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V(D)J recombinase-mediated HPRT mutations in peripheral blood lymphocytes of normal children.

Somatic mutations in the hypoxanthine-guanine phosphoribosyltransferase (hprt) gene are rare occurrences in T-lymphocytes of normal individuals. Lacking pathogenic significance, these events can serve as reporters for assessing environmental genotoxicity. The present molecular analyses of hprt mutations arising spontaneously in normal children show that 30-35% of the genomic hprt changes in children under 5 years of age have approximately 20 Kb deletions encompassing exons 2 and 3. The frequency of these specific changes are dramatically decreased in older children. Sequence analysis of these deletion breakpoint and joining regions reveal the molecular hallmarks of V(D)J recombinase-mediated recombination events. This early childhood hprt mutational spectrum is quite distinct from the adult background spectrum but similar to that reported previously for newborns, as determined in lymphocytes from placental cord blood. The present study also demonstrates that definition of sequences in the hprt deletion joining regions that are analogous to the N-nucleotide insertion hypervariable regions of rearranged T-cell receptor genes allows the same identification of in vivo clonality of mutants as does analysis of the T-cell receptor gene rearrangements themselves. These methods reveal an in vivo clonal amplification of a V(D)J recombinase-mediated hprt mutant clone in one child in the present study. This newly found age-frequency distribution of V(D)J recombinase-mediated hprt mutations correlates with the age-frequency distribution of childhood acute lymphocytic leukemia. A significant number of these malignancies, including acute T-cell leukemia, are also characterized by V(D)J recombinase-mediated recombinations but in critical regions of the genome. hprt, therefore, captures a pathogenic mutagenic mechanism as a harmless mistake which, when it occurs in other genetic regions, may result in malignancy.

Adolescent↗

Investigation of aciclovir-resistant herpes simplex virus I infection in a bone marrow transplantation unit: genotyping shows that different strains are involved.

Over an eight-month period from October 1997 to May 1998, four patients who had received a bone marrow transplant (BMT) from an unrelated donor presented with severe mucosal cutaneous infections involving aciclovir resistant herpes simplex virus 1 (HSV-1). The emergence within a short period of resistant HSV-1 strains in the bone marrow transplantation unit raised fears of hospital-acquired infections. The hypothesis was investigated by restriction fragment length polymorphism (RFLP), sequencing of the thymidine kinase (TK) gene and genotyping of hypervariable regions of these four strains. Restriction fragment length polymorphism proved to be poorly discriminant and the TK sequence did not rule out transmission between these patients. Amplification of reiterating hypervariable genomic HSV-1 regions designated Re IV and Re VII clearly differentiated patients' strains. Thus, in this study, there was no evidence of nosocomial transmission of HSV-1 strains between the four patients.

Acyclovir↗

N-linked glycosylation in the V3 region of HIV type 1 surface antigen modulates coreceptor usage in viral infection.

The V3 hypervariable region of HIV-1 surface protein has been identified as a major determinant for viral tropism and coreceptor usage. However, the role of the highly conserved N-linked glycan at the V3 loop remains controversial. To further examine its role in viral infection, we introduced a conservative amino acid substitution (asparagine to glutamine) in the V3-proximal glycosylation motif (Asn-X-Ser/Thr) in the surface glycoprotein of a CXCR4-using virus (BRU), a CCR5-using virus (SF162), and a dual-tropic virus (89.6). The effect of the mutation was determined by complementation assays, and by infectivity on CEMx174 and U373-MAGI cells expressing either CXCR4 or CCR5. The mutation resulted in decreased CXCR4 usage by SHIV89.6, but increased usage by BRU. Similarly, it abrogated CCR5 usage by SHIV89.6, but had no effect on SF162. This effect was not dependent on the specific amino acid substitution used, because a threonine-toalanine mutation in the same motif in 89.6 Env yielded identical results as the asparagine-to-glutamine mutation. These findings support the notion that multiple factors, including glycosylation at V3, contribute to coreceptor usage and that the particular effects exerted by the N-linked glycan itself appear to be isolate dependent.

Amino Acid Motifs↗

Genetic heterogeneity of the envelope 2 gene and eradication of hepatitis C virus after a second course of interferon-alpha.

