A basic/helix-loop-helix transcription factor controls leaf shape by regulating auxin signaling in apple

Enrichment of two important metabolites D-galacturonic acid and D-glucuronic acid inhibits MdHb1-mediated fruit softening in apple

In apples, fruit firmness is a crucial quality trait influencing fruit storability, transportability, shelf life and consumer preference. However, the genetic network underlying this trait remains unclear. Therefore, the present study investigated the changes in apple fruit at different stages of postharvest storage using a combination of transcriptomic and metabolomic analyses. With prolonged storage, we detected a significant increase in two metabolites, D-galacturonic acid (D-GalUA) and D-glucuronic acid (D-GlcA), which are associated with a key class 1 non-symbiotic haemoglobin (MdHb1). We innovatively found that MdHb1 regulates fruit softening by catalysing the conversion from protopectin to water-soluble pectin. Biochemical analysis demonstrated that MdMYB2/MdNAC14/MdNTL9 transcription factors directly bind to the MdHb1 promoter to activate its transcriptional expression and promote fruit softening. Further injection experiments in apple fruit and histological as well as transmission electron microscopy analyses of the fruit samples revealed that D-GalUA and D-GlcA reduce the transcription of MdHb1, or through the MdMYB2/MdNAC14/MdNTL9-MdHb1 regulatory module, thereby delaying fruit softening. Our study provides novel insights into the role of two important metabolites, D-GalUA and D-GlcA, in the regulation of MdHb1-mediated fruit softening in apples.

Kiwifruit spatiotemporal multiomics networks uncover key tissue-specific regulatory processes throughout the life cycle

Kiwifruit (Actinidia chinensis), a recently commercialized horticultural crop, is rich in various nutrient compounds. However, the regulatory networks controlling the dynamic changes in key metabolites among different tissues remain largely unknown. Here, high-resolution spatiotemporal datasets obtained by ultraperformance liquid chromatography-tandem mass spectrometry methodology and RNA-seq were employed to investigate the dynamic changes in the metabolic and transcriptional landscape of major kiwifruit tissues across different developmental stages, including from fruit skin, outer pericarp, inner pericarp, and fruit core. Kiwifruit spatiotemporal regulatory networks (KSRN) were constructed by integrating the 1,243 identified metabolites and co-expressed genes into 10 different clusters and 11 modules based on their biological functions. These networks allowed the generation of a global map for the major metabolic and transcriptional changes occurring throughout the life cycle of different kiwifruit tissues and discovery of the underlying regulatory networks. KSRN predictions confirmed previously established regulatory networks, including the spatiotemporal accumulation of anthocyanin and ascorbic acid (AsA). More importantly, the networks led to the functional characterization of three transcription factors: an A. chinensis ethylene response factor 1, which negatively controls sugar accumulation and ethylene production by perceiving the ripening signal, a basic-leucine zipper 60 (AcbZIP60) transcription factor, which is involved in the biosynthesis of AsA as part of the L-galactose pathway, and a transcription factor related to apetala 2.4 (RAP2.4), which directly activates the expression of the kiwi fruit aroma terpene synthase gene AcTPS1b. Our findings provide insights into spatiotemporal changes in kiwifruit metabolism and generate a valuable resource for the study of metabolic regulatory processes in kiwifruit as well as other fruits.

GH3 Gene Family Identification in Chinese White Pear (Pyrus bretschneideri) and the Functional Analysis of PbrGH3.5 in Fe Deficiency Responses in Tomato

