scholarly journals Roles of the GA-mediated SPL Gene Family and miR156 in the Floral Development of Chinese Chestnut (Castanea mollissima)

2019 ◽  
Vol 20 (7) ◽  
pp. 1577 ◽  
Author(s):  
Guosong Chen ◽  
Jingtong Li ◽  
Yang Liu ◽  
Qing Zhang ◽  
Yuerong Gao ◽  
...  
Keyword(s):  
Target Genes ◽  
Floral Development ◽  
Binding Protein ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Deciduous Tree ◽  
Main Function ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Castanea Mollissima

Chestnut (Castanea mollissima) is a deciduous tree species with major economic and ecological value that is widely used in the study of floral development in woody plants due its monoecious and out-of-proportion characteristics. Squamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that plays an important role in floral development. In this study, a total of 18 SPL genes were identified in the chestnut genome, of which 10 SPL genes have complementary regions of CmmiR156. An analysis of the phylogenetic tree of the squamosa promoter-binding protein (SBP) domains of the SPL genes of Arabidopsis thaliana, Populus trichocarpa, and C. mollissima divided these SPL genes into eight groups. The evolutionary relationship between poplar and chestnut in the same group was similar. A structural analysis of the protein-coding regions (CDSs) showed that the domains have the main function of SBP domains and that other domains also play an important role in determining gene function. The expression patterns of CmmiR156 and CmSPLs in different floral organs of chestnut were analyzed by real-time quantitative PCR. Some CmSPLs with similar structural patterns showed similar expression patterns, indicating that the gene structures determine the synergy of the gene functions. The application of gibberellin (GA) and its inhibitor (Paclobutrazol, PP333) to chestnut trees revealed that these exert a significant effect on the number and length of the male and female chestnut flowers. GA treatment significantly increased CmmiR156 expression and thus significantly decreased the expression of its target gene, CmSPL6/CmSPL9/CmSPL16, during floral bud development. This finding indicates that GA might indirectly affect the expression of some of the SPL target genes through miR156. In addition, RNA ligase-mediated rapid amplification of the 5′ cDNA ends (RLM-RACE) experiments revealed that CmmiR156 cleaves CmSPL9 and CmSPL16 at the 10th and 12th bases of the complementary region. These results laid an important foundation for further study of the biological function of CmSPLs in the floral development of C. mollissima.

scholarly journals SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 354
Author(s):  
Shaokun Li ◽  
Li Li ◽  
Yang Jiang ◽  
Jun Wu ◽  
Honghua Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Panax Ginseng ◽  
Interaction Analysis ◽  
Binding Protein ◽  
Expression Patterns ◽  
Evolutionary Analysis ◽  
Main Function ◽  
Squamosa Promoter Binding Protein ◽  
Expression Characteristics ◽  
Spl Gene

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

scholarly journals Molecular Cloning and Characterization of SQUAMOSA-Promoter Binding Protein-Like Gene FvSPL10 from Woodland Strawberry (Fragaria vesca)

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 342 ◽  
Author(s):  
Jinsong Xiong ◽  
Yibo Bai ◽  
Chuangju Ma ◽  
Hongyu Zhu ◽  
Dan Zheng ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth And Development ◽  
Binding Protein ◽  
Ectopic Expression ◽  
Plant Growth And Development ◽  
Woodland Strawberry ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes

SQUAMOSA-promoter binding protein-like (SPL) proteins are plant-specific transcript factors that play essential roles in plant growth and development. Although many SPL genes have been well characterized in model plants like Arabidopsis, rice and tomato, the functions of SPLs in strawberry are still largely elusive. In the present study, we cloned and characterized FvSPL10, the ortholog of AtSPL9, from woodland strawberry. Subcellular localization shows FvSPL10 localizes in the cell nucleus. The luciferase system assay indicates FvSPL10 is a transcriptional activator, and both in vitro and in vivo assays indicate FvSPL10 could bind to the promoter of FvAP1 and activate its expression. Ectopic expression of FvSPL10 in Arabidopsis promotes early flowering and increases organs size. These results demonstrate the multiple regulatory roles of FvSPL10 in plant growth and development and lay a foundation for investigating the biological functions of FvSPL10 in strawberry.

scholarly journals Genome-Wide Identification and Characterization of SQUAMOSA—Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina

Biomolecules ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 66 ◽  
Author(s):  
Ren-Fang Zeng ◽  
Jing-Jing Zhou ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Floral Induction ◽  
Binding Protein ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Specific Expression ◽  
Water Deficits ◽  
Citrus Clementina ◽  
Squamosa Promoter Binding Protein ◽  
Gene Structures

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.

