Expression of recombinant S-locus F-box-S2 protein and computational modeling of protein interaction at the self-incompatibility locus of Rosaceae

Philosophiae Doctor - PhDSelf-incompatibility (SI) is a major mechanism that prevents inbreeding in ow-ering plants, which was identi ed in Rosaceae, Solanaceae and Scrophulariace. In these families, SI is gametophytic and retains inter-speci c genetic variations by out-crossing promotion. Self-incompatibility is genetically controlled by an S- locus where both male (pollen) and female (pistil) S-determinants are encoded. The female determinant (SRNase) has been extensively studied, whereas its male counterpart (SLF/SFB) has only recently been characterized as a pollen-expressed protein, which encodes for an F-box domain. However, the exact mechanism of in- teraction between SLF/SFB and SRNase is still largely unclear in Rosaceae. This study takes a closer look at the mechanism of self-incompatibility to gain a clearer understanding of the ligand-receptor binding mechanism of SI using molecular evolutionary analysis, structure prediction and binding speci city characteriza- tion, the outcome of which, will translate into a guideline for future studies. The major aims of this study were to derive an evolutionary pattern for GSI in Rosaceae subfamilies and to further assess the collaborative non-self recognition in Malus domestica Borkh.. The evolutionary analysis suggests a di erence in the evolution- ary pattern of Prunoideae and Maloideae S-genes, hence proposing a di erence in their GSI systems. Furthermore, sites responsible for this divergence are identi ed as critical amino acids in GSI function. To maintain GSI it is expected that the S-genes must be linked and co-evolve as a genetic unit. The results of this study show that these genes have co-existed, while SRNase have experienced a higher rate of evolution compared to SLF, thus rejecting the co-evolution of these genes in Maloideae. Furthermore, positively selected sites of S-locus pistil and pollen genes were identi ed that are likely to be responsible for speci city determination. Di erent numbers of these sites are found for both S-genes, while SRNase holds a larger number of positively selected sites. Additionally a model of speci city is introduced that supports the collaborative non-self recognition in Malus GSI, while critical sites responsible for such speci city are proposed and mapped to the predicted ancestral tertiary structure of SRNase and SLF/SFB. The identi cation of regions determining pollen pistil speci city as well as proposing a Collaborative Non-self Recognition model for Malus domestica Borkh. provide greater in-sight into how pollen-pistil communication system works in Maloideae (Rosaceae subfamily)

Glycosyltransferase gene expression profiles classify cancer types and propose prognostic subtypes

Aberrant glycosylation in tumours stem from altered glycosyltransferase (GT) gene expression but can the expression profiles of these signature genes be used to classify cancer types and lead to cancer subtype discovery? The differential structural changes to cellular glycan structures are predominantly regulated by the expression patterns of GT genes and are a hallmark of neoplastic cell metamorphoses. We found that the expression of 210 GT genes taken from 1893 cancer patient samples in The Cancer Genome Atlas (TCGA) microarray data are able to classify six cancers; breast, ovarian, glioblastoma, kidney, colon and lung. The GT gene expression profiles are used to develop cancer classifiers and propose subtypes. The subclassification of breast cancer solid tumour samples illustrates the discovery of subgroups from GT genes that match well against basal-like and HER2-enriched subtypes and correlates to clinical, mutation and survival data. This cancer type glycosyltransferase gene signature finding provides foundational evidence for the centrality of glycosylation in cancer

A simple, high-throughput modeling approach reveals insights into the mechanism of gametophytic self-incompatibility

Specificity in the GSI response results from the S-haplotype-specific molecular interaction of S-locus F-box (SLF/SFB) and SRNase proteins in the self-incompatibility locus (S-locus). The answer to the question of how these two components of the S-locus (SRNase and SLF/SFB) interact has been gathered from several models. Since there is not enough evidence as to which one is the definitive model, none of them can be ruled out. Despite the identification of interacting protein elements, the mechanism by which SLF/SFB and SRNase interact to differently trigger the self-incompatibility among families and subfamilies remain uncertain. The high-throughput modeling approach demonstrates structural visions into the possible existence of a Collaborative Non-Self Recognition model in apple. These findings postulate several prospects for future investigation providing useful information to guide the implementation of breeding strategies

Meta-Analysis Suggests Evidence of Novel Stress-Related Pathway Components in Orsay Virus - Caenorhabditis Elegans Viral Model

The genetic model organism, Caenorhabditis elegans (C. elegans), shares many genes with humans and is the best-annotated of the eukaryotic genome. Therefore, the identification of new genes and pathways is unlikely. Nevertheless, host-pathogen interaction studies from viruses, recently discovered in the environment, has created new opportunity to discover these pathways. For example, the exogenous RNAi response in C. elegans by the Orsay virus as seen in plants and other eukaryotes is not systemic and transgenerational, suggesting different RNAi pathways between these organisms. Using a bioinformatics meta-analysis approach, we show that the top 17 genes differentially-expressed during C. elegans infection by Orsay virus are functionally uncharacterized genes. Furthermore, functional annotation using similarity search and comparative modeling, was able to predict folds correctly, but could not assign easily function to the majority. However, we could identify gene expression studies that showed a similar pattern of gene expression related to toxicity, stress and immune response. Those results were strengthened using protein-protein interaction network analysis. This study shows that novel molecular pathway components, of viral innate immune response, can be identified and provides models that can be further used as a framework for experimental studies. Whether these features are reminiscent of an ancient mechanism evolutionarily conserved, or part of a novel pathway, remain to be established. These results reaffirm the tremendous value of this approach to broaden our understanding of viral immunity in C. elegans