Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review

During their long evolutionary history viruses generated many proteins de novo by a mechanism called “overprinting”. Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open reading frame (ORF). Overlapping genes represent an intriguing example of adaptive conflict, because they simultaneously encode two proteins whose freedom to change is constrained by each other. However, overlapping genes are also a source of genetic novelties, as the constraints under which alternative ORFs evolve can give rise to proteins with unusual sequence properties, most importantly the potential for novel functions. Starting with the discovery of overlapping genes in phages infecting Escherichia coli, this review covers a range of studies dealing with detection of overlapping genes in small eukaryotic viruses (genomic length below 30 kb) and recognition of their critical role in the evolution of pathogenicity. Origin of overlapping genes, what factors favor their birth and retention, and how they manage their inherent adaptive conflict are extensively reviewed. Special attention is paid to the assembly of overlapping genes into ad hoc databases, suitable for future studies, and to the development of statistical methods for exploring viral genome sequences in search of undiscovered overlaps.

A Golgi-localized peptide encoded by the CENP-R transcript provides a valuable tool for live cell imaging

Understanding cell biological behaviors requires the ability to visualize different cellular structures and compartments. Excellent markers and tagged proteins exist to detect key cellular structures such as the ER and mitochondrion, where minimal targeting motifs can be used to image and target proteins to these specific organelles (Raykhel et al., 2007); (Bear, 2000; Kim & Hwang, 2013). These markers make visualizing these organelles robust and easy, and provide insights into the requirements for targeting proteins to these subcellular compartments. In the course of our ongoing work, we identified a 37 amino acid peptide that is encoded by a hypothetical alternative open reading frame (altORF) within the mRNA produced for the CENP-R gene. Unlike the centromere-localized canonical CENP-R protein, we find that this small peptide localizes specifically to the Golgi compartment. Our studies demonstrate that this altORF peptide can act as a valuable tool for cell biology experimentation to visualize the Golgi for both fixed and live cell analyses.

Characterisation of the nucleic acid binding features of the PRRSV 7ap and its ability to induce antinuclear antibodies

A short alternative open reading frame named ORF7a has recently been discovered within the nucleocapsid gene of the porcine reproductive and respiratory syndrome virus (PRRSV) genome. Proteins (7ap) translated from the ORF7a of two divergent strains — a type I and a type II — are able to completely reduce the motility of nucleic acids at relatively high molar charge ratios in gel retardation assays indicating strong dsDNA- and ssRNA-binding capability. Conserved RNA- and DNA-binding properties suggest that nucleic acid binding is a functional property of the divergent 7aps, and not an arbitrary consequence of their net positive charge. Sera from Hu7ap-immunised pigs and mice did not react with Hu7ap or Hu7ap-GFP; however, antinuclear antibodies were detected in the sera of the immunised animals, suggesting an ability of Hu7ap to interact with or mimic autoantigenic macromolecules.