Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis

Comparative Anatomical and Transcriptomics Reveal the Larger Cell Size as a Major Contributor to Larger Fruit Size in Apricot

Fruit size is one of the essential quality traits and influences the economic value of apricots. To explore the underlying mechanisms of the formation of differences in fruit size in apricots, we performed a comparative analysis of anatomical and transcriptomics dynamics during fruit growth and development in two apricot cultivars with contrasting fruit sizes (large-fruit Prunus armeniaca 'Sungold' and small-fruit P. sibirica 'F43'). Our analysis identified that the difference in fruit size was mainly caused by the difference in cell size between the two apricot cultivars. Compared with 'F43', the transcriptional programs exhibited significant differences in 'Sungold', mainly in the cell expansion period. After analysis, key differentially expressed genes (DEGs) most likely to influence cell size were screened out, including genes involved in auxin signal transduction and cell wall loosening mechanisms. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that PRE6/bHLH was identified as a hub gene, which interacted with 1 TIR1, 3 AUX/IAAs, 4 SAURs, 3 EXPs, and 1 CEL. Hence, a total of 13 key candidate genes were identified as positive regulators of fruit size in apricots. The results provide new insights into the molecular basis of fruit size control and lay a foundation for future breeding and cultivation of larger fruits in apricot.

Comparative transcriptome analysis reveals the function of SlPRE2 in multiple phytohormones biosynthesis, signal transduction and stomatal development in tomato

KEY MESSAGE

Transcriptomic, physiological, and qRT-PCR analysis revealed the potential mechanism by which SlPRE2 regulates plant growth and stomatal size via multiple phytohormone pathways in tomato. Paclobutrazol resistance proteins (PREs) are atypical members of the basic/helix-loop-helix (bHLH) transcription factor family that regulate plant morphology, cell size, pigment metabolism and abiotic stress in response to different phytohormones. However, little is known about the network regulatory mechanisms of PREs in plant growth and development in tomato. In this study, the function and mechanism of SlPRE2 in tomato plant growth and development were investigated. The quantitative RT-PCR results showed that the expression of SlPRE2 was regulated by multiple phytohormones and abiotic stresses. It showed light-repressed expression during the photoperiod. The RNA-seq results revealed that SlPRE2 regulated many genes involved in photosynthesis, chlorophyll metabolism, phytohormone metabolism and signaling, and carbohydrate metabolism, suggesting the role of SlPRE2 in gibberellin, brassinosteroid, auxin, cytokinin, abscisic acid and salicylic acid regulated plant development processes. Moreover, SlPRE2 overexpression plants showed widely opened stomata in young leaves, and four genes involved in stomatal development showed altered expression. Overall, the results demonstrated the mechanism by which SlPRE2 regulates phytohormone and stress responses and revealed the function of SlPRE2 in stomatal development in tomato. These findings provide useful clues for understanding the molecular mechanisms of SlPRE2-regulated plant growth and development in tomato.

Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis

Changes in ambient temperature immensely affect developmental programs in many species. Plants adapt to high ambient growth temperature in part by vegetative and reproductive developmental reprogramming, known as thermo-morphogenesis. Thermo-morphogenesis is accompanied by massive changes in the transcriptome upon temperature change. Here, we show that transcriptome changes induced by warm ambient temperature require VERNALIZATION INSENSITIVE 3-LIKE 1 (VIL1), a facultative component of the Polycomb repressive complex PRC2, in Arabidopsis. Warm growth temperature elicits genome-wide accumulation of H3K27me3 and VIL1 is necessary for the warm temperature-mediated accumulation of H3K27me3. Consistent with its role as a mediator of thermo-morphogenesis, loss of function of VIL1 results in hypo-responsiveness to warm ambient temperature. Our results show that VIL1 is a major chromatin regulator in responses to high ambient temperature.

H+-pyrophosphatases enhance low nitrogen stress tolerance in transgenic Arabidopsis and wheat by interacting with a receptor-like protein kinase

INTRODUCTION

Nitrogen is a major abiotic stress that affects plant productivity. Previous studies have shown that plant H+-pyrophosphatases (H+-PPases) enhance plant resistance to low nitrogen stress. However, the molecular mechanism underlying H+-PPase-mediated regulation of plant responses to low nitrogen stress is still unknown. In this study, we aimed to investigate the regulatory mechanism of AtAVP1 in response to low nitrogen stress.

