Restriction Endonuclease Fragments Research Articles

Frequent mutations of the β- catenin gene in mouse colon tumors induced by azoxymethane

The beta-catenin gene is frequently mutated at codons 33, 41 and 45 of the glycogen synthase kinase-3beta phosphorylation motif in human colon cancers in patients without APC mutations. Frequent mutations at codons 32 and 34, as well as 33 and 41, have been detected in rat colon tumors induced by azoxymethane (AOM), with the second G of CTGGA sequences being considered as a mutational hot-spot. In the present study, exon 3 of the beta-catenin gene in mouse colon tumors induced by AOM was amplified by PCR and mutations were detected by the single strand conformation polymorphism method, restriction enzyme fragment length polymorphism and direct sequencing. All 10 colon tumors tested were found to have beta-catenin mutations, four in codon 34, three in codon 33, two in codon 41 and one in codon 37, nine being G:C-->A:T transitions. However, no mutations were found in codon 32 of the mouse beta-catenin gene. On immmunostaining, beta-catenin was observed in the cytoplasm and nucleus of the tumor cells. The cytoplasmic staining was homogeneous, while both homogeneous and heterogeneous patterns were noted for the nuclei. Highly frequent mutations of the beta-catenin gene in AOM-induced mouse colon tumors suggest that consequent alterations in the stability and localization of the protein may play an important role in this colon carcinogenesis model.

Survival of infectiousPseudomonas aeruginosa genotypes in occupational saturation diving environment and the significance of these genotypes for recurrent skin infections

Occupational saturation divers suffer from various skin disorders, of which skin infections are the most serious and frequent. Pseudomonas aeruginosa is the microbe most often isolated. P. aeruginosa isolates from 292 skin infections in operational saturation divers and about 800 isolates from occupational saturation diving systems have been collected during the period 1986 to 1998. Genotyping of the isolates has been performed by using restriction enzyme fragmentation and pulsed field gel electrophoresis. Four hundred and seventy-two P. aeruginosa isolates have been analyzed, of which 181 originate from skin infections in divers. Ninety-seven significantly different P. aeruginosa genotypes have been defined. Some of these genotypes are solely found from skin infections, some solely from the saturation environment and about 25% were found both from infections and from the saturation environment. Eight frequent infectious genotypes have been identified, and these are shown to be present over several years, both in infections and in the saturation environment. The study suggests that skin infections in occupational saturation divers are commonly caused by environmental strains.

Contamination of Marek's disease vaccine suspensions with Enterococcus faecalis and its possible role in amyloid arthropathy

Samples of hatchery air (hatcher and processing room), Marek's disease vaccine suspensions and injection needles collected during chick processing, revealed variable levels (< 500 to 106 colony forming units (cfu)/m3 air, < 10 to 106 cfu/ml vaccine suspension, and 9500 to 61000 cfu/needle) of Enterococcus faecalis contamination. This observation suggests a possible infection route in 1-day-old chickens through intramuscular vaccination of Marek's disease vaccine contaminated with arthropathic and amyloidogenic E. faecalis, which could lead to amyloid arthropathy. Pulsed-field gel electrophoresis (PFGE) DNA restriction endonuclease fragment analysis of E. faecalis strains obtained from two hatcheries revealed a predominant PFGE pattern in one hatchery, while one isolate with an almost identical PFGE pattern to an amyloid arthropathy inducing isolate was found.

Terminal restriction fragment length polymorphism monitoring of genes amplified directly from bacterial communities in soils and sediments.

Terminal Restriction Fragment Length Polymorphism (T-RFLP) or Fluorescent Polymerase Chain Reaction/Restriction Fragment Length Polymorphism (FluRFLP) have made a significant impact on the way in which PCR products amplified from mixed community DNA extracts have been assessed. Technically, these approaches are essentially the same. PCR products are generated that contain at one 5' end label, typically a fluorescent moiety, that will be detected by a DNA sequencing machine. Upon digestion using a specific restriction endonuclease, labeled and unlabeled fragments are generated. This restriction endonuclease is chosen such that following this digestion, each labeled fragment corresponds to a different sequence variant. During electrophoretic separation, the DNA sequencing machine detects only these labeled fragments and therefore detects only the sequence variants. The aim of this article is to describe the protocols and demonstrate that this profiling can be performed using different DNA sequencing machines. The analysis and applications of this approach are also discussed.