Iron (Fe) deficiency poses a major threat to pear (Pyrus spp.) fruit yield and quality. The Gretchen Hagen 3 (GH3) plays a vital part in plant stress responses. However, the GH3 gene family is yet to be characterized, and little focus has been given to the function of the GH3 gene in Fe deficiency responses. Here, we identified 15 GH3 proteins from the proteome of Chinese white pear (Pyrus bretschneideri) and analyzed their features using bioinformatics approaches. Structure domain and motif analyses showed that these PbrGH3s were relatively conserved, and phylogenetic investigation displayed that they were clustered into two groups (GH3 I and GH3 II). Meanwhile, cis-acting regulatory element searches of the corresponding promoters revealed that these PbrGH3s might be involved in ABA- and drought-mediated responses. Moreover, the analysis of gene expression patterns exhibited that most of the PbrGH3s were highly expressed in the calyxes, ovaries, and stems of pear plants, and some genes were significantly differentially expressed in normal and Fe-deficient pear leaves, especially for PbrGH3.5. Subsequently, the sequence of PbrGH3.5 was isolated from the pear, and the transgenic tomato plants with PbrGH3.5 overexpression (OE) were generated to investigate its role in Fe deficiency responses. It was found that the OE plants were more sensitive to Fe deficiency stress. Compared with wild-type (WT) plants, the rhizosphere acidification and ferric reductase activities were markedly weakened, and the capacity to scavenge reactive oxygen species was prominently impaired in OE plants under Fe starvation conditions. Moreover, the expressions of Fe-acquisition-associated genes, such as SlAHA4, SlFRO1, SlIRT1, and SlFER, were all greatly repressed in OE leaves under Fe depravation stress, and the free IAA level was dramatically reduced, while the conjugated IAA contents were notably escalated. Combined, our findings suggest that pear PbrGH3.5 negatively regulates Fe deficiency responses in tomato plants, and might help enrich the molecular basis of Fe deficiency responses in woody plants.

The BTB-BACK-TAZ domain protein MdBT2 reduces drought resistance by weakening the positive regulatory effect of MdHDZ27 on apple drought tolerance via ubiquitination

Drought stress is one of the dominating challenges to the growth and productivity in crop plants. Elucidating the molecular mechanisms of plants responses to drought stress is fundamental to improve fruit quality. However, such molecular mechanisms are poorly understood in apple (Malus domestica Borkh.). In this study, we explored that the BTB-BACK-TAZ protein, MdBT2, negatively modulates the drought tolerance of apple plantlets. Moreover, we identified a novel Homeodomain-leucine zipper (HD-Zip) transcription factor, MdHDZ27, using a yeast two-hybrid (Y2H) screen with MdBT2 as the bait. Overexpression of MdHDZ27 in apple plantlets, calli, and tomato plantlets enhanced their drought tolerance by promoting the expression of drought tolerance-related genes [responsive to dehydration 29A (MdRD29A) and MdRD29B]. Biochemical analyses demonstrated that MdHDZ27 directly binds to and activates the promoters of MdRD29A and MdRD29B. Furthermore, in vitro and in vivo assays indicate that MdBT2 interacts with and ubiquitinates MdHDZ27, via the ubiquitin/26S proteasome pathway. This ubiquitination results in the degradation of MdHDZ27 and weakens the transcriptional activation of MdHDZ27 on MdRD29A and MdRD29B. Finally, a series of transgenic analyses in apple plantlets further clarified the role of the relationship between MdBT2 and MdHDZ27, as well as the effect of their interaction on drought resistance in apple plantlets. Collectively, our findings reveal a novel mechanism by which the MdBT2-MdHDZ27 regulatory module controls drought tolerance, which is of great significance for enhancing the drought resistance of apple and other plants.

