BBX proteins in green plants: insights into their evolution, structure, feature and functional diversification

The B-box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis

The optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B-box (BBX) family of transcription factors regulates several light-mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II BBX family member, BBX13/COL15, as a negative regulator of flowering under long-day conditions. BBX13 is primarily expressed in the leaf vasculature, buds, and flowers, showing a similar spatial expression pattern to the major flowering time regulators CO and FT. bbx13 mutants flower early, while BBX13-overexpressors exhibit delayed flowering under long days. Genetic analyses showed that BBX13 acts upstream to CO and FT and negatively regulates their expression. BBX13 physically interacts with CO and inhibits the CO-mediated transcriptional activation of FT. In addition, BBX13 directly binds to the CORE2 motif on the FT promoter, where CO also binds. Chromatin immunoprecipitation data indicates that BBX13 reduces the in vivo binding of CO on the FT promoter. Through luciferase assay, we found that BBX13 inhibits the CO-mediated transcriptional activation of FT. Together, these findings suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating the binding of CO on the FT promoter.

BBX21 Integrates Brassinosteroid Biosynthesis and Signaling in the Inhibition of Hypocotyl Growth under Shade

B-Box-containing zinc finger transcription factors (BBX) are involved in light-mediated growth, affecting processes such as hypocotyl elongation in Arabidopsis thaliana. However, the molecular and hormonal framework that regulates plant growth through BBX proteins is incomplete. Here, we demonstrate that BBX21 inhibits the hypocotyl elongation through the brassinosteroid (BR) pathway. BBX21 reduces the sensitivity to 24-epiBL, a synthetic active BR, principally at very low concentrations in simulated shade. The biosynthesis profile of BRs showed that two active BR-brassinolide and 28-homobrassinolide-and 8 of 11 intermediates can be repressed by BBX21 under white light (WL) or simulated shade. Furthermore, BBX21 represses the expression of CYTOCHROME P450 90B1 (DWF4/CYP90B1), BRASSINOSTEROID-6-OXIDASE 1 (BR6OX1, CYP85A1) and BR6OX2 (CYP85A2) genes involved in the BR biosynthesis in WL while specifically promoting DWF4 and PHYB ACTIVATION TAGGED SUPPRESSOR 1 (CYP2B1/BAS1) expression in WL supplemented with far-red (WL + FR), a treatment that simulates shade. In addition, BBX21 represses BR signaling genes, such as PACLOBUTRAZOL RESISTANCE1 (PRE1), PRE3 and ARABIDOPSIS MYB-LIKE 2 (MYBL2), and auxin-related and expansin genes, such as INDOLE-3-ACETIC ACID INDUCIBLE 1 (IAA1), IAA4 and EXPANSIN 11 in short-term shade. By a genetic approach, we found that BBX21 acts genetically upstream of BRASSINAZOLE-RESISTANT 1 (BZR1) for the promotion of DWF4 and BAS1 gene expression in shade. We propose that BBX21 integrates the BR homeostasis and shade-light signaling, allowing the fine-tuning of hypocotyl elongation in Arabidopsis.

BBX Genes of Cymbidium ensifolium Exhibited Intense Response to Blue Light in Meristem Induction through Artificial Control

Cymbidium ensifolium, a prominent orchid species, is both highly valued for its ornamental qualities and commercially cultivated. However, the species has a considerable challenge in its breeding efforts due to the lengthy period of 7-8 years required for it to transition from seed germination to flowering. BBXs are multifunctional proteins that modulate the actions of critical regulators including HY5 and COP1 in response to blue light, ultimately impacting photomorphogenic processes. In this study, BBX proteins, known for their essential roles in regulating developmental processes under various light conditions, were chosen as the main subject of investigation. The outcome reveals the presence of 19 BBX genes in their genome. The genes are classified into four separate clades and dispersed among 12 out of the 20 chromosomes. Located in the nuclear, physicochemical properties of proteins, analysis of the promoter region reveals the existence of almost 800 cis-acting elements, highlighting the complex regulatory mechanisms that control the expression of the CeBBXs in various organs, as well as their response to light and hormone inputs. Moreover, the examination of differential expression under blue light therapy reveals their involvement in photomorphogenic reactions. The expression of CeBBXs exhibits substantial alterations as the duration of exposure to blue light increases. These findings contribute to a deeper understanding of the roles that BBX genes serve in C. ensifolium, providing a basis for future studies on the functions and regulatory mechanisms of BBX members in the context of floral initiation and development within this species.

Genome-Wide Identification of B-Box Family Genes and Their Potential Roles in Seed Development under Shading Conditions in Rapeseed

B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development.

Involvement of the tomato BBX16 and BBX17 microProteins in reproductive development

BBXs are B-Box zinc finger proteins that can act as transcription factors and regulators of protein complexes. Several BBX proteins play important roles in plant development. Two Arabidopsis thaliana microProteins belonging to the BBX family, named miP1a and miP1b, homotypically interact with and modulate the activity of other BBX proteins, including CONSTANS, which transcriptionally activates the florigen, FLOWERING LOCUS T. Arabidopsis plants overexpressing miP1a and miP1b showed delayed flowering. In tomato, the closest homologs of miP1a and miP1b are the microProteins SlBBX16 and SlBBX17. This study was aimed at investigating whether the constitutive expression of SlBBX16/17 in Arabidopsis and tomato impacted reproductive development. The heterologous expression of the two tomato microProteins in Arabidopsis caused a delay in the flowering transition; however, the effect was weaker than that observed when the native miP1a/b were overexpressed. In tomato, overexpression of SlBBX17 prolonged the flowering period; this effect was accompanied by downregulation of the flowering inhibitors Self Pruning (SP) and SP5G. SlBBX16 and SlBBX17 can hetero-oligomerize with TCMP-2, a cystine-knot peptide involved in flowering pattern regulation and early fruit development in tomato. The increased expression of both microProteins also caused alterations in tomato fruit development: we observed in the case of SlBBX17 a decrease in the number and size of ripe fruits as compared to WT plants, while for SlBBX16, a delay in fruit production up to the breaker stage. These effects were associated with changes in the expression of GA-responsive genes.

Promotion of seedling germination in Arabidopsis by B-box zinc-finger protein BBX32

Seed germination represents a determinant for plants to enter ecosystems and is thus regarded as a key ecological and agronomic trait. It is tightly regulated by a variety of environmental cues to ensure that seeds germinate under favorable conditions. Here, we characterize BBX32, a B-box zinc-finger protein, as an imbibition-stimulated positive regulator of seed germination. Belonging to subgroup V of the BBX family, BBX32 exhibits distinct characteristics compared with its close counterparts within the same subgroup. BBX32 is transiently induced at both the transcriptional and post-transcriptional levels in the embryo upon water absorption. Genetic evidence indicates that BBX32 acts upstream of the master transcription factor PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) to facilitate light-induced seed germination. BBX32 directly interacts with PIF1, suppressing its protein-interacting and DNA-binding capabilities, thereby relieving PIF1's repression on seed germination. Furthermore, the imbibition-stimulated BBX32 functions in parallel with the light-induced transcription regulator HFR1 to collectively attenuate the transcriptional activities of PIF1. The BBX32-PIF1 de-repression module serves as a molecular connection that enables plants to integrate signals of water availability and light exposure, effectively coordinating the initiation of seed germination.

Genome-wide identification and expression analysis of the CONSTANS-like family in potato (Solanum tuberosum L.)

The CONSTANS-like (COL) gene plays important roles in plant growth, development, and abiotic stress. A total of 15 COL genes are unevenly distributed on eight chromosomes in the potato genome. The amino acid length of the family members was 347-453 aa, the molecular weight was 38.65-49.92 kD, and the isoelectric point was 5.13-6.09. The StCOL family can be divided into three subfamilies by evolutionary tree analysis, with conserved motifs and similar gene structure positions in each subfamily. The analysis of promoter cis-acting elements showed 17 cis-acting elements related to plant hormones, stress, and light response. Collinearity analysis of COL genes of tomato, potato, and Arabidopsis showed that 13 StCOL genes in the different species may have a common ancestor. A total of 10 conserved motifs and six kinds of post-translational modifications in the 15 StCOL proteins were identified. The 15 StCOL genes exhibit a genomic structure consisting of exons and introns, typically ranging from two to four in number. The results showed that 10 genes displayed significant expression across all potato tissues, while the remaining five genes were down-expressed in potato transcriptome data. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis exhibited differential expression of 8 StCOL genes in the potato leaves and tubers at different growth stages, as well as 7 StCOL genes under 2°C treatment conditions. These results suggested that the StCOL gene family may play an important role in regulating potato tuberization and responding to cold stress.

