Ubiquitin protein ligase 3 mediates the proteasomal degradation of GLABROUS 3 and ENHANCER OF GLABROUS 3, regulators of trichome development and flavonoid biosynthesis in Arabidopsis

Defects in Glabrous 3 (GL3) functionality underlie the absence of trichomes in Brassica napus

Previously, expression of the Arabidopsis thaliana GLABRA3 (GL3) induced trichome formation in Brassica napus. GL3 orthologues were examined from glabrous (B. oleracea), semi-glabrous (B. napus), moderately hirsute (B. rapa), and very hirsute (B. villosa) Brassica species. Ectopic expression of BnGL3, BrGL3 alleles, or BvGL3 induced trichome formation in glabrous B. napus with the effect on trichome number commensurate with density in the original accessions. Chimeric GL3 proteins in which the B. napus amino terminal region, which interacts with MYB proteins, or the middle region, which interacts with the WD40 protein TTG1, was exchanged with corresponding regions from A. thaliana were as stimulatory to trichome production as AtGL3. Exchange of the carboxy-terminal region containing a bHLH domain and an ACT domain did not alter the trichome stimulatory activity, although modeling of the ACT domain identified differences that could affect GL3 dimerization. B. napus A- and C-genomes orthologues differed in their abilities to form homo- and heterodimers. Modeling of the amino-terminal region revealed a conserved domain that may represent the MYB factor binding pocket. This region interacted with the MYB factors GL1, CPC, and TRY, as well as with JAZ8, which is involved in jasmonic acid-mediated regulation of MYC-like transcription factors. Protein interaction studies indicated that GL1 interaction with GL3 from B. napus and A. thaliana may underlie the difference in their respective abilities to induce trichome formation.

Comparative proteomics in tall fescue to reveal underlying mechanisms for improving Photosystem II thermotolerance during heat stress memory

BACKGROUND

The escalating impacts of global warming intensify the detrimental effects of heat stress on crop growth and yield. Among the earliest and most vulnerable sites of damage is Photosystem II (PSII). Plants exposed to recurring high temperatures develop heat stress memory, a phenomenon that enables them to retain information from previous stress events to better cope with subsequent one. Understanding the components and regulatory networks associated with heat stress memory is crucial for the development of heat-resistant crops.

RESULTS

Physiological assays revealed that heat priming (HP) enabled tall fescue to possess higher Photosystem II photochemical activity when subjected to trigger stress. To investigate the underlying mechanisms of heat stress memory, we performed comparative proteomic analyses on tall fescue leaves at S0 (control), R4 (primed), and S5 (triggering), using an integrated approach of Tandem Mass Tag (TMT) labeling and Liquid Chromatography-Mass Spectrometry. A total of 3,851 proteins were detected, with quantitative information available for 3,835 proteins. Among these, we identified 1,423 differentially abundant proteins (DAPs), including 526 proteins that were classified as Heat Stress Memory Proteins (HSMPs). GO and KEGG enrichment analyses revealed that the HSMPs were primarily associated with the "autophagy" in R4 and with "PSII repair", "HSP binding", and "peptidase activity" in S5. Notably, we identified 7 chloroplast-localized HSMPs (HSP21, DJC77, EGY3, LHCA4, LQY1, PSBR and DEGP8, R4/S0 > 1.2, S5/S0 > 1.2), which were considered to be effectors linked to PSII heat stress memory, predominantly in cluster 4. Protein-protein interaction (PPI) analysis indicated that the ubiquitin-proteasome system, with key nodes at UPL3, RAD23b, and UCH3, might play a role in the selective retention of memory effectors in the R4 stage. Furthermore, we conducted RT-qPCR validation on 12 genes, and the results showed that in comparison to the S5 stage, the R4 stage exhibited reduced consistency between transcript and protein levels, providing additional evidence for post-transcriptional regulation in R4.

CONCLUSIONS

These findings provide valuable insights into the establishment of heat stress memory under recurring high-temperature episodes and offer a conceptual framework for breeding thermotolerant crops with improved PSII functionality.

Characterization and expression analysis of GLABRA3 (GL3) genes in cotton: insights into trichome development and hormonal regulation

BACKGROUND

GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3) genes encode a typical helix-loop-helix (bHLH) transcription factors that primarily regulate trichome branching and root hair development, DNA endoreduplication, trichoblast size, and stomatal formation. The functions of GL3 genes in cotton crop have been poorly characterized. In this study, we performed comprehensive genome-wide scans for GL3 and EGL3 homologs to enhance our comprehension of their potential roles in trichome and fiber development in cotton crop.

METHODS AND RESULTS

Our findings paraded that Gossypium hirsutum and G. barbadense have 6 GL3s each, unevenly distributed on 4 chromosomes whereas, G. arboreum, and G. raimondii have 3 GL3s each, unevenly distributed on 2 chromosomes. Gh_A08G2088 and Gb_A09G2187, despite having the same bHLH domain as the other GL3 genes, were excluded due to remarkable short sequences and limited number of motifs, indicating a lack of potential functional activity. The phylogenetic analysis categorized remaining 16 GL3s into three subfamilies (Group I-III) closely related to A. thaliana. The 16 GL3s have complete bHLH domain, encompassing 590-631 amino acids, with molecular weights (MWs) ranging from 65.92 to 71.36 kDa. Within each subfamily GL3s depicted shared similar gene structures and motifs, indicating conserved characteristics within respective groups. Promoter region analysis revealed 27 cis-acting elements, these elements were responsive to salicylic acid, abscisic acid (ABA), methyl jasmonate (MeJA), and gibberellin. The expression of GL3 genes was analyzed across 12 tissues in both G. barbadense and G. hirsutum using the publicly available RNA-seq data. Among GL3s, Gb_D11G0219, Gb_D11G0214, and Gb_D08G2182, were identified as relatively highly expressed across different tissues, consequently selected for hormone treatment and expression validation in G. barbadense. RT-qPCR results demonstrated significant alterations in the expression levels of Gb_D11G0219 and Gb_D11G0214 following MeJA, GA, and ABA treatment. Subcellular localization prediction revealed that most GL3 proteins were predominantly expressed in the nucleus, while a few were localized in the cytoplasm and chloroplasts.

CONCLUSIONS

In summary, this study lays the foundation for subsequent functional validation of GL3 genes by identifying hormonal regulation patterns and probable sites of action in cotton trichome formation and fiber development. The results stipulate a rationale to elucidate the roles and regulatory mechanisms of GL3 genes in the intricate process of cotton fibre and trichome development.

HECT-type ubiquitin ligase KAKTUS mediates the proteasome-dependent degradation of cyclin-dependent kinase inhibitor KRP2 during trichome morphogenesis in Arabidopsis

Trichome development is a fascinating model to elaborate the plant cell differentiation and growth processes. A wealth of information has pointed to the contributions of the components associated with cell cycle control and ubiquitin/26S proteasome system (UPS) to trichome morphogenesis, but how these two pathways are connected remains obscure. Here, we report that HECT‐type ubiquitin ligase KAKTUS (KAK) targets the cyclin‐dependent kinase (CDK) inhibitor KRP2 (for kip‐related protein 2) for proteasome‐dependent degradation during trichome branching in Arabidopsis. We show that over‐expression of KRP2 promotes trichome branching and endoreduplication which is similar to kak loss of function mutants. KAK directly interacts with KRP2 and mediates KRP2 degradation. Mutation of KAK results in the accumulation of steady‐state KRP2. Consistently, in kak pKRP2:KRP2‐GFP plants, the trichome branching is further induced compared with the single mutant. Taken together, our studies bridge the cell cycle control and UPS pathways during trichome development and underscore the importance of post‐translational control in epidermal differentiation.

UPL3 Promotes BZR1 Degradation, Growth Arrest, and Seedling Survival under Starvation Stress in Arabidopsis

BRASSINAZONE RESISTANT 1 (BZR1) is a key transcription factor of the brassinosteroid signaling pathway but also a signaling hub that integrates diverse signals that modulate plant growth. Previous studies have shown that starvation causes BZR1 degradation, but the underlying mechanisms are not understood. Here we performed quantitative proteomic analysis of BZR1 interactome under starvation conditions and identified two BZR1-interacting ubiquitin ligases, BAF1 and UPL3. Compared to the wild type, the upl3 mutants show long hypocotyl and increased BZR1 levels when grown under sugar starvation conditions but not when grown on sugar-containing media, indicating a role of UPL3 in BZR1 degradation specifically under starvation conditions. The upl3 mutants showed a reduced survival rate after starvation treatment, supporting the importance of UPL3-mediated BZR1 degradation and growth arrest for starvation survival. Treatments with inhibitors of TARGET of RAPAMYCIN (TOR) and autophagy altered BZR1 level in the wild type but were less effective in upl3 , suggesting that UPL3 mediates the TOR-regulated and autophagy-dependent degradation of BZR1. Further, the UPL3 protein level is increased posttranscriptionally by starvation but decreased by sugar treatment. Our study identifies UPL3 as a key component that mediates sugar regulation of hormone signaling pathways, important for optimal growth and survival in plants.

