SBP Gene Research Articles

Exploring solute binding proteins in Pseudomonas aeruginosa that bind to γ-aminobutyrate and 5-aminovalerate and their role in activating sensor kinases.

The standard method of receptor activation involves the binding of signals or signal-loaded solute binding proteins (SBPs) to sensor domains. Many sensor histidine kinases (SHKs), which are activated by SBP binding, are encoded adjacent to their corresponding sbp gene. We examined three SBPs of Pseudomonas aeruginosa PAO1, encoded near the genes for the AgtS (PA0600) and AruS (PA4982) SHKs, to determine how common this arrangement is. Ligand screening and microcalorimetric studies revealed that the SBPs PA0602 and PA4985 preferentially bind to GABA (KD = 2.3 and 0.58 μM, respectively), followed by 5-aminovalerate (KD = 30 and 1.6 μM, respectively) and ethanoldiamine (KD = 2.3 and 0.58 μM, respectively). In contrast, AgtB (PA0604) exclusively recognizes 5-aminovaleric acid (KD = 2.9 μM). However, microcalorimetric titrations did not show any binding between the AgtS sensor domain and AgtB or PA0602, regardless of the presence of ligands. Similarly, bacterial two-hybrid assays did not demonstrate an interaction between PA4985 and the AruS sensor domain. Therefore, sbp and shk genes located nearby are not always functionally linked. We previously identified PA0222 as a GABA-specific SBP. The presence of three SBPs for GABA may be linked to GABA's role as a trigger for P. aeruginosa virulence.

The maize gene ZmSBP17 encoding an SBP transcription factor confers osmotic resistance in transgenic Arabidopsis.

Among the major abiotic stresses, salt and drought have considerably affected agricultural development globally by interfering with gene expression profiles and cell metabolism. Transcription factors play crucial roles in activating or inhibiting the expression of stress-related genes in response to abiotic stress in plants. In this study, the Zea mays L. SQUAMOSA promoter-binding protein gene (ZmSBP17) was identified, and the molecular regulatory mechanism of osmotic stress tolerance was analyzed. Phylogenetic analysis confirmed that ZmSBP17 is part of the SBP gene family and is closely related to OsSBP17. The ZmSBP17-GFP fusion protein exhibited green fluorescence in the nucleus, as determined via tobacco epidermal transient transformation system. Acting as a transcriptional activator, the overexpression of ZmSBP17 in Arabidopsis significantly enhanced the expression of genes encoding superoxide dismutases (CSD1/2, MSD1), catalases (CAT1/2), ascorbate peroxidase 1 (APX1), and myeloblastosis transcription factors (AtMYB53/65), which increased the activity of reactive oxygen species (ROS)-scavenging enzymes and reduced ROS levels. Additionally, the expression of abiotic stress-related genes, such as AtDREB2A and AtNHX1, was significantly upregulated by ZmSBP17. Furthermore, ZmSBP17 specifically bound to cis-acting elements containing GTAC core sequences in the promoters of stress-related genes, suggesting that ZmSBP17 regulates the transcription of certain genes by recognizing these sequences. These results indicate that the overexpression of ZmSBP17 in Arabidopsis thaliana significantly increased tolerance to osmotic stress during the germination and seedling stages, which may enhance our understanding of the biological functions of SBPs in maize under abiotic stresses.

Genome-wide identification and analysis of the evolution and expression pattern of the SBP gene family in two Chimonanthus species.

Chimonanthus praecox and Chimonanthus salicifolius are closely related species that diverged approximately six million years ago. While both C. praecox and C. salicifolius could withstand brief periods of low temperatures of -15°C. Their flowering times are different, C. praecox blooms in early spring, whereas C. salicifolius blooms in autumn. The SBP-box (SQUAMOSA promoter-binding protein) is a plant-specific gene family that plays a crucial vital role in regulating plant flowering. Although extensively studied in various plants, the SBP gene family remains uncharacterized in Calycanthaceae. We conducted genome-wide identification of SBP genes in both C. praecox and C. salicifolius and comprehensively characterized the chromosomal localization, gene structure, conserved motifs, and domains of the identified SBP genes. In total, 15 and 18 SBP genes were identified in C. praecox and C. salicifolius, respectively. According to phylogenetic analysis, the SBP genes from Arabidopsis, C. praecox, and C. salicifolius were clustered into eight groups. Analysis of the gene structure and conserved protein motifs showed that SBP proteins of the same subfamily have similar motif structures. The expression patterns of SBP genes were analyzed using transcriptome data. The results revealed that more than half of the genes exhibited lower expression levels in leaves than in flowers, suggesting their potential involvement in the flower development process and may be linked to the winter and autumn flowering of C. praecox and C. salicifolius. Thirty-three SBPs were identified in C. praecox and C. salicifolius. The evolutionary characteristics and expression patterns were examined in this study. These results provide valuable information to elucidate the evolutionary relationships of the SBP family and help determine the functional characteristics of the SBP genes in subsequent studies.

