Reverse transcriptase rides again

Mutations in the primer grip region of HIV reverse transcriptase can increase replication fidelity

Mutations in the primer grip region of human immunodeficiency virus reverse transcriptase (HIV-RT) affect its replication fidelity. The primer grip region (residues 227-235) correctly positions the 3'-ends of primers. Point mutations were created by alanine substitution at positions 224-235. Error frequencies were measured by extension of a dG:dA primer-template mismatch. Mutants E224A, P225A, P226A, L228A, and E233A were approximately equal to the wild type in their ability to extend the mismatch. Mutants F227A, W229A, M230A, G231A, and Y232A extended 40, 66, 54, 72, and 76% less efficiently past a dG:dA mismatch compared with the wild type. We also examined the misinsertion rates of dG, dC, or dA across from a DNA template dA using RT mutants F227A and W229A. Mutant W229A exhibited high fidelity and did not produce a dG:dA or dC:dA mismatch. Interestingly, mutant F227A displayed high fidelity for dG:dA and dC:dA mismatches but low fidelity for dA:dA misinsertions. This indicates that F227A discriminates against particular base substitutions. However, a primer extension assay with three dNTPs showed that F227A generally displays higher fidelity than the wild type RT. Clearly, primer grip mutations can improve or worsen either the overall or base-specific fidelity of HIV-RT. We hypothesize that wild type RT has evolved to a fidelity that allows genetic variation without compromising yield of viable viruses.

Presence of a retroviral encapsidation sequence in nonretroviral RNA increases the efficiency of formation of cDNA genes

We showed previously that retrovirus vector particles can encapsidate RNAs without retroviral cis-acting sequences, that such RNAs are reverse transcribed in infected target cells, and that the cDNA copies are inserted into the host genome resulting in cDNA genes (R. Dornburg and H. M. Temin, Mol. Cell. Biol. 8:2328-2334, 1988). To provide further evidence that this retrovirus-mediated gene transfer occurred through an RNA intermediate, we constructed retroviral vectors containing an intron from a cellular gene. This intron was lost in a cDNA gene formed after infection with retroviral particles, establishing that an RNA intermediate had existed. Retroviral vectors with additional encapsidation sequences were constructed. The presence of a murine leukemia virus encapsidation sequence in an mRNA transcribed from the hygromycin B phosphotransferase gene increased the efficiency of encapsidation into spleen necrosis virus vector particles and the formation of cDNA genes by approximately 2 orders of magnitude.

cDNA genes formed after infection with retroviral vector particles lack the hallmarks of natural processed pseudogenes

Retroviral proteins can encapsidate RNAs without retroviral cis-acting sequences. Such RNAs are reverse transcribed and inserted into the genomes of infected target cells to form cDNA genes. Previous investigations by Southern blot analysis of such cDNA genes suggested that they were truncated at the 3' and the 5' ends (R. Dornburg and H. M. Temin, Mol. Cell. Biol. 8:2328-2334, 1988). To analyze such cDNA genes further, we cloned three cDNA genes (derived from a hygromycin B phosphotransferase gene) in lambda vectors and analyzed them by DNA sequencing. We found that they did not correspond to the full-length mRNA: they were truncated at both the 3' and the 5' ends, did not contain a poly(A) tract, and were not flanked by direct repeats. The 3'-end junctions to chromosomal DNA of five more cDNA genes were amplified by polymerase chain reaction, cloned in pUC vectors, and sequenced. All of these cDNA genes had 3'-end truncations, and no poly(A) tracts were found. Further polymerase chain reaction experiments were performed to detect hygromycin B phosphotransferase cDNA genes with a poly(A) tract in DNA extracted from a pool of about 500 colonies of cells containing cDNA genes. No hygromycin B phosphotransferase cDNA gene with a poly(A) tract was found. Investigation of two preintegration sites by Southern analysis revealed that deletions were present in chromosomal DNA at the site of the integration of the cDNA genes. Naturally occurring processed pseudogenes correspond to the full-length mRNA, contain a poly(A) sequence, and are flanked by direct repeats. Our data indicate that cDNA genes formed by infection with retrovirus particles lack the hallmarks or natural processed pseudogenes. Thus, it appears that natural processed pseudogenes were not generated by retrovirus proteins.