IN A NUTSHELL

Background: The coordination between signaling pathways that monitor the levels of photosynthate and growth hormones is crucial for optimizing growth and survival, but the underlying mechanisms are not fully understood. When the sugar level is low, the BZR1 transcription factor of the brassinosteroid (BR) signaling pathway is degraded, and hence growth is attenuated to prevent starvation and enhance survival. When sugar is sufficient, sugar signaling inhibits BZR1 degradation and enables BR promotion of plant growth. The key component that mediates starvation-induced BZR1 degradation remains unknown.Question: What proteins interact with BZR1 and mediate its degradation under sugar starvation?Finding: We performed immunoprecipitation mass spectrometry analysis of BZR1 in starvation-treated Arabidopsis and identified many BZR1-interacting proteins, including two E3 ligases UPL3 and BAF1. Genetic analysis showed that UPL3 plays a specific and prominent role in promoting autophagy-dependent BZR1 degradation and plant survival under sugar-starvation conditions.Next step: How sugar-TOR signaling regulates UPL3 level remains to be studied in the future.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

Advances in understanding epigenetic regulation of plant trichome development: a comprehensive review

Plant growth and development are controlled by a complex gene regulatory network, which is currently a focal point of research. It has been established that epigenetic factors play a crucial role in plant growth. Trichomes, specialized appendages that arise from epidermal cells, are of great significance in plant growth and development. As a model system for studying plant development, trichomes possess both commercial and research value. Epigenetic regulation has only recently been implicated in the development of trichomes in a limited number of studies, and microRNA-mediated post-transcriptional regulation appears to dominate in this context. In light of this, we have conducted a review that explores the interplay between epigenetic regulations and the formation of plant trichomes, building upon existing knowledge of hormones and transcription factors in trichome development. Through this review, we aim to deepen our understanding of the regulatory mechanisms underlying trichome formation and shed light on future avenues of research in the field of epigenetics as it pertains to epidermal hair growth.

TOE1/TOE2 Interacting with GIS to Control Trichome Development in Arabidopsis

Trichomes are common appendages originating and projecting from the epidermal cell layer of most terrestrial plants. They act as a first line of defense and protect plants against different types of adverse environmental factors. GL3/EGL3-GL1-TTG1 transcriptional activator complex and GIS family genes regulate trichome initiation through gibberellin (GA) signaling in Arabidopsis. Here, our novel findings show that TOE1/TOE2, which are involved in developmental timing, control the initiation of the main-stem inflorescence trichome in Arabidopsis. Phenotype analysis showed that the 35S:TOE1 transgenic line increases trichome density of the main-stem inflorescence in Arabidopsis, while 35S:miR172b, toe1, toe2 and toe1toe2 have the opposite phenotypes. Quantitative RT-PCR results showed that TOE1/TOE2 positively regulate the expression of GL3 and GL1. In addition, protein-protein interaction analysis experiments further demonstrated that TOE1/TOE2 interacting with GIS/GIS2/ZFP8 regulate trichome initiation in Arabidopsis. Furthermore, phenotype and expression analysis also demonstrated that TOE1 is involved in GA signaling to control trichome initiation in Arabidopsis. Taken together, our results suggest that TOE1/TOE2 interact with GIS to control trichome development in Arabidopsis. This report could provide valuable information for further study of the interaction of TOE1/TOE2 with GIS in controlling trichome development in plants.

Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to salt tolerance in sorghum (Sorghum bicolor L.)

Plant U-box (PUB) E3 ubiquitin ligases play essential roles in many biological processes and stress responses, but little is known about their functions in sorghum (Sorghum bicolor L.). In the present study, 59 SbPUB genes were identified in the sorghum genome. Based on the phylogenetic analysis, the 59 SbPUB genes were clustered into five groups, which were also supported by the conserved motifs and structures of these genes. SbPUB genes were found to be unevenly distributed on the 10 chromosomes of sorghum. Most PUB genes (16) were found on chromosome 4, but there were no PUB genes on chromosome 5. Analysis of cis-acting elements showed that SbPUB genes were involved in many important biological processes, particularly in response to salt stress. From proteomic and transcriptomic data, we found that several SbPUB genes had diverse expressions under different salt treatments. To verify the expression of SbPUBs, qRT-PCR analyses also were conducted under salt stress, and the result was consistent with the expression analysis. Furthermore, 12 SbPUB genes were found to contain MYB-related elements, which are important regulators of flavonoid biosynthesis. These results, which were consistent with our previous multi-omics analysis of sorghum salt stress, laid a solid foundation for further mechanistic study of salt tolerance in sorghum. Our study showed that PUB genes play a crucial role in regulating salt stress, and might serve as promising targets for the breeding of salt-tolerant sorghum in the future.

Comparative Transcriptomic Analysis Revealed the Suppression and Alternative Splicing of Kiwifruit (Actinidia latifolia) NAP1 Gene Mediating Trichome Development

Kiwifruit (Actinidia chinensis) is commonly covered by fruit hairs (trichomes) that affect kiwifruit popularity in the commercial market. However, it remains largely unknown which gene mediates trichome development in kiwifruit. In this study, we analyzed two kiwifruit species, A. eriantha (Ae) with long, straight, and bushy trichomes and A. latifolia (Al) with short, distorted, and spare trichomes, by second- and third-generation RNA sequencing. Transcriptomic analysis indicated that the expression of the NAP1 gene, a positive regulator of trichome development, was suppressed in Al compared with that in Ae. Additionally, the alternative splicing of AlNAP1 produced two short transcripts (AlNAP1-AS1 and AlNAP1-AS2) lacking multiple exons, in addition to a full-length transcript of AlNAP1-FL. The defects of trichome development (short and distorted trichome) in Arabidopsis nap1 mutant were rescued by AlNAP1-FL but not by AlNAP1-AS1. AlNAP1-FL gene does not affect trichome density in nap1 mutant. The qRT-PCR analysis indicated that the alternative splicing further reduces the level of functional transcripts. These results indicated that the short and distorted trichomes in Al might be caused by the suppression and alternative splicing of AlNAP1. Together, we revealed that AlNAP1 mediates trichome development and is a good candidate target for genetic modification of trichome length in kiwifruit.

Identification of genes for seed isoflavones based on bulk segregant analysis sequencing in soybean natural population

We identified four hub genes for isoflavone biosynthesis based on BSA-seq and WGCNA methods and validated that GmIE3-1 positively contribute to isoflavone accumulation in soybean. Soybean isoflavones are secondary metabolites of great interest owing to their beneficial impact on human health. Herein, we profiled the seed isoflavone content by HPLC in 1551 soybean accessions grown in two locations for two years and constructed two extreme pools with high (4065.1 µg g^-1) and low (1427.23 µg g^-1) isoflavone contents to identify candidate genes involved in isoflavone biosynthesis pathways using bulk segregant analysis sequencing (BSA-seq) approach. The results showed that the average sequencing depths were 50.3× and 65.7× in high and low pools, respectively. A total of 23,626 polymorphic SNPs and 5299 InDels were detected between both pools and 1492 genes with different variations were identified. Based on differential genes in BSA-seq and weighted gene co-expression network analysis (WGCNA), four hub genes, Glyma.06G290400 (designated as GmIE3-1), Glyma.01G239200, Glyma.01G241500, Glyma.13G256100 were identified, encoding E3 ubiquitin-protein ligase, arm repeat protein interacting with ABF2, zinc metallopeptidase EGY3, and dynamin-related protein 3A, respectively. The allelic variation in GmIE3-1 showed a significant influence on isoflavone accumulation. The virus-induced gene silencing (VIGS) and RNAi hairy root transformation of GmIE3-1 revealed partial suppression of this gene could cause a significant decrease (P < 0.0001) of total isoflavone content, suggesting GmIE3-1 is a positive regulator for isoflavones. The present study demonstrated that the BSA-seq approach combined with WGCNA, VIGS and hairy root transformation can efficiently identify isoflavone candidate genes in soybean natural population.

