BEL1-LIKE HOMEODOMAIN4 regulates chlorophyll accumulation, chloroplast development, and cell wall metabolism in tomato fruit

Cotton BLH1 and KNOX6 antagonistically modulate fiber elongation via regulation of linolenic acid biosynthesis

BEL1-LIKE HOMEODOMAIN (BLH) proteins are known to function in various plant developmental processes. However, the role of BLHs in regulating plant cell elongation is still unknown. Here, we identify a BLH gene, GhBLH1, that positively regulates fiber cell elongation. Combined transcriptomic and biochemical analyses reveal that GhBLH1 enhances linolenic acid accumulation to promote cotton fiber cell elongation by activating the transcription of GhFAD7A-1 via binding of the POX domain of GhBLH1 to the TGGA cis-element in the GhFAD7A-1 promoter. Knockout of GhFAD7A-1 in cotton significantly reduces fiber length, whereas overexpression of GhFAD7A-1 results in longer fibers. The K2 domain of GhKNOX6 directly interacts with the POX domain of GhBLH1 to form a functional heterodimer, which interferes with the transcriptional activation of GhFAD7A-1 via the POX domain of GhBLH1. Overexpression of GhKNOX6 leads to a significant reduction in cotton fiber length, whereas knockout of GhKNOX6 results in longer cotton fibers. An examination of the hybrid progeny of GhBLH1 and GhKNOX6 transgenic cotton lines provides evidence that GhKNOX6 negatively regulates GhBLH1-mediated cotton fiber elongation. Our results show that the interplay between GhBLH1 and GhKNOX6 modulates regulation of linolenic acid synthesis and thus contributes to plant cell elongation.

Epigenetic insights into an epimutant colorless non-ripening: from fruit ripening to stress responses

The epigenetic machinery has received extensive attention due to its involvement in plant growth, development, and adaptation to environmental changes. Recent studies often highlight the epigenetic regulatory network by discussing various epigenetic mutants across various plant species. However, a systemic understanding of essential epigenetic regulatory mechanisms remains limited due to a lack of representative mutants involved in multiple biological processes. Colorless Non-ripening (Cnr), a spontaneous epimutant isolated from a commercial population, was initially characterized for its role in fruit ripening regulation. Cnr fruits exhibit an immature phenotype with yellow skin, attributed to hypermethylation of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE-CNR (SlSPL-CNR) promoter, resulting in the repression of gene expression. In addition to DNA methylation, this process also involves histone modification and microRNA, integrating multiple epigenetic regulatory factors. Interestingly, knockout mutants of SlSPL-CNR display phenotypical distinctions from Cnr in fruit ripening, indicating complex genetic and epigenetic control over the non-ripening phenotype in Cnr fruits. Accumulating evidence suggests that Cnr epimutation is pleiotropic, participating in various biological processes such as Cd stress, Fe deficiency, vivipary, and cell death. Therefore, the Cnr epimutant serve as an excellent model for unveiling how epigenetic mechanisms are involved in diverse biological processes. This review paper focuses on recent research advances regarding the Cnr epimutant, delving into its complex genetic and epigenetic regulatory mechanisms, with the aim of enhancing our understanding and facilitating the development of high-quality, high-yield crops through epigenetic modification.

Quantitative Trait Loci Sequencing and Genetic Mapping Reveal Two Main Regulatory Genes for Stem Color in Wax Gourds

Stem color is an important agronomic trait of wax gourds. However, its regulatory genes have not been identified. In this study, 105 inbred lines constructed from two parents (GX-71 and MY-1) were sequenced and quantitative trait loci sequencing was used to mine the genes that regulate stem color in wax gourds. The results identified two quantitative trait loci related to stem color, qSC5 and qSC12, located on Chr05 (11,134,567-16,459,268) and Chr12 (74,618,168-75,712,335), respectively. The qSC5 had a phenotypic variation rate of 36.9% and a maximum limit of detection of 16.9. And the qSC12 had a phenotypic variation rate of 20.9%, and a maximum limit of detection of 11.2. Bch05G003950 (named BchAPRR2) and Bch12G020400 were identified as candidate genes involved in stem color regulation in wax gourds. The chlorophyll content and expression of BchAPRR2 and Bch12G020400 were significantly higher in green-stemmed wax gourds than in white-stemmed ones. Therefore, BchAPRR2 and Bch12G020400 were considered the main and secondary regulatory genes for wax gourd stem color, respectively. Finally, InDel markers closely linked to BchAPRR2 were developed to validate the prediction of wax gourd stem color traits in 55 germplasm lines, with an accuracy of 81.8%. These findings lay the foundation for exploring the genetic regulation of wax gourd stem color and future research on wax gourd breeding.

