Search Results (15)

Tieguanyin tea, a renowned oolong tea, is one of the ten most famous teas in China. The Squamosa Promoter Binding Protein (SBP)-box transcription factor family, widely present in plants, plays a crucial role in plant development, growth, and stress responses. In this study, we identify and analyze 22 CsSBP genes at the genome-wide level. These genes were distributed unevenly across 11 chromosomes. Using Arabidopsis thaliana and Solanum lycopersicum L. as model organisms, we constructed a phylogenetic tree to classify these genes into six distinct subfamilies. Collinearity analysis revealed 20 homologous gene pairs between AtSBP and CsSBP, 21 pairs between SiSBP and CsSBP, and 14 pairs between OsSBP and CsSBP. Cis-acting element analysis indicated that light-responsive elements were the most abundant among the CsSBP genes. Protein motif, domain, and gene architecture analyses demonstrated that members of the same subgroup shared similar exon–intron structures and motif arrangements. Furthermore, we evaluated the expression profiles of nine CsSBP genes under light, shade, and cold stress using qRT-PCR analysis. Notably, CsSBP1, CsSBP17, and CsSBP19 were significantly upregulated under all three stresses. This study provides fundamental insights into the CsSBP gene family and offers a novel perspective on the mechanisms of SBP transcription factor-mediated stress responses, as well as Tieguanyin tea’s adaptation to environmental variations. Full article

The loquat (Eriobotrya japonica L.) is a special evergreen tree, and its fruit is of high medical and health value as well as having stable market demand around the world. In recent years, research on the accumulation of nutrients in loquat fruit, such as carotenoids, flavonoids, and terpenoids, has become a hotspot. The SBP-box gene family encodes transcription factors involved in plant growth and development. However, there has been no report on the SBP-box gene family in the loquat genome and their functions in carotenoid biosynthesis and fruit ripening. In this study, we identified 28 EjSBP genes in the loquat genome, which were unevenly distributed on 12 chromosomes. We also systematically investigated the phylogenetic relationship, collinearity, gene structure, conserved motifs, and cis-elements of EjSBP proteins. Most EjSBP genes showed high expression in the root, stem, leaf, and inflorescence, while only five EjSBP genes were highly expressed in the fruit. Gene expression analysis revealed eight differentially expressed EjSBP genes between yellow- and white-fleshed fruits, suggesting that the EjSBP genes play important roles in loquat fruit development at the breaker stage. Notably, EjSBP01 and EjSBP19 exhibited completely opposite expression patterns between white- and yellow-fleshed fruits during fruit development, and showed a close relationship with SlCnr involved in carotenoid biosynthesis and fruit ripening, indicating that these two genes may participate in the synthesis and accumulation of carotenoids in loquat fruit. In summary, this study provides comprehensive information about the SBP-box gene family in the loquat, and identified two EjSBP genes as candidates involved in carotenoid synthesis and accumulation during loquat fruit development. Full article

Transcription factors are crucial for plant growth and development. MADS-box, WRKY, NAC, and SBP-box, some of the most vital transcription factors, are not well identified in Diospyros spp., and their floral development and sex differentiation related functions remain unknown. We identified and analysed 53 MADS-box, 66 WRKY, 83 NAC, and 17 SBP-box transcription factors using the chromosomal D. oleifera genome. There were six DolSBPs identified as miR156 and miR157 targets. According to the multiple sequence alignments of Arabidopsis and D. oleifera proteins and their conserved domains and motifs, DolMADSs were divided into 23 type I and 30 type II. The DolWRKYs, DolNACs, and DolSBPs were divided into 7, 16, and 6 subgroups, respectively. It was found that one DolMADS, five DolWRKYs, one DolNAC, and four DolSBPs may promote unisexual female flowers development, while three DolMADSs, four DolWRKYs, and one DolNAC may enhance unisexual male flowers development. The functions among the different members of the same family may, thus, vary widely. The results will help to elucidate the evolution of the MADS-box, WRKY, NAC, and SBP-box genes families in D. oleifera and to determine their functions in flower development for Diospyros spp. Full article

Black pepper (Piper nigrum L.), is dubbed “the King of Spices”. However, the lack of genic knowledge has limited the understanding of its physiological processes and hindered the development of its molecular breeding. The SBP-box gene family is an important family in plant development and integrates multiple physiological processes. Here, we made a genome-wide identification of the pepper SBP-box gene family to provide evolutionary and functional information about this conserved transcription factor. In total, 34 SBP genes were identified in pepper. All these pepper SBP genes were clustered into eight groups, and one pepper group was not found in Arabidopsis thaliana. Segment duplications played the most important role in the expansion process of pepper SBP genes, and all these duplications were subjected to purifying selection. Half of pepper SBP genes were found miR156 target sites, and 17 miR156s were predicted. The tissue expression analysis revealed the differential expression of pepper SBP genes. Eleven SBP genes were found in four co-expression networks, and the GO enrichment further provides a functional prediction for pepper SBP genes. This study lays a foundation for further studies of pepper and provides a valuable reference for functional mining of pepper SBP genes. Full article

MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development. Full article

SBP-box is an important plant-specific transcription factor family and is involved in diverse biological processes. Here, we identified a total of 15 SBP-BOX genes in the important fruit crop sweet orange (Citrus sinensis) and characterized their gene structures, conserved domain and motif, chromosomal location, and cis-acting regulatory elements. SBP genes were classified into four subfamilies based on the amino acid sequence homology, and the classification is equally strongly supported by the gene and protein structures. Our analysis revealed that segmental duplication events were the main driving force in the evolution of CsSBP genes, and gene pairs might undergo extensive purifying selection. Further synteny analysis of the SBP members among sweet orange and other plant species provides valuable information for clarifying the CsSBP family evolutionary relationship. According to publicly available RNA-seq data and qRT-PCR analysis from various sweet orange tissues, CsSBP genes may be expressed in different tissues and developmental stages. Gene expression analysis showed variable expression profiles of CsSBP genes under various abiotic stresses, such as high and low-temperature, salt, and wound treatments, demonstrating the potential role of SBP members in sweet orange response to abiotic stress. Noticeably, all CsSBP genes were also downregulated in sweet orange upon the infection of an important fungal pathogen Diaporthe citri. Our results provide valuable information for exploring the role of SBP-Box in sweet orange. Full article

Squamosa promoter binding protein (SBP)-box genes are plant-specific transcription factors involved in plant growth and development, morphogenesis and biotic and abiotic stress responses. However, these genes have been understudied in pepper, especially with respect to defense responses to Phytophthora capsici infection. CaSBP11 is a SBP-box family gene in pepper that was identified in our previous research. Silencing CaSBP11 enhanced the defense response of pepper plants to Phytophthora capsici. Without treatment, the expression of defense-related genes (CaBPR1, CaPO1, CaSAR8.2 and CaDEF1) increased in CaSBP11-silenced plants. However, the expression levels of these genes were inhibited under transient CaSBP11 expression. CaSBP11 overexpression in transgenic Nicotiana benthamiana decreased defense responses, while in Arabidopsis, it induced or inhibited the expression of genes in the salicylic acid and jasmonic acid signaling pathways. CaSBP11 overexpression in sid2-2 mutants induced AtNPR1, AtNPR3, AtNPR4, AtPAD4, AtEDS1, AtEDS5, AtMPK4 and AtNDR1 expression, while AtSARD1 and AtTGA6 expression was inhibited. CaSBP11 overexpression in coi1-21 and coi1-22 mutants, respectively, inhibited AtPDF1.2 expression and induced AtPR1 expression. These results indicate CaSBP11 has a negative regulatory effect on defense responses to Phytophthora capsici. Moreover, it may participate in the defense response of pepper to Phytophthora capsici by regulating defense-related genes and the salicylic and jasmonic acid-mediated disease resistance signaling pathways. Full article

Conservative gene families in plants, which are closely related to innovations in flowering plants, have long and complex evolutionary histories. Here, we used the SQUAMOSA promoter-binding protein (SBP-box) gene family as an example to study conservative gene families in flowering plants. In total, 11 groups, including nine angiosperm-conservative groups and two monocot- and eudicot-specific groups, were identified. Among the nine angiosperm-conservative groups, four are conserved in all land plants and the remaining five are angiosperm-specific. The five angiosperm-specific groups exhibit structural and functional diversity and evolved together, along with the evolution of flowering plants. The expansion of SBP genes was affected by miR156, and the miR156-regulated SBP genes tend to retain more copies. Our results reflect the dynamic evolutionary process of the different groups, with the identification of two genetic lines via synteny analyses. In addition, miR156 showed a close evolutionary relationship with SBP genes, suggesting that it may originate from face-to-face tandem duplication of SBP genes. SBP genes without an miR156 binding locus are usually functionally conservative or housekeeping like, belonging to the terrestrial-conservative group. In contrast, SBP genes with miR156 binding sites are selected by angiosperms to regulate more complex physiological processes. Full article

Transcription factors (TFs) play fundamental roles in the developmental processes of all living organisms. Squamosa Promoter Binding Protein-like (SBP/SBP-Box) is a major family of plant-specific TFs, which plays important roles in multiple processes involving plant growth and development. While some work has been done, there is a lot more that is yet to be discovered in the hexaploid wheat SBP (TaSBP) family. With the completion of whole genome sequencing, genome-wide analysis of SBPs in common hexaploid wheat is now possible. In this study, we used protein–protein Basic Local Alignment Search Tool (BLASTp) to hunt the newly released reference genome sequence of hexaploid wheat (Chinese spring). Seventy-four TaSBP proteins (belonging to 56 genes) were identified and clustered into five groups. Gene structure and motif analysis indicated that most TaSBPs have relatively conserved exon–intron arrangements and motif composition. Analysis of transcriptional data showed that many TaSBP genes responded to some biological and abiotic stresses with different expression patterns. Moreover, three TaSBP genes were generally expressed in the majority of tissues throughout the wheat growth and also responded to many environmental biotic and abiotic stresses. Collectively, the detailed analyses presented here will help in understanding the roles of the TaSBP and also provide a reference for the further study of its biological function in wheat. Full article

SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron–exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis. Full article

SBP-box (Squamosa-promoter binding protein) genes are a type of plant-specific transcription factor and play important roles in plant growth, signal transduction and stress response. However, little is known about the SBP-box genes in pepper (CaSBP), especially in the process of Phytophthora capsici infection. In this study, a novel gene (CaSBP12) was selected from the CaSBP gene family, which was isolated from the pepper genome database in our previous study. The CaSBP12 gene was located in the nucleus of the cell and its silencing in the pepper plant enhanced the defense response against Phytophthora capsici infection. After inoculation with Phytophthora capsici, the root activity of the CaSBP12-silenced plants is compared to control plants, while malondialdehyde (MDA) content is compared viceversa. Additionally, the expression of defense related genes (CaPO1, CaSAR8.2, CaBPR1, and CaDEF1) in the silenced plants were induced to different degrees and the peak of CaSAR8.2 and CaBPR1 were higher than that of CaDEF1. The CaSBP12 over-expressed Nicotiana benthamiana plants were more susceptible to Phytophthora capsici infection with higher EC (electrical conductivity) and MDA contents as compared to the wild-type. The relative expression of defense related genes (NbDEF, NbNPR1, NbPR1a, and NbPR1b) in transgenic and wild-type Nicotiana benthamiana plants were induced, especially the NbPR1a and NbPR1b. In conclusion, these results indicate that CaSBP12 gene negative regulates the defense response against Phytophthora capsici infection which suggests their potentially significant role in plant defense. To our knowledge, this is the first report on CaSBP gene which negative regulate defense response. Full article

The SQUAMOSA promoter binding protein (SBP)-box gene family is a plant-specific transcription factor family. This family plays a crucial role in plant growth and development. In this study, 20 SBP-box genes were identified in the tea plant genome and classified into six groups. The genes in each group shared similar exon-intron structures and motif positions. Expression pattern analyses in five different tissues demonstrated that expression in the buds and leaves was higher than that in other tissues. The cis-elements and expression patterns of the CsSBP genes suggested that the CsSBP genes play active roles in abiotic stress responses; these responses may depend on the abscisic acid (ABA), gibberellic acid (GA), and methyl jasmonate (MeJA) signaling pathways. Our work provides a comprehensive understanding of the CsSBP family and will aid in genetically improving tea plants. Full article

Salinity and drought are two major abiotic stresses that limit grape productivity. Responses to stress in grape are known to be regulated by several families of transcription factors. However, little is known about the role of grape Squamosa promoter binding protein (SBP)-box transcription factor genes in response to abiotic stress. To better understand the functions of the grape SBP-box genes in abiotic stress tolerance, a full-length complementary DNA (cDNA) sequence of the putative SBP-box transcription factor gene, VpSBP16 was amplified from Chinese wild grapevine Vitis pseudoreticulata clone “Baihe-35-1”. We observed that the VpSBP16 protein fused to the green fluorescent protein (GFP) reporter accumulated in the nucleus when transiently expressed in onion epidermal cells. Moreover, VpSBP16 was shown to have transcriptional activation activity using a yeast trans-activation assay. We performed a VpSBP16 functional analysis through the characterization of transgenic Arabidopsis thaliana plants constitutively over-expressing VpSBP16. The transgenic lines had longer roots and the seeds had a higher germination rate than the wild type (WT) under osmotic stress. In addition, the accumulation of reactive oxygen species (ROS) of transgenic seedlings was significantly lower than WT in the transgenic lines, as was electrolyte leakage. VpSBP16 overexpression also elevated expression levels of stress-response genes involved in the salt overly sensitive (SOS) pathway. These results indicate that overexpression VpSBP16 in A. thaliana enhances tolerance of salt and drought stress during seed germination, as well in seedlings and mature plants, by regulating SOS and ROS signaling cascades. Full article

Transcription factors play vital roles in the developmental processes of plants. The SQUAMOSA promoter binding protein (SBP) genes encode a family of plant-specific transcription factors and plays many crucial roles in plant development. In this study, 16 SBP-box gene family members were identified in Ziziphus jujuba Mill. Dongzao (Dongzao), which were distributed over 8 chromosomes. They were classified into seven groups according to their phylogenetic relationships with other SBP-box gene families. Within each group, genes shared similar exon-intron structures and motif locations. The number of exons varied among the groups. We identified 12 homologous gene pairs between Dongzao and Arabidopsis. Expression profiling revealed that ZjSBP02 and ZjSBP14 expressed highly in mature fruits, ZjSBP01 expressed higher in mature leaves than other tissues and the expression level of ZjSBP12 was much higher in the flowers. The transcriptome analysis indicated that ZjSBPs had different expression patterns in various tissues. This study represents the first systematic analysis of the SBP-box gene family in Z. jujuba. The data presented here provides a foundation for understanding the crucial roles of ZjSBP genes in plant growth and development. Full article

The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis. Full article