Vitamin D receptor interactions with the rat parathyroid hormone gene: synergistic effects between two negative vitamin D response elements.

Vitamin D response elements (VDREs) that are required for negative regulation of rat parathyroid hormone (rPTH) gene expression have been characterized. Gel mobility shift assays using DNA restriction enzyme fragments and recombinant proteins for vitamin D and retinoic acid X receptors (VDR/RXR) revealed a sequence between -793 and -779 that bound a VDR/RXR heterodimer with high affinity (VDRE1). Furthermore, a lower affinity site (VDRE2) was detected that acted in combination with VDRE1 to bind a second VDR/RXR complex. As determined by ethylation interference analysis, the nucleotide sequence of VDRE1 consisted of GGTTCA GTG AGGTAC, which is remarkably similar to the sequence of the negative VDRE found in the chicken PTH (cPTH) gene. Using the same technique, VDRE2 was identified between positions -760 and -746 and contained the sequence AGGCTA GCC AGTTCA. Functional analysis was determined by transfection studies with plasmid constructs that expressed the gene for chloramphenicol acetyl transferase (CAT). The ability of the VDREs to regulate gene expression was tested in their native context with the rPTH promoter as well as when positioned immediately upstream from the cPTH promoter. With either plasmid construct, exposure to 10(-8)M 1,25(OH)2D3 resulted in a 60-70% decrease in CAT gene expression when both VDRE1 and VDRE2 were present. Examination of the individual VDREs showed that inhibition by 10(-8) M 1,25(OH)2D3 was only 35-40% when just VDRE1 was present. By itself, VDRE2 was even less effective, as significant inhibition of CAT activity (20%) was observed only in the presence of higher concentrations of 1, 25(OH)2D3 (10(-7)M) or when a plasmid vector that overexpressed the VDR protein was cotransfected. In conclusion, the rPTH gene contains two negative VDREs that act in concert to bind two RXR/VDR heterodimer complexes and that both VDREs are required for maximal inhibition by 1,25(OH)2D3.

Characterization of a Nucleopolyhedrovirus from the Black Cutworm, Agrotis ipsilon (Lepidoptera: Noctuidae)

The black cutworm, Agrotis ipsilon (Hufnagel) (Lepidoptera: Noctuidae), is a serious localized pest of vegetable and field crops. We have characterized a newly discovered baculovirus, the Agrotis ipsilon multicapsid nucleopolyhedrovirus (AgipMNPV), that was isolated from A. ipsilon in Illinois. Restriction enzyme fragment profiles of AgipMNPV DNA were distinct from those of previously described nucleopolyhedroviruses. Electron microscopy of AgipMNPV-infected tissues indicated that nucleocapsids of this virus are multiply enveloped. A. ipsilon was highly susceptible to infection by AgipMNPV and significantly more susceptible to infection by AgipMNPV than by Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV). Host range studies showed that Heliothis virescens and Helicoverpa zea were moderately susceptible to infection; Pseudaletia unipuncta and Spodoptera frugiperda were only partially susceptible, and Anticarsia gemmatalis, Spodoptera exigua, Trichoplusia ni, and Ostrinia nubilalis were not susceptible to infection by AgipMNPV. Because of its high virulence, AgipMNPV has potential as an alternative to chemical insecticides for control of A. ipsilon.