Identification of the differential distribution patterns of mRNAs and consensus binding sequences for mouse DAF-16 homologues

2000 ◽  
Vol 349 (2) ◽  
pp. 629-634 ◽  
Author(s):  
Tatsuo FURUYAMA ◽  
Toru NAKAZAWA ◽  
Itsuko NAKANO ◽  
Nozomu MORI
Keyword(s):  
Target Genes ◽  
Binding Protein ◽  
Expression Patterns ◽  
Distribution Patterns ◽  
Mobility Shift ◽  
Differential Distribution ◽  
C Elegans ◽  
Core Sequence ◽  
Mobility Shift Assay ◽  
Responsive Element

daf-16 is a forkhead-type transcription factor, functioning downstream of insulin-like signals, and is known to be critical to the regulation of life span in Caenorhabditis elegans. Mammalian DAF-16 homologues include AFX, FKHR and FKHRL1, which contain a conserved forkhead domain and three putative phosphorylation sites for the Ser/Thr kinase Akt/protein kinase B (PKB), as well as for DAF-16. To assess the function of the homologues, we examined tissue distribution patterns of mRNAs for DAF-16 homologues in mice. In the embryos, expressions of AFX, FKHR and FKHRL1 mRNAs were complementary to each other and were highest in muscle, adipose tissue and embryonic liver. The characteristic expression pattern remained in the adult, except that signals of FKHRL1 became evident in more tissues, including the brain. In order to clarify whether each DAF-16 homologue had different target genes, we determined the consensus sequences for the binding of DAF-16 and the mouse homologues. The binding sequences for all four proteins shared a core sequence, TTGTTTAC, daf-16 family protein-binding element (DBE) binding protein. However, electrophoretic mobility shift assay showed that the binding affinity of DAF-16 homologues to the core sequence was stronger than that to the insulin-responsive element in the insulin-like growth factor binding protein-1 promoter region, which has been identified as a binding sequence for them. We identified one copy of the DBE upstream of the first exon of sod-3 by searching the genomic database of C. elegans. Taken together, DAF-16 homologues can fundamentally regulate the common target genes in insulin-responsive tissues and the specificity to target genes of each protein is partially determined by the differences in their expression patterns.

scholarly journals Comparative analysis of the SPL genes among four Ipomoea species and the evidence for a role of some IbSPLs in storage root development in sweet potato (Ipomoea batatas)

2021 ◽  
Author(s):  
Haoyun Sun ◽  
Jingzhao Mei ◽  
Wenqian Hou ◽  
Yang Zhang ◽  
Tao Xu ◽  
...  
Keyword(s):  
Root Development ◽  
Ipomoea Batatas ◽  
Target Genes ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Evolutionary Analysis ◽  
Storage Root ◽  
Storage Roots ◽  
Spl Genes ◽  
Storage Root Development

Abstract Background As a major family of plant-specific transcription factors, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes play crucial regulatory roles in plant growth, development, and stress tolerance. SPL transcription factor family has been widely studied in various plant species, however, there are no systematic studies on SPL genes in genus Ipomoea. Results In this study, a total of 29, 27, 26, 23 SPL genes were identified in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Phylogenetic analysis indicated that Ipomoea SPL genes could be clustered into eight clades. SPL members within the same clade showed similar gene structures, domain organizations, and cis-acting element compositions, suggesting similarity of biological function potentially. Evolutionary analysis revealed that segmental duplication events played a major role in the Ipomoea genus-specific expansion of SPL genes. Of these Ipomoea SPL genes, 69 were predicted as the target genes of miR156, and 7 IbSPL genes were further confirmed by degradome data. Additionally, IbSPL genes showed diverse expression patterns in various tissues, implying their functional conservation and divergence. Finally, by combining the information from expression patterns and regulatory sub-networks, we found that four IbSPL genes (IbSPL16/IbSPL17/IbSPL21/IbSPL28) may be involved in the formation and development of storage roots. Conclusions This study not only provides novel insights into the evolutionary and functional divergence of the SPL genes in all available sequenced species in genus Ipomoea, but also lays a foundation for further elucidation of the potential functional roles of IbSPL genes during storage root development.

