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R A Katz

Publications and source records attributed to R A Katz.

At least 37 records · Page 2Linked to original sources

The retroviral enzymes.

We have reviewed the current state of knowledge concerning the three enzymes common to all retroviruses. It is informative to consider them together, since their activities are interrelated. The enzymatic activities of RT and IN depend on processing of polyprotein precursors by PR. Furthermore, RT produces the viral DNA substrate to be acted upon by IN. All three of these retroviral enzymes function as multimers, and it is conceivable that specific polyprotein precursor interactions facilitate the multimerization of all of them. The multimeric structures of the enzymes are, however, quite different. PR is a symmetric homodimer whose subunits contribute to formation of a single active site. RT (of HIV, at least) is an asymmetric heterodimer in which one subunit appears to contribute all of the catalytic activity and the second is catalytically inactive, but structurally important. IN also functions minimally as a dimer for processing and joining. The retroviral enzymes represent important targets for antiviral therapy. Considerable effort continues to be focused on developing PR and RT inhibitors. As more is learned about IN, such efforts can be extended. Since these enzymes are critical at different stages in the retroviral life cycle, one optimistic hope is that a combination of drugs that target all of them may be maximally effective as therapy for AIDS.

DNA Nucleotidyltransferases↗

Requirement for a conserved serine in both processing and joining activities of retroviral integrase.

Retroviruses encode a protein, the integrase (IN), that is required for insertion of the viral DNA into the host cell chromosome. IN alone can carry out the integration reaction in vitro. The reaction involves endonucleolytic cleavage near the 3' ends of both viral DNA strands (the processing step), followed by joining of these new viral DNA ends to host DNA (the joining step). Based on their evolutionary conservation, we have previously identified at least 11 amino acid residues of IN that may be essential for the reaction. Here we report that even conservative replacements of one of these residues, an invariant serine, produce severe reductions in both the processing and joining activities of Rous sarcoma virus IN in vitro. Replacement of the analogous serine of the type 1 human immunodeficiency virus IN had similar effects on processing activity. These results suggest that this single conserved serine is a component of the active site and that one active site is used for both processing and joining. Replacement of this serine with certain amino acids resulted in a loss or reduction in DNA binding activities, while other replacements at this position appeared to affect later steps in catalysis. All of the defective Rous sarcoma virus INs were able to compete with the wild-type protein, which supports a model in which IN functions in a multimeric complex.

Avian Sarcoma Viruses↗

Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases.

Our comparison of deduced amino acid sequences for retroviral/retrotransposon integrase (IN) proteins of several organisms, including Drosophila melanogaster and Schizosaccharomyces pombe, reveals strong conservation of a constellation of amino acids characterized by two invariant aspartate (D) residues and a glutamate (E) residue, which we refer to as the D,D(35)E region. The same constellation is found in the transposases of a number of bacterial insertion sequences. The conservation of this region suggests that the component residues are involved in DNA recognition, cutting, and joining, since these properties are shared among these proteins of divergent origin. We introduced amino acid substitutions in invariant residues and selected conserved and nonconserved residues throughout the D,D(35)E region of Rous sarcoma virus IN and in human immunodeficiency virus IN and assessed their effect upon the activities of the purified, mutant proteins in vitro. Changes of the invariant and conserved residues typically produce similar impairment of both viral long terminal repeat (LTR) oligonucleotide cleavage referred to as the processing reaction and the subsequent joining of the processed LTR-based oligonucleotides to DNA targets. The severity of the defects depended upon the site and the nature of the amino acid substitution(s). All substitutions of the invariant acidic D and E residues in both Rous sarcoma virus and human immunodeficiency virus IN dramatically reduced LTR oligonucleotide processing and joining to a few percent or less of wild type, suggesting that they are essential components of the active site for both reactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Retroviral integrase domains: DNA binding and the recognition of LTR sequences.