Polymorphism in the regulatory regions of the HLA-DPB1 gene

Nucleotide sequencing of approximately 400 basepairs upstream from exon 1 of the DPB1 gene and sequence specific oligonucleotide hybridisation identified eight nucleotide positions to be polymorphic which were in linkage disequilibrium (LD) with DPA1 and DPB1 alleles. Substitutions at two sites (−230 and −224) formed three genotypes (DP-PRO1-3). DP-PRO 1 was the most common genotype and was in LD with DPA1∗0103, ∗0202 and DPB1∗0401, ∗0501. DP-PRO 2 was observed in LD with DPB1∗02012, ∗1601, ∗1701 and DPA1∗0104. DP-PRO3 was in LD with DPB1∗0901, ∗1001 and DPA1∗0201. Electrophoretic Mobility Shift Assays (EMSA) performed with restriction enzyme fragments showed substitutions at −230 and −224 not to be involved in binding nuclear proteins. Six substitutions were found on a single genotype (DP-PRO4) which was observed in seven samples; 67% of DP-PRO4 inferred haplotypes were HLA-A2-B46, DRB1∗0901, DQB1∗03032, DPA1∗0401, DPB1∗1301. Three of the substitutions occurred in conserved regulatory region boxes, W′, X and Y, and three in the signal and leader sequences. EMSA competitive binding assays performed with oligonucleotide probes for the substitutions showed no difference in binding affinity for W′ and X probes. The DP-PRO4 Y box had a decreased nuclear protein binding affinity compared to DP-PRO1-3. Whether the sum of the differences in DP-PRO4 relate to a change in the cell surface expression of HLA-DP is yet to be determined.

Mitochondrial DNA polymorphisms of a west Algerian population (Oran region)

Mitochondrial DNA codes for enzymes involved in the cellular energetic pathway. The polymorphism of this genome has been extensively analyzed for disease associations, but can also be used to characterize anthropological distances between populations. This study presents the results of mitochondrial DNA (mtDNA) sequence variation for a population sample of 50 unrelated individuals originating from western Algeria. The samples were studied with the recently developed long PCR technique followed by RFLP analysis using six restriction endonucleases: HpaI, BamHI, HaeII, MspI, AvaII and HincII One new morph for HpaI (named Hpal-9 Alg) was detected, and was found to be derived from the combination of the already known morphs 3 and 4. mtDNA restriction endonuclease fragment patterns were analyzed for potential site gain or loss and classified into 18 mtDNA types by the sequence-comparison method. Three mtDNA types (97 Alg; 2-1-7-1-1, 98 Alg; 2-1-1-8-37 and 99 Alg; 9 Alg-1-1-1-3) were detected for the first time. Another mtDNA marker — the presence of the 9 by deletion in the COII/tRNA Lys region - was also studied in the Algerian sample. No deletions were observed. Our results indicate that the Algerians are genetically related to the Israeli-Arab population, with certain characteristics found in southern Europeans and others found in sub-Saharan Africans.

Fluorescent PCR and automated fragment analysis in preimplantation genetic diagnosis for 21-hydroxylase deficiency in congenital adrenal hyperplasia

Congenital adrenal hyperplasia (CAH) is an autosomal recessive disease which is most often caused by a deficiency in steroid 21-hydroxylase. The disease is characterized by a range of impaired adrenal cortisol and aldosterone synthesis combined with an increased androgen synthesis. These metabolic abnormalities lead to an inability to conserve sodium and virilization of females. The most common mutation causing the severe form of CAH is a conversion of an A or C at nucleotide (nt) 656 to a G in the second intron of the steroid 21-hydroxylase gene (CYP21) causing aberrant splicing of mRNA. A couple was referred to our centre for preimplantation genetic diagnosis (PGD) for 21-hydroxylase deficiency in CAH. A PGD was set up to detect the nt656 A/C-->G mutation using fluorescent polymerase chain reaction (PCR) and subsequent restriction enzyme digestion and fragment analysis on an automated sequencer. Using DNA or single cells from the father, the normal allele could not be amplified. Non-amplification of the normal allele has been previously described in asymptomatic carriers, therefore the PCR was further developed using heterozygous lymphoblasts from the mother. The PCR was shown to be highly efficient (96% amplification), accurate (0% contamination) and reliable (0% allelic drop-out). The couple started PGD treatment and the second PGD cycle resulted in a twin pregnancy. The genotype of the fetuses was determined in our laboratory using chorionic villus sampling material using the method described here. Both fetuses were shown to be heterozygous carriers of the mutation, and two healthy girls were born.

