Number Of Amino Acid Changes Research Articles

The molecular basis of adaptive evolution of squirrelfish rhodopsins.

The wavelengths of maximal absorption (lambdamax) of the rhodopsins of nine squirrelfishes (N. sammara, N. argenteus, S. punctatissimum, S. microstoma, S. diadema, S. xantherythrum, S. spiniferum, N. aurolineatus, and S. tiere) and two soldierfishes (M. violacea and M. berndti) vary between 481 and 502 nm. Phylogenetic and mutagenesis analyses suggest that the common ancestor of these pigments had a lambdamax value of approximately 493 nm, and the contemporary lambdamax values were generated mostly by amino acid replacements E122M, F261Y, and A292S. The probability of observing all these amino acid replacements at specific branches of the phylogenetic tree is only 2.5 x 10(-9); it is highly unlikely that these changes have occurred by neutral evolution. Because of a close association between the lambdamax values of these pigments and the wavelengths of light available to the corresponding species, the excess number of amino acid changes at specific branches in the phylogenetic tree strongly suggests that the rhodopsins have undergone adaptive changes at various stages of the holocentrid evolution.

Update of the standard numbering scheme for class B beta-lactamases.

Update of the standard numbering scheme for class B beta-lactamases.

Human-Specific Amino Acid Changes Found in 103 Protein-Coding Genes

We humans have many characteristics that are different from those of the great apes. These human-specific characters must have arisen through mutations accumulated in the genome of our direct ancestor after the divergence of the last common ancestor with chimpanzee. Gene trees of human and great apes are necessary for extracting these human-specific genetic changes. We conducted a systematic analysis of 103 protein-coding genes for human, chimpanzee, gorilla, and orangutan. Nucleotide sequences for 18 genes were newly determined for this study, and those for the remaining genes were retrieved from the DDBJ/EMBL/GenBank database. The total number of amino acid changes in the human lineage was 147 for 26,199 codons (0.56%). The total number of amino acid changes in the human genome was, thus, estimated to be about 80,000. We applied the acceleration index test and Fisher's synonymous/nonsynonymous exact test for each gene tree to detect any human-specific enhancement of amino acid changes compared with ape branches. Six and two genes were shown to have significantly higher nonsynonymous changes at the human lineage from the acceleration index and exact tests, respectively. We also compared the distribution of the differences of the nonsynonymous substitutions on the human lineage and those on the great ape lineage. Two genes were more conserved in the ape lineage, whereas one gene was more conserved in the human lineage. These results suggest that a small proportion of protein-coding genes started to evolve differently in the human lineage after it diverged from the ape lineage.

Fine mapping of the interaction of neutralizing and nonneutralizing monoclonal antibodies with the CD4 binding site of human immunodeficiency virus type 1 gp120.

Alanine scanning mutagenesis was performed on monomeric gp120 of human immunodeficiency virus type 1 to systematically identify residues important for gp120 recognition by neutralizing and nonneutralizing monoclonal antibodies (MAbs) to the CD4 binding site (CD4bs). Substitutions that affected the binding of broadly neutralizing antibody b12 were compared to substitutions that affected the binding of CD4 and of two nonneutralizing anti-CD4bs antibodies (b3 and b6) with affinities for monomeric gp120 comparable to that of b12. Not surprisingly, the sensitivities to a number of amino acid changes were similar for the MAbs and for CD4. However, in contrast to what was seen for the MAbs, no enhancing mutations were observed for CD4, suggesting that the virus has evolved toward an optimal gp120-CD4 interaction. Although the epitope maps of the MAbs overlapped, a number of key differences between b12 and the other two antibodies were observed. These differences may explain why b12, in contrast to nonneutralizing antibodies, is able to interact not only with monomeric gp120 but also with functional oligomeric gp120 at the virion surface. Neutralization assays performed with pseudovirions bearing envelopes from a selection of alanine mutants mostly showed a reasonable correlation between the effects of the mutations on b12 binding to monomeric gp120 and neutralization efficacy. However, some mutations produced an effect on b12 neutralization counter to that predicted from gp120 binding data. It appears that these mutations have different effects on the b12 epitope on monomeric gp120 and functional oligomeric gp120. To determine whether monomeric gp120 can be engineered to preferentially bind MAb b12, recombinant gp120s were generated containing combinations of alanine substitutions shown to uniquely enhance b12 binding. Whereas b12 binding was maintained or increased, binding by five nonneutralizing anti-CD4bs MAbs (b3, b6, F105, 15e, and F91) was reduced or completely abolished. These reengineered gp120s are prospective immunogens that may prove capable of eliciting broadly neutralizing antibodies.

Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies.

Pax genes are defined by the presence of a paired box that encodes a DNA-binding domain of 128 amino acids. They are involved in the development of the central nervous system, organogenesis, and oncogenesis. The known Pax genes are divided into five groups within two supergroups. By means of a novel combination of evolutionary analysis, in vitro binding assays and in vivo functional analyses, we have identified the key residues that determine the differing DNA-binding properties of the two supergroups and of the Pax-2, 5, 8 and Pax-6 subgroups within supergroup I. The differences in binding properties between the two supergroups are largely caused by amino acid changes at residues 20 and 121 of the paired domain. Although the paired domains of the Pax-2, 5, 8 and the Pax-6 group differ by >19 amino acids, their distinct DNA-binding properties are determined almost completely by a single amino acid change. Thus, a small number of amino acid changes can account in large part for the divergence in binding properties among the known paired domains. Our approach for selecting candidate sites responsible for the functional divergence between genes should also be useful for studying other gene families.

The Function of OmpA in Escherichia coli

Outer membrane protein A (OmpA) is a major protein in the Escherichia coli outer membrane. In this study, the function of OmpA in E. coli stress survival was examined. An E. coli K1 ompA-deletion mutant was significantly more sensitive than that of its parent strain to sodium dodecyl sulfate (SDS), cholate, acidic environment, high osmolarity, and pooled human serum. A number of amino acid changes at the extracellular loops of OmpA did not affect the viability of E. coli, while short peptide insertions in the periplasmic turns of the OmpA β-barrel decreased E. coli resistance to environmental stresses. Moreover, ompA mutants were found to survive much better within brain microvascular endothelial cells than the wild-type strain, supporting that OmpA is a major target in mammalian host cell defense. These results indicated that OmpA plays a vital structural role in E. coli, and suggested that a perfect β-barrel structure of OmpA is important for outer membrane stability. Based on these results and the published OmpA structural analyses, I propose that OmpA is composed of three functional domains including a hydrophilic extracellular mass, a β-barrel transmembrane structure, and a peptidoglycan binding domain.

Genetic characterization of wild-type genotype VII hepatitis A virus.

The complete genome sequence of the only identified genotype VII hepatitis A virus (HAV), strain SLF88, was obtained from PCR amplicons generated by a modified long PCR approach. There was 90% nucleotide identity in the 5' untranslated region compared to other known HAV sequences. In the remainder of the genome containing the long open reading frame, there was about 85% nucleotide identity to human HAV genotypes IA and IB and 80% identity to simian HAV genotype V. Compared to HAV strain HM-175, the capsid amino acids were highly conserved, with only four homologous amino acid changes, while an increasing number of amino acid differences was seen in the P2 and P3 genome regions. While nucleotide variability within the three functional coding regions did not differ, the P3D region was found to have the largest number of amino acid changes compared to HM-175.

High amino acid variability within the NS5A of hepatitis C virus (HCV) is associated with hepatocellular carcinoma in patients with HCV-1b–related cirrhosis

