Gene structure, phylogeny and expression profile of the sucrose synthase gene family in cacao (Theobroma cacao L.)

VaSUS2 confers cold tolerance in transgenic tomato and Arabidopsis by regulation of sucrose metabolism and ROS homeostasis

VaSUS2 enhances cold tolerance of transgenic tomato and Arabidopsis by regulating sucrose metabolism and improving antioxidant enzymes activity. Sucrose synthetase (SUS) is a key enzyme of sugar metabolism, and plays an important role in response to abiotic stress in plant. However, the function of VaSUS2 remains unknown in cold tolerance. Here, the cloning and functional characterization of the plasma membrane-localized VaSUS2 gene isolated from Vitis amurensis was studied. The transcript level of VaSUS2 was up-regulated under cold stress in Vitis amurensis. Heterologous expression of VaSUS2 in tomato increased SUS activity, which promoted the accumulation of glucose and fructose under cold treatment. The transgenic tomato and Arabidopsis exhibited higher levels of antioxidant enzymes activity, lower relative electrolyte leakage (REL), malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) content compared to wild type under cold stress. Importantly, the ability of scavenging reactive oxygen species (ROS) in transgenic plants was significantly improved. Moreover, yeast two-hybrid (Y2H) indicated that VaSnRK1 might be a potential interaction protein of VaSUS2. qRT-PCR showed that sucrose metabolism-related genes SlSUS, SlSPS and SlINV were significantly up-regulated in transgenic tomatoes. Meanwhile, the expression levels of antioxidant enzyme genes and cold-related genes CBF1, COR47 and ICE1 were up-regulated in transgenic plants. Taken together, these results suggested that VaSUS2 was involved in cold tolerance by increasing the levels of soluble sugars, improving the activity of antioxidant enzymes, and up-regulating the expression of cold-related genes in transgenic tomatoes and Arabidopsis.

A Comprehensive Analysis of the DUF4228 Gene Family in Gossypium Reveals the Role of GhDUF4228-67 in Salt Tolerance

Soil salinization conditions seriously restrict cotton yield and quality. Related studies have shown that the DUF4228 proteins are pivotal in plant resistance to abiotic stress. However, there has been no systematic identification and analysis of the DUF4228 gene family in cotton and their role in abiotic stress. In this study, a total of 308 DUF4228 genes were identified in four Gossypium species, which were divided into five subfamilies. Gene structure and protein motifs analysis showed that the GhDUF4228 proteins were conserved in each subfamily. In addition, whole genome duplication (WGD) events and allopolyploidization might play an essential role in the expansion of the DUF4228 genes. Besides, many stress-responsive (MYB, MYC) and hormone-responsive (ABA, MeJA) related cis-elements were detected in the promoters of the DUF4228 genes. The qRT-PCR results showed that GhDUF4228 genes might be involved in the response to abiotic stress. VIGS assays and the measurement of relative water content (RWC), Proline content, POD activity, and malondialdehyde (MDA) content indicated that GhDUF4228-67 might be a positive regulator of cotton response to salt stress. The results in this study systematically characterized the DUF4228s in Gossypium species and will provide helpful information to further research the role of DUF4228s in salt tolerance.

Molecular identification and expression analysis of five sucrose synthase genes in Sorghum Bicolor

In higher plants, sucrose synthase (Susy, EC 2.4.1.13) as an enzyme with a core function, involved in the synthesis and breakdown of sugars, and plays an important role in growth and metabolism. Although, the different genes encoding Susy isozyme proteins have been cloned and functionally verified in several plant species, to date detailed information about the Susy genes is lacking in Sorghum. Here, we demonstrated the identification of five novel Susy genes from the sorghum genome database. Sequence, structure and phylogenetic analyses of these five SbSusy genes revealed evolutionary conservation through Susy gene family members across Sorghum and other crop plants. The expression of sorghum Susy genes was investigated via transcriptome database in various developmental stages and different tissues. Further qRT-PCR was performed to reveal the induction of SbSusy genes under salt, drought and sugar induction. The results indicated that all Susy genes were differentially expressed in various tissues and highly associated with sucrose metabolism. This study shows a theoretical reference of Susy genes in Sorghum, which provides new insights for the knowledge of the evolution relationships, and basic information to help clarify the molecular mechanism of Susy synthase genes in Sorghum.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01166-8.

Identification and expression analysis of the sucrose synthase gene family in pomegranate (Punica granatum L.)

BACKGROUND

Sucrose synthase (SUS, EC 2.4.1.13) is one of the major enzymes of sucrose metabolism in higher plants. It has been associated with C allocation, biomass accumulation, and sink strength. The SUS gene families have been broadly explored and characterized in a number of plants. The pomegranate (Punica granatum) genome is known, however, it lacks a comprehensive study on its SUS genes family.

METHODS

PgSUS genes were identified from the pomegranate genome using a genome-wide search method. The PgSUS gene family was comprehensively analyzed by physicochemical properties, evolutionary relationship, gene structure, conserved motifs and domains, protein structure, syntenic relationships, and cis-acting elements using bioinformatics methods. The expression pattern of the PgSUS gene in different organs and fruit development stages were assayed with RNA-seq obtained from the NCBI SRA database as well as real-time quantitative polymerase chain reaction (qPCR).

RESULTS

Five pomegranate SUS genes, located on four different chromosomes, were divided into three subgroupsaccording to the classification of other seven species. The PgSUS family was found to be highly conserved during evolution after studying the gene structure, motifs, and domain analysis. Furthermore, the predicted PgSUS proteins showed similar secondary and tertiary structures. Syntenic analysis demonstrated that four PgSUS genes showed syntenic relationships with four species, with the exception of PgSUS2. Predictive promoter analysis indicated that PgSUS genes may be responsive to light, hormone signaling, and stress stimulation. RNA-seq analysis revealed that PgSUS1/3/4 were highly expressed in sink organs, including the root, flower, and fruit, and particularly in the outer seed coats. qPCR analysis showed also that PgSUS1, PgSUS3, and PgSUS4 were remarkably expressed during fruit seed coat development. Our results provide a systematic overview of the PgSUS gene family in pomegranate, developing the framework for further research and use of functional PgSUS genes.

The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis

The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T.cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs.

Sucrose synthase gene family in Brassica juncea: genomic organization, evolutionary comparisons, and expression regulation

Sucrose synthase (SUS) plays an important role in sucrose metabolism and plant development. The SUS gene family has been identified in many plants, however, there is no definitive study of SUS gene in Brassica juncea. In this study, 14 SUS family genes were identified and comprehensively analyzed using bioinformatics tools. The analyzed parameters included their family member characteristics, chromosomal locations, gene structures and phylogenetic as well as transcript expression profiles. Phylogenetic analysis revealed that the 14 members could be allocated into three groups: SUS I, SUS II and SUS III. Comparisons of the exon/intron structure of the mustard SUS gene indicated that its structure is highly conserved. The conserved structure is attributed to purification selection during evolution. Expansion of the SUS gene family is associated with fragment and tandem duplications of the mustard SUS gene family. Collinearity analysis among species revealed that the SUS gene family could be lost or mutated to varying degrees after the genome was doubled, or when Brassica rapa and Brassica nigra hybridized to form Brassica juncea. The expression patterns of BjuSUSs vary among different stages of mustard stem swelling. Transcriptomics revealed that the BjuSUS01-04 expression levels were the most elevated. It has been hypothesized that they play an important role in sucrose metabolism during stem development. The expression levels of some BjuSUSs were significantly up-regulated when they were treated with plant hormones. However, when subjected to abiotic stress factors, their expression levels were suppressed. This study establishes SUS gene functions during mustard stem development and stress.

Genome-wide identification and analysis of the sucrose synthase gene family in cassava (Manihot esculenta Crantz)

Sucrose synthase (SUS), a key enzyme of the sucrose metabolism pathway, is encoded by a multi-gene family in plants. To date, dozens of SUS gene families have been characterized in various plant genomes. However, only a few studies have performed comprehensive analyses in tropical crops like cassava (Manihot esculenta Crantz). In the present study, seven non-redundant members of the SUS gene family (MeSUS1-7) were identified and characterized from the cassava genome. The MeSUS genes were distributed on five chromosomes (Chr1, Chr2, Chr3, Chr14, and Chr16) and the encoded proteins could be classified into three major groups with other SUS proteins from both dicot and monocot species (SUS I, SUS II, and SUS III). The spatio-temporal expression profiles of MeSUS genes showed a developmental stage-dependent, partially overlapping pattern, mainly expressed in the source and sink tissues. Cold and drought treatments significantly induced the expressions of MeSUS2, MeSUS4, MeSUS6, and MeSUS7 and the activities of the encoded enzymes, indicating that these genes may play crucial roles in resistance against abiotic stresses. These results provide new insights into the multifaceted role of the SUS gene family members in various physiological processes, especially sucrose transport and starch accumulation in cassava roots.

The evolutionary history of the sucrose synthase gene family in higher plants

BACKGROUND

Sucrose synthase (SUS) is widely considered a key enzyme participating in sucrose metabolism in higher plants and regarded as a biochemical marker for sink strength in crops. However, despite significant progress in characterizing the physiological functions of the SUS gene family, knowledge of the trajectory of evolutionary processes and significance of the family in higher plants remains incomplete.