Galactinol synthase 2 influences the metabolism of chlorophyll, carotenoids, and ethylene in tomato fruits

Galactinol synthase (GolS), which catalyses the synthesis of galactinol, is the first critical enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs) and contributes to plant growth and development, and resistance mechanisms. However, its role in fruit development remains largely unknown. In this study, we used CRISPR/Cas9 gene-editing technology in tomato (Solanum lycopersicum) to create the gols2 mutant showing uniformly green fruits without dark-green shoulders, and promoting fruit ripening. Analysis indicated that galactinol was undetectable in the ovaries and fruits of the mutant, and the accumulation of chlorophyll and chloroplast development was suppressed in the fruits. RNA-sequencing analysis showed that genes related to chlorophyll accumulation and chloroplast development were down-regulated, including PROTOCHLOROPHYLLIDE OXIDOREDUCTASE, GOLDEN 2-LIKE 2, and CHLOROPHYLL A/B-BINDING PROTEINS. In addition, early color transformation and ethylene release was prompted in the gols2 lines by regulation of the expression of genes involved in carotenoid and ethylene metabolism (e.g. PHYTOENE SYNTHASE 1, CAROTENE CIS-TRANS ISOMERASE, and 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE2/4) and fruit ripening (e.g. RIPENING INHIBITOR, NON-RIPENING, and APETALA2a). Our results provide evidence for the involvement of GolS2 in pigment and ethylene metabolism of tomato fruits.

Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit

Knotted1-like homeodomain (KNOX) proteins are essential in regulating plant organ differentiation. Land plants, including tomato (Solanum lycopersicum), have two classes of the KNOX protein family, namely, class I (KNOX I) and class II KNOX (KNOX II). While tomato KNOX I proteins are known to stimulate chloroplast development in fruit, affecting fruit coloration, the role of KNOX II proteins in this context remains unclear. In this study, we employ CRISPR/Cas9 to generate knockout mutants of the KNOX II member, SlKN5. These mutants display increased leaf complexity, a phenotype commonly associated with reduced KNOX II activity, as well as enhanced accumulation of chloroplasts and chlorophylls in smaller cells within young, unripe fruit. RNA-seq data analyses indicate that SlKN5 suppresses the transcriptions of genes involved in chloroplast biogenesis, chlorophyll biosynthesis, and gibberellin catabolism. Furthermore, protein-protein interaction assays reveal that SlKN5 physically interacts with three transcriptional repressors from the BLH1-clade of BEL1-like homeodomain (BLH) protein family, SlBLH4, SlBLH5, and SlBLH7, with SlBLH7 showing the strongest interaction. CRISPR/Cas9-mediated knockout of these SlBLH genes confirmed their overlapping roles in suppressing chloroplast biogenesis, chlorophyll biosynthesis, and lycopene cyclization. Transient assays further demonstrate that the SlKN5-SlBLH7 interaction enhances binding capacity to regulatory regions of key chloroplast- and chlorophyll-related genes, including SlAPRR2-like1, SlCAB-1C, and SlGUN4. Collectively, our findings elucidate that the KNOX II SlKN5-SlBLH regulatory modules serve to inhibit fruit greening and subsequently promote lycopene accumulation, thereby fine-tuning the color transition from immature green fruit to mature red fruit.