Genome-scale identification, expression and evolution analysis of B-box members in Dendrobium huoshanense

B-box (BBX) proteins have been recognized as vital determinants in plant development, morphogenesis, and adaptive responses to a myriad of environmental stresses. These zinc-finger proteins play a pivotal role in various biological processes. Their influence spans photomorphogenesis, the regulation of flowering, and imparting resilience to a wide array of challenges, encompassing both biotic and abiotic factors. Chromosome localization, gene structure and conserved motifs, phylogenetic analysis, collinearity analysis, expression profiling, fluorescence quantitative analysis, and tobacco transient transformation methods were used for functional localization and expression pattern analysis of the DhBBX gene. A total of 23 DhBBX members were identified from Dendrobium huoshanense. Subsequent phylogenetic evaluations effectively segregated these genes into five discrete evolutionary subsets. The predictions of subcellular localizations revealed that all these proteins were localized in the nucleus. The genetic composition and patterns showed that the majority of these genes consisted of several exons, with a few variations that could be attributed to transposon insertion. A comprehensive analysis using qRT-PCR was conducted to unravel the expression patterns of these genes in D. huoshanense, with a specific concentration on their responses to various hormone treatments and cold stress. Subcellular localization reveals that DhBBX21 and DhBBX9 are located in the nucleus. Our results provide a deep comprehension of the complex regulatory mechanisms of BBXs in response to various environmental and hormonal stimuli. These discoveries encourage further detailed and focused investigations into the operational dynamics of the BBX gene family in a wider range of plant species.

Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.)

BACKGROUND

Mung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking.

RESULTS

In this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response.

CONCLUSIONS

In this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.

Allelic variation of BBX24 is a dominant determinant controlling red coloration and dwarfism in pear

Variation in anthocyanin biosynthesis in pear fruit provides genetic germplasm resources for breeding, while dwarfing is an important agronomic trait, which is beneficial to reduce the management costs and allow for the implementation of high-density cultivation. Here, we combined bulked segregant analysis (BSA), quantitative trait loci (QTL), and structural variation (SV) analysis to identify a 14-bp deletion which caused a frame shift mutation and resulted in the premature translation termination of a B-box (BBX) family of zinc transcription factor, PyBBX24, and its allelic variation termed PyBBX24ΔN14. PyBBX24ΔN14 overexpression promotes anthocyanin biosynthesis in pear, strawberry, Arabidopsis, tobacco, and tomato, while that of PyBBX24 did not. PyBBX24ΔN14 directly activates the transcription of PyUFGT and PyMYB10 through interaction with PyHY5. Moreover, stable overexpression of PyBBX24ΔN14 exhibits a dwarfing phenotype in Arabidopsis, tobacco, and tomato plants. PyBBX24ΔN14 can activate the expression of PyGA2ox8 via directly binding to its promoter, thereby deactivating bioactive GAs and reducing the plant height. However, the nuclear localization signal (NLS) and Valine-Proline (VP) motifs in the C-terminus of PyBBX24 reverse these effects. Interestingly, mutations leading to premature termination of PyBBX24 were also identified in red sports of un-related European pear varieties. We conclude that mutations in PyBBX24 gene link both an increase in pigmentation and a decrease in plant height.

Genome-Wide Analysis of BBX Gene Family in Three Medicago Species Provides Insights into Expression Patterns under Hormonal and Salt Stresses

BBX protein is a class of zinc finger transcription factors that have B-box domains at the N-terminus, and some of these proteins contain a CCT domain at the C-terminus. It plays an important role in plant growth, development, and metabolism. However, the expression pattern of BBX genes in alfalfa under hormonal and salt stresses is still unclear. In this study, we identified a total of 125 BBX gene family members by the available Medicago reference genome in diploid alfalfa (Medicago sativa spp. Caerulea), a model plant (M. truncatula), and tetraploid alfalfa (M. sativa), and divided these members into five subfamilies. We found that the conserved motifs of BBXs of the same subfamily reveal similarities. We analyzed the collinearity relationship and duplication mode of these BBX genes and found that the expression pattern of BBX genes is specific in different tissues. Analysis of the available transcriptome data suggests that some members of the BBX gene family are involved in multiple abiotic stress responses, and the highly expressed genes are often clustered together. Furthermore, we identified different expression patterns of some BBX genes under salt, ethylene, salt and ethylene, salicylic acid, and salt and salicylic acid treatments, verified by qRT-PCR, and analyzed the subcellular localization of MsBBX2, MsBBX17, and MsBBX32 using transient expression in tobacco. The results showed that BBX genes were localized in the nucleus. This study systematically analyzed the BBX gene family in Medicago plants, which provides a basis for the study of BBX gene family tolerance to abiotic stresses.

The DBB Family in Populus trichocarpa: Identification, Characterization, Evolution and Expression Profiles

The B-box proteins (BBXs) encode a family of zinc-finger transcription factors that regulate the plant circadian rhythm and early light morphogenesis. The double B-box (DBB) family is in the class of the B-box family, which contains two conserved B-box domains and lacks a CCT (CO, CO-like and TOC1) motif. In this study, the identity, classification, structures, conserved motifs, chromosomal location, cis elements, duplication events, and expression profiles of the PtrDBB genes were analyzed in the woody model plant Populus trichocarpa. Here, 12 PtrDBB genes (PtrDBB1-PtrDBB12) were identified and classified into four distinct groups, and all of them were homogeneously spread among eight out of seventeen poplar chromosomes. The collinearity analysis of the DBB family genes from P. trichocarpa and two other species (Z. mays and A. thaliana) indicated that segmental duplication gene pairs and high-level conservation were identified. The analysis of duplication events demonstrates an insight into the evolutionary patterns of DBB genes. The previously published transcriptome data showed that PtrDBB genes represented distinct expression patterns in various tissues at different stages. In addition, it was speculated that several PtrDBBs are involved in the responsive to drought stress, light/dark, and ABA and MeJA treatments, which implied that they might function in abiotic stress and phytohormone responses. In summary, our results contribute to the further understanding of the DBB family and provide a reference for potential functional studies of PtrDBB genes in P. trichocarpa.

Natural variation in the promoter of FLOWERING LOCUS T-LIKE 2 in pumpkin (Cucurbita moschata Duch.) is associated with flowering time under short-day conditions

Late flowering is a serious bottleneck in pumpkin (Cucurbita moschata Duch.) agriculture production. Although key genes governing flowering time have been reported in many species, the regulatory network of flowering in pumpkin remains largely obscure, thereby impeding the resolution of industry-wide challenges associated with delayed fruit ripening in pumpkin cultivation. Here, we report an early flowering pumpkin germplasm accession (LXX-4). Using LXX-4 and a late flowering germplasm accession (HYM-9), we constructed an F2 segregation population. A significant difference in FLOWERING LOCUS T-LIKE 2 (FTL2) expression level was identified to be the causal factor of the flowering time trait discrepancy in LXX-4 and HYM-9. Moreover, we have shown that a 21 bp InDel in the FTL2 promoter was the key reason for the waxing and waning of its transcript level. The 21 bp deletion excluded a repressor-AGL19 and recruited activators-BBX7, WRKY40 and SVP to the FTL2 promoter in LXX-4. Together, our data add a useful element to our knowledge which could be used to simplify breeding efforts for early-maturing pumpkin.

COL2-dependent photoperiodic floral induction in Nicotiana sylvestris seems to be lost in the N. sylvestris × N. tomentosiformis hybrid N. tabacum

Introduction

Plants are sessile organisms that maximize reproductive success by adapting to their environment. One of the key steps in the reproductive phase of angiosperms is flower development, requiring the perception of multiple endogenous and exogenous signals integrated via a complex regulatory network. Key floral regulators, including the main transcription factor of the photoperiodic pathway (CONSTANS, CO) and the central floral pathway integrator (FLOWERING LOCUS T, FT), are known in many species.

