Complete genomic sequence and comparative analysis of the tumorigenic poxvirus Yaba monkey tumor virus

Abstract

The Yatapoxvirus genus of poxviruses is comprised of Yaba monkey tumor virus (YMTV), Tanapox virus, and Yaba-like disease virus (YLDV), which all have the ability to infect primates, including humans. Unlike other poxviruses, YMTV induces formation of focalized histiocytomas upon infection. To gain a greater understanding of the Yatapoxvirus genus and the unique tumor formation properties of YMTV, we sequenced the 134,721-bp genome of YMTV. The genome of YMTV encodes at least 140 open reading frames, all of which are also found as orthologs in the closely related YLDV. However, 13 open reading frames found in YLDV are completely absent from YMTV. Common to both YLDV and YMTV are the unusually large noncoding regions between many open reading frames. To determine whether any of these noncoding regions might be functionally significant, we carried out a comparative analysis between the putative noncoding regions of YMTV and similar noncoding regions from other poxviruses. This approach identified three new gene poxvirus families, defined as orthologs of YMTV23.5L, YMTV28.5L, and YMTV120.5L, which are highly conserved in virtually all poxvirus species. Furthermore, the comparative analysis also revealed a 40-bp nucleotide sequence at approximately 14,700 bases from the left terminus that was 100% identical in the comparable intergene site within members of the Yatapoxvirus, Suipoxvirus, and Capripoxvirus genera and 95% conserved in the Leporipoxvirus genus. This conserved sequence was shown to function as a poxvirus late promoter element in transfected and infected cells, but other functions, such as an involvement in viral replication or packaging, cannot be excluded. Finally, we summarize the predicted immunomodulatory protein repertoire in the Yatapoxvirus genus as a whole.

FIG. 1.

YMTV genomic map. The assigned ORFs of YMTV are displayed, with an arrow indicating the direction of transcription. Each ORF is colored to indicate a general functional category. In addition, the black arrows above the ORFs at either end of the genome indicate the TIR.

FIG. 2.

YMTV and YLDV each contain an apparent pseudogene within the noncoding region of the termini. An alignment of the assigned SPV002 ORF (3) with a portion of the noncoding region of the YMTV and YLDV termini is shown.

FIG. 3.

Comparative analysis of the noncoding region between YMTV22L and YMTV24L. (a) Schematic arrangement of ORFs in the region of the 23.5L orthologs in YMTV and YLDV. A 42-base conserved sequence (CS) is shown as a black box. (b) Alignment of orthologs of 23.5L in YMTV, YLDV, LSDV (LSDV023), myxoma virus (M018L), vaccinia virus (vv F8L), fowlpox (FPV113), and molluscum contagiosum virus (MC014.1L). The SPV (SPV20.5) sequence is also shown, although it lacks a start codon in the published sequence (3).

FIG. 4.

Analysis of the conserved promoter-like sequence between YMTV23.5L and YMTV24L. (a) Alignment of a conserved sequence found between orthologs of YMTV23.5L and YMTV24L. The sequence within the red boxes labeled “A” and “B” represents the 9-bp repeat. The numbers above the grey box indicate the nucleotide positions. (b) Schematic of the orientation of the promoterless GFP with respect to the orientation of the cloned myxoma virus conserved sequence. R-GFP contains the conserved sequence from bases 2 to 41. L-GFP contains the reverse complement of the conserved sequence. The red boxes show the location of the two repeats in panel a. (c) Cells were either mock infected or infected with myxoma virus and subsequently transfected with either a promoterless GFP, R-GFP, or L-GFP construct. Forty-eight hours postinfection, the cells were visualized using a fluorescence microscope.

FIG. 5.

Alignment of two conserved ORF clusters in a variety of poxvirus genera. (a) Alignment of predicted ORFs from representative members from seven of the eight poxvirus genera. Two regions of the genome are shown, the orthologous region between YMTV027L and YMTV029L and the region between YMTV120L and YMTV121L. Orthologous ORFs share the same color. (b) Analysis of the region between YMTV027L/029L and YMTV120L/121L revealed two new conserved gene families. The proposed arrangements of these ORFs are shown, highlighting the arrangement of the two new gene families YMTV028.5L and YMTV120.5L.

FIG. 6.

Alignments of the predicted YMTV28.5L and YMTV120.5L protein families. (a) Arrangement of YMTV 28.5L orthologs in YMTV, YLDV, and myxoma virus. (b) Alignment of orthologs of YMTV28.5L, including YLDV28.5L, LSDV (LSDV28.5), myxoma virus (M023.5L), vaccinia virus (vvF14L), SPV (SPV26.5), and molluscum contagiosum virus (MC022.1L). (c) Alignment of orthologs of YMTV120.5L, including YLDV120.5L, LSDV (LSDV120.5), myxoma virus (M119L), vaccinia virus (vvA30.5L), swinepox virus (SPV117.5), fowlpox virus (FPV194.5L), and molluscum contagiosum virus (MC137L).