Pathogen Proteins Eliciting Antibodies Do Not Share Epitopes with Host Proteins: A Bioinformatics Approach

The best way to prevent diseases caused by pathogens is by the use of vaccines. The advent of genomics enables genome-wide searches of new vaccine candidates, called reverse vaccinology. The most common strategy to apply reverse vaccinology is by designing subunit recombinant vaccines, which usually generate an humoral immune response due to B-cell epitopes in proteins. A major problem for this strategy is the identification of protective immunogenic proteins from the surfome of the pathogen. Epitope mimicry may lead to auto-immune phenomena related to several human diseases. A sequence-based computational analysis has been carried out applying the BLASTP algorithm. Therefore, two huge databases have been created, one with the most complete and current linear B-cell epitopes, and the other one with the surface-protein sequences of the main human respiratory bacterial pathogens. We found that none of the 7353 linear B-cell epitopes analysed shares any sequence identity region with human proteins capable of generating antibodies, and that only 1% of the 2175 exposed proteins analysed contain a stretch of shared sequence with the human proteome. These findings suggest the existence of a mechanism to avoid autoimmunity. We also propose a strategy for corroborating or warning about the viability of a protein linear B-cell epitope as a putative vaccine candidate in a reverse vaccinology study; so, epitopes without any sequence identity with human proteins should be very good vaccine candidates, and the other way around

Polar Microalgae: Functional Genomics, Physiology, and the Environment

Microalgae underpin most foodwebs in polar regions as terrestrial primary production is too limited to support these complex and productive ecosystems. The success of microalgae in these extreme and highly variable ecosystems is rooted in their evolution and adaptation. The recent application of omics approaches in addition to biochemical and physiological measurements enabled a step change in our understanding of how these important organisms are adapted to their environment and how they have evolved from non-polar anchestors. This chapter is focused on diatoms and green algae as both groups of microalgae are most prevalent in polar regions. First genomes, transcriptomes, and reverse genetic tools have recently become available for representative species from both groups. They serve as important platforms to advance studies on their ecology, evolution, and adaptation. We highlight some of the key findings from these studies and link them with biochemical and physiological data to give insights into how genes and their products have shaped important microalgae in their diverse polar environments such as oceans, sea ice, permanently frozen lakes, snow and glaciers. Data from these studies will pave the way for understanding how these key organisms and their communities are going to respond to global climate change. They already provide novel genetic resources for various different biotechnological applications