METHODS AND RESULTS

AtAVP1 in Arabidopsis thaliana and EdVP1 in Elymus dahuricus belong to the H+-PPase gene family. In this study, we found that AtAVP1 overexpression was more tolerant to low nitrogen stress than was wild type (WT), whereas the avp1-1 mutant was less tolerant to low nitrogen stress than WT. Plant height, root length, aboveground fresh and dry weights, and underground fresh and dry weights of EdVP1 overexpression wheat were considerably higher than those of SHI366 under low nitrogen treatment during the seedling stage. Two consecutive years of low nitrogen tolerance experiments in the field showed that grain yield and number of grains per spike of EdVP1 overexpression wheat were increased compared to those in SHI366, which indicated that EdVP1 conferred low nitrogen stress tolerance in the field. Furthermore, we screened interaction proteins in Arabidopsis; subcellular localization analysis demonstrated that AtAVP1 and Arabidopsis thaliana receptor-like protein kinase (AtRLK) were located on the plasma membrane. Yeast two-hybrid and luciferase complementary imaging assays showed that the AtRLK interacted with AtAVP1. Under low nitrogen stress, the Arabidopsis mutants rlk and avp1-1 had the same phenotypes.

DISCUSSION

These results indicate that AtAVP1 regulates low nitrogen stress responses by interacting with AtRLK, which provides a novel insight into the regulatory pathway related to H+-pyrophosphatase function in plants.

Characterization of Transcriptome Dynamics during Early Fruit Development in Olive (Olea europaea L.)

In the olive (Olea europaea L.), an economically leading oil crop worldwide, fruit size and yield are determined by the early stages of fruit development. However, few detailed analyses of this stage of fruit development are available. This study offers an extensive characterization of the various processes involved in early olive fruit growth (cell division, cell cycle regulation, and cell expansion). For this, cytological, hormonal, and transcriptional changes characterizing the phases of early fruit development were analyzed in olive fruit of the cv. 'Picual'. First, the surface area and mitotic activity (by flow cytometry) of fruit cells were investigated during early olive fruit development, from 0 to 42 days post-anthesis (DPA). The results demonstrate that the cell division phase extends up to 21 DPA, during which the maximal proportion of 4C cells in olive fruits was reached at 14 DPA, indicating that intensive cell division was activated in olive fruits at that time. Subsequently, fruit cell expansion lasted as long as 3 weeks more before endocarp lignification. Finally, the molecular mechanisms controlling the early fruit development were investigated by analyzing the transcriptome of olive flowers at anthesis (fruit set) as well as olive fruits at 14 DPA (cell division phase) and at 28 DPA (cell expansion phase). Sequential induction of the cell cycle regulating genes is associated with the upregulation of genes involved in cell wall remodeling and ion fluxes, and with a shift in plant hormone metabolism and signaling genes during early olive fruit development. This occurs together with transcriptional activity of subtilisin-like protease proteins together with transcription factors potentially involved in early fruit growth signaling. This gene expression profile, together with hormonal regulators, offers new insights for understanding the processes that regulate cell division and expansion, and ultimately fruit yield and olive size.

Morphological and physiological mechanism of cytoplasmic inheritance stigma exsertion trait expression in tobacco (Nicotiana tabacum)

Stigma exsertion is an essential outcrossing trait that can improve hybrid seed production efficiencies. In this study, the morphological and physiological mechanisms of cytoplasmic inheritance stigma exsertion trait expression in a tobacco line (MSK326SE) which generated from a stigma exsertion tobacco mutant through continuous backcross were investigated. Compared with its homonuclear-heteroplasmic lines (MSK326 and K326 with inserted stigmas), the exserted stigma phenotype of MSK326SE was mainly caused by corolla shortening, while was stable under different environmental temperature. The different responses of mainly endogenous hormones and expression of cell division- and expansion-related genes caused the differences in cell division and expansion in different flower organs, which further determined the lengths of the corolla. Furthermore, the significant decrease of MSK326SE corolla epidermal cell size caused corolla shortening and finally resulting in stigma exsertion. Exogenous JA could shorten the corolla and more effective increased stigma exsertion degree of MSK326SE, suggesting a potential relationship between stigma exsertion and high JA levels during early bud development. The hybrid seed production efficiency could be improved in tobacco. Our results provide a basis for elucidating the cytoplasmic inheritance stigma exsertion trait expression in tobacco while helping to improve hybrid seed production efficiency.

