Genome-wide in silico characterization and stress induced expression analysis of BcL-2 associated athanogene (BAG) family in Musa spp.

Programmed cell death (PCD) is a genetically controlled process for the selective removal of damaged cells. Though understanding about plant PCD has improved over years, the mechanisms are yet to be fully deciphered. Among the several molecular players of PCD in plants, B cell lymphoma 2 (Bcl-2)-associated athanogene (BAG) family of co-chaperones are evolutionary conserved and regulate cell death, growth and development. In this study, we performed a genome-wide in silico analysis of the MusaBAG gene family in a globally important fruit crop banana. Thirteen MusaBAG genes were identified, out of which MusaBAG1, 7 and 8 genes were found to have multiple copies. MusaBAG genes were distributed on seven out of 11 chromosomes in banana. Except for one paralog of MusaBAG8 all the other 12 proteins have characteristic BAG domain. MusaBAG1, 2 and 4 have an additional ubiquitin-like domain whereas MusaBAG5-8 have a calmodulin binding motif. Most of the MusaBAG proteins were predicted to be localized in the nucleus and mitochondria or chloroplast. The in silico cis-regulatory element analysis suggested regulation associated with photoperiodic control, abiotic and biotic stress. The phylogenetic analysis revealed 2 major clusters. Digital gene expression analysis and quantitative real-time RT-PCR depicted the differential expression pattern of MusaBAG genes under abiotic and biotic stress conditions. Further studies are warranted to uncover the role of each of these proteins in growth, PCD and stress responses so as to explore them as candidate genes for engineering transgenic banana plants with improved agronomic traits.

The Gene FvTST1 From Strawberry Modulates Endogenous Sugars Enhancing Plant Growth and Fruit Ripening

Sugar is an important carbon source and contributes significantly to the improvement of plant growth and fruit flavor quality. Sugar transport through the tonoplast is important for intracellular homeostasis and metabolic balance in plant cells. There are four tonoplast sugar transporters (FvTST1-4) in strawberry genome. The qRT-PCR results indicated that FvTST1 has a differential expression pattern in different tissues and developmental stages, and exhibited highest expression level in mature fruits. The yeast complementation assay showed that FvTST1 can mediate the uptake of different sugars, such as fructose, glucose, sucrose, and mannose. Subcellular localization analyses revealed that FvTST1 was mainly targeted to the tonoplast. Transient expression of FvTST1 in strawberry fruits enhanced both fruit ripening and sugar accumulation. Furthermore, FvTST1-transformed tomato plants exhibited higher sucrose and auxin content, enhanced seed germination and vegetative growth, higher photosynthetic rate, early flowering, and bore fruit; fructose and glucose levels were higher in transgenic fruits than those in the control. Transcriptomic analysis indicated that the auxin signaling pathway was highly enriched pathway in up-regulated Gene-ontology terms. In transgenic plants, genes encoding transcription factors, such as phytochrome-interacting factors PIF1, -3, and -4, as well as their potential target genes, were also induced. Collectively, the results show that FvTST1 enhances plant growth and fruit ripening by modulating endogenous sugars, and highlight the biological significance of this gene for future breeding purposes.

Nematode RALF-Like 1 Targets Soybean Malectin-Like Receptor Kinase to Facilitate Parasitism

Soybean [Glycine max (L.) Merr. ] is one of the most strategical oilseed crops that provides sustainable source of protein and oil worldwide. Cultivation of soybean is severely affected by root-knot nematode (RKN). However, the mechanism of RKN parasitism to soybeans is largely unknown. In this study, we identify GmLMM1, which encodes a homolog of FERONIA-like receptor kinase in soybean, as a susceptible gene toward nematode. Mutations of GmLMM1 exhibit enhanced resistance against the RKN Meloidogyne incognita. RNA-sequencing (RNA-seq) analysis reveals a similar differential expression pattern for genes regulated by GmLMM1 (Gmlmm1 vs. wild-type) and M. incognita (M. incognita vs. mock), supporting the role of GmLMM1 in M. incognita infection. Unlike FERONIA in Arabidopsis, GmLMM1 specifically binds to MiRALF1 and AtRALF23 that suppress plant immunity, but not MiRALF3 and AtRALF1. Moreover, we found that the single-nucleotide polymorphism (SNP) in GmLMM1 leads to the natural resistance against RKNs in soybeans. Collectively, these findings uncover GmLMM1 as a susceptible target of nematode RALF-like 1 and provide new genetic resource for nematode resistant breeding.

