Single nucleotide polymorphisms (SNPs) are one of the most common determinants and potential biomarkers of human disease pathogenesis. SNPs could alter amino acid residues, leading to the loss of structural and functional integrity of the encoded protein. In humans, members of the minichromosome maintenance (MCM) family play a vital role in cell proliferation and have a significant impact on tumorigenesis. Among the MCM members, the molecular mechanism of how missense SNPs of minichromosome maintenance complex component 6 (MCM6) contribute to DNA replication and tumor pathogenesis is underexplored and needs to be elucidated. Hence, a series of sequence and structure-based computational tools were utilized to determine how mutations affect the corresponding MCM6 protein. From the dbSNP database, among 15,009 SNPs in the MCM6 gene, 642 missense SNPs (4.28%), 291 synonymous SNPs (1.94%), and 12,500 intron SNPs (83.28%) were observed. Out of the 642 missense SNPs, 33 were found to be deleterious during the SIFT analysis. Among these, 11 missense SNPs (I123S, R207C, R222C, L449F, V456M, D463G, H556Y, R602H, R633W, R658C, and P815T) were found as deleterious, probably damaging, affective and disease-associated. Then, I123S, R207C, R222C, V456M, D463G, R602H, R633W, and R658C missense SNPs were found to be highly harmful. Six missense SNPs (I123S, R207C, V456M, D463G, R602H, and R633W) had the potential to destabilize the corresponding protein as predicted by DynaMut2. Interestingly, five high-risk mutations (I123S, V456M, D463G, R602H, and R633W) were distributed in two domains (PF00493 and PF14551). During molecular dynamics simulations analysis, consistent fluctuation in RMSD and RMSF values, high Rg and hydrogen bonds in mutant proteins compared to wild-type revealed that these mutations might alter the protein structure and stability of the corresponding protein. Hence, the results from the analyses guide the exploration of the mechanism by which these missense SNPs of the MCM6 gene alter the structural integrity and functional properties of the protein, which could guide the identification of ways to minimize the harmful effects of these mutations in humans.

Muscadine grape is rich in stilbenes, which include resveratrol, piceid, viniferin, pterostilbene, etc. Resveratrol has been extensively studied for its biological activities; however, the synergistic effect of stilbene compounds in berry extracts is poorly understood. The aim of this study was to evaluate the anti-cancer activity of stilbene-rich muscadine berry extract and pure resveratrol. Stilbenes were extracted from ripened berries of muscadine grape cultivars, Pineapple, and Southern Home. HPLC analysis was performed to determine quantity of stilbenes. The extracts were tested for their cytotoxic activity against A549 (lung carcinoma cells), triple negative breast cancer (HCC-1806) and HepG2 (human liver cancer) cells. The stilbene-rich extracts of the muscadine berry extracts showed cytotoxic activity against all of the cells tested. The extracts at 1 μg/mL induced death in 50–80% of cells by 72 h of treatment. About 50 μg/mL of resveratrol was required to induce a similar response in the cells. Further, modulation of genes involved in tumor progression and suppression was significantly (p < 0.0005) higher with the HepG2 cells treated with stilbene-rich berry extracts than the pure resveratrol. This shows that the synergistic activity of stilbenes present in muscadine grape berries have more potent anti-cancer activity than the resveratrol alone.

Reduced expression of MADS-box gene AGAMOUS-LIKE11 (VviAGL11) is responsible for stenospermocarpic seedlessness in bunch grapes. This study is aimed to characterize the VviAGL11 orthologous gene (VroAGL11) in native muscadine grapes (Vitis rotundifolia) at the molecular level and analyze its divergence from other plants. The VroAGL11 transcripts were found in all muscadine cultivars tested and highly expressed in berries while barely detectable in leaves. RT-PCR and sequencing of predicted ORFs from diverse grape species showed that AGL11 transcripts were conservatively spliced. The encoded VroAGL11 protein contains highly conserved MADS-MEF2-like domain, MADS domain, K box, putative phosphorylation site and two sumoylation motifs. The muscadine VroAGL11 proteins are almost identical (99%) to that of seeded bunch cultivar, Chardonnay, except in one amino acid (A79G), but differs from mutant protein of seedless bunch grape, Sultanina, in two amino acids, R197L and T210A. Phylogenetic analysis showed that AGL11 gene of muscadine and other Vitis species formed a separate clade than that of other eudicots and monocots. Muscadine grape cultivar “Jane Bell” containing the highest percentage of seed content in berry (7.2% of berry weight) had the highest VroAGL11 expression, but almost none to nominal expression in seedless cultivars Fry Seedless (muscadine) and Reliance Seedless (bunch). These findings suggest that VroAGL11 gene controls the seed morphogenesis in muscadine grapes like in bunch grape and can be manipulated to induce stenospermocarpic seedlessness using gene editing technology.

Sugars are the structural building blocks of carbohydrates, which are transported through a series of transporters in plant. To explore the molecular mechanisms of how transporters, play roles in uptake, transport and mobilization of sugars in maize, a series of bioinformatics analyses were done to identify and characterize the transporters. Following the analyses, 60 sugar transporters were identified in maize, which shared eight (STP, PLT, ERD6, INT, TMT, pGlcT, SUC, and VGT) clades during phylogenetic analysis. Due to having significant differences in molecular weight, multiple beta-strands, transmembrane helices, and 11–12 transmembrane domains, the transports might play significant variations in functional properties. Since most transporters are plasma membrane bound, and have the highest homolog pairs (39) with S. bicolor during synteny analysis, the transporters might be involved in intercellular sugar transport that are conserved and significantly duplicated during the process of evolution. The lowest binding affinity (ΔG: − 7.1 kcal/mol) in ZmVGT1-Suc docked complex, and most commonly found hydrogen bond mediated attachment of valine residue ligand might represent the complex stability and functional integrity of the complex. Indeed, the RMSD deviation of 1 (for ZmST10-Gal) to 3 Å (for ZmST10-Glu) among the docked complexes might guide the subtle conformational differences that could impact the functional roles of the complexes. Next, during co-expression analysis, clustering of 491 genes with 43 maize sugar transporter into four co-expression clusters and five different metabolic pathways might guide their inter regulatory roles in interacting different metabolic pathways. More specifically, co-expression of ZmSTP9 and ZmPLT10 with the MYB8 and A6b stress-responsive transcription factors might guide their stress regulatory mechanisms. The RNA-Seq based observation of differential tissue specific expression and expression under salinity, drought, nitrogen deficiency, and heat stress and qRT-PCR mediated validation of differential tissue specific expression and upregulation of ZmPLT1 , ZmPLT8 , ZmSTP1 , ZmTMT1 , and ZmSUC3 under salinity stress might guide their potential roles in abiotic stress tolerance. The plasma membrane localized validation of subcellular localization of ZmPLT1 and ZmPLT8 proteins might guide the consistent results between dry and wet lab experiments. Therefore, the identified and characterized maize sugar transporters through integrated dry and wet lab experiments might guide the future research in developing abiotic stress tolerant maize and exploring the molecular mechanism of stress tolerance trough transporter guided regulation of maize abiotic stress signaling pathways following circuit enabled synthetic biology approaches.