The Tonoplastic Inositol Transporter INT1 From Arabidopsis thaliana Impacts Cell Elongation in a Sucrose-Dependent Way

Genome-wide exploration: Evolution, structural characterization, molecular docking, molecular dynamics simulation and expression analysis of sugar transporter (ST) gene family in potato (Solanum tuberosum)

Sugars are the basic structural components of carbohydrates. Sugar transport is crucial for plants to ensure their optimal growth and development. Long-distance sugar transport occurs through either diffusion-based passive or active transport mediated by transporter proteins. In potatoes, STs play a vital role in sugar transport and total sugar accumulation. To better understand the roles of these transporters, in-depth structural, protein characterization, and tissue-specific expression analysis were performed. A total of 61 StSTs were identified and classified into eight sub-families (STP, PLT, ERD6L, INT, TMT, pGlcT, SUC, and VGT). The majority of StSTs were found in the plasma membrane, and all of them were dispersed throughout the 12 chromosomes. Exon and motif counts ranged from 1-18 and 1-10, respectively. In synteny analysis with four plant genomes, the highest (38) orthologous gene pair was found with S. lycopersicum (tomato). In 3D protein modeling, the alpha helix and transmembrane helices range varied from 32 % to 78 % and 53 %-57 %, respectively. During molecular docking analysis, the lowest binding energy was observed for Glu-StINT1 (ΔG: - 6.6 kcal/mol), Fru-StVGT1 (ΔG: - 6.1 kcal/mol), Gal-StSTP10 (ΔG: - 6.5 kcal/mol), and Suc-StINT2 (ΔG: - 7.5 kcal/mol), among 244 docking results. These complexes showed significant hydrogen and hydrophobic interactions, due to having significant amino acid residues. The molecular dynamics (MD) simulation of four complexes (Glu-StINT1, Fru-StVGT1, Gal-StSTP10, and Suc-StINT2) validated the ligand's stable attachment to the intended target proteins and it can be predicted that these complexes are the best sugar transporters of potato. In RNA-seq mediated expression analysis, StSTP12, StERD6L-6, 12, StpGlcT3, StVGT1, and StVGT2, were significantly upregulated in vegetative tissues/organs, revealing their significant role in vegetative organ development. In addition, stu-miRNA395 was the largest family interacting with StERD6L-1 and StTMT2 genes, demonstrating their significant role in sulfate metabolism. The detection and visualization of potential transcription factors (TFs) like ERF, Dof, MYB, BBR-BPC, LBD, and NAC in conjunction with the StSTs gene indicate their significant contribution to stress tolerance and DNA conversion and transcription into RNA. A significant interaction of StSTs in the PPI network might be due to their cumulative role in the same signaling pathways. The integration of these findings will guide the development of programming-based sugar transporter-mediated genetic circuits to improve the sugar accumulation in potatoes using synthetic biology approaches.

The Vacuolar Inositol Transporter BvINT1;1 Contributes to Raffinose Biosynthesis and Reactive Oxygen Species Scavenging During Cold Stress in Sugar Beet

Despite a high sucrose accumulation in its taproot vacuoles, sugar beet (Beta vulgaris subsp. vulgaris) is sensitive to freezing. Earlier, a taproot-specific accumulation of raffinose was shown to have beneficial effects on the freezing tolerance of the plant. However, synthesis of raffinose and other oligosaccharides of the raffinose family depends on the availability of myo-inositol. Since inositol and inositol-metabolising enzymes reside in different organelles, functional inositol metabolism and raffinose synthesis depend on inositol transporters. We identified five homologues of putative inositol transporters in the sugar beet genome, two of which, BvINT1;1 and BvINT1;2, are localised at the tonoplast. Among these, only the transcript of BvINT1;1 is highly upregulated in sugar beet taproots under cold. BvINT1;1 exhibits a high transport specificity for inositol and sugar beet mutants lacking functional BvINT1;1 contain increased inositol levels, likely accumulating in the vacuole, and decreased raffinose contents under cold treatment. Due to the quenching capacity of raffinose for Reactive Oxygen Species (ROS), which accumulate under cold stress, bvint1;1 sugar beet plants show increased expression of both, ROS marker genes and detoxifying enzymes. Based on these findings, we conclude that the vacuolar inositol transporter BvINT1;1 is contributing to ROS-homoeostasis in the cold metabolism of sugar beet.

Genome-wide transcript expression analysis reveals major chickpea and lentil genes associated with plant branching

The search for elite cultivars with better architecture has been a demand by farmers of the chickpea and lentil crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. Herein, this work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested. A total of 1,624 and 2,512 transcripts were identified as differentially expressed among different tissues and contrasting cultivars of chickpea and lentil, respectively. Several gene categories were significantly modulated such as cell cycle, DNA transcription, energy metabolism, hormonal biosynthesis and signaling, proteolysis, and vegetative development between apical and axillary tissues and contrasting cultivars of chickpea and lentil. Based on differential expression and branching-associated biological function, ten chickpea genes and seven lentil genes were considered the main players involved in differentially regulating the plant branching between contrasting cultivars. These collective data putatively revealed the general mechanism and high-effect genes associated with the regulation of branching in chickpea and lentil, which are potential targets for manipulation through genome editing and transgenesis aiming to improve plant architecture.

Genome-wide analysis of sugar transporter genes in maize (Zea mays L.): identification, characterization and their expression profiles during kernel development

Sugar transporters (STs) play a crucial role in the development of maize kernels. However, very limited information about STs in maize is known. In this study, sixty-eight ZmST genes were identified from the maize genome and classified into eight major groups based on phylogenetic relationship. Gene structure analysis revealed that members within the same group shared similar exon numbers. Synteny analysis indicated that ZmSTs underwent 15 segmental duplication events under purifying selection. Three-dimensional structure of ZmSTs demonstrated the formation of a compact helix bundle composed of 8-13 trans-membrane domains. Various development-related cis-acting elements, enriched in promoter regions, were correlated with the transcriptional response of ZmSTs during kernel development. Transcriptional expression profiles exhibited expression diversity of various ZmST genes in roots, stems, leaves, tassels, cobs, embryos, endosperms and seeds tissues. During kernel development, the expression of 24 ZmST genes was significantly upregulated in the early stage of grain filling. This upregulation coincided with the sharply increased grain-filling rate observed in the early stage. Overall, our findings shed light on the characteristics of ZmST genes in maize and provide a foundation for further functional studies.

Comparative Proteomic Analysis of Two Wild Soybean (Glycine soja) Genotypes Reveals Positive Regulation of Saline-Alkaline Stress Tolerance by Tonoplast Transporters

Soil saline-alkalization is a significant constraint for soybean production. Owing to higher genetic diversity of wild soybean, we compared the proteomic landscape of saline-alkaline stress-tolerant (SWBY032) and stress-sensitive (SWLJ092) wild soybean (Glycine soja) strains under saline and saline-alkaline stress. Out of 346 differentially expressed proteins (DEPs) specifically involved in saline-alkaline stress, 159 and 133 DEPs were identified in only SWLJ092 and SWBY032, respectively. Functional annotations revealed that more ribosome proteins were downregulated in SWLJ092, whereas more membrane transporters were upregulated in SWBY032. Moreover, protein-protein interaction analysis of 133 DEPs revealed that 14 protein-synthesis- and 2 TCA-cycle-related DEPs might alter saline-alkaline tolerance by affecting protein synthesis and amino acid metabolism. Furthermore, we confirmed G. soja tonoplast intrinsic protein (GsTIP2-1 and GsTIP2-2), inositol transporter (GsINT1), sucrose transport protein (GsSUC4), and autoinhibited Ca2+-ATPase (GsACA11) as tonoplast transporters can synergistically improve saline-alkaline tolerance in soybean, possibly by relieving the inhibition of protein synthesis and amino acid metabolism. Overall, our findings provided a foundation for molecular breeding of a saline-alkaline stress-tolerant soybean.

A genome-wide association study of freezing tolerance in red clover (Trifolium pratense L.) germplasm of European origin

Improvement of persistency is an important breeding goal in red clover (Trifolium pratense L.). In areas with cold winters, lack of persistency is often due to poor winter survival, of which low freezing tolerance (FT) is an important component. We conducted a genome wide association study (GWAS) to identify loci associated with freezing tolerance in a collection of 393 red clover accessions, mostly of European origin, and performed analyses of linkage disequilibrium and inbreeding. Accessions were genotyped as pools of individuals using genotyping-by-sequencing (pool-GBS), generating both single nucleotide polymorphism (SNP) and haplotype allele frequency data at accession level. Linkage disequilibrium was determined as a squared partial correlation between the allele frequencies of pairs of SNPs and found to decay at extremely short distances (< 1 kb). The level of inbreeding, inferred from the diagonal elements of a genomic relationship matrix, varied considerably between different groups of accessions, with the strongest inbreeding found among ecotypes from Iberia and Great Britain, and the least found among landraces. Considerable variation in FT was found, with LT50-values (temperature at which 50% of the plants are killed) ranging from -6.0°C to -11.5°C. SNP and haplotype-based GWAS identified eight and six loci significantly associated with FT (of which only one was shared), explaining 30% and 26% of the phenotypic variation, respectively. Ten of the loci were found within or at a short distance (<0.5 kb) from genes possibly involved in mechanisms affecting FT. These include a caffeoyl shikimate esterase, an inositol transporter, and other genes involved in signaling, transport, lignin synthesis and amino acid or carbohydrate metabolism. This study paves the way for a better understanding of the genetic control of FT and for the development of molecular tools for the improvement of this trait in red clover through genomics assisted breeding.

Exogenously Applied Cyclitols and Biosynthesized Silver Nanoparticles Affect the Soluble Carbohydrate Profiles of Wheat (Triticum aestivum L.) Seedling

Cyclitols, such as myo-inositol and its isomers and methyl derivatives (i.e., d-chiro-inositol and d-pinitol (3-O-methyl-chiro-inositol)), are classified as osmolytes and osmoprotectants and are significantly involved in plant responses to abiotic stresses, such as drought, salinity and cold. Moreover, d-pinitol demonstrates a synergistic effect with glutathione (GSH), increasing its antioxidant properties. However, the role of cyclitols in plant protection against stresses caused by metal nanoparticles is not yet known. Therefore, the present study examined the effects of myo-inositol, d-chiro-inositol and d-pinitol on wheat germination, seedling growth and changes in the profile of soluble carbohydrates in response to biologically synthesized silver nanoparticles ((Bio)Ag NPs). It was found that cyclitols were absorbed by germinating grains and transported within the growing seedlings but this process was disrupted by (Bio)Ag NPs. Cyclitols applied alone induced sucrose and 1-kestose accumulation in seedlings slightly, while (Bio)Ag NP doubled the concentrations of both sugars. This coincided with a decrease in monosaccharides; i.e., fructose and glucose. Cyclitols and (Bio)Ag NPs present in the endosperm resulted in reductions in monosaccharides, maltose and maltotriose, with no effect on sucrose and 1-kestose. Similar changes occurred in seedlings developing from primed grains. Cyclitols that accumulated in grain and seedlings during grain priming with d-pinitol and glutathione did not prevent the phytotoxic effects of (Bio)Ag NPs.

Genome-wide characterization of the inositol transporters gene family in Populus and functional characterization of PtINT1b in response to salt stress

Inositol transporters (INTs) can mediate the transmembrane transport of inositol, and play crucial roles in plant growth, development and stress resistance. However, the INT gene family in Populus has not been reported. Herein, nine INT genes were identified in the Populus trichocarpa genome and divided into three clades. Tandem duplication and whole-genome duplication events could induce the expansion of PtINT gene family. It was worth noting that PtINT1c* and 1d* formed by twice tandem gene duplication events of PtINT1b, but both had undergone partial structural loss during evolution. PtINT2_p1* and PtINT2_p2* might be originated from one INT2 gene by stop codon- and start codon-gain variants. Different members of PtINTs were localized to the plasma membrane or vacuolar membrane. PtINTs had diversified tissue expression profiles, and many members were significantly induced or suppressed after salt and drought treatments. PtINT1b was induced by drought and salinity stresses, and encoded a vacuolar inositol transporter. Overexpression of PtINT1b rendered the transgenic Arabidopsis plants more resistant to salt stress. In conclusion, this study provides valuable clues for future research on the function of PtINTs, and PtINT1b was identified as a candidate gene for genetic engineering to enhance salinity tolerance in plants.