cDNA genes formed after infection with retroviral vector particles lack the hallmarks of natural processed pseudogenes

Retroviral proteins can encapsidate RNAs without retroviral cis-acting sequences. Such RNAs are reverse transcribed and inserted into the genomes of infected target cells to form cDNA genes. Previous investigations by Southern blot analysis of such cDNA genes suggested that they were truncated at the 3' and the 5' ends (R. Dornburg and H. M. Temin, Mol. Cell. Biol. 8:2328-2334, 1988). To analyze such cDNA genes further, we cloned three cDNA genes (derived from a hygromycin B phosphotransferase gene) in lambda vectors and analyzed them by DNA sequencing. We found that they did not correspond to the full-length mRNA: they were truncated at both the 3' and the 5' ends, did not contain a poly(A) tract, and were not flanked by direct repeats. The 3'-end junctions to chromosomal DNA of five more cDNA genes were amplified by polymerase chain reaction, cloned in pUC vectors, and sequenced. All of these cDNA genes had 3'-end truncations, and no poly(A) tracts were found. Further polymerase chain reaction experiments were performed to detect hygromycin B phosphotransferase cDNA genes with a poly(A) tract in DNA extracted from a pool of about 500 colonies of cells containing cDNA genes. No hygromycin B phosphotransferase cDNA gene with a poly(A) tract was found. Investigation of two preintegration sites by Southern analysis revealed that deletions were present in chromosomal DNA at the site of the integration of the cDNA genes. Naturally occurring processed pseudogenes correspond to the full-length mRNA, contain a poly(A) sequence, and are flanked by direct repeats. Our data indicate that cDNA genes formed by infection with retrovirus particles lack the hallmarks or natural processed pseudogenes. Thus, it appears that natural processed pseudogenes were not generated by retrovirus proteins.

Reverse transcriptase in a clinical strain of Escherichia coli: production of branched RNA-linked msDNA

Branched RNA-linked multicopy single-stranded DNA (msDNA) originally detected in myxobacteria has now been found in a clinical isolate of Escherichia coli. Although lacking homology in the primary structure, the E. coli msDNA is similar in secondary structure to the myxobacterial msDNA's, including the 2',5'-phosphodiester linkage between RNA and DNA. A chromosomal DNA fragment responsible for the production of msDNA was cloned in an E. coli K12 strain; its DNA sequence revealed an open reading frame (ORF) of 586 amino acid residues. The ORF shows sequence similarity with retroviral reverse transcriptases and ribonuclease H. Disruption of the ORF blocked msDNA production, indicating that this gene is essential for msDNA synthesis.

Reverse transcriptase associated with the biosynthesis of the branched RNA-linked msDNA in Myxococcus xanthus

Myxobacteria have been shown to produce a peculiar RNA-DNA complex called msDNA, in which a single-stranded DNA is branched out from a RNA molecule (msdRNA) by a 2',5' phosphodiester linkage. It has been predicted that reverse transcriptase is required for msDNA biosynthesis. We identified a gene for reverse transcriptase in M. xanthus in the region that has been demonstrated to code for a cis- or transacting element for msDNA synthesis. This gene is located immediately downstream of the msdRNA coding region, and codes for a polypeptide of 485 amino acid residues. The polypeptide shows sequence similarity with retroviral reverse transcriptases. This fact, together with the mode of msDNA synthesis, suggests a possible relationship between retroviruses and the msDNA system. The analysis of the gene and the distribution of the msDNA system in independent isolates of M. xanthus indicate that the element is as old as other essential genes in M. xanthus and that it was not recently acquired into the genome.

Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics

Transposable elements can be identified by their ability to induce mutant alleles at new loci. The retrotransposon family is thought to transpose through an RNA intermediate and has many similarities to vertebrate proretroviruses. In plants, retrotransposons have been described in maize, Arabidopsis and wheat, and non-viral retroposons in maize. Most of these elements, however, have been found as non-mobile integrated units. Here, we report the isolation of the first tobacco (Nicotiana tabacum) transposable element, Tnt1, which seems to be the most complete mobile retrotransposon characterized in higher plants. Tnt1 has been isolated after its transposition into the nitrate reductase (NR) structural gene of tobacco, and transposition events have been detected through in vitro selection of spontaneous NR-deficient (NR-) mutant lines in cell cultures derived from tobacco mesophyll protoplasts. Tnt1 is 5,334 nucleotides long, contains two 610-base-pair-long terminal repeats and a single open reading frame of 3,984 nucleotides. Comparison of the Tnt1 open reading frame coding potential with those of the Drosophila melanogaster copia retrotransposon, yeast Ty retrotransposon, and vertebrate proretroviruses revealed that Tnt1 is closely related to copia and carries all the functions known to be required for autonomous transposition by reverse transcription.

Biosynthesis of the reverse transcriptase of hepatitis B viruses involves de novo translational initiation not ribosomal frameshifting

Retroviruses and many other types of genetic elements replicate by reverse transcription of RNA. Although structurally and biologically very diverse, such elements carry conserved polymerase genes (pol) that encode proteins required for reverse transcription. In most cases, the pol gene is preceded by an overlapping gene encoding one or more nucleocapsid proteins, in a different reading frame. Because both coding regions are represented in a single mRNA, the question arises of how the reverse transcriptase in the alternative reading frame is expressed. In retroviruses and retrotransposons it is expressed as a nucleocapsid-polymerase fusion protein by ribosomal frameshifting during translation of the overlapping region. We have examined the mechanism of polymerase biosynthesis in another family of animal viruses that use reverse transcription, the hepatitis B viruses. Genetic and biochemical studies reveal that these viruses do not use ribosomal frameshifting to generate this enzyme, but instead direct translation initiation at an internal initiation (AUG) codon in the polymerase gene.

Analysis of the primary structure of the long terminal repeat and the gag and pol genes of the human spumaretrovirus

The nucleotide sequence of the human spumaretrovirus (HSRV) genome was determined. The 5' long terminal repeat region was analyzed by strong stop cDNA synthesis and S1 nuclease mapping. The length of the RU5 region was determined and found to be 346 nucleotides long. The 5' long terminal repeat is 1,123 base pairs long and is bound by an 18-base-pair primer-binding site complementary to the 3' end of mammalian lysine-1,2-specific tRNA. Open reading frames for gag and pol genes were identified. Surprisingly, the HSRV gag protein does not contain the cysteine motif of the nucleic acid-binding proteins found in and typical of all other retroviral gag proteins; instead the HSRV gag gene encodes a strongly basic protein reminiscent of those of hepatitis B virus and retrotransposons. The carboxy-terminal part of the HSRV gag gene products encodes a protease domain. The pol gene overlaps the gag gene and is postulated to be synthesized as a gag/pol precursor via translational frameshifting analogous to that of Rous sarcoma virus, with 7 nucleotides immediately upstream of the termination codons of gag conserved between the two viral genomes. The HSRV pol gene is 2,730 nucleotides long, and its deduced protein sequence is readily subdivided into three well-conserved domains, the reverse transcriptase, the RNase H, and the integrase. Although the degree of homology of the HSRV reverse transcriptase domain is highest to that of murine leukemia virus, the HSRV genomic organization is more similar to that of human and simian immunodeficiency viruses. The data justify classifying the spumaretroviruses as a third subfamily of Retroviridae.

Translation products of cauliflower mosaic virus ORF V, the coding region corresponding to the retrovirus pol gene

Open reading frame (ORF) V of cauliflower mosaic virus (CaMV), the candidate for the reverse transcriptase gene, has been expressed in E. coli under control of the PR promoter of bacteriophage lambda either as an N-terminal polypeptide fused to beta-galactosidase or as the total ORF V without fusion. Antibodies against these proteins were used to analyze extracts from CaMV-infected plants by immunoblotting. ORF V-specific polypeptides of 80, 62, 58, 22, and 18 kD apparent molecular weights were detected, with the largest species corresponding to the full length translation product. The 62 and 22 kD species could be assigned to the N-terminus and the remaining two species to the C-terminus of the ORF.

Nucleotide sequence analysis of a cloned DNA fragment from human cells reveals homology to retrotransposons

During molecular cloning of proviral DNA of human spumaretrovirus, various recombinant clones were established and analyzed. Blot hybridization revealed that one of the recombinant plasmids had the characteristic features of a member of the long interspersed repetitive sequences family. The DNA element was analyzed by restriction mapping and nucleotide sequencing. It showed a high degree of amino acid sequence homology of 54.3% when compared with the 5'-terminal part of the pol gene product of the murine retrotransposon LIMd. The 3' region of the cloned DNA element encodes proteins with an even higher degree of homology of 67.4% in comparison to the corresponding parts of a member of the primate KpnI sequence family.

RNA-dependent DNA polymerase activity in Paramecium tetraurelia: what for?

Protein extracts from the protozoan ciliate Paramecium tetraurelia revealed high levels of RNA-dependent DNA polymerase activity (reverse transcriptase). Stable and constant during the somatic phase of the cell cycle, the reverse transcriptase activity quickly diminished following the completion of the sexual phases of the cell cycle: conjugation and autogamy. The Paramecium reverse transcriptase presented a number of common features with retroviral polymerases: ability to copy synthetic templates such as poly(rCm).oligo(dG) as well as mRNA; sensitivity to various reverse transcriptase inhibitors such as HPA 23, suramin, phosphonoformate and ethidium bromide; insensitivity to the action of other DNA and RNA polymerase inhibitors and, finally, the requirement for divalent cations before the enzyme can function: either magnesium or manganese. Although the reverse transcriptase activity was not proven to be independent from one of the DNA polymerases in paramecia, its high activity predicts a role in the paramecia cell cycle. From what we are able to conceive today two possible roles could be envisaged. Participation in the anlage macronucleus formation: micronuclear sequences are first transcripted and, after rearrangements of the RNA molecules, these are retrotranscribed into the macronuclear DNA molecules or association with retrotransposons that participate in the movement of certain macronuclear sequences into the germ-line micronucleus.

Nucleotide sequence analysis of a cloned DNA fragment from human cells reveals homology to retrotransposons

During molecular cloning of proviral DNA of human spumaretrovirus, various recombinant clones were established and analyzed. Blot hybridization revealed that one of the recombinant plasmids had the characteristic features of a member of the long interspersed repetitive sequences family. The DNA element was analyzed by restriction mapping and nucleotide sequencing. It showed a high degree of amino acid sequence homology of 54.3% when compared with the 5'-terminal part of the pol gene product of the murine retrotransposon LIMd. The 3' region of the cloned DNA element encodes proteins with an even higher degree of homology of 67.4% in comparison to the corresponding parts of a member of the primate KpnI sequence family.

Hepadnaviruses and retroviruses share genome homology and features of replication

The hepadnavirus family includes hepatitis B virus (HBV), woodchuck hepatitis virus (WHV), ground squirrel hepatitis virus (GSHV) and duck hepatitis B virus (DHBV). These viruses share unique ultrastructural, molecular and biological features. HBV has great medical importance in many parts of the world. More important numerically than acute hepatitis B in high prevalence geographic regions is the liver disease associated with chronic infection. There appear to be more than 200 million chronically infected humans in the world, and these HBV infections appear to be the single most common cause of chronic liver disease and liver cancer in man. All hepadnaviruses share the propensity for silent infection in early life leading to persistence of the virus, and hepatocellular carcinoma (HCC) is clearly associated with long-standing persistent infection in man, woodchucks and ground squirrels. Although the viral DNA has been found to be integrated in cellular DNA of many HCC in man, woodchucks and ground squirrels, the precise role of the virus in tumor formation has not been defined. Hepadna viruses have an interesting molecular structure and mechanisms of replication, and they appear to share certain important features with retroviruses as reviewed here. It is of interest to define similarities and differences between hepadnaviruses and retroviruses in order to understand their evolutionary relationship and to determine whether they share a common oncogenic mechanism, since infection with members of both virus families is associated with neoplastic disease.