Methods and results

We identified several CO-like (COL) proteins in tobacco (Nicotiana tabacum). The NtCOL2a/b proteins in the day-neutral plant N. tabacum were most closely related to Arabidopsis CO. We characterized the diurnal expression profiles of corresponding genes in leaves under short-day (SD) and long-day (LD) conditions and confirmed their expression in phloem companion cells. Furthermore, we analyzed the orthologs of NtCOL2a/b in the maternal LD ancestor (N. sylvestris) and paternal, facultative SD ancestor (N. tomentosiformis) of N. tabacum and found that they were expressed in the same diurnal manner. NtCOL2a/b overexpression or knock-out using the CRISPR/Cas9 system did not support a substantial role for the CO homologs in the control of floral transition in N. tabacum. However, NsCOL2 overexpression induced flowering in N. sylvestris under typically non-inductive SD conditions, correlating with the upregulation of the endogenous NsFTd gene.

Discussion

Our results suggest that NsFTd is transcriptionally regulated by NsCOL2 and that this COL2-dependent photoperiodic floral induction seems to be lost in N. tabacum, providing insight into the diverse genetics of photoperiod-dependent flowering in different Nicotiana species.

Involvement of CONSTANS-like Proteins in Plant Flowering and Abiotic Stress Response

The process of flowering in plants is a pivotal stage in their life cycle, and the CONSTANS-like (COL) protein family, known for its photoperiod sensing ability, plays a crucial role in regulating plant flowering. Over the past two decades, homologous genes of COL have been identified in various plant species, leading to significant advancements in comprehending their involvement in the flowering pathway and response to abiotic stress. This article presents novel research progress on the structural aspects of COL proteins and their regulatory patterns within transcription complexes. Additionally, we reviewed recent information about their participation in flowering and abiotic stress response, aiming to provide a more comprehensive understanding of the functions of COL proteins.

Identification and Characterization of the BBX Gene Family in Bambusa pervariabilis × Dendrocalamopsis grandis and Their Potential Role under Adverse Environmental Stresses

Zinc finger protein (ZFP) transcription factors play a pivotal role in regulating plant growth, development, and response to biotic and abiotic stresses. Although extensively characterized in model organisms, these genes have yet to be reported in bamboo plants, and their expression information is lacking. Therefore, we identified 21 B-box (BBX) genes from a transcriptome analysis of Bambusa pervariabilis × Dendrocalamopsis grandis. Consequently, multiple sequence alignments and an analysis of conserved motifs showed that they all had highly similar structures. The BBX genes were divided into four subgroups according to their phylogenetic relationships and conserved domains. A GO analysis predicted multiple functions of the BBX genes in photomorphogenesis, metabolic processes, and biological regulation. We assessed the expression profiles of 21 BBX genes via qRT-PCR under different adversity conditions. Among them, eight genes were significantly up-regulated under water deficit stress (BBX4, BBX10, BBX11, BBX14, BBX15, BBX16, BBX17, and BBX21), nine under salt stress (BBX2, BBX3, BBX7, BBX9, BBX10, BBX12, BBX15, BBX16, and BBX21), twelve under cold stress (BBX1, BBX2, BBX4, BBX7, BBX10, BBX12, BBX14, BBX15, BBX17, BBX18, BBX19, and BBX21), and twelve under pathogen infestation stress (BBX1, BBX2, BBX4, BBX7, BBX10, BBX12, BBX14, BBX15, BBX17, BBX18, BBX19, and BBX21). Three genes (BBX10, BBX15, and BBX21) were significantly up-regulated under both biotic and abiotic stresses. These results suggest that the BBX gene family is integral to plant growth, development, and response to multivariate stresses. In conclusion, we have comprehensively analyzed the BDBBX genes under various adversity stress conditions, thus providing valuable information for further functional studies of this gene family.

Insights into the molecular mechanisms underlying responses of apple trees to abiotic stresses

Apple (Malus[Formula: see text]domestica) is a popular temperate fruit crop worldwide. However, its growth, productivity, and quality are often adversely affected by abiotic stresses such as drought, extreme temperature, and high salinity. Due to the long juvenile phase and highly heterozygous genome, the conventional breeding approaches for stress-tolerant cultivars are time-consuming and resource-intensive. These issues may be resolved by feasible molecular breeding techniques for apples, such as gene editing and marker-assisted selection. Therefore, it is necessary to acquire a more comprehensive comprehension of the molecular mechanisms underpinning apples' response to abiotic stress. In this review, we summarize the latest research progress in the molecular response of apples to abiotic stressors, including the gene expression regulation, protein modifications, and epigenetic modifications. We also provide updates on new approaches for improving apple abiotic stress tolerance, while discussing current challenges and future perspectives for apple molecular breeding.

Comprehensive Characterization of B-Box Zinc Finger Genes in Citrullus lanatus and Their Response to Hormone and Abiotic Stresses

Plant B-BOX (BBX) zinc finger transcription factors play crucial roles in growth and development and the stress response. Although the BBX family has been characterized in various plants, systematic analysis in watermelon is still lacking. In this study, 25 watermelon ClBBX genes were identified. ClBBXs were grouped into five clades (Clade I, II, III, IV, and V) based on their conserved domains and phylogenetic relationships. Most of the ClBBXs (84%) might be localized in the nuclei or cytoplasm. The classification of ClBBXs was consistent with their gene structures. They were unevenly distributed in nine chromosomes except for Chr4 and Chr10, with the largest number of six members in Chr2. Segmental duplications were the major factor in ClBBX family expansion. Some BBXs of watermelon and Arabidopsis evolved from a common ancestor. In total, 254 hormonal and stress-responsive cis elements were discovered in ClBBX promoters. ClBBXs were differentially expressed in tissues, and the expression levels of ClBBX15 and 16 were higher in aboveground tissues than in roots, while the patterns of ClBBX21a, 21b, 21c, 28 and 30b were the opposite. With salicylic acid, methyl jasmonate and salt stress conditions, 17, 18 and 18 ClBBXs exhibited significant expression changes, respectively. In addition, many ClBBXs, including ClBBX29b, 30a and 30b, were also responsive to cold and osmotic stress. In summary, the simultaneous response of multiple ClBBXs to hormonal or abiotic stress suggests that they may have functional interactions in the stress hormone network. Clarifying the roles of key ClBBXs in transcriptional regulation and mediating protein interactions will be an important task. Our comprehensive characterization of the watermelon ClBBX family provides vital clues for the in-depth analysis of their biological functions in stress and hormone signaling pathways.

Identification of BBX gene family and its function in the regulation of microtuber formation in yam

BBX proteins play important roles in all of the major light-regulated developmental processes. However, no systematic analysis of BBX gene family regarding the regulation of photoperiodic microtuber formation has been previously performed in yam. In this study, a systematic analysis on the BBX gene family was conducted in three yam species, with the results, indicating that this gene plays a role in regulating photoperiodic microtuber formation. These analyses included identification the BBX gene family in three yam species, their evolutionary relationships, conserved domains, motifs, gene structure, cis-acting elements, and expressional patterns. Based on these analyses, DoBBX2/DoCOL5 and DoBBX8/DoCOL8 showing the most opposite pattern of expression during microtuber formation were selected as candidate genes for further investigation. Gene expression analysis showed DoBBX2/DoCOL5 and DoBBX8/DoCOL8 were highest expressed in leaves and exhibited photoperiod responsive expression patterns. Besides, the overexpression of DoBBX2/DoCOL5 and DoBBX8/DoCOL8 in potato accelerated tuber formation under short-day (SD) conditions, whereas only the overexpression of DoBBX8/DoCOL8 enhanced the accelerating effect of dark conditions on tuber induction. Tuber number was increased in DoBBX8/DoCOL8 overexpressing plants under dark, as well as in DoBBX2/DoCOL5 overexpressing plants under SD. Overall, the data generated in this study may form the basis of future functional characterizations of BBX genes in yam, especially regarding their regulation of microtuber formation via the photoperiodic response pathway.

Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.)

The B-box (BBX) protein, which is a zinc-finger protein containing one or two B-box domains, plays a crucial role in the growth and development of plants. Plant B-box genes are generally involved in morphogenesis, the growth of floral organs, and various life activities in response to stress. In this study, the sugar beet B-box genes (hereafter referred to as BvBBXs) were identified by searching the homologous sequences of the Arabidopsis thaliana B-box gene family. The gene structure, protein physicochemical properties, and phylogenetic analysis of these genes were systematically analyzed. In this study, 17 B-box gene family members were identified from the sugar beet genome. A B-box domain can be found in all sugar beet BBX proteins. BvBBXs encode 135 to 517 amino acids with a theoretical isoelectric point of 4.12 to 6.70. Chromosome localization studies revealed that BvBBXs were dispersed across nine sugar beet chromosomes except chromosomes 5 and 7. The sugar beet BBX gene family was divided into five subfamilies using phylogenetic analysis. The gene architectures of subfamily members on the same evolutionary tree branch are quite similar. Light, hormonal, and stress-related cis-acting elements can be found in the promoter region of BvBBXs. The BvBBX gene family was differently expressed in sugar beet following Cercospora leaf spot infection, according to RT-qPCR data. It is shown that the BvBBX gene family may influence how the plant reacts to a pathogen infection.

