Sequence Properties of the MAAP Protein and of the VP1 Capsid Protein of Adeno-Associated Viruses

Abstract

Adeno-associated viruses (AAVs, genus dependoparvovirus) are promising gene therapy vectors. In strains AAV1-12, the capsid gene VP1 encodes a recently discovered protein, MAAP, in an overlapping frame.MAAP binds the cell membrane by an unknown mechanism. We discovered that MAAP is also encoded in bovine AAV and in porcine AAVs (which have shown promise for gene transfer into muscle tissues), in which it is probably translated from a non-canonical start codon. MAAP is predicted to be mostly disordered except for a predicted C-terminal, membrane-binding amphipathic α-helix. MAAP has a highly unusual composition. In particular, it lacks internal methionines, and is devoid of tyrosines in most strains.Unexpectedly, we discovered that the N-terminus of VP1 also lacks several amino acids. In all AAVs that encode MAAP, the first 200 aas of VP1 are devoid of internal methionines, probably owing to a selection against ATG codons that could prevent translation of MAAP and of capsid isoforms (VP2, VP3). The Nterminus of VP1 also lacks cysteines, likely to avoid the formation of disulfide bridges when it becomes exposed outside of the capsid during post-endocytic trafficking. Finally, the region common to VP1 and VP2 lacks tyrosine in the vast majority of AAVs that encode MAAP. Avoiding these "forbidden" aas in MAAP and VP1 when creating recombinant AAV capsids might increase the efficiency of capsid design. Conversely, the presence of "forbidden" aas in some rare strains probably indicates that they have unusual properties that could help us understand the viral cycle.Preprints (www.preprints.org) | NOT PEER-REVIEWED |

Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene

“…While a systematic effort has been made to discover overlapping genes in RNA viruses by sequence analyses [16], this has not yet been the case in DNA viruses. Our findings confirm (if that were needed) that overlapping genes remain to be discovered in DNA viruses (we know of at least another case already flagged by sequence analyses, in human However, we note that the predicted sequence features of MAAP differ radically from those of X and ARF1: the region of MAAP that overlaps PLA2 is disordered and T/S-rich, while in X it contains a transmembrane region [54]. Thus, regardless of whether they have a common origin, there is no rationale for thinking that the MAAP protein has a similar function to X or to ARF1.…”

“…The X and ARF1 ORFs overlap the same location of the VP1 gene (corresponding to the PLA2 domain), in the same frame (+1) relative to VP1, and encode proteins with similar properties. In the genus Dependoparvovirus , another ORF, MAAP, whose translation has been proven experimentally, also overlaps the same region of the VP1 gene in the +1 reading frame [ 54 , 55 ]. This similarity begs the question: do X, ARF1, and MAAP have a common origin and a similar function?…”

“…However, we note that the predicted sequence features of MAAP differ radically from those of X and ARF1: the region of MAAP that overlaps PLA2 is disordered and T/S-rich, while in X it contains a transmembrane region [ 54 ]. Thus, regardless of whether they have a common origin, there is no rationale for thinking that the MAAP protein has a similar function to X or to ARF1.…”