression was examined in C. colocynthis leaves, and using reporter (pCcNAC1, 2::GUS) lines in Arabidopsis. Furthermore, the effects of constitutive overexpression (OE-CcNAC1, 2) in Arabidopsis were also examined under a range of conditions to confirm reporter line linkages. White, blue, red, and far-red light treatments resulted in similar patterns of quantitative changes in CcNAC1and CcNAC2 expression in both species, with the highest transcript increases following red light. Photomorphogenic changes in Arabidopsis hypocotyls were correlated with gene transcript levels. In the absence of light, hypocotyls of OE-CcNAC1/CcNAC2 lines were significantly longer as compared to WT. The addition of exogenous auxin (+IAA) to growth medium also resulted in changes to the hypocotyl lengths of overexpression lines and spatiotemporal reporter line changes in seedlings. Our data suggest that CcNAC1, 2 might be functionally important in the light signaling pathway, and appear connected to the hormone auxin. This is the first study to indicate that NAC genes might play a role in both light and auxin signaling pathways.

Arabidopsis CAM7 and HY5 physically interact and directly bind to the HY5 promoter to regulate its expression and thereby promote photomorphogenesis

Arabidopsis thaliana CALMODULIN7 (CAM7), a unique member of the calmodulin gene family, plays a crucial role as a transcriptional regulator in seedling development. The elongated HYPOCOTYL5 (HY5) bZIP protein, an integrator of multiple signaling pathways, also plays an important role in photomorphogenic growth and light-regulated gene expression. CAM7 acts synergistically with HY5 to promote photomorphogenesis at various wavelengths of light. Although the genetic relationships between CAM7 and HY5 in light-mediated seedling development have been demonstrated, the molecular connectivity between CAM7 and HY5 is unknown. Furthermore, whereas HY5-mediated gene regulation has been fairly well investigated, the transcriptional regulation of HY5 is largely unknown. Here, we report that HY5 expression is regulated by HY5 and CAM7 at various wavelengths of light and also at various stages of development. In vitro and in vivo DNA-protein interaction studies suggest that HY5 and CAM7 bind to closely located T/G- and E-box cis-acting elements present in the HY5 promoter, respectively. Furthermore, CAM7 and HY5 physically interact and regulate the expression of HY5 in a concerted manner. Taken together, these results demonstrate that CAM7 and HY5 directly interact with the HY5 promoter to mediate the transcriptional activity of HY5 during Arabidopsis seedling development.

LeMYC2 acts as a negative regulator of blue light mediated photomorphogenic growth, and promotes the growth of adult tomato plants

BACKGROUND

Arabidopsis ZBF1/MYC2bHLH transcription factor is a repressor of photomorphogenesis, and acts as a point of cross talk in light, abscisic acid (ABA) and jasmonic acid (JA) signaling pathways. MYC2 also functions as a positive regulator of lateral root development and flowering time under long day conditions. However, the function of MYC2 in growth and development remains unknown in crop plants.

RESULTS

Here, we report the functional analyses of LeMYC2 in tomato (Lycopersicon esculentum). The amino acid sequence of LeMYC2 showed extensive homology with Arabidopsis MYC2, containing the conserved bHLH domain. To study the function of LeMYC2 in tomato, overexpression and RNA interference (RNAi) LeMYC2 tomato transgenic plants were generated. Examination of seedling morphology, physiological responses and light regulated gene expression has revealed that LeMYC2 works as a negative regulator of blue light mediated photomorphogenesis. Furthermore, LeMYC2 specifically binds to the G-box of LeRBCS-3A promoter. Overexpression of LeMYC2 has led to increased root length with more number of lateral roots. The tomato plants overexpressing LeMYC2 have reduced internode distance with more branches, and display the opposite morphology to RNAi transgenic lines. Furthermore, this study shows that LeMYC2 promotes ABA and JA responsiveness.

CONCLUSIONS

Collectively, this study highlights that working in light, ABA and JA signaling pathways LeMYC2 works as an important regulator for growth and development in tomato plants.

Z-box binding transcription factors (ZBFs): a new class of transcription factors in Arabidopsis seedling development

One set of genes encoding diverse groups of transcription factors that interact with the Z-box (ATACGTGT; a potential Z-DNA forming sequence) is called ZBFs (Z-box Binding Factors). ZBFs include ZBF1, ZBF2, and ZBF3, which encode ZBF1/MYC2 (bHLH), ZBF2/GBF1 (bZIP), and ZBF3/CAM7 (Calmodulin) proteins, respectively. With several recent reports, it is becoming increasingly evident that ZBFs play crucial roles in Arabidopsis seedling photomorphogenesis. ZBFs integrate signals from various wavelengths of light to coordinate the regulation of transcriptional networks that affect multiple facets of plant growth and development. The function of each ZBF is qualitatively and quantitatively distinct. The zbf mutants display pleiotropic effects including altered hypocotyl elongation, cotyledon expansion, lateral root development, and flowering time. In this inaugural review, we discuss the identification, molecular functions, and interacting partners of ZBFs in light-mediated Arabidopsis seedling development.

