The WD-repeat protein superfamily in Arabidopsis: conservation and divergence in structure and function

Optimum chalcone synthase for flavonoid biosynthesis in microorganisms

Chalcones and the subsequently generated flavonoids, as well as flavonoid derivatives, have been proven to have a variety of physiological activities and are widely used in: the pharmaceutical, food, feed, and cosmetic industries. As the content of chalcones and downstream products in native plants is low, the production of these compounds by microorganisms has gained the attention of many researchers and has a history of more than 20 years. The mining and engineering of chalcone synthase (CHS) could be one of the most important ways to achieve more efficient production of chalcones and downstream products in microorganisms. CHS has a broad spectrum of substrates, and its enzyme activity and expression level can significantly affect the efficiency of the biosynthesis of flavonoids. This review summarizes the recent advances in the: structure, mechanism, evolution, substrate spectrum, transformation, and expression regulation in the flavonoid biosynthesis of this vital enzyme. Future development directions were also suggested. The findings may further promote the research and development of flavonoids and health products, making them vital in the fields of human diet and health.

Research progress of fruit color development in apple (Malus domestica Borkh.)

Apple (Malus domestica Borkh.) is one of the most widely produced and economically important fruits in temperate regions. Fruit color development in apple is a major focus for both breeders and researchers as consumers associate brightly colored red apples with ripeness and a good flavor. In recent years, great progress has been made in the research of apple fruit color development, but its development mechanism has not been systematic dissected from the aspects of genetics, transcription or environmental factors. Here, we summarize research on the coloration of apple fruit, including the development of important genomic databases to identify important genomic regions and genes, genetic and transcriptional factors that regulate pigment accumulation, environmental factors that affect anthocyanin synthesis, and the current breeding progress of red-skinned and red-fleshed apples. We describe key transcription factors, such as MYB, bHLH, and WD40, which are involved in the regulation of anthocyanin synthesis and fruit color development in apple. We also discuss the regulation of apple color by external environmental factors such as light, temperature, and water. The aim of this review is to provide insights into the molecular mechanisms underlying anthocyanin biosynthesis in apple. This information will provide significant guidance for the breeding of high-quality red-skinned and red-fleshed apple varieties.

Fine mapping identifies NAD-ME1 as a candidate underlying a major locus controlling temporal variation in primary and specialized metabolism in Arabidopsis

Plant metabolism is modulated by a complex interplay between internal signals and external cues. A major goal of all quantitative metabolomic studies is to clone the underlying genes to understand the mechanistic basis of this variation. Using fine-scale genetic mapping, in this work we report the identification and initial characterization of NAD-DEPENDENT MALIC ENZYME 1 (NAD-ME1) as the candidate gene underlying the pleiotropic network Met.II.15 quantitative trait locus controlling variation in plant metabolism and circadian clock outputs in the Bay × Sha Arabidopsis population. Transcript abundance and promoter analysis in NAD-ME1^Bay-0 and NAD-ME1^Sha alleles confirmed allele-specific expression that appears to be due a polymorphism disrupting a putative circadian cis-element binding site. Analysis of transfer DNA insertion lines and heterogeneous inbred families showed that transcript variation of the NAD-ME1 gene led to temporal shifts of tricarboxylic acid cycle intermediates, glucosinolate (GSL) accumulation, and altered regulation of several GSL biosynthesis pathway genes. Untargeted metabolomic analyses revealed complex regulatory networks of NAD-ME1 dependent upon the daytime. The mutant led to shifts in plant primary metabolites, cell wall components, isoprenoids, fatty acids, and plant immunity phytochemicals, among others. Our findings suggest that NAD-ME1 may act as a key gene to coordinate plant primary and secondary metabolism in a time-dependent manner.

Flourishing in water: the early evolution and diversification of plant receptor-like kinases

Receptor-like kinases (RLKs) play significant roles in mediating innate immunity and development of plants. The evolution of plant RLKs has been characterized by extensive variation in copy numbers and domain configurations. However, much remains unknown about the origin, evolution, and early diversification of plant RLKs. Here, we perform phylogenomic analyses of RLKs across plants (Archaeplastida), including embryophytes, charophytes, chlorophytes, prasinodermophytes, glaucophytes, and rhodophytes. We identify the presence of RLKs in all the streptophytes (land plants and charophytes), nine out of 18 chlorophytes, one prasinodermophyte, and one glaucophyte, but not in rhodophytes. Interestingly, the copy number of RLKs increased drastically in streptophytes after the split of the clade of Mesostigmatophyceae and Chlorokybophyceae and other streptophytes. Moreover, phylogenetic analyses suggest RLKs from charophytes form diverse distinct clusters, and are dispersed along the diversity of land plant RLKs, indicating that RLKs have extensively diversified in charophytes and charophyte RLKs seeded the major diversity of land plant RLKs. We identify at least 81 and 76 different kinase-associated domains for charophyte and land plant RLKs, 23 of which are shared, suggesting that RLKs might have evolved in a modular fashion through frequent domain gains or losses. We also detect signatures of positive selection for many charophyte RLK groups, indicating potential functions in host-microbe interaction. Taken together, our findings provide significant insights into the early evolution and diversification of plant RLKs and the ancient evolution of plant-microbe symbiosis.

Genomic analysis of WD40 protein family in the mango reveals a TTG1 protein enhances root growth and abiotic tolerance in Arabidopsis

WD40 domain-containing proteins constitute one of the most abundant protein families in all higher plants and play vital roles in the regulation of plant growth and developmental processes. To date, WD40 protein members have been identified in several plant species, but no report is available on the WD40 protein family in mango (Mangifera indica L.). In this study, a total of 315 WD40 protein members were identified in mango and further divided into 11 subgroups according to the phylogenetic tree. Here, we reported mango TRANSPARENT TESTA GLABRA 1 (MiTTG1) protein as a novel factor that functions in the regulation of Arabidopsis root growth and development. Bimolecular fluorescence complementation (BiFC) assay in tobacco leaves revealed that MiTTG1 protein physically interacts with MiMYB0, MiTT8 and MibHLH1, implying the formation of a new ternary regulatory complex (MYB-bHLH-WD40) in mango. Furthermore, the MiTTG1 transgenic lines were more adapted to abiotic stresses (mannitol, salt and drought stress) in terms of promoted root hairs and root lengths. Together, our findings indicated that MiTTG1 functions as a novel factor to modulate protein-protein interactions and enhance the plants abilities to adjust different abiotic stress responses.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

Identification of Transcription Factor Genes and Functional Characterization of PlMYB1 From Pueraria lobata

Kudzu, Pueraria lobata, is a traditional Chinese food and medicinal herb that has been commonly used since ancient times. Kudzu roots are rich sources of isoflavonoids, e.g., puerarin, with beneficial effects on human health. To gain global information on the isoflavonoid biosynthetic regulation network in kudzu, de novo transcriptome sequencings were performed using two genotypes of kudzu with and without puerarin accumulation in roots. RNAseq data showed that the genes of the isoflavonoid biosynthetic pathway were significantly represented in the upregulated genes in the kudzu with puerarin. To discover regulatory genes, 105, 112, and 143 genes encoding MYB, bHLH, and WD40 transcription regulators were identified and classified, respectively. Among them, three MYB, four bHLHs, and one WD40 gene were found to be highly identical to their orthologs involved in flavonoid biosynthesis in other plants. Notably, the expression profiles of PlMYB1, PlHLH3-4, and PlWD40-1 genes were closely correlated with isoflavonoid accumulation profiles in different tissues and cell cultures of kudzu. Over-expression of PlMYB1 in Arabidopsis thaliana significantly increased the accumulation of anthocyanins in leaves and proanthocyanidins in seeds, by activating AtDFR, AtANR, and AtANS genes. Our study provided valuable comparative transcriptome information for further identification of regulatory or structural genes involved in the isoflavonoid pathway in P. lobata, as well as for bioengineering of bioactive isoflavonoid compounds.

Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty acid biosynthesis while maintaining healthy nodules

Developing soybean lines with high levels of stearic acid is a primary goal of the soybean industry. Most high-stearic-acid soybeans carry different GmSACPD-C mutated alleles. However, due to the dual role of GmSACPD-C in seeds and nodule development, all derived deleterious GmSACPD-C mutant alleles are of extremely poor agronomic value because of defective nodulation. The soybean stearoyl-acyl carrier protein desaturase (GmSACPD) gene family is composed of five members. Comparative genomics analysis indicated that SACPD genes were duplicated and derived from a common ancestor that is still present in chlorophytic algae. Synteny analysis showed the presence of segment duplications between GmSACPD-A/GmSACPD-B, and GmSACPD-C/GmSACPD-D. GmSACPD-E was not contained in any duplicated segment and may be the result of tandem duplication. We developed a TILLING by Target Capture Sequencing (Tilling-by-Sequencing+) technology, a versatile extension of the conventional TILLING by sequencing, and successfully identified 12, 14, and 18 ethyl methanesulfonate mutants at the GmSACPD-A, GmSACPD-B, and GmSACPD-D genes, respectively. Functional analysis of all identified mutants revealed an unprecedented role of GmSACPD-A, GmSACPD-B, and GmSACPD-D in unsaturated fatty acid biosynthesis without affecting nodule development and structure. This discovery will positively impact the development of high-stearic-acid lines to enhance soybean nutritional value without potential developmental tradeoffs.

From the Outside to the Inside: New Insights on the Main Factors That Guide Seed Dormancy and Germination

The transition from a dormant to a germinating seed represents a crucial developmental switch in the life cycle of a plant. Subsequent transition from a germinating seed to an autotrophic organism also requires a robust and multi-layered control. Seed germination and seedling growth are multistep processes, involving both internal and external signals, which lead to a fine-tuning control network. In recent years, numerous studies have contributed to elucidate the molecular mechanisms underlying these processes: from light signaling and light-hormone crosstalk to the effects of abiotic stresses, from epigenetic regulation to translational control. However, there are still many open questions and molecular elements to be identified. This review will focus on the different aspects of the molecular control of seed dormancy and germination, pointing out new molecular elements and how these integrate in the signaling pathways already known.

Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica

Rice (Oryza sativa L.) is one of the most important cereal crops for one third of the world population. However, the grain quality as well as yield of rice is severely affected by various abiotic stresses. Environmental stresses affect the expression of various microRNAs (miRNAs) which in turn negatively regulate gene expression at the post-transcriptional level either by degrading the target mRNA genes or suppressing translation in plants. Plant homeo-domain (PHD) finger proteins are known to be involved in the plant response to salinity stress. In the present study, we identified 44 putative OsPHD finger genes in Oryza sativa Indica, using Ensembl Plants Database. Using computational approach, potential miRNAs that target OsPHD finger genes were identified. Out of the 44 OsPHD finger genes only three OsPHD finger genes i.e., OsPHD2, OsPHD35 and OsPHD11, were found to be targeted by five newly identified putative miRNAs i.e., ath-miRf10010-akr, ath-miRf10110-akr, osa-miR1857–3p, osa-miRf10863-akr, and osa-miRf11806-akr. This is the first report of these five identified miRNAs on targeting PHD finger in Oryza sativa Indica. Further, expression analysis of 44 PHD finger genes under salinity was also performed using quantitative Real-Time PCR. The expression profile of 8 genes were found to be differentially regulated, among them two genes were significantly up regulated i.e., OsPHD6 and OsPHD12. In silico protein-protein interaction analysis using STRING database showed interaction of the OsPHD finger proteins with other protein partners that are directly or indirectly involved in development and abiotic stress tolerance.

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Total of 44 Plant homeo-domain (PHD) finger proteins were identified & classified into 10 groups in Oryza sativa Indica.

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This is the first report showing 5 newly identified putative miRNAs targeting three OsPHD genes i.e., OsPHD2, 11 and 35.

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Expression analysis of PHD finger genes showed up-regulation of the 2 genes OsPHD 6 & 12 under salinity stress treatment.

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Protein-protein network of OsPHDs showed protein partners that are involved in plant growth and abiotic stress tolerance.

Plant Cyclophilins: Multifaceted Proteins With Versatile Roles

Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.

WDR5a functions in cadmium-inhibited root meristem growth by regulating nitric oxide accumulation in Arabidopsis

Cadmium stress induces WDR5a expression to promote NO accumulation to repress root meristem growth via suppressing auxin transport and synthesis in Arabidopsis. Nitric oxide (NO) synthase (NOS)-like activity plays a vital role in toxic cadmium (Cd)-induced NO production and inhibition of root meristem growth, while factor(s) regulating NOS-like activity and root meristem growth in plant response to Cd has not been identified yet. Here, we report that WD40 repeat 5a (WDR5a) functions in Cd-induced NOS-like activity, NO accumulation and root meristem growth suppression. We found that wdr5a-1 mutant root has increased root meristem growth with lower NOS-like activity and NO accumulation than wild type upon Cd exposure, and exogenous NO donors sodium nitroprusside or nitrosoglutathione can restore its reduced Cd sensitivity. In addition, Cd activates WDR5a expression in roots, and overexpressing WDR5a results in increased NO accumulation and suppressed root meristem growth similar to Cd-stressed wild-type roots, while scavenging NO or inhibiting NOS-like activity significantly reverts these effects of Cd. Furthermore, WDR5a acts in Cd-repressed auxin accumulation through reducing the levels of auxin efflux carriers PIN1/3/7 and biosynthetic enzyme TAA1, and reduced sensitivity of wdr5a-1 root meristem to Cd can be partially reverted by inhibiting TAA1 activity pharmaceutically or mutating TAA1 genetically. This study identified WDR5a as a key factor modulating NO accumulation and root meristem growth in plant response to Cd.

Association of host protein VARICOSE with HCPro within a multiprotein complex is crucial for RNA silencing suppression, translation, encapsidation and systemic spread of potato virus A infection

In this study, we investigated the significance of a conserved five-amino acid motif 'AELPR' in the C-terminal region of helper component-proteinase (HCPro) for potato virus A (PVA; genus Potyvirus) infection. This motif is a putative interaction site for WD40 domain-containing proteins, including VARICOSE (VCS). We abolished the interaction site in HCPro by replacing glutamic acid (E) and arginine (R) with alanines (A) to generate HCProWD. These mutations partially eliminated HCPro-VCS co-localization in cells. We have earlier described potyvirus-induced RNA granules (PGs) in which HCPro and VCS co-localize and proposed that they have a role in RNA silencing suppression. We now demonstrate that the ability of HCProWD to induce PGs, introduce VCS into PGs, and suppress RNA silencing was impaired. Accordingly, PVA carrying HCProWD (PVAWD) infected Nicotiana benthamiana less efficiently than wild-type PVA (PVAWT) and HCProWD complemented the lack of HCPro in PVA gene expression only partially. HCPro was purified from PVA-infected leaves as part of high molecular weight (HMW) ribonucleoprotein (RNP) complexes. These complexes were more stable when associated with wild-type HCPro than with HCProWD. Moreover, VCS and two viral components of the HMW-complexes, viral protein genome-linked and cylindrical inclusion protein were specifically decreased in HCProWD-containing HMW-complexes. A VPg-mediated boost in translation of replication-deficient PVA (PVAΔGDD) was observed only if viral RNA expressed wild-type HCPro. The role of VCS-VPg-HCPro coordination in PVA translation was further supported by results from VCS silencing and overexpression experiments and by significantly elevated PVA-derived Renilla luciferase vs PVA RNA ratio upon VPg-VCS co-expression. Finally, we found that PVAWD was unable to form virus particles or to spread systemically in the infected plant. We highlight the role of HCPro-VCS containing multiprotein assemblies associated with PVA RNA in protecting it from degradation, ensuring efficient translation, formation of stable virions and establishment of systemic infection.

Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R² between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

WD40-Repeat Proteins in Ciliopathies and Congenital Disorders of Endocrine System

WD40-repeat (WDR)-containing proteins constitute an evolutionarily conserved large protein family with a broad range of biological functions. In human proteome, WDR makes up one of the most abundant protein-protein interaction domains. Members of the WDR protein family play important roles in nearly all major cellular signalling pathways. Mutations of WDR proteins have been associated with various human pathologies including neurological disorders, cancer, obesity, ciliopathies and endocrine disorders. This review provides an updated overview of the biological functions of WDR proteins and their mutations found in congenital disorders. We also highlight the significant role of WDR proteins in ciliopathies and endocrine disorders. The new insights may help develop therapeutic approaches targeting WDR motifs.

Genome-wide identification of WD40 genes reveals a functional diversification of COP1-like genes in Rosaceae

Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and photomorphogenesis, with strong functional diversification in Rosaceae. WD40 proteins play crucial roles in a broad spectrum of developmental and physiological processes. Here, we conducted a systematic characterization of this family of genes in Rosa chinensis 'Old Blush' (OB), a founder genotype for modern rose domestication. We identified 187 rose WD40 genes and classified them into 5 clusters and 15 subfamilies with 11 of RcWD40s presumably generated via tandem duplication. We found RcWD40 genes were expressed differentially following stages of vegetative and reproductive development. We detected a duplication of CONSTITUTIVE PHOTOMORPHOGENIC1-like genes in rose (RcCOP1 and RcCOP1L) and other Rosaceae plants. Featuring a distinct expression pattern and a different profile of cis-regulatory-elements in the transcriptional regulatory regions, RcCOP1 seemed being evolutionarily conserved while RcCOP1L did not dimerize with RcHY5 and RcSPA4. Our data thus reveals a functional diversification of COP1-like genes in Rosacaeae plants, and provides a valuable resource to explore the potential function and evolution of WD40-like genes in Rosaceae plants.

Expression profiling of WD40 family genes including DDB1- and CUL4- associated factor (DCAF) genes in mice and human suggests important regulatory roles in testicular development and spermatogenesis

BACKGROUND

The WD40-repeat containing proteins, including DDB1-CUL4-associated factors (DCAFs), are abundant and conserved proteins that play important roles in different cellular processes including spermatogenesis. DCAFs are subset of WD40 family proteins that contain WDxR motif and have been proposed to function as substrate receptor for Cullin4-RING-based E3 ubiquitin ligase complexes to recruit diverse proteins for ubiquitination, a vital process in spermatogenesis. Large number of WD40 genes has been identified in different species including mouse and human. However, a systematic expression profiling of WD40 genes in different tissues of mouse and human has not been investigated. We hypothesize that large number of WD40 genes may express highly or specifically in the testis, where their expression is uniquely regulated during testis development and spermatogenesis. Therefore, the objective of this study is to mine and characterize expression patterns of WD40 genes in different tissues of mouse and human with particular emphasis on DCAF genes expressions during mouse testicular development.

RESULTS

Publically available RNA sequencing (RNA seq) data mining identified 347 and 349 WD40 genes in mouse and human, respectively. Hierarchical clustering and heat map analyses of RNA seq datasets revealed differential expression patterns of WD40 genes with around 60-73% of the genes were highly or specifically expressed in testis. Similarly, around 74-83% of DCAF genes were predominantly or specifically expressed in testis. Moreover, WD40 genes showed distinct expression patterns during embryonic and postnatal testis development in mice. Finally, different germ cell populations of testis showed specific patterns of WD40 genes expression. Predicted gene ontology analyses revealed more than 80% of these proteins are implicated in cellular, metabolic, biological regulation and cell localization processes.

CONCLUSIONS

We have identified large number of WD40 family genes that are highly or specifically expressed in the testes of mouse and human. Moreover, WD40 genes have distinct expression patterns during embryonic and postnatal development of the testis in mice. Further, different germ cell populations within the testis showed specific patterns of WD40 genes expression. These results provide foundation for further research towards understanding the functional genomics and molecular mechanisms of mammalian testis development and spermatogenesis.

Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium

The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.

Systematic analysis of SmWD40s, and responding of SmWD40-170 to drought stress by regulation of ABA- and H2O2-induced stomal movement in Salvia miltiorrhiza bunge

WD40 proteins play crucial roles in response to abiotic stress. By screening the genome sequences of Salvia miltiorrhiza Bunge, 225 SmWD40 genes were identified and divided into 9 subfamilies (I-IX). Physiological, biochemical, gene structure, conserved protein motif and GO annotation analyses were performed on SmWD40 family members. The SmWD40-170 was found in 110 SmWD40 genes that contain drought response elements, SmWD40-170 was one of these genes whose response in terms of expression under drought was significant. The expression of SmWD40-170 was also up-regulated by ABA and H₂O₂. Through observed the stomatal phenotype of SmWD40-170 transgenic lines, the stomatal closure was abolished under dehydration, ABA and H₂O₂ treatment in SmWD40-170 knockdown lines. Abscisic acid (ABA), as the key phytohormone, elevates reactive oxygen species (ROS) levels under drought stress. The ABA-ROS interaction mediated the generation of H₂O₂ and the activation of anion channel in guard cells. The osmolality alteration of guard cells further accelerated the stomatal closure. As a second messenger, nitric oxide (NO) regulated ABA signaling, the NO stimulated protein kinase activity inhibited the K⁺ influx which result in stomatal closure. These NO-relevant events were essential for ABA-induced stomatal closure. The reduction of NO production was also observed in the guard cells of SmWD40-170 knockdown lines. The abolished of stomatal closure attributed to the SmWD40-170 deficiency induced the reduction of NO content. In general, the SmWD40-170 is a critical drought response gene in SmWD40 gene family and regulates ABA- and H₂O₂-induced stomatal movement by affecting the synthesis of NO.

A mutation in the essential and widely conserved DAMAGED DNA BINDING1-Cullin4 ASSOCIATED FACTOR gene OZS3 causes hypersensitivity to zinc excess, cold and UV stress in Arabidopsis thaliana

The overly zinc sensitive Arabidopsis thaliana mutant ozs3 shows reduced growth of the primary root, which is exacerbated by an excess specifically of Zn ions. In addition, ozs3 plants display various subtle developmental phenotypes, such as longer petioles and early flowering. Also, ozs3 seedlings are completely but reversibly growth-arrested when shifted to 4°C. The causal mutation was mapped to a gene encoding a putative substrate-recognition receptor of cullin4 E3 ligases. OZS3 orthologous genes can be found in almost all eukaryotic genomes. Most species from Schizosaccharomyces pombe to Homo sapiens, and including A. thaliana, possess one ortholog. No functional data are available for these genes in any of the multicellular model systems. CRISPR-Cas9-mediated knockout demonstrated that a complete loss of OZS3 function is embryo-lethal, indicating essentiality of OZS3 and its orthologs. The OZS3 protein interacts with the adaptor protein DAMAGED DNA BINDING1 (DDB1) in the nucleus. Thus, it is indeed a member of the large yet poorly characterized family of DDB1-cullin4 associated factors in plants. Mutant phenotypes of ozs3 plants are apparently caused by the weakened DDB1-OZS3 interaction as a result of the exchange of a conserved amino acid near the conserved WDxR motif.

