5''-terminal nucleotide sequences of the Rauscher leukemia virus and gibbon ape leukemia virus genomes exhibit a high degree of correspondence.

The 5'-terminal regions of gibbon ape leukemia virus-Hall's Island and Rauscher murine leukemia virus have been completely sequenced. The chain length for the 5'-terminal region of Rauscher murine leukemia virus is 140 nucleotides, and that for gibbon ape leukemia virus-Hall's Island is 144 nucleotides. An alignment of the sequences maximizing the number of ocrrespondences with the minimum introduction of gaps shows 81% nucleotide matches. From the complementary RNA, secondary structures of this region have been proposed. These data demonstrate the conservation of the 5'-terminal genetic sequences of these viruses and strongly reinforce the concept that viruses of murine origin and viruses of the gibbon ape leukemia virus-Simian sarcoma-associated virus group are closely related.     

Quantitative analysis of the rescue of RNA sequences by mammalian type C viruses.

The specificity and quantitation of the rescue of RNA sequences by mammalian type C viruses has been investigated. Type C virus can package with specificity only type C viral RNA. Type C viruses do not encapsidate with comparable efficiency either type B viral or cellular globin mRNA. Conversely, a non-type C mammalian retravirus, MP-MV, cannot encapsidate type C RNA. A revertant of Kirsten sarcoma virus (Ki-SV)-transformed nonproducer cells which fails to rescue biologically active Ki-SV after superinfection with helper virus had no detectable intracellular Ki-SV-specific RNA. The results suggest specific mechanisms by which type C viral proteins can package type C viral RNA and provide an approach to classifying RNA of potentially defective endogenous retraviruses as type C in origin.     

The 3''-terminal nucleotide sequences of adenovirus types 2 and 5 DNA.

Short nucleotide sequences at the 3'-termini of adenovirus types 2 and 5 DNA have been determined using T4 DNA polymerase as described by P. T. Englund (1972). The terminal sequences of both serotypes appear to be completely identical. Both molecular ends of type 2 as well as of type 5 DNA terminate with the sequence ...pCpC...pGpApTpG3', consistent with the presence of an inverted terminal repetition in adenovirus DNA.     

Alignment of U3 region sequences of mammalian type C viruses: identification of highly conserved motifs and implications for enhancer design.

We aligned published sequences for the U3 region of 35 type C mammalian retroviruses. The alignment reveals that certain sequence motifs within the U3 region are strikingly conserved. A number of these motifs correspond to previously identified sites. In particular, we found that the enhancer region of most of the viruses examined contains a binding site for leukemia virus factor b, a viral corelike element, the consensus motif for nuclear factor 1, and the glucocorticoid response element. Most viruses containing more than one copy of enhancer sequences include these binding sites in both copies of the repeat. We consider this set of binding sites to constitute a framework for the enhancers of this set of viruses. Other highly conserved motifs in the U3 region include the retrovirus inverted repeat sequence, a negative regulatory element, and the CCAAT and TATA boxes. In addition, we identified two novel motifs in the promoter region that were exceptionally highly conserved but have not been previously described.     

There appear to be conserved constraints on the distribution of nucleotide sequences in cellular genomes

Summary The data from a genomic library can be sorted into the frequencies of every possible tetranucleotide in the sequence. This tabulation, a short sequence distribution, contains the frequency of occurrence of the 256 tetranucleotides and thus seems to serve as a vehicle for averaging sequence information. Two such distributions can be readily compared by correlation. Reported here are correlations (Spearmanr _s) of the distributions from all of the genomic libraries in GenBank 44.0 with sizes equal to or larger than that ofSalmonella typhimurium, except for the data for mouse and humans. All of the organisms examined showed highly significant correlations between the two DNA strands (not the complementarity expected from base pairing). Of 155 comparisons between libraries, 132 showed significant correlations at the 99% confidence level. Application of the correlation coefficients as a similarity matrix clustered most organisms in a phenogram in a pattern consistent with other hypotheses. This suggests a highly conserved pattern underlying all other genetic information in cellular DNA and affecting both DNA strands, perhaps caused by interaction with conserved factors necessary for DNA packaging.     

Comparative studies on the structural phosphoproteins of mammalian type C viruses.