Tx1: a transposable element from Xenopus laevis with some unusual properties

A family of transposable genetic elements in the genome of the frog, Xenopus laevis, is described. They are designated Tx1. Transposability of the elements was deduced by characterization of a chromosomal locus which is polymorphic for the presence or absence of a Tx1 element. Nucleotide sequence analysis suggested that Tx1 elements show target site specificity, as they are inserted at the pentanucleotide TTTAA in all four cases that were examined. The elements appear to have 19-base-pair (bp) inverted terminal repeats, and they are flanked by 4-bp target duplications (TTAA), although the possibility that they do not create target site duplications is discussed. Tx1 elements have several unusual characteristics: the central portion of each element is comprised of a variable number of two types of 393-bp repeating units; the rightmost 1,000 bp of the element contains separate regions potentially capable of forming bends, left-handed Z-form DNA, and alternative stem-loop structures. Comparisons among single frogs suggest that germ line transposition is relatively infrequent and that variations in numbers of internal repeats accumulate quite slowly at any locus.

Mitochondrial plasmids of Neurospora: integration into mitochondrial DNA and evidence for reverse transcription in mitochondria

The Mauriceville (3.6 kb) and Varkud (3.8 kb) mitochondrial plasmids of Neurospora are closely related, closed circular DNAs whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retrotransposons. Here we isolated mutants whose growth is impaired as a result of malevolent behavior of these plasmids. All 12 mutants contain variant plasmids that are suppressive relative to mtDNA, and ten also contain defective mtDNAs. All the suppressive plasmids contain small insertions, generally including a mitochondrial tRNA sequence, at or near the major 5' RNA start site. The structure of the suppressive plasmids suggests that they were generated via an RNA intermediate and a reverse transcription step. At least three of the mutants contain defective mtDNAs into which mitochondrial plasmid sequences have integrated. Sequences at the plasmid-mtDNA junctions are also consistent with integration via an RNA intermediate.

Complete nucleotide sequence of the fast skeletal troponin T gene. Alternatively spliced exons exhibit unusual interspecies divergence

The continuous nucleotide sequence of the rat fast skeletal muscle troponin T gene is reported, complementing the previous determinations of its structural organization and its capacity to encode multiple isoforms via alternative RNA splicing. Canonical promoter elements, as well as consensus sequences that may be involved in the 3' processing of the primary transcript, are present. All exons are flanked by conventional donor and acceptor splice sites, which can hybridize to U1 RNA. Extensive computer-assisted analyses of the genomic sequence do not reveal cis elements that unambiguously distinguish alternative from constitutive exons. Local RNA secondary structures can be predicted, however, that sequester exons or their splice sites in stem-and-loop formations, and which may also pair with small nuclear RNAs. These interactions might, in theory, contribute to differential exon usage. The structural features of exon organization that characterize this rat skeletal gene are closely conserved in the chicken cardiac troponin T gene, but the former exhibits a more diversified capacity for differential splicing. Implications for the mechanisms of alternative RNA splicing are considered. Comparisons of troponin T amino acid sequences among several species reveal striking dissimilarities, in contrast to the otherwise highly conserved contractile proteins. These divergences involve entire peptide subsegments and are concentrated in the same domains as are encoded by alternatively spliced exons, suggesting that exon shuffling may have contributed to the evolution of troponin T.

Tx1: a transposable element from Xenopus laevis with some unusual properties

A family of transposable genetic elements in the genome of the frog, Xenopus laevis, is described. They are designated Tx1. Transposability of the elements was deduced by characterization of a chromosomal locus which is polymorphic for the presence or absence of a Tx1 element. Nucleotide sequence analysis suggested that Tx1 elements show target site specificity, as they are inserted at the pentanucleotide TTTAA in all four cases that were examined. The elements appear to have 19-base-pair (bp) inverted terminal repeats, and they are flanked by 4-bp target duplications (TTAA), although the possibility that they do not create target site duplications is discussed. Tx1 elements have several unusual characteristics: the central portion of each element is comprised of a variable number of two types of 393-bp repeating units; the rightmost 1,000 bp of the element contains separate regions potentially capable of forming bends, left-handed Z-form DNA, and alternative stem-loop structures. Comparisons among single frogs suggest that germ line transposition is relatively infrequent and that variations in numbers of internal repeats accumulate quite slowly at any locus.