The 3'-untranslated region polymorphism of the gene for skeletal muscle-specific glycogen-targeting subunit of protein phosphatase 1 in the type 2 diabetic Japanese population.

A newly identified 3'-untranslated region (UTR) polymorphism of the gene for skeletal muscle-specific glycogen-targeting subunit of protein phosphatase 1 (PPP1R3) was associated with insulin resistance and type 2 diabetes in Pima Indians (Xia J, Scherers W, Cohen PTW, Majer M, Xi T, Norman RA, Knowler WC, Bogardus C, Prochazka M: A common variant in PP1R3 associated with insulin resistance and type 2 diabetes. Diabetes 47:1519-1524, 1998). Thus, we investigated the frequency of polymorphism of the adenine- and thymine-rich element (ARE-1 and its variant ARE-2) in 426 Japanese type 2 diabetic and 380 nondiabetic subjects using a polymerase chain reaction (PCR)-restriction enzyme fragment length polymorphism (RFLP) method. The allele frequency of the ARE-2 variant in diabetic subjects was higher than that in nondiabetic subjects (0.34 vs. 0.29; P < 0.05), even though its frequency in Japanese subjects was lower (P < 0.001) than the reported value in Pima Indians (0.56). An aspartate polymorphism at codon 905 was 100% coupled to the ARE-2 allele, and its allele frequency was higher also in diabetic subjects. Although a serine substitution at codon 883 was partially linked with the ARE-2 allele, there was no difference between diabetic and nondiabetic subjects. These results indicate that the frequency of polymorphism of the PPP1R3 gene (ARE-2 and Asp905) is different between two ethnic groups and is increased in Japanese people with type 2 diabetes, suggesting that these variants may be a possible marker for searching for diabetogenic genes.

Purification and partial genome characterization of a herpes-like virus infecting the Japanese oyster, Crassostrea gigas.

First observed in 1972 in Crassostrea virginica, herpes-like viruses of bivalves were more recently found to be associated with high mortality rates in other cultured oyster species, such as Crassostrea gigas and Ostrea edulis. The diagnosis of herpes-like virus infections is performed currently by laborious histological and transmission electron microscope examinations. Preparation of specific reagents for use in more amenable diagnostic techniques prompted purification of virus particles and investigation of the viral genome. This paper is the first description of the purification of a virus pathogen from a bivalve mollusc. A procedure was developed which facilitated purification of large amounts of virus particles on the 40-50% interface of sucrose gradients. Transmission electron microscopy showed that a purified virus suspension contained capsids and enveloped virus particles. High molecular mass viral DNA was extracted, and the genome size was estimated by the summation of the sizes of restriction endonuclease fragments to be approximately 180 kbp. Partial cloning of the virus genome was achieved and the specificity of certain cloned fragments was established by dot blot hybridization.

Geographically diverse Australian isolates of Melissococcus pluton exhibit minimal genotypic diversity by restriction endonuclease analysis.