The major phosphoprotein common to woolly monkey sarcoma virus, gibbon ape lymphosarcoma virus, and type C viruses of the lower mammalian species (mouse, rat, cat), with the exception of the endogenous cat virus (RD-114), is the polypeptide of about 12,000 molecular weight. The protein-phosphate bond in this polypeptide of several viruses is of the phosphoserine variety excepting gibbon ape virus, which contains both phosphoserine and phosphothreonine. The primary phosphoprotein of RD-114 virus and the endogenous baboon type C virus, on the other hand, is the polypeptide of about 15,000 molecular weight which contains phosphothreonine as its phosphoamino acid. A second major phosphoprotein of molecular weight of 10,000 is detected only in viruses genetically related to rat species including those derived from the RPL cell line, from Sprague-Dawley rat embryo cells, and the Kirsten mouse sarcoma virus which was recovered from a mouse erythroblastosis virus after in vivo propagation through rat. These phosphorylated polypeptides of molecular weight 15,000, 12,000, or 10,000 are present in the virion structure in several different but nonrandom phosphorylated states.     

Prokaryotic SPHINX replication sequences are conserved in mammalian brain and participate in neurodegeneration

A new class of viral mammalian Slow Progressive Hidden INfections of variable (X) latency (“SPHINX”) DNAs, represented by the 1.8 and 2.4 kb nuclease-protected circular elements, were discovered in highly infectious cytoplasmic particles isolated from Creutzfeldt-Jakob Disease (CJD) and scrapie samples. These DNAs contained replication initiation sequences (REPs) with approximately 70% homology to those of environmental Acinetobacter phage. Antibodies against REP peptides from the 1.8 kb DNA highlighted a 41 kDa protein (spx) on Western blots, and in situ studies previously revealed its peripheral tissue expression, for example, in pancreatic islet cells, keratinocytes, kidney tubules, and oocytes but not pancreatic exocrine cells, alveoli, and striated muscle. To determine if spx concentrated in specific neurons and synapses, and also maintained a conserved pattern of architectural organization in mammalian brains, we evaluated mouse, rat, hamster, guinea pig (GP), and human samples. Most outstanding was the cross-species concentration of spx in huge excitatory synapses of mossy fibers and small internal granule neuron synapses, the only excitatory neuron within the cerebellum. Spx also localized to excitatory glutamate type synapses in the hippocampus, and both cerebellar and hippocampal synaptic spx was demonstrable ultrastructurally. Studies of two well-characterized models of sporadic CJD (sCJD) revealed novel spx pathology. Vacuolar loss of cerebellar synaptic complexes, thinning of the internal granule cell layer, and fibrillar spx accumulations within Purkinje neurons were prominent in sCJD GP brains. In rats, comparable spx fibrillar changes appeared in hippocampal pyramidal neurons, and they preceded prion protein misfolding. Hence, spx is an integral player in progressive neurodegeneration. The evolutionary origin, spread, and neuropathology of SPHINX 1.8 REP sequences opens another unanticipated chapter for mammalian symbiotic interactions with environmental microbes.     

Recognition sequences of type II restriction systems are constrained by the G + C content of host genomes

I show that the recognition sequences of Type II restriction systems are correlated with the G + C content of the host bacterial DNA. Almost all restriction systems with G + C rich tetranucleotide recognition sequences are found in species with A + T rich genomes, whereas G + C rich hexanucleotide and octanucleotide recognition sequences are found almost exclusively in species with G + C rich genomes. Most hexanucleotide recognition sequences found in species with A + T rich genomes are A + T rich. This distribution eliminates a substantial proportion of the potential variance in the frequency of restriction recognition sequences in the host genomes. As a consequence, almost all restriction recognition sequences, including those eight base pairs in length (Not I and Sfi I), are predicted to occur with a frequency ranging from once every 300 to once every 5,000 base pairs in the host genome. Since the G + C content of bacteriophage DNA and of the host genome are also correlated, the data presented is evidence that most Type II "restriction systems" are indeed involved in phage restriction.     

Avian reticuloendotheliosis viruses: evolutionary linkage with mammalian type C retroviruses.

Reticuloendotheliