RNA-dependent DNA polymerase activity in cauliflower mosaic virus-infected plant leaves

Predicted structure of the hepatitis B virus polymerase reveals an ancient conserved protein fold

Hepatitis B virus (HBV) chronically infects >250 million people. It replicates by a unique protein-primed reverse transcription mechanism, and the primary anti-HBV drugs are nucleos(t)ide analogs targeting the viral polymerase (P). P has four domains compared to only two in most reverse transcriptases: the terminal protein (TP) that primes DNA synthesis, a spacer, the reverse transcriptase (RT), and the ribonuclease H (RNase H). Despite being a major drug target and catalyzing a reverse transcription pathway very different from the retroviruses, HBV P has resisted structural analysis for decades. Here, we exploited computational advances to model P. The TP wrapped around the RT domain rather than forming the anticipated globular domain, with the priming tyrosine poised over the RT active site. The orientation of the RT and RNase H domains resembled that of the retroviral enzymes despite the lack of sequences analogous to the retroviral linker region. The model was validated by mapping residues with known surface exposures, docking nucleic acids, mechanistically interpreting mutations with strong phenotypes, and docking inhibitors into the RT and RNase H active sites. The HBV P fold, including the orientation of the TP domain, was conserved among hepadnaviruses infecting rodent to fish hosts and a nackednavirus, but not in other non-retroviral RTs. Therefore, this protein fold has persisted since the hepadnaviruses diverged from nackednaviruses >400 million years ago. This model will advance mechanistic analyses into the poorly understood enzymology of HBV reverse transcription and will enable drug development against non-active site targets for the first time.

50th anniversary of the discovery of reverse transcriptase

The simultaneous discovery in 1970 of reverse transcriptase in virions of retroviruses by Howard Temin and David Baltimore was perhaps the most dramatic scientific moment of the second half of the 20th century. Ten years previously, Temin's observation of cells transformed by Rous Sarcoma virus led him to the conclusion that retroviruses replicate through a DNA intermediate he called the provirus. This heretical hypothesis was greeted with derision by fellow scientists; Temin and Baltimore performed a simple experiment, rapidly reproduced, and convincing to all. Its result was a major paradigm shift-reversal of the central dogma of molecular biology. It immediately grabbed the attention of both the scientific and lay press. It also came at a key time for cancer research, at the start of the "War on Cancer." As a theoretical base and fundamental molecular tool, it enabled a decade of (largely fruitless) search for human oncogenic retroviruses but laid the foundation for the discovery of HIV 13 years later, leading to the development of effective therapy. I had the good fortune, as a student in Temin's lab, to witness these events. I am honored to be able to share my recollection on the occasion of their 50th anniversary.

Processing of the minor capsid protein of the cauliflower mosaic virus requires a cysteine proteinase

The major capsid protein of the cauliflower mosaic virus (CaMV) is processed in vivo. The viral aspartic proteinase that catalyses this maturation has been characterized previously and is coded by the CaMV gene V. This virus has a second capsid protein, a minor component, encoded by gene III. This protein, P3, is also processed at its C-terminus in vivo. To determine whether P3 is matured by the CaMV proteinase P5, we expressed, in Saccharomyces cerevisiae, P3, P5 and a fusion protein P7-P4, containing potential sites of cleavage. P5 was found to be involved in maturation of P7-P4 but did not cleave P3. The latter result was confirmed by experiments carried out with an in vitro translation system (the reticulocyte lysate) and with preparations of replication complexes purified from infected plants. Moreover, [N-(L-3-trans-carboxyoxiran-2-carbonyl)-L-leu cyl]-amido(4-guanido)butane, a specific inhibitor of cysteine proteinases, inhibited the maturation of P3, suggesting that the two CaMV capsid proteins are not processed by the same proteolytic event.

Cauliflower mosaic virus gene I product detected in a cell-wall-enriched fraction

Gene I product of cauliflower mosaic virus was immunodetected in a cell-wall-enriched fraction from infected turnip leaves in addition to its detection in viroplasms and replication complexes. The immunoreaction was carried out with an antiserum raised against a 15 amino acid long synthetic peptide corresponding to the carboxy-terminus of potential gene I protein (P1). The presence of P1 in different subcellular fractions was investigated as a function of time during viral multiplication. At late infection times, P1 was found only in the cell-wall-enriched fraction.