Melissococcus pluton, the causative agent of European foulbrood is an economically significant disease of honey bees (Apis mellifera) across most regions of the world and is prevalent throughout most states of Australia. 49 Isolates of M. pluton recovered from diseased colonies or honey samples in New South Wales, Queensland, South Australia, Tasmania and Victoria were compared using SDS-PAGE, Western immunoblotting and restriction endonuclease analyses. DNA profiles of all 49 geographically diverse isolates showed remarkably similar AluI profiles although four isolates (one each from Queensland, South Australia, New South Wales and Victoria) displayed minor profile variations compared to AluI patterns of all other isolates. DNA from a subset of the 49 Australian and three isolates from the United Kingdom were digested separately with the restriction endonucleases CfoI, RsaI and DraI. Restriction endonuclease fragment patterns generated using these enzymes were also similar although minor variations were noted. SDS-PAGE of whole cell proteins from 13 of the 49 isolates from different states of Australia, including the four isolates which displayed minor profile variations (AluI) produced indistinguishable patterns. Major immunoreactive proteins of approximate molecular masses of 21, 24, 28, 30, 36, 40, 44, 56, 60, 71, 79 and 95 kDa were observed in immunoblots of whole cell lysates of 22 of the 49 isolates and reacted with rabbit hyperimmune antibodies raised against M. pluton whole cells. Neither SDS-PAGE or immunoblotting was capable of distinguishing differences between geographically diverse isolates of M. pluton. Collectively these data confirm that Australian isolates of M. pluton are genetically homogeneous and that this species may be clonal. Plasmid DNA was not detected in whole cell DNA profiles of any isolate resolved using agarose gel electrophoresis.

Geographically diverse Australian isolates of Melissococcus pluton exhibit minimal genotypic diversity by restriction endonuclease analysis

Melissococcus pluton, the causative agent of European foulbrood is an economically significant disease of honey bees ( Apis mellifera) across most regions of the world and is prevalent throughout most states of Australia. 49 Isolates of M. pluton recovered from diseased colonies or honey samples in New South Wales, Queensland, South Australia, Tasmania and Victoria were compared using SDS-PAGE, Western immunoblotting and restriction endonuclease analyses. DNA profiles of all 49 geographically diverse isolates showed remarkably similar AluI profiles although four isolates (one each from Queensland, South Australia, New South Wales and Victoria) displayed minor profile variations compared to AluI patterns of all other isolates. DNA from a subset of the 49 Australian and three isolates from the United Kingdom were digested separately with the restriction endonucleases CfoI, RsaI and DraI. Restriction endonuclease fragment patterns generated using these enzymes were also similar although minor variations were noted. SDS-PAGE of whole cell proteins from 13 of the 49 isolates from different states of Australia, including the four isolates which displayed minor profile variations ( AluI) produced indistinguishable patterns. Major immunoreactive proteins of approximate molecular masses of 21, 24, 28, 30, 36, 40, 44, 56, 60, 71, 79 and 95 kDa were observed in immunoblots of whole cell lysates of 22 of the 49 isolates and reacted with rabbit hyperimmune antibodies raised against M. pluton whole cells. Neither SDS-PAGE or immunoblotting was capable of distinguishing differences between geographically diverse isolates of M. pluton. Collectively these data confirm that Australian isolates of M. pluton are genetically homogeneous and that this species may be clonal. Plasmid DNA was not detected in whole cell DNA profiles of any isolate resolved using agarose gel electrophoresis.

Tumor necrosis factor genetic polymorphisms correlate with infections after liver transplantation. NEMC TNF Study Group. New England Medical Center Tumor Necrosis Factor.

Tumor necrosis factor-alpha (TNF-alpha) is a pro-inflammatory mediator of the immune response to allogenic and infectious stimuli. Non-immunosuppressed individuals possessing a NcoI restriction enzyme site in the TNF gene locus produce less TNF-alpha in vitro and in vivo compared with individuals lacking this restriction site. We performed polymerase chain reaction amplification and restriction enzyme fragment length analysis of the TNF locus from 86 liver transplant recipients to determine if presence of the NcoI site is associated with the frequency of rejection or infection, time to rejection or infection, and patient and graft survival. We controlled for recipient primary diagnosis, age, sex, United Network for Organ Sharing status, year of transplant, type of immunosuppression, use of anti-lymphocyte agents, and graft ischemia time. Fifty-six recipients possessed the NcoI+/low TNF-alpha genotype and 30 were NcoI-/high TNF-alpha genotype. In the first year after transplant, there were no significant differences in the frequency, or time to first rejections or the overall number of rejection episodes between the two genotypes. NcoI+/low TNF-alpha genotype recipients had significantly more infections (1.52 vs. 0.87, P=0.014). In a linear regression, multivariate model controlling for all marginally significant variables, the NcoI+/low TNF-alpha genotype was still associated with significantly more infections (P=0.0031). Patient and graft survival were equal for the two groups. One implication of this study, in individuals genetically predetermined to be low TNF-alpha producers, is that additional inhibition of TNF-alpha production by routine immunosuppression may be excessive, rendering these individuals less able to respond to infectious stimuli. These patients may benefit from lower doses or withdrawal of corticosteroids.