Exploring the influence of a single-nucleotide mutation in EIN4 on tomato fruit firmness diversity through fruit pericarp microstructure

Tomato (Solanum lycopersicum) stands as one of the most valuable vegetable crops globally, and fruit firmness significantly impacts storage and transportation. To identify genes governing tomato firmness, we scrutinized the firmness of 266 accessions from core collections. Our study pinpointed an ethylene receptor gene, SlEIN4, located on chromosome 4 through a genome-wide association study (GWAS) of fruit firmness in the 266 tomato core accessions. A single-nucleotide polymorphism (SNP) (A → G) of SlEIN4 distinguished lower (AA) and higher (GG) fruit firmness genotypes. Through experiments, we observed that overexpression of SlEIN4AA significantly delayed tomato fruit ripening and dramatically reduced fruit firmness at the red ripe stage compared with the control. Conversely, gene editing of SlEIN4AA with CRISPR/Cas9 notably accelerated fruit ripening and significantly increased fruit firmness at the red ripe stage compared with the control. Further investigations revealed that fruit firmness is associated with alterations in the microstructure of the fruit pericarp. Additionally, SlEIN4AA positively regulates pectinase activity. The transient transformation assay verified that the SNP (A → G) on SlEIN4 caused different genetic effects, as overexpression of SlEIN4GG increased fruit firmness. Moreover, SlEIN4 exerts a negative regulatory role in tomato ripening by impacting ethylene evolution through the abundant expression of ethylene pathway regulatory genes. This study presents the first evidence of the role of ethylene receptor genes in regulating fruit firmness. These significant findings will facilitate the effective utilization of firmness and ripening traits in tomato improvement, offering promising opportunities for enhancing tomato storage and transportation capabilities.

SlBEL11 regulates flavonoid biosynthesis, thus fine-tuning auxin efflux to prevent premature fruit drop in tomato

Auxin regulates flower and fruit abscission, but how developmental signals mediate auxin transport in abscission remains unclear. Here, we reveal the role of the transcription factor BEL1-LIKE HOMEODOMAIN11 (SlBEL11) in regulating auxin transport during abscission in tomato (Solanum lycopersicum). SlBEL11 is highly expressed in the fruit abscission zone, and its expression increases during fruit development. Knockdown of SlBEL11 expression by RNA interference (RNAi) caused premature fruit drop at the breaker (Br) and 3 d post-breaker (Br+3) stages of fruit development. Transcriptome and metabolome analysis of SlBEL11-RNAi lines revealed impaired flavonoid biosynthesis and decreased levels of most flavonoids, especially quercetin, which functions as an auxin transport inhibitor. This suggested that SlBEL11 prevents premature fruit abscission by modulating auxin efflux from fruits, which is crucial for the formation of an auxin response gradient. Indeed, quercetin treatment suppressed premature fruit drop in SlBEL11-RNAi plants. DNA affinity purification sequencing (DAP-seq) analysis indicated that SlBEL11 induced expression of the transcription factor gene SlMYB111 by directly binding to its promoter. Chromatin immunoprecipitation-quantitative polymerase chain reaction and electrophoretic mobility shift assay showed that S. lycopersicum MYELOBLASTOSIS VIRAL ONCOGENE HOMOLOG111 (SlMYB111) induces the expression of the core flavonoid biosynthesis genes SlCHS1, SlCHI, SlF3H, and SlFLS by directly binding to their promoters. Our findings suggest that the SlBEL11-SlMYB111 module modulates flavonoid biosynthesis to fine-tune auxin efflux from fruits and thus maintain an auxin response gradient in the pedicel, thereby preventing premature fruit drop.

The SlGRAS9-SlZHD17 transcriptional cascade regulates chlorophyll and carbohydrate metabolism contributing to fruit quality traits in tomato