Interferon therapy may decrease the risk of hepatocellular carcinoma in patients with hepatitis C virus (HCV)-related liver cirrhosis. Interaction of the cellular protein kinase PKR with the PKR-binding domain (PKR-bd) of HCV-NS5A protein may affect cellular growth control and viral resistance to interferon therapy. Mutations within the PKR-bd, which comprises the interferon sensitivity determining region (ISDR), have been associated with interferon sensitivity. To determine whether or not there is an association between HCV heterogeneity and the presence of hepatocellular carcinoma, HCV-1b genomic regions were amplified and directly sequenced from serum samples obtained from 82 patients with liver cirrhosis, 53 with, and 29 without hepatocellular carcinoma. None of them had received antiviral therapy. When compared with the deduced consensus sequence, the median number of amino acid changes in the PKR-bd was higher among samples from patients with (4.22) than from those without hepatocellular carcinoma (1.62; P < .001), and isolates with 3 or more amino acid changes were significantly more common among the former (60%) than among the later (6%, P < .001). No such differences were observed in other viral regions, including Core, E2-HVR-1, E2-PePHD, NS3, and the 5′ and 3′ PKR-bd flanking regions. In addition, amino acid variation in viral regions other than HVR-1 did not accumulate over time in the analyzed sequential serum samples obtained from patients with or without hepatocellular carcinoma. Therefore, a mutated HCV-PKR-bd phenotype is very common in cirrhotic patients with hepatocellular carcinoma. (HEPATOLOGY 2001;34:158-167.)

Molecular Analysis of the Epidermal Growth Factor-like Short Consensus Repeat Domain-mediated Protein-Protein Interactions: DISSECTION OF THE CD97-CD55 COMPLEX

Epidermal growth factor-like (EGF) and short consensus repeat (SCR) domains are commonly found in cell surface and soluble proteins that mediate specific protein-protein recognition events. Unlike the immunoglobulin (Ig) superfamily, very little is known about the general properties of intermolecular interactions encoded by these common modules, and in particular, how specificity of binding is achieved. We have dissected the binding of CD97 (a member of the EGF-TM7 family) to the complement regulator CD55, two cell surface modular proteins that contain EGF and SCR domains, respectively. We demonstrate that the interaction is mediated solely by these domains and is characterized by a low affinity (86 microm) and rapid off-rate (at least 0.6 s(-1)). The interaction is Ca(2+) -dependent but is unaffected by glycosylation of the EGF domains. Using biotinylated multimerized peptides in cell binding assays and surface plasmon resonance, we show that a CD97-related EGF-TM7 molecule (termed EMR2), differing by only three amino acids within the EGF domains, binds CD55 with a K(D) at least an order of magnitude weaker than that of CD97. These results suggest that low affinity cell-cell interactions may be a general feature of highly expressed cell surface proteins and that specificity of SCR-EGF binding can be finely tuned by a small number of amino acid changes on the EGF module surface.

Differential selection after duplication in mammalian developmental genes.

Gene duplication provides the opportunity for subsequent refinement of distinct functions of the duplicated copies. Either through changes in coding sequence or changes in regulatory regions, duplicate copies appear to obtain new or tissue-specific functions. If this divergence were driven by natural selection, we would expect duplicated copies to have differentiated patterns of substitutions. We tested this hypothesis using genes that duplicated before the human/mouse split and whose orthologous relations were clear. The null hypothesis is that the number of amino acid changes between humans and mice was distributed similarly across different paralogs. We used a method modified from Tang and Lewontin to detect heterogeneity in the amino acid substitution pattern between those different paralogs. Our results show that many of the paralogous gene pairs appear to be under differential selection in the human/mouse comparison. The properties that led to diversification appear to have arisen before the split of the human and mouse lineages. Further study of the diverged genes revealed insights regarding the patterns of amino acid substitution that resulted in differences in function and/or expression of these genes. This approach has utility in the study of newly identified members of gene families in genomewide data mining and for contrasting the merits of alternative hypotheses for the evolutionary divergence of function of duplicated genes.

Mutations of Respiratory Syncytial Virus Attachment Glycoprotein G Associated with Resistance to Neutralization by Primate Polyclonal Antibodies

The respiratory syncytial (RS) virus attachment glycoprotein G is a type II transmembrane glycoprotein and an important target of the host immune response. Antigenic variability of the G protein is postulated to contribute to the ability of the virus to evade established immune responses. A glycoprotein G monospecific polyclonal antiserum from a nonhuman primate was used to select for an antibody resistant RS virus. The mutant virus was resistant to neutralization by the selecting antiserum and by the sera from three other G-protein immunized primates. G-protein amino acid changes were found at residues 61 (Phe to Leu), 174 (Ser to Cys), and 183 (Trp to Leu). Thus the mutant protein had amino acid changes in the transmembrane domain (61) and the central ectodomain (174 and 183). The change at amino acid 174 resulted in five rather than the usual four Cys found in the conserved central region of the ectodomain. These data demonstrate that an RS virus with resistance to neutralization by polyclonal antibodies can be selected readily in cell culture. In addition, only a limited number of amino acid changes is required to produce the resistant phenotype.