A Global Transcriptome and Co-expression Analysis Reveals Robust Host Defense Pathway Reprogramming and Identifies Key Regulators of Early Phases of Cicer-Ascochyta Interactions

Ascochyta blight (AB) caused by the filamentous fungus Ascochyta rabiei is a major threat to global chickpea production. The mechanisms underlying chickpea response to A. rabiei remain elusive to date. Here, we investigated the comparative transcriptional dynamics of AB-resistant and -susceptible chickpea genotypes upon A. rabiei infection, to understand the early host defense response. Our findings revealed that AB-resistant plants underwent rapid and extensive transcriptional reprogramming compared with a susceptible host. At the early stage (24 h postinoculation [hpi]), mainly cell-wall remodeling and secondary metabolite pathways were highly activated, while differentially expressed genes related to signaling components, such as protein kinases, transcription factors, and hormonal pathways, show a remarkable upsurge at 72 hpi, especially in the resistant genotype. Notably, our data suggest an imperative role of jasmonic acid, ethylene, and abscisic acid signaling in providing immunity against A. rabiei. Furthermore, gene co-expression networks and modules corroborated the importance of cell-wall remodeling, signal transduction, and phytohormone pathways. Hub genes such as MYB14, PRE6, and MADS-SOC1 discovered in these modules might be the master regulators governing chickpea immunity. Overall, we not only provide novel insights for comprehensive understanding of immune signaling components mediating AB resistance and susceptibility at early Cicer-Ascochyta interactions but, also, offer a valuable resource for developing AB-resistant chickpea. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Overexpression of SlPRE5, an atypical bHLH transcription factor, affects plant morphology and chlorophyll accumulation in tomato

The basic helix-loop-helix (bHLH) transcription factors play vital regulatory roles in a series of metabolic, physiological, and developmental processes of plants. Here, SlPRE5, an atypical bHLH gene, was isolated from tomato. SlPRE5 was noticeably expressed in young leaves, sepals, and flowers. SlPRE5-overexpressing plants exhibited rolling leaves with reduced chlorophyll content, increased stem internode length, leaf angle, and compound leaf length. The water loss rate of mature leaves and the content of starch were significantly reduced, while the content of gibberellin was significantly increased in transgenic plants. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) showed that SlPRE5 could interact with SlAIF1, SlAIF2, and SlPAR1. qRT-PCR and RNA-seq results revealed that the expression levels of genes related to chloroplast development, chlorophyll metabolism, gibberellin metabolism and signal transduction, starch, photosynthesis, and cell expansion were significantly altered in SlPRE5-overexpression plants. Collectively, our results suggest that SlPRE5 is a crucial transcription factor involved in plant morphology and chlorophyll accumulation in tomato leaves.

Genetic Mapping of the Gmpgl3 Mutant Reveals the Function of GmTic110a in Soybean Chloroplast Development

The generation of oxygen and organic matter in plants mainly depends on photosynthesis, which directly affects plant growth and development. The chloroplast is the main organelle in which photosynthesis occurs. In this study, a Glycine max pale green leaf 3-1 (Gmpgl3-1) mutant was isolated from the soybean mutagenized population. The Gmpgl3-1 mutant presented with decreased chlorophyll contents, reduced chloroplast stroma thylakoids, reduced yields, and decreased numbers of pods per plant. Bulked segregant analysis (BSA) together with map-based cloning revealed a single-nucleotide non-synonymous mutation at the 341st nucleotide of the first exon of the chloroplast development-related GmTic110a gene. The phenotype of the knockout plants was the same as that of the mutant. The GmTic110a gene was highly expressed in the leaves at various developmental stages, and its protein was localized to the inner chloroplast membrane. Split luciferase complementation assays and coimmunoprecipitation (co-IP) experiments revealed that GmTic110a interacted with GmTic20, GmTic40a, and GmTic40b in tobacco leaves. These results indicated that the GmTic110a gene plays an important role in chloroplast development.

Regulation of lignin biosynthesis by an atypical bHLH protein CmHLB in Chrysanthemum

Stem mechanical strength is one of the most important agronomic traits that affects the resistance of plants against insects and lodging, and plays an essential role in the quality and yield of plants. Several transcription factors regulate mechanical strength in crops. However, mechanisms of stem strength formation and regulation remain largely unexplored, especially in ornamental plants. In this study, we identified an atypical bHLH transcription factor CmHLB (HLH PROTEIN INVOLVED IN LIGNIN BIOSYNTHESIS) in chrysanthemum, belonging to a small bHLH sub-family - the PACLOBUTRAZOL RESISTANCE (PRE) family. Overexpression of CmHLB in chrysanthemum significantly increased mechanical strength of the stem, cell wall thickness, and lignin content, compared with the wild type. In contrast, CmHLB RNA interference lines exhibited the opposite phenotypes. RNA-seq analysis indicated that CmHLB promoted the expression of genes involved in lignin biosynthesis. Furthermore, we demonstrated that CmHLB interacted with Chrysanthemum KNOTTED ARABIDOPSIS THALIANA7 (CmKNAT7) through the KNOX2 domain, which has a conserved function, i.e. it negatively regulates secondary cell wall formation of fibres and lignin biosynthesis. Collectively, our results reveal a novel role for CmHLB in regulating lignin biosynthesis by interacting with CmKNAT7 and affecting stem mechanical strength in Chrysanthemum.