Some essential components of fleshy fruits are dependent on photosynthetic activity and carbohydrate metabolism. Nevertheless, the regulatory mechanisms linking chlorophyll and carbohydrate metabolism remain partially understood. Here, we uncovered the role of SlGRAS9 and SlZHD17 transcription factors in controlling chlorophyll and carbohydrate accumulation in tomato fruit. Knockout or knockdown of SlGRAS9 or SlZHD17 resulted in marked increase in chlorophyll content, reprogrammed chloroplast biogenesis and enhanced accumulation of starch and soluble sugars. Combined genome-wide transcriptomic profiling and promoter-binding experiments unveiled a complex mechanism in which the SlGRAS9/SlZHD17 regulatory module modulates the expression of chloroplast and sugar metabolism either via a sequential transcriptional cascade or through binding of both TFs to the same gene promoters, or, alternatively, via parallel pathways where each of the TFs act on different target genes. For instance, the regulation of SlAGPaseS1 and SlSUS1 is mediated by SlZHD17 whereas that of SlVI and SlGLK1 occurs only through SlGRAS9 without the intervention of SlZHD17. Both SlGRAS9 and SlZHD17 can also directly bind the promoter of SlPOR-B to regulate its expression. Taken together, our findings uncover two important regulators acting synergistically to manipulate chlorophyll and carbohydrate accumulation and provide new potential breeding targets for improving fruit quality in fleshy fruits.

New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches

The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.

BEL transcription factors in prominent Solanaceae crops: the missing pieces of the jigsaw in plant development

MAIN CONCLUSION

Understanding BEL transcription factors roles in potato and tomato varies considerably with little overlap. The review suggests reciprocal use of gained results to proceed with the knowledge in both crops The proper development of organs that plants use for reproduction, like fruits or tubers, is crucial for the survival and competitiveness of the species and thus subject to strict regulations. Interestingly, the controls of potato (Solanum tuberosum) tuber and tomato (S. lycopersicum) fruit development use common mechanisms, including the action of the BEL transcription factors (TFs). Although more than ten BEL genes have been identified in either genome, only a few of them have been characterized. The review summarizes knowledge of BEL TFs' roles in these closely related Solanaceae species, focusing on those that are essential for tuberization in potato, namely StBEL5, StBEL11 and StBEL29, and for fruit development in tomato - SlBEL11, SlBL2 and SIBL4. Comprehension of the roles of individual BEL TFs, however, is not yet sufficient. Different levels of understanding of important characteristics are described, such as BEL transcript accumulation patterns, their mobility, BEL protein interaction with KNOX partners, subcellular localisation, and their target genes during initiation and development of the organs in question. A comparison of the knowledge on BEL TFs and their mechanisms of action in potato and tomato may provide inspiration for faster progress in the study of both models through the exchange of information and ideas. Both crops are extremely important for human nutrition. In addition, their production is likely to be threatened by the upcoming climate change, so there is a particular need for breeding using a deep knowledge of control mechanisms.

MaBEL1 regulates banana fruit ripening by activating cell wall and starch degradation-related genes

Banana is a typical subtropical fruit, sensitive to chilling injuries and prone to softening disorder. However, the underlying regulatory mechanisms of the softening disorder caused by cold stress remain obscure. Herein, we found that BEL1-LIKE HOMEODOMAIN transcription factor 1 (MaBEL1) and its associated proteins regulate the fruit softening and ripening process. The transcript and protein levels of MaBEL1 were up-regulated with fruit ripening but severely repressed by the chilling stress. Moreover, the MaBEL1 protein interacted directly with the promoters of the cell wall and starch degradation-related genes, such as MaAMY3, MaXYL32, and MaEXP-A8. The transient overexpression of MaBEL1 alleviated fruit chilling injury and ripening disorder caused by cold stress and promoted fruit softening and ripening of "Fenjiao" banana by inducing ethylene production and starch and cell wall degradation. The accelerated ripening was also validated by the ectopic overexpression in tomatoes. Conversely, MaBEL1-silencing aggravated the chilling injury and ripening disorder and repressed fruit softening and ripening by inhibiting ethylene production and starch and cell wall degradation. MaABI5-like and MaEBF1, the two positive regulators of the fruit softening process, interacted with MaBEL1 to enhance the promoter activity of the starch and cell wall degradation-related genes. Moreover, the F-box protein MaEBF1 does not modulate the degradation of MaBEL1, which regulates the transcription of MaABI5-like protein. Overall, we report a novel MaBEL1-MaEBF1-MaABI5-like complex system that mediates the fruit softening and ripening disorder in "Fenjiao" bananas caused by cold stress.

