Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2)

The nucleotide sequence of molecular clones of DNA from a retrovirus, ARV-2, associated with the acquired immune deficiency syndrome (AIDS) was determined. Proviral DNA of ARV-2 (9737 base pairs) has long terminal repeat structures (636 base pairs) and long open reading frames encoding gag (506 codons), pol (1003 codons), and env (863 codons) genes. Two additional open reading frames were identified. Significant amino acid homology with several other retroviruses was noted in the predicted product of gag and pol, but ARV-2 was as closely related to murine and avian retroviruses as it was to human T-cell leukemia viruses (HTLV-I and HTLV-II). By means of an SV-40 vector in transfected simian cells, the cloned gag and env genes of ARV-2 were shown to express viral proteins.     

HTLV x-gene product: requirement for the env methionine initiation codon

The human T-cell leukemia viruses (HTLV) are replication-competent retroviruses whose genomes contain gag, pol, and env genes as well as a fourth gene, termed x, which is believed to be the transforming gene of HTLV. The product of the x gene is now shown to be encoded by a 2.1-kilobase messenger RNA derived by splicing of at least two introns. By means of S1 nuclease mapping of this RNA and nucleic acid sequence analysis of a complementary DNA clone, the complete primary structure of the x-gene product has been determined. It is encoded by sequences containing the env initiation codon and one nucleotide of the next codon spliced to the major open reading frame of the HTLV-I and HTLV-II x gene.     

Complete nucleotide sequence and organization of the Moloney murine sarcoma virus genome

The complete nucleotide sequence of a mammalian transforming retrovirus. Moloney murine sarcoma virus, has been determined. MSV, recombinant virus derived of helper viral and cellular sequences, possesses termini resembling prokaryotic transposable elements. The viral genome has the coding capacity for the Moloney murine leukemia virus gag gene product and contains large deletions in pol and env genes. A large open reading frame encompassing its cell-derived sequences codes for its putative transforming protein. The nature of some of the important domains in the viral genome has been established, and their structure is discussed in relation to their function.     

A new class of endogenous human retroviral genomes

Human DNA contains multiple copies of a novel class of endogenous retroviral genomes. Analysis of a human recombinant DNA clone (HLM-2) containing one such proviral genome revealed that it is a mosaic of retroviral-related sequences with the organization and length of known endogenous retroviral genomes. The HLM-2 long terminal repeat hybridized with the long terminal repeat of the squirrel monkey virus, a type D retrovirus. The HLM-2 gag and pol genes share extensive nucleotide sequence homology with those of the M432 retrovirus (a type A-related retrovirus), mouse mammary tumor virus (a type B retrovirus), and the avian Rous sarcoma virus (a type C retrovirus). Nucleotide sequence analysis revealed regions in the HLM-2 pol gene that were as much as 70 percent identical to the mouse mammary tumor virus pol gene. A portion of the putative HLM-2 env gene hybridized with the corresponding region of the M432 viral genome.     

Isolation and characterization of a novel protein (X-ORF product) from SIV and HIV-2

A protein designated p14 was purified from a simian immunodeficiency virus (SIVMne) and was shown by amino acid sequence analysis to be nearly identical to the predicted translational product of a unique open reading frame (X-ORF) in the nucleotide sequences of SIVmac and human immunodeficiency virus type 2 (HIV-2). Thus the X-ORF is proven to be a new retroviral gene. The p14 is present in SIVMne in molar amounts equivalent to those of the gag proteins. This is the first example of a retrovirus that contains a substantial quantity of a viral protein that is not a product of the gag, pro, pol, or env genes. SIV p14 and its homolog in HIV-2 may function as nucleic acid binding proteins since purified p14 binds to single-stranded nucleic acids in vitro. Antisera to the purified protein detected p14 in SIVMne, SIVmac, and a homologous protein (16 kilodaltons) in HIV-2 but did not react with HIV-1. Diagnostic procedures based on this novel protein will distinguish between HIV-1 and HIV-2.     

A new HTLV-III/LAV protein encoded by a gene found in cytopathic retroviruses

The DNA of the HTLV-III/LAV group of retroviruses contains certain additional open reading frames that are not found in typical avian or mammalian retroviruses. The role of these sequences in encoding for gene products that may be related to pathogenesis remains to be resolved. An open reading frame whose 5' end overlaps with the pol gene, but is unrelated to the env gene, has been observed in HTLV-III/LAV and visna virus, both cytopathic mammalian retroviruses. Evidence presented here shows that this open reading frame is a bona fide coding sequence of HTLV-III/LAV and that its product, a protein with a molecular weight of 23,000, induces antibody production in the natural course of infection.     

