Using iodinated single-stranded M13 probes to facilitate rapid DNA sequence analysis--nucleotide sequence of a mouse lysine tRNA gene

Generation and characterization of a SIVmac239 clone corrected at four suboptimal nucleotides

BACKGROUND

SIVmac239 is a commonly used virus in non-human primate models of HIV transmission and pathogenesis. Previous studies identified four suboptimal nucleotides in the SIVmac239 genome, which putatively inhibit its replicative capacity. Since all four suboptimal changes revert to the optimal nucleotide consensus sequence during viral replication in vitro and in vivo, we sought to eliminate the variability of generating these mutations de novo and increase the overall consistency of viral replication by introducing the optimal nucleotides directly to the infectious molecular clone.

RESULTS

Using site directed mutagenesis of the full-length/nef-open SIVmac239 clone, we reverted all four nucleotides to the consensus/optimal base to generate SIVmac239Opt and subsequently tested its infectivity and replicative capacity in vitro and in vivo. In primary and cell line cultures, we observed that the optimized virus displayed consistent modest but not statistically significant increases in replicative kinetics compared to wild type. In vivo, SIVmac239Opt replicated to high peak titers with an average of 1.2 × 10(8) viral RNA copies/ml at day 12 following intrarectal challenge, reaching set-point viremia of 1.2 × 10(6) viral RNA copies/ml by day 28. Although the peak and set point viremia means were not statistically different from the original "wild type" SIVmac239, viral load variation at set point was greater for SIVmac239WT compared to SIVmac239Opt (p = 0.0015) demonstrating a greater consistency of the optimized virus. Synonymous mutations were added to the integrase gene of SIVmac239Opt to generate a molecular tag consisting of ten genetically distinguishable viral variants referred to as SIVmac239OptX (Del Prete et al., J Virol. doi: 10.1128/JVI.01026-14 , 2014). Replication dynamics in vitro of these optimized clones were not statistically different from the parental clones. Interestingly, the consistently observed rapid reversion of the primer binding site suboptimal nucleotide is not due to viral RT error but is changed post-integration of a mismatched base via host proofreading mechanisms.

CONCLUSIONS

Overall, our results demonstrate that SIVmac239Opt is a functional alternative to parental SIVmac239 with marginally faster replication dynamics and with increased replication uniformity providing a more consistent and reproducible infection model in nonhuman primates.

Reduced replication of human immunodeficiency virus type 1 mutants that use reverse transcription primers other than the natural tRNA(3Lys)

Replication of the human immunodeficiency virus type 1 (HIV-1) and other retroviruses involves reverse transcription of the viral RNA genome into a double-stranded DNA. This reaction is primed by the cellular tRNA(3Lys) molecule, which binds to a complementary sequence in the viral genome, referred to as the primer-binding site (PBS). In order to study the specificity of primer usage, we constructed a set of HIV-1 mutants with altered PBS sites corresponding to other tRNA species (tRNA(Ile), tRNA(1,2Lys), tRNA(Phe), tRNA(Pro), tRNA(Trp)). These mutant viruses were able to replicate, although with delayed replication kinetics compared with wild-type HIV-1. Identification of the tRNA species associated with the genomic RNA demonstrated binding of tRNAs complementary to the new PBS sites. However, the occupancy of the mutant PBS sites by these new primers was reduced and correlated well with the replication potential of the mutant viruses. These results suggest that the PBS sequence is not sufficient for annealing of the tRNA primer. Upon prolonged culturing, all mutants reverted to the wild-type PBS(3Lys) sequence. Minor sequence changes in the nucleotides flanking the PBS site indicate that these reversions resulted from annealing of the wild-type tRNA(3Lys) primer onto the mutant PBS sites, followed by copying of part of the tRNA(3Lys) sequence during reverse transcription. Furthermore, the reversion efficiency of the different PBS mutants was found to correlate with their tRNA(Lys)3 binding capacity. A remarkable reversion pathway was observed for the PBSPro variant (PBSPro-->PBSIle-->PBSwt). This pathway can be explained by efficient base pairing of tRNA(Ile) to PBSPro, followed by annealing of tRNA(3Lys) onto the PBSIle intermediate. These results demonstrate that HIV-1 is dedicated to the tRNA(3Lys) primer and that factors other than the PBS sequence determine the selective primer usage of this retrovirus.