TRANSPARENT TESTA GLABRA1, a Key Regulator in Plants with Multiple Roles and Multiple Function Mechanisms

TRANSPARENT TESTA GLABRA1 (TTG1) is a WD40 repeat protein. The phenotypes caused by loss-of-function of TTG1 were observed about half a century ago, but the TTG1 gene was identified only about twenty years ago. Since then, TTG1 has been found to be a plant-specific regulator with multiple roles and multiple functional mechanisms. TTG1 is involved in the regulation of cell fate determination, secondary metabolisms, accumulation of seed storage reserves, plant responses to biotic and abiotic stresses, and flowering time in plants. In some processes, TTG1 may directly or indirectly regulate the expression of downstream target genes via forming transcription activator complexes with R2R3 MYB and bHLH transcription factors. Whereas in other processes, TTG1 may function alone or interact with other proteins to regulate downstream target genes. On the other hand, the studies on the regulation of TTG1 are very limited. So far, only the B3-domain family transcription factor FUSCA3 (FUS3) has been found to regulate the expression of TTG1, phosphorylation of TTG1 affects its interaction with bHLH transcription factor TT2, and TTG1 proteins can be targeted for degradation by the 26S proteasome. Here, we provide an overview of TTG1, including the identification of TTG1, the functions of TTG1, the possible function mechanisms of TTG1, and the regulation of TTG1. We also proposed potential research directions that may shed new light on the regulation and functional mechanisms of TTG1 in plants.

The Conserved and Particular Roles of the R2R3-MYB Regulator FhPAP1 from Freesia hybrida in Flower Anthocyanin Biosynthesis

Anthocyanin biosynthesis is mainly controlled by MYB-bHLH-WD40 (MBW) complexes that modulate the expression of anthocyanin biosynthetic genes (ABGs). The MYB regulators involved in anthocyanin biosynthesis arose early during plant evolution and thus might function divergently in different evolutionary lineages. Although the anthocyanin-promoting R2R3-MYB regulators in eudicots have been comprehensively explored, little consensus has been reached about functional discrepancies versus conservation among MYB regulators from different plant lineages. Here, we integrated transcriptome analysis, gene expression profiles, gain-of-function experiments and transient protoplast transfection assays to functionally characterize the monocot Freesia hybrida anthocyanin MYB regulator gene FhPAP1, which showed correlations with late ABGs. FhPAP1 could activate ABGs as well as TT8-clade genes FhTT8L, AtTT8 and NtAN1 when overexpressed in Freesia, Arabidopsis and tobacco, respectively. Consistently, FhPAP1 could interact with FhTT8L and FhTTG1 to form the conserved MBW complex and shared similar target genes with its orthologs from Arabidopsis. Most prominently, FhPAP1 displayed higher transactivation capacity than its homologs in Arabidopsis and tobacco, which was instantiated in its powerful regulation on ABGs. Moreover, we found that FhPAP1 might be the selected gene during the domestication and rapid evolution of the wild Freesia species to generate intensive flower pigmentation. These results showed that while the MBW complex was highly evolutionarily conserved between tested monocot and core eudicot plants, participating MYB regulators showed functional differences in transactivation capacity according to their activation domain and played important roles in the flower coloration domestication and evolution of angiosperms.

The transcription factor MML4_D12 regulates fiber development through interplay with the WD40-repeat protein WDR in cotton

In planta, a vital regulatory complex, MYB-basic helix-loop-helix (bHLH)-WD40 (MBW), is involved in trichome development and synthesis of anthocyanin and proanthocyanin in Arabidopsis. Usually, WD40 proteins provide a scaffold for protein-protein interaction between MYB and bHLH proteins. Members of subgroup 9 of the R2R3 MYB transcription factors, which includes MYBMIXTA-Like (MML) genes important for plant cell differentiation, are unable to interact with bHLH. In this study, we report that a cotton (Gossypium hirsutum) seed trichome or lint fiber-related GhMML factor, GhMML4_D12, interacts with a diverged WD40 protein (GhWDR) in a process similar to but different from that of the MBW ternary complex involved in Arabidopsis trichome development. Amino acids 250-267 of GhMML4_D12 and the first and third WD40 repeat domains of GhWDR determine their interaction. GhWDR could rescue Arabidopsis ttg1 to its wild type, confirming its orthologous function in trichome development. Our findings shed more light towards understanding the key role of the MML and WD40 families in plants and in the improvement of cotton fiber production.

Comparative transcriptome analysis of anthocyanin synthesis in black and pink peanut

In recent years, black testa peanut (Arachis hypogaea L.) has been favored because of its nutritional value and health function. To explore the genetic basis of peanut testa color, high-throughput sequencing technology was used to sequence the transcriptome of black testa peanut 'ZH9' and pink testa peanut 'ZH8.' Over 18 million high-quality reads were assembled into 49,404-52,578 genes for these two cultivars using a combined assembly strategy. Totally, 4,122 differentially expressed genes (DEGs) were identified between ZH8 and ZH9, among which 1317 (32%) were up-regulated and 2805 (68%) were down-regulated. KEGG analysis showed that the pathways of anthocyanin biosynthesis, isoflavonoid biosynthesis, flavone and flavonol biosynthesis, and phenylpropanoid biosynthesis were in the top 20 differentially expressed genes enriched pathways. Further analysis showed that the formation of the black color of ZH9 testa was mainly due to the reduction of lignin biosynthesis and isoflavonoid biosynthesis, and as a result, more substrate flow to anthocyanin biosynthesis. The up-regulation of all genes associated with DFR, a key enzyme determining flavonoid synthesis or anthocyanin synthesis in the flavonoid metabolic pathway, is also a strategy for increasing dihydroflavonol, a substrate for anthocyanin and flavonol biosynthesis. In addition, we identified three up-regulated R2R3MYB transcription factors associated with anthocyanin biosynthesis in ZH9. Finally, we verified the expressions of 15 genes that encode key enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).

GRWD1 promotes cell proliferation and migration in non-small cell lung cancer by activating the Notch pathway

GRWD1 is a member of the WD repeat protein family that is over-expressed in various cancer cell lines and associated with poor prognosis in patients with cancer. However, its biological function and mechanism in non-small cell lung cancer (NSCLC) remain unclear. In this study, we aimed to elucidate the role of GRWD1 in NSCLC. Immunohistochemistry on tumor specimens from 170 patients showed that GRWD1 is highly expressed in NSCLC tissues and positively correlated with tumor size, lymph node metastasis, and P-TNM stage, but negatively correlated with differentiation and prognosis. We found that GRWD1 promotes cell colony formation by affecting the expression of Cyclin B1, CDK1, and p27 and inducing G2/M transition. GRWD1 was also found to stimulate cell migration through RhoA, RhoC, and CDC42, and induce epithelial-mesenchymal transition by affecting the expression of E-cadherin, N-cadherin, Vimentin, Snail, Zeb1, and ZO-1. Our results indicated that the GRWD1 can activate the Notch signaling pathway by affecting the Notch intracellular domain and promoting the expression of Hes1. Our use of DAPT to suppress Notch signaling confirmed that GRWD1 promotes the progression of NSCLC through the Notch signaling pathway and may be a potential prognostic biomarker and therapeutic target for this disease.