Integration of retroviral DNA into the host chromosome requires a virus-encoded integrase (IN). IN recognizes, cuts and then joins specific viral DNA sequences (LTR ends) to essentially random sites in host DNA. We have used computer-assisted protein alignments and mutagenesis in an attempt to localize these functions within the avian retroviral IN protein. A comparison of the deduced amino acid sequences for 80 retroviral/retrotransposon IN proteins reveals strong conservation of an HHCC N-terminal 'Zn finger'-like domain, and a central D(35)E region which exhibits striking similarities with sequences deduced for bacterial IS elements. We demonstrate that the HHCC region is not required for DNA binding, but contributes to specific recognition of viral LTRs in the cutting and joining reactions. Deletions which extend into the D(35)E region destroy the ability of IN to bind DNA. Thus, we propose that the D(35)E region may specify a DNA-binding/cutting domain that is conserved throughout evolution in enzymes with similar functions.

Amino Acid Sequence↗

The role of branchpoint and 3'-exon sequences in the control of balanced splicing of avian retrovirus RNA.

We previously described an avian sarcoma-leukosis virus (ASLV) insertion mutation that causes a decrease in the ratio of unspliced to spliced RNA in vivo, resulting in a replication defect. Pseudorevertant viruses containing cis-acting suppressor mutations that restored the normal ratio were isolated. One class of the suppressor mutations consists of single-base changes or small deletions near the 3' splice site, while another consists of deletions in the 3' exon. In this paper we report results from an in vitro analysis of wild-type, mutant, and pseudorevertant pre-mRNA splicing. We find that wild-type RNA is spliced inefficiently in vitro, and that the insertion mutation and suppressors act directly at the level of splicing. Characterization of splicing intermediates reveals that the insertion mutation and suppressor mutations located within the intron alter the pattern of lariat formation. In contrast, suppressor mutations consisting of 3' exon deletions act at an earlier step in the splicing pathway. Thus, the efficiency of splicing at the env 3' splice site can be affected at the level of spliceosome assembly, lariat formation, or cleavage at the 3' splice site and exon ligation.

Avian Sarcoma Viruses↗

The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro.

The integration of viral DNA into the host cell chromosome is an essential feature of the retroviral life cycle. The integration reaction requires cis-acting sequences at the ends of linear viral DNA and a trans-acting product of the pol gene, the integration protein (IN). Previously, we demonstrated that avian sarcoma-leukosis virus (ASLV) IN is able to carry out the first step in the integration process in vitro: nicking of the ends of linear viral DNA. In this paper, using two independent assays, we demonstrate that IN, alone, is sufficient to carry out the second step: cleavage and joining to the target DNA. These results demonstrate that the retroviral IN protein is an integrase.

Alpharetrovirus↗

EEG suppression and increased blood-brain barrier permeability following intracarotid injection of iothalamate meglumine (Conray) in dogs.

Over a 2-year period we observed three cases of unilateral suppression of the electroencephalogram (EEG) lasting from 45 s to 4 min following intracarotid injection of 60% iothalamate meglumine (Conray) for intraoperative carotid angiography postendarterectomy. As a result of these cases we undertook studies in 11 dogs anesthetized with isoflurane to examine causes of EEG suppression following intracarotid contrast medium injection. In group 1 (n = 6) cerebral blood flow (CBF), the cerebral metabolic rate for oxygen (CMRO2), EEG activity, and permeability of the blood-brain barrier (BBB) were determined. In group 2 (n = 5) cerebrospinal fluid (CSF) pressure, EEG activity, and BBB permeability were determined. Intracarotid injection of 5 ml of 60% Conray was associated with unilateral EEG suppression and increased BBB permeability in 1 of 11 dogs. Injection of contrast material caused no change in CBF or CMRO2 and caused a statistically significant but physiologically unimportant increase of CSF pressure (from 12 +/- 1 to 16 +/- 1 cm H2O, mean +/- SEM). It is concluded that EEG suppression following intracarotid injection of Conray is a rare event. It seems unlikely that EEG suppression resulted from cerebral ischemia or hypoxia, but rather was associated with increased BBB permeability. Increased BBB permeability likely was caused by the osmotic effect of Conray and not by hypoxic-ischemic microvascular injury or loss of autoregulation of CBF.

Journal Article↗

Control of retroviral RNA splicing through maintenance of suboptimal processing signals.