Dark secrets of phytomelatonin

Phytomelatonin is a newly identified plant hormone, and its primary functions in plant growth and development remain relatively poorly appraised. Phytomelatonin is a master regulator of reactive oxygen species (ROS) signaling and acts as a darkness signal in circadian stomatal closure. Plants exhibit at least three interrelated patterns of interaction between phytomelatonin and ROS production. Exogenous melatonin can induce flavonoid biosynthesis, which might be required for maintenance of antioxidant capacity under stress, after harvest, and in leaf senescence conditions. However, several genetic studies have provided direct evidence that phytomelatonin plays a negative role in the biosynthesis of flavonoids under non-stress conditions. Phytomelatonin delays flowering time in both dicot and monocot plants, probably via its receptor PMTR1 and interactions with the gibberellin, strigolactone, and ROS signaling pathways. Furthermore, phytomelatonin signaling also functions in hypocotyl and shoot growth in skotomorphogenesis and ultraviolet B (UV-B) exposure; the G protein α-subunit (Arabidopsis GPA1 and rice RGA1) and constitutive photomorphogenic1 (COP1) are important signal components during this process. Taken together, these findings indicate that phytomelatonin acts as a darkness signal with important regulatory roles in circadian stomatal closure, flavonoid biosynthesis, flowering, and hypocotyl and shoot growth.

Transcription factor CmbHLH16 regulates petal anthocyanin homeostasis under different lights in Chrysanthemum

Light is essential to plant survival and elicits a wide range of plant developmental and physiological responses under different light conditions. A low red-to-far red (R/FR) light ratio induces shade-avoidance responses, including decreased anthocyanin accumulation, whereas a high R/FR light ratio promotes anthocyanin biosynthesis. However, the detailed molecular mechanism underpinning how different R/FR light ratios regulate anthocyanin homeostasis remains elusive, especially in non-model species. Here, we demonstrate that a low R/FR light ratio induced the expression of CmMYB4, which suppressed the anthocyanin activator complex CmMYB6-CmbHLH2, leading to the reduction of anthocyanin accumulation in Chrysanthemum (Chrysanthemum morifolium) petals. Specifically, CmMYB4 recruited the corepressor CmTPL (TOPLESS) to directly bind the CmbHLH2 promoter and suppressed its transcription by impairing histone H3 acetylation. Moreover, the low R/FR light ratio inhibited the PHYTOCHROME INTERACTING FACTOR family transcription factor CmbHLH16, which can competitively bind to CmMYB4 and destabilize the CmMYB4-CmTPL protein complex. Under the high R/FR light ratio, CmbHLH16 was upregulated, which impeded the formation of the CmMYB4-CmTPL complex and released the suppression of CmbHLH2, thus promoting anthocyanin accumulation in Chrysanthemum petals. Our findings reveal a mechanism by which different R/FR light ratios fine-tune anthocyanin homeostasis in flower petals.

A dual-function transcription factor, SlJAF13, promotes anthocyanin biosynthesis in tomato

Unlike modern tomato (Solanum lycopersicum) cultivars, cv. LA1996 harbors the dominant Aft allele, which is associated with anthocyanin synthesis in tomato fruit peel. However, the control of Aft anthocyanin biosynthesis remains unclear. Here, we used ethyl methanesulfonate-induced and CRISPR/Cas9-mediated mutation of LA1996 to show, respectively, that two class IIIf basic helix-loop-helix (bHLH) transcription factors, SlJAF13 and SlAN1, are involved in the control of anthocyanin synthesis. These transcription factors are key components of the MYB-bHLH-WD40 (MBW) complex, which positively regulates anthocyanin synthesis. Molecular and genetic analyses showed that SlJAF13 functions as an upstream activation factor of SlAN1 by binding directly to the G-Box motif of its promoter region. On the other hand, SlJAZ2, a JA signaling repressor, interferes with formation of the MBW complex to suppress anthocyanin synthesis by directly binding these two bHLH components. Unexpectedly, the transcript level of SlJAZ2 was in turn repressed in a SlJAF13-dependent manner. Mechanistically, SlJAF13 interacts with SlMYC2, inhibiting SlMYC2 activation of SlJAZ2 transcription, thus constituting a negative feedback loop governing anthocyanin accumulation. Taken together, our findings support a sophisticated regulatory network, in which SlJAF13 acts as an upstream dual-function regulator that fine tunes anthocyanin biosynthesis in tomato.

A newly characterized allele of ZmR1 increases anthocyanin content in whole maize plant and the regulation mechanism of different ZmR1 alleles

The novel ZmR1^CQ01 allele for maize anthocyanin synthesis was identified, and the biological function and regulatory molecular mechanisms of three ZmR1 alleles were unveiled. Anthocyanins in maize are valuable to human health. The R1 gene family is one of the important regulatory genes for the tissue-specific distribution of anthocyanins. R1 gene allelic variations are abundant and its biological function and regulatory molecular mechanisms are not fully understood. By exploiting genetic mapping and transgenic verification, we found that anthocyanin pigmentation in maize leaf midrib was controlled by ZmR1 on chromosome 10. Allelism test of maize zmr1 EMS mutants confirmed that anthocyanin pigmentation in leaf sheath was also controlled by ZmR1. ZmR1^CQ01 was a novel ZmR1 allelic variation obtained from purple maize. Its overexpression caused the whole maize plant to turn purple. ZmR1^B73 allele confers anthocyanin accumulation in near ground leaf sheath rather than in leaf midribs. The mRNA expression level of ZmR1^B73 was low in leaf midribs, resulting in no anthocyanin accumulation. ZmR1^B73 overexpression promoted anthocyanin accumulation in leaf midribs. Loss of exon 5 resulted in ZmR1^ZN3 allele function destruction and no anthocyanin accumulation in leaf midrib and leaf sheath. DNA affinity purification sequencing revealed 1010 genes targeted by ZmR1^CQ01, including the bz2 in anthocyanin synthesis pathway. RNA-seq analysis showed 55 genes targeted by ZmR1^CQ01 changed the expression level significantly, and the expression of genes encoding key enzymes in flavonoid and phenylpropanoid biosynthesis pathways were significantly up-regulated. ZmR1 functional molecular marker was developed. These results revealed the effects of transcriptional regulation and sequence variation on ZmR1 function and identified the genes targeted by ZmR1^CQ01 at the genome-wide level.

HECT ubiquitin ligases as accessory proteins of the plant proteasome

The proteasome plays vital roles in eukaryotic cells by orchestrating the regulated degradation of large repertoires of substrates involved in numerous biological processes. Proteasome dysfunction is associated with a wide variety of human pathologies and in plants severely affects growth, development and responses to stress. The activity of E3 ubiquitin ligases marks proteins fated for degradation with chains of the post-translational modifier, ubiquitin. Proteasomal processing of ubiquitinated substrates involves ubiquitin chain recognition, deubiquitination, ATP-mediated unfolding and translocation, and proteolytic digestion. This complex series of steps is made possible not only by the many specialised subunits of the 1.5 MDa proteasome complex but also by a range of accessory proteins that are recruited to the proteasome. A surprising class of accessory proteins are members of the HECT-type family of ubiquitin ligases that utilise a unique mechanism for post-translational attachment of ubiquitin to their substrates. So why do proteasomes that already contain all the necessary machinery to recognise ubiquitinated substrates, harbour HECT ligase activity? It is now clear that some ubiquitin ligases physically relay their substrates to proteasome-associated HECT ligases, which prevent substrate stalling at the proteasome. Moreover, HECT ligases ubiquitinate proteasome subunits, thereby modifying the proteasome's ability to recognise substrates. They may therefore enable proteasomes to be both non-specific and extraordinarily selective in a complex substrate environment. Understanding the relationship between the proteasome and accessory HECT ligases will reveal how the proteasome controls so many diverse plant developmental and stress responses.

Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence

The HECT-type UPL3 ligase plays critical roles in plant development and stress protection, but understanding of its regulation remains limited. Here, the multi-omics analyses of ubiquitinated proteins in <i>upl3</i> mutants were performed. A landscape of UPL3-dependent ubiquitinated proteins is constructed: Preferential ubiquitination of proteins related to carbon fixation represented the largest set of proteins with increased ubiquitination in the <i>upl3</i> plant, including most of carbohydrate metabolic enzymes, BRM, and variant histone, whereas a small set of proteins with reduced ubiquitination caused by the <i>upl3</i> mutation were linked to cysteine/methionine synthesis, as well as hexokinase 1 (HXK1) and phosphoenolpyruvate carboxylase 2 (PPC2). Notably, ubiquitin hydrolase 12 (UBP12), BRM, HXK1, and PPC2 were identified as the UPL3-interacting partners in vivo and in vitro. Characterization of <i>brm</i>, <i>upl3</i>, <i>ppc2</i>, <i>gin2</i>, and <i>ubp12</i> mutant plants and proteomic and transcriptomic analysis suggested that UPL3 fine-tunes carbohydrate metabolism, mediating cellular senescence by interacting with UBP12, BRM, HXK1, and PPC2. Our results highlight a regulatory pattern of UPL3 with UBP12 as a hub of regulator on proteolysis-independent regulation and proteolysis-dependent degradation.

Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton

Plant trichomes are specialized epidermal cells that are widely distributed on plant aerial tissues. The initiation and progression of trichomes are controlled in a coordinated sequence of multiple molecular events. During the past decade, major breakthroughs in the molecular understanding of trichome development were achieved through the characterization of various trichomes defective mutants and trichome-associated genes, which revealed a highly complex molecular regulatory network underlying plant trichome development. This review focuses on the recent millstone in plant trichomes research obtained using genetic and molecular studies, as well as 'omics' analyses in model plant Arabidopsis and fiber crop cotton. In particular, we discuss the latest understanding and insights into the underlying molecular mechanisms of trichomes formation at multiple dimensions, including at the chromatin, transcriptional, post-transcriptional, and post-translational levels. We summarize that the integration of multi-dimensional trichome-associated genes will enable us to systematically understand the molecular regulation network that landscapes the development of the plant trichomes. These advances will enable us to address the unresolved questions regarding the molecular crosstalk that coordinate concurrent and ordered the changes in cotton fiber initiation and progression, together with their possible implications for genetic improvement of cotton fiber.

Anthocyanins: From Mechanisms of Regulation in Plants to Health Benefits in Foods

Anthocyanins represent the major red, purple, and blue pigments in many flowers, fruits, vegetables, and cereals. They are also recognized as important health-promoting components in the human diet with protective effects against many chronic diseases, including cardiovascular diseases, obesity, and cancer. Anthocyanin biosynthesis has been studied extensively, and both biosynthetic and key regulatory genes have been isolated in many plant species. Here, we will provide an overview of recent progress in understanding the anthocyanin biosynthetic pathway in plants, focusing on the transcription factors controlling activation or repression of anthocyanin accumulation in cereals and fruits of different plant species, with special emphasis on the differences in molecular mechanisms between monocot and dicot plants. Recently, new insight into the transcriptional regulation of the anthocyanin biosynthesis, including positive and negative feedback control as well as epigenetic and post-translational regulation of MYB-bHLH-WD40 complexes, has been gained. We will consider how knowledge of regulatory mechanisms has helped to produce anthocyanin-enriched foods through conventional breeding and metabolic engineering. Additionally, we will briefly discuss the biological activities of anthocyanins as components of the human diet and recent findings demonstrating the important health benefits of anthocyanin-rich foods against chronic diseases.

A Class II TCP Transcription Factor PaTCP4 from Platanus acerifolia Regulates Trichome Formation in Arabidopsis

London plane tree is widely grown as a landscaping and street tree, but the release of its trichomes creates a serious air-borne pollution problem. Identifying the key genes that regulate the development of trichomes is, therefore, an important tool for the molecular breeding of Platanus acerifolia. In this study, a sequence homologous with the Arabidopsis Class II TCP subfamily was identified from London plane, and named PaTCP4. The expression of PaTCP4 was detected in various organs of London plane trees, significantly in the trichomes. Overexpression of PaTCP4 in Arabidopsis reduced the trichome density on the first pair of true leaves, and atypical 5-branched trichomes were also detected on those leaves. The expression of endogenous AtCPC and AtTCL2 was significantly increased in PaTCP4 transgenic lines, and was associated with a decrease in the expression of endogenous AtGL2. Furthermore, the expression of endogenous AtGL3 was significantly increased. In addition, the protein product of PaTCP4 was shown to directly activate AtCPC, AtTCL2, AtGL3, AtGIS, PaGIS, and PaGL3 in yeast one-hybrid assays and in the dual-luciferase reporter system. Taken together, these results identify a role for PaTCP4 in trichome initiation and branching in Arabidopsis. Thus, PaTCP4 represents a strong candidate gene for regulating the development of trichomes in London plane trees.

A transcriptional hub integrating gibberellin-brassinosteroid signals to promote seed germination in Arabidopsis

Seed germination is regulated by multiple phytohormones, including gibberellins (GAs) and brassinosteroids (BRs); however, the molecular mechanism underlying GA and BR co-induced seed germination is not well elucidated. We demonstrated that BRs induce seed germination through promoting testa and endosperm rupture in Arabidopsis. BRs promote cell elongation, rather than cell division, at the hypocotyl-radicle transition region of the embryonic axis during endosperm rupture. Two key basic helix-loop-helix transcription factors in the BR signaling pathway, HBI1 and BEE2, are involved in the regulation of endosperm rupture. Expression of HBI1 and BEE2 was induced in response to BR and GA treatment. In addition, HBI1- or BEE2-overexpressing Arabidopsis plants are less sensitive to the BR biosynthesis inhibitor, brassinazole, and the GA biosynthesis inhibitor, paclobutrazol. HBI1 and BEE2 promote endosperm rupture and seed germination by directly regulating the GA-Stimulated Arabidopsis 6 (GASA6) gene. Expression of GASA6 was altered in Arabidopsis overexpressing HBI1, BEE2, or SRDX-repressor forms of the two transcription factors. In addition, HBI1 interacts with BEE2 to synergistically activate GASA6 expression. Our findings define a new role for GASA6 in GA and BR signaling and reveal a regulatory module that controls GA and BR co-induced seed germination in Arabidopsis.

Factors that affect protein abundance of a positive regulator of abscisic acid signalling, the basic leucine zipper transcription factor ABRE-binding factor 2 (ABF2)

Most members of basic leucine zipper (bZIP) transcription factor (TF) subgroup A play important roles as positive effectors in abscisic acid (ABA) signaling during germination and/or in vegetative stress responses. In multiple plant species, one member, ABA insensitive 5 (ABI5), is a major TF that promotes seed maturation and blocks early seeding growth in response to ABA. Other members, referred to as either ABRE-binding factors (ABFs), ABRE-binding proteins (AREBs), or D3 protein-binding factors (DPBFs), are implicated as major players in stress responses during vegetative growth. Studies on the proteolytic regulation of ABI5, ABF1, and ABF3 in Arabidopsis thaliana have shown that the proteins have moderate degradation rates and accumulate in the presence of the proteasome inhibitor MG132. Exogenous ABA slows their degradation and the ubiquitin E3 ligase called KEEP ON GOING (KEG) is important for their degradation. However, there are some reported differences in degradation among subgroup A members. The conserved C-terminal sequences (referred to as the C4 region) enhance degradation of ABI5 but stabilize ABF1 and ABF3. To better understand the proteolytic regulation of the ABI5/ABFs and determine whether there are differences between vegetative ABFs and ABI5, we studied the degradation of an additional family member, ABF2, and compared its in vitro degradation to that of ABI5. As previously seen for ABI5, ABF1, and ABF3, epitope-tagged constitutively expressed ABF2 degrades in seedlings treated with cycloheximide and is stabilized following treatment with the proteasome inhibitor MG132. Tagged ABF2 protein accumulates when seedlings are treated with ABA, but its mRNA levels do not increase, suggesting that the protein is stabilized in the presence of ABA. ABF2 is also an in vitro ubiquitination substrate of the E3 ligase KEG and recombinant ABF2 is stable in keg lysates. ABF2 with a C4 deletion degrades more quickly in vitro than full-length ABF2, as previously observed for ABF1 and ABF3, suggesting that the conserved C4 region contributes to its stability. In contrast to ABF2 and consistent with previously published work, ABI5 with C terminal deletions including an analogous C4 deletion is stabilized in vitro compared to full length ABI5. In vivo expression of an ABF1 C4 deletion protein appears to have reduced activity compared to equivalent levels of full length ABF1. Additional group A family members show similar proteolytic regulation by MG132 and ABA. Altogether, these results together with other work on ABI5 regulation suggest that the vegetative ABFs share proteolytic regulatory mechanisms that are not completely shared with ABI5.

The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice

Panicle size and grain number are important agronomic traits and influence grain yield in rice (Oryza sativa), but the molecular and genetic mechanisms underlying panicle size and grain number control remain largely unknown in crops. Here we report that LARGE2 encodes a HECT-domain E3 ubiquitin ligase OsUPL2 and regulates panicle size and grain number in rice. The loss of function large2 mutants produce large panicles with increased grain number, wide grains and leaves, and thick culms. LARGE2 regulates panicle size and grain number by repressing meristematic activity. LARGE2 is highly expressed in young panicles and grains. Biochemical analyses show that LARGE2 physically associates with ABERRANT PANICLE ORGANIZATION1 (APO1) and APO2, two positive regulators of panicle size and grain number, and modulates their stabilities. Genetic analyses support that LARGE2 functions with APO1 and APO2 in a common pathway to regulate panicle size and grain number. These findings reveal a novel genetic and molecular mechanism of the LARGE2-APO1/APO2 module-mediated control of panicle size and grain number in rice, suggesting that this module is a promising target for improving panicle size and grain number in crops.