Nucleocytoplasmic Trafficking of the Arabidopsis WD40 Repeat Protein XIW1 Regulates ABI5 Stability and Abscisic Acid Responses

WD40 repeat-containing proteins (WD40 proteins) serve as versatile scaffolds for protein-protein interactions, modulating a variety of cellular processes such as plant stress and hormone responses. Here we report the identification of a WD40 protein, XIW1 (for XPO1-interacting WD40 protein 1), which positively regulates the abscisic acid (ABA) response in Arabidopsis. XIW1 is located in the cytoplasm and nucleus. We found that it interacts with the nuclear transport receptor XPO1 and is exported by XPO1 from the nucleus. Mutation of XIW1 reduces the induction of ABA-responsive genes and the accumulation of ABA Insensitive 5 (ABI5), causing mutant plants with ABA-insensitive phenotypes during seed germination and seedling growth, and decreased drought stress resistance. ABA treatment upregulates the expression of XIW1, and both ABA and abiotic stresses promote XIW1 accumulation in the nucleus, where it interacts with ABI5. Loss of XIW1 function results in rapid proteasomal degradation of ABI5. Taken together, these findings suggest that XIW1 is a nucleocytoplasmic shuttling protein and plays a positive role in ABA responses by interacting with and maintaining the stability of ABI5 in the nucleus.

Sequence characteristics of Medicago truncatula cyclophilin family members and function analysis of MsCYP20-3B involved in axillary shoot development

Cyclophilins (CYPs) belonging to the immunophilin family are present in all organisms and widely distributed in various cells associated with the activity of peptidyl-prolyl cis/trans isomerase. Plant CYPs are members of a multi-gene family and are involved in a series of biological processes. However, little is known about their structure, evolution, developmental expression and functional analysis in Medicago truncatula. In this study, a total of 33 CYP genes were identified and found to be unevenly distributed on eight chromosomes. Among them, 21 are single-domain and 12 are multi-domain proteins, and most were predicted to be localized in the cytosol, nucleus or chloroplast. Phylogenetic and gene structure analysis revealed seven segmental gene pairs, indicating that segmental duplication probably made a large contribution to the expansion of MtCYP gene family. Furthermore, gene expression analysis revealed that about 10 MtCYP genes (were) highly expressed involved in vegetative and reproduction tissues in M. truncatula, and MsCYP20-3B was mainly upregulated in stems, leaves and flower buds in alfalfa (Medicago sativa). Overexpression of MsCYP20-3B was shown to regulate axillary shoot development associated with higher jasmonic acid and abscisic acid contents in M. truncatula. Our study suggests the importance of the CYP genes family in development, reproduction and stress responses, and provides a reference for future studies and application of CYP genes for alfalfa genetic improvement.

Characterization and diagnostic marker for TTG1 regulating tannin and anthocyanin biosynthesis in faba bean

Condensed tannins, found in coloured-flowering varieties of faba bean (Vicia faba L) are, after vicine and convicine, one of the major anti-nutritional factors for monogastric animals. The development of tannin-free cultivars is a key goal in breeding to broaden the use of this legume in the animal feed industry. Two recessive genes, zt-1 and zt-2, control the zero-tannin content and promote white-flowered plants. Previous studies exploiting synteny with the model Medicago truncatula reported a mutation in TTG1, a gene encoding a WD40 transcription factor located in chromosome II, as the responsible for the zt-1 phenotypes. Here a comprehensive analysis of VfTTG1 (including phylogenetic relationships, gene structure and gene expression) has been conducted to confirm the identity of the gene and to reveal structural changes that may result in different functional alleles. The results confirmed the identity of the candidate and revealed the existence of two different alleles responsible for the phenotype: ttg1-a, probably due to a mutation in the promoter region, and ttg1-b caused by a deletion at the 5′end of VfTTG1. Based on the sequencing results, an allele-specific diagnostic marker was designed that differentiate zt-1 from wild and zt-2 genotypes and facilitates its deployment in faba bean breeding programs.

Genome-wide identification and functional analysis of the WDR protein family in potato

WD-repeat (WDR) proteins are highly abundant and participate in a seemingly wide range of interactions and cellular functions acting as scaffolding molecules. However, WDR identification in potato has not been conducted so far. In this study, we demonstrated the presence of at least 168 WDR genes in potato (Solanum tuberosum L.) which can be subdivided into five discrete clusters (Cluster I-V) and 10 classes inferred from their phylogenetic features of the constituent genes and the distribution of domains. These genes are distributed on all 12 chromosomes, of which chromosome 3 carries the most genes with 26 StWDRs. The expression of potato WDR genes showed tissue specificity with a high expression in carpels, callus and roots, and the expression patterns were obviously different among different genes. Transcript profiling of 168 StWDR genes revealed the particular tissues in which the 168 StWDR are expressed, and displayed a high expression in carpels, callus and roots. Most StWDRs were modulated by salt, ABA and Verticillium dahliae stresses, of which StWD092 was found to be highly expressed under all the three stresses. These outcomes revealed the intricate crosstalk between WDRs and other regulatory networks in the event of adverse milieu.

A genome-wide association and meta-analysis reveal regions associated with seed size in cowpea [Vigna unguiculata (L.) Walp]

This paper combined GWAS, meta-analysis and sequence homology comparison with common bean to identify regions associated with seed size variation in domesticated cowpea. Seed size is an important trait for yield and commercial value in dry-grain cowpea. Seed size varies widely among different cowpea accessions, and the genetic basis of such variation is not yet well understood. To better decipher the genetic basis of seed size, a genome-wide association study (GWAS) and meta-analysis were conducted on a panel of 368 cowpea diverse accessions from 51 countries. Four traits, including seed weight, length, width and density were evaluated across three locations. Using 51,128 single nucleotide polymorphisms covering the cowpea genome, 17 loci were identified for these traits. One locus was common to weight, width and length, suggesting pleiotropy. By integrating synteny-based analysis with common bean, six candidate genes (Vigun05g036000, Vigun05g039600, Vigun05g204200, Vigun08g217000, Vigun11g187000, and Vigun11g191300) which are implicated in multiple functional categories related to seed size such as endosperm development, embryo development, and cell elongation were identified. These results suggest that a combination of GWAS meta-analysis with synteny comparison in a related plant is an efficient approach to identify candidate gene (s) for complex traits in cowpea. The identified loci and candidate genes provide useful information for improving cowpea varieties and for molecular investigation of seed size.

De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway

Gymnema sylvestre is a highly valuable medicinal plant in traditional Indian system of medicine and used in many polyherbal formulations especially in treating diabetes. However, the lack of genomic resources has impeded its research at molecular level. The present study investigated functional gene profile of G. sylvestre via RNA sequencing technology. The de novo assembly of 88.9 million high quality reads yielded 23,126 unigenes, of which 18116 were annotated against databases such as NCBI nr database, gene ontology (GO), KEGG, Pfam, CDD, PlantTFcat, UniProt & GreeNC. Total 808 unigenes mapped to 78 different Transcription Factor families, whereas 39 unigenes assigned to CYP450 and 111 unigenes coding for enzymes involved in the biosynthesis of terpenoids including transcripts for synthesis of important compounds like Vitamin E, beta-amyrin and squalene. Among them, presence of six important enzyme coding transcripts were validated using qRT-PCR, which showed high expression of enzymes involved in methyl-erythritol phosphate (MEP) pathway. This study also revealed 1428 simple sequence repeats (SSRs), which may aid in molecular breeding studies. Besides this, 8 putative long non-coding RNAs (lncRNAs) were predicted from un-annotated sequences, which may hold key role in regulation of essential biological processes in G. sylvestre. The study provides an opportunity for future functional genomic studies and to uncover functions of the lncRNAs in G. sylvestre.