The full-length retroviral transcript serves as genomic RNA for progeny virions, as an mRNA for structural proteins and enzymes, and as a pre-mRNA substrate for splicing that yields subgenomic mRNAs that encode other essential proteins. Thus, RNA splicing to form subgenomic mRNAs must be incomplete or regulated in order to preserve some of the full-length transcripts. We have used the avian sarcoma virus system to delineate the viral functions that are required in the regulation of the splicing event that forms the envelope glycoprotein (env) subgenomic mRNA. We observed previously that a specific insertion mutation just 5' of the env splice acceptor site resulted in nearly complete splicing to form env mRNA and a concomitant replication defect which is presumably due to a deficit of the full-length transcript. Replication-competent pseudorevertants contained second-site mutations that restored splicing control, and these mapped either just upstream or downstream of the env splice acceptor site. In this report, we show that splicing control at this site does not require expression of any known viral replication protein(s), nor does it appear to require the viral splice donor site. From these results and analysis of additional splicing mutations obtained by in vivo selection, we conclude that splicing is controlled through the maintenance of suboptimal cis-acting signals in the viral RNA that alter the efficiency of recognition by the cellular splicing machinery.

Animals↗

Generation of diversity in retroviruses.

Retroviruses are unique in that their propagation includes transfer of genetic information from RNA to DNA. Two enzymes (RT and RNA polymerase II) that participate in their replication process do not encode editing functions and are thus "error prone." Current estimates indicate that up to one nucleotide substitution per genome occurs per retrovirus replication cycle. In addition, rearrangements can occur during reverse transcription. These mutations result in viral populations in which the wild-type sequence can only be defined by consensus. Retroviruses are also unusual among viruses in their high recombination frequency, which is the result of the copackaging, and then reverse transcribing of two different RNA genomes in the same particle. Recombinants are formed during copying of RNA templates into DNA. With the ability to mutate and recombine genetic information at a higher rate, retroviral populations are poised to respond to selective forces, which may increase or decrease replication of particular genotypes. Interspecies transmission of retroviruses or retroviral genes also likely plays a role in generating diversity. Endogenous proviruses exist in the germline of many vertebrates; pedigrees indicate that recent infections of the germline have also occurred. Thus, the selective forces that mold the retroviral genome may be opposing: selection for efficient replication as exogenous viruses versus selection for passive replication as endogenous proviruses. The latter may be more advantageous over the course of evolution since the survival of the retrovirus is ensured by survival of the host organism. Segments of endogenous viruses may reappear in exogenous viruses through recombination and thus these endogenous sequences are perpetuated.

Animals↗

Terminal nucleotides of the preintegrative linear form of HIV-1 DNA deduced from the sequence of circular DNA junctions.

The termini of integrated retroviral DNAs are characterized by highly conserved dinucleotide sequences: 5'TG...//...CA3'. For the avian and murine C-type retroviruses, the dinucleotide sequences reside two deoxynucleotides (usually AA and TT) from the LTR ends of unintegrated viral DNA (5' AATG...//...CATT3'). The number and identity of terminal deoxynucleotides in unintegrated HIV-1 linear DNA that extend beyond the conserved dinucleotides have not been determined. However, they had been presumed to consist of a single nucleotide (5'CTG...//...CAG3') on each end, based on inspection of the nucleotide sequence between the end of the supposed primer sites for retroviral DNA synthesis and the conserved proviral termini. We have utilized the polymerase chain reaction (PCR) to amplify segments representing the joined ends of linear DNA present in covalently closed circular HIV-1 DNA molecules isolated from infected T cells. These fragments were cloned and the nucleotide sequence of the LTR-LTR circle junction of several independent clones determined. Based upon the results, we predict that, like the avian and murine viruses, HIV-1 linear DNA contains two nucleotides beyond the conserved dinucleotides: 5'ACTG...//...CAGT3'. Models for the origin of these termini and other observed junction sequences are proposed.

Base Sequence↗

Avian retroviral protease and cellular aspartic proteases are distinguished by activities on peptide substrates.