Genome-Wide Identification of Apple Atypical bHLH Subfamily PRE Members and Functional Characterization of MdPRE4.3 in Response to Abiotic Stress

Paclobutrazol Resistance (PRE) genes encode atypical basic helix–loop–helix (bHLH) transcription factor family. Typical bHLH proteins contain a bifunctional structure with a basic region involved in DNA binding and an adjacent helix–loop–helix domain involved in protein–protein interaction. PRE members lack the basic region but retain the HLH domain, which interacts with other typical bHLH proteins to suppress or enhance their DNA-binding activity. PRE proteins are involved in phytohormone responses, light signal transduction, and fruit pigment accumulation. However, apple (Malus domestica) PRE protein functions have not been studied. In this study, nine MdPRE genes were identified from the apple GDDH13 v1.1 reference genome and were mapped to seven chromosomes. The cis-acting element analysis revealed that MdPRE promoters possessed various elements related to hormones, light, and stress responses. Expression pattern analysis showed that MdPRE genes have different tissue expression profiles. Hormonal and abiotic stress treatments can induce the expression of several MdPRE genes. Moreover, we provide molecular and genetic evidence showing that MdPRE4.3 increases the apple’s sensitivity to NaCl, abscisic acid (ABA), and indoleacetic acid (IAA) and improves tolerance to brassinosteroids (BR); however, it does not affect the apple’s response to gibberellin (GA). Finally, the protein interaction network among the MdPRES proteins was predicted, which could help us elucidate the molecular and biological functions of atypical bHLH transcription factors in the apple.

The NAC transcription factor ATAF2 promotes ethylene biosynthesis and response in Arabidopsis thaliana seedlings

Arabidopsis thaliana ACTIVATING FACTOR 2 (ATAF2) plays extensive regulatory roles in pathogenesis, seedling development, and stress responses. Here, we performed transcriptome analysis on ATAF2 loss- and gain-of-function mutants to identify differentially expressed genes (DEGs). Gene ontology analyses on DEGs reveal that ATAF2 enhances seedling responses to multiple hormone and stress signals. In particular, our transcriptome analysis suggests that ATAF2 promotes ethylene biosynthesis and responses via activating relevant genes. This novel role of ATAF2 was further demonstrated by using multiple ATAF2 null and overexpression lines for reverse transcription quantitative PCR verification, ethylene production measurements, and assays of seedlings growth responses to the ethylene immediate biosynthetic precursor 1-aminocyclopropane-1-carboxylic acid (ACC). ACC suppresses ATAF2 expression to form a negative feedback regulation loop.

Deciphering Novel Transcriptional Regulators of Soybean Hypocotyl Elongation Based on Gene Co-expression Network Analysis

Hypocotyl elongation is the key step of soybean seed germination, as well an important symbol of seedling vitality, but the regulatory mechanisms remain largely elusive. To address the problem, bioinformatics approaches along with the weighted gene co-expression network analysis (WGCNA) were carried out to elucidate the regulatory networks and identify key regulators underlying soybean hypocotyl elongation at transcriptional level. Combining results from WGCNA, yeast one hybridization, and phenotypic analysis of transgenic plants, a cyan module significantly associated with hypocotyl elongation was discerned, from which two novel regulatory submodules were identified as key candidates underpinning soybean hypocotyl elongation by modulating auxin and light responsive signaling pathways. Taken together, our results constructed the regulatory network and identified novel transcriptional regulators of soybean hypocotyl elongation based on WGCNA, which provide new insights into the global regulatory basis of soybean hypocotyl elongation and offer potential targets for soybean improvement to acquire cultivars with well-tuned hypocotyl elongation and seed germination vigor.

