Polyomavirus JC in the context of immunosuppression: a series of adaptive, DNA replication-driven recombination events in the development of progressive multifocal leukoencephalopathy

Abstract

Polyomavirus JC (JCV) is the etiological agent of progressive multifocal leukoencephalopathy (PML), a demyelinating infection of oligodendrocytes in the brain. PML, a frequently fatal opportunistic infection in AIDS, has also emerged as a consequence of treatment with several new immunosuppressive therapeutic agents. Although nearly 80% of adults are seropositive, JCV attains an ability to infect glial cells in only a minority of people. Data suggest that JCV undergoes sequence alterations that accompany this ability, and these changes can be derived from an archetype strain by mutation, deletion, and duplication. While the introductory source and primary tissue reservoir of JCV remain unknown, lymphoid cells have been identified as potential intermediaries in progression of JCV to the brain. This review is focused on sequence changes in the noncoding control region (NCCR) of the virus. We propose an adaptive mechanism that involves a sequential series of DNA replication-driven NCCR recombination events involving stalled DNA replication forks at NCCR palindromic secondary structures. We shall describe how the NCCR sequence changes point to a model in which viral DNA replication drives NCCR recombination, allowing JCV adaptation to different cell types in its progression to neurovirulence.

Figure 1

DNA deletions and duplication in a JCV archetype sequence leading to a Mad-1 sequence implicated in PML: position of an internal palindrome. (a) The sequence of the noncoding control region (NCCR) termed archetype [31] here is from strain JAL (gb:JX273163). The sequence rearrangements leading to Mad-1 have been documented [28, 39]. The core origin of DNA replication (ori, not altered) is shaded in light blue. A 23 bp deletion is shaded in red. A 66 bp deletion is shaded in yellow. After shown deletions, the sequence underlined and in bold is tandemly duplicated in Mad-1. (b) A potentially stable internal hairpin, positioned at the 5′ end of the 66 bp deletion, is typed in blue and boxed. A sequence most frequently deleted in several reported cases of PML [4] is located within the 66 bp deletion and typed in red.

Figure 2

Potential stability of palindromes folded as hairpins in the NCCR region of JCV archetype and Mad-1 strains. Folding [72] was modeled at 55°C using JCV circular, single strands in 0.14 M NaCl and 3 mM MgCl₂. NCCR regions are highlighted in pink. The arrow denotes the palindrome typed in blue and boxed in Figure 1(b). Note that sequence rearrangements in Mad-1 remove internal hairpins present in the archetype.

Figure 3

Recombination between replicating plasmids or viral DNA bearing an SV40 ori sequence. Electron micrographs showing in vitro replication of plasmids pSVod (3.3 kb), pSV2-neo (5.6 kb), or SV40 (5.2 kb) are reprinted from Jenab and Johnson [74] with permission from Elsevier. (a) A theta form with replication forks indicated by arrows. (b) A theta form with a dsb creating a free DNA end. (c) Two pSVod circles connected by a DNA bridge. (d) A DNA bridge (arrows) indicating recombination between plasmid pSVod and SV40 viral DNA. (e) A DNA bridge indicating recombination between plasmids pSVod and pSV2-neo. No dual-circular forms or theta forms were seen in the absence of either an SV40 ori or large T-antigen. The drawing at bottom depicts potential dual circular recombination generated by dsb followed by strand invasion.

Figure 4

A sequential order of DNA sequence alterations in progression of the JCV archetype NCCR to a neurovirulent type. In this model mutations precede deletions, and deletions precede tandem duplication. Deletions may occur due to slippage and/or homologous recombination, and duplication may result from various forms of recombination. The possibility of specialized forms of recombination, such as V(D)J-like recombination, occurring within this series cannot be ruled out. Both deletion and duplication may be triggered by dsb caused by replication fork pausing or stalling. No individual step, denoted by an arrow, need be an extremely rare event, but the end result, a neurovirulent JCV form, would be a rarity.