Structural requirements for enzymatic activities of foamy virus protease-reverse transcriptase

Structures of Substrate Complexes of Foamy Viral Protease-Reverse Transcriptase

Reverse transcriptases (RTs) use their DNA polymerase and RNase H activities to catalyze the conversion of single-stranded RNA to double-stranded DNA (dsDNA), a crucial process for the replication of retroviruses. Foamy viruses (FVs) possess a unique RT, which is a fusion with the protease (PR) domain. The mechanism of substrate binding by this enzyme has been unknown. Here, we report a crystal structure of monomeric full-length marmoset FV (MFV) PR-RT in complex with an RNA/DNA hybrid substrate. We also describe a structure of MFV PR-RT with an RNase H deletion in complex with a dsDNA substrate in which the enzyme forms an asymmetric homodimer. Cryo-electron microscopy reconstruction of the full-length MFV PR-RT–dsDNA complex confirmed the dimeric architecture. These findings represent the first structural description of nucleic acid binding by a foamy viral RT and demonstrate its ability to change its oligomeric state depending on the type of bound nucleic acid.

IMPORTANCE Reverse transcriptases (RTs) are intriguing enzymes converting single-stranded RNA to dsDNA. Their activity is essential for retroviruses, which are divided into two subfamilies differing significantly in their life cycles: Orthoretrovirinae and Spumaretrovirinae. The latter family is much more ancient and comprises five genera. A unique feature of foamy viral RTs is that they contain N-terminal protease (PR) domains, which are not present in orthoretroviral enzymes. So far, no structural information for full-length foamy viral PR-RT interacting with nucleic substrates has been reported. Here, we present crystal and cryo-electron microscopy structures of marmoset foamy virus (MFV) PR-RT. These structures revealed the mode of binding of RNA/DNA and dsDNA substrates. Moreover, unexpectedly, the structures and biochemical data showed that foamy viral PR-RT can adopt both a monomeric configuration, which is observed in our structures in the presence of an RNA/DNA hybrid, and an asymmetric dimer arrangement, which we observed in the presence of dsDNA.

RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features

N2-methylguanosine is a post-transcriptional modification of RNA that is found in eukaryotes and archaea. The biological function of m2G modification discovered so far is to control and stabilize the three-dimensional structure of tRNA and the dynamic barrier of reverse transcription. To discover additional biological functions of m2G, it is necessary to develop time-saving and labor-saving calculation tools to identify m2G. In this paper, based on hybrid features and a random forest, a novel predictor, RFhy-m2G, was developed to identify the m2G modification sites for three species. The hybrid feature used by the predictor is used to fuse the three features of ENAC, PseDNC, and NPPS. These three features include primary sequence derivation properties, physicochemical properties, and position-specific properties. Since there are redundant features in hybrid features, MRMD2.0 is used for optimal feature selection. Through feature analysis, it is found that the optimal hybrid features obtained still contain three kinds of properties, and the hybrid features can more accurately identify m2G modification sites and improve prediction performance. Based on five-fold cross-validation and independent testing to evaluate the prediction model, the accuracies obtained were 0.9982 and 0.9417, respectively. The robustness of the predictor is demonstrated by comparisons with other predictors.

iRNA-m2G: Identifying N2-methylguanosine Sites Based on Sequence-Derived Information

RNA N²-methylguanosine (m2G) is one kind of posttranscriptional modification and plays crucial roles in the control and stabilization of tRNA. However, our knowledge about the biological functions of m2G is still limited. The key step of revealing its new function is to recognize the m2G sites in the transcriptome. Since there is no effective method for detecting m2G sites, it is desirable to develop new methods to identify m2G sites. In this study, a computational predictor called iRNA-m2G was proposed to identify m2G sites in eukaryotic transcriptomes. In iRNA-m2G, the RNA sequences were encoded by using nucleotide chemical property and accumulated nucleotide frequency. iRNA-m2G was not only validated by the rigorous jackknife test on the benchmark dataset but also examined by performing cross-species validations. In addition, iRNA-m2G was also tested on an independent dataset. It was found that the accuracies obtained by iRNA-m2G were all quite promising in these tests, indicating that the proposed method could become a powerful tool for identifying m2G sites. Finally, a user-friendly web server for iRNA-m2G is freely accessible at http://lin-group.cn/server/iRNA-m2G.php.

Structural and Functional Aspects of Foamy Virus Protease-Reverse Transcriptase

Reverse transcription describes the process of the transformation of single-stranded RNA into double-stranded DNA via an RNA/DNA duplex intermediate, and is catalyzed by the viral enzyme reverse transcriptase (RT). This event is a pivotal step in the life cycle of all retroviruses. In contrast to orthoretroviruses, the domain structure of the mature RT of foamy viruses is different, i.e., it harbors the protease (PR) domain at its N-terminus, thus being a PR-RT. This structural feature has consequences on PR activation, since the enzyme is monomeric in solution and retroviral PRs are only active as dimers. This review focuses on the structural and functional aspects of simian and prototype foamy virus reverse transcription and reverse transcriptase, as well as special features of reverse transcription that deviate from orthoretroviral processes, e.g., PR activation.