Transcriptomic analysis reveals the gene regulatory networks involved in leaf and root response to osmotic stress in tomato

Introduction

Tomato (Solanum lycopersicum L.) is a major horticultural crop that is cultivated worldwide and is characteristic of the Mediterranean agricultural system. It represents a key component of the diet of billion people and an important source of vitamins and carotenoids. Tomato cultivation in open field often experiences drought episodes, leading to severe yield losses, since most modern cultivars are sensitive to water deficit. Water stress leads to changes in the expression of stress-responsive genes in different plant tissues, and transcriptomics can support the identification of genes and pathways regulating this response.

Methods

Here, we performed a transcriptomic analysis of two tomato genotypes, M82 and Tondo, in response to a PEG-mediated osmotic treatment. The analysis was conducted separately on leaves and roots to characterize the specific response of these two organs.

Results

A total of 6,267 differentially expressed transcripts related to stress response was detected. The construction of gene co-expression networks defined the molecular pathways of the common and specific responses of leaf and root. The common response was characterized by ABA-dependent and ABA-independent signaling pathways, and by the interconnection between ABA and JA signaling. The root-specific response concerned genes involved in cell wall metabolism and remodeling, whereas the leaf-specific response was principally related to leaf senescence and ethylene signaling. The transcription factors representing the hubs of these regulatory networks were identified. Some of them have not yet been characterized and can represent novel candidates for tolerance.

Discussion

This work shed new light on the regulatory networks occurring in tomato leaf and root under osmotic stress and set the base for an in-depth characterization of novel stress-related genes that may represent potential candidates for improving tolerance to abiotic stress in tomato.

The BELL1-like homeobox gene MdBLH14 from apple controls flowering and plant height via repression of MdGA20ox3

Apple growth and yield are largely dependent on plant height and flowering characteristics. The BELL1-like homeobox (BLH) transcription factors regulate extensive plant biological processes. However, the BLH-mediated regulation of plant height and flowering in apple remains elusive. In the current study, 19 members of the MdBLH family were identified in the apple genome. Segmental duplication and purifying selection are the main reasons for the evolution of the MdBLH genes. A BLH1-like gene, MdBLH14, was isolated and functionally characterized. The MdBLH14 was preferentially expressed in flower buds, and downregulated during the floral induction period. The subcellular localization in tobacco leaves indicated that MdBLH14 is a nuclear protein. Overexpression of MdBLH14 in Arabidopsis led to a significant dwarfing and late-flowering phenotype by hindering active GA accumulation. Additionally, MdKNOX19, another member of the TALE superfamily, physically interacts with MdBLH14 and synergistically inhibits the expression of MdGA20ox3. This is the first report on the function of the MdBLH14 from apple, and its mechanism involving plant flower induction and growth. The data presented here provide a theoretical basis for genetically breeding new apple varieties.

Transcription factor SlBEL2 interferes with GOLDEN2-LIKE and influences green shoulder formation in tomato fruits

Chloroplasts play a crucial role in plant growth and fruit quality. However, the molecular mechanisms of chloroplast development are still poorly understood in fruits. In this study, we investigated the role of the transcription factor SlBEL2 (BEL1-LIKE HOMEODOMAIN 2) in fruit of Solanum lycopersicum (tomato). Phenotypic analysis of SlBEL2 overexpression (OE-SlBEL2) and SlBEL2 knockout (KO-SlBEL2) plants revealed that SlBEL2 has the function of inhibiting green shoulder formation in tomato fruits by affecting the development of fruit chloroplasts. Transcriptome profiling revealed that the expression of chloroplast-related genes such as SlGLK2 and SlLHCB1 changed significantly in the fruit of OE-SlBEL2 and KO-SlBEL2 plants. Further analysis showed that SlBEL2 could not only bind to the promoter of SlGLK2 to inhibit its transcription, but also interacted with the SlGLK2 protein to inhibit the transcriptional activity of SlGLK2 and its downstream target genes. SlGLK2 knockout (KO-SlGLK2) plants exhibited a complete absence of the green shoulder, which was consistent with the fruit phenotype of OE-SlBEL2 plants. SlBEL2 showed an expression gradient in fruits, in contrast with that reported for SlGLK2. In conclusion, our study reveals that SlBEL2 affects the formation of green shoulder in tomato fruits by negatively regulating the gradient expression of SlGLK2, thus providing new insights into the molecular mechanism of fruit green shoulder formation.