Profiling of H3K4me3 and H3K27me3 and Their Roles in Gene Subfunctionalization in Allotetraploid Cotton

Cotton is an excellent model for studying crop polyploidization and domestication. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenomes in allotetraploid cotton. However, the detailed profiling and functional characterization of broad H3K4me3 and H3K27me3 are still understudied in cotton. In this study, we conducted H3K4me3- and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating the expression of genes between A and D subgenomes, respectively. More importantly, H3K4me3 exhibited enrichment level-, position-, and distance-related impacts on expression levels of related genes. Distinct GO term enrichment occurred between A/D-specific and homeologous genes with broad H3K4me3 enrichment in promoters and gene bodies, suggesting that broad H3K4me3-marked genes might have some unique biological functions between A and D subgenome. An anticorrelation between H3K27me3 enrichment and expression levels of homeologous genes was more pronounced in the A subgenome relative to the D subgenome, reflecting distinct enrichment of H3K27me3 in homeologous genes between A and D subgenome. In addition, H3K4me3 and H3K27me3 marks can indirectly influence gene expression through regulatory networks with TF mediation. Thus, our study provides detailed insights into functions of H3K4me3 and H3K27me3 in regulating differential gene expression and subfunctionalization of homeologous genes, therefore serving as a driving force for polyploidization and domestication in cotton.

Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor gene families in Arabidopsis thaliana, and contains a bHLH motif that is highly conserved throughout eukaryotic organisms. Members of this family have two conserved motifs, a basic DNA binding region and a helix-loop-helix (HLH) region. These proteins containing bHLH domain usually act as homo- or heterodimers to regulate the expression of their target genes, which are involved in many physiological processes and have a broad range of functions in biosynthesis, metabolism and transduction of plant hormones. Although there are a number of articles on different aspects to provide detailed information on this family in plants, an overall summary is not available. In this review, we summarize various aspects of related studies that provide an overview of insights into the pleiotropic regulatory roles of these transcription factors in plant growth and development, stress response, biochemical functions and the web of signaling networks. We then provide an overview of the functional profile of the bHLH family and the regulatory mechanisms of other proteins.

Comparative transcriptome analysis of the peanut semi-dwarf mutant 1 reveals regulatory mechanism involved in plant height

Plant height is a fundamentally crucial agronomic trait to control crop growth and high yield cultivation. Several studies have been conducted on the understanding ofmolecular genetic bases of plant height in model plants and crops. However, the molecular mechanism underlying peanut plant height development is stilluncertain. In the present study, we created a peanut mutant library by fast neutron irradiation using peanut variety SH13 and identified a semi-dwarf mutant 1 (sdm1). At 84 DAP (days after planting), the main stem of sdm1 was only about 62% of SH13. The internode length of sdm1 hydroponic seedlings was found significantly shorter than that of SH13 at 14 DAP. In addition, the foliar spraying of exogenous IAA could partially restore the semi-dwarf phenotype of sdm1. Transcriptome data indicated that the differentially expressed genes (DEGs) between sdm1 and SH13 significantly enriched in diterpenoid biosynthesis, alpha-linolenic acid metabolism, brassinosteroid biosynthesis, tryptophan metabolism and plant hormone signal transduction. The expression trend of most of the genes involved in IAA and JA pathway showed significantly down- and up- regulation, which may be one of the key factors of the sdm1 semi-dwarf phenotype. Moreover, several transcription factorsand cell wall relatedgenes were expressed differentially between sdm1 and SH13. Conclusively, this research work not only provided important clues to unveil the molecular mechanism of peanut plant height regulation, but also presented basic materials for breeding peanut cultivars with ideal plant height.

PIP2, An Auxin Induced Plant Peptide Hormone Regulates Root and Hypocotyl Elongation in Arabidopsis