Genome-Wide Analysis of the BBX Genes in Platanus × acerifolia and Their Relationship with Flowering and/or Dormancy

The B-BOX (BBX) gene family is widely distributed in animals and plants and is involved in the regulation of their growth and development. In plants, BBX genes play important roles in hormone signaling, biotic and abiotic stress, light-regulated photomorphogenesis, flowering, shade response, and pigment accumulation. However, there has been no systematic analysis of the BBX family in Platanus × acerifolia. In this study, we identified 39 BBX genes from the P. × acerifolia genome, and used TBtools, MEGA, MEME, NCBI CCD, PLANTCARE and other tools for gene collinearity analysis, phylogenetic analysis, gene structure, conserved domain analysis, and promoter cis-element analysis, and used the qRT-PCR and transcriptome data for analyzing expression pattern of the PaBBX genes. Collinearity analysis indicated segmental duplication was the main driver of the BBX family in P. × acerifolia, and phylogenetic analysis showed that the PaBBX family was divided into five subfamilies: I, II, III, IV and V. Gene structure analysis showed that some PaBBX genes contained super-long introns that may regulate their own expression. Moreover, the promoter of PaBBX genes contained a significant number of cis-acting elements that are associated with plant growth and development, as well as hormone and stress responses. The qRT-PCR results and transcriptome data indicated that certain PaBBX genes exhibited tissue-specific and stage-specific expression patterns, suggesting that these genes may have distinct regulatory roles in P. × acerifolia growth and development. In addition, some PaBBX genes were regularly expressed during the annual growth of P. × acerifolia, corresponding to different stages of flower transition, dormancy, and bud break, indicating that these genes may be involved in the regulation of flowering and/or dormancy of P. × acerifolia. This article provided new ideas for the study of dormancy regulation and annual growth patterns in perennial deciduous plants.

AtBBX29 integrates photomorphogenesis and defense responses in Arabidopsis

Light is an environmental signal that modulates plant defenses against attackers. Recent research has focused on the effects of light on defense hormone signaling; however, the connections between light signaling pathways and the biosynthesis of specialized metabolites involved in plant defense have been relatively unexplored. Here, we show that Arabidopsis BBX29, a protein that belongs to the B-Box transcription factor (TF) family, integrates photomorphogenic signaling with defense responses by promoting flavonoid, sinapate and glucosinolate accumulation in Arabidopsis leaves. AtBBX29 transcript levels were up regulated by light, through photoreceptor signaling pathways. Genetic evidence indicated that AtBBX29 up-regulates MYB12 gene expression, a TF known to induce genes related to flavonoid biosynthesis in a light-dependent manner, and MYB34 and MYB51, which encode TFs involved in the regulation of glucosinolate biosynthesis. Thus, bbx29 knockout mutants displayed low expression levels of key genes of the flavonoid biosynthetic pathway, and the opposite was true in BBX29 overexpression lines. In agreement with the transcriptomic data, bbx29 mutant plants accumulated lower levels of kaempferol glucosides, sinapoyl malate, indol-3-ylmethyl glucosinolate (I3M), 4-methylsulfinylbutyl glucosinolate (4MSOB) and 3-methylthiopropyl glucosinolate (3MSP) in rosette leaves compared to the wild-type, and showed increased susceptibility to the necrotrophic fungus Botrytis cinerea and to the herbivore Spodoptera frugiperda. In contrast, BBX29 overexpressing plants displayed increased resistance to both attackers. In addition, we found that AtBBX29 plays an important role in mediating the effects of ultraviolet-B (UV-B) radiation on plant defense against B. cinerea. Taken together, these results suggest that AtBBX29 orchestrates the accumulation of specific light-induced metabolites and regulates Arabidopsis resistance against pathogens and herbivores.

Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum

BACKGROUND

B-box (BBX) zinc-finger transcription factors play crucial roles in plant growth, development, and abiotic stress responses. Nevertheless, little information is available on sugarcane (Saccharum spp.) BBX genes and their expression profiles.

RESULTS

In the present study, we characterized 25 SsBBX genes in the Saccharum spontaneum genome database. The phylogenetic relationships, gene structures, and expression patterns of these genes during plant growth and under low-nitrogen conditions were systematically analyzed. The SsBBXs were divided into five groups based on phylogenetic analysis. The evolutionary analysis further revealed that whole-genome duplications or segmental duplications were the main driving force for the expansion of the SsBBX gene family. The expression data suggested that many BBX genes (e.g., SsBBX1 and SsBBX13) may be helpful in both plant growth and low-nitrogen stress tolerance.

CONCLUSIONS

The results of this study offer new evolutionary insight into the BBX family members in how sugarcane grows and responds to stress, which will facilitate their utilization in cultivated sugarcane breeding.

NbMLP43 Ubiquitination and Proteasomal Degradation via the Light Responsive Factor NbBBX24 to Promote Viral Infection

The ubiquitin-proteasome system (UPS) plays an important role in virus-host interactions. However, the mechanism by which the UPS is involved in innate immunity remains unclear. In this study, we identified a novel major latex protein-like protein 43 (NbMLP43) that conferred resistance to Nicotiana benthamiana against potato virus Y (PVY) infection. PVY infection strongly induced NbMLP43 transcription but decreased NbMLP43 at the protein level. We verified that B-box zinc finger protein 24 (NbBBX24) interacted directly with NbMLP43 and that NbBBX24, a light responsive factor, acted as an essential intermediate component targeting NbMLP43 for its ubiquitination and degradation via the UPS. PVY, tobacco mosaic virus, (TMV) and cucumber mosaic virus (CMV) infections could promote NbMLP43 ubiquitination and proteasomal degradation to enhance viral infection. Ubiquitination occurred at lysine 38 (K38) within NbMLP43, and non-ubiquitinated NbMLP43(K38R) conferred stronger resistance to RNA viruses. Overall, our results indicate that the novel NbMLP43 protein is a target of the UPS in the competition between defense and viral anti-defense and enriches existing theoretical studies on the use of UPS by viruses to promote infection.

Overexpression of two CONSTANS-like 2 (MiCOL2) genes from mango delays flowering and enhances tolerance to abiotic stress in transgenic Arabidopsis

The CO/COL gene family plays an important role in regulating photoperiod-dependent flowering time in plants. In this study, two COL2 gene homologs, MiCOL2A and MiCOL2B, were isolated from 'SiJiMi' mango, and their expression patterns and functions were characterized. The MiCOL2A and MiCOL2B genes both belonged to the group Ⅰ of CO/COL gene family. MiCOL2A and MiCOL2B exhibited distinct circadian rhythms and were highly expressed in leaves during the flowering induction period. Subcellular localization analysis revealed that MiCOL2A and MiCOL2B are localized in the nucleus. The overexpression of MiCOL2A and MiCOL2B significantly delayed flowering time in Arabidopsis under both long-day (LD) and short-day (SD) conditions. The MiCOL2A and MiCOL2B overexpression Arabidopsis plants exhibited more tolerance to slat and drought stress after abiotic stress treatments, with greater ROS scavenging capacity and protective enzyme activity, less cell damage and death and higher expression of stress response genes than wild type plants. Bimolecular fluorescence complementation (BiFC) analysis showed that MiCOL2A and MiCOL2B interacted with several stress-related proteins, including zinc finger protein 4 (MiZFP4), MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1) and RING zinc finger protein 34 (MiRZFP34). The results indicate that MiCOL2A and MiCOL2B are not only involved in flowering time but also play a positive role in abiotic stress responses in plants.

Multi-layered roles of BBX proteins in plant growth and development

Light and phytohormone are external and internal cues that regulate plant growth and development throughout their life cycle. BBXs (B-box domain proteins) are a group of zinc finger proteins that not only directly govern the transcription of target genes but also associate with other factors to create a meticulous regulatory network to precisely regulate numerous aspects of growth and developmental processes in plants. Recent studies demonstrate that BBXs play pivotal roles in light-controlled plant growth and development. Besides, BBXs have been documented to regulate phytohormone-mediated physiological procedures. In this review, we summarize and highlight the multi-faced role of BBXs, with a focus in photomorphogenesis, photoperiodic flowering, shade avoidance, abiotic stress, and phytohormone-mediated growth and development in plant.