Replicative and cytopathic potential of HTLV-III/LAV with sor gene deletions

The genome of the human T-lymphotropic virus type III (HTLV-III/LAV) has the potential to encode at least three polypeptides in addition to those encoded by the gag, pol, and env genes. In this study, the product of the sor (short open reading frame) region, which overlaps the 3' end of the pol gene, was found to be a protein with a molecular weight of 23,000. An assay was developed for testing the ability of cloned HTLV-III proviruses to produce viruses cytopathic for T4+ lymphocytes. In the cell line used, C8166, neither the HTLV-III sor gene product nor the complete 3'-orf gene product were necessary for the replication or cytopathic effects of the HTLV-III.     

Expression in Escherichia coli of open reading frame gene segments of HTLV-III

Human T-cell lymphotropic virus type III (HTLV-III), the causative agent of the acquired immune deficiency syndrome (AIDS), was recently isolated and its genomic structure analyzed by DNA cloning methods. In the studies reported here a combined cloning and expression system was used to identify HTLV-III encoded peptides that react immunologically with antibodies in sera from AIDS patients. Cloned HTLV-III DNA was sheared into approximately 500-base-pair fragments and inserted into an "open reading frame" expression vector, pMR100. The inserted DNA was expressed in Escherichia coli transformants as a polypeptide fused to the lambda CI protein at its amino terminus and to beta-galactosidase at its carboxyl terminus. Sera from AIDS patients containing antibodies to HTLV-III were then used to screen for immunoreactive fusion proteins. Twenty clones, each specifying a fusion protein strongly reactive with AIDS serum, were identified. DNA sequence analysis indicated that the HTLV-III fragments were derived from the open reading frame DNA segments corresponding to the gag and pol gene coding regions and also the large open reading frame region (env-lor) located near the 3' end of the viral genome.     

Identification of HTLV-III/LAV sor gene product and detection of antibodies in human sera

The nucleotide sequence of the genome of HTLV-III, the infectious agent etiologically associated with the acquired immune deficiency syndrome, predicts a small open reading frame, termed sor, located between the pol and env genes. A DNA segment containing 82 percent of the sor region was inserted into a prokaryotic expression vector, pJL6, to determine whether sor encodes a viral protein and to gain some insight into its possible function. The bacterially synthesized sor protein reacted with sera from individuals infected with HTLV-III, indicating that sor is expressed as a protein product or products that are immunogenic in vivo. Antibodies to the purified, bacterially synthesized sor protein were found to react specifically with the same protein and also with a protein of molecular weight 23,000 (23K) in HTLV-III-infected H9 cell extracts. The 23K protein comigrated with a protein immunoprecipitated by the serum of a hemophiliac patient with antibodies to HTLV-III, suggesting that this protein is probably the sor gene product.     

Structure of genes coding the envelope proteins of the avian influenza a virus and bovine leucosis virus

This paper comparatively analyzes the density of nucleotide sequences potentially predisposed to the formation of noncanonical DNA structures (G4 quadruplexes) on the hemagglutinin (HA) and neuraminidase (NA) genes of the avian influenza A virus (H5N1) and the env and pol genes of the bovine leucosis virus. The higher genetic heterogeneity of the HA gene in comparison with the NA gene coincided with the high frequency of the nucleotide sequences predisposed to the formation of G4 quadruplexes. The same tendency was observed when comparing the distribution of potential G4 quadruplexes in the env and pol genes of the bovine leucosis virus. We discuss a possible relation between the increased density of the noncanonical DNA structures in the genes whose products interact with the receptor system of target cells of a retrovirus infection and their genetic heterogeneity maintained in the host-pathogen system.     

Sequence homology and morphologic similarity of HTLV-III and visna virus, a pathogenic lentivirus

A study was conducted of the genetic relation between human T-cell lymphotropic retroviruses and visna virus. The human T-cell lymphotropic viruses include those associated with T-cell malignancies (HTLV-I and HTLV-II) as well as the etiologic agent of the acquired immune deficiency syndrome (HTLV-III). Visna virus, a slowly replicating and pathogenic but nononcogenic retrovirus of sheep, is a member of the subfamily Lentivirinae. Results obtained by molecular hybridization and heteroduplex analysis indicated that a greater extent of nucleotide sequence homology exists between HTLV-III and visna virus than between HTLV-III and any of the other viruses. The homology observed under conditions of low stringency spanned the entire genome, but was strongest in the gag/pol region. The morphogenesis and fine structure of HTLV-III and visna virus also demonstrated striking similarities. The data provide strong evidence for a close taxonomic and thus evolutionary relation between HTLV-III and the Lentivirinae subfamily.     