Varlitinib induced differential Protein Expression analysis on oral carcinoma cell line: A therapeutic approach

Receptor-ligand complex mediated signaling significantly contributesin cellular activities such as growth, proliferation, differentiation, and survival. However, augmented expression of signal transducing receptors and ligands is the most frequent molecular event and major hallmark of oral carcinogenesis. Among these receptors, Epidermal Growth Factor Receptor (EGFR) with intracellular tyrosine kinase activity is the most frequently overexpressed molecule by Squamous epithelial cells of oral cavity. Aberrated EGFR mediated signaling has laid the foundation of targeted therapy thus providing rationale for the conducted study. We have selected EGFR pathway as targeted intracellular signaling cascade inOral squamous cell carcinoma (OSCC). Deactivating EGFR by blocking the binding sites is likely to result in prevention of intracellular downstream signaling. In this context, Tyrosine Kinase Inhibitors (TKIs) have come into play. Quinazolines (aromatic heterocyclic compounds) and their derivatives have shown promising clinical outcomes. Present study focused to investigate anti-EGFR potential of quinazoline derivative, varlitinib-a pan-EGFR inhibitor on oral squamous epithelial cell lines. We performed proteomic analyses to identify differential expression pattern of proteins in SCC-25 cells in response to varlitinib treatment. Identified proteins include Binding Immunoglobulin Protein (BiP), Heat Shock Protein 7C (HSP7C), Protein Disulfide Isomerase 1 A (PDIA1), Vimentin (VIME), Keratin type I Cytoskeletal 14 (K1C14), and β-Actin (ACTB). Among these, five proteinswere found to be downregulated upon varlitinib treatment whereas only Keratin type I Cytoskeletal 14 was upregulated. Differential expression of proteins and possible role of varlitinib as potential antitumor drug in oral carcinoma is discussed.

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

Background SQUAMOSA 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. Results In 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. Conclusions The 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.

PSII-17 The differential expression pattern of messenger RNA for key hepatic glycogen metabolizing proteins is consistent with hepatic glycogen content in suckling pigs

The effect of developmental age (d) on expression of genes responsible for hepatic glycogen (GLY) synthesis and degradation, glucose flux, and GLY content, was determined in crossbred pigs euthanized (n = 6) at birth (d 0, pre-suckle), 1, 3, 7, 14, and 21 d. Liver GLY content and relative abundance of mRNA (RT-PCR) was determined. The relative content of liver mRNA was determined in 2 experiments, d 0, 1, 3, 7 (Experiment 1) and d 0, 1, 7, 14, 21 (Experiment 2). Within each experiment, data were analyzed using the GLM procedure of SAS. Fisher’s protected LSD procedure was used to separate treatment means. Day 0 (76.0) GLY content (mg/g) decreased (P < 0.01) 82% from d 0 to d 1, increased (P < 0.05) from d 1 (13.8) through d 14 (28.4), and did not differ (P = 0.07) between d 1 and 21. In Experiment 1, mRNA content of GLY synthesis proteins GYG1 and GYS1 was greatest (P < 0.01) at d 3 and 7; and 1 and 3; respectively, whereas mRNA content of GLY degrading proteins PGM1, PGM2, and PGM5 was greatest (P ≤ 0.01) at d 1; d 0; and d 1 and 7; respectively. In Experiment 2, mRNA content of GLY synthesis proteins GBE1 and GYS1 was greatest (P < 0.01) at d 0 and 21; and d 1 and 21; respectively, whereas mRNA content of GLY degrading proteins AGL, PGM2, PGM2L, and PGM5 was greatest (P < 0.01) at d 21; d 0; d 7, 14, and 21; and d 14 and 21; respectively. Glucose transporter SGLT1 mRNA content was greatest (P < 0.01) at d 14 and 21. These findings indicate that the pattern of mRNA content of key hepatic GLY degradation and synthesis proteins was consistent with GLY content of suckling pigs.

Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance

Background Alfalfa (Medicago sativa L.) production decreases under salt stress. Identification of genes associated with salt tolerance in alfalfa is essential for the development of molecular markers used for breeding and genetic improvement. Result An RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with salt stress in two alfalfa cultivars: salt tolerant ‘Halo’ and salt intolerant ‘Vernal’. Leaf and root tissues were sampled for RNA extraction at 0 h, 3 h, and 27 h under 12 dS m− 1 salt stress maintained by NaCl. The sequencing generated a total of 381 million clean sequence reads and 84.8% were mapped on to the alfalfa reference genome. A total of 237 DEGs were identified in leaves and 295 DEGs in roots of the two alfalfa cultivars. In leaf tissue, the two cultivars had a similar number of DEGs at 3 h and 27 h of salt stress, with 31 and 49 DEGs for ‘Halo’, 34 and 50 for ‘Vernal’, respectively. In root tissue, ‘Halo’ maintained 55 and 56 DEGs at 3 h and 27 h, respectively, while the number of DEGs decreased from 42 to 10 for ‘Vernal’. This differential expression pattern highlights different genetic responses of the two cultivars to salt stress at different time points. Interestingly, 28 (leaf) and 31 (root) salt responsive candidate genes were highly expressed in ‘Halo’ compared to ‘Vernal’ under salt stress, of which 13 candidate genes were common for leaf and root tissues. About 60% of DEGs were assigned to known gene ontology (GO) categories. The genes were involved in transmembrane protein function, photosynthesis, carbohydrate metabolism, defense against oxidative damage, cell wall modification and protection against lipid peroxidation. Ion binding was found to be a key molecular activity for salt tolerance in alfalfa under salt stress. Conclusion The identified DEGs are significant for understanding the genetic basis of salt tolerance in alfalfa. The generated genomic information is useful for molecular marker development for alfalfa genetic improvement for salt tolerance.

Loss of Function of OsFBX267 and OsGA20ox2 in Rice Promotes Early Maturing and Semi-Dwarfism in γ-Irradiated IWP and Genome-Edited Pusa Basmati-1

Targeted mutagenesis is now becoming the most favored methodology to improve traits in popular rice cultivars selectively. Understanding the genetic basis of already available mutants could be the first step in designing such experiment. Improved White Ponni (IWP), a popularly grown South Indian rice variety, was subjected to γ irradiation to develop WP-22-2, an M6 line superior in semi-dwarfism, early flowering, and high yield, and it has grain qualities similar to those of IWP. The exogenous application of gibberellic acid (GA3) on WP-22-2 resulted in the elongation of shorter internodes to a level similar to IWP. The expression profiling of six genes regulating plant height showed their differential expression pattern at different time points post GA3 treatment. Furthermore, the sequencing of WP-22-2 and IWP genomes revealed several single nucleotide polymorphisms (SNPs) and large-scale deletions in WP-22-2. The conversion of functional codons to stop codons was observed in OsGA20ox2 and OsFBX267, which have been reported to have roles in regulating semi-dwarfism and early flowering, respectively. The loss of function of OsGA20ox2 and OsFBX267 in WP-22-2 resulted in reduced plant height as well as early flowering, and the same has been confirmed by editing OsGA20ox2 in the rice variety Pusa Basmati1 (PB1) using the CRISPR-Cas9 approach. The targeted editing of OsGA20ox2 in PB1 conferred shorter plant height to the edited lines compared with the wild type. Altogether, the study provides evidence on mutating OsGA20ox2 and OsFBX267 genes to develop early maturing and semi-dwarf varieties that can be released to farmers after functional characterization and field trials.

Effect of Banana Bunchy Top Virus on the Heat Shock Protein Genes of Pentalonia nigronervosa during Temperature Susceptibility and Its Effect on Virus Transmission

Acquisition of plant viruses is known to exert various effects on vectors’ developmental biology. Pentalonia nigronervosa is the only known vector of banana bunchy top virus (BBTV), which is an economically detrimental virus infecting banana cultivars all over the world. In the present study, the developmental biology of viruliferous (Vr) and non-viruliferous (NVr) aphids was compared, with a marked reduction noted in the lifespan of aphids upon acquisition of BBTV. Among all the environmental parameters temperature is an important determinant of an insect’s abundance and geographical distribution. Temperature susceptibility of P. nigronervosa was scrutinized by comparing the mortality percentage and differential expression pattern of three heat shock proteins (Hsps; Hsp40, Hsp70, and Hsp90) at the mRNA level between NVr and Vr aphids. After exposure to different temperature stress (5 °C, 15 °C, 38 °C and 25 °C as control) highest mortality of Vr aphids were recorded at 5 °C. Analysis of expression levels of Hsp genes using qPCR showed that both cold and heat shock treatment stimulated higher expression of the three Hsps at various rates in Vr than NVr aphids.. Finally, the effect of temperature stress on the BBTV titer level and their transmission by P.nigronervosa was determined by absolute quantification. The transmission efficiency along with the virus titer was found to be the lowest at 15 °C compared to 38 °C. Overall, our results provide a novel insight into the intricate interaction between aphid fitness and thermal stress concerning the acquisition and transmission of BBTV, which could be a roadmap for the future epidemiological control system.