The sweet potato B-box transcription factor gene IbBBX28 negatively regulates drought tolerance in transgenic Arabidopsis

B-box (BBX) which are a class of zinc finger transcription factors, play an important role in regulating of photoperiod, photomorphogenesis, and biotic and abiotic stresses in plants. However, there are few studies on the involvement of BBX transcription factors in response to abiotic stresses in sweet potato. In this paper, we cloned the DNA and promoter sequences of IbBBX28. There was one B-box conserved domain in IbBBX28, and the expression of IbBBX28 was induced under drought stress. Under drought stress, compared to wild type Arabidopsis, the protective enzyme activities (SOD, POD, and CAT) were all decreased in IbBBX28-overexpression Arabidopsis but increased in the mutant line bbx28, while the MDA content was increased in the IbBBX28-overexpression Arabidopsis and decreased in the bbx28. Moreover, the expression levels of the resistance-related genes showed the same trend as the protective enzyme activities. These results showed that IbBBX28 negatively regulates drought tolerance in transgenic Arabidopsis. Additionally, the yeast two-hybrid and BiFC assays verified that IbBBX28 interacted with IbHOX11 and IbZMAT2. The above results provide important clues for further studies on the role of IbBBX28 in regulating the stress response in sweet potato.

AcBBX5, a B-box transcription factor from pineapple, regulates flowering time and floral organ development in plants

Flowering is an important factor to ensure the success of plant reproduction, and reasonable flowering time is crucial to the crop yield. BBX transcription factors can regulate several growth and development processes. However, there is little research on whether BBX is involved in flower formation and floral organ development of pineapple. In this study, AcBBX5, a BBX family gene with two conserved B-box domains, was identified from pineapple. Subcellular localization analysis showed that AcBBX5 was located in the nucleus. Transactivation analysis indicated that AcBBX5 had no significant toxic effects on the yeast system and presented transcriptional activation activity in yeast. Overexpression of AcBBX5 delayed flowering time and enlarged flower morphology in Arabidopsis. Meanwhile, the expression levels of AtFT, AtSOC1, AtFUL and AtSEP3 were decreased, and the transcription levels of AtFLC and AtSVP were increased in AcBBX5-overexpressing Arabidopsis, which might lead to delayed flowering of transgenic plants. Furthermore, transcriptome data and QRT-PCR results showed that AcBBX5 was expressed in all floral organs, with the high expression levels in stamens, ovaries and petals. Yeast one-hybrid and dual luciferase assay results showed that AcBBX5 bound to AcFT promoter and inhibited AcFT gene expression. In conclusion, AcBBX5 was involved in flower bud differentiation and floral organ development, which provides an important reference for studying the functions of BBX and the molecular regulation of flower.

Transcription factors BBX11 and HY5 interdependently regulate the molecular and metabolic responses to UV-B

UV-B radiation acts as a developmental cue and a stress factor for plants, depending on dose. Activation of the transcription factor ELONGATED HYPOCOTYL 5 (HY5) in a UV RESISTANCE LOCUS 8 (UVR8)-dependent manner leads to the induction of a broad set of genes under UV-B. However, the underlying molecular mechanisms regulating this process are less understood. Here, we use molecular, biochemical, genetic, and metabolomic tools to identify the B-BOX transcription factor B-BOX PROTEIN 11 (BBX11) as a component of the molecular response to UV-B in Arabidopsis (Arabidopsis thaliana). BBX11 expression is induced by UV-B in a dose-dependent manner. Under low UV-B, BBX11 regulates hypocotyl growth suppression, whereas it protects plants exposed to high UV-B radiation by promoting the accumulation of photo-protective phenolics and antioxidants, and inducing DNA repair genes. Our genetic studies indicate that BBX11 regulates hypocotyl elongation under UV-B partially dependent on HY5. Overexpression of BBX11 can partially rescue the high UV-B sensitivity of hy5, suggesting that HY5-mediated UV-B stress tolerance is partially dependent on BBX11. HY5 regulates the UV-B-mediated induction of BBX11 by directly binding to its promoter. BBX11 reciprocally regulates the mRNA and protein levels of HY5. We report here the role of a BBX11-HY5 feedback loop in regulating photomorphogenesis and stress tolerance under UV-B.

Rice and Arabidopsis BBX proteins: toward genetic engineering of abiotic stress resistant crops

Productivity of crop plants are enormously affected by biotic and abiotic stresses. The co-occurrence of several abiotic stresses may lead to death of crop plants. Hence, it is the responsibility of plant scientists to develop crop plants equipped with multistress tolerance pathways. A subgroup of zinc finger transcription factor family, known as B-box (BBX) proteins, play a key role in light and hormonal regulation pathways. In addition, BBX proteins act as key regulatory proteins in many abiotic stress regulatory pathways, including Ultraviolet-B (UV-B), salinity, drought, heat and cold, and heavy metal stresses. Most of the BBX proteins identified in Arabidopsis and rice respond to more than one abiotic stress. Considering the requirement of improving rice for multistress tolerance, this review discusses functionally characterized Arabidopsis and rice BBX proteins in the development of abiotic stress responses. Furthermore, it highlights the participation of BBX proteins in multistress regulation and crop improvement through genetic engineering.

Genome-Wide Identification and Analysis of the BBX Gene Family and Its Role in Carotenoid Biosynthesis in Wolfberry (Lycium barbarum L.)

The B-box proteins (BBXs) are a family of zinc-finger transcription factors with one/two B-Box domain(s) and play important roles in plant growth and development as well as stress responses. Wolfberry (Lycium barbarum L.) is an important traditional medicinal and food supplement in China, and its genome has recently been released. However, comprehensive studies of BBX genes in Lycium species are lacking. In this study, 28 LbaBBX genes were identified and classified into five clades by a phylogeny analysis with BBX proteins from Arabidopsis thaliana and the LbaBBXs have similar protein motifs and gene structures. Promoter cis-regulatory element prediction revealed that LbaBBXs might be highly responsive to light, phytohormone, and stress conditions. A synteny analysis indicated that 23, 20, 8, and 5 LbaBBX genes were orthologous to Solanum lycopersicum, Solanum melongena, Capsicum annuum, and Arabidopsis thaliana, respectively. The gene pairs encoding LbaBBX proteins evolved under strong purifying selection. In addition, the carotenoid content and expression patterns of selected LbaBBX genes were analyzed. LbaBBX2 and LbaBBX4 might play key roles in the regulation of zeaxanthin and antheraxanthin biosynthesis. Overall, this study improves our understanding of LbaBBX gene family characteristics and identifies genes involved in the regulation of carotenoid biosynthesis in wolfberry.

Genome-Wide Identification, Characterization, and Expression Profile Analysis of CONSTANS-like Genes in Woodland Strawberry (Fragaria vesca)

CONSTANS-like (CO-like) gene is one of the most important regulators in the flowering process of the plant, playing a core role in the photoperiodic flowering induction pathway. In this study, we identified 10 distinct CO-like genes (FveCOs) in woodland strawberry (Fragaria vesca). They were classified into three groups with specific gene structure characteristics or protein domains in each group. The effect of selection pressure on the FveCOs in the woodland strawberry was tested by Ka/Ks, and it was shown that the evolution rate of FveCOs was controlled by purification selection factors. Intraspecific synteny analysis of woodland strawberry FveCOs showed that at least one duplication event existed in the gene family members. Collinearity analysis of woodland strawberry genome with genomes of Arabidopsis, rice (Oryza sativa), and apple (Malus × domestica) showed that CO-like genes of F. vesca and Malus × domestica owned higher similarity for their similar genomes compared with those of other two species. The FveCOs showed different tissue-specific expression patterns. Moreover, real-time quantitative PCR results revealed that the expressions of the most FveCOs followed a 24-h rhythm oscillation under both long-day (LD) and short-day (SD) conditions. Further expression analysis showed that the individual expression changing profile of FveCO3 and FveCO5 was opposite to each other under both LD and SD conditions. Moreover, the expression of FveCO3 and FveCO5 was both negatively correlated with the flowering time variation of the woodland strawberry grown under LD and SD conditions, indicating their potential vital roles in the photoperiodic flowering regulation. Further protein interaction network analysis also showed that most of the candidate interaction proteins of FveCO3 and FveCO5 were predicted to be the flowering regulators. Finally, LUC assay indicated that both FveCO3 and FveCO5 could bind to the promoter of FveFT1, the key regulator of flowering regulation in the woodland strawberry, and thus activate its expression. Taken together, this study laid a foundation for understanding the exact roles of FveCOs in the reproductive development regulation of the woodland strawberry, especially in the photoperiodic flowering process.