Comparative transcriptome analysis of root types in salt tolerant and sensitive rice varieties in response to salinity stress

Salinity tolerance in rice is a very important trait, especially in areas that are affected by soil salinity, such as tsunami-devastated areas and coastal regions in rice-producing countries. The roots are the key organs that first detect and respond to salinity stress; thus, it is important to have an understanding of how roots contribute to salinity tolerance in agricultural crops. After salinity treatment of the salt tolerant (Mulai) and sensitive (IR29) rice varieties, it appeared that among the three types of roots, the L-type lateral roots (LLR) were the most sensitive to salinity stress in Mulai and the most tolerant in IR29. The nodal roots (NR) and the S-type lateral roots (SLR) were all negatively affected by salinity treatment in both rice varieties. In order to elucidate the molecular mechanism of the difference in stress response among rice root types, the RNA-seq transcriptome profiles of NR, LLR, and SLR were analyzed in Mulai and IR29. Between the two rice varieties, more transporters were found to participate in the regulation of salt tolerance in Mulai roots, such as those involved in ion and sugar transport. In IR29, many of the genes detected were associated with transcription regulation, including stress-inducible genes such as NAC, WRKY and MYB. Among the different root types, gene expression in LLR and SLR were significantly regulated in both rice varieties. Taken together, the genes identified in this study may be utilized in the varietal improvement of rice with very specific root traits that can enhance tolerance to salinity stress.

Molecular mechanism of sugar transport in plants unveiled by structures of glucose/H+ symporter STP10

Sugars are essential sources of energy and carbon and also function as key signalling molecules in plants. Sugar transport proteins (STP) are proton-coupled symporters responsible for uptake of glucose from the apoplast into plant cells. They are integral to organ development in symplastically isolated tissues such as seed, pollen and fruit. Additionally, STPs play a vital role in plant responses to stressors such as dehydration and prevalent fungal infections like rust and mildew. Here we present a structure of Arabidopsis thaliana STP10 in the inward-open conformation at 2.6 Å resolution and a structure of the outward-occluded conformation at improved 1.8 Å resolution, both with glucose and protons bound. The two structures describe key states in the STP transport cycle. Together with molecular dynamics simulations that establish protonation states and biochemical analysis, they pinpoint structural elements, conserved in all STPs, that clarify the basis of proton-to-glucose coupling. These results advance our understanding of monosaccharide uptake, which is essential for plant organ development, and set the stage for bioengineering strategies in crops.

Myo-inositol transport and metabolism participate in salt tolerance of halophyte ice plant seedlings

Myo-inositol and its metabolic derivatives such as pinitol, galactinol, and raffinose affect growth and development and are also involved in stress adaptation. Previous studies have identified myo-inositol transporters (INTs) as transporters of Na⁺ from root to shoot in the halophyte ice plant (Mesembryanthemum crystallinum). We found that the supply of myo-inositol could alleviate the dehydration effects of salt-stressed ice plant seedlings by decreasing the Na/K ratio in roots and increasing the Na/K ratio in shoots. Analyses of the uptake of exogenous myo-inositol revealed that ice plant seedlings contained intrinsic high-affinity transporters and inducible low-affinity uptake systems. The presence of Na⁺ facilitated both high- and low-affinity myo-inositol uptake. Six INT genes were identified from the ice plant transcriptome and named McINT1a, 1b, 2, 4a, 4b, and 4c, according to the classification of the Arabidopsis INT family. In seedlings treated with myo-inositol, salt, or myo-inositol plus salt, the expression patterns of all McINT members differed in shoot and root, which indicates organ-specific regulation of McINTs by salt and myo-inositol. The expression of McINT2, 4a, 4b, and 4c was induced by salt stress in shoot and root, but that of McINT1a and 1b was salt-induced only in shoot. The expression of pinitol biosynthesis gene IMT1 was induced by salt and myo-inositol, and their combination had a synergistic effect on the accumulation of pinitol. Supply of myo-inositol to salt-treated seedlings alleviated the detrimental effects by maintaining a low root Na/K ratio and providing precursors for the synthesis of compatible solute to maintain the osmotic balance.

MdINT1 enhances apple salinity tolerance by regulating the antioxidant system, homeostasis of ions, and osmosis

Myo-inositol is a versatile compound and plays a vital role in plant growth and stress tolerance. Previously, we found that exogenous application of myo-inositol enhanced the salinity tolerance in Malus hupehensis Rehd. by enhancing myo-inositol metabolism. In this study, we found that the tonoplast-localized myo-inositol transporter 1 (MdINT1) was involved in myo-inositol accumulation and conferred salinity tolerance in apple. MdINT1 is characterized by the highest transcripts among the four apple INT-like genes and could be induced by salt stress at the transcriptional level. Also, it was shown that myo-inositol level was slightly decreased in the leaves of transgenic apple lines over-expressing MdINT1, but was significantly increased in the leaves and roots of MdINT1 silencing line. Interestingly, overexpression of MdINT1 enhanced salinity tolerance by promoting Na⁺ and K⁺ balance, antioxidant activity, and accumulation of osmoprotectants in transgenic apple lines. In contrast, under salinity conditions, the MdINT1-mediated protective roles in the antioxidant activity, homeostasis of ions and osmosis were compromised, which in turn increased the risk of salt intolerance in the MdINT1 silencing line.