Genome-wide characterization of the TALE homeodomain family and the KNOX-BLH interaction network in tomato

Comprehensive yeast and protoplast two-hybrid analyses illustrated the protein-protein interaction network of the TALE homeodomain protein family, KNOX and BLH proteins, in tomato leaf and fruit development. KNOTTED-like (KNOX, KN) proteins and BELL1-like (BLH) proteins, which belong to the same TALE homeodomain family, act together by forming KNOX-BLH heterodimer modules. These modules play crucial roles in regulating multiple developmental processes in plants, like organ differentiation. However, despite the increasing knowledge about individual KNOX and BLH functions, a comprehensive view of their functional protein-protein interaction (PPI) network remains elusive in most plants, including tomato (Solanum lycopersicum), an important model plant to study fruit and leaf development. Here, we characterized eight tomato KNOX genes (SlKN1 to SlKN8) and fourteen tomato BLH genes (SlBLH1 to SlBLH14) by expression profiling, co-expression analysis, and PPI network analysis using two-hybrid techniques in yeasts (Y2H) and protoplasts (P2H). We identified 75 pairwise KNOX-BLH interactions, including ten novel interactors of SlKN2/TKN2, a primary class I KNOX protein, and nine novel interactors of SlKN5, a primary class II KNOX protein. Based on these data, we classified KNOX-BLH modules into several categories, which made us infer the order and combination of the KNOX-BLH modules involved in differentiation processes in leaf and fruit. Notably, the co-expression and interaction of SlKN5 and fruit preferentially expressing BLH1-clade paralogs (SlBLH5/SlBEL11 and SlBLH7) suggest their important roles in regulating fruit differentiation. Furthermore, in silico modeling of the KNOX-BLH modules, sequence analysis, and P2H assay identified several residues and a linker region potentially influencing the affinity of BLHs to KNOXs within their conserved dimerization domains. Together, these findings provide insights into the regulatory mechanism of KNOX-BLH modules underlying tomato organ differentiation.

Identification of TALE Transcription Factor Family and Expression Patterns Related to Fruit Chloroplast Development in Tomato (Solanum lycopersicum L.)

The TALE gene family is an important transcription factor family that regulates meristem formation, organ morphogenesis, signal transduction, and fruit development. A total of 24 genes of the TALE family were identified and analyzed in tomato. The 24 SlTALE family members could be classified into five BELL subfamilies and four KNOX subfamilies. SlTALE genes were unevenly distributed on every tomato chromosome, lacked syntenic gene pairs, and had conserved structures but diverse regulatory functions. Promoter activity analysis showed that cis-elements responsive to light, phytohormone, developmental regulation, and environmental stress were enriched in the promoter of SlTALE genes, and the light response elements were the most abundant. An abundance of TF binding sites was also enriched in the promoter of SlTALE genes. Phenotype identification revealed that the green shoulder (GS) mutant fruits showed significantly enhanced chloroplast development and chlorophyll accumulation, and a significant increase of chlorophyll fluorescence parameters in the fruit shoulder region. Analysis of gene expression patterns indicated that six SlTALE genes were highly expressed in the GS fruit shoulder region, and four SlTALE genes were highly expressed in the parts with less-developed chloroplasts. The protein-protein interaction networks predicted interaction combinations among these SlTALE genes, especially between the BELL subfamilies and the KNOX subfamilies, indicating a complex regulatory network of these SlTALE genes in chloroplast development and green fruit shoulder formation. In conclusion, our result provides detailed knowledge of the SlTALE gene for functional research and the utilization of the TALE gene family in fruit quality improvement.