禽流感病毒新疆株A/Duck/XJ/4的M基因的序列分析

利用RT-PCR技术对禽流感病毒新疆株A/Duck/XJ/4的M基因进行了扩增与克隆,得到了全长核苷酸序列为1 016 bp的M基因,序列分析表明,M基因最大的开放阅读框位于19～1 000碱基;M1蛋白位于19～777碱基,编码252个氨基酸.M2蛋白位于19～44碱基和733～1 000碱基,编码97个氨基酸.同源性分析显示,A/Duck/XJ/4 株M基因的核苷酸序列和氨基酸序列与所选H5N1亚型的参考毒株以及所选不同HA亚型的参考毒株均有很高的同源性.     

HTLV-III gag protein is processed in yeast cells by the virus pol-protease

The gag-pol gene of HTLV-III (human T-lymphotropic virus), the virus linked to AIDS (acquired immune deficiency syndrome), was expressed in yeast, and processing of the gag precursor into proteins of the same size as those in the virion was observed. Processing of the gag gene in yeast cells mimics the process that naturally occurs in mammalian cells during maturation of virions. Therefore it was possible to perform mutational analysis of the virus genome to localize the gene that codes for the protease function to the amino terminal coding region of the pol gene. Since this region overlaps the gag gene, it is likely that ribosomal frameshifting occurs from gag to pol. Antibodies in all of the AIDS patients' sera tested recognized the yeast synthesized gag proteins, although the sera showed differences in relative reactivity to the individual gag proteins and the precursor. This yeast system should be valuable not only for production of viral proteins for diagnostic or vaccine purposes but also for analysis of the genetics and biochemistry of viral gene functions--parameters that are difficult to study otherwise with this virus.     

小麦属Xa 21-类似蛋白激酶基因的克隆及与同源位点序列比较

对小麦属Xa21-类似蛋白激酶基因进行了克隆及与同源序列比较研究.在小麦(Triticum aestivum)高分子量麦谷蛋白基因位点附近有一个编码LRR-类受体蛋白激酶的基因位点(暂标记为TaXa),编码蛋白与水稻(O ryza sativa)抗病蛋白Xa 21类似.通过反转录PCR途径,从普通小麦和二粒小麦(Triticum turgidum)的TaXa同源位点分离了3个cDNA克隆,ZS 860(GenBank查询号:EF 394367),ZS 2000(GenBank查询号:EF 394368)和ZS 2001(GenBank查询号:EF 394369).TaXa位点的祖先基因可能编码1 028个氨基酸组成的多肽.一个完整的TaXa蛋白包括N-端保守区、LRR结构域、一个跨膜区和位于C—端的丝氨酸—苏氨酸蛋白激酶功能域.在基因进化过程中,由于碱基代换、缺失和插入导致了开放读码框的改变,使该位点基因的编码多肽缩短.本研究对小麦属TaXa同源位点编码氨基酸序列和1个大麦(Hordeum vulgare)中的同源蛋白进行了详细比较.     

Transcription of novel open reading frames of AIDS retrovirus during infection of lymphocytes

The retrovirus frequently isolated from patients with the acquired immune deficiency syndrome (AIDS) has two novel open reading frames previously designated "A" and "B." The "A" region was found to be specifically expressed as polyadenylated RNA's of 5.5 and 5.0 kilobases in infected cells. The "B" region was expressed as 1.8- to 2.0-kilobase RNA species. Additional full-length and spliced messenger RNA's of the env region were also identified.     

疣粒野生稻半胱氨酸蛋白酶基因ME085的cDNA全长克隆及序列分析

为了发掘疣粒野生稻抗性基因,从受白叶枯菌诱导的疣粒野生稻叶片抑制差减文库(SSH文库)中选择抗病相关的EST序列,运用cDNA末端快速扩增法(RACE)获得一个基因全长,命名为ME085。通过生物信息学分析表明该基因全长1 171bp,具有一个750bp的开放阅读框,编码249个氨基酸,其理论等电点为5.76,相对分子质量为27 580.1,存在一个明显的半胱氨酸蛋白酶结构域。推测该基因是一个半胱氨酸蛋白酶基因。