A hydrophobic residue stabilizes dimers of regulatory ACT-like domains in plant basic helix-loop-helix transcription factors

About a third of the plant basic helix–loop–helix (bHLH) transcription factors harbor a C-terminal aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain, which was originally identified in the maize R regulator of anthocyanin biosynthesis, where it modulates the ability of the bHLH to dimerize and bind DNA. Characterization of other bHLH ACT-like domains, such as the one in the Arabidopsis R ortholog, GL3, has not definitively confirmed dimerization, raising the question of the overall role of this potential regulatory domain. To learn more, we compared the dimerization of the ACT-like domains of R (R^ACT) and GL3 (GL3^ACT). We show that R^ACT dimerizes with a dissociation constant around 100 nM, over an order of magnitude stronger than GL3^ACT. Structural predictions combined with mutational analyses demonstrated that V568, located in a hydrophobic pocket in R^ACT, is important: when mutated to the Ser residue present in GL3^ACT, dimerization affinity dropped by almost an order of magnitude. The converse S595V mutation in GL3^ACT significantly increased the dimerization strength. We cloned and assayed dimerization for all identified maize ACT-like domains and determined that 12 of 42 formed heterodimers in yeast two-hybrid assays, irrespective of whether they harbored V568, which was often replaced by other aliphatic amino acids. Moreover, we determined that the presence of polar residues at that position occurs only in a small subset of anthocyanin regulators. The combined results provide new insights into possibly regulatory mechanisms and suggest that many of the other plant ACT-like domains associate to modulate fundamental cellular processes.

Protein phosphatase NtPP2C2b and MAP kinase NtMPK4 act in concert to modulate nicotine biosynthesis

Protein phosphatases (PPs) and protein kinases (PKs) regulate numerous developmental, defense, and phytohormone signaling processes in plants. However, the underlying regulatory mechanism governing biosynthesis of specialized metabolites, such as alkaloids, by the combined effects of PPs and PKs, is insufficiently understood. Here, we report the characterization of a group B protein phosphatase type 2C, NtPP2C2b, that likely acts upstream of the NICOTINE2 locus APETALA 2/Ethylene Response Factors (AP2/ERFs), to regulate nicotine biosynthesis in tobacco. Similar to the nicotine pathway genes, NtPP2C2b is highly expressed in roots and induced by jasmonic acid (JA). Overexpression of NtPP2C2b in transgenic hairy roots or stable transgenic tobacco plants repressed nicotine pathway gene expression and reduced nicotine accumulation. Additionally, transient overexpression of NtPP2C2b, together with the NtERF221, repressed transactivation of the quinolinate phosphoribosyltransferase promoter in tobacco cells. We further demonstrate that the JA-responsive tobacco mitogen-activated protein kinase (MAPK) 4 interacts with NtPP2C2b in yeast and plant cells. Conditional overexpression of NtMPK4 in tobacco hairy roots up-regulated nicotine pathway gene expression and increased nicotine accumulation. Our findings suggest that a previously uncharacterized PP-PK module acts to modulate alkaloid biosynthesis, highlighting the importance of post-translational control in the biosynthesis of specialized plant metabolites.

Genome-wide identification and evolution of HECT genes in wheat

Background

As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops.

Methods

Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana.

Results

The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

Genetic determinism of prickles in rose

KEY MESSAGE

The genetic determinism of prickle in rose is complex, with a major locus on LG3 that controls the absence/presence of prickles on the rose stem. Rose is one of the major ornamental plants. The selection of glabrous cultivars is an important breeding target but remains a difficult task due to our limited genetic knowledge. Our objective was to understand the genetic and molecular determinism of prickles. Using a segregating diploid rose F1 population, we detected two types of prickles (glandular and non-glandular) in the progeny. We scored the number of non-glandular prickles on the floral and main stems for three years. We performed QTL analysis and detected four prickle loci on LG1, 3, 4 and 6. We determined the credible interval on the reference genome. The QTL on LG3 is a major locus that controls the presence of prickles, and three QTLs (LG3, 4 and 1) may be responsible for prickle density. We further revealed that glabrous hybrids are caused by the combination of the two recessive alleles from both parents. In order to test whether rose prickles could originate from a 'trichome-like structure,' we used a candidate approach to characterize rose gene homologues known in Arabidopsis, involved in trichome initiation. Four of these homologues were located within the overlapping credible interval of the detected QTLs. Transcript accumulation analysis weakly supports the involvement of trichome homologous genes, in the molecular control of prickle initiation. Our studies provide strong evidence for a complex genetic determinism of stem prickle and could help to establish guidelines for glabrous rose breeding. New insights into the relationship between prickles and trichomes constitute valuable information for reverse genetic research on prickles.

Transcriptome analysis of near-isogenic lines for glume hairiness of wheat

Hairiness, which is a phenotypic trait common among land plants, primarily affects the stem, leaf, and floral organs. Plant hairiness is associated with complex functions. For example, glume hairiness in wheat is related to the resistance to biotic and abiotic stresses, and may also influence human health. In the present study, two pairs of near-isogenic lines (NILs) for glume hairiness, which were derived from a cross between a Tibetan semi-wild wheat accession (Triticum aestivum ssp. tibetanum Q1028) and a common wheat cultivar (T. aestivum 'Zhengmai 9023'), underwent a glume transcriptome analysis. We detected 27,935 novel genes, of which 18,027 were annotated. Additionally, 488 and 600 differentially expressed genes (DEGs) were detected in NIL1 and NIL2, respectively, with 37 DEGs detected in both NIL pairs. Moreover, 987 and 1584 single nucleotide polymorphisms (SNPs) were detected in NIL1 and NIL2, respectively, with 39 SNPs detected in both NIL pairs, of which most were located in the Hairy glume (Hg) gene region on chromosome arm 1AS. The annotation of the DEGs with gene ontology terms revealed that genes associated with hairiness in Arabidopsis and rice were similarly enriched. The possible functions of these genes related to glume hairiness were examined. The study results provide useful information for identifying candidate genes and the fine-mapping of Hg in the wheat genome.

The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host

Plant-parasitic nematodes secrete effectors that manipulate plant cell morphology and physiology to achieve host invasion and establish permanent feeding sites. Effectors from the highly expanded SPRYSEC (SPRY domain with a signal peptide for secretion) family in potato cyst nematodes have been implicated in activation and suppression of plant immunity, but the mechanisms underlying these activities remain largely unexplored. To study the host mechanisms used by SPRYSEC effectors, we identified plant targets of GpRbp-1 from the potato cyst nematode Globodera pallida. Here, we show that GpRbp-1 interacts in yeast and in planta with a functional potato homologue of the Homology to E6-AP C-Terminus (HECT)-type ubiquitin E3 ligase UPL3, which is located in the nucleus. Potato lines lacking StUPL3 are not available, but the Arabidopsis mutant upl3-5 displaying a reduced UPL3 expression showed a consistently small but not significant decrease in susceptibility to cyst nematodes. We observed a major impact on the root transcriptome by the lower levels of AtUPL3 in the upl3-5 mutant, but surprisingly only in association with infections by cyst nematodes. To our knowledge, this is the first example that a HECT-type ubiquitin E3 ligase is targeted by a pathogen effector and that a member of this class of proteins specifically regulates gene expression under biotic stress conditions. Together, our data suggest that GpRbp-1 targets a specific component of the plant ubiquitination machinery to manipulate the stress response in host cells.

New Aspects of HECT-E3 Ligases in Cell Senescence and Cell Death of Plants

Plant cells undergo massive orderly changes in structure, biochemistry, and gene expression during cell senescence. These changes cannot be distinguished from the hydrolysis/degradation function controlled by the ubiquitination pathway, autophagy, and various hydrolases in cells. In this mini-review, we summarized current research progress that the human HECT (homologous to the E6AP carboxyl terminus)-type ubiquitin E3 ligases have non-redundant functions in regulating specific signaling pathways, involved in a number of human diseases, especially aging-related diseases, through the influence of DNA repair, protein stability, and removal efficiency of damaged proteins or organelles. We further compared HECT E3 ligases’ structure and functions between plant and mammalian cells, and speculated new aspects acting as degrading signals and regulating signals of HECT E3 ligase in cell senescence and the cell death of plants.

Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus

Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.

Chalcone synthase is ubiquitinated and degraded via interactions with a RING-H2 protein in petals of Paeonia 'He Xie'

Flavonoids are secondary metabolites widely distributed among angiosperms, where they play diverse roles in plant growth, development, and evolution. The regulation of flavonoid biosynthesis in plants has been extensively studied at the transcriptional level, but post-transcriptional, translational, and post-translational control of flavonoid biosynthesis remain poorly understood. In this study, we analysed post-translational regulation of flavonoid biosynthesis in the ornamental plant Paeonia, using proteome and ubiquitylome profiling, in conjunction with transcriptome data. Three enzymes involved in flavonoid biosynthesis were identified as being putative targets of ubiquitin-mediated degradation. Among these, chalcone synthase (PhCHS) was shown to have the greatest number of ubiquitination sites. We examined PhCHS abundance in petals using PhCHS-specific antibody and found that its accumulation decreased at later developmental stages, resulting from 26S proteasome-mediated degradation. We further identified a ring domain-containing protein (PhRING-H2) that physically interacts with PhCHS and demonstrated that PhRING-H2 is required for PhCHS ubiquitination. Taken together, our results suggest that PhRING-H2-mediates PhCHS ubiquitination and degradation is an important mechanism of post-translational regulation of flavonoid biosynthesis in Paeonia, providing a theoretical basis for the manipulation of flavonoid biosynthesis in plants.

Updates on molecular mechanisms in the development of branched trichome in Arabidopsis and nonbranched in cotton

Trichomes are specialized epidermal cells and a vital plant organ that protect plants from various harms and provide valuable resources for plant development and use. Some key genes related to trichomes have been identified in the model plant Arabidopsis thaliana through glabrous mutants and gene cloning, and the hub MYB-bHLH-WD40, consisting of several factors including GLABRA1 (GL1), GL3, TRANSPARENT TESTA GLABRA1 (TTG1), and ENHANCER OF GLABRA3 (EGL3), has been established. Subsequently, some upstream transcription factors, phytohormones and epigenetic modification factors have also been studied in depth. In cotton, a very important fibre and oil crop globally, in addition to the key MYB-like factors, more important regulators and potential molecular mechanisms (e.g. epigenetic modifiers, distinct metabolic pathways) are being exploited during different fibre developmental stages. This occurs due to increased cotton research, resulting in the discovery of more complex regulation mechanisms from the allotetraploid genome of cotton. In addition, some conservative as well as specific mediators are involved in trichome development in other species. This study summarizes molecular mechanisms in trichome development and provides a detailed comparison of the similarities and differences between Arabidopsis and cotton, analyses the possible reasons for the discrepancy in identification of regulators, and raises future questions and foci for understanding trichome development in more detail.

The Dynamic Genetic-Hormonal Regulatory Network Controlling the Trichome Development in Leaves

Plant trichomes are outgrowths developed from an epidermal pavement cells of leaves and other organs. Trichomes (also called 'hairs') play well-recognized roles in defense against insect herbivores, forming a physical barrier that obstructs insect movement and mediating chemical defenses. In addition, trichomes can act as a mechanosensory switch, transducing mechanical stimuli (e.g., insect movement) into physiological signals, helping the plant to respond to insect attacks. Hairs can also modulate plant responses to abiotic stresses, such as water loss, an excess of light and temperature, and reflect light to protect plants against UV radiation. The structure of trichomes is species-specific and this trait is generally related to their function. These outgrowths are easily analyzed and their origin represents an outstanding subject to study epidermal cell fate and patterning in plant organs. In leaves, the developmental control of the trichomatous complement has highlighted a regulatory network based on four fundamental elements: (i) genes that activate and/or modify the normal cell cycle of epidermal pavement cells (i.e., endoreduplication cycles); (ii) transcription factors that create an activator/repressor complex with a central role in determining cell fate, initiation, and differentiation of an epidermal cell in trichomes; (iii) evidence that underlines the interplay of the aforesaid complex with different classes of phytohormones; (iv) epigenetic mechanisms involved in trichome development. Here, we reviewed the role of genes in the development of trichomes, as well as the interaction between genes and hormones. Furthermore, we reported basic studies about the regulation of the cell cycle and the complexity of trichomes. Finally, this review focused on the epigenetic factors involved in the initiation and development of hairs, mainly on leaves.

Regulation of anthocyanin accumulation via MYB75/HAT1/TPL-mediated transcriptional repression

Anthocyanin is part of secondary metabolites, which is induced by environmental stimuli and developmental signals, such as high light and sucrose. Anthocyanin accumulation is activated by the MYB-bHLH-WD40 (MBW) protein complex in plants. But the evidence of how plants maintain anthocyanin in response to signals is lacking. Here we perform molecular and genetic evidence to display that HAT1 plays a new breaker of anthocyanin accumulation via post-translational regulations of MBW protein complex. Loss of function of HAT1 in the Arabidopsis seedlings exhibits increased anthocyanin accumulation, whereas overexpression of HAT1 significantly repressed anthocyanin accumulation. We found that HAT1 interacted with MYB75 and thereby interfered with MBW protein complex. Overexpression of HAT1 suppresses abundant anthocyanin phenotype of pap1-D plant. HAT1 is characterized as a transcriptional repressor possessing an N-terminal EAR motif, which determines to interact with TOPLESS corepressor. Repression activity of HAT1 in regulation of gene expression and anthocyanin accumulation can be abolished by deletion or mutation of the EAR motif 1. Chromatin immunoprecipitation assays revealed that MYB75 formed a transcriptional repressor complex with HAT1-TPL by histone H3 deacetylation in target genes. We proposed that HAT1 restrained anthocyanin accumulation by inhibiting the activities of MBW protein complex through blocking the formation of MBW protein complex and recruiting the TPL corepressor to epigenetically modulate the anthocyanin late biosynthetic genes (LBGs).

Anthocyanins, a class of flavonoids distributed ubiquitously in the plant kingdom, are induced by environmental stimuli and developmental signals, such as high light and sucrose. It is well established that anthocyanin accumulation is regulated by the MYB-bHLH-WD40 (MBW) protein complex in plants. But little is known about the regulation of MBW protein complex by other factors. Here, we show that an HD-ZIP II transcription factor HAT1 negatively regulates anthocyanin accumulation via post-translational regulation of MBW protein complex. Loss of function of HAT1 in the Arabidopsis seedlings exhibits increased anthocyanin accumulation, whereas overexpression of HAT1 significantly repressed anthocyanin accumulation. We reveal that HAT1 interacted with MYB75 and thereby sequestered MBW protein complex. Overexpression of HAT1 in pap1-D mutant suppresses abundant anthocyanin phenotype of the pap1-D mutant. HAT1 identified was as a transcriptional repressor possessing an N-terminal EAR motif, which determines the interaction with TOPLESS corepressor. The deletion or mutation of the EAR motif 1 of HAT1 partially eliminates the repression activity of HAT1 in regulation of gene expression and anthocyanin accumulation. Our results illustrate a new repressor HAT1 which helps plants fine-tune anthocyanin accumulation.

VvWRKY8 represses stilbene synthase genes through direct interaction with VvMYB14 to control resveratrol biosynthesis in grapevine

Resveratrol (Res) is a stilbenoid, a group of plant phenolic metabolites derived from stilbene that possess activities against pests, pathogens, and abiotic stresses. Only a few species, including grapevine (Vitis), synthesize and accumulate Res. Although stilbene synthases (STSs) have been isolated and characterized in several species, the gene regulatory mechanisms underlying stilbene biosynthesis are still largely unknown. Here, we characterize a grapevine WRKY transcription factor, VvWRKY8, that regulates the Res biosynthetic pathway. Transient and stable overexpression of VvWRKY8 in grapevine results in decreased expression of VvSTS15/21 and VvMYB14, as well as in a reduction of Res accumulation. VvWRKY8 does not bind to or activate the promoters of VvMYB14 and VvSTS15/21; however, it physically interacts with VvMYB14 proteins through their N-terminal domains to prevent them from binding to the VvSTS15/21 promoter. Application of exogenous Res results in the stimulation of VvWRKY8 expression and in a decrease of VvMYB14 and VvSTS15/21 expression in grapevine suspension cells, and in the activation of the VvWRKY8 promoter in tobacco leaves. These results demonstrate that VvWRKY8 represses VvSTS15/21 expression and Res biosynthesis through interaction with VvMYB14. In this context, the VvMYB14-VvSTS15/21-Res-VvWRKY8 regulatory loop may be an important mechanism for the fine-tuning of Res biosynthesis in grapevine.

Proteasome-associated HECT-type ubiquitin ligase activity is required for plant immunity

Regulated degradation of proteins by the 26S proteasome plays important roles in maintenance and signalling in eukaryotic cells. Proteins are marked for degradation by the action of E3 ligases that site-specifically modify their substrates by adding chains of ubiquitin. Innate immune signalling in plants is deeply reliant on the ubiquitin-26S proteasome system. While progress has been made in understanding substrate ubiquitination during plant immunity, how these substrates are processed upon arrival at the proteasome remains unclear. Here we show that specific members of the HECT domain-containing family of ubiquitin protein ligases (UPL) play important roles in proteasomal substrate processing during plant immunity. Mutations in UPL1, UPL3 and UPL5 significantly diminished immune responses activated by the immune hormone salicylic acid (SA). In depth analyses of upl3 mutants indicated that these plants were impaired in reprogramming of nearly the entire SA-induced transcriptome and failed to establish immunity against a hemi-biotrophic pathogen. UPL3 was found to physically interact with the regulatory particle of the proteasome and with other ubiquitin-26S proteasome pathway components. In agreement, we demonstrate that UPL3 enabled proteasomes to form polyubiquitin chains, thereby regulating total cellular polyubiquitination levels. Taken together, our findings suggest that proteasome-associated ubiquitin ligase activity of UPL3 promotes proteasomal processivity and is indispensable for development of plant immunity.