The heterogeneity of the envelope 2 (E2) gene of the hepatitis C virus (HCV) was involved in the sensitivity of HCV to interferon-alpha (IFN-alpha). To assess the factors leading to virus eradication by IFN-alpha, patients whose first treatment by IFN-alpha failed and who had virus eradication after a second treatment were studied. These patients were paired with subjects in whom both treatments failed. The phosphorylation homology domain of the E2 gene (E2-PHD) had no sequence variation between the two stages in both groups of patients. Therefore, this region has no clinical predictive value within a specific genotype. The hypervariable region 1 (HVR1) was analyzed by cloning and sequencing 20 clones per sample. Comparison of samples showed that the change in quasispecies induced by the first IFN-alpha therapy could be associated with virus elimination obtained after a second treatment. The greater proportion of nonsynonymous mutations that was noted before the second treatment in responders suggest that pretherapeutic immune response is a major factor determining virus elimination and that the immune status of these patients changed between the first and the second treatment.

Adult↗

Genomic typing of hepatitis C viruses from Korean patients: implications of genome variation in the E2/NS1 region.

Comparative nucleotide sequence studies of a 2.4-kb cDNA fragment (nt -49 to 2361) of Korean-type hepatitis C virus (HCV) were carried out. The nt sequences of the Korean HCV isolates have stronger sequence homologies with type II HCV (Japanese HCV-BK) than with types I (HCV-1) or III (HCV-6). In addition, the net sequences of a part of the core region of ten different samples confirmed that prevalent HCV in Korea belongs to type II with the exception of one sample which belongs to type III. The nt sequence of a cDNA fragment of E2/NS1 region of HCV, from six different serum samples, which comprises the hypervariable regions-1 (HVR-1) and -2 (HVR-2), revealed sequence heterogeneity with type II HCV (75.4 to 80.7% nt homology and 75.5 to 79.7% amino acid homology). However, it was relatively well conserved among the Korean isolates, in fact, aa sequences of HVR-2 as well as HVR-1, converged into two groups. Also we found consensus sequences (T.V.G..AGRTT.G..SLE......K) in HVR-1. Thus, we propose that the conserved patterns in HVR-1 and -2 are characteristics of the six different Korean isolates.

Amino Acid Sequence↗

Phylogenetic analysis of hepatitis E virus isolates from India (1976-1993).

Seventeen Indian hepatitis E virus (HEV) isolates, representing epidemic and sporadic hepatitis E cases during 1976-1991, were sequenced in the RNA polymerase (RNAP) region. Five isolates were also sequenced in the non-structural hypervariable region of open reading frame 1. Open reading frames 2 and 3 were sequenced only for the prototype isolate. On the basis of the comparison of all the available sequences of the conserved RNAP region, the HEV isolates were divided into three genotypes, differing from each other by >15%. Genotype I included African and Asian isolates, whereas II and III were represented by Mexican and US isolates, respectively. Genotype I was further divided into four sub-genotypes. The majority of the Indian isolates (15/20), along with the Burmese and Nepali isolates, belonged to genotype IA. Genotype IB included HEV isolates from China, Pakistan and the former USSR and 2/20 Indian isolates, which represented the oldest (1976) HEV sequenced so far. Genotype IC included both the African isolates, whereas 3/20 Indian isolates formed genotype ID. Nucleotide sequence analysis of other regions of the HEV genome also placed isolates in the same genotypes. Both the Indian cities experiencing second HEV epidemics, after intervals of 8 and 10 years, showed shifts in the sub-genotypes found; from IB (Ahm-76) to IA (Ahm-84) and from IA (Kol-81) to ID (Kol-91). However, no major shift in the genotypes was noted. Overall, HEV genotypes appear to be segregated geographically.

DNA-Directed RNA Polymerases↗

High adhesiveness of encapsulated Neisseria meningitidis to epithelial cells is associated with the formation of bundles of pili.

Pili are indispensable in adhesion of encapsulated Neisseria meningitidis (MC) to eukaryotic cells. Intrastrain variability with respect to the degree of adhesion is the result of pilin antigenic variation. We have localized the region responsible for this variability to the 20-amino-acid hypervariable domain of pilin. The replacement of an aspartic acid, located in the hypervariable region of a low-adhesive variant by a lysine restored high adhesiveness. To assess whether hyperadhesiveness conferred by some pilin variants was related to the generation of a new pilus-associated ligand, high- and low-adhesive variants were purified. In a first step, low- and high-adhesive pilins were fused to maltose binding protein (MBP). These hybrid proteins bound epithelial cells with the same affinity. Truncated MBP pilin fusions identified a cell-binding domain within the 77 residues of the N-terminal end of mature pilin. This region of the protein is common to low- and high-adhesive derivatives used in this work, thus eliminating the possibility that high adhesiveness conferred by some pilin variants was because of the generation of a new pilus-associated ligand. Electron-microscopic examination showed that low-adhesive derivatives expressed long and distinct pili and adhered as single cells. In contrast, pili of derivatives expressing high-adhesive pilins, either wild type or mutagenized from the low-adhesive variant, formed large bundles which bound bacteria and caused them to grow as colonies on infected monolayers. These data demonstrate that aggregative pili promote high adhesiveness of encapsulated MC.