A novel Tartary buckwheat gene FtIST1, associated with salt tolerance, was isolated and identified via over-expression and VIGS

FtIST1 is a novel SBP gene isolated from salt-responsive Tartary buckwheat, and its molecular characteristics and function in salt tolerance are unclear. With the use of DNAMAN and MEGA7.0 software and online analysis program SOPMA, we performed the bioinformatics analysis of the novel FtIST1 gene. We also identified the function of FtIST1 gene via over-expression and VIGS (virus-induced gene silencing). FtIST1 gene was cloned from Tartary buckwheat, and its GenBank accession number is MK799640. FtIST1 belongs to the SBP transcription factor gene family, it is 374 bp long and encodes 99 amino acids. The molecular weight and isoelectric point of FtIST1 protein are 11.7 kDa and 8.78, which is predicted to be a soluble hydrophilic protein. Through analyzing the physiological characteristics of transgenic Arabidopsis, it was found that the activities of antioxidant enzymes (SOD, POD and CAT), chlorophyll content, Fv/Fm, Fv/F0, net photosynthetic rate, fresh weight and dry weight, K+ and Mg2+ content increased significantly in Arabidopsis with over-expression of FtIST1 gene, while the plasmalemma permeability, chlorophyll a fluorescence F0 and Na+ content of leaves decreased significantly, indicating that the over-expression of FtIST1 gene can obviously improve the physiological characteristics of Arabidopsis under salt stress and the salt tolerance of transgenic Arabidopsis. After successfully inhibiting the expression of FtIST1 gene in Tartary buckwheat by VIGS technology, the activities of antioxidant enzymes such as SOD, POD and CAT in Tartary buckwheat decreased significantly, while the plasmalemma permeability and Na+ content of leaves increased significantly, indicating that the loss of FtIST1 gene expression in Tartary buckwheat led to the decrease of antioxidant capacity, the increase of cell membrane damage, the increase of Na+ content in shoot and the obvious decrease of salt tolerance. Our data indicate that FtIST1 is a salt tolerance gene, which is closely associated with salt tolerance of Tartary buckwheat.

Comparative transcriptome analysis of melon (Cucumis melo L.) reveals candidate genes and pathways involved in powdery mildew resistance

Powdery mildew is a major disease in melon, primarily caused by Podosphaera xanthii (Px). Some melon varieties were resistant to powdery mildew, while others were susceptible. However, the candidate genes associated with resistance and the mechanism of resistance/susceptibility to powdery mildew in melon remain unclear. In this study, disease-resistant melon cultivar TG-1 and disease-susceptible melon cultivar TG-5 were selected for comparative transcriptome analysis. The results suggested that the numbers of differentially expressed genes (DEGs) in TG-5 was always more than that in TG-1 at each of the four time points after Px infection, indicating that their responses to Px infection may be different and that the active response of TG-5 to Px infection may be earlier than that of TG-1. Transcription factors (TFs) analysis among the DEGs revealed that the bHLH, ERF, and MYB families in TG-1 may play a vital role in the interaction between melon and powdery mildew pathogens. GO enrichment analysis of these DEGs in TG-5 showed that the SBP, HSF, and ERF gene families may play important roles in the early stage of melon development after Px infection. Finally, we speculated on the regulatory pathways of melon powdery mildew and found PTI and ABA signaling genes may be associated with the response to Px infection in melon.

Genomic analysis of SBP gene family in Saccharum spontaneum reveals their association with vegetative and reproductive development

BackgroundSQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane.ResultsIn the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues.ConclusionsThe sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes.

Global analysis of SBP gene family in Brachypodiumdistachyon reveals its association with spike development

