Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology

Abstract

Epizootic bovine abortion (EBA), or “foothill abortion,” is the leading cause of beef cattle abortion in California and has also been reported in Nevada and Oregon. In the 1970s, the soft-shelled tick Ornithodoros coriaceus, or “pajaroello tick,” was confirmed as the disease-transmitting vector. In 2005, a novel Deltaproteobacterium was discovered as the etiologic agent of EBA (aoEBA), recently named Pajaroellobacter abortibovis. This organism cannot be grown in culture using traditional microbiological techniques; it can only be grown in experimentally-infected severe combined immunodeficient (SCID) mice. The objectives of this study were to perform a de novo genome assembly for P. abortibovis and identify and validate potential antigenic proteins as candidates for future recombinant vaccine development. DNA and RNA were extracted from spleen tissue collected from experimentally-infected SCID mice following exposure to P. abortibovis. This combination of mouse and bacterial DNA was sequenced and aligned to the mouse genome. Mouse sequences were subtracted from the sequence pool and the remaining sequences were de novo assembled at 50x coverage into a 1.82 Mbp complete closed circular Deltaproteobacterial genome containing 2250 putative protein-coding sequences. Phylogenetic analysis of P. abortibovis predicts that this bacterium is most closely related to the organisms of the order Myxococcales, referred to as Myxobacteria. In silico prediction of vaccine candidates was performed using a reverse vaccinology approach resulting in the identification and ranking of the top 10 candidate proteins that are likely to be antigenic. Immunologic testing of these candidate proteins confirmed antigenicity of seven of the nine expressed protein candidates using serum from P. abortibovis immunized mice.

In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides

“…Most of the myxobacteria are strict aerobes and have genomes > 9 Mb in size. The exceptions include Pajaroellobacter , Anaeromyxobacter and Vulgatibacter, which have small genomes, between 2 and 6 Mbp [ 66 , 86 , 87 ]. Among these, Pajaroellobacter , a strict anaerobic pathogen of cows, have no proteins with a PAS domain.…”

The Impact of Bioinformatics on Vaccine Design and Development

“…Thereafter, this technology has been used to study pathogenic agents including eukaryotic organisms and those involved in diseases transmited by vectors [13], to design and obtain not only vaccines for humans but also for animals [5]. The majority of new vaccines against infectious diseases that have been developed with this technology are currently found in preclinical or clinical trial.…”

“…In addition to the invaluable role of traditional vaccines to prevent diseases, the society has observed remarkable scientiic and technological progress since the last century in the improvement of these vaccines and the generation of new ones. This has been possible by the fusion of computational technologies with the application of recombinant DNA technology, the fast growth of biological and genomic information in database banks, and the possibility of accelerated and massive sequencing of complete genomes [3][4][5]. This has aided in expanding the concept and application of vaccines beyond their traditional immunoprophylactic function of preventing infectious diseases, and also serving as therapeutic products capable of modifying the evolution of a disease and even cure it [3].…”

Immunogenicity Prediction by VaxiJen: A Ten Year Overview

“…As this bacterium cannot be grown in culture, DNA and RNA was extracted from spleen tissue collected from experimentally-infected mice [164]. In silico prediction of vaccine candidates was performed and the top 10 candidate proteins, as ranked by VaxiJen, were tested using serum from P. abortibovis immunized mice.…”