Auxin is one of the traditional plant hormones, whereas peptide hormones are peptides with hormone activities. Both auxin and plant peptide hormones regulate multiple aspects of plant growth and development, and there are cross-talks between auxin and plant peptide hormones. PAMP-INDUCED SECRETED PEPTIDES (PIPs) and PIP-LIKEs (PIPLs) are a new family of plant peptide hormone, and PIPL3/TARGET OF LBD SIXTEEN 2 (TOLS2) has been shown to regulate lateral root formation in Arabidopsis. We report here the identification of PIP2 as an auxin response gene, and we found it plays a role in regulating root and hypocotyl development in Arabidopsis. By using quantitative RT-PCR, we found that the expression of PIP2 but not PIP1 and PIP3 was induced by auxin, and auxin induced expression of PIP2 was reduced in nph4-1 and arf19-4, the lost-of-function mutants of Auxin Response Factor 7 (ARF7) and ARF19, respectively. By generating and characterizing overexpressing transgenic lines and gene edited mutants for PIP2, we found that root length in the PIP2 overexpression plant seedlings was slightly shorter when compared with that in the Col wild type plants, but root length of the pip2 mutant seedlings remained largely unchanged. For comparison, we also generated overexpressing transgenic lines and gene edited mutants for PIP3, as well as pip2 pip3 double mutants. Surprisingly, we found that root length in the PIP3 overexpression plant seedlings is shorter than that of the PIP2 overexpression plant seedlings, and the pip3 mutant seedlings also produced short roots. However, root length in the pip2 pip3 double mutant seedlings is largely similar to that in the pip3 single mutant seedlings. On the other hand, hypocotyl elongation assays indicate that only the 35S:PIP2 transgenic plant seedlings produced longer hypocotyls when compared with the Col wild type seedlings. Further analysis indicates that PIP2 promotes cell division as well as cell elongation in hypocotyls. Taken together, our results suggest that PIP2 is an auxin response gene, and PIP2 plays a role in regulating root and hypocotyl elongation in Arabidopsis likely via regulating cell division and cell elongation.

Ectopic expression of the atypical HLH FaPRE1 gene determines changes in cell size and morphology

PACLOBUTRAZOL RESISTANCE (PRE) genes code atypical HLH transcriptional regulators characterized by the absence of a DNA-binding domain but present an HLH dimerization domain. In vegetative tissues, the function of these HLH proteins has been related with cell elongation processes. In strawberry, three FaPRE genes are expressed, two of them (FaPRE2 and FaPRE3) in vegetative tissues while FaPRE1 is fruit receptacle-specific. Ubiquitous FaPRE1 accumulation produced elongated flower receptacles and plants due to the elongation of the main aerial vegetative organs, with the exception of leaves. Histological analysis clearly demonstrated that the observed phenotype was due to significant changes in the parenchymal cell's morphology. In addition, transcriptomic studies of the transgenic elongated flower receptacles allowed to identify a small group of differentially expressed genes that encode cell wall-modifying enzymes. Together, the data seem to indicate that, in the strawberry plant vegetative organs, FaPRE proteins could modulate the expression of genes related with the determination of the size and shape of the parenchymal cells.

Bulk RNA-Seq analysis to dissect the regulation of stigma position in tomato

Transcriptomic analysis of tomato genotypes contrasting for stigma position suggests that stigma insertion occurred by the disruption of a process that finds a parallel in Arabidopsis gynoecium development. Domestication of cultivated tomato (Solanum lycopersicum L.) included the transition from allogamy to autogamy that occurred through the loss of self-incompatibilty and the retraction of the stigma within the antheridial cone. Although the inserted stigma is an established phenotype in modern tomatoes, an exserted stigma is still present in several landraces or vintage varieties. Moreover, exsertion of the stigma is a frequent response to high temperature stress and, being a cause of reduced fertility, a trait of increasing importance. Few QTLs for stigma position have been described and only one of the underlying genes identified. To gain insights on genes involved in stigma position in tomato, a bulk RNA sequencing (RNA-Seq) approach was adopted, using two groups of contrasting genotypes. Phenotypic analysis confirmed the extent and the stability of stigma position in the selected genotypes, whereas they were highly heterogeneous for other reproductive and productive traits. The RNA-Seq analysis yielded 801 differentially expressed genes (DEGs), 566 up-regulated and 235 down-regulated in the genotypes with exserted stigma. Validation by quantitative PCR indicated a high reliability of the RNA-Seq data. Up-regulated DEGs were enriched for genes involved in the cell wall metabolism, lipid transport, auxin response and flavonoid biosynthesis. Down-regulated DEGs were enriched for genes involved in translation. Validation of selected genes on pistil tissue of the 26 single genotypes revealed that differences between bulks could both be due to a general trend of the bulk or to the behaviour of single genotypes. Novel candidate genes potentially involved in the control of stigma position in tomato are discussed.

Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley (Hordeum vulgare L.)

Background

The basic helix-loop-helix (bHLH) transcription factor is one of the most important gene families in plants, playing a key role in diverse metabolic, physiological, and developmental processes. Although it has been well characterized in many plants, the significance of the bHLH family in barley is not well understood at present.

Methods

Through a genome-wide search against the updated barley reference genome, the genomic organization, evolution and expression of the bHLH family in barley were systematically analyzed.