SQUAMOSA-promoter binding like proteins (SBPs/SPLs) are plant specific transcription factors targeted by miR156 and involved in various biological pathways, playing multi-faceted developmental roles. This gene family is not well characterized in Brachypodium. We identified a total of 18 SBP genes in B.distachyon genome. Phylogenetic analysis revealed that SBP gene family in Brachypodium expanded through large scale duplication. A total of 10 BdSBP genes were identified as targets of miR156. Transcript cleavage analysis of selected BdSBPs by miR156 confirmed their antagonistic connection. Alternative splicing was observed playing an important role in BdSBPs and miR156 interaction. Characterization of T-DNA Bdsbp9 mutant showed reduced plant growth and spike length, reflecting its involvement in the spike development. Expression of a majority of BdSBPs elevated during spikelet initiation. Specifically, BdSBP1 and BdSBP3 differentially expressed in response to vernalization. Differential transcript abundance of BdSBP1,BdSBP3,BdSBP8,BdSBP9,BdSBP14,BdSBP18 and BdSBP23 genes was observed during the spike development under high temperature. Co-expression network, protein–protein interaction and biological pathway analysis indicate that BdSBP genes mainly regulate transcription, hormone, RNA and transport pathways. Our work reveals the multi-layered control of SBP genes and demonstrates their association with spike development and temperature sensitivity in Brachypodium.

Autophagy and mTOR Pathways Mediate the Potential Renoprotective Effects of Vitamin D on Diabetic Nephropathy.

Introduction Not only is diabetic nephropathy (DN) the most common cause of end-stage renal disease worldwide, but it also increases the risk of mortality up to fourteen times compared to normoalbuminuric diabetic patients. Aim The aim of the current study was the evaluation of the renoprotective effects of vitamin D in DN and the possible interplay between autophagy and mTOR pathways. Materials and Methods Fifty male Wistar albino rats were divided (10/group) into control, DN group, insulin-treated DN group, vitamin D-treated DN group, and combined insulin and vitamin D-treated DN group. Assessments of systolic blood pressure, albuminuria, creatinine clearance, serum glucose, insulin, urea, creatinine, inflammatory cytokines, oxidative stress markers, and rat kidney gene expression of mTOR were performed. Histopathological and immunohistochemical assessments of autophagy marker LC3 in rat kidneys were also performed. Results DN was associated with significant increases in SBP, urinary albumin, serum glucose, urea, creatinine, inflammatory cytokines, MDA, and mTOR gene expression (P < 0.05). However, there was significant decrease in creatinine clearance, serum insulin, GSH, and H score value of LC3 when compared with control group (P < 0.05). The combination of insulin and vitamin D treatment significantly restored DN changes when compared with the other treated groups, except in oxidative stress markers where there was an insignificant difference between the combination-treated and insulin-treated groups (P > 0.05). Conclusion It has been concluded that vitamin D is a potent adjuvant therapy in treatment of DN via downregulation of mTOR gene expression, stimulation of autophagy, and antioxidant, anti-inflammatory, and hypotensive effects.

Genome-wide identification of the SPL gene family in Tartary Buckwheat (Fagopyrum tataricum) and expression analysis during fruit development stages

BackgroundSPL (SQUAMOSA promoter binding protein-like) is a class of plant-specific transcription factors that play important roles in many growth and developmental processes, including shoot and inflorescence branching, embryonic development, signal transduction, leaf initiation, phase transition, and flower and fruit development. The SPL gene family has been identified and characterized in many species but has not been well studied in tartary buckwheat, which is an important edible and medicinal crop.ResultsIn this study, 24 Fagopyrum tataricum SPL (FtSPL) genes were identified and renamed according to the chromosomal distribution of the FtSPL genes. According to the amino acid sequence of the SBP domain and gene structure, the SPL genes were divided into eight groups (group I to group VII) by phylogenetic tree analysis. A total of 10 motifs were detected in the tartary buckwheat SPL genes. The expression patterns of 23 SPL genes in different tissues and fruits at different developmental stages (green fruit stage, discoloration stage and initial maturity stage) were determined by quantitative real-time polymerase chain reaction (qRT-PCR).ConclusionsThe tartary buckwheat genome contained 24 SPL genes, and most of the genes were expressed in different tissues. qRT-PCR showed that FtSPLs played important roles in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This work provides a comprehensive understanding of the SBP-box gene family in tartary buckwheat and lays a significant foundation for further studies on the functional characteristics of FtSPL genes and improvement of tartary buckwheat crops.

Expression of genes SBP and leginsulin in contrasting soybean seed coats

ABSTRACT: Evaluation of differential candidate gene expression in contrasting soybean seeds is an auxiliary tool in the partial elucidation of processes involved in seeds formation, as well as it contributes to the generation of new information that can be used in future research or in the development of r genetic superior constitutions. The aim of this study was to evaluate the expression of two candidate genes, SBP and leginsulin genes, possibly involved in seed quality, in contrasting coats of four soybean genotypes. Two cultivars of yellow soybeans were used, BMX Potência RR and CD 202, and two lines of black soybean, TP and IAC. Gene expression was evaluated using qPCR in seven stages of development from seed coats for four genotypes, at 25, 30, 35, 40, 45, 50, and 55 days after anthesis. The design was completely randomized, with three replications. Data were subjected to analysis of variance and means compared by Tukey's test at 5% probability. SBP and leginsulin gene have higher expression in the early phases of development from seed coats of BMX Potência RR cultivar, followed by the IAC line. These genotypes are therefore of interest for further research involving these genes.