High WDR34 mRNA expression as a potential prognostic biomarker in patients with breast cancer as determined by integrated bioinformatics analysis

The WD-repeat domain (WDR) family is distributed in the majority of eukaryotes and has several unique biological functions. It serves important roles in signal transduction, cytoskeleton assembly, protein transport, RNA processing, chromatin modification and transcription mechanisms. WD repeat domain 34 (WDR34) has been recently identified as a member of the WDR family. Overexpression of WDR34 was accompanied by the presence of multiple centrioles in the cell, suggesting that it was associated with tumor occurrence. However, its association with breast cancer was unclear. To the best of our knowledge, it has not yet been confirmed whether WDR34 gene expression is associated with breast cancer. Therefore, the current study attempted to clarify this by performing a comprehensive study using multiple datasets in the Oncomine, Breast Cancer Gene-Expression Miner and Kaplan-Meier Plotter databases. The analysis indicated that the mRNA expression levels of WDR34 were increased in breast cancer tissues compared with normal tissues. Consistent with this result, the Broad-Novartis Cancer Cell Line Encyclopedia revealed that WDR34 mRNA expression levels were upregulated in breast cancer cell lines compared with other cancer cells. It was noted that high WDR34 mRNA expression was associated with forkhead box M1 and PTTG1 regulator of sister chromatid separation, securing in co-expression analysis. Expression profile characteristics of WDR34 mRNA were identified in different molecular subtypes of breast cancer. Furthermore, survival analysis revealed that increased expression levels of WDR34 mRNA were associated with poor overall survival in patients with breast cancer, particularly in luminal B, lymph node status-positive and estrogen receptor (ER)-negative subgroups. Additionally, Kaplan-Meier curves revealed that high WDR34 mRNA expression was associated with shorter relapse-free survival in patients with breast cancer, particularly in ER-positive, human epidermal growth factor receptor 2-negative and progesterone receptor-positive subgroups. These results suggested that WDR34 may be used as a prognosis predictor in breast cancer and may provide a novel target for the diagnosis and treatment of breast cancer.

Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome

A hub protein in protein interaction networks will typically have a large number of diverse interactions. Determining the core interactions and the function of such a hub protein remains a significant challenge in the study of networks. Proteins with WD40 repeats represent a large class of proteins that can be hub proteins. WDR76 is a poorly characterized WD40 repeat protein with possible involvement in DNA damage repair, cell-cycle progression, apoptosis, gene expression regulation, and protein quality control. WDR76 has a large and diverse interaction network that has made its study challenging. Here we rigorously carry out a series of affinity purification coupled to mass spectrometry (AP-MS) analyses to map out the WDR76 interactome through different biochemical conditions. We apply AP-MS analysis coupled to size-exclusion chromatography to resolve WDR76-based protein complexes. Furthermore, we also show that WDR76 interacts with the CCT complex via its WD40 repeat domain and with DNA-PK-KU, PARP1, GAN, SIRT1, and histones outside of the WD40 domain. An evaluation of the stability of WDR76 interactions led to focused and streamlined reciprocal analyses that validate the interactions with GAN and SIRT1. Overall, the approaches used to study WDR76 would be valuable to study other proteins containing WD40 repeat domains, which are conserved in a large number of proteins in many organisms.

AtWDS1 negatively regulates age-dependent and dark-induced leaf senescence in Arabidopsis

Although the involvement of ROS (reactive oxygen species) in leaf senescence is well known, the factors governing this accumulation of ROS are not fully characterized. In this study, analysis of transgenic overexpressing and knock out lines of AtWDS1 (encoding a WD repeat protein), indicates that AtWDS1 negatively regulates age-dependent and dark-induced leaf senescence. Furthermore, we observed ROS accumulation and altered tolerance of oxidative stress in atwds1 plants, as well as upregulated expression of oxidative stress-responsive genes. The location of an EGFP-AtWDS1 fusion protein in the nucleus of transformed cells and plants indicates that AtWDS1 is a nuclear protein, and, using a Dual-Luciferase assay, we showed that AtWDS1 can act as a transcription activator. However, the lack of a nuclear localization sequence in AtWDS1 suggests that its presence in the nucleus must depend on interactions with other proteins. Indeed, we found that AtWDS1 interacts directly with AtRanBPM, and that mutation of the AtRanBPM gene results in partial mislocalization of AtWDS1 in the cytoplasm. Together, these results suggest a role for AtWDS1 as a novel modulator of redox homeostasis, which responds to developmental and stress signals to regulate leaf senescence.

A functional homologue of Arabidopsis TTG1 from Freesia interacts with bHLH proteins to regulate anthocyanin and proanthocyanidin biosynthesis in both Freesia hybrida and Arabidopsis thaliana

The MBW complex, consisting of MYB, basic helix-loop-helix (bHLH) and WD40 proteins, regulates multiple traits in plants, such as anthocyanin and proanthocyanidin biosynthesis and cell fate determination. The complex has been widely identified in dicot plants, whereas few studies are concentrated on monocot plants which are of crucial importance to decipher its functional diversities among angiosperms during evolution. In present study, a WD40 gene from Freesia hybrida, designated as FhTTG1, was cloned and functionally characterized. Real-time PCR analysis indicated that it was expressed synchronously with the accumulation of both proanthocyanidins and anthocyanins in Freesia flowers. Transient protoplast transfection and biomolecular fluorescence complementation (BiFC) assays demonstrated that FhTTG1 could interact with FhbHLH proteins (FhTT8L and FhGL3L) to constitute the MBW complex. Moreover, the transportation of FhTTG1 to nucleus was found to rely on FhbHLH factors. Outstandingly, FhTTG1 could highly activate the anthocyanin or proanthocyanidin biosynthesis related gene promoters when co-transfected with MYB and bHLH partners, implying that FhTTG1 functioned as a member of MBW complex to control the anthocyanin or proanthocyanidin biosynthesis in Freesia hybrida. Further ectopic expression assays in Arabidopsis ttg1-1 showed the defective phenotypes of ttg1-1 were partially restored. Molecular biological assays validated FhTTG1 might interact with the endogenous bHLH factors to up-regulate genes responsible for anthocyanin and proanthocyanidin biosynthesis and trichome formation, indicating that FhTTG1 might perform exchangeable roles with AtTTG1. These results will not only contribute to the characterization of FhTTG1 in Freesia but also shed light on the establishment of flavonoid regulatory system in monocot plants, especially in Freesia hybrida.

Evolutionary comparison of competitive protein-complex formation of MYB, bHLH, and WDR proteins in plants

A protein complex consisting of a MYB, basic Helix-Loop-Helix, and a WDR protein, the MBW complex, regulates five traits, namely the production of anthocyanidin, proanthocyanidin, and seed-coat mucilage, and the development of trichomes and root hairs. For complexes involved in trichome and root hair development it has been shown that the interaction of two MBW proteins can be counteracted by the respective third protein (called competitive complex formation). We examined competitive complex formation for selected MBW proteins from Arabidopsis thaliana, Arabis alpina, Gossypium hirsutum, Petunia hybrida, and Zea mays. Quantitative analyses of the competitive binding of MYBs and WDRs to bHLHs were done by pull-down assays using ProtA- and luciferase-tagged proteins expressed in human HEC cells. We found that some bHLHs show competitive complex formation whilst others do not. Competitive complex formation strongly correlated with a phylogenetic tree constructed with the bHLH proteins under investigation, suggesting a functional relevance. We demonstrate that this different behavior can be explained by changes in one amino acid and that this position is functionally relevant in trichome development but not in anthocyanidin regulation.