Genetic alterations in the S gene of hepatitis B virus in patients with acute hepatitis B, chronic hepatitis B and hepatitis B liver cirrhosis before and after liver transplantation.

Several studies have shown that hepatitis B immunoglobulin (HBIG) imposes a selection pressure on the hepatitis B virus (HBV) S gene, and that the emergence of mutations in this region would make reinfection after orthotopic liver transplantation (OLT) possible. This study was undertaken to analyze the presence of HBV S-gene mutations in the different stages of HBV infection and the relationship between HBIG therapy and the emergence of mutations in liver transplant recipients. The frequency and location of mutations in the coding region of the HBV S gene were studied by PCR and direct sequencing in 30 patients (7 with acute self-limited hepatitis B, 16 with chronic hepatitis B and 7 recipients of (OLT) for HBV-related end stage liver disease who became reinfected). The average number of amino acid changes was higher in patients with a more advanced stage of disease, 0.57 mutations/100 positions in acute hepatitis B and 1.57 in chronic hepatitis B (1.28 in HBeAg-positive and 1.8 in anti-HBe-positive patients). The average number of substitutions in the transplanted patients was 2.7 before OLT and 3 after OLT. No amino acid substitutions were detected in the "a" determinant of HBsAg in acute hepatitis B, however, 8 substitutions were observed in 6 chronic patients. In 3 OLT patients, 4 substitutions were observed in samples before and after OLT. One of these patients, who had protective levels of anti-HBs, showed 3 additional new amino acid substitutions after OLT, suggesting escape mutant selection by the effect of HBIG therapy. No changes were observed between the consensus sequences obtained several years before and after transplantation, indicating consensus sequence stability. These results show that there is an accumulation of HBV S-gene mutations in HBV-related end-stage liver disease. Prophylaxis with HBIG mainly obtained from acute self-limited hepatitis patients who have a highly homogeneous viral population, may be one factor underlying the reinfection after liver transplantation.

Molecular bases of color vision in vertebrates.

Visual pigments initiate vision and are characterized by their wavelengths of maximal absorption (λmax). Modifications of the λmax values of visual pigments have allowed organisms to adapt to diverse light environments. The availability of the functional assays of these visual pigments using cultured cells makes vision an ideal genetic system to study the molecular bases of adaptation and genetics of color vision in vertebrates. The visual pigments in vertebrate retinas are distinguished into five evolutionarily distinct groups RH1 (λmax = 490-500 nm), RH2 (470-510 nm), SWS1 (360-420 nm), SWS2 (440-455), and LWS/MWS (510-570 nm). Here, we review amino acid replacements that are associated with the shifts in the λmax values of these visual pigments. The λmax-shifts in several RH1 pigments seem to reflect adaptive changes to blue environments of the organisms and are explained mostly by amino acid replacements D83N (D → N at residue 83), E122Q, and A292S. Similarly, the blue-shifts in the λmax values of the RH2 pigments can be explained by D83N, E122Q, A164S, and M207L. For the SWS1 pigments of birds, only one amino acid replacement S84C seems to be responsible for the transformation of ultraviolet pigments from the violet pigment. For the LWS/MWS pigments, the additive effects of amino acid differences at 180, 197, 277, 285, and 308 fully explain the red-green color vision in a wide range of vertebrates. All of these observations suggest that the evolution of the extant visual pigments can be explained by amino acid replacements at only a small number of sites. Visual pigments, a group of G-protein-coupled receptors, initiate visual excitation (Wald 1968). Each visual pigment consists of a transmembrane protein, opsin, and the chromophore, 11-cis-retinal, and can be characterized by its wavelength of maximal absorption (λmax). Human color vision is mediated by `blue', `green', and `red' visual pigments. The `blue' pigments absorb wavelengths ranging from about 370 nm to 570 nm with a λmax at 420 nm, while both `green' and `red' pigments are sensitive to wavelength about 450-620 nm with λmax values at 530 nm and 560 nm, respectively (Nathans 1989). The molecular bases of the spectral tuning of these and other visual pigments in vertebrates are still not well understood. Recently, however, some significant progress has been made on this subject. To evaluate the mechanisms of the functional properties of visual pigments, a large number of amino acid changes have been introduced into the bovine rod-specific visual pigment (rhodopsin) by several groups of vision scientists (for a review, see Yokoyama 1997). In most of these analyses, charged amino acids have been considered. For example, an amino acid change from glutamic acid at residue 113 (E113) to glutamine (E113Q) shifts the λmax of the pigment from 500 nm to 380 nm (Sakmar et al. 1989; Zhukovsky and Oprian 1989; Nathans 1990a, b). E113 is the negatively charged counterion to the positively charged protonated Schiff base and the modification of this opsin structure causes a drastic shift in the λmax value of the pigment. Unfortunately, most of these amino acid changes, including E113Q, have not been found in nature. Thus, it is not immediately clear how these mutagenesis results are helpful in elucidating the molecular basis for the divergence of λmax values of visual pigments in nature (Yokoyama 1995, 1997). Since this abstract exceeds the limit of the space allocated to abstract, the last paragraph has to be deleted. Please refer to PDF for the rest of the abstract.