Amino Acid Sequence↗

Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone.

Intraclonal genome diversity of Pseudomonas aeruginosa was studied in one of the most diverse mosaic regions of the P. aeruginosa chromosome. The ca. 110-kb large hypervariable region located near the lipH gene in two members of the predominant P. aeruginosa clone C, strain C and strain SG17M, was sequenced. In both strains the region consists of an individual strain-specific gene island of 111 (strain C) or 106 (SG17M) open reading frames (ORFs) and of a 7-kb stretch of clone C-specific sequence of 9 ORFs. The gene islands are integrated into conserved tRNA(Gly) genes and have a bipartite structure. The first part adjacent to the tRNA gene consists of strain-specific ORFs encoding metabolic functions and transporters, the majority of which have homologs of known function in other eubacteria, such as hemophores, cytochrome c biosynthesis, or mercury resistance. The second part is made up mostly of ORFs of yet-unknown function. Forty-seven of these ORFs are mutual homologs with a pairwise amino acid sequence identity of 35 to 88% and are arranged in the same order in the two gene islands. We hypothesize that this novel type of gene island derives from mobile elements which, upon integration, endow the recipient with strain-specific metabolic properties, thus possibly conferring on it a selective advantage in its specific habitat.

Bacterial Proteins↗

The capsid protein of vesicular exanthema of swine virus serotype A48: relationship to the capsid protein of other animal caliciviruses.

Vesicular exanthema of swine virus (VESV), the prototype calicivirus, is the etiologic agent of the porcine disease vesicular exanthema of swine (VES). VES is characterized by vesicle formation on the extremities, mouth and snout and causes abortions and stillbirths if infection occurs during pregnancy. VESV is considered an exotic agent in the US, following its eradication in 1956. The single capsid protein gene of VESV serotype A48 was cloned and sequenced. The capsid amino acid sequence was 69% similar to the San Miguel sea lion virus serotype 1 (SMSV 1) and 89% similar to the SMSV serotype 4 (SMSV 4) capsid proteins. The six functional regions (A-F) previously identified in SMSV 1, SMSV 4, feline calicivirus and rabbit hemorrhagic disease virus capsid proteins were present in VESV A48. Two sets of PCR primers were designed which directed amplification of the 5' end (A region) and the hypervariable (E region) sequences of the capsid protein precursor gene of these viruses, as well as seven additional SMSV serotypes. Alignment and phylogenetic analysis of the N-terminal sequences demonstrated the close relationship of these viruses. Alignment of the hypervariable region amino acid sequences of the ten viruses confirmed that a great variety of sequence exists in this region; however, a consensus sequence (NxT(N/H)F(K/R)GxYI(C/M)GxLx(T/R)) was derived which is also present in the feline calicivirus capsid protein. Comparison of the E region sequences provides further evidence that this area of animal calicivirus capsid protein may contain the major antigenic determinants.

Amino Acid Sequence↗

Genetic polymorphism of the 3' VNTR region of the human dopaminergic function gene DAT1 (human dopamine transporter gene) in the Mongolian population.

The hypervariable region of the dopamine transporter gene (DAT1) was amplified from samples in the Mongolian population. This region includes a variable number of tandem repeats of a 40-bp core unit in the 3' untranslated region of DAT1. Vandenbergh et al. (1992) reported variability in the number of repeats of this 3' flanking region ranging from 3 to 11 times in white and black populations. We examined polymorphism at the DAT1 locus in 78 native Mongolian subjects. We found alleles with 7 to 13 repeats, which is different from the findings of Vandenbergh et al. (1992). The allele distribution of the Mongolian population is similar to that in the Japanese population, reported previously by Nakatome et al. (1995). Chi-square analysis showed a significant lack of homogeneity between our findings in Mongolian subjects and those reported previously in white and black populations. The DAT1 locus was estimated to have a heterozygosity index of 14.1%, and the polymorphic information content was calculated to be 0.16.

Base Sequence↗

[Highly polymorphic regions of the genes for apolipoprotein B and angiotensin-converting enzyme in the Udmurt population].