Identification and characterization of WD40 superfamily genes in peach

The WD40 transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. To our knowledge, to date, WD40 superfamily genes have been identified and characterized in several plant species, but little information is available on the WD40 superfamily genes in peach. In this study, we identified 220 members of the WD40 superfamily in the peach genome, and these members were further classified into five subfamilies based on phylogenetic comparison with those in Arabidopsis. The members within each subfamily had conserved motifs and gene structures. The WD40 genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. Additionally, 58 pairs of paralog WD40 members were found on eight chromosomes in peach, and 242 pairs of orthologous WD40 genes in peach and Arabidopsis were matched. The 54 selected putative WD40 genes in peach had diverse expression patterns in red-fleshed and white-fleshed peach fruits at five developmental stages. Prupe.6G211800.1 was located only on the cytomembrane, while Prupe.1G428200.1 and Prupe.I003200.1 were located on both the cytomembrane and in the nucleus; Prupe.1G558700.1 was densely localized around the nuclear rim but relatively faintly localized in the nucleoplasm; Prupe.5G116300.1 was located in the nucleus and cytomembrane with strong signals but showed weak signals in the cytoplasm; and Prupe.8G212400.1 and Prupe.1G053600.1 were located mainly in the nuclear envelope and cytomembrane but relatively faintly in the nucleoplasm. This study provides a foundation for the further functional verification of WD40 genes in peach.

Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max)

Whole-genome re-sequencing is a powerful approach to detect gene variants, but it is expensive to analyse only the target genes. To circumvent this problem, we attempted to detect novel variants of flowering time-related genes and their homologues in soybean mini-core collection by target re-sequencing using AmpliSeq technology. The average depth of 382 amplicons targeting 29 genes was 1,237 with 99.85% of the sequence data mapped to the reference genome. Totally, 461 variants were detected, of which 150 sites were novel and not registered in dbSNP. Known and novel variants were detected in the classical maturity loci-E1, E2, E3, and E4. Additionally, large indel alleles, E1-nl and E3-tr, were successfully identified. Novel loss-of-function and missense variants were found in FT2a, MADS-box, WDR61, phytochromes, and two-component response regulators. The multiple regression analysis showed that four genes-E2, E3, Dt1, and two-component response regulator-can explain 51.1-52.3% of the variation in flowering time of the mini-core collection. Among them, the two-component response regulator with a premature stop codon is a novel gene that has not been reported as a soybean flowering time-related gene. These data suggest that the AmpliSeq technology is a powerful tool to identify novel alleles.

Integration of RACK1 and ethylene signaling regulates plant growth and development in Arabidopsis

Arabidopsis RACK1 (Receptors for Activated C Kinase 1) are versatile scaffold proteins that have been shown to be involved in the regulation of plant response to plant hormones including auxin, ABA, gibberellin and brassinosteroid, but not ethylene. By characterizing the double and triple mutants of RACK1 genes, we found that rack1 mutants showed reduced sensitivity to ethylene. By characterizing double and high order mutants generated between ein2, a loss-of-function mutant of the key ethylene signaling regulator gene EIN2 (Ethylene INsensitive 2), and rack1 mutants, we found that loss-of-function of EIN2 partially recovered some phenotypes observed in the rack1 mutants, such as low-fertility and reduced root length and rosette size. On the other hand, the ein2 rack1 mutants produced more rosette leaves, and flowered late when compared with ein2 and the corresponding rack1 mutants. We also found that the curled leaves and twisted petioles phenotypes observed in the ein2 mutants were enhanced in the ein2 rack1 mutants. However, assays in yeast indicated that EIN2 may not physically interact with RACK1. On the other hand, RT-PCR results showed that the expression level of EIN2 was reduced in the rack1 mutants. Taken together, our results suggest that RACKl may integrate ethylene signaling to regulate plant growth and development in Arabidopsis.

GmZPR3d Interacts with GmHD-ZIP III Proteins and Regulates Soybean Root and Nodule Vascular Development

Fabaceans produce two major classes of symbiotic nodules: the indeterminate type characterized by a persistent meristem, and the determinate type that lacks a persistent meristem. The class III homeodomain leucine zipper (HD-ZIP III) transcription factor family influence development of multiple lateral organs and meristem maintenance, but their role in determinate nodule development is not known. HD-ZIP III protein activity is post-translationally regulated by members of the small leucine zipper protein (ZPR) family in arabidopsis. We characterized the ZPR gene family in soybean and evaluated their ability to interact with two key members of GmHD-ZIP III family through yeast two-hybrid assays. GmZPR3d displayed the strongest interaction with GmHD-ZIP III-2 among the different pairs evaluated. GmHD-ZIP III-1, -2, and GmZPR3d showed overlapping expression patterns in the root stele and in nodule parenchyma tissues. Over-expression of GmZPR3d resulted in ectopic root secondary xylem formation, and enhanced expression of vessel-specific master switch genes in soybean. The nodules in ZPR3d over-expressing roots were larger in size, had a relatively larger central zone and displayed increased nodule vascular branching. The results from this study point to a key role for GmZPR3d in soybean root and nodule development.

Genome Wide Analysis of WD40 Proteins in Saccharomyces cerevisiae and Their Orthologs in Candida albicans

The WD40 domain containing proteins are present in the lower organisms (Monera) to higher complex metazoans with involvement in diverse cellular processes. The WD40 repeats fold into β propeller structure due to which the proteins harbouring WD40 domains function as scaffold by offering platform for interactions, bring together diverse cellular proteins to form a single complex for mediating downstream effects. Multiple functions of WD40 domain containing proteins in lower eukaryote as in Fungi have been reported with involvement in vegetative and reproductive growth, virulence etc. In this article insilico analysis of the WDR proteins in the budding yeast Saccharomyces cerevisiae was performed. By WDSP software 83 proteins in S. cerevisiae were identified with at least one WD40 motif. WD40 proteins with 6 or more WD40 motifs were considered for further studies. The WD40 proteins in yeast which are involved in various biological processes show distribution on all chromosomes (16 chromosomes in yeast) except chromosome 1. Besides the WD40 domain some of these proteins also contain other protein domains which might be responsible for the diversity in the functions of WD40 proteins in the budding yeast. These proteins in budding yeast were analysed by DAVID and Blast2Go software for functional and domains categorization. Candida albicans, an opportunistic fungal pathogen also have orthologs of these WD40 proteins with possible similar functions. This is the first time genome wide analysis of WD40 proteins in lower eukaryote i.e. budding yeast. This data may be useful in further study of the functional diversity of yeast proteomes.

Comparative Transcriptome Analysis of the Skin-Specific Accumulation of Anthocyanins in Black Peanut ( Arachis hypogaea L.)

As an oil crop with good taste and profuse nutrition, peanut ( Arachis hypogaea L.) is grown worldwide, mainly for edible seeds. Black peanuts attract more attention for their appealing color and health-promoting anthocyanins. Here, two cyanidin-based anthocyanins and four quercetin-based flavonols were separated and identified from skins of two black cultivars (Zi Yu and Zi Guan) by HPLC-ESI-Q-TOF-MS. To study the anthocyanin accumulation, libraries constructed from the mRNA of skins of Zi Yu and white cultivar (Bai Yu) were sequenced, and 4042 differentially expressed genes were identified. Gene ontology and KEGG pathway analysis underlined the importance of the high expression of flavonoid biosynthetic and regulatory genes in seed skin of Zi Yu. Furthermore, expression profiles of these genes were analyzed carefully in four representative peanut cultivars. Altogether, these results strongly indicate that the up-regulation of transcriptional activators (AhMYB1, AhMYB2, and AhTT8) accounts for the skin-specific accumulation of anthocyanins in black peanut.