The regulation of the Z- and G-box containing promoters by light signaling components, SPA1 and MYC2, in Arabidopsis

Although many transcription factors and regulatory proteins have been identified and functionally characterized in light signaling pathways, photoperception to transcription remains largely fragmented. The Z-box is one of the LREs (Light responsive elements) that plays important role in the regulation of transcription during light-controlled Arabidopsis seedling development. The involvement of photoreceptors in the modulation of the activity of the Z-box containing promoters has been demonstrated. However, the role of downstream signaling components such as SPA1 and MYC2/ZBF1, which are functionally interrelated, remains unknown. In this study, we have investigated the regulation of the Z-box containing synthetic and native promoters by SPA1 and MYC2 by using stable transgenic lines. Our studies suggest that SPA1 negatively regulates the expression of CAB1 native promoter. MYC2 negatively regulates the activity of Z- and/or G-box containing synthetic as well as native promoters irrespective of light quality. Moreover, MYC2 negatively regulates the expression of Z/G-NOS101-GUS even in the darkness. Furthermore, analyses of tissue specific expression in adult plants suggest that MYC2 strongly regulates the activity of Z- and G-box containing promoters specifically in leaves and stems. In roots, whereas MYC2 positively regulates the activity of the Z-box containing synthetic promoter, it does not seem to control the activity of the G-box containing promoters. Taken together, these results provide insights into SPA1- and MYC2-mediated transcriptional regulation of the Z- and G-box containing promoters in light signaling pathways.

Molecular interactions of GBF1 with HY5 and HYH proteins during light-mediated seedling development in Arabidopsis thaliana

Arabidopsis bZIP transcription factor, GBF1, acts as a differential regulator of cryptochrome-mediated blue light signaling. Whereas the bZIP proteins, HY5 (elongated hypocotyl 5) and HYH (HY5 homologue), are degraded by COP1-mediated proteasomal pathways, GBF1 is degraded by a proteasomal pathway independent of COP1. In this study, we have investigated the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development. The genetic studies using double and triple mutants reveal that GBF1 largely acts antagonistically with HY5 and HYH in Arabidopsis seedling development. Further, GBF1 and HY5 play more important roles than HYH in blue light-mediated photomorphogenic growth. This study reveals that GBF1 is able to form a G-box-binding heterodimer with HY5 but not with HYH. The in vitro and in vivo studies demonstrate that GBF1 co-localizes with HY5 or HYH in the nucleus and physically interacts with both of the proteins. The protein-protein interaction studies further reveal that the bZIP domain of GBF1 is essential and sufficient for the interaction with HY5 or HYH. Taken together, these data demonstrate the functional interrelations of GBF1 with HY5 and HYH in Arabidopsis seedling development.

MYC2, a bHLH transcription factor, modulates the adult phenotype of SPA1

MYC2 and SPA1 are two key regulatory proteins that negatively regulate light-controlled Arabidopsis seedling development. We have recently demonstrated the genetic and molecular relationships of MYC2 and SPA1 in light and JA (jasmonic acid) signaling pathways. Here, we have further shown the genetic interactions between these two proteins in flowering time and lateral root development.

Computing gene expression data with a knowledge-based gene clustering approach

Computational analysis methods for gene expression data gathered in microarray experiments can be used to identify the functions of previously unstudied genes. While obtaining the expression data is not a difficult task, interpreting and extracting the information from the datasets is challenging. In this study, a knowledge-based approach which identifies and saves important functional genes before filtering based on variability and fold change differences was utilized to study light regulation. Two clustering methods were used to cluster the filtered datasets, and clusters containing a key light regulatory gene were located. The common genes to both of these clusters were identified, and the genes in the common cluster were ranked based on their coexpression to the key gene. This process was repeated for 11 key genes in 3 treatment combinations. The initial filtering method reduced the dataset size from 22,814 probes to an average of 1134 genes, and the resulting common cluster lists contained an average of only 14 genes. These common cluster lists scored higher gene enrichment scores than two individual clustering methods. In addition, the filtering method increased the proportion of light responsive genes in the dataset from 1.8% to 15.2%, and the cluster lists increased this proportion to 18.4%. The relatively short length of these common cluster lists compared to gene groups generated through typical clustering methods or coexpression networks narrows the search for novel functional genes while increasing the likelihood that they are biologically relevant.

SHW1, a common regulator of abscisic acid (ABA) and light signaling pathways

In our recent paper in Plant Physiology, we have reported the identification and functional characterization of a unique regulator, SHW1, a serine-arginine-aspartate rich protein in Arabidopsis seedling development.1 Genetic and molecular analyses have revealed that SHW1 functions in an independent and interdependent manner with COP1, and differentially regulates photomorphogenic growth and light regulated gene expression. Here, we show the involvement of photoreceptors in the function of SHW1. Our results have further revealed that SHW1 is a common regulator of light and ABA signaling pathways. These results along with some data described in Plant Physiology paper have been discussed here in a broader perspective.