Temporal dynamics of genetic architecture governing leaf development in Populus

Leaf development is a multifaceted and dynamic process orchestrated by a myriad of genes to shape the proper size and morphology. The dynamic genetic network underlying leaf development remains largely unknown. Utilizing a synergistic genetic approach encompassing dynamic genome-wide association study (GWAS), time-ordered gene co-expression network (TO-GCN) analyses and gene manipulation, we explored the temporal genetic architecture and regulatory network governing leaf development in Populus. We identified 42 time-specific and 18 consecutive genes that displayed different patterns of expression at various time points. We then constructed eight TO-GCNs that covered the cell proliferation, transition, and cell expansion stages of leaf development. Integrating GWAS and TO-GCN, we postulated the functions of 27 causative genes for GWAS and identified PtoGRF9 as a key player in leaf development. Genetic manipulation via overexpression and suppression of PtoGRF9 revealed its primary influence on leaf development by modulating cell proliferation. Furthermore, we elucidated that PtoGRF9 governs leaf development by activating PtoHB21 during the cell proliferation stage and attenuating PtoLD during the transition stage. Our study provides insights into the dynamic genetic underpinnings of leaf development and understanding the regulatory mechanism of PtoGRF9 in this dynamic process.

MdbHLH93 confers drought tolerance by activating MdTyDC expression and promoting dopamine biosynthesis

Dopamine and its biosynthesis-limiting enzyme tyrosine decarboxylase (TyDC) play a vital part in mediating plant growth and the response to drought stress. However, the underlying molecular mechanism remains poorly understood. Here, drought stress markedly induced the expression of Malus domestica bHLH93 (MdbHLH93), the apple basic helix-loop-helix transcription factor. Moreover, MdbHLH93 directly bound to the Malus domestica TyDC (MdTyDC) promoter and positively regulated its expression, which resulted in dopamine synthesis and enhanced drought tolerance. Furthermore, the additive effect of overexpressing MdbHLH93 and MdTyDC simultaneously promoted dopamine synthesis and drought tolerance in apples, while the interference of MdbHLH93 inhibited this effect, indicating that MdTyDC-regulated dopamine synthesis and drought tolerance were positively regulated by MdbHLH93. Taken together, these findings suggest the positive regulation of dopamine accumulation by MdbHLH93 through its transcriptional regulation of MdTyDC and show that increased dopamine content confers drought tolerance in apples.

The Roles of GRETCHEN HAGEN3 (GH3)-Dependent Auxin Conjugation in the Regulation of Plant Development and Stress Adaptation

The precise control of free auxin (indole-3-acetic acid, IAA) gradient, which is orchestrated by biosynthesis, conjugation, degradation, hydrolyzation, and transport, is critical for all aspects of plant growth and development. Of these, the GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetase family, pivotal in conjugating IAA with amino acids, has garnered significant interest. Recent advances in understanding GH3-dependent IAA conjugation have positioned GH3 functional elucidation as a hot topic of research. This review aims to consolidate and discuss recent findings on (i) the enzymatic mechanisms driving GH3 activity, (ii) the influence of chemical inhibitor on GH3 function, and (iii) the transcriptional regulation of GH3 and its impact on plant development and stress response. Additionally, we explore the distinct biological functions attributed to IAA-amino acid conjugates.

A New Function of MbIAA19 Identified to Modulate Malus Plants Dwarfing Growth

The primary determinants of apple (Malus) tree architecture include plant height and internode length, which are the significant criteria for evaluating apple dwarf rootstocks. Plant height and internode length are predominantly governed by phytohormones. In this study, we aimed to assess the mechanisms underlying dwarfism in a mutant of Malus baccata. M. baccata dwarf mutant (Dwf) was previously obtained through natural mutation. It has considerably reduced plant height and internode length. A comparative transcriptome analysis of wild-type (WT) and Dwf mutant was performed to identify and annotate the differentially expressed genes responsible for the Dwf phenotype using RNA-seq and GO and KEGG pathway enrichment analyses. Multiple DEGs involved in hormone signaling pathways, particularly auxin signaling pathways, were identified. Moreover, the levels of endogenous indole-3-acetic acid (IAA) were lower in Dwf mutant than in WT. The Aux/IAA transcription factor gene MbIAA19 was downregulated in Dwf mutant due to a single nucleotide sequence change in its promoter. Genetic transformation assay demonstrated strong association between MbIAA19 and the dwarf phenotype. RNAi-IAA19 lines clearly exhibited reduced plant height, internode length, and endogenous IAA levels. Our study revealed that MbIAA19 plays a role in the regulation of dwarfism and endogenous IAA levels in M. baccata.