Identification of SSR markers associated with saccharification yield using pool-based genome-wide association mapping in sorghum

Saccharification describes the conversion of plant biomass by cellulase into glucose. Because plants have never been selected for high saccharification yield, cellulosic ethanol production faces a significant bottleneck. To improve saccharification yield, it is critical to identify the genes that affect this process. In this study, we used pool-based genome-wide association mapping to identify simple sequence repeat (SSR) markers associated with saccharification yield. Screening of 703 SSR markers against the low and high saccharification pools identified two markers on the sorghum chromosomes 2 (23-1062) and 4 (74-508c) associated with saccharification yield. The association was significant at 1% using either general or mixed linear models. Localization of these markers based on the whole genome sequence indicates that 23-1062 is 223 kb from a β-glucanase (Bg) gene and 74-508c is 81 kb from a steroid-binding protein (Sbp) gene. Bg is critical for cell wall assembly and degradation, but Sbp can suppress the expression of Bg as demonstrated in Arabidopsis (Yang et al. 2005). These markers are found physically close to genes encoding plant cell wall synthesis enzymes such as xyloglucan fucosyltransferase (149 kb from 74-508c) and UDP-D-glucose 4-epimerase (46 kb from 23-1062). Genetic transformation of selected candidate genes is in progress to examine their effect on saccharification yield in plants.

Lotus japonicus Gene Ljsbp Is Highly Conserved Among Plants and Animals and Encodes a Homologue to the Mammalian Selenium-Binding Proteins

We have isolated and characterized a Lotus japonicus gene (Ljsbp) encoding a putative polypeptide with striking homology to the mammalian 56-kDa selenium-binding protein (SBP). cDNA clones homologous to LjSBP were also isolated from soybean, Medicago sativa, and Arabidopsis thaliana. Comparative expression studies in L japonicus and A. thaliana showed that sbp transcripts are present in various tissues and at different levels. Especially in L japonicus nodules and seedpods and A. thaliana siliques, sbp expression appears to be developmentally up-regulated. sbp Gene transcripts were localized by in situ hybridization in the infected cells and vascular bundles of young nodules, while in mature nodules, low levels of expression were only detected in the parenchymatous cells. Expression of sbp transcripts in young seedpods and siliques was clearly visible in vascular tissues and embryos, while in embryos, low levels of expression were detected in the root epidermis and the vascular bundles. Polyclonal antibodies raised against a truncated LjSBP recombinant protein recognized a polypeptide of about 60 kDa in nodule extracts. Immunohistochemical experiments showed that accumulation of LjSBP occurred in root hairs, in the root epidermis above the nodule primordium, in the phloem of the vasculature, and abundantly in the infected cells of young nodules. Irrespective of the presence of rhizobia, expression of SBP was also observed in root tips, where it was confined in the root epidermis and protophloem cells. We hypothesize that LjSBP may have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport, or both.

Antisense and sense expression of a sucrose binding protein homologue gene from soybean in transgenic tobacco affects plant growth and carbohydrate partitioning in leaves

We isolated a cDNA from a soybean library, which encodes sucrose binding protein (SBP) homologue, designated S-64. To analyze the function of the SBP homologue, transgenic tobacco plants were obtained by introducing chimeric genes containing the s-64 coding region linked to the 35S CaMV promoter, either in the sense or antisense orientation, via Agrobacterium tumefaciens-mediated transformation. The accumulation of the SBP homologue was increased in transgenic plants expressing the heterologous sbp gene, whereas those expressing the antisense construct had reduced levels of the protein. The antisense transgenic plants developed symptoms characteristic of an inhibition of sucrose translocation and displayed a reduction in plant growth and development. In contrast, overexpression of the protein accelerated plant growth and the onset of flowering induction. The overall developmental performance of the transgenic plants was correlated with their photosynthetic rate under normal conditions. While photosynthesis in the antisense lines was decreased, in the sense lines photosynthetic rates were increased. Furthermore, both antisense repression and overexpression of the SBP homologue in transgenic lines altered carbohydrate partitioning in mature leaves. Taken together, these results indicate that S-64 protein is functionally analogous to SBP, representing an important component of the sucrose translocation pathway in plants.

Cloning and expression of the pea gene encoding SBP65, a seed-specific biotinylated protein.