The avian sarcoma/leukemia virus protease (PR), purified from avian myeloblastosis virus has a native molecular mass of 26 kDa, suggesting a dimer structure. The enzymatic activity of PR has been characterized using synthetic peptide substrates. PR is most active at pH 5.5, 35 degrees C and 2-3 M NaCl. Under these conditions PR cleaves decapeptides which are resistant in low ionic strength. This high, nonphysiological, salt concentration also increases the proteolytic activity of a cellular aspartic protease, pepsin. PR and pepsin show additional similarities: they both cleave a synthetic decapeptide at the same Tyr-Pro bond in low and high salt, while the cleavage site preferences of human renin and cathepsin-D in this substrate are altered at high salt concentrations. In addition, iodination of the tyrosine residue in this decapeptide causes an increase in the rates of hydrolysis by both PR and pepsin. However, Km values are too high to be estimated accurately for PR using Tyr-Pro and Tyr(I)-Pro decapeptides as substrates. Comparison of the digestion products of two additional decapeptides, altered in a single amino acid residue, shows that PR cleaves at fewer sites than all three cellular enzymes. Furthermore pepstatin, a strong inhibitor of pepsin, renin, and cathepsin-D has little effect on PR.

Avian Leukosis Virus↗

What is the role of the cys-his motif in retroviral nucleocapsid (NC) proteins?

Retroviruses encode a small, basic nucleocapsid (NC) protein that is found complexed to genomic RNA within the viral particle. The NC protein appears to function not only in a histone-like manner in packaging the RNA into the particle but also in specifically selecting the viral genomic RNA for packaging. A cysteine-histidine (cys-his) region, usually composed of 14 amino acids and reminiscent of the 'zinc fingers' of transcription factors, is the only highly conserved sequence element among the retroviral NC proteins. This review discusses the biochemical properties of NC, and its possible role(s) in retroviral replication. We also speculate on how the biochemical properties may relate to its function in RNA recognition and packaging.

Amino Acid Sequence↗

Autoregulation of cerebral blood flow during normocapnia and hypocapnia in dogs.

The effect of hypocapnia on autoregulation of cerebral blood flow (CBF) and the lower limit of autoregulation (LLA) was determined in dogs anesthetized with nitrous oxide (66%) and halothane (0.2%, end-expired concentration). CBF and cerebral vascular resistance (CVR) were determined during both normocapnia and hypocapnia (PaCO2 21-22 mmHg) at control cerebral perfusion pressure (CPP) and after reducing CPP (by hemorrhage) to 80%, 60%, 50%, and 40% of control. At control CPP hypocapnia decreased CBF from 75 +/- 5 to 48 +/- 3 ml.100 g-1.min-1 (mean +/- SEM, P less than 0.05). During both normocapnia and hypocapnia CVR decreased and CBF did not change as CPP was reduced to 60% of control. When CPP was reduced to 50% or 40% of control, CVR remained decreased and CBF fell sharply. The LLA during hypocapnia, 61 +/- 2% of control CPP, was not different than that during normocapnia, 59 +/- 3% of control CPP. Below the LLA the CBF-CPP slopes differed from zero but did not differ between hypocapnia and normocapnia. Hypocapnia does not produce a substantial shift of the LLA, and over the range of CPP values studied here, autoregulatory cerebral vasodilation only partially abolishes hypocapnia-induced cerebral vasoconstriction. The results suggest that when cerebral autoregulation is intact and in the absence of cerebrovascular disease, hypocapnia does not reduce global CBF to a level that is likely to produce ischemia and remains a useful therapeutic treatment so long as CPP remains above the LLA.

Animals↗

Cerebral blood volume and CSF pressure following administration of ketamine in dogs; modification by pre- or posttreatment with hypocapnia or diazepam.