Genome-wide identification and stress response analysis of cyclophilin gene family in apple (Malus × domestica)

BACKGROUND

Cyclophilin (CYP) belongs to the immunophilin family and has peptidyl-prolyl cis-trans isomerase (PPIase) activity, which catalyzes the cis-trans isomerization process of proline residues. CYPs widely exist in eukaryotes and prokaryotes, and contain a conserved cyclophilin-like domain (CLD). Plant cyclophilins are widely involved in a range of biological processes including stress response, metabolic regulation, and growth and development.

RESULT

In this study, 30 cyclophilin genes on 15 chromosomes were identified from the 'Golden Delicious' apple (M. domestica) genome. Phylogenetic analysis showed that the cyclophilin family genes can be divided into three clades in Malus. Collinear analysis showed that ten gene pairs were the result of segmental duplication. Analysis of gene and protein structure further supported the phylogenetic tree and collinearity analysis. The expression of MdCYPs in different organs was higher in leaves, flowers, and fruits. Ten and eight CYPs responded to drought and salt stress, respectively. MdCYP16, a nuclear-localized MD CYP, was screened from the intersection of the two expression profiling datasets and was highly sensitive to drought and salt stress. GUS staining of transgenic Arabidopsis indicated that MdCYP16 may be involved in the regulation of abiotic stress.

CONCLUSION

This study systematically analyzed members of the apple cyclophilin family and confirmed the involvement of MdCYP16 as a nuclear-localized MD cyclophilin that acts in response to salt and drought stress in apple. Our work identifies members of the apple cyclophilin gene family, and provides an important theoretical basis for in-depth study of cyclophilin function. Additionally, the analysis provides candidate genes that may be involved in stress response in apple.

Plant responses to metals stress: microRNAs in focus

Metal toxicity can largely affect the growth and yield of numerous plant species. Plants have developed specific mechanisms to withstand the varying amounts of metals. One approach involves utilization of microRNAs (miRNAs) that are known for cleaving transcripts or inhibiting translation to mediate post-transcriptional control. Use of transcription factors (TFs) or gene regulation in metal detoxification largely depends on metal-responsive miRNAs. Moreover, systemic signals and physiological processes for plants response to metal toxicities are likewise controlled by miRNAs. Therefore, it is necessary to understand miRNAs and their regulatory networks in relation to metal stress. The miRNA-based approach can be important to produce metal-tolerant plant species. Here, we have reviewed the importance of plant miRNAs and their role in mitigating metal toxicities. The current review also discusses the specific advances that have occurred as a result of the identification and validation of several metal stress-responsive miRNAs.

Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree (Vernicia fordii)

The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms.

Loss of function of the bHLH transcription factor Nrd1 in tomato enhances resistance to Pseudomonas syringae

Basic helix-loop-helix (bHLH) transcription factors constitute a superfamily in eukaryotes, but their roles in plant immunity remain largely uncharacterized. We found that the transcript abundance in tomato (Solanum lycopersicum) leaves of one bHLH transcription factor-encoding gene, negative regulator of resistance to DC3000 1 (Nrd1), increased significantly after treatment with the immunity-inducing flgII-28 peptide. Plants carrying a loss-of-function mutation in Nrd1 (Δnrd1) showed enhanced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 although early pattern-triggered immunity responses, such as generation of reactive oxygen species and activation of mitogen-activated protein kinases after treatment with flagellin-derived flg22 and flgII-28 peptides, were unaltered compared to wild-type plants. RNA-sequencing (RNA-seq) analysis identified a gene, Arabinogalactan protein 1 (Agp1), whose expression is strongly suppressed in an Nrd1-dependent manner. Agp1 encodes an arabinogalactan protein, and overexpression of the Agp1 gene in Nicotiana benthamiana led to ∼10-fold less Pst growth compared to the control. These results suggest that the Nrd1 protein promotes tomato susceptibility to Pst by suppressing the defense gene Agp1. RNA-seq also revealed that the loss of Nrd1 function has no effect on the transcript abundance of immunity-associated genes, including AvrPtoB tomato-interacting 9 (Bti9), Cold-shock protein receptor (Core), Flagellin sensing 2 (Fls2), Flagellin sensing (Fls3), and Wall-associated kinase 1 (Wak1) upon Pst inoculation, suggesting that the enhanced immunity observed in the Δnrd1 mutants is due to the activation of key PRR signaling components as well as the loss of Nrd1-regulated suppression of Agp1.