Viral reverse transcriptases

Reverse transcriptases (RTs) play a major role in the replication of Retroviridae, Metaviridae, Pseudoviridae, Hepadnaviridae and Caulimoviridae. RTs are enzymes that are able to synthesize DNA using RNA or DNA as templates (DNA polymerase activity), and degrade RNA when forming RNA/DNA hybrids (ribonuclease H activity). In retroviruses and LTR retrotransposons (Metaviridae and Pseudoviridae), the coordinated action of both enzymatic activities converts single-stranded RNA into a double-stranded DNA that is flanked by identical sequences known as long terminal repeats (LTRs). RTs of retroviruses and LTR retrotransposons are active as monomers (e.g. murine leukemia virus RT), homodimers (e.g. Ty3 RT) or heterodimers (e.g. human immunodeficiency virus type 1 (HIV-1) RT). RTs lack proofreading activity and display high intrinsic error rates. Besides, high recombination rates observed in retroviruses are promoted by poor processivity that causes template switching, a hallmark of reverse transcription. HIV-1 RT inhibitors acting on its polymerase activity constitute the backbone of current antiretroviral therapies, although novel drugs, including ribonuclease H inhibitors, are still necessary to fight HIV infections. In Hepadnaviridae and Caulimoviridae, reverse transcription leads to the formation of nicked circular DNAs that will be converted into episomal DNA in the host cell nucleus. Structural and biochemical information on their polymerases is limited, although several drugs inhibiting HIV-1 RT are known to be effective against the human hepatitis B virus polymerase. In this review, we summarize current knowledge on reverse transcription in the five virus families and discuss available biochemical and structural information on RTs, including their biosynthesis, enzymatic activities, and potential inhibition.

Foamy Virus Protein-Nucleic Acid Interactions during Particle Morphogenesis

Compared with orthoretroviruses, our understanding of the molecular and cellular replication mechanism of foamy viruses (FVs), a subfamily of retroviruses, is less advanced. The FV replication cycle differs in several key aspects from orthoretroviruses, which leaves established retroviral models debatable for FVs. Here, we review the general aspect of the FV protein-nucleic acid interactions during virus morphogenesis. We provide a summary of the current knowledge of the FV genome structure and essential sequence motifs required for RNA encapsidation as well as Gag and Pol binding in combination with details about the Gag and Pol biosynthesis. This leads us to address open questions in FV RNA engagement, binding and packaging. Based on recent findings, we propose to shift the point of view from individual glycine-arginine-rich motifs having functions in RNA interactions towards envisioning the FV Gag C-terminus as a general RNA binding protein module. We encourage further investigating a potential new retroviral RNA packaging mechanism, which seems more complex in terms of the components that need to be gathered to form an infectious particle. Additional molecular insights into retroviral protein-nucleic acid interactions help us to develop safer, more specific and more efficient vectors in an era of booming genome engineering and gene therapy approaches.

A deep phylogeny of viral and cellular right-hand polymerases

Right-hand polymerases are important players in genome replication and repair in cellular organisms as well as in viruses. All right-hand polymerases are grouped into seven related protein families: viral RNA-dependent RNA polymerases, reverse transcriptases, single-subunit RNA polymerases, and DNA polymerase families A, B, D, and Y. Although the evolutionary relationships of right-hand polymerases within each family have been proposed, evolutionary relationships between families remain elusive because their sequence similarity is too low to allow classical phylogenetic analyses. The structure of viral RNA-dependent RNA polymerases recently was shown to be useful in inferring their evolution. Here, we address evolutionary relationships between right-hand polymerase families by combining sequence and structure information. We used a set of 22 viral and cellular polymerases representing all right-hand polymerase families with known protein structure. In contrast to previous studies, which focused only on the evolution of particular families, the current approach allowed us to present the first robust phylogenetic analysis unifying evolution of all right-hand polymerase families. All polymerase families branched into discrete lineages, following a fairly robust adjacency pattern. Only single-subunit RNA polymerases formed an inner group within DNA polymerase family A. RNA-dependent RNA polymerases of RNA viruses and reverse transcriptases of retroviruses formed two sister groups and were distinguishable from all other polymerases. DNA polymerases of DNA bacteriophages did not form a monophyletic group and are phylogenetically mixed with cellular DNA polymerase families A and B. Based on the highest genetic variability and structural simplicity, we assume that RNA-dependent RNA polymerases are the most ancient group of right-hand polymerases, in agreement with the RNA World hypothesis, because RNA-dependent RNA polymerases are enzymes that could serve in replication of RNA genomes. Moreover, our results show that protein structure can be used in phylogenetic analyses of distantly related proteins that share only limited sequence similarity.