APhaseolus vulgaris mitochondrial tRNA(Leu) is identical to its cytoplasmic counterpart: sequencing andin vivo transcription of the gene corresponding to the cytoplasmic tRNA(Leu.)

We report here that the sequence ofP. vulgaris mitochondrial and cytoplasmic tRNA(Leu) (NAA) are identical except for a post-transcriptional modification. There is an unidentified modification at the "wobble" position which, from the sequence of the nuclear tRNA(Leu) gene, we identify as a derivative of C. We also show that thisP. vulgaris nuclear gene is functional by demonstrating its transcription in anin vivo eukaryotic transcription system.

The sequences of two nuclear genes and a pseudogene for tRNA(Pro) from the higher plant Phaseolus vulgaris

A genomic bank of nuclear DNA (nDNA) from the higher plant Phaseolus vulgaris, constructed using the lambda EMBL-4 vector, has been screened for the presence of tRNA genes. One of the many positive recombinants was found to hybridise several times stronger than the other positives, and has been shown to contain several tRNA genes. We report the structure of two nuclear tRNA genes for tRNA(Pro), namely tRNA(Pro)(UGG) and tRNA(Pro)(AGG), and that of a 'pseudogene' for tRNA(Pro). This 'pseudogene', despite showing 95% homology with the other tRNA(Pro) species presented here, has several features which are likely to affect its transcription or its functioning as a tRNA.

Sandwich nucleic acid hybridization: a method with a universally usable labeled probe for various specific tests

Nucleic acid hybridization is widely used for scientific applications but essentially restricted to specialized laboratories. The use of recombinant m 13 phages as hybridization probes (Hu and Messing (1980) Gene 17, 271; Messing (1983) Methods Enzymol. 101, 20) offers a considerable advantage over the commonly used recombinant plasmids as the preparation of the DNA probe is very simple and it can easily be labeled directly, e.g. with isotopes with long half-life like 125I (Commerford (1971) Biochemistry 10, 11 (1983); Gu et al. (1983) Cancer (China) 2, 129; Han and Harding (1983) Nucleic Acids Res. 11, 14) and used for hybridization. However, as the application of nucleic acid hybridization for diagnostic and epidemiological purposes becomes almost unavoidable, the logistic problems of keeping numerous individually labeled hybridization probes increase considerably and may reach prohibitory levels in less well-equipped laboratories. In a new sandwich technique, the first step involves hybridization with an unlabeled recombinant m 13 DNA carrying an insert of the desired specificity. In a second step a universally usable labeled probe directed against the m 13 part of the recombinant phage DNA is applied. This reduces considerably the problems of preparing and keeping multiple labeled probes in stock.

Detection of pseudorabies virus DNA in the inner ear of intranasally infected BALB/c mice with nucleic acid hybridization in situ

Evidence for the pathogenicity of pseudorabies virus for the auditory and vestibular organs of experimentally infected mice is presented. We demonstrate viral genomes in cells of the peripheral sensory organs, the nerve structures, and the affected areas of the brain in single sections from an entire cranium of an adult mouse. The data were obtained by an in situ hybridization technique adapted for use with fixed, plastic-embedded materials. In contrast to conventional methods which use frozen sections, we were able to analyze cartilaginous and bony materials with high resolution.

Structure and evolution of mammalian tRNA genes: sequence of a mouse tRNAiMet gene, the 5'-flanking region of which is homologous to a human gene

From a recombinant lambda phage, we have determined a 317-bp sequence containing a mouse tRNAiMet gene. The coding region is precisely homologous to mammalian tRNAiMet if post-transcriptional modifications (including addition of the 3'-terminal CCA) are not considered. The gene does not contain introns and has a typical RNA polymerase III termination site in the 3'-flanking region. It is transcribed by RNA polymerase III in the HeLa cell S-100 system in vitro. Notably, the 5'-flanking region of the mouse tRNAiMet gene shares a "patchwork" pattern of homology with one of the human tRNAiMet genes of Santos and Zasloff [Cell 23 (1981) 699-710]. The 5'-flanking regions of the two genes contain strings of nucleotides, 6 to 32 bp in length, the homology of which is 76-100%. These are separated by short strings of unrelated nucleotides. This is one of the first examples of tRNA genes containing homologous 5'-flanking regions isolated from distantly related mammals. We also report a novel method for constructing deletion mutants of sequences cloned in M13 vectors.

