Determining the mechanism of HPV18 replication is paramount for identifying possible drug targets against HPV infection. We used two-dimensional and three-dimensional gel electrophoresis techniques to identify replication intermediates arising during the initial amplification of HPV18 episomal genomes. We determined that the first rounds of HPV18 replication proceed via bidirectional theta structures; however, a notable accumulation of almost fully replicated HPV18 genomes indicates difficulties with the completion of theta replication. We also observed intermediates that were created by a second replication mechanism during the initial amplification of HPV18 genomes. The second replication mechanism does not utilize specific initiation or termination sequences and proceeds via a unidirectional replication fork. We suggest a significant role for the second replication mechanism during the initial replication of the HPV18 genome and propose that the second replication mechanism is recombination-dependent replication.

We describe the extensive and progressive oligomerization of human papillomavirus (HPV) genomes after transfection into the U2OS cell line. The HPV genomic oligomers are extrachromosomal concatemeric molecules containing the viral genome in a head-to-tail orientation. The process of oligomerization does not depend on the topology of the input DNA, and it does not require any other viral factors besides replication proteins E1 and E2. We provide evidence that oligomerization of the HPV18 and HPV11 genomes involves homologous recombination. We also demonstrate oligomerization of the HPV18 and HPV11 genomes in SiHa, HeLa, and C-33 A cell lines and provide examples of oligomeric HPV genomes in clinical samples obtained from HPVinfected patients. Human papillomaviruses (HPV) are important pathogens that cause different epithelial hyperplastic lesions, most commonly manifesting as benign warts or papillomas. Over 100 HPV types have been identified to date (1). These epitheliotropic viruses can be categorized based on their ability to infect mucosal or cutaneous keratinocytes. The mucosal viruses can be further subdivided into low-and high-risk HPVs. A potential for malignant progression is characteristic of high-risk HPV types, such as HPV18, HPV16, HPV31, and HPV45, whereas types such as HPV6 and HPV11 do not show similar associations and are considered low risk (2). Essentially all cervical carcinomas (3) and a quarter of reported head and neck cancers (4) are associated with HPV infections.HPV is a small DNA virus with an approximately 8-kbp genome. During infection of stratified cutaneous or mucosal epithelia, the viral genomes replicate as multicopy extrachromosomal genetic elements in the nuclei of host cells. HPV genomes undergo a three-phase replication cycle linked to the host cell differentiation program (5). The first stage of HPV DNA replication occurs in undifferentiated basal keratinocytes after infection and is referred to as transient amplificational replication. During the first phase, the viral replication factors are produced and the HPV genome is amplified up to 100 of copies per cell during the S phase of the cell cycle. After initial amplification, the expression of viral replication proteins is downregulated to a level sufficient for the stable maintenance phase of episomal genomes in HPV-infected basal cells. Upon differentiation of the infected cells, the regulated expression of viral proteins initiates a second amplification of the viral genome, the production of capsid proteins, and the assembly of viral particles in the uppermost layers of terminally differentiated epithelium. The mechanisms regulating the switch from the initial HPV genome replication to HPV genome maintenance and, subsequently, to vegetative amplification are not entirely understood.Replication of the HPV genome is carried out by the cellular replication machinery, which is directed to the viral origin by the viral replication proteins E1 and E2. The mechanism underlying the initiation of DNA replication is well described...

Viruses manipulate the cell cycle of the host cell to optimize conditions for more efficient viral genome replication. One strategy utilized by DNA viruses is to replicate their genomes non-concurrently with the host genome; in this case, the viral genome is amplified outside S phase. This phenomenon has also been described for human papillomavirus (HPV) vegetative genome replication, which occurs in G2-arrested cells; however, the precise timing of viral DNA replication during initial and stable replication phases has not been studied. We developed a new method to quantitate newly synthesized DNA levels and used this method in combination with cell cycle synchronization to show that viral DNA replication is initiated during S phase and is extended to G2 during initial amplification but follows the replication pattern of cellular DNA during S phase in the stable maintenance phase. E1 and E2 protein overexpression changes the replication time from S only to both the S and G2 phases in cells that stably maintain viral episomes. These data demonstrate that the active synthesis and replication of the HPV genome are extended into the G2 phase to amplify its copy number and the duration of HPV genome replication is controlled by the level of the viral replication proteins E1 and E2. Using the G2 phase for genome amplification may be an important adaptation that allows exploitation of changing cellular conditions during cell cycle progression. We also describe a new method to quantify newly synthesized viral DNA levels and discuss its benefits for HPV research.

This unit includes the necessary information to conduct neutral/neutral and neutral/alkaline two-dimensional and neutral/neutral/alkaline three-dimensional agarose gel electrophoresis. The methodology has been optimized over the years to gain a better outcome from the hard-to-interpret signals of human papilloma virus replication intermediates obtained from two- and three-dimensional agarose gels. Examples of typical results and interpretation of replication intermediate patterns are included, and the outcomes of multiple-dimension assays are assessed using previously published experimental data. © 2017 by John Wiley & Sons, Inc.