Besides biotin-dependent carboxylases, which play key roles in basic metabolism, SBP65 (seed biotinylated protein of 65 kDa of apparent molecular mass), an atypical biotinylated protein, has been described in pea plants. This seed-specific protein is devoid of any carboxylase activity, and shares many physiological and molecular features with late embryogenesis-abundant (Lea) proteins. In a first step toward understanding the role of this peculiar protein, we have demonstrated the role of abscisic acid (ABA) and of the osmotic environment on its expression using northern blot analysis from immature embryos cultured in vitro and germinating mature seeds. Moreover, the cloning and characterization of its gene (referred to as sbp gene) allowed us to define various potential cis-acting elements within the promoter region to account for the observed strict seed-specific expression. The results described in this paper are consistent with a model in which ABA regulates, at least in part, expression of this gene. However, unlike most lea genes, ABA regulation of the sbp gene seems to occur in a very restricted fashion, being confined only to particular stages of embryo development. Such a strict spatial and temporal expression pattern is dependent on the osmotic environment of the developing embryos and on tissue-specific factors, presumably preventing biotin depletion in cells requiring this essential cofactor for basic metabolic activity.

A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA.

Several sites of nuclear protein interaction within the promoter region of the Antirrhinum majus floral meristem identity gene SQUAMOSA were detected using an electrophoretic mobility shift assay. One of these sites displayed a particularly clear interaction with nuclear protein extracted from inflorescences but not with nuclear protein extracted from young, nonflowering plants. This site could thus represent a binding motif for a transcriptional activator. A South-western screen of an inflorescence cDNA expression library resulted in the isolation of several cDNAs representing two different genes named SBP1 and SBP2 (for SQUAMOSA-pROMOTER BINDING PROTEIN gene 1 and 2). Both genes encode highly similar protein domains which were found to be necessary and sufficient for binding DNA in a sequence-specific manner. This DNA-binding domain showed no similarity to known proteins in the databases. However, it is characteristic for a small family of gene products in A. majus and other plant species. Expression of SBP1 and 2 is developmentally regulated and their transcriptional activation precedes that of SQUAMOSA. The data presented support the idea that members of the newly identified SBP gene family function as transcription factors involved in the control of early flower development.

The Bacillus subtilis cell-division 135–137° region contains an essential orf with significant similarity to murB and a dispensable sbp gene

Sequence similarity analysis has revealed that orf2, in the cell division 135-137° region of the Bacillus subtilis (Bs) chromosome, is the probable homolog of Escherichia coli murB (encoding a reductase involved in peptidoglycan synthesis). The amino-acid sequences of the two protein products show 24% identity (47% overall similarity), with several regions of higher similarity which may represent functional domains of the proteins. Attempts to insertionally inactivate orf2 were unsuccessful, strongly suggesting that it is an essential Bs gene. A small gene found in the same region as orf2, sbp (encoding the ‘small basic protein’), was shown to be non-essential in Bs.

Roles of anions in cells: studies on a Cl(-)-translocating ATPase and sulfate uptake system in Acetabularia acetabulum

Biochemical and molecular biological approaches to two anion translocators, a Cl(-)-translocating ATPase and sulfate permease were described for Acetabularia acetabulum, a unicellular marine alga. The primary structures of an almost complete cDNA clone of the 50 kDa subunit and a partial cDNA clone of the 54 kDa subunit of the Cl(-)-ATPase were highly similar to the beta and alpha subunits of the F type ATPase, respectively. A partial cDNA clone encoding the alpha subunit of chloroplast ATPase, and partial cDNA clones coding for the beta subunits of chloroplast and mitochondrial ATPases were also obtained from A. acetabulum. The presence of a small multigene family for the F type ATPases with different ion specificities was strongly suggested for the organism. Sulfate uptake system in this organism was also studied and partial cDNA clones encoding CysA and sulfate binding proteins were obtained. ca. 1.7 kb RNA for cysA gene and 1.55 kb for sbp gene were detected by Northern analysis, respectively. A putative malK gene was also partially cloned.

The plasma sex steroid binding protein (SBP or SHBG). A critical review of recent developments on the structure, molecular biology and function

Significant developments have taken place within the past five years on the characterization, molecular biology and function of the plasma sex steroid-binding protein, SBP (or sex hormone binding globulin, SHBG). During the span of that time, amino acid sequences of two SBPs have been established, amino acid residues in the steroid-binding site have been identified, the structure of the human SBP gene has been deduced and evidence for the possible existence of a SBP membrane receptor has been presented. This review covers the salient aspects of these and other developments including a critical analysis of the various proposed models and interpretations with regards to the structure, evolution, molecular biology and function of SBP.