Retroviral DNA Integration

Lesbats, Paul; Engelman, Alan; Cherepanov, Peter

doi:10.1021/acs.chemrev.6b00125

Cited by 196 publications

(218 citation statements)

References 400 publications

(1,016 reference statements)

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“…The crystal structure of the Mos1 strand transfer complex suggests that the A metal ion activates the 3′-hydroxyl at the end of the transposon for the integration step (Figure 6B, right element) (32). This is the same as in Tn 5 and the retroviral integrases (50,51). If we now work backward in the reaction pathway: the structure of Mos1 with an uncleaved transferred strand suggests that the B metal ion activates the nucleophilic water for the cleavage step (31).…”

Section: Discussionmentioning

confidence: 89%

A single active site in the mariner transposase cleaves DNA strands of opposite polarity

Bouuaert

Chalmers

2017

Nucleic Acids Research

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The RNase H structural fold defines a large family of nucleic acid metabolizing enzymes that catalyze phosphoryl transfer reactions using two divalent metal ions in the active site. Almost all of these reactions involve only one strand of the nucleic acid substrates. In contrast, cut-and-paste transposases cleave two DNA strands of opposite polarity, which is usually achieved via an elegant hairpin mechanism. In the mariner transposons, the hairpin intermediate is absent and key aspects of the mechanism by which the transposon ends are cleaved remained unknown. Here, we characterize complexes involved prior to catalysis, which define an asymmetric pathway for transpososome assembly. Using mixtures of wild-type and catalytically inactive transposases, we show that all the catalytic steps of transposition occur within the context of a dimeric transpososome. Crucially, we find that each active site of a transposase dimer is responsible for two hydrolysis and one transesterification reaction at the same transposon end. These results provide the first strong evidence that a DDE/D active site can hydrolyze DNA strands of opposite polarity, a mechanism that has rarely been observed with any type of nuclease.

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Section: Discussionmentioning

confidence: 89%

A single active site in the mariner transposase cleaves DNA strands of opposite polarity

Bouuaert

Chalmers

2017

Nucleic Acids Research

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“…The organization of these large, LTR-dense loci is similar to that of piRNA clusters [30]: piRNA-producing loci in the genome that result from the accumulation of TE fragments (due to non-random LTR integrase-directed integration)[31]. To assess the ability of these loci to produce piRNAs, we performed small RNA sequencing, employing a procedure to enrich for bona fide piRNAs (see STAR methods).…”

Section: Resultsmentioning

confidence: 99%

The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome

et al. 2017

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SUMMARY The Aedes aegypti mosquito transmits arboviruses including dengue, chikungunya and Zika virus. Understanding the mechanisms underlying mosquito immunity could provide new tools to control arbovirus spread. Insects exploit two different RNAi pathways to combat viral and transposon infection: short-interfering RNA (siRNAs) and PIWI-interacting RNAs (piRNAs) [1, 2]. Endogenous viral elements (EVEs) are sequences from non-retroviral RNA viruses that are inserted into the mosquito genome and act as templates for the production of piRNAs [3, 4]. EVEs therefore represent a record of past infections and a reservoir of potential immune memory [5]. The large-scale organization of EVEs has been difficult to resolve with short-read sequencing because they tend to integrate into repetitive regions of the genome. To define the diversity, organization and function of EVEs, we took advantage of the contiguity associated with long-read sequencing to generate a high-quality assembly of the Ae. aegypti-derived Aag2 cell line genome, an important and widely used model system. We show EVEs are acquired through recombination with specific classes of LTR retrotransposons and organize into large loci (>50kbp) characterized by high LTR density. These EVE-containing loci have increased density of piRNAs compared to similar regions without EVEs. Furthermore, we detected EVE-derived piRNAs consistent with a targeted processing of persistently infecting virus genomes. We propose that comparisons of EVEs across mosquito populations may explain differences in vector competence and further study of the structure and function of these elements in the genome of mosquitoes may lead to epidemiological interventions.

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“…This subtle reconfiguration prevents the reversal of transesterification, which, by itself, is an energy-neutral process. More detailed reviews of the PFV intasome structure and the mechanism of retroviral DNA integration can be found elsewhere [9,10]. …”

Section: Prototype Foamy Virus Intasome Structuresmentioning

confidence: 99%

Retroviral intasomes arising

Engelman

Cherepanov

2017

Current Opinion in Structural Biology

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Retroviral DNA integration takes place within the context of the intasome nucleoprotein complex. X-ray crystal structures of functional spumaviral intasomes were previously revealed to harbor a homotetramer of integrase, and it was generally believed that integrase tetramers catalyzed the integration of other retroviruses. The elucidation of new structures from four different retroviruses over the past year has however revealed this is not the case. The number of integrase molecules required to construct the conserved intasome core structure differs between viral species. While four subunits suffice for spumaviruses, α- and β-retroviruses require eight and the lentiviruses use up to sixteen. Herein we described these alternative architectures, highlighting both evolutionary and structural constraints that result in the different integrase-DNA stoichiometries across Retroviridae.

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Retroviral DNA Integration

Cited by 196 publications

References 400 publications

A single active site in the mariner transposase cleaves DNA strands of opposite polarity

A single active site in the mariner transposase cleaves DNA strands of opposite polarity

The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome

Retroviral intasomes arising

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