Putative reverse transcriptase intermediates of human hepatitis B virus in primary liver carcinomas

Nucleocapsid-pol fusion proteins have been detected by serological screening hepatocellular carcinoma tissues that contain hepatitis B virus (HBV) DNA. The existence of these fusion proteins suggests that HBV may synthesize its reverse transcriptase in a fashion analogous to the way that retroviruses synthesize and process a precursor. The accumulation of HBV reverse transcriptase intermediates in tumorous tissues and not in other tissues may be related to the absence of viral core particles and possibly contributes to tumor development.

Murine mammary tumor virus pol-related sequences in human DNA: characterization and sequence comparison with the complete murine mammary tumor virus pol gene

Sequences in the human genome with homology to the murine mammary tumor virus (MMTV) pol gene were isolated from a human phage library. Ten clones with extensive pol homology were shown to define five separate loci. These loci share common sequences immediately adjacent to the pol-like segments and, in addition, contain a related repeat element which bounds this region. This organization is suggestive of a proviral structure. We estimate that the human genome contains 30 to 40 copies of these pol-related sequences. The pol region of one of the cloned segments (HM16) and the complete MMTV pol gene were sequenced and compared. The nucleotide homology between these pol sequences is 52% and is concentrated in the terminal regions. The MMTV pol gene contains a single long open reading frame encoding 899 amino acids and is demarcated from the partially overlapping putative gag gene by termination codons and a shift in translational reading frame. The pol sequence of HM16 is multiply terminated but does contain open reading frames which encode 370, 105, and 112 amino acid residues in separate reading frames. We deduced a composite pol protein sequence for HM16 by aligning it to the MMTV pol gene and then compared these sequences with other retroviral pol protein sequences. Conserved sequences occur in both the amino and carboxyl regions which lie within the polymerase and endonuclease domains of pol, respectively.

Amino acid sequence homology in gag region of reverse transcribing elements and the coat protein gene of cauliflower mosaic virus

A nucleic acid binding protein (NBP) derived from the gag gene of retroviruses that is thought to interact with genomic RNA in virion cores, contains a highly conserved arrangement of cysteine residues. A search of available nucleic acid and protein sequences has revealed that the motif CysX2CysX4HisX4Cys (NBPcys) is invarient in all replication competent retroviruses, a Syrian hamster intracisternal A-particle gene, the Drosophila retrotransposon copia and in cauliflower mosaic virus (CaMV). In each case, NBPcys is located in that part of the 'gag-pol' region just preceding a conserved protease amino acid sequence. This is of special significance for CaMV as NBPcys is in the coat protein gene (ORF IV) upstream of the putative reverse transcriptase gene (ORF V) and demonstrates that the gag-pol arrangement of reverse transcribing elements is preserved in CaMV. Moreover, CaMV differs from all other known NBPcys-containing elements in that it packages a DNA genome in virions.

Retroviral gag and DNA endonuclease coding sequences in IgE-binding factor gene

Immunoglobulin-binding factors are known to regulate the synthesis of B-cell-derived immunoglobulin heavy-chain isotypes. Cloning and nucleotide sequence determination of complementary DNA encoding rodent IgE-binding factors (IgE-BF) revealed that messenger RNA encodes a glycoprotein of 557 amino acids which is expressed as a precursor of relative molecular mass (Mr) 60,000 (60K) in COS7 monkey cells. We report here that the 3' two-thirds of the IgE-BF coding sequence shows a surprising homology (72%) at the DNA level with coding sequences of the gag and pol (DNA endonuclease) genes of the Syrian hamster intracisternal A particle (IAP H18), an endogenous retrovirus. This marked homology demonstrates that the rodent gene encoding IgE-BF is a hybrid gene which evolved very recently by integrating genes of viral origin, and that the encoded polypeptide comprises three separate domains: an IgE-BF domain and retrovirus-derived gag and DNA endonuclease-like domains. This may represent the first report of a cellular gene containing a virus-derived coding sequence.