Lysine tRNAs from rat liver: lysine tRNA sequences are highly conserved

The two major lysine tRNAs from rat liver, tRNA2Lys and tRNA5Lys, were sequenced by rapid gel or chromatogram readout methods. The major tRNA2Lys differs from a minor form only by a base pair in positions 29 and 41; both tRNAs have an unidentified nucleotide, U**, in the third position of the anticodon. Although highly related, the major tRNA2Lys and tRNA5Lys differ in four base pairs and four unpaired nucleotides, including the first position of the anticodons, but have the same base pair in positions 29 and 41. The three tRNAs maintain a m2G-U pair in the acceptor stem. Detection of this m2G is in contrast to other reports of lysine tRNAs. Sequences of lysine tRNAs are strongly conserved in higher eukaryotes.

Screening recombinant phage M13 plaques with RNA probes; a one-step procedure which identifies clones containing either of the complementary DNA strands

We describe a method for detecting specific DNA sequences cloned in M13 phage vectors, based on the procedure of Woo (in Wu, R., Methods in Enzymology, Vol. 68, Academic Press, New York, 1979, pp. 389-395). M13 plaques are adsorbed to a nitrocellulose filter that has been pre-saturated with bacteria. The filter is incubated on an agar plate to amplify the phage; the DNA is alkali-denatured and then hybridized with a radioactive RNA probe. Unlike standard procedures, this method detects and distinguishes M13 plaques containing phage particles which harbor either the coding or non-coding (RNA-like) DNA strand, when single-stranded RNA is used as probe. We have optimized this procedure with M13 clones containing mouse histidine tRNA gene sequences and have used it to determine the sequence of both strands of a mouse glycine tRNA gene.

Molecular cloning, sequence analysis and in vitro expression of a rat tRNA gene cluster

A rat genomic DNA fragment containing a tRNA gene cluster was isolated from a lambda phage library. Hybridization and nucleotide sequence analysis revealed the presence of a 83 bp tRNALeuCUG gene and a 72 bp tRNAAspGUG gene. Both genes possessed intact coding regions and putative transcription termination signals at their respective 3' ends. In vitro transcription analysis of the two subcloned genes in a HeLa cell S-100 system demonstrated the specific synthesis of a number of RNAs by RNA polymerase III. Studies carried out in the presence of alpha-amanitin showed that the larger RNAs are precursors for the final processed transcripts of the tRNALeu and tRNAAsp genes, respectively. Further nucleotide sequence analysis of the cluster revealed the presence of tRNAGly and a tRNAGlu pseudogenes with missing areas within their coding regions which are essential for transcription by RNA polymerase III. Within the region of DNA between the tRNALeu and tRNAAsp genes is a sequence which is 65% homologous to a region of the rat B1 element. The significance of this latter structure within the gene cluster is unknown.

Structure and evolution of a mouse tRNA gene cluster encoding tRNAAsp, tRNAGly and tRNAGlu and an unlinked, solitary gene encoding tRNAAsp

We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al., 1981, Nucleic Acids Res. 9, 2239-2250). The mouse and rat tRNAAsp and tRNAGly coding regions are identical. The tRNAGlu coding regions differ at two positions. The flanking sequences contain 3 non-homologous areas: a c. 100 bp insertion in the first mouse spacer, short tandemly repeated sequences in the second spacers and unrelated sequences at the 3' ends of the clusters. In contrast, most of the flanking regions are homologous, consisting of strings of consecutive, identical residues (5-17 bp) separated by single base differences and short insertions/deletions. The latter are often associated with short repeats. The homology of the flanking regions is c. 75%, similar to other murine genes. The second lambda clone contains a solitary mouse tRNAAsp gene. The coding region is identical to that of the clustered tRNAAsp gene. The 5' flanking regions of the two genes contain homologous areas (10-25 bp) separated by unrelated sequences. Overall, the flanking regions of the two mouse tRNAAsp genes are less homologous than those of the mouse and rat clusters.