The duck hepatitis B virus DNA polymerase is tightly associated with the viral core structure and unable to switch to an exogenous template

The duck hepatitis B virus (DHBV) has a DNA polymerase associated with it which uses the incomplete viral genome as endogenous template. A prerequisite for studying this polymerase is the availability of conditions to open viral cores without destroying their enzymatic activity. In this study, this was achieved by a brief treatment with low pH. DHBV DNA in low-pH-treated cores was susceptible to digestion with deoxyribonuclease I and restriction enzymes, and large restriction fragments diffused out of the viral cores. However, the DHBV polymerase remained tightly associated with its DNA template in the viral core structure and could still incorporate nucleotides into those DNA fragments which carried the DNA-bound protein and remained in the core. The DHBV polymerase could not switch to any of several exogenously supplied templates although these were most likely accessible to it. The manner in which this tight association of the DHBV polymerase with the core may occur, and the possible implications of this interaction during the DHBV replication cycle, is discussed.

Main properties of duck hepatitis B virus DNA polymerase: comparison with the human and woodchuck hepatitis B virus DNA polymerases

The main properties of the duck hepatitis B virus (DHBV) DNA polymerase have been studied and compared with those of the human hepatitis B virus (HBV) and of the woodchuck hepatitis virus (WHV) DNA polymerases. All 3 enzymes are active under high salt conditions in the presence of high magnesium concentration. DHBV DNA polymerase was found less sensitive to ethanol and to operate at higher optimal pH than the HBV and WHV DNA polymerases. Like the other two viral endogenous DNA polymerases, the DHBV enzyme was strongly inhibited by phosphonoformic acid but not by aphidicolin, sulfhydryl group blockers or phosphonoacetic acid. Inhibition of DHBV DNA polymerase by the triphosphate derivatives of several nucleoside analogs appeared similar to that reported for HBV or WHV endogenous polymerase. FIACTP was the most, and ACVTP the least effective inhibitor; BVdUTP was of intermediary potency; araCTP and araTTP had a greater inhibitory effect on DHBV DNA polymerase than HBV or WHV DNA polymerase. The similarities in the properties of DHBV and HBV DNA polymerase justify the use of the duck hepatitis B polymerase model for screening and evaluation of potentially active drugs against HBV infection.

Detection of a potential transcription control sequence on the cauliflower mosaic virus genome by dinucleotide primed "in vitro" transcription

The three sites of selective dinucleotide-primed "in vitro" transcription initiation on a cloned cauliflower mosaic virus DNA fragment have been localised by S1 nuclease mapping. Two of these sites lie within a region which has been shown to be essential for transcription complex formation on the viral sequences, one corresponding to a nuclease S1 hypersensitive site and the other to an imperfect repeat 100bp downstream. These sequences show striking homology with known transcription control sequences. These observations and the effect of the sequences on "in vitro" transcription raise the possibility that they may be involved in control of transcription of the viral genome.

Selective dinucleotide-primed in vitro transcription of a cloned fragment of cauliflower mosaic virus DNA is dependent on a limited region of the viral genome

We have previously shown that plant RNA polymerase II preferentially forms ternary transcription complexes on a cloned fragment of the cauliflower mosaic virus genome in the presence of a particular dinucleotide/purine NTP combination (ApG + ATP). This preferential interaction is observed when the viral sequences are present on a discrete circular molecule. Deletion of a 205-bases-pair region abolishes this selectivity. The deleted region contains a considerable number of symmetrical or repeating elements. The use of nuclease S1 as a probe shows that this region contains a homopurine-homopyrimidine sequence which is extremely sensitive to this enzyme, indicating its capacity to adopt a non-B DNA conformation. A possible alternative structure of these sequences, which may explain the preferential interaction with the RNA polymerase, is presented.

Biochemical and genetic evidence for the hepatitis B virus replication strategy

Hepatitis B viruses synthesize their open circular DNA genomes by reverse transcription of an RNA intermediate. The details of this process have been examined with the use of mammalian hepatitis B viruses to map the sites for initiation and termination of DNA synthesis and to explore the consequences of mutations introduced at short, separated direct repeats (DR1 and DR2) implicated in the mechanisms of initiation. The first DNA strand to be synthesized is initiated within DR1, apparently by a protein primer, and the completed strand has a short terminal redundancy. In contrast, the second DNA strand begins with the sequence adjacent to DR2, but its 5' end is joined to an oligoribonucleotide that contains DR1; thus the putative RNA primer has been transposed to the position of DR2. It is now possible to propose a detailed strategy for reverse transcription by hepatitis B viruses that can be instructively compared with that used by retroviruses.

Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus

We have made a computer-assisted search for homology among polymerases or putative polymerases of various viruses and a transposable element, the Drosophila copia-like element 17.6. The search revealed that the putative polymerase (second open reading frame) of the copia-like element 17.6 bears close resemblance in overall structural organization to the pol gene product of Moloney murine leukaemia virus (M-MuLV): they show significant homology to each other at both the N- and C-terminal portions, suggesting that the 17.6 putative polymerase carries two enzymatic activities, related to reverse transcriptase and DNA endonuclease. The putative polymerase of cauliflower mosaic virus (CaMV) shows striking homology with the putative polymerase of 17.6 over almost its entire length, but it lacks the DNA endonuclease-related sequence. Furthermore, it was shown that the N-terminal ends of the M-MuLV pol product and the CaMV and 17.6 putative polymerases exhibit strong sequence homology with the gag-specific protease (p15) of Rous sarcoma virus (RSV) as well as the amino acid sequence predicted from the gag/pol spacer sequence of human adult T-cell leukaemia virus (HTLV). These p15-related sequences contain a highly conserved stretch of amino acids which show a close similarity with sequences around the active site amino acids Asp-Thr-Gly of the acid protease family, suggesting that they have an activity similar to acid protease. On the basis of the alignment of reverse transcriptase-related sequences, a dendrogram representing phylogenetic relationships among all the viruses compared together with 17.6 was constructed and its evolutionary implication is discussed.

Immunological detection of cauliflower mosaic virus gene V protein produced in engineered bacteria or infected plants

Antiserum was prepared against a synthetic peptide corresponding to the C-terminal 25 amino acids (aa) of the protein encoded by cauliflower mosaic virus (CaMV) gene V, which is thought to be a reverse transcriptase involved in viral DNA replication. This antiserum was used to detect the expression of CaMV gene V either in Escherichia coli JM103 transformed by an expression vector containing CaMV gene V or in CaMV-infected plants. In both cases, an 80-kDal protein has been detected.

Partial characterisation of different classes of viral DNA, and kinetics of DNA synthesis in turnip protoplasts infected with cauliflower mosaic virus

Turnip protoplasts infected with cauliflower mosaic virus (CaMV) have been used to examine the kinetics of CaMV DNA synthesis, and the different classes of CaMV DNA found in vivo partially characterised. Differential extraction techniques for DNA from infected protoplasts has identified several distinct classes of viral DNA. The same approach applied to virus preparations revealed that while the majority of virion DNA was stably encapsidated, some small DNAs and a heterogeneous population 3.8-ca. 5.0 Kb were not. The structural relationship of sa-DNA (3) with the particle is such that only its 5' RNA moeity is susceptible to nuclease attack. Two-dimensional gel electrophoresis of total CaMV DNA from infected protoplasts revealed all the DNA species found in virion DNA, those species representing the 'free' DNA class and a further class of molecules, rich in DNA of (-) polarity (24), to which the role of reverse transcription intermediates has been ascribed. 'Free' DNA contains 8 Kb supercoiled DNA (Form I DNA), an 8 Kb open circle (Form II), an 8 Kb linear (Form III) and a truncated molecule with an extension of the (-) strand previously observed from infected plants (10). Kinetic experiments show that the accumulation of total CaMV-DNA parallels the accumulation of progeny virions to reach a maximum around 72 h post-inoculation and that there is not a separation of CaMV-DNA synthesis into clearly defined early and late stages.

Cauliflower Mosaic Virus replication complexes: characterization of the associated enzymes and of the polarity of the DNA synthesized in vitro

The synthesis of both strands of CaMV-DNA has been studied in vitro using viral replication complexes obtained by hypotonic extraction of infected plant organelles. Hybridization of the DNA synthesized in vitro to single stranded CaMV DNA probes cloned in bacteriophage M 13 confirmed that the 35 S RNA served as a template for the synthesis of the (-) DNA strand. The response of CaMV DNA synthesis to various inhibitors suggests that a single enzyme directs both steps of the replication cycle. A comparative activity gel analysis of the DNA polymerases present in nuclear extracts from healthy and CaMV-infected turnips revealed an increase of a DNA polymerase species migrating in the 75 Kd range in infected tissue. When the enzyme activity associated with the isolated replicative complexes was similarly analyzed, the 75 Kd polymerase was markedly predominant, confirming that DNA polymerases of the α-type (MW in the 110 Kd range) are not involved in the aphidicolin-insensitive CaMV DNA replication. It seems therefore increasingly probable that CaMV codes for its own polymerase.