scholarly journals Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

Agronomy ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 527 ◽  
Author(s):  
Song ◽  
Ma ◽  
Yin ◽  
Yang ◽  
He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Hexaploid Wheat ◽  
Abiotic Stresses ◽  
Binding Protein ◽  
Expression Patterns ◽  
Local Alignment ◽  
Composition Analysis ◽  
Motif Analysis ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein

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.

scholarly journals miR156-targeted SPL10 controls Arabidopsis root meristem activity and root-derived de novo shoot regeneration via cytokinin responses

2019 ◽  
Vol 71 (3) ◽  
pp. 934-950 ◽  
Author(s):  
Carlos Hernán Barrera-Rojas ◽  
Gabriel Henrique Braga Rocha ◽  
Laura Polverari ◽  
Diego Armando Pinheiro Brito ◽  
Diego Silva Batista ◽  
...  
Keyword(s):  
Shoot Regeneration ◽  
Root Meristem ◽  
De Novo ◽  
Expression Patterns ◽  
Primary Root ◽  
Loss Of Function ◽  
Arabidopsis Root ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Dependent Pathway

Abstract Root growth is modulated by different factors, including phytohormones, transcription factors, and microRNAs (miRNAs). MicroRNA156 and its targets, the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, define an age-dependent pathway that controls several developmental processes, including lateral root emergence. However, it remains unclear whether miR156-regulated SPLs control root meristem activity and root-derived de novo shoot regeneration. Here, we show that MIR156 and SPL genes have opposing expression patterns during the progression of primary root (PR) growth in Arabidopsis, suggesting that age cues may modulate root development. Plants with high miR156 levels display reduced meristem size, resulting in shorter primary root (PRs). Conversely, plants with reduced miR156 levels show higher meristem activity. Importantly, loss of function of SPL10 decreases meristem activity, while SPL10 de-repression increases it. Meristem activity is regulated by SPL10 probably through the reduction of cytokinin responses, via the modulation of type-B ARABIDOPSIS RESPONSE REGULATOR1(ARR1) expression. We also show that SPL10 de-repression in the PRs abolishes de novo shoot regenerative capacity by attenuating cytokinin responses. Our results reveal a cooperative regulation of root meristem activity and root-derived de novo shoot regeneration by integrating age cues with cytokinin responses via miR156-targeted SPL10.

Genome-wide identification and expression analysis of the SPL gene family in woodland strawberry Fragaria vesca

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 675-683 ◽  
Author(s):  
Jin-Song Xiong ◽  
Dan Zheng ◽  
Hong-Yu Zhu ◽  
Jian-Qiu Chen ◽  
Ran Na ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Growth And Development ◽  
Expression Patterns ◽  
Systematic Research ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Localization Analysis

SQUAMOSA promoter-binding protein-like (SPL) is a class of plant-specific transcription factors that play critical roles in regulating plant growth and development. However, little systematic research on SPL genes has been conducted in strawberry. In this study, 14 SPL genes were identified in the genome of woodland strawberry (Fragaria vesca), one of the model plants of the family Rosaceae. Chromosome localization analysis indicated that the 14 FvSPL genes were unevenly distributed on six chromosomes. Phylogenetic analysis indicated that the FvSPL proteins could be clustered into six groups (G1 to G6). Genes with similar structure were classified into the same group, implying their functional redundancy. In addition, nine out of the 14 FvSPL genes, belonging to G1, G2, and G5, were found to be the putative targets of FvmiR156 genes. Expression analysis indicated FvSPL genes exhibited highly diverse expression patterns in the tissues and organs examined. The transcript levels of most FvmiR156-targeted FvSPL genes in fruit were lower than those non-miR156-targeted genes. In addition, the expression of the FvmiR156-targeted FvSPL genes decreased during fruit ripening, whereas the expression of FvmiR156 genes increased in fruit during this process. The results provide a foundation for future functional analysis of FvSPL genes in strawberry growth and development.

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