The sugar transporter system of strawberry: genome-wide identification and expression correlation with fruit soluble sugar-related traits in a Fragaria × ananassa germplasm collection

Sugar from plant photosynthesis is a basic requirement for life activities. Sugar transporters are the proteins that mediate sugar allocation among or within source/sink organs. The transporters of the major facilitator superfamily (MFS) targeting carbohydrates represent the largest family of sugar transporters in many plants. Strawberry (Fragaria × ananassa Duchesne) is an important crop appreciated worldwide for its unique fruit flavor. The involvement of MFS sugar transporters (STs) in cultivated strawberry fruit sugar accumulation is largely unknown. In this work, we characterized the genetic variation associated with fruit soluble sugars in a collection including 154 varieties. Then, a total of 67 ST genes were identified in the v4.0 genome integrated with the v4.0.a2 protein database of F. vesca, the dominant subgenome provider for modern cultivated strawberry. Phylogenetic analysis updated the nomenclature of strawberry ST homoeologs. Both the chromosomal distribution and structural characteristics of the ST family were improved. Semi-RT-PCR analysis in nine tissues from cv. Benihoppe screened 34 highly expressed ST genes in fruits. In three varieties with dramatically differing fruit sugar levels, qPCR integrated with correlation analysis between ST transcript abundance and sugar content identified 13 sugar-correlated genes. The correlations were re-evaluated across 19 varieties, including major commercial cultivars grown in China. Finally, a model of the contribution of the sugar transporter system to subcellular sugar allocation in strawberry fruits was proposed. Our work highlights the involvement of STs in controlling strawberry fruit soluble sugars and provides candidates for the future functional study of STs in strawberry development and responses and a new approach for strawberry genetic engineering and molecular breeding.

Metabolic Profiling of γ-Irradiated Barley Plants Identifies Reallocation of Nitrogen Metabolism and Metabolic Stress Response

The favorable responses of crop species to low-dose γ irradiation can help to develop cultivars with increased productivity and improved stress tolerance. In the present study, we tried to reveal the candidate metabolites involved in growth stimulation of barley seedlings after applying low-dose γ-radiation (⁶⁰Co) to seeds. Stimulating doses (5-20 Gy) provided a significant increase in shoot length and biomass, while relatively high dose of 100 Gy led to significant inhibition of growth. Gas chromatography–mass spectrometry metabolomic analysis uncovered several compounds that may take part in radiation hormesis establishment in irradiated plants. This includes molecules involved in nitrogen redistribution (arginine, glutamine, asparagine, and γ-aminobutyric acid) and stress-responsive metabolites, such as ascorbate, myo-inositol and its derivates, and free amino acids (l-serine, β-alanine, pipecolate, and GABA). These results contribute to the understanding of the molecular mechanisms of hormesis phenomenon.

More Transporters, More Substrates: The Arabidopsis Major Facilitator Superfamily Revisited

The Major Facilitator Superfamily (MFS) is ubiquitous in living organisms and represents the largest group of secondary active membrane transporters. In plants, significant research efforts have focused on the role of specific families within the MFS, particularly those transporting macronutrients (C, N, and P) that constitute the vast majority of the members of this superfamily. Other MFS families remain less explored, although a plethora of additional substrates and physiological functions have been uncovered. Nevertheless, the lack of a systematic approach to analyzing the MFS as a whole has obscured the high diversity and versatility of these transporters. Here, we present a phylogenetic analysis of all annotated MFS domain-containing proteins encoded in the Arabidopsis thaliana genome and propose that this superfamily of transporters consists of 218 members, clustered in 22 families. In reviewing the available information regarding the diversity in biological functions and substrates of Arabidopsis MFS members, we provide arguments for intensified research on these membrane transporters to unveil the breadth of their physiological relevance, disclose the molecular mechanisms underlying their mode of action, and explore their biotechnological potential.