The Roles of BLH Transcription Factors in Plant Development and Environmental Response

Despite recent advancements in plant molecular biology and biotechnology, providing enough, and safe, food for an increasing world population remains a challenge. The research into plant development and environmental adaptability has attracted more and more attention from various countries. The transcription of some genes, regulated by transcript factors (TFs), and their response to biological and abiotic stresses, are activated or inhibited during plant development; examples include, rooting, flowering, fruit ripening, drought, flooding, high temperature, pathogen infection, etc. Therefore, the screening and characterization of transcription factors have increasingly become a hot topic in the field of plant research. BLH/BELL (BEL1-like homeodomain) transcription factors belong to a subfamily of the TALE (three-amino-acid-loop-extension) superfamily and its members are involved in the regulation of many vital biological processes, during plant development and environmental response. This review focuses on the advances in our understanding of the function of BLH/BELL TFs in different plants and their involvement in the development of meristems, flower, fruit, plant morphogenesis, plant cell wall structure, the response to the environment, including light and plant resistance to stress, biosynthesis and signaling of ABA (Abscisic acid), IAA (Indoleacetic acid), GA (Gibberellic Acid) and JA (Jasmonic Acid). We discuss the theoretical basis and potential regulatory models for BLH/BELL TFs’ action and provide a comprehensive view of their multiple roles in modulating different aspects of plant development and response to environmental stress and phytohormones. We also present the value of BLHs in the molecular breeding of improved crop varieties and the future research direction of the BLH gene family.

Identification and characterization of the BEL1-like genes reveal their potential roles in plant growth and abiotic stress response in tomato

BEL1-like (BELL) transcription factors, belonging to three-amino acid-loop-extension (TALE) superfamily, are ubiquitous in plants. BELLs regulate a wide range of plant biological processes, but the understanding of the BELL family in tomato (Solanum lycopersicum) remains fragmentary. In this study, a total of 14 members of the SlBELL family were identified in tomato. SlBELL proteins contained the conserved BELL and SKY domains that served as typical structures of the BELL family. Syntenic analysis indicated that the BELL orthologs between tomato and other dicots had close evolutionary relationships. Furthermore, the promoters of SlBELLs contained numerous cis-elements related to plant growth, development, and stress response. The SlBELL genes exhibited different tissue-specific expression profiles and responded to cold, heat, and drought stresses, implying their potential functions in regulating multiple aspects of plant growth, as well as in response to abiotic stresses. Through the interaction network prediction, we found that most SlBELL proteins displayed probable interactions with the KNOTTED1-like (KNOX) proteins, another kind of transcription factor in the TALE superfamily. These findings laid foundations for further dissection of the functions of SlBELL genes in tomato, as well as for exploration of the evolutionary relationships of BELL homologs among different plant species.

Integrated analysis of the transcriptome, sRNAome, and degradome reveals the network regulating fruit skin coloration in sponge gourd (Luffa cylindrica)

Sponge gourd fruit skin color is an important quality-related trait because it substantially influences consumer preferences. However, little is known about the miRNAs and genes regulating sponge gourd fruit skin coloration. This study involved an integrated analysis of the transcriptome, sRNAome, and degradome of sponge gourd fruit skins with green skin (GS) and white skin (WS). A total of 4,331 genes were differentially expressed between the GS and WS, with 2,442 down-regulated and 1,889 up-regulated genes in WS. The crucial genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection were identified (e.g., HEMA, CHLM, CRD1, POR, CAO, CLH, SGR, CAB, BEL1-like, KNAT, ARF, and peroxidase genes). Additionally, 167 differentially expressed miRNAs were identified, with 70 up-regulated and 97 down-regulated miRNAs in WS. Degradome sequencing identified 125 differentially expressed miRNAs and their 521 differentially expressed target genes. The miR156, miR159, miR166, miR167, miR172, and miR393 targeted the genes involved in chlorophyll metabolism, chloroplast development, and chloroplast protection. Moreover, a flavonoid biosynthesis regulatory network was established involving miR159, miR166, miR169, miR319, miR390, miR396, and their targets CHS, 4CL, bHLH, and MYB. The qRT-PCR data for the differentially expressed genes were generally consistent with the transcriptome results. Subcellular localization analysis of selected proteins revealed their locations in different cellular compartments, including nucleus, cytoplasm and endoplasmic reticulum. The study findings revealed the important miRNAs, their target genes, and the regulatory network controlling fruit skin coloration in sponge gourd.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