Clinical and haematological consequences of recurrent G6PD mutations and a single new mutation causing chronic nonspherocytic haemolytic anaemia.

We have determined the causative mutation in 12 cases of glucose-6-phosphate dehydrogenase deficiency associated with chronic non-spherocytic haemolytic anaemia. In 11 of them the mutation we found had been previously reported in unrelated individuals. These mutations comprise seven different missense mutations and a 24 base pair deletion. G6PD Nara, previously found in a Japanese boy. Repeated findings of the same mutations suggests that a limited number of amino acid changes can produce the CNSHA phenotype and be compatible with normal development. The one new mutation we have found, G6PD Serres, is 1082 C-->T causing a 361 Ala-->Val substitution in the dimer interface where most other severe G6PD mutations are found. Now that several patients with the same mutation have been reported we can compare the resulting clinical phenotypes. For each mutation we find a reasonably consistent clinical picture, ranging from mild (G6PD Clinic) through moderate (G6PD Nashville) to severe (G6PD Beverly Hills and G6PD Nara).

Activation of the Xmrk proto-oncogene of Xiphophorus by overexpression and mutational alterations.

Xmrk is a receptor tyrosine kinase closely related to the human EGF receptor. In the teleost fish Xiphophorus two versions of the Xmrk gene exist, an oncogene (ONC) and a proto-oncogene (INV). While ONC-Xmrk is the melanoma-inducing gene, INV-Xmrk appears not to be involved in transformation of pigment cells. To elucidate the mechanism that converts the proto-oncogene into a transforming oncogene a comparative analysis of the structure, expression and function of both versions of the gene was performed. In contrast to ONC-Xmrk which is expressed at high levels in melanoma cells, the proto-oncogene INV-Xmrk is ubiquitously expressed at very low levels indicating overexpression as one possible reason for tumorigenicity by ONC-Xmrk. As sequence comparison of the proto-oncogene and the oncogene revealed a number of amino acid changes, a possible effect of these mutations on the activation of the ONC-Xmrk receptor was determined. A constitutive activation of the oncogenic receptor was found and ectopic expression of INV-Xmrk after microinjection into medakafish embryos did not lead to the high tumour rate in transgenic fish as observed for the oncogene. Our data therefore suggest that overexpression of the receptor alone is not sufficient for melanoma induction, but that in addition activating mutations in ONC-Xmrk are responsible for its full tumorigenic potential.

Sensitivity of human immunodeficiency virus to bicyclam derivatives is influenced by the three-dimensional structure of gp120.

The bicyclams are a new class of anti-human immunodeficiency virus (anti-HIV) compounds targeted at viral entry. From marker rescue experiments, it appears that the envelope gp120 glycoprotein plays an important role in the anti-HIV activity of the bicyclams. Bicyclam-resistant strains contain a number of amino acid changes scattered over the V2 to V5 region of gp120. Experiments aimed at estimating the relative importance of particular amino acid changes with regard to the overall resistance pattern are described. The sequences of some partially bicyclam-resistant virus strains, obtained during the resistance development process, were analyzed, and the corresponding 50% effective concentrations were determined. Selected mutations observed in bicyclam-resistant strains were introduced in the wild-type background by site-directed mutagenesis. In addition, some amino acids were back-mutated to their wild-type counterparts in an otherwise JM3100-resistant strain. The sensitivities of these mutant viruses to bicyclams were determined. Construction of chimeric viruses, carrying the V3 loop of JM3100-resistant virus in a wild-type HIV type 1 HXB2 background, enabled us to investigate the importance of the mutations in the V3 loop of JM3100-resistant virus. From the results described in the report, it can be concluded that single amino acid substitutions do not influence the observed resistance to JM3100. Also, the mutations in the V3 loop are not sufficient to engender even a partially resistant phenotype. We postulate that the overall conformation of gp120 determines the degree of sensitivity or resistance of HIV strains to bicyclams.

The molecular basis of virulence of the encephalitogenic flaviviruses.

Summary: Studies of flavivirus virulence have focussed on variants with differing neurovirulence or neuroinvasiveness in animal models, with the majority based on determining the contribution of viral structural proteins, in particular the envelope glycoprotein. Specific virulence determinants on protein E have recently been identified by the application of several experimental techniques such as selection and characterization of neutralization escape variants in the presence of anti-E protein MAbs or by site-directed mutagenesis of the E gene of infectious cDNA clones (see Fig. 2, Tables 2 And 3). However, the association of particular amino acid substitutions in protein E with loss of neurovirulence and/or neuroinvasiveness appears to be dependent on the virus system under study and thus the mechanism by which protein E controls these two virulence phenotypes is unclear. Existing data show that neurovirulence and neuroinvasiveness determinants map to identical regions of protein E, including the lateral surface of domain III (the putative receptor binding site) and the base of domain II (thought to be involved in pH-dependent fusion activity). Attenuation of some domain II and III variants is associated with changes in binding to cell membrane proteins or in pH-dependent fusion activity, suggesting that defects in the early events of virus replication are responsible for virulence attenuation. A small number of amino acid changes in domain I are associated with attenuation of virulence, including mutations in the protein E glycosylation site which result in significant reductions in viral glycoprotein expression. The mechanism of attenuation associated with other mutations in domain I is unknown. Several studies have identified putative neurovirulence determinants within other regions of the genome (e.g. non-structural protein genes, 3′ UTR), and in one example the mutation attenuates neurovirulence without alteration in neuroinvasiveness. Further work is necessary to map neurovirulence determinants within these regions. It is likely that significant advances in this field will come from the application of infectious cDNA clone technology.

Association between frequency of amino acid changes in core region of hepatitis B virus (HBV) and the presence of precore mutation in Japanese HBV carriers.

To elucidate the relationship between the frequency of core mutations and precore mutation of hepatitis B virus (HBV) in Japanese HBV carriers, we investigated the nucleotide sequence of the precore/core region of HBV in 26 Japanese HBV carriers [15 who were HBe antigen-negative (HBeAg-) and 11 who were HBeAg-positive (HBeAg+)]. The number of amino acid changes (5.9 +/- 3.8) in the core region of HBV in HBeAg-carriers was significantly greater than that in the HBeAg+ carriers (1.5 +/- 1.0; P < 0.005). The precore stop codon mutation was found in 93.3% of HBeAg-negative HBV carriers, while no precore mutation was found in the HBeAg-positive HBV carriers, suggesting that the frequency of core mutations may be associated with the presence of the precore stop codon mutation. However, there was no significant difference in the frequency of amino acid changes among HBeAg-HBV carriers. The mean number of core amino acid changes of liver cirrhosis patients, chronic active hepatitis patients, chronic persistent hepatitis patients, and asymptomatic carriers were 2.7 +/- 1.5, 6.0 +/- 2.2, 4.7 +/- 1.2, and 8.4 +/- 5.3, respectively. We detected hot spots for core mutations, which showed characteristic localizations and specific substitutions: Gly-87, Leu-97, and Thr-130 were detected exclusively in patients with chronic liver disease with or without HBeAg. To address further the relationship between frequency of core mutations and the presence of the precore stop codon mutation, we investigated the precore/core nucleotide sequence serially along with seroconversion in three patients with chronic hepatitis B in whom the hepatitis either became inactive or remained active after the seroconversion. Emergence of the precore stop codon mutation and a significant increase in core amino-acid changes after seroconversion were noted in all three patients. Our results suggest a close association between the frequency of core amino acid changes and the presence of the precore stop codon mutation; some characteristic core mutations may be associated with the clinical course of chronic hepatitis B in Japanese patients.