NbGIS regulates glandular trichome initiation through GA signaling in tobacco

KEY MESSAGE

A novel gene NbGIS positively regulates glandular trichome initiation through GA Signaling in tobacco. NbMYB123-like regulates glandular trichome initiation by acting downstream of NbGIS in tobacco. Glandular trichome is a specialized multicellular structure which has capability to synthesize and secrete secondary metabolites and protects plants from biotic and abiotic stresses. Our previous results revealed that a C2H2 zinc-finger transcription factor GIS and its sub-family genes act upstream of GL3/EGL3-GL1-TTG1 transcriptional activator complex to regulate trichome initiation in Arabidopsis. In this present study, we found that NbGIS could positively regulate glandular trichome development in Nicotiana benthamiana (tobacco). Our result demonstrated that 35S:NbGIS lines exhibited much higher densities of trichome on leaves, main stems, lateral branches and sepals than WT plants, while NbGIS:RNAi lines had the opposite phenotypes. Furthermore, our results also showed that NbGIS was required in response to GA signal to control glandular trichome initiation in Nicotiana benthamiana. In addition, our results also showed that NbGIS significantly influenced GA accumulation and expressions of marker genes of the GA biosynthesis, might result in the changes of growth and maturation in tobacco. Lastly, our results also showed that NbMYB123-like regulated glandular trichome initiation in tobacco by acting downstream of NbGIS. These findings provide new insights to discover the molecular mechanism by which C2H2 transcriptional factors regulates glandular trichome initiation through GA signaling pathway in tobacco.

Cross-family transcription factor interaction between MYC2 and GBFs modulates terpenoid indole alkaloid biosynthesis

Biosynthesis of medicinally valuable terpenoid indole alkaloids (TIAs) in Catharanthus roseus is regulated by transcriptional activators such as the basic helix-loop-helix factor CrMYC2. However, the transactivation effects are often buffered by repressors, such as the bZIP factors CrGBF1 and CrGBF2, possibly to fine-tune the accumulation of cytotoxic TIAs. Questions remain as to whether and how these factors interact to modulate TIA production. We demonstrated that overexpression of CrMYC2 induces CrGBF expression and results in reduced alkaloid accumulation in C. roseus hairy roots. We found that CrGBF1 and CrGBF2 form homo- and heterodimers to repress the transcriptional activities of key TIA pathway gene promoters. We showed that CrGBFs dimerize with CrMYC2, and CrGBF1 binds to the same cis-elements (T/G-box) as CrMYC2 in the target gene promoters. Our findings suggest that CrGBFs antagonize CrMYC2 transactivation possibly by competitive binding to the T/G-box in the target promoters and/or protein-protein interaction that forms a non-DNA binding complex that prevents CrMYC2 from binding to its target promoters. Homo- and heterodimer formation allows fine-tuning of the amplitude of TIA gene expression. Our findings reveal a previously undescribed regulatory mechanism that governs the TIA pathway genes to balance metabolic flux for TIA production in C. roseus.

Isolation and characterization of a salt stress-responsive betaine aldehyde dehydrogenase in Lycium ruthenicum Murr

As compatible solute, glycine betaine (GB) plays a significant role in salinity tolerance in GB accumulating plants. Solanaceous crops such as tomato (Solanum lycopersicum) and tobacco (Nicotiana tabacum) are salt sensitive and naturally GB non-accumulators. In Solanaceae, only the Lycium genus has been recorded as halophytes in China, and several Lycium species have been reported as GB accumulators. The last biosynthetic step of GB is catalyzed by aminoaldehyde dehydrogenase (AMADH) with betaine aldehyde dehydrogenase (BADH) activities. Failure of GB synthesis in tomato and tobacco was attributed to lack of BADH activity. Here, by comparing the BADH functional residues of AMADHs between the Lycium genus and solanaceous crops, we predict that all studied AMADH1s have low BADH activities while only LbAMADH2 from L. barbarum has high BADH activity. For two AMADHs in L. ruthenicum, results from substrate enzyme assays confirmed low BADH activity of LrAMADH1 and no BADH activity of LrAMADH2. Despite the very low GB contents in L. ruthenicum seedlings (< 0.5 μmol g^-1 fresh weight), GB contents in fruits are up to 150 μmol g^-1 FW, inferring fruits of L. ruthenicum as good GB sources. In NaCl treated seedlings, accompanied by elevated GB accumulation, expression of LrAMADH1 was up-regulated, indicating response of LrAMADH1 to salt stress in L. ruthenicum. Virus-induced silence of LrAMADH1 leads to less GB accumulation than control, revealing that LrAMADH1 participates in GB synthesis in planta. Collectively, our results show that LrAMADH1 is the bona fide BADH, which responds to salt stress in L. ruthenicum.

A network of jasmonate-responsive bHLH factors modulate monoterpenoid indole alkaloid biosynthesis in Catharanthus roseus

The pharmaceutically valuable monoterpene indole alkaloids (MIAs) in Catharanthus roseus are derived from the indole and iridoid pathways that respond to jasmonate (JA) signaling. Two classes of JA-responsive bHLH transcription factor (TF), CrMYC2 and BIS1/BIS2, are known to regulate the indole and iridoid pathways, respectively. However, upregulation of either one of the TF genes does not lead to increased MIA accumulation. Moreover, little is known about the interconnection between the CrMYC2 and BIS transcriptional cascades and the hierarchical position of BIS1/BIS2 in JA signaling. Here, we report that a newly identified bHLH factor, Repressor of MYC2 Targets 1 (RMT1), is activated by CrMYC2 and BIS1, and acts as a repressor of the CrMYC2 targets. In addition, we isolated and functionally characterized the core C. roseus JA signaling components, including CORONATINE INSENSITIVE 1 (COI1) and JASMONATE ZIM domain (JAZ) proteins. CrMYC2 and BIS1 are repressed by the JAZ proteins in the absence of JA, but de-repressed by the SCF^COI1 complex on perception of JA. Our findings suggest that the repressors, JAZs and RMT1, mediate crosstalk between the CrMYC2 and BIS regulatory cascades to balance the metabolic flux in MIA biosynthesis.

Degradation of the stress-responsive enzyme formate dehydrogenase by the RING-type E3 ligase Keep on Going and the ubiquitin 26S proteasome system

KEG is involved in mediating the proteasome-dependent degradation of FDH, a stress-responsive enzyme. The UPS may function to suppress FDH mediated stress responses under favorable growth conditions. Formate dehydrogenase (FDH) has been studied in bacteria and yeasts for the purpose of industrial application of NADH co-factor regeneration. In plants, FDH is regarded as a universal stress protein involved in responses to various abiotic and biotic stresses. Here we show that FDH abundance is regulated by the ubiquitin proteasome system (UPS). FDH is ubiquitinated in planta and degraded by the 26S proteasome. Interaction assays identified FDH as a potential substrate for the RING-type ubiquitin ligase Keep on Going (KEG). KEG is capable of attaching ubiquitin to FDH in in vitro assays and the turnover of FDH was increased when co-expressed with a functional KEG in planta, suggesting that KEG contributes to FDH degradation. Consistent with a role in regulating FDH abundance, transgenic plants overexpressing KEG were more sensitive to the inhibitory effects of formate. In addition, FDH is a phosphoprotein and dephosphorylation was found to increase the stability of FDH in degradation assays. Based on results from this and previous studies, we propose a model where KEG mediates the ubiquitination and subsequent degradation of phosphorylated FDH and, in response to unfavourable growth conditions, reduction in FDH phosphorylation levels may prohibit turnover allowing the stabilized FDH to facilitate stress responses.