SlZHD17 is involved in the control of chlorophyll and carotenoid metabolism in tomato fruit

Chlorophylls and carotenoids are essential and beneficial substances for both plant and human health. Identifying the regulatory network of these pigments is necessary for improving fruit quality. In a previous study, we identified an R2R3-MYB transcription factor, SlMYB72, that plays an important role in chlorophyll and carotenoid metabolism in tomato fruit. Here, we demonstrated that the SlMYB72-interacting protein SlZHD17, which belongs to the zinc-finger homeodomain transcription factor family, also functions in chlorophyll and carotenoid metabolism. Silencing SlZHD17 in tomato improved multiple beneficial agronomic traits, including dwarfism, accelerated flowering, and earlier fruit harvest. More importantly, downregulating SlZHD17 in fruits resulted in larger chloroplasts and a higher chlorophyll content. Dual-luciferase, yeast one-hybrid and electrophoretic mobility shift assays clarified that SlZHD17 regulates the chlorophyll biosynthesis gene SlPOR-B and chloroplast developmental regulator SlTKN2 in a direct manner. Chlorophyll degradation and plastid transformation were also retarded after suppression of SlZHD17 in fruits, which was caused by the inhibition of SlSGR1, a crucial factor in chlorophyll degradation. On the other hand, the expression of the carotenoid biosynthesis genes SlPSY1 and SlZISO was also suppressed and directly regulated by SlZHD17, which induced uneven pigmentation and decreased the lycopene content in fruits with SlZHD17 suppression at the ripe stage. Furthermore, the protein-protein interactions between SlZHD17 and other pigment regulators, including SlARF4, SlBEL11, and SlTAGL1, were also presented. This study provides new insight into the complex pigment regulatory network and provides new options for breeding strategies aiming to improve fruit quality.

Tomato SlBL4 plays an important role in fruit pedicel organogenesis and abscission

Abscission, a cell separation process, is an important trait that influences grain and fruit yield. We previously reported that BEL1-LIKE HOMEODOMAIN 4 (SlBL4) is involved in chloroplast development and cell wall metabolism in tomato fruit. In the present study, we showed that silencing SlBL4 resulted in the enlargement and pre-abscission of the tomato (Solanum lycopersicum cv. Micro-TOM) fruit pedicel. The anatomic analysis showed the presence of more epidermal cell layers and no obvious abscission zone (AZ) in the SlBL4 RNAi lines compared with the wild-type plants. RNA-seq analysis indicated that the regulation of abscission by SlBL4 was associated with the altered abundance of genes related to key meristems, auxin transporters, signaling components, and cell wall metabolism. Furthermore, SlBL4 positively affected the auxin concentration in the abscission zone. A dual-luciferase reporter assay revealed that SlBL4 activated the transcription of the JOINTLESS, OVATE, PIN1, and LAX3 genes. We reported a novel function of SlBL4, which plays key roles in fruit pedicel organogenesis and abscission in tomatoes.

Progress on Understanding Transcriptional Regulation of Chloroplast Development in Fleshy Fruit

Edible fleshy fruits are important food sources in the human diet. Their yield and nutritional quality have long been considered as breeding targets for improvement. Various developing fleshy fruits with functional chloroplasts are capable of photosynthesis and contribute to fruit photosynthate, leading to the accumulation of metabolites associated with nutritional quality in ripe fruit. Although tomato high-pigment mutants with dark-green fruits have been isolated for more than 100 years, our understanding of the mechanism of chloroplast development in fleshy fruit remain poor. During the past few years, several transcription factors that regulate chloroplast development in fleshy fruit were identified through map-based cloning. In addition, substantial progress has been made in elucidating the mechanisms that how these transcription factors regulate chloroplast development. This review provides a summary and update on this progress, with a framework for further investigations of the multifaceted and hierarchical regulation of chloroplast development in fleshy fruit.