Mutations in the nonstructural 5A gene of European hepatitis C virus isolates and response to interferon alfa.

The response rate to interferon alfa (IFN-alpha) in patients infected with hepatitis C virus (HCV) genotype 1 isolates is poor. A region associated with sensitivity to IFN has been identified in subtype HCV-1b isolates from Japanese patients in the carboxyterminal half of the nonstructural protein NS5A (between codon 2209 and 2248). HCV-1b isolates with at least four amino acid changes in this region compared with the HCV-1b prototype sequence were sensitive, whereas isolates identical to the prototype sequence were resistant to IFN-alpha. Patients infected with HCV-1b isolates carrying 1 to 3 mutations in NS5A(2209-2248) showed an intermediate response pattern. Because of the large geographical differences observed for HCV it is unknown whether this putative IFN-alpha sensitivity determining region is also predictive for European isolates. We analyzed 32 patients chronically infected with HCV-1a or HCV-1b isolates who were treated with 3 million units of recombinant IFN-alpha three times per week for 1 year. Before initiation, during, and after treatment serum HCV-RNA levels were assessed by a quantitative reverse-transcription polymerase chain reaction (RT-PCR) assay. The amino acid sequence of NS5A(2209-2248)was determined by direct sequencing of the PCR-amplified HCV genome and was compared with the reference sequence HCV-J. In patients chronically infected with subtype HCV-1a or HCV-1b the initial or sustained response to IFN-alpha was not related to the number of amino acid substitutions in the NS5A(2209-2248) region. In addition, the number of amino acid changes in NS5A(2209-2248) was not related to pretreatment HCV-RNA serum levels. In three patients with a pronounced initial decline of HCV-RNA levels (>3 log) sequence analyses of NS5A(2209-2248) were performed before and after therapy. Compared with the pretreatment amino acid sequence the HCV isolates of these patients revealed more mutations in the NS5A(2209-2248) region after therapy. These findings from European patients indicate that the NS5A(2209-2248) region of HCV does not represent a common interferon sensitivity determining region.

Novel Variation in the N Protein of Avian Infectious Bronchitis Virus

The nucleocapsid protein of coronaviruses has been considered highly conserved, showing greater than 94% conservation within strains of a given species. We determined the nucleotide sequence of the N gene and the 3′ untranslated region (UTR) of eight naturally occurring strains of IBV which differed in pathogenicity and tissue tropism. In pairwise comparisons, the deduced amino acid sequences of N of five strains Vic S, N1/62, N9/74, N2/75, and V5/90 (group I) shared 92.3–98.8% identity. The three strains N1/88, Q3/88, and V18/91 (group II) shared 85.8–89.2% identity with each other, but only 60.0–63.3% identity with viruses of group I. Amino acid substitutions, deletions, and insertions occurred throughout the N protein and involved regions previously identified as being conserved. Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. In addition, all strains contained approximately 30 serine residues of which 10 were conserved, the majority occurring between positions 168 and 194. As for all other coronaviruses, the region between positions 92 and 103 was highly conserved. Hence, a large number of amino acid changes can be tolerated within the N protein without affecting its integrity or functioning. The 3′ UTR immediately downstream from the N gene was highly heterogeneous with extensive deletions occurring in the group II strains.