An alternative inverse PCR (IPCR) method to amplify DNA sequences flanking Tn5 transposon insertions

We have developed an alternative method to amplify DNA sequences flanking Tn5 transposon insertions. This method relies on the identical sequences of inverted terminal repeats, located at the 5′ and 3′ ends of Tn5, to determine the location and orientation of a transposon insertion within a restriction endonuclease fragment. From this information, PCR primers can be designed to selectively amplify by inverse PCR the DNA flanking one side of the transposon. This method avoids the problem of amplifying or cloning long sequences flanking Tn5. To demonstrate the applicability of this method, we generated Tn5 transposon mutants of Pseudomonas abietaniphila BKME-9 which no longer grew on dehydroabietic acid (DhA). The flanking sequence of one of the mutant (strain BKME-941) which accumulated 7-oxoDhA, was amplified.

Transformation and laccase mutant isolation inCoprinus congregatusby restriction enzyme-mediated integration

Coprinus congregatus did not show any growth on a minimal medium in the presence of phosphinothricin which inhibited glutamine synthetase. Genetic transformation to phosphinothricin resistance in C. congregatus was carried out successfully by restriction enzyme-mediated integration. The procedure was improved to yield 550 transformants per μg of DNA, and three laccase mutants were generated. The vector pBARGEM 7-1 which had the phosphinothricin resistance gene was detected in the restriction enzyme fragments of chromosomal DNA from the transformants by Southern hybridization. Transformants showed identical electrophoretic banding patterns but CL1430b had a faster moving band when analyzed by native PAGE.

Transformation and laccase mutant isolation in Coprinus congregatus by restriction enzyme-mediated integration

Coprinus congregatus did not show any growth on a minimal medium in the presence of phosphinothricin which inhibited glutamine synthetase. Genetic transformation to phosphinothricin resistance in C. congregatus was carried out successfully by restriction enzyme-mediated integration. The procedure was improved to yield 550 transformants per μg of DNA, and three laccase mutants were generated. The vector pBARGEM 7-1 which had the phosphinothricin resistance gene was detected in the restriction enzyme fragments of chromosomal DNA from the transformants by Southern hybridization. Transformants showed identical electrophoretic banding patterns but CL1430b had a faster moving band when analyzed by native PAGE.

Immunologic characterization of a recombinant American cockroach (Periplaneta americana) Per a 1 (Cr-PII) allergen.

Previously, we have identified several Per a 1 (Cr-PII) allergens from a deltagt22A cDNA library of Periplaneta americana. This study aimed to sequence clone C42 and determine its molecular and antigenic properties. The cDNA of C42 was sequenced and ligated into a bacteria expression vector, pET21. The recombinant proteins were purified by ion-exchange and affinity chromatographies. Their antigenicities were analyzed by immunoblotting, ELISA, and binding inhibition with human IgE. The nucleotide of the cDNA has been sequenced and the deduced amino acid which encodes a 446-amino-acid protein (50kDa) determined. The recombinant C42 protein can bind both anti-Per a 1 monoclonal antibodies and human IgE and showed a 54.4% (12/22) skin reactivity in atopic patients. Sequence homology searches revealed a high degree of identity to two other members of the Per a 1 family, C17 and C6, and the German cockroach (Blattella germanica) Bla g Bd90K allergen. Interestingly, these allergens all contain internal repeats, and the crude B. germanica extract, Per a 1, and recombinant allergens share similar antigenic determinant(s) as defined by ELISA and IgE-binding inhibition studies. In IgE-binding epitope studies, an immunopositive C42 fragment was first identified from partial protease digestion. Overlapping peptides were then generated by expression of restriction enzyme fragments in E. coli. The shortest peptide, C42-P560, identified by monoclonal antibodies and human specific IgE, can inhibit IgE binding to C42. An additional Per a 1 allergen has been defined at the molecular level and characterized and preliminary results showed that a potential IgE-reactive region is located within amino-acid residue 358-446 of C42, which is an internal repeat. The results defined the boundaries of the antigenic site and will facilitate further epitope-mapping studies.