Results

We identified 141 bHLHs in the barley genome (HvbHLHs) and further classified them into 24 subfamilies based on phylogenetic analysis. It was found that HvbHLHs in the same subfamily shared a similar conserved motif composition and exon-intron structures. Chromosome distribution and gene duplication analysis revealed that segmental duplication mainly contributed to the expansion of HvbHLHs and the duplicated genes were subjected to strong purifying selection. Furthermore, expression analysis revealed that HvbHLHs were widely expressed in different tissues and also involved in response to diverse abiotic stresses. The co-expression network was further analyzed to underpin the regulatory function of HvbHLHs. Finally, 25 genes were selected for qRT-PCR validation, the expression profiles of HvbHLHs showed diverse patterns, demonstrating their potential roles in relation to stress tolerance regulation.

Conclusion

This study reported the genome organization, evolutionary characteristics and expression profile of the bHLH family in barley, which not only provide the targets for further functional analysis, but also facilitate better understanding of the regulatory network bHLH genes involved in stress tolerance in barley.

Phospho-Mutant Activity Assays Provide Evidence for the Negative Regulation of Transcriptional Regulator PRE1 by Phosphorylation

The PACLOBUTRAZOL-RESISTANCE (PRE) gene family encodes a group of atypical helix-loop-helix (HLH) proteins that act as the major hub integrating a wide range of environmental and hormonal signals to regulate plant growth and development. PRE1, as a positive regulator of cell elongation, activates HBI1 DNA binding by sequestering its inhibitor IBH1. Furthermore, PRE1 can be phosphorylated at Ser-46 and Ser-67, but how this phosphorylation regulates the functions of PRE1 remains unclear. Here, we used a phospho-mutant activity assay to reveal that the phosphorylation at Ser-67 negatively regulates the functions of PRE1 on cell elongation. Both of mutations of serine 46, either to phospho-dead alanine or phospho-mimicking glutamic acid, had no significant effects on the functions of PRE1. However, the mutation of serine 67 to glutamic acid (PRE1^S67E-Ox), but not alanine (PRE1^S67A-Ox), significantly reduced the promoting effects of PRE1 on cell elongation. The mutation of Ser-67 to Glu-67 impaired the interaction of PRE1 with IBH1 and resulted in PRE1 failing to inhibit the interaction between IBH1 and HBI1, losing the ability to induce the expression of the subsequent cell elongation-related genes. Furthermore, we showed that PRE1-Ox and PRE1^S67A-Ox both suppressed but PRE1^S67E-Ox had no strong effects on the dwarf phenotypes of IBH1-Ox. Our study demonstrated that the PRE1 activity is negatively regulated by the phosphorylation at Ser-67.

A Gas-and-Brake Mechanism of bHLH Proteins Modulates Shade Avoidance

Plants detect proximity of competitors through reduction in the ratio between red and far-red light that triggers the shade avoidance syndrome, inducing responses such as accelerated shoot elongation and early flowering. Shade avoidance is regulated by PHYTOCHROME INTERACTING FACTORs, a group of basic helix-loop-helix (bHLH) transcription factors. Another (b)HLH protein, KIDARI (KDR), which is non-DNA-binding, was identified in de-etiolation studies and proposed to interact with LONG HYPOCOTYL IN FAR-RED1 (HFR1), a (b)HLH protein that inhibits shade avoidance. Here, we established roles of KDR in regulating shade avoidance in Arabidopsis (Arabidopsis thaliana) and investigated how KDR regulates the shade avoidance network. We showed that KDR is a positive regulator of shade avoidance and interacts with several negative growth regulators. We identified KDR interactors using a combination of yeast two-hybrid screening and dedicated confirmations with bimolecular fluorescence complementation. We demonstrated that KDR is translocated primarily to the nucleus when coexpressed with these interactors. A genetic approach confirmed that several of these interactions play a functional role in shade avoidance; however, we propose that KDR does not interact with HFR1 to regulate shade avoidance. Based on these observations, we propose that shade avoidance is regulated by a three-layered gas-and-brake mechanism of bHLH protein interactions, adding a layer of complexity to what was previously known.

The bHLH network underlying plant shade-avoidance

Shade is a potential threat to many plant species. When shade-intolerant plants detect neighbours, they elongate their stems and leaves in an effort to maximise their light capture. This developmental programme, known as 'shade-avoidance' is tightly controlled by specialised photoreceptors and a suite of transcriptional regulators. The basic helix-loop-helix (bHLH) family of transcription factors are particularly important for shade-induced elongation. In recent years, it has become apparent that many members of this family heterodimerise and that together they form a complex regulatory network. This review summarises recent work into the structure of the bHLH network and how it regulates elongation growth. In addition to this, we highlight how photoreceptors modulate the function of the network via direct interaction with transcription factors. It is hoped that the information integrated in this review will provide a useful theoretical framework for future studies on the molecular basis of shade-avoidance in plants.