Beyond Arabidopsis: Differential UV-B Response Mediated by UVR8 in Diverse Species

Ultraviolet-B radiation (UV-B, 280-315 nm) is an important environmental signal that regulates growth and development in plants. Two dose-dependent UV-B response pathways were described in plants: a specific one, mediated by UVR8 (the specific UV-B receptor) and an unspecific one, activated by the oxidative damage produced by radiation. The constitutively expressed receptor appears inactive as a dimer, with the two monomers dissociating upon UV-B irradiation. The monomer then interacts with COP1, an ubiquitin ligase, hindering its ability to poly-ubiquitinate transcriptional factor HY5, thus averting its degradation and activating the photomorphogenic response. HY5 induces the synthesis of proteins RUP1 and RUP2, which interact with UVR8, releasing COP1, and inducing the re-dimerization of UVR8. This mechanism has been thoroughly characterized in Arabidopsis, where studies have demonstrated that the UVR8 receptor is key in UV-B response. Although Arabidopsis importance as a model plant many mechanisms described in this specie differ in other plants. In this paper, we review the latest information regarding UV-B response mediated by UVR8 in different species, focusing on the differences reported compared to Arabidopsis. For instance, UVR8 is not only induced by UV-B but also by other agents that are expressed differentially in diverse tissues. Also, in some of the species analyzed, proteins with low homology to RUP1 and RUP2 were detected. We also discuss how UVR8 is involved in other developmental and stress processes unrelated to UV-B. We conclude that the receptor is highly versatile, showing differences among species.

Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression

CULLIN4 (CUL4) RING ligase (CRL4) complexes contain a CUL4 scaffold protein, associated to RBX1 and to DDB1 proteins and have traditionally been associated to protein degradation events. Through DDB1, these complexes can associate with numerous DCAF proteins, which directly interact with specific targets promoting their ubiquitination and subsequent degradation by the proteasome. A characteristic feature of the majority of DCAF proteins that associate with DDB1 is the presence of the DWD motif. DWD-containing proteins sum up to 85 in the plant model species Arabidopsis. In the last decade, numerous Arabidopsis DWD proteins have been studied and their molecular functions uncovered. Independently of whether their association with CRL4 has been confirmed or not, DWD proteins are often found as components of additional multimeric protein complexes that play key roles in essential nuclear events. For most of them, the significance of their complex partnership is still unexplored. Here, we summarize recent findings involving both confirmed and putative CRL4-associated DCAF proteins in regulating nuclei architecture remodelling, DNA damage repair, histone post-translational modification, mRNA processing and export, and ribosome biogenesis, that definitely have an impact in gene expression and de novo protein synthesis. We hypothesized that, by maintaining accurate levels of regulatory proteins through targeted degradation and transcriptional control, CRL4 complexes help to surveil nuclear processes essential for plant development and survival.

Wheat WD40-repeat protein TaHOS15 functions in a histone deacetylase complex to fine-tune defense responses to Blumeria graminis f.sp. tritici

Powdery mildew caused by Blumeria graminis f.sp. tritici (Bgt) seriously threatens the production of common wheat (Triticum aestivum). In eukaryotes, WD40-repeat (WDR) proteins usually participate in assembling protein complexes involved in a wide range of cellular processes, including defense responses. However, the potential function of WDR proteins in regulating crop resistance to biotrophic fungal pathogens, such as Bgt, remains unclear. In this study, we isolated TaHOS15, encoding a WDR protein, from the Bgt-susceptible wheat cultivar Jing411 and demonstrated that knockdown of TaHOS15 expression using virus- or transient-induced gene-silencing attenuated wheat susceptibility to Bgt. Biochemical and molecular-biological assays revealed that TaHOS15 interacts with TaHDA6, a wheat homolog of Arabidopsis histone deacetylase AtHDA6, to constitute a transcriptional repressor complex. We determined the role of TaHOS15, which might act as an adaptor protein recruiting TaHDA6 to the chromatin of wheat defense-related genes including TaPR1, TaPR2, TaPR5, and TaWRKY45, where they repress histone acetylation. Reduced TaHOS15 or TaHDA6 transcript levels led to decreased susceptibility to Bgt together with enhanced defense-related transcription under Bgt infection. Collectively, these results demonstrate that TaHOS15 functions in a histone deacetylase complex with TaHDA6 to fine-tune the defense response to Bgt in common wheat.

HOS15 Interacts with the Histone Deacetylase HDA9 and the Evening Complex to Epigenetically Regulate the Floral Activator GIGANTEA

In plants, seasonal inputs such as photoperiod and temperature modulate the plant's internal genetic program to regulate the timing of the developmental transition from vegetative to reproductive growth. This regulation of the floral transition involves chromatin remodeling, including covalent modification of histones. Here, we report that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), a WD40 repeat protein, associates with a histone deacetylase complex to repress transcription of the GIGANTEA (GI)-mediated photoperiodic flowering pathway in Arabidopsis (Arabidopsis thaliana). Loss of function of HOS15 confers early flowering under long-day conditions because elevated GI expression. LUX ARRHYTHMO (LUX), a DNA binding transcription factor and component of the Evening Complex (EC), is important for the binding of HOS15 to the GI promoter. In wild type, HOS15 associates with the EC components LUX, EARLY FLOWERING 3 (ELF3), and ELF4 and the histone deacetylase HDA9 at the GI promoter, resulting in histone deacetylation and reduced GI expression. In the hos15-2 mutant, the levels of histone acetylation are elevated at the GI promoter, resulting in increased GI expression. Our data suggest that the HOS15-EC-HDA9 histone-modifying complex regulates photoperiodic flowering via the transcriptional repression of GI.

Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.)

BACKGROUND

WD40 domains are abundant in eukaryotes, and they are essential subunits of large multiprotein complexes, which serve as scaffolds. WD40 proteins participate in various cellular processes, such as histone modification, transcription regulation, and signal transduction. WD40 proteins are regarded as crucial regulators of plant development processes. However, the systematic identification and analysis of WD40 proteins have yet to be reported in wheat.

RESULTS

In this study, a total of 743 WD40 proteins were identified in wheat, and they were grouped into 5 clusters and 11 subfamilies. Their gene structures, chromosomal locations, and evolutionary relationships were analyzed. Among them, 39 and 46 pairs of TaWD40s were distinguished as tandem duplication and segmental duplication genes. The 123 OsWD40s were identified to exhibit synteny with TaWD40s. TaWD40s showed the specific characteristics at the reproductive developmental stage, and numerous TaWD40s were involved in responses to stresses, including cold, heat, drought, and powdery mildew infection pathogen, based on the result of RNA-seq data analysis. The expression profiles of some TaWD40s in wheat seed development were confirmed through qRT-PCR technique.

CONCLUSION

In this study, 743 TaWD40s were identified from the wheat genome. As the main driving force of evolution, duplication events were observed, and homologous recombination was another driving force of evolution. The expression profiles of TaWD40s revealed their importance for the growth and development of wheat and their response to biotic and abiotic stresses. Our study also provided important information for further functional characterization of some WD40 proteins in wheat.