RESULTS

In this study, we identified over 100 SUS genes in 19 plant species and reconstructed their phylogenies, presenting a potential framework of SUS gene family evolution in higher plants. Three anciently diverged SUS gene subfamilies (SUS I, II and III) were distinguished based on their phylogenetic relationships and unique intron/exon structures in angiosperms, and they were found to have evolved independently in monocots and dicots. Each subfamily of SUS genes exhibited distinct expression patterns in a wide range of plants, implying that their functional differentiation occurred before the divergence of monocots and dicots. Furthermore, SUS III genes evolved under relaxed purifying selection in dicots and displayed narrowed expression profiles. In addition, for all three subfamilies of SUS genes, the GT-B domain was more conserved than the "regulatory" domain.

CONCLUSIONS

The present study reveals the evolution of the SUS gene family in higher plants and provides new insights into the evolutionary conservation and functional divergence of angiosperm SUS genes.

Genome-wide identification and expression analysis of sucrose synthase genes in allotetraploid Brassica juncea

Sucrose plays pivotal role in energy metabolism and regulating gene expression of several physiological processes in higher plants. Here, fourteen sucrose synthase (SUS) genes have been identified in the allotetraploid genome of Indian mustard, Brassica juncea. The identified SUS genes in B. juncea (BjSUS) were derived from the two-progenitor species, B. rapa and B. nigra. Intron-exon analysis indicated loss or gain of 1-3 introns in diversification of SUS gene family. Phylogenetic analysis revealed discrete evolutionary paths for the BjSUS genes, originating from three ancestor groups, SUS I, SUS II and SUS III. Gene expression study revealed significant variability in expression of the BjSUS paralogs across the different tissues. BjSUS genes showed transcriptional activation in response to defense hormones and a late response to wounding. Tissue and temporal specificity of expression revealed importance of specific SUS paralogs at different developmental stages and under different stress conditions. The study highlighted differential involvement of SUS paralogs in sucrose metabolism across the tissues and stress-responses, in a major oilseed crop B. juncea.

An Overview of Sucrose Synthases in Plants

Sucrose is the end product of photosynthesis and the primary sugar transported in the phloem of most plants. Sucrose synthase (SuSy) is a glycosyl transferase enzyme that plays a key role in sugar metabolism, primarily in sink tissues. SuSy catalyzes the reversible cleavage of sucrose into fructose and either uridine diphosphate glucose (UDP-G) or adenosine diphosphate glucose (ADP-G). The products of sucrose cleavage by SuSy are available for many metabolic pathways, such as energy production, primary-metabolite production, and the synthesis of complex carbohydrates. SuSy proteins are usually homotetramers with an average monomeric molecular weight of about 90 kD (about 800 amino acids long). Plant SuSy isozymes are mainly located in the cytosol or adjacent to plasma membrane, but some SuSy proteins are found in the cell wall, vacuoles, and mitochondria. Plant SUS gene families are usually small, containing between four to seven genes, with distinct exon-intron structures. Plant SUS genes are divided into three separate clades, which are present in both monocots and dicots. A comprehensive phylogenetic analysis indicates that a first SUS duplication event may have occurred before the divergence of the gymnosperms and angiosperms and a second duplication event probably occurred in a common angiosperm ancestor, leading to the existence of all three clades in both monocots and dicots. Plants with reduced SuSy activity have been shown to have reduced growth, reduced starch, cellulose or callose synthesis, reduced tolerance to anaerobic-stress conditions and altered shoot apical meristem function and leaf morphology. Plants overexpressing SUS have shown increased growth, increased xylem area and xylem cell-wall width, and increased cellulose and starch contents, making SUS high-potential candidate genes for the improvement of agricultural traits in crop plants. This review summarizes the current knowledge regarding plant SuSy, including newly discovered possible developmental roles for SuSy in meristem functioning that involve sugar and hormonal signaling.

Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta

Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways. The pattern of occurrence of these cis-elements (overrepresentation/common) decipher the mechanism of stress-responsive upregulation of downstream genes, simultaneously forming a molecular bridge between primary and specialized metabolisms. Though many studies have been conducted on the transcriptional regulation of stress-mediated primary or specialized metabolism genes, but not much data is available with regard to cis-element signatures and transcription factors that simultaneously modulate both pathway genes. Hence, our major focus would be to present a comprehensive analysis of the stress-mediated interconnection between primary and specialized metabolism genes via the interaction between different transcription factors and their corresponding cis-elements. In future, this study could be further utilized for the overexpression of the specific transcription factors that upregulate both primary and specialized metabolism, thereby simultaneously improving the yield and therapeutic content of plants.