The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana

Trichomes are the first cell type to be differentiated during the morphogenesis of leaf epidermis and serve as an ideal model to study cellular differentiation. Many genes involved in the patterning and differentiation of trichome cells have been studied over the past decades, and the majority of these genes encode transcription factors that specifically regulate epidermal cell development. However, the upstream regulators of these genes that link early leaf morphogenesis with cell type differentiation are less studied. The TCP proteins are the plant-specific transcription factors involved in regulating diverse aspects of plant development including lateral organ morphogenesis by modulating cell proliferation and differentiation. Here, we show that the miR319-regulated class II TCP proteins, notably TCP4, suppress trichome branching in Arabidopsis leaves and inflorescence stem by direct transcriptional activation of GLABROUS INFLORESCENCE STEMS (GIS), a known negative regulator of trichome branching. The trichome branch number is increased in plants with reduced TCP activity and decreased in the gain-of-function lines of TCP4. Biochemical analyses show that TCP4 binds to the upstream regulatory region of GIS and activates its expression. Detailed genetic analyses show that GIS and TCP4 work in same pathway and GIS function is required for TCP4-mediated regulation of trichome differentiation. Taken together, these results identify a role for the class II TCP genes in trichome differentiation, thus providing a connection between organ morphogenesis and cellular differentiation.

TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis

The flavonoid composition of various tissues throughout plant development is of biological relevance and particular interest for breeding. Arabidopsis thaliana TRANSPARENT TESTA GLABRA 1 (AtTTG1) is an essential regulator of late structural genes in flavonoid biosynthesis. Here, we provide a review of the regulation of the pathway's core enzymes through AtTTG1-containing R2R3-MYELOBLASTOSIS-basic HELIX-LOOP-HELIX-WD40 repeat (MBW(AtTTG1)) complexes embedded in an evolutionary context. We present a comprehensive collection of A. thalianattg1 mutants and AtTTG1 orthologs. A plethora of MBW(AtTTG1) mechanisms in regulating the five major TTG1-dependent traits is highlighted.

An ubiquitin-like protein SDE2 negatively affects sucrose-induced anthocyanin biosynthesis in Arabidopsis

Anthocyanin biosynthesis is regulated by a conserved transcriptional MBW complex composed of MYB, bHLH and WD40 subunits. However, molecular mechanisms underlying transcriptional regulation of these MBW subunits remain largely elusive. In this study, we isolated an Arabidopsis mutant that displays a constitutive red color in aboveground tissues with retarded growth phenotypes. In the presence of sucrose, the mutant accumulates more than 3-fold anthocyanins of the wild type (WT), but cannot produce anthocyanins as WT in the absence of sucrose. Map-based cloning results demonstrated that the mutation occurs in the locus At4G01000, which encodes a conserved nuclear-localized ubiquitin-like (UBL) superfamily protein, silencing defective 2 (SDE2), in eukaryotes. SDE2 is ubiquitously expressed in various tissues. In the sucrose-induced anthocyanin biosynthesis, SDE2 expression was not responded to sucrose treatment at the early stage but was enhanced at the late stage. SDE2 mutations result in up-regulation of anthocyanin biosynthetic and regulatory genes. Yeast-two hybrid analysis indicated that SDE2 has no direct interaction with the MYB transcription factor PAP1 and bHLH factor TT8, indicating that SDE2 is a indirect factor to affect anthocyanin accumulation. Taking together, our data suggest that SDE2 may play a role in finely coordinating anthocyanin biosynthesis with other biological processes.

Similarities between plant traits based on their connection to underlying gene functions

Understanding of phenotypes and their genetic basis is a major focus in current plant biology. Large amounts of phenotype data are being generated, both for macroscopic phenotypes such as size or yield, and for molecular phenotypes such as expression levels and metabolite levels. More insight in the underlying genetic and molecular mechanisms that influence phenotypes will enable a better understanding of how various phenotypes are related to each other. This will be a major step forward in understanding plant biology, with immediate value for plant breeding and academic plant research. Currently the genetic basis of most phenotypes remains however to be discovered, and the relatedness of different traits is unclear. We here present a novel approach to connect phenotypes to underlying biological processes and molecular functions. These connections define similarities between different types of phenotypes. The approach starts by using Quantitative Trait Locus (QTL) data, which are abundantly available for many phenotypes of interest. Overrepresentation analysis of gene functions based on Gene Ontology term enrichment across multiple QTL regions for a given phenotype, be it macroscopic or molecular, results in a small set of biological processes and molecular functions for each phenotype. Subsequently, similarity between different phenotypes can be defined in terms of these gene functions. Using publicly available rice data as example, a close relationship with defined molecular phenotypes is demonstrated for many macroscopic phenotypes. This includes for example a link between 'leaf senescence' and 'aspartic acid', as well as between 'days to maturity' and 'choline'. Relationships between macroscopic and molecular phenotypes may result in more efficient marker-assisted breeding and are likely to direct future research aimed at a better understanding of plant phenotypes.

A differentially regulated AP2/ERF transcription factor gene cluster acts downstream of a MAP kinase cascade to modulate terpenoid indole alkaloid biosynthesis in Catharanthus roseus

Catharanthus roseus produces bioactive terpenoid indole alkaloids (TIAs), including the chemotherapeutics, vincristine and vinblastine. Transcriptional regulation of TIA biosynthesis is not fully understood. The jasmonic acid (JA)-responsive AP2/ERF transcription factor (TF), ORCA3, and its regulator, CrMYC2, play key roles in TIA biosynthesis. ORCA3 forms a physical cluster with two uncharacterized AP2/ERFs, ORCA4 and 5. Here, we report that (1) the ORCA gene cluster is differentially regulated; (2) ORCA4, while overlapping functionally with ORCA3, modulates an additional set of TIA genes. Unlike ORCA3, ORCA4 overexpression resulted in dramatic increase of TIA accumulation in C. roseus hairy roots. In addition, CrMYC2 is capable of activating ORCA3 and co-regulating TIA pathway genes concomitantly with ORCA3. The ORCA gene cluster and CrMYC2 act downstream of a MAP kinase cascade that includes a previously uncharacterized MAP kinase kinase, CrMAPKK1. Overexpression of CrMAPKK1 in C. roseus hairy roots upregulated TIA pathways genes and increased TIA accumulation. This work provides detailed characterization of a TF gene cluster and advances our understanding of the transcriptional and post-translational regulatory mechanisms that govern TIA biosynthesis in C. roseus.

Whole Plant Temperature Manipulation Affects Flavonoid Metabolism and the Transcriptome of Grapevine Berries

Among environmental factors, temperature is the one that poses serious threats to viticulture in the present and future scenarios of global climate change. In this work, we evaluated the effects on berry ripening of two thermal regimes, imposed from veraison to harvest. Potted vines were grown in two air-conditioned greenhouses with High Temperature (HT) and Low Temperature (LT) regimes characterized by 26 and 21°C as average and 42 and 35°C as maximum air daily temperature, respectively. We conducted analyses of the main berry compositional parameters, berry skin flavonoids and berry skin transcriptome on HT and LT berries sampled during ripening. The two thermal conditions strongly differentiated the berries. HT regime increased sugar accumulation at the beginning of ripening, but not at harvest, when HT treatment contributed to a slight total acidity reduction and pH increase. Conversely, growing temperatures greatly impacted on anthocyanin and flavonol concentrations, which resulted as strongly reduced, while no effects were found on skin tannins accumulation. Berry transcriptome was analyzed with several approaches in order to identify genes with different expression profile in berries ripened under HT or LT conditions. The analysis of whole transcriptome showed that the main differences emerging from this approach appeared to be more due to a shift in the ripening process, rather than to a strong rearrangement at transcriptional level, revealing that the LT temperature regime could delay berry ripening, at least in the early stages. Moreover, the results of the in-depth screening of genes differentially expressed in HT and LT did not highlight differences in the expression of transcripts involved in the biosynthesis of flavonoids (with the exception of PAL and STS) despite the enzymatic activities of PALs and UFGT being significantly higher in LT than HT. This suggests only a partial correlation between molecular and biochemical data in our conditions and the putative existence of post-transcriptional and post-translational mechanisms playing significant roles in the regulation of flavonoid metabolic pathways and in particular of anthocyanins.

Regulation of the WD-repeat/bHLH/MYB complex by gibberellin and jasmonate

The phytohormones gibberellin (GA) and jasmonate (JA) regulate various aspects of plant development, growth and defense. Previous studies showed that both DELLA repressors in GA pathway and JA-ZIM domain (JAZ) proteins in JA pathway interact with and repress the WD-repeat/bHLH/MYB transcriptional complex to inhibit trichome initiation, and GA and JA respectively induce DELLAs and JAZs degradation to synergistically enhance trichome formation. In this study, we showed that the DELLA protein RGA and JAZ1 competitively bind to ENHANCER OF GLABRA3 (EGL3), a bHLH component of the WD-repeat/bHLH/MYB complex. GA and JA differently affect the expression and protein stability of the components of the WD-repeat/bHLH/MYB complex, and EGL3 and GL3 repress the expression of JAZ genes as a feedback. The novel findings help to understand the mechanism of the WD-repeat/bHLH/MYB complex in GA/JA-regulated trichome formation.