Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicum L.).

Genome-wide association study (GWAS) is effective in identifying favorable alleles for traits of interest with high mapping resolution in crop species. In this study, we conducted GWAS to explore quantitative trait loci (QTL) for eight fruit traits using 162 tomato accessions with diverse genetic backgrounds. The eight traits included fruit weight, fruit width, fruit height, fruit shape index, pericarp thickness, locule number, fruit firmness, and brix. Phenotypic variations of these traits in the tomato collection were evaluated with three replicates in field trials over three years. We filtered 34,550 confident SNPs from the 51 K Axiom® tomato array based on < 10% of missing data and > 5% of minor allele frequency for association analysis. The 162 tomato accessions were divided into seven clusters and their membership coefficients were used to account for population structure along with a kinship matrix. To identify marker-trait associations (MTAs), four phenotypic data sets representing each of three years and combined were independently analyzed in the multilocus mixed model (MLMM). A total of 30 significant MTAs was detected over data sets for eight fruit traits at P < 0.0005. The number of MTA per trait ranged from one (brix) to seven (fruit weight and fruit width). Two SNP markers on chromosomes 1 and 2 were significantly associated with multiple traits, suggesting pleiotropic effects of QTL. Furthermore, 16 of 30 MTAs suggest potential novel QTL for eight fruit traits. These results facilitate genetic dissection of tomato fruit traits and provide a useful resource to develop molecular tools for improving fruit traits via marker-assisted selection and genomic selection in tomato breeding programs.

Intracellular delivery of immunoglobulin G at nanomolar concentrations with domain Z-fused multimeric α-helical cell penetrating peptides.

A new vehicle is designed for the intracellular delivery of antibodies at nanomolar concentrations by combination of domain Z, a small affibody with strong binding affinity to Fc regions of immunoglobulin G (IgG), and the multimers of LK sequences, α-helical cell penetrating peptides (CPP) with powerful cell penetrating activities. Domain Z and multimeric LK are fused together to form LK-domain Z proteins. The LK-domain Z can bind with IgG at a specific ratio at nanomolar concentrations by simple mixing. The IgG/LK-domain Z complexes can successfully penetrate live cells at nanomolar concentration and the delivery efficiency is strongly dependent upon the concentrations of IgG/LK-domain Z complex as well as the species and subclasses of IgGs. The IgG/LK-domain Z complexes penetrate cells via ATP-dependent endocytosis pathway and the majority of delivered IgG seems to escape endosome to cytosol. Remarkably, the delivered IgGs are able to control the targeted intracellular signaling pathway as shown in the down-regulation of pro-survival genes by the delivery of anti-NF-κB using an LK-domain Z vehicle with a cathepsin B-cleavable linker between the LK sequence and domain Z. The simple but very efficient intracellular delivery method of antibodies at nanomolar concentrations is expected to facilitate profound understanding of cell mechanisms and development of new future therapeutics on the basis of intracellular antibodies.

pH-Activatable cell penetrating peptide dimers for potent delivery of anticancer drug to triple-negative breast cancer.

We developed a pH-activatable cell-penetrating peptide dimer LH2 with histidine residues, which can penetrate cells, specifically in weak acidic conditions, even at few tens of nanomolar concentrations. LH2 effectively delivered paclitaxel into triple-negative breast cancer cells, MDA-MB-231, via formation of non-covalent complexes (PTX-LH2(M)) or covalent conjugates (PTX-LH2(C)). Moreover, LH2 showed prolonged circulation in the body and enhanced accumulation in tumors. Both PTX-LH2(M) and PTX-LH2(C) showed strong antitumor effects in a triple-negative breast cancer grafted mouse model at an extremely low dosage.

Reversible Protein Conjugation on Live Cell Surfaces by Specific Recognition between Coiled-Coil Motifs of Natural Amino Acid Sequences.

In this study, we propose a reversible covalent conjugation method for peptides, proteins, and even live cells based on specific recognition between natural amino acid sequences. Two heptad sequences can specifically recognize each other and induce the formation of a disulfide bond between cysteine residues. We show the covalent bond formation and dissociation between peptides and proteins in cell-free conditions and on the surface of live cells. Because heptad sequences consist of natural amino acids, they are expressed in cells without additional preparation and can be used to selectively conjugate peptides, proteins, and cells.

Augmented osteogenesis of mesenchymal stem cells using a fragmented Runx2 mixed with cell-penetrating, dimeric a-helical peptide.

The intracellular delivery of transcription factor/cofactor using cell penetrating peptide (CPP) can lead to selective osteogenesis. The present work investigates the cell-penetrating potential of the a cyclic, α-helical cell-penetrating peptide based on leucine and lysine residues (cLK) for intracellular delivery in MC3T3 cells and the osteogenic effects of a C-terminal proline­serine­threonine-rich (PST) domain of Runx2 using cLK in rat mesenchymal stem cells (MSCs). We confirmed that the combination of cLK and fluorescein 5-isothiocyanate (FITC)-fragmented-Runx2 (fRunx2) showed an enhanced cell-penetrating activity of FITC-fRunx2 compared with FITC-fRunx2 alone. In addition, the fRunx2-cLK group showed strong staining with alizarin red compared with other groups and the degree of alizarin red staining in the fRunx2-cLK group was also 1.2-fold higher than that in the fRunx2-Tat group. The ALP and osteocalcin gene expression levels in the fRunx2-cLK group were higher than those in the other groups. The fRunx2 transferred effectively into the cytoplasm aided by the cLK peptide and augmented the osteogenic differentiation of MSCs.

Photoswitching of Cell Penetration of Amphipathic Peptides by Control of α-Helical Conformation.

We stapled an amphipathic peptide mainly consisting of leucine (L) and lysine (K) by an azobenzene (Ab) linker for photocontrol of the secondary structure. The cis- trans isomerization of the Ab moieties could stabilize and destabilize the α-helical conformation of the LK peptide along with dramatic change of associated peptide structures in a reversible manner by UV-vis irradiation. The cell-penetrating activities of the LK peptide can be readily regulated by the photocontrol, as the stabilized cis-Ab-LK peptide showed remarkable increase of cell penetration compared to the destabilized trans-Ab-LK peptide. The photoswitchable cell-penetrating peptides would provide important structural information for cell permeability as well as an effective targeting strategy for peptide-based pharmaceuticals with spatiotemporal specificity.

Biological control and plant growth promoting capacity of rhizobacteria on pepper under greenhouse and field conditions.

Plant growth promoting rhizobacteria Ochrobactrum lupini KUDC1013 and Novosphingobium pentaromativorans KUDC1065 isolated from Dokdo Island, S. Korea are capable of eliciting induced systemic resistance (ISR) in pepper against bacterial spot disease. The present study aimed to determine whether plant growth-promoting rhizobacteria (PGPR) strains including strain KUDC1013, strain KUDC1065, and Paenibacillus polymyxa E681 either singly or in combinations were evaluated to have the capacity for potential biological control and plant growth promotion effect in the field trials. Under greenhouse conditions, the induced systemic resistance (ISR) effect of treatment with strains KUDC1013 and KUDC1065 differed according to pepper growth stages. Drenching of 3-week-old pepper seedlings with the KUDC-1013 strain significantly reduced the disease symptoms. In contrast, treatment with the KUDC1065 strain significantly protected 5-week-old pepper seedlings. Under field conditions, peppers treated with PGPR mixtures containing E681 and KUDC1013, either in a two-way combination, were showed greater effect on plant growth than those treated with an individual treatment. Collectively, the application of mixtures of PGPR strains on pepper might be considered as a potential biological control under greenhouse and field conditions.