Overlapping reading frames in closely related human papillomaviruses result in modular rates of selection within E2

Abstract

A core group of four open reading frames (ORFs) is present in all known papillomaviruses (PVs): the E1 and E2 replication/transcription proteins and the L1 and L2 structural proteins. Because they are involved in processes that are essential to PV propagation, the sequences of these proteins are well-conserved. However, sequencing of novel subtypes for human papillomaviruses (HPV) 54 (AE9) and 82 (AE2/IS39), coupled to analysis of four other closely related genital HPV pairs, indicated that E2 has a higher dN/dS ratio than E1, L1 or L2. The elevated ratio is not homogeneous across the length of the ORF, but instead varies with respect to E2's three domains. The E2 hinge region is of particular interest, because its hypervariability (dN/dS>1) differs markedly from the two domains that it joins: the transcription-activation domain and the DNA-binding domain. Deciphering whether the hinge region's high rate of non-synonymous change is the result of positive Darwinian selection or relaxed constraint depends on the evolutionary behaviour of E4, an ORF that overlaps E2. The E2 hinge region is contained within E4 and non-synonymous changes in the hinge are associated with a disproportionate amount of synonymous change in E4, a case of simultaneous positive and purifying selection in overlapping reading frames. Modular rates of selection among E2 domains are a likely consequence of the presence of an embedded E4. E4 appears to be positioned in a part of the HPV genome that can tolerate non-synonymous change and purifying selection of E4 may be indicative of its functional importance. INTRODUCTIONHuman papillomaviruses (HPVs) include a group of closedcircular, double-stranded DNA viruses established as the aetiological agents of cervical neoplasia and invasive cervical cancer Muñoz et al., 2003). Over 100 putative HPVs have been described, more than 90 of which have been cloned and officially designated (de Villiers et al., 2004). Despite an array of types, the development of cervical carcinoma is restricted to a subset of high-risk viruses, of which HPV16 and HPV18 together account for nearly two-thirds of observed cases (Muñoz et al., 2003). Classification of HPV types into categories, such as 'cancer-causing' and 'non-cancer-causing' or cutaneous and mucosal, is based on both epidemiological and phylogenetic studies (Chan et al., 1995;Pfister & Fuchs, 1994;Van Ranst et al., 1992, 1993. Most oncogenic types share a common ancestor and most common ancestors radiate within an ecological niche, such as the skin or mucosa.The typical HPV genome contains six open reading frames (ORFs) encoding the structural proteins (L1 and L2), proteins that mediate the viral life cycle (E1 and E2) and proteins that regulate host-cell DNA replication and transformation (E6 and E7) (Knipe et al., 2001). E6 and E7 bind the cell-cycle regulators p53 and pRb, respectively. Among highly cancerous types, these oncogenes degrade p53 and pRb, resulting in host-cell immortalization and proliferation (reviewed by Fehrmann & Laimins, 2003). Some p...

Phylogenetic Incongruence among Oncogenic Genital Alpha Human Papillomaviruses

“…Figure 4 shows that the E1 or L1 ORFs were similar between all clades. E2 displayed divergence across all species, especially in the hinge region (16). Two distinct populations are apparent in the E6/E7 region, corresponding to the high-and low-risk species.…”

“…E5 was not used because homologous ORFs were not found throughout this data set. E4, embedded within E2, is also excluded from the analysis, but it is treated in depth elsewhere (16). The total-evidence tree shown in Fig.…”

Human Papillomaviruses: Genetic Basis of Carcinogenicity

“…To date, 5 genital ␣-HPV types have variants meeting the definition of subtypes, and include HPVs 34, 44, 54, 68 and 82 (see table 1 for alias names). Some of these subtypes differ from their closest relative by as much as 6-8% [22][23][24] . At this point, it is unclear whether subtype is a useful designation to describe type variants exceeding 2% differences.…”

Introducing Protein Intrinsic Disorder

“…295 In that study, the authors propose that beyond affording a broad partnership, the wide occurrence of disordered regions in viral proteins could also be related to the typical high mutation rates of RNA viruses, representing a strategy for buffering the deleterious effects of mutations. 295 Taking into account these considerations, as well as the correlation between overlapping genes and disorder, [296][297][298] it has been proposed [299][300][301][302] that the main advantage of the abundance of disorder within viruses would reside in pleiotropy and genetic compaction. Indeed, disorder provides a solution to reduce both genome size and molecular crowding, where a single gene would (i) encode a single (regulatory) protein product that can establish multiple interactions via its disordered regions and hence exert multiple concomitant biological effects, and/or (ii) would encode more than one product by means of overlapping reading frames.…”