Viral oncogenes, noncoding RNAs, and RNA splicing in human tumor viruses

Abstract

Viral oncogenes are responsible for oncogenesis resulting from persistent virus infection. Although different human tumor viruses express different viral oncogenes and induce different tumors, their oncoproteins often target similar sets of cellular tumor suppressors or signal pathways to immortalize and/or transform infected cells. Expression of the viral E6 and E7 oncogenes in papillomavirus, E1A and E1B oncogenes in adenovirus, large T and small t antigen in polyomavirus, and Tax oncogene in HTLV-1 are regulated by alternative RNA splicing. However, this regulation is only partially understood. DNA tumor viruses also encode noncoding RNAs, including viral microRNAs, that disturb normal cell functions. Among the determined viral microRNA precursors, EBV encodes 25 from two major clusters (BART and BHRF1), KSHV encodes 12 from a latent region, human polyomavirus MCV produce only one microRNA from the late region antisense to early transcripts, but HPVs appears to produce no viral microRNAs.

Keywords: Epstein-Barr virus; Human papillomaviruses; Kaposi sarcoma-associated herpesvirus; RNA splicing; adenovirus; human T-cell leukemia virus; polyomavirus; viral microRNA; viral noncoding RNA.

Figure 1

Schematic structures of oncoproteins E6 and E7. A. Protein structure and functions of HPV16 E6. Four zinc-binding motifs are shown as grey boxes. The F47 position in E6 appears to be responsible for p53 destabilization . Nuclear localization signals (NLS) and the PDZ-binding domain in the protein are indicated by underlines. B. Protein structure and functions of HPV16 E7. Relative locations of the regions with sequence motifs similar to a portion of conserved region 1 (CR1) and the entire CR2 of adenovirus E1A are shown with the pRB-binding site LXCXE in the CR2. Grey boxes indicate zinc-binding motifs. CKII, casein kinase II phosphorylation sites. Arrows in this figure and the following figures for individual proteins indicate functions of the protein, not its domains or motifs.

Figure 2

Schematic structures of adenovirus E1A protein and mRNAs. A. Structure of E1A protein (full-length 289R variant) and its biological functions. Four conserved regions (CR1-CR4) in E1A and mapped domains in E1A are diagramed . B. RNA structure and alternative spliced species of E1A pre-mRNA. A bidirectional splicing enhancer (BSE) is shown in exon 2 in green, and cellular splicing factors or regulators that control selection of each splice site are indicated by arrows. The panel is modified from reference , with permission. Dotted lines indicate splicing directions.

Figure 3

Schematic structures of adenovirus E1B protein and mRNAs. A. E1B protein structure and its biological functions. NES, nuclear export sequences; NLS, nuclear localization sequences; RNP, ribonucleoprotein motif; CKI/II, casein kinase I/II phosphorylation site. See other reference for more information about E1B . B. RNA structure and alternatively spliced species of E1B pre-mRNA.

Figure 4

Diagrammatic representation of the SV40 large T antigen and its RNA splicing. A. Schematic protein structure of SV40 large T antigen. J, DnaJ domain; OBD, origin DNA-binding domain. B. Alternative splicing of SV40 T antigen pre-mRNA leads to production of Large T, 17K T, and small t mRNAs. Black dots indicate stop codon locations on spliced RNAs.

Figure 5

Schematic structures of EBV LMP1 protein and its RNAs. A. Full-length LMP1 protein. Both the N-terminal and C-terminal cytoplasmic domains are white boxes and the transmembrane domain is a shaded box. Protein-protein interacting motifs are indicated as colored ovals, and a 30-nt deletion (del.) or duplication (dupl.) region often seen in nasopharyngeal carcinomas or B cells is underlined. TRAF, TNFR-associated factor; TRADD, TNFR-associated death domain protein; JAK3, Janus kinase 3. B. Schematic structure of LMP1 mRNAs. Promoters driving the expression of LMP1 and truncated LMP1 are shown relative to the EBV genome. Black dots indicate the first AUG on each transcript that is used for translation initiation.

Figure 6

Schematic structure of the HTLV-1 Tax protein and production of Tax mRNA by alternative RNA splicing. A. Functional regions of HTLV-1 Tax protein. NLS, nuclear localization signal; Zn, zinc finger; LZR, leucine-zipper-like region; NES, nuclear export signal; GLM, Golgi localization motif; SM, secretion motif; PDZ, PDZ-binding domain. B. HTLV-1 Tax expression by alternative RNA splicing. The HTLV-1 genome structure is shown at the top of the panel, with nine species of mRNAs diagramed below. Boxes above RNA exons (solid lines) show an ORF in each spliced mRNA that is used for translation of an individual accessory protein. Introns and splicing directions for each mRNA species are indicated by the dotted lines. Six accessory proteins expressed by alternative RNA splicing all originate from a single pre-mRNA transcribed from the 5' LTR, and their cellular localizations are shown at the right. In addition, HTLV-1 basic leucine zipper factor (HBZ) minus-strand RNA is transcribed from the 3' LTR in an antisense fashion ,, and its encoded protein is a nuclear protein , as shown at the right. Panel B is modified from reference with permission.

Figure 7

Intron 1 splicing in the E6 ORF in HPV16 or HPV18 E6E7 pre-mRNA is essential for E7 production. The HPV16 or HPV18 E6E7 pre-mRNA contains three exons (colored boxes) and two introns (lines). The majority of the E6E7 RNA species in cervical cancer tissues and cervical cancer-derived cell lines are fully spliced E6*I mRNAs, which are utilized for E7 translation. However, the presence of a minimal amount of partially spliced E6 with retention of intron 1 has been detected in cervical cancer tissues and cervical cancer-derived cell lines. This RNA species contains an entire E6 ORF and functions as an E6 mRNA for E6 translation .