Euryale Small Auxin Up RNA62 promotes cell elongation and seed size by altering the distribution of indole-3-acetic acid under the light

Euryale (Euryale ferox Salisb.) is an aquatic crop used as both food and drug in Asia, but its utilization is seriously limited due to low yield. Previously, we hypothesized that Euryale small auxin up RNAs (EuSAURs) regulate seed size, but the underlying biological functions and molecular mechanisms remain unclear. Here, we observed that the hybrid Euryale lines (HL) generate larger seeds with higher indole-3-acetic acid (IAA) concentrations than those in the North Gordon Euryale (WT). Histological analysis suggested that a larger ovary in HL is attributed to longer cells around. Overexpression of EuSAUR62 in rice (Oryza sativa L.) resulted in larger glumes and grains and increased the length of glume cells. Immunofluorescence and protein interaction assays revealed that EuSAUR62 modulates IAA accumulation around the rice ovary by interacting with the rice PIN-FORMED 9, an auxin efflux carrier protein. Euryale basic region/leucine zipper 55 (EubZIP55), which was highly expressed in HL, directly binds to the EuSAUR62 promoter and activated the expression of EuSAUR62. Constant light increased the expression of both EubZIP55 and EuSAUR62 with auxin-mediated hook curvature in HL seedlings. Overall, we proposed that EuSAUR62 is a molecular bridge between light and IAA and plays a crucial role in regulating the size of the Euryale seed.

Roles of Auxin in the Growth, Development, and Stress Tolerance of Horticultural Plants

Auxin, a plant hormone, regulates virtually every aspect of plant growth and development. Many current studies on auxin focus on the model plant Arabidopsis thaliana, or on field crops, such as rice and wheat. There are relatively few studies on what role auxin plays in various physiological processes of a range of horticultural plants. In this paper, recent studies on the role of auxin in horticultural plant growth, development, and stress response are reviewed to provide novel insights for horticultural researchers and cultivators to improve the quality and application of horticultural crops.

MdbHLH3 modulates apple soluble sugar content by activating phosphofructokinase gene expression

Sugars are involved in plant growth, fruit quality, and signaling perception. Therefore, understanding the mechanisms involved in soluble sugar accumulation is essential to understand fruit development. Here, we report that MdPFPβ, a pyrophosphate-dependent phosphofructokinase gene, regulates soluble sugar accumulation by enhancing the photosynthetic performance and sugar-metabolizing enzyme activities in apple (Malus domestica Borkh.). Biochemical analysis revealed that a basic helix-loop-helix (bHLH) transcription factor, MdbHLH3, binds to the MdPFPβ promoter and activates its expression, thus promoting soluble sugar accumulation in apple fruit. In addition, MdPFPβ overexpression in tomato influenced photosynthesis and carbon metabolism in the plant. Furthermore, we determined that MdbHLH3 increases photosynthetic rates and soluble sugar accumulation in apple by activating MdPFPβ expression. Our results thus shed light on the mechanism of soluble sugar accumulation in apple leaves and fruit: MdbHLH3 regulates soluble sugar accumulation by activating MdPFPβ gene expression and coordinating carbohydrate allocation.