Analysis of a phenobarbital-responsive enhancer sequence located in the 5' flanking region of the chicken CYP2H1 gene: identification and characterization of functional protein-binding sites.

We previously identified in the chicken CYP2H1 gene an upstream enhancer domain (-5900/-1100) that responds to phenobarbital. Deletion and restriction enzyme analyses of this domain have now identified two separate enhancer regions that respond to phenobarbital (from -5900 to -4550 and from -1956 to -1400). We have focused here on the latter and in particular a resident 240-base pair (bp) restriction enzyme fragment that retains drug responsiveness. Using deletion analysis and in vitro DNase I footprinting, transcription factor binding sites have been located in the 240-bp fragment. The sites identified are an E-box-like element, a consensus hepatocyte nuclear factor 1 site, a CCAAT box motif, and a novel site. Mutagenesis demonstrated that each site contributed to enhancer activity, although there was a weaker contribution from the CCAAT box, and that no individual site was critical for responsiveness. In keeping with the tissue-restricted expression of the CYP2H1 gene, gel shift experiments established that the proteins binding to these enhancer sites are enriched in chicken liver, kidney, and small intestine. In vitro footprint experiments showed a stronger protection with liver nuclear extracts from drug-treated chickens compared with control extracts on the E-box-like element, the CCAAT box motif, and the novel binding site; however, the basis for this apparent increase in binding remains to be determined. The proteins binding to the 240-bp fragment are different from those recently reported to be required for the activity of the phenobarbital responsive enhancer domains of rodent CYP2 genes.

Importance of the Intracytoplasmic Domain of the Simian Immunodeficiency Virus (SIV) Envelope Glycoprotein for Pathogenesis

SIVmac1A11 and SIVmac239 are nonpathogenic and pathogenic molecular clones in rhesus macaques, respectively. Although these viruses exhibit ∼98% nucleotide and amino acid sequence homology, differences are found in the length of the translation frames for several genes. SIVmac239 has a premature stop codon innef, whereas SIVmac1A11 has a premature stop codon invprand two premature stop codons in the intracytoplasmic domain of theenv-transmembrane (TM) subunit. Recombinant viruses, constructed through reciprocal exchange of large DNA restriction enzyme fragments between SIVmac1A11 and SIVmac239, were evaluated in adult rhesus macaques. Thisin vivoanalysis revealed that two or more regions of the SIVmac genome were essential for high virus load and disease progression (Marthaset al.,1993.J. Virol.67, 6047–6055). An important gap in knowledge remaining from this study was whether the premature stop codons inenv-TM of recombinant virus SIV1A11/239gag-env/1A11 (full-lengthvprandnef, two stop codons inenv-TM) reverted to coding tripletsin vivo. Here, we report that viral sequences in macaques, which succumbed to an AIDS-like disease after infection with SIV1A11/239gag-env/1A11, exhibited reversion of bothenv-TM stop codons. In addition, antibodies to the intracytoplasmic domain ofenv-TM were detected in macaques containing revertant virus and showing disease; this finding indicates that this domain of theenvglycoprotein was expressedin vivo. Thus selection for viral variants with full-lengthenv-TM demonstrated that the cytoplasmic domain of the SIVmacenvglycoprotein plays a role in viral persistence and immunodeficiency in primates.