Apple SINA E3 ligase MdSINA3 negatively mediates JA-triggered leaf senescence by ubiquitinating and degrading the MdBBX37 protein

Jasmonic acid (JA) induces chlorophyll degradation and leaf senescence. B-box (BBX) proteins play important roles in the modulation of leaf senescence, but the molecular mechanism of BBX protein-mediated leaf senescence remains to be further studied. Here, we identified the BBX protein MdBBX37 as a positive regulator of JA-induced leaf senescence in Malus domestica (apple). Further studies showed that MdBBX37 interacted with the senescence regulatory protein MdbHLH93 to enhance its transcriptional activation on the senescence-associated gene MdSAG18, thereby promoting leaf senescence. Moreover, the JA signaling repressor MdJAZ2 interacted with MdBBX37 and interfered with the interaction between MdBBX37 and MdbHLH93, thereby negatively mediating MdBBX37-promoted leaf senescence. In addition, the E3 ubiquitin ligase MdSINA3 delayed MdBBX37-promoted leaf senescence through targeting MdBBX37 for degradation. The MdJAZ2-MdBBX37-MdbHLH93-MdSAG18 and MdSINA3-MdBBX37 modules realized the precise modulation of JA on leaf senescence. In parallel, our data demonstrate that MdBBX37 was involved in abscisic acid (ABA)- and ethylene-mediated leaf senescence through interacting with the ABA signaling regulatory protein MdABI5 and ethylene signaling regulatory protein MdEIL1, respectively. Taken together, our results not only reveal the role of MdBBX37 as an integration node in JA-, ABA- and ethylene-mediated leaf senescence, but also provide new insights into the post-translational modification of BBX proteins.

Two B-Box Proteins, MaBBX20 and MaBBX51, Coordinate Light-Induced Anthocyanin Biosynthesis in Grape Hyacinth

Floral colour is an important agronomic trait that influences the commercial value of ornamental plants. Anthocyanins are a class of flavonoids and confer diverse colours, and elucidating the molecular mechanisms that regulate their pigmentation could facilitate artificial manipulation of flower colour in ornamental plants. Here, we investigated the regulatory mechanism of light-induced anthocyanin biosynthesis during flower colouration in grape hyacinth (Muscari spp.). We studied the function of two B-box proteins, MaBBX20 and MaBBX51. The qPCR revealed that MaBBX20 and MaBBX51 were associated with light-induced anthocyanin biosynthesis. Both MaBBX20 and MaBBX51 are transcript factors and are specifically localised in the nucleus. Besides, overexpression of MaBBX20 in tobacco slightly increased the anthocyanin content of the petals, but reduced in MaBBX51 overexpression lines. The yeast one-hybrid assays indicated that MaBBX20 and MaBBX51 did not directly bind to the MaMybA or MaDFR promoters, but MaHY5 did. The BiFC assay revealed that MaBBX20 and MaBBX51 physically interact with MaHY5. A dual luciferase assay further confirmed that the MaBBX20-MaHY5 complex can strongly activate the MaMybA and MaDFR transcription in tobacco. Moreover, MaBBX51 hampered MaBBX20-MaHY5 complex formation and repressed MaMybA and MaDFR transcription by physically interacting with MaHY5 and MaBBX20. Overall, the results suggest that MaBBX20 positively regulates light-induced anthocyanin biosynthesis in grape hyacinth, whereas MaBBX51 is a negative regulator.

Activation and negative feedback regulation of SlHY5 transcription by the SlBBX20/21-SlHY5 transcription factor module in UV-B signaling

In tomato (Solanum lycopersicum) and other plants, the photoreceptor UV-RESISTANCE LOCUS 8 regulates plant UV-B photomorphogenesis by modulating the transcription of many genes, the majority of which depends on the transcription factor ELONGATED HYPOCOTYL 5 (HY5). HY5 transcription is induced and then rapidly attenuated by UV-B. However, neither the transcription factors that activate HY5 transcription nor the mechanism for its attenuation during UV-B signaling is known. Here, we report that the tomato B-BOX (BBX) transcription factors SlBBX20 and SlBBX21 interact with SlHY5 and bind to the SlHY5 promoter to activate its transcription. UV-B-induced SlHY5 expression and SlHY5-controlled UV-B responses are normal in slbbx20 and slbbx21 single mutants, but strongly compromised in the slbbx20 slbbx21 double mutant. Surprisingly, UV-B responses are also compromised in lines overexpressing SlBBX20 or SlBBX21. Both SlHY5 and SlBBX20 bind to G-box1 in the SlHY5 promoter. SlHY5 outcompetes SlBBX20 for binding to the SlHY5 promoter in vitro, and inhibits the association of SlBBX20 with the SlHY5 promoter in vivo. Overexpressing 35S:SlHY5-FLAG in the WT background inhibits UV-B-induced endogenous SlHY5 expression. Together, our results reveal the critical role of the SlBBX20/21-SlHY5 module in activating the expression of SlHY5, the gene product of which inhibits its own gene transcription under UV-B, forming an autoregulatory negative feedback loop that balances SlHY5 transcription in plants.

Genome-Wide Identification of the B-Box Gene Family and Expression Analysis Suggests Their Potential Role in Photoperiod-Mediated β-Carotene Accumulation in the Endocarp of Cucumber (Cucumis sativus L.) Fruit

Carotenoids are indispensable to plants and essential for human nutrition and health. Carotenoid contents are strongly influenced by light through light-responsive genes such as B-Box (BBX) genes. BBX proteins, a class of zinc-finger transcription factors, mediate many light-signaling pathways, leading to the biosynthesis of important metabolites in plants. However, the identification of the BBX gene family and expression analysis in response to photoperiod-mediated carotenoid accumulation in cucumber remains unexplored. We performed a genome-wide study and determined the expression of cucumber BBX genes (hereafter referred to as CsaBBXs genes) in the endocarp of Xishuangbanna cucumber fruit (a special type of cucumber accumulating a high level of β-carotene in the endocarp) using an RNA-seq analysis of plants previously subjected to two photoperiodic conditions. Here, 26 BBX family genes were identified in the cucumber genome and named serially CsaBBX1 through CsaBBX26. We characterized CsaBBX genes in terms of their phylogenetic relationships, exon-intron structures, cis-acting elements, and syntenic relationships with Arabidopsis thaliana (L.) Heynh. RNA-seq analysis revealed a varied expression of CsaBBX genes under photoperiod treatment. The analysis of CsaBBXs genes revealed a strong positive correlation between CsaBBX17 and carotenoid biosynthetic pathway genes (phytoene synthase, ζ-carotene desaturase, lycopene ε-cyclase, β-carotene hydroxylase-1), thus suggesting its involvement in β-carotene biosynthesis. Additionally, nine CsaBBX genes (CsaBBX 4, 5, 7, 9, 11, 13, 15, 17 and 22) showed a significant positive correlation with β-carotene content. The selected CsaBBX genes were verified by qRT-PCR and confirmed the validity of RNA-seq data. The results of this study established the genome-wide analysis of the cucumber BBX family and provide a framework for understanding their biological role in carotenoid accumulation and photoperiodic responses. Further investigations of CsaBBX genes are vital since they are promising candidate genes for the functional analysis of carotenoid biosynthesis and can provide genetic tools for the molecular breeding of carotenoids in plants.