AZT resistance alters enzymatic properties and creates an ATP-binding site in SFVmac reverse transcriptase

BACKGROUND

The replication of simian foamy virus from macaques can be inhibited by the nucleoside reverse transcriptase inhibitor azidothymidine (AZT, zidovudine). Four substitutions in the protease-reverse transcriptase (PR-RT) protein (K211I, I224T, S345T, E350K) are necessary to obtain highly AZT resistant and fully replication competent virus. AZT resistance is based on the excision of the incorporated AZTMP in the presence of ATP. I224T is a polymorphism which is not essential for AZT resistance per se, but is important for regaining efficient replication of the resistant virus.

RESULTS

We constructed PR-RT enzymes harboring one to four amino acid substitutions to analyze them biochemically and to determine their ability to remove the incorporated AZTMP. S345T is the only single substitution variant exhibiting significant AZTMP excision activity. Although K211I alone showed no AZTMP excision activity, excision efficiency doubled when K211I was present in combination with S345T and E350K. K211I also decreased nucleotide binding affinity and increased fidelity. NMR titration experiments revealed that a truncated version of the highly AZT resistant mt4 variant, comprising only the fingers-palm subdomains was able to bind ATP with a KD-value of ca. 7.6 mM, whereas no ATP binding could be detected in the corresponding wild type protein. We could show by NMR spectroscopy that S345T is responsible for ATP binding, probably by making a tryptophan residue accessible.

CONCLUSION

Although AZT resistance in SFVmac is based on excision of the incorporated AZTMP like in HIV-1, the functions of the resistance substitutions in SFVmac PR-RT appear to be different. No mutation resulting in an aromatic residue like F/Y215 in HIV, which is responsible for π-π-stacking interactions with ATP, is present in SFVmac. Instead, S345T is responsible for creating an ATP binding site, probably by making an already existing tryptophan more accessible, which in turn can interact with ATP. This is in contrast to HIV-1 RT, in which an ATP binding site is present in the WT RT but differs from that of the AZT resistant enzyme.

Retroviral DNA Transposition: Themes and Variations

Retroviruses and LTR retrotransposons are transposable elements that encapsidate the RNAs that are intermediates in the transposition of DNA copies of their genomes (proviruses), from one cell (or one locus) to another. Mechanistic similarities in DNA transposase enzymes and retroviral/retrotransposon integrases underscore the close evolutionary relationship among these elements. The retroviruses are very ancient infectious agents, presumed to have evolved from Ty3/Gypsy LTR retrotransposons (1), and DNA copies of their sequences can be found embedded in the genomes of most, if not all, members of the tree of life. All retroviruses share a specific gene arrangement and similar replication strategies. However, given their ancestries and occupation of diverse evolutionary niches, it should not be surprising that unique sequences have been acquired in some retroviral genomes and that the details of the mechanism by which their transposition is accomplished can vary. While every step in the retrovirus lifecycle is, in some sense, relevant to transposition, this Chapter focuses mainly on the early phase of retroviral replication, during which viral DNA is synthesized and integrated into its host genome. Some of the initial studies that set the stage for current understanding are highlighted, as well as more recent findings obtained through use of an ever-expanding technological toolbox including genomics, proteomics, and siRNA screening. Persistence in the area of structural biology has provided new insight into conserved mechanisms as well as variations in detail among retroviruses, which can also be instructive.

The p66 immature precursor of HIV-1 reverse transcriptase

In contrast to the wealth of structural data available for the mature p66/p51 heterodimeric human immunodeficiency virus type 1 reverse transcriptase (RT), the structure of the homodimeric p66 precursor remains unknown. In all X-ray structures of mature RT, free or complexed, the processing site in the p66 subunit, for generating the p51 subunit, is sequestered into a β-strand within the folded ribonuclease H (RNH) domain and is not readily accessible to proteolysis, rendering it difficult to propose a simple and straightforward mechanism of the maturation step. Here, we investigated, by solution NMR, the conformation of the RT p66 homodimer. Our data demonstrate that the RNH and Thumb domains in the p66 homodimer are folded and possess conformations very similar to those in mature RT. This finding suggests that maturation models which invoke a complete or predominantly unfolded RNH domain are unlikely. The present study lays the foundation for further in-depth mechanistic investigations at the atomic level.

Determination of the protease cleavage site repertoire--the RNase H but not the RT domain is essential for foamy viral protease activity

In contrast to orthoretroviruses, the foamy virus protease is only active as a protease-reverse transcriptase fusion protein and requires viral RNA for activation. Maturation of foamy viral proteins seems to be restricted to a single cleavage site in Gag and Pol. We provide evidence that unprocessed Gag is required for optimal infectivity, which is unique among retroviruses. Analyses of the cleavage site sequences of the Gag and Pol cleavage sites revealed a high similarity compared to those of Lentiviruses. We show that positions P2׳ and P2 are invariant and that Gag and Pol cleavage sites are processed with similar efficiencies. The RNase H domain is essential for protease activity, but can functionally be substituted by RNase H domains of other retroviruses. Thus, the RNase H domain might be involved in the stabilization of the protease dimer, while the RT domain is essential for RNA dependent protease activation.