The effects of ketamine (2 mg/kg) on cerebral blood (CBV) and cerebrospinal fluid (CSF) pressure, and the modification of ketamine's effects by pre- or posttreatment with hypocapnia (PaCO2 of 20-25 mm Hg) or diazepam (0.3 mg/kg) were determined in 26 dogs. In Group I (n = 7), the sequence of experimental treatments was as follows: control, ketamine, hypocapnia, and normocapnia. In Group II (n = 7), the sequence was control, hypocapnia, ketamine, and normocapnia. In Group III (n = 6), the sequence was control, ketamine, and diazepam. In Group IV In (n = 6), the sequence was control, diazepam, and ketamine. Ketamine alone increased CBV by 11.7 +/- 6.6 (Group III) to 12.4 +/- 6.9% (Group I) (mean +/- SD) and increased CSF pressure by 6.0 +/- 3.9 (Group I) to 10.7 +/- 5.2 (Group III) cm H2O. Pretreatment with hypocapnia or diazepam reduced CSF pressure and CBV so that when ketamine was administered after 15 min of hypocapnia or diazepam, CSF pressure and CBV rose only to prehypocapnia or prediazepam levels. When hypocapnia or diazepam were administered 15 min after ketamine, CSF pressure and CBV decreased to preketamine levels. For all treatments, CSF pressure changed in parallel with CBV in the absence of significant changes in PaCO2, expired CO2, or mean arterial blood pressure (except for a decrease of mean arterial blood pressure with diazepam pretreatment). We conclude the following: (a) ketamine increases CBV concomitant with increases in CSF pressure, (b) ketamine increases CBV and CSF pressure independent of significant change in PaCO2, and (c) pre- or posttreatment with hypocapnia or diazepam reverses ketamine-induced increase of CBV and CSF pressure in dogs with normal CSF pressure and no cerebrovascular damage.

Journal Article↗

The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration.

The purified integration protein (IN) of avian myeloblastosis virus is shown to nick double-stranded oligodeoxynucleotide substrates that mimic the ends of the linear form of viral DNA. In the presence of Mg2+, nicks are created 2 nucleotides from the 3' OH ends of both the U5 plus strand and the U3 minus strand. Similar cleavage is observed in the presence of Mn2+ but only when the extent of the reaction is limited. Neither the complementary strands nor sequences representing the termini of human immunodeficiency virus type 1 DNA were cleaved at analogous positions. Analysis of a series of substrates containing U5 base substitutions has defined the sequence requirements for site-selective nicking; nucleotides near the cleavage site are most critical for activity. The minimum substrate size required to demonstrate significant activity corresponds to the nearly perfect 15-base terminal inverted repeat. This in vitro activity of IN thus produces viral DNA ends that are joined to host DNA in vivo and corresponds to an expected early step in the integrative recombination reaction. These results provide the first enzymatic support using purified retroviral proteins for a linear DNA precursor to the integrated provirus.

Avian Leukosis Virus↗

Site-directed mutagenesis of the avian retrovirus nucleocapsid protein, pp 12. Mutation which affects RNA binding in vitro blocks viral replication.

Site-directed mutagenesis was used to replace the lysine residues of the avian retrovirus nucleocapsid protein pp 12 that have previously been shown to be important for RNA binding. Single amino acid substitutions at Lys-36, -37, and -39 of the protein were not sufficient to affect virus production as measured by reverse transcriptase activity in virus particles released from transfected cells. However, when Lys-36 and Lys-37 were simultaneously replaced by isoleucine residues, there was a complete block of viral replication. As expected from the single mutant analyses, the wild type phenotype could be restored by reverting either or both of the isoleucine residues to lysine residues. Analysis of a bacterially produced rp 12 protein containing Ile-36 and Ile-37 indicated that the protein has a low affinity binding for RNA, as compared to wild type protein. Unlike wild type, the binding is independent of phosphorylation at Ser-40, the major site of phosphorylation of the protein in vivo. A quail cell line was established that expresses virus particles containing the doubly mutated pp 12. Analysis of these particles indicated that they lack viral RNA. Thus, the binding defect in pp 12 is correlated with the inability to package viral RNA.

Animals↗

Synthetic peptides as substrates and inhibitors of a retroviral protease.

Processing of the gag and pol gene precursor proteins of retroviruses is essential for infectivity and is directed by a viral protease that is itself included in one of these precursors. We demonstrate here that small synthetic peptides can be used as both model substrates and inhibitors to investigate the specificity and molecular parameters of the reaction. The results indicate that a peptide that extends five amino acids but not three amino acids in both directions from a known cleavage site is accurately hydrolyzed by the protease of avian sarcoma-leukosis virus. Substitutions of the amino acids to either side of the peptide bond to be cleaved affect the ability of the peptide (as well as a larger precursor protein) to serve as a substrate. The specificity is more stringent for the amino acid that will become the carboxyl end after cleavage. Some substitutions produced peptides that were not cleaved but could act as inhibitors of cleavage of a susceptible peptide. Thus, small model substrates may be used to explore both the binding and catalytic properties of these important proteases.

Alpharetrovirus↗