The hypervariable regions of the 3'-end of the apolipoprotein B gene (APOB3'-VNTR) and angiotensin converting enzyme gene (ACE), which had 10-15 alleles each, were studied in a sample from the Udmurt population by means of polymerase chain reaction (PCR). From the literature data, the genetic position of Udmurts among 12 groups of Caucasoid, Mongoloid, and Negroid populations was determined. The data obtained by the method of principal components indicated that Udmurts held an isolated position in the northern branch of the Caucasoid race.

Alleles↗

Human rotavirus VP4 contains strain-specific, serotype-specific and cross-reactive neutralization sites.

The neutralization epitopes of human rotavirus VP4 were studied by using a panel of neutralization monoclonal antibodies previously shown to be strain-specific (RV-3:3), serotype-specific (RV-5:2, ST-3:3) or cross-reactive (F45:4). Antigenic variants of human rotaviruses RV-3, ST-3, RV-5 and F45 resistant to neutralization by the appropriate of VP4 specific monoclonal antibodies (RV-3:3, ST-3:3, RV-5:2 and F45:4 respectively) were selected. By nucleotide sequence analysis and single strand conformational polymorphism analysis of these variants, three sites of neutralization on VP5* and one site on VP8* were identified. At or near to the putative fusion region on VP5*, a strain-specific site (aa383), a serotype P1A-P2 cross-reactive site (aa392) and a serotype P2-specific site (aa397) were found. On VP8*, a serotype P1B-specific site at aa148 was detected. These results confirmed the importance of the putative fusion region in neutralization and have identified a new neutralization site in the hypervariable region of VP8* which is specific for serotype P1B human rotaviruses.

Amino Acid Sequence↗

Non-specific cross-reacting antigen: characterization of specific and cross-reacting epitopes.

A cDNA for NCA-50 was cloned into the inducible expression vector pTRB1, using the polylinker site at the C-terminus of the lac Z' gene. An NCA-specific MAb (N1), NCA and CEA cross-reactive MAbs (T84.1, 192) and polyclonal antisera (anti-NCA and anti-CEA, as well as anti-PS beta G) detected the fusion protein, with a mol. wt of 155,000, which constituted about 5% of the total bacterial protein. Deletion and mutation analysis showed that all MAbs which stained positive in western blots mapped to a small region within the last third of the N-terminal domain. Superimposition of the deduced amino acid sequence of NCA-50 on the known structure of immunoglobulins reveals that the antigenic region is located on a surface loop, which corresponds to a fourth hypervariable region on the immunoglobulin heavy chain variable regions. By oligonucleotide directed site-specific mutagenesis amino acids were deduced, which constitute part of an epitope, to which the NCA-50-specific MAb, N1, binds.

Amino Acid Sequence↗

Nucleotide sequence analysis of the env gene of a new Zairian isolate of HIV-1.

As a further step in the continuing process of defining the extent and nature of variability of the envelope (env) gene of HIV-1, we have cloned a new Zairian isolate, JY1, and sequenced the env gene of this isolate. Although the restriction map of the env region of JY1 was found to be more similar to that of the American prototype, BH10, than maps of all previously reported Zairian isolates and some American isolates, nucleotide sequencing of the JY1 env gene showed that it is among the most divergent from BH10 yet reported and that it differs from previously reported Zairian isolates almost to the same extent that it differs from BH10. A typical pattern of variable and constant regions was seen. A number of complex duplications were found in the hypervariable regions of JY1. The unique and highly divergent nature of the env gene of JY1 enhances its usefulness as part of a panel of HIV-1 isolates being evaluated in biologic and immunologic studies toward vaccine development.

Amino Acid Sequence↗

Molecular epidemiology of a hepatitis C virus outbreak in a hemodialysis unit.

We analyzed a hepatitis C virus (HCV) transmission case in the hemodialysis unit of a private clinic by sequencing two genome regions of virus isolates from a number of patients attending this unit and some external controls. The analysis of 337 nucleotides (nt) in the NS5B region did not provide enough resolution to ascertain which patients were actually involved in the outbreak and the potential source. Nevertheless, this region allowed the exclusion of several patients as putative sources of the transmission case based on their genotypes and phylogenetic relationships. On the other hand, the analysis of several 472-nt-long clone sequences per sample in a more rapidly evolving region of the HCV genome, coding for the envelope proteins and encompassing hypervariable region 1, allowed us to establish the existence of at least two independent transmission events involving two different source patients and three recipients. The direction of the transmissions was further corroborated by different measures of genetic variability within and among samples.

Cross Infection↗

Beta-D-glycan synthases and the CesA gene family: lessons to be learned from the mixed-linkage (1-->3),(1-->4)beta-D-glucan synthase.

