Unravelling structural, functional, evolutionary and genetic basis of SWEET transporters regulating abiotic stress tolerance in maize

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.

Identification of the maize drought-resistant gene Zinc-finger Inflorescence Meristem 23 through high-resolution temporal transcriptome analysis

Drought is a major abiotic stress that significantly limits maize productivity. However, previous transcriptomic studies with limited time-point sampling have hindered the construction of robust co-expression networks, making it challenging to identify reliable hub genes involved in drought tolerance. To overcome this limitation, we generated a high-temporal-resolution transcriptome dataset spanning 108 time points from maize seedlings subjected to two consecutive rounds of drought and re-watering treatments. A total of 8477 drought-responsive genes (DRGs) were identified by comparing drought-stressed and well-watered controls. Using weighted gene co-expression network analysis (WGCNA), we constructed 17 co-expression modules, of which 8 were strongly associated with drought stress responses and collectively contained 353 hub genes. Among them, we validated the drought resistance functions of ZmCPK35, a known drought-responsive gene, and Zinc-finger Inflorescence Meristem 23 (ZmZIM23), a newly identified drought-regulatory gene, within the M10 module. Functional analysis revealed that ZmZIM23 enhances drought tolerance by improving water-use efficiency, reducing transpiration rates, and promoting biomass accumulation. Furthermore, yeast one-hybrid (Y1H) and dual-luciferase (LUC) assays demonstrated that ZmWRKY40, another M10 module member, transcriptionally regulates both ZmZIM23 and ZmCPK35. By integrating high-resolution transcriptomic data with co-expression network analyses, this study unveils key drought-responsive regulatory networks in maize and identifies novel candidate genes for improving drought tolerance. These findings provide valuable insights into the genetic foundation of drought adaptation and offer potential targets for the development of drought-resistant maize cultivars.

Genome-Wide Characterization, Comparative Analysis, and Expression Profiling of SWEET Genes Family in Four Cymbidium Species (Orchidaceae)

The SWEET (Sugar Will Eventually be Exported Transporters) protein family plays a key role in plant growth, adaptation, and stress responses by facilitating soluble sugar transport. However, their functions in Cymbidium remain poorly understood. This study identified 59 SWEET genes across four Cymbidium species, encoding conserved MtN3/saliva domains. Despite variations in exon-intron structures, gene motifs and domains were highly conserved. Phylogenetic analysis grouped 95 SWEET proteins from six species into four clades, with gene expansion driven by whole-genome, segmental, and tandem duplications. Cis-element analysis and expression profiling across 72 samples revealed diverse regulatory patterns. Notably, SWEET genes showed peak expression in floral development, leaf morph variations, and diurnal rhythms. qRT-PCR and transcription factor binding analysis further highlighted their regulatory roles in floral patterning, leaf variation, and metabolic rhythms. These findings provide a foundation for future studies on SWEET gene function and their potential molecular breeding value in orchids.

Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection

BACKGROUND

The nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.).

RESULTS

The genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains.

CONCLUSION

The identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.

Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses

Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.

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.

Genome-Wide Identification, Expression, and Response to Fusarium Infection of the SWEET Gene Family in Garlic (Allium sativum L.)

Proteins of the SWEET (Sugar Will Eventually be Exported Transporters) family play an important role in plant development, adaptation, and stress response by functioning as transmembrane uniporters of soluble sugars. However, the information on the SWEET family in the plants of the Allium genus, which includes many crop species, is lacking. In this study, we performed a genome-wide analysis of garlic (Allium sativum L.) and identified 27 genes putatively encoding clade I-IV SWEET proteins. The promoters of the A. sativum (As) SWEET genes contained hormone- and stress-sensitive elements associated with plant response to phytopathogens. AsSWEET genes had distinct expression patterns in garlic organs. The expression levels and dynamics of clade III AsSWEET3, AsSWEET9, and AsSWEET11 genes significantly differed between Fusarium-resistant and -susceptible garlic cultivars subjected to F. proliferatum infection, suggesting the role of these genes in the garlic defense against the pathogen. Our results provide insights into the role of SWEET sugar uniporters in A. sativum and may be useful for breeding Fusarium-resistant Allium cultivars.