Recombinant Origins of Pathogenic and Nonpathogenic Mouse Gammaretroviruses with Polytropic Host Range

Abstract

Ecotropic, xenotropic, and polytropic mouse leukemia viruses (E-, X-, and P-MLVs) exist in mice as infectious viruses and endogenous retroviruses (ERVs) inserted into mouse chromosomes. All three MLV subgroups are linked to leukemogenesis, which involves generation of recombinants with polytropic host range. Although P-MLVs are deemed to be the proximal agents of disease induction, few biologically characterized infectious P-MLVs have been sequenced for comparative analysis. We analyzed the complete genomes of 16 naturally occurring infectious P-MLVs, 12 of which were typed for pathogenic potential. We sought to identify ERV progenitors, recombinational hot spots, and segments that are always replaced, never replaced, or linked to pathogenesis or host range. Each P-MLV has an E-MLV backbone with P- or X-ERV replacements that together cover 100% of the recombinant genomes, with different substitution patterns for X- and P-ERVs. Two segments are always replaced, both coding for envelope (Env) protein segments: the N terminus of the surface subunit and the cytoplasmic tail R peptide. Viral gene replacements are influenced by host restriction genes and Pathogenic potential maps to the transmembrane subunit segment encoding the N-heptad repeat (HR1). Molecular dynamics simulations identified three novel interdomain salt bridges in the lymphomagenic virus HR1 that could affect structural stability, entry or sensitivity to host immune responses. The long terminal repeats of lymphomagenic P-MLVs are differentially altered by recombinations, duplications, or mutations. This analysis of the naturally occurring, sometimes pathogenic P-MLV recombinants defines the limits and extent of intersubgroup recombination and identifies specific sequence changes linked to pathogenesis and host interactions. During virus-induced leukemogenesis, ecotropic mouse leukemia viruses (MLVs) recombine with nonecotropic endogenous retroviruses (ERVs) to produce polytropic MLVs (P-MLVs). Analysis of 16 P-MLV genomes identified two segments consistently replaced: one at the envelope N terminus that alters receptor choice and one in the R peptide at the envelope C terminus, which is removed during virus assembly. Genome-wide analysis shows that nonecotropic replacements in the progenitor ecotropic MLV genome are more extensive than previously appreciated, covering 100% of the genome; contributions from xenotropic and polytropic ERVs differentially alter the regions responsible for receptor determination or subject to APOBEC3 and Fv1 restriction. All pathogenic viruses had modifications in the regulatory elements in their long terminal repeats and differed in a helical segment of envelope involved in entry and targeted by the host immune system. Virus-induced leukemogenesis thus involves generation of complex recombinants, and specific replacements are linked to pathogenesis and host restrictions.

Human APOBEC3G Prevents Emergence of Infectious Endogenous Retrovirus in Mice

“…Our data ( Fig. 1A) are consistent with previously published findings that the generation of replication-competent ERV requires multiple recombination events to restore polymerase function and endow the Emv2-based virus with a nonrestricted capsid (7,51). We and others (10) observe that several generations of breeding are required for this infectious ERV emergence to occur.…”

Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model

“…The recombinants identified within the IN (Region 1) had crossover junctions distinct from that of the MCF247 and C58v2 recombinant MLVs, with TP -6 having partial overlap with the previously identified crossover region of M965 MLV ( Fig 3B, black boxes) [46]. Similarly, within Region 3, the crossover identified in TP -7 partially overlapped that previously described for PTV-1 [46]. Notably, the presence of recombination did not correlate with tumorigenesis in the MYC/Runx2 mouse.…”

“…Thus, 3' and 5' sequence junctions of M-MLV/polytopic ERV recombinants were determined. Polytropic ERV (P-ERV) DNA segments from TP -6, 7, 9 had close homology to the P-ERV Pmv20 [46,47]. The 5' junction points for the recombinants were found to be within the IN region, with those of TP -6 and TP -9 within the IN CCD ( Fig 3A and 3B, region 1, green) and that of TP-7 within the IN CTD ( Fig 3A and 3B, region 2, blue).…”

Xenotropic Mouse Gammaretroviruses Isolated from Pre-Leukemic Tissues Include a Recombinant

“…There are two subclasses of P-ERVs, the polytropic murine viruses ( Pmvs ) and modified polytropic murine viruses ( Mpmvs ) [ 11 ]. None of the infectious P-MLVs derive directly from Pmvs or Mpmvs , although these P-ERVs can contribute to the generation of intersubgroup recombinant viruses that have the distinctive P-MLV host range [ 12 , 13 , 14 , 15 ].…”

“…Our recent analyses of nonecotropic MLVs from leukemic and pre-leukemic tissues focused on the E-MLV derived P-MLVs [ 15 ], but the P-ERV substitutions have also been found in the lymphomagenic viruses from the mice infected with amphotropic MLVs [ 20 ], and there are multiple examples of intersubtype recombination involving Xmvs . For example, the melanoma associated MelARV MLV is a recombinant of the Emv2 E-MLV and Xmv45 / XmvIV1 [ 21 ], the XMRV X-MLV is a recombinant of two nonecotropic ERV sequences [ 22 ], and some P-MLV recombinants can incorporate Xmv- and Pmv -derived sequences [ 15 ]. The analyses of the other infectious and endogenous MLVs of the inbred and wild mice suggest that some are recombinants that include X-MLV-related sequences [ 23 , 24 ].…”