Genome-wide survey of the bHLH super gene family in Brassica napus

BACKGROUND

The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus.

RESULTS

We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function.

CONCLUSION

The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing

rRNA processing and assembly of ribosomal proteins during maturation of ribosomes involve many ribosome biogenesis factors (RBFs). Recent studies identified differences in the set of RBFs in humans and yeast, and the existence of plant-specific RBFs has been proposed as well. To identify such plant-specific RBFs, we characterized T-DNA insertion mutants of 15 Arabidopsis thaliana genes encoding nuclear proteins with nucleotide binding properties that are not orthologues to yeast or human RBFs. Mutants of nine genes show an altered rRNA processing ranging from inhibition of initial 35S pre-rRNA cleavage to final maturation events like the 6S pre-rRNA processing. These phenotypes led to their annotation as 'involved in rRNA processing' - IRP. The irp mutants are either lethal or show developmental and stress related phenotypes. We identified IRPs for maturation of the plant-specific precursor 5'-5.8S and one affecting the pathway with ITS2 first cleavage of the 35S pre-rRNA transcript. Moreover, we realized that 5'-5.8S processing is essential, while a mutant causing 6S accumulation shows only a weak phenotype. Thus, we demonstrate the importance of the maturation of the plant-specific precursor 5'-5.8S for plant development as well as the occurrence of an ITS2 first cleavage pathway in fast dividing tissues.

The non-DNA binding bHLH transcription factor Paclobutrazol Resistances are involved in the regulation of ABA and salt responses in Arabidopsis

Abscisic acid (ABA) is the key hormone that regulating plant responses to abiotic stresses. Several basic helix-loop-helix (bHLH) transcription factors have been reported to regulate ABA signaling in Arabidopsis. Paclobutrazol Resistances (PREs) are non-DNA binding bHLH transcription factors involved in the regulation of plant response to several different plant hormones including gibberellin, brassinosteroid and auxin. Here, we show that PREs are involved in the regulation of ABA and salt responses in Arabidopsis. Quantitative RT-PCR results showed that the expression levels of PRE6 as well as several other PRE genes were reduced in response to ABA treatment, but increased to salt treatment. Seed germination assays indicated that ABA sensitivity is reduced in the pre6 mutants, but increased in transgenic plants overexpressing PRE6. On the other hand, the 35S:PRE6 transgenic plants showed enhanced tolerance to salt, whereas little, if any changes were observed in the pre6 mutants. Similar responses to ABA and salt treatments were observed in the pre2 mutants and the transgenic plants overexpressing PRE2, and a slight increased resistance to ABA in seed germination was observed in the pre2 pre6 double mutants. Taken together, our results suggest that at least some of the PRE genes are ABA responsive genes, and PREs may function redundantly to regulate ABA and salt responses in Arabidopsis.

PACLOBUTRAZOL-RESISTANCE Gene Family Regulates Floral Organ Growth with Unequal Genetic Redundancy in Arabidopsis thaliana

A PACLOBUTRAZOL-RESISTANCE (PRE) gene family, consisting of six genes in Arabidopsis thaliana, encodes a group of helix-loop-helix proteins that act in the growth-promoting transcriptional network. To delineate the specific role of each of the PRE genes in organ growth, we took a reverse genetic approach by constructing high order pre loss-of-function mutants of Arabidopsis thaliana. In addition to dwarf vegetative growth, some double or high order pre mutants exhibited defective floral development, resulting in reduced fertility. While pre2pre5 is normally fertile, both pre2pre6 and pre5pre6 showed reduced fertility. Further, the reduced fertility was exacerbated in the pre2pre5pre6 mutant, indicative of the redundant and critical roles of these PREs. Self-pollination assay and scanning electron microscopy analysis showed that the sterility of pre2pre5pre6 was mainly ascribed to the reduced cell elongation of anther filament, limiting access of pollens to stigma. We found that the expression of a subset of flower-development related genes including ARGOS, IAA19, ACS8, and MYB24 was downregulated in the pre2pre5pre6 flowers. Given these results, we propose that PREs, with unequal functional redundancy, take part in the coordinated growth of floral organs, contributing to successful autogamous reproduction in Arabidopsis thaliana.