Cellulose synthase genes (CesAs) encode a broad range of processive glycosyltransferases that synthesize (1-->4)beta-D-glycosyl units. The proteins predicted to be encoded by these genes contain up to eight membrane-spanning domains and four 'U-motifs' with conserved aspartate residues and a QxxRW motif that are essential for substrate binding and catalysis. In higher plants, the domain structure includes two plant-specific regions, one that is relatively conserved and a second, so-called 'hypervariable region' (HVR). Analysis of the phylogenetic relationships among members of the CesA multi-gene families from two grass species, Oryza sativa and Zea mays, with Arabidopsis thaliana and other dicotyledonous species reveals that the CesA genes cluster into several distinct sub-classes. Whereas some sub-classes are populated by CesAs from all species, two sub-classes are populated solely by CesAs from grass species. The sub-class identity is primarily defined by the HVR, and the sequence in this region does not vary substantially among members of the same sub-class. Hence, we suggest that the region is more aptly termed a 'class-specific region' (CSR). Several motifs containing cysteine, basic, acidic and aromatic residues indicate that the CSR may function in substrate binding specificity and catalysis. Similar motifs are conserved in bacterial cellulose synthases, the Dictyostelium discoideum cellulose synthase, and other processive glycosyltransferases involved in the synthesis of non-cellulosic polymers with (1-->4)beta-linked backbones, including chitin, heparan, and hyaluronan. These analyses re-open the question whether all the CesA genes encode cellulose synthases or whether some of the sub-class members may encode other non-cellulosic (1-->4)beta-glycan synthases in plants. For example, the mixed-linkage (1-->3)(1-->4)beta-D-glucan synthase is found specifically in grasses and possesses many features more similar to those of cellulose synthase than to those of other beta-linked cross-linking glycans. In this respect, the enzymatic properties of the mixed-linkage beta-glucan synthases not only provide special insight into the mechanisms of (1-->4)beta-glycan synthesis but may also uncover the genes that encode the synthases themselves.

Amino Acid Sequence↗

Genomic and antigenic variations of porcine reproductive and respiratory syndrome virus major envelope GP5 glycoprotein.

The objective of the present study was to evaluate the importance of genomic and antigenic variations which may have affected the major envelope glycoprotein GP5 of porcine reproductive and respiratory syndrome virus (PRRSV) isolates responsible for outbreaks in Quebec and Ontario, in comparison with the modified-live U.S. vaccine strain (MLV) and the European prototype strain from Lelystad (LV). Nucleotide sequence analyses of the open reading frame (ORF)5 genes showed that all of the isolates studied were heterogenous, amino acid (aa) identities varied from 88 to 99% with the MLV strain, and between 51 and 54% with the LV strain. The aa substitutions were randomly scattered across the protein, although one region between residues 26 and 39 was found to correspond to a hypervariable region which involved 0 to 3 potential N-glycosylation sites. The ORF5 encoded products of 5 of these isolates, including the MLV and LV strains, were expressed in E. coli as recombinant proteins fused to the glutathione S-transferase (GST) protein and used to raise hyperimmune anti-ORF5 sera in rabbits. The reactivity patterns of strain-specific hyperimmune anti-ORF5 sera and a panel of 4 monoclonal antibodies directed against the ORF5 gene product of the Quebec IAF-Klop strain of PRRSV, indicated that GP5 of field isolates also underwent antigenic variations. The data suggest that neutralizing epitopes, independent of conformation and glycosylation, are also associated with antigenic variability of the GP5 of PRRSV.

Amino Acid Sequence↗

A family exhibiting heteroplasmy in the human mitochondrial DNA control region reveals both somatic mosaicism and pronounced segregation of mitotypes.

A family exhibiting heteroplasmy at position 16355 in hypervariable region I of the human mtDNA control region has been identified. This family consists of a mother, daughter, and son. DNA samples extracted from blood stains, buccal swabs, and hairs from these individuals were amplified by PCR and sequenced utilizing fluoresence-labeled dye terminator chemistry in an automated DNA sequencer. In both the daughter and mother, heteroplasmy was observed in DNA extracted from blood stains, buccal swabs, and hairs. In the blood stains, the proportion of cytosine was greater than thymine in both individuals. Buccal swab extracts showed a more balanced contribution from the two nucleotides. Telogenic hair root and hair shaft samples exhibited a wide range of nucleotide contributions at this position, from predominately cytosine in some samples to predominately thymine in others. The apparent stochastic segregation of mitotypes in hair samples is discussed from a forensic viewpoint, and the mechanism of mtDNA heteroplasmy is considered.

DNA, Mitochondrial↗