Phytochrome interacting factor MdPIF7 modulates anthocyanin biosynthesis and hypocotyl growth in apple

Light affects many physiological and developmental processes of plants by regulating the expression and activity of light-responsive proteins. Among them, phytochrome interacting factors (PIFs) play pivotal roles in the regulation of anthocyanin accumulation and hypocotyl growth. However, the molecular mechanism is not well understood, especially in woody plants, such as apple (Malus × domestica). In this study, we identified a light-responsive PIF protein, MdPIF7, in apple and investigated the molecular mechanism of its regulation of anthocyanin biosynthesis and hypocotyl growth. We found that overexpression of MdPIF7 decreased anthocyanin accumulation in transgenic apple materials and promoted hypocotyl elongation in ectopically expressed Arabidopsis (Arabidopsis thaliana). Further investigation showed that MdPIF7 functioned by interacting with B-box 23 (MdBBX23), a positive regulator of anthocyanin biosynthesis in apple and hypocotyl growth inhibition in ectopically expressed Arabidopsis, and attenuating the transcriptional activation of MdBBX23 on LONG HYPOCOTYL 5 (MdHY5). In addition, MdPIF7 interacted with basic region leucine zipper 44 (MdbZIP44) and ethylene response factor 38 (MdERF38), two positive regulators of anthocyanin biosynthesis, and it negatively regulated MdbZIP44- and MdERF38-promoted anthocyanin accumulation by interfering with the interaction between MdbZIP44/MdERF38 and MdMYB1. Taken together, our results reveal that MdPIF7 regulates anthocyanin biosynthesis in apple and hypocotyl growth in ectopically expressed Arabidopsis through MdPIF7-MdBBX23-MdHY5 and MdPIF7-MdbZIP44/MdERF38-MdMYB1 modules. Our findings enrich the functional studies of PIF proteins and provide insights into the molecular mechanism of PIF-mediated anthocyanin biosynthesis and hypocotyl growth.

Genome-Wide Characterization and Anthocyanin-Related Expression Analysis of the B-BOX Gene Family in Capsicum annuum L

The transcription factors, B-box (BBX), belong to a subfamily of the zinc finger family of proteins and exhibit multiple biological functions in plant growth, development, and abiotic stress response pathways. In this study, a total of 23 CaBBX members were identified using the pepper reference genome database. According to the gene structure, conserved domains, and the phylogenetic tree, 23 CaBBX genes were divided into four groups, wherein the analysis of the promoter region indicated the presence of cis-acting elements related to plant development, hormones, and stress response. Interspecies collinearity analysis showed that the CaBBXs had three duplicated gene pairs, and the highest gene density was found on chromosomes 2 and 7. Transcriptome RNA-seq data and quantitative polymerase chain reaction (qRT-PCR) analysis of pepper plants spanning the entire period showed that more than half of the CaBBX genes were widely expressed in diversity tissues of pepper. Co-expression network analysis indicated that the CaBBXs and the anthocyanin structural genes had a close co-expression relationship. Thus, it was reasonably speculated that the CaBBX genes may be involved in the regulation of anthocyanin biosynthesis. Overall, this study involved the genome-wide characterization of the CaBBX family and may serve as a solid foundation for further investigations on CaBBX genes involved in the anthocyanin synthesis mechanisms and development in pepper.

The IbBBX24-IbTOE3-IbPRX17 module enhances abiotic stress tolerance by scavenging reactive oxygen species in sweet potato

Soil salinity and drought limit sweet potato yield. Scavenging of reactive oxygen species (ROS) by peroxidases (PRXs) is essential during plant stress responses, but how PRX expression is regulated under abiotic stress is not well understood. Here, we report that the B-box (BBX) family transcription factor IbBBX24 activates the expression of the class III peroxidase gene IbPRX17 by binding to its promoter. Overexpression of IbBBX24 and IbPRX17 significantly improved the tolerance of sweet potato to salt and drought stresses, whereas reducing IbBBX24 expression increased their susceptibility. Under abiotic stress, IbBBX24- and IbPRX17-overexpression lines showed higher peroxidase activity and lower H₂ O₂ accumulation compared with the wild-type. RNA sequencing analysis revealed that IbBBX24 modulates the expression of genes encoding ROS scavenging enzymes, including PRXs. Moreover, interaction between IbBBX24 and the APETALA2 (AP2) protein IbTOE3 enhances the ability of IbBBX24 to activate IbPRX17 transcription. Overexpression of IbTOE3 improved the tolerance of tobacco plants to salt and drought stresses by scavenging ROS. Together, our findings elucidate the mechanism underlying the IbBBX24-IbTOE3-IbPRX17 module in response to abiotic stress in sweet potato and identify candidate genes for developing elite crop varieties with enhanced abiotic stress tolerance.

B-box containing protein 1 from Malus domestica (MdBBX1) is involved in the abiotic stress response

B-box proteins (BBXs), which act as transcription factors, mainly regulate photomorphogenesis. However, the molecular functions underlying the activity of plant BBXs in response to abiotic stress remain largely unclear. In this investigation, we found that a BBX from Malus domestica (MdBBX1) was involved in the response to various abiotic stresses. The expression of MdBBX1 was significantly upregulated in response to abiotic stresses and abscisic acid (ABA). Recombinant MdBBX1 increased stress tolerance in Escherichia coli cells. In addition, overexpression of MdBBX1 in Arabidopsis decreased sensitivity to exogenous ABA, resulting in a germination rate and root length that were greater and longer, respectively, than those of wild-type (WT) plants. Moreover, the expression of ABI5 was decreased in MdBBX1-overexpressing lines under ABA treatment. After salt and drought treatments, compared with the WT plants, the MdBBX1 transgenic plants displayed enhanced tolerance and had a higher survival rate. Furthermore, under salt stress, increased proline (PRO) contents, decreased levels of malondialdehyde (MDA), increased activity of antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX)) and decreased accumulation of reactive oxygen species (ROS) were observed in the MdBBX1-overexpressing plants. Overall, our results provide evidence that MdBBX1 might play a critical role in the regulation of abiotic stress tolerance by reducing the generation of ROS.

Zinc-finger protein MdBBX7/MdCOL9, a target of MdMIEL1 E3 ligase, confers drought tolerance in apple

Water deficit is one of the main challenges for apple (Malus × domestica) growth and productivity. Breeding drought-tolerant cultivars depends on a thorough understanding of the drought responses of apple trees. Here, we identified the zinc-finger protein B-BOX 7/CONSTANS-LIKE 9 (MdBBX7/MdCOL9), which plays a positive role in apple drought tolerance. The overexpression of MdBBX7 enhanced drought tolerance, whereas knocking down MdBBX7 expression reduced it. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis identified one cis-element of MdBBX7, CCTTG, as well as its known binding motif, the T/G box. ChIP-seq and RNA-seq identified 1,197 direct targets of MdBBX7, including ETHYLENE RESPONSE FACTOR (ERF1), EARLY RESPONSIVE TO DEHYDRATION 15 (ERD15), and GOLDEN2-LIKE 1 (GLK1) and these were further verified by ChIP-qPCR and electronic mobility shift assays. Yeast two-hybrid screen identified an interacting protein of MdBBX7, RING-type E3 ligase MYB30-INTERACTING E3 LIGASE 1 (MIEL1). Further examination revealed that MdMIEL1 could mediate the ubiquitination and degradation of MdBBX7 by the 26S proteasome pathway. Genetic interaction analysis suggested that MdMIEL1 acts as an upstream factor of MdBBX7. In addition, MdMIEL1 was a negative regulator of the apple drought stress response. Taken together, our results illustrate the molecular mechanisms by which the MdMIEL1-MdBBX7 module influences the response of apple to drought stress.

BBX21 reduces abscisic acid sensitivity, mesophyll conductance and chloroplast electron transport capacity to increase photosynthesis and water use efficiency in potato plants cultivated under moderated drought

The B-box (BBX) proteins are zinc-finger transcription factors with a key role in growth and developmental regulatory networks mediated by light. AtBBX21 overexpressing (BBX21-OE) potato (Solanum tuberosum) plants, cultivated in optimal water conditions, have a higher photosynthesis rate and stomatal conductance without penalty in water use efficiency (WUE) and with a higher tuber yield. In this work, we cultivated potato plants in two water regimes: 100 and 35% field capacity of water restriction that imposed leaf water potentials between -0.3 and -1.2 MPa for vegetative and tuber growth during 14 or 28 days, respectively. We found that 42-day-old plants of BBX21-OE were more tolerant to water restriction with higher levels of chlorophylls and tuber yield than wild-type spunta (WT) plants. In addition, the BBX21-OE lines showed higher photosynthesis rates and WUE under water restriction during the morning. Mechanistically, we found that BBX21-OE lines were more tolerant to moderated drought by enhancing mesophyll conductance (g_m ) and maximum capacity of electron transport (J_max ), and by reducing abscisic acid (ABA) sensitivity in plant tissues. By RNA-seq analysis, we found 204 genes whose expression decreased by drought in WT plants and expressed independently of the water condition in BBX21-OE lines as SAP12, MYB73, EGYP1, TIP2-1 and DREB2A, and expressions were confirmed by quantitative polymerase chain reaction. These results suggest that BBX21 interplays with the ABA and growth signaling networks, improving the photosynthetic behavior in suboptimal water conditions with an increase in potato tuber yield.

Transcriptomic study of the night break in Chenopodium rubrum reveals possible upstream regulators of the floral activator CrFTL1

The transition from vegetative to reproductive phases is the most fundamental and tightly controlled switch in the life of flowering plants. The short-day plant Chenopodium rubrum is a fast cycling annual plant lacking a juvenile phase. It can be induced to flowering at the seedling stage by exposure to a single period of darkness. This floral induction may then be cancelled by a short pulse of red light at midnight called night break (NB), which also inhibits the floral activator FLOWERING LOCUS T LIKE 1 (CrFTL1). We performed a comparative transcriptomic study between C. rubrum seedlings treated by NB and ones growing through uninterrupted night, and found about six hundred differentially expressed genes, including the B-BOX DOMAIN (BBX) genes. We focused on the CrBBX19 and BOLTING TIME CONTROL 1 (BTC1) genes, homologous to the upstream regulators of the BvFT2, a floral inducer in sugar beet. The transcription patterns of the two genes were compatible with their putative role as a sensor of the dark period length optimal for flowering (CrBBX19), and a signal of lights-on (CrBTC1), but the participation of other genes cannot be excluded. The expression profiles of CrBBX19 and the homolog of the core endogenous clock gene LATE ELONGATED HYPOCOTYL (LHY) were highly similar, which suggested their co-regulation.

Genome-Wide Identification, Evolution, and Comparative Analysis of B-Box Genes in Brassica rapa, B. oleracea, and B. napus and Their Expression Profiling in B. rapa in Response to Multiple Hormones and Abiotic Stresses

The B-box zinc-finger transcription factors are important for plant growth, development, and various physiological processes such as photomorphogenesis, light signaling, and flowering, as well as for several biotic and abiotic stress responses. However, there is relatively little information available regarding Brassica B-box genes and their expression. In this study, we identified 51, 52, and 101 non-redundant genes encoding B-box proteins in Brassica rapa (BrBBX genes), B. oleracea (BoBBX genes), and B. napus (BnBBX genes), respectively. A whole-genome identification, characterization, and evolutionary analysis (synteny and orthology) of the B-box gene families in the diploid species B. rapa (A genome) and B. oleracea (C genome) and in the allotetraploid species B. napus (AC genome) revealed segmental duplications were the major contributors to the expansion of the BrassicaBBX gene families. The BrassicaBBX genes were classified into five subgroups according to phylogenetic relationships, gene structures, and conserved domains. Light-responsive cis-regulatory elements were detected in many of the BBX gene promoters. Additionally, BrBBX expression profiles in different tissues and in response to various abiotic stresses (heat, cold, salt, and drought) or hormones (abscisic acid, methyl jasmonate, and gibberellic acid) were analyzed by qRT-PCR. The data indicated that many B-box genes (e.g., BrBBX13, BrBBX15, and BrBBX17) may contribute to plant development and growth as well as abiotic stress tolerance. Overall, the identified BBX genes may be useful as functional genetic markers for multiple stress responses and plant developmental processes.

CpBBX19, a B-Box Transcription Factor Gene of Chimonanthus praecox, Improves Salt and Drought Tolerance in Arabidopsis

Zinc-finger proteins are important transcription factors in plants, responding to adversity and regulating the growth and development of plants. However, the roles of the BBX gene family of zinc-finger proteins in wintersweet (Chimonanthus praecox) have yet to be elucidated. In this study, a group IV subfamily BBX gene, CpBBX19, was identified and isolated from wintersweet. Quantitative real-time PCR (qRT-PCR) analyses revealed that CpBBX19 was expressed in all tissues and that expression was highest in cotyledons and inner petals. CpBBX19 was also expressed in all flower development stages, with the highest expression detected in early initiating bloom, followed by late initiating bloom and bloom. In addition, the expression of CpBBX19 was induced by different abiotic stress (cold, heat, NaCl, and drought) and hormone (ABA and MeJA) treatments. Heterologous expression of CpBBX19 in Arabidopsis thaliana (Arabidopsis) enhanced the tolerance of this plant to salt and drought stress as electrolyte leakage and malondialdehyde (MDA) concentrations in transgenic Arabidopsis after stress treatments were significantly lower than those in wild-type (WT) plants. In conclusion, this research demonstrated that CpBBX19 plays a role in the abiotic stress tolerance of wintersweet. These findings lay a foundation for future studies on the BBX gene family of wintersweet and enrich understanding of the molecular mechanism of stress resistance in wintersweet.

Genome-wide analysis of BBX gene family in Tartary buckwheat (Fagopyrum tataricum)

BBX (B-box), a zinc finger transcription factor with one or two B-box domains, plays an important role in plant photomorphogenesis, growth, and development as well as response to environmental changes. In this study, 28 Tartary buckwheat BBX (FtBBX) genes were identified and screened using a comparison program. Their physicochemical properties, gene structures, conserved motifs, distribution in chromosomal, and phylogeny of the coding proteins, as well as their expression patterns, were analyzed. In addition, multiple collinearity analysis in three monocots and three dicot species illustrated that the BBX proteins identified from monocots clustered separately from those of dicots. Moreover, the expression of 11 candidate BBX genes with probable involvement in the regulation of anthocyanin biosynthesis was analyzed in the sprouts of Tartary buckwheat during light treatment. The results of gene structure analysis showed that all the 28 BBX genes contained B-box domain, three genes lacked introns, and these genes were unevenly distributed on the other seven chromosomes except for chromosome 6. The 28 proteins contained 10 conserved motifs and could be divided into five subfamilies. BBX genes of Tartary buckwheat showed varying expression under different conditions demonstrating that FtBBXs might play important roles in Tartary buckwheat growth and development. This study lays a foundation for further understanding of Tartary buckwheat BBX genes and their functions in growth and development as well as regulation of pigmentation in Tartary buckwheat.

The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles

BACKGROUND

The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized in many model organisms, genome-wide identification of the BBX family genes have not yet been reported in Moso bamboo (Phyllostachys edulis), and the biological functions of this family remain unknown.

RESULT

In the present study, we identified 27 BBX genes in the genome of Moso bamboo, and analysis of their conserved motifs and multiple sequence alignments revealed that they all shared highly similar structures. Additionally, phylogenetic and homology analyses indicated that PeBBX genes were divided into three clusters, with whole-genome duplication (WGD) events having facilitated the expansion of this gene family. Light-responsive and stress-related cis-elements were identified by analyzing cis-elements in the promoters of all PeBBX genes. Short time-series expression miner (STEM) analysis revealed that the PeBBX genes had spatiotemporal-specific expression patterns and were likely involved in the growth and development of bamboo shoots. We further explored the downstream target genes of PeBBXs, and GO/KEGG enrichment analysis predicted multiple functions of BBX target genes, including those encoding enzymes involved in plant photosynthesis, pyruvate metabolism and glycolysis/gluconeogenesis.

CONCLUSIONS

In conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family.

Genome-wide identification of Brassicaceae B-BOX genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed

BACKGROUND

B-box (BBX) genes play important roles in plant growth regulation and responses to abiotic stresses. The plant growth and yield production of allotetraploid rapeseed is usually hindered by diverse nutrient stresses. However, no systematic analysis of Brassicaceae BBXs and the roles of BBXs in the regulation of nutrient stress responses have not been identified and characterized previously.

RESULTS

In this study, a total of 536 BBXs were identified from nine brassicaceae species, including 32 AtBBXs, 66 BnaBBXs, 41 BoBBXs, 43 BrBBXs, 26 CrBBXs, 81 CsBBXs, 52 BnBBXs, 93 BjBBXs, and 102 BcBBXs. Syntenic analysis showed that great differences in the gene number of Brassicaceae BBXs might be caused by genome duplication. The BBXs were respectively divided into five subclasses according to their phylogenetic relationships and conserved domains, indicating their diversified functions. Promoter cis-element analysis showed that BBXs probably participated in diverse stress responses. Protein-protein interactions between BnaBBXs indicated their functions in flower induction. The expression profiles of BnaBBXs were investigated in rapeseed plants under boron deficiency, boron toxicity, nitrate limitation, phosphate shortage, potassium starvation, ammonium excess, cadmium toxicity, and salt stress conditions using RNA-seq data. The results showed that different BnaBBXs showed differential transcriptional responses to nutrient stresses, and some of them were simultaneously responsive to diverse nutrient stresses.

CONCLUSIONS

Taken together, the findings investigated in this study provided rich resources for studying Brassicaceae BBX gene family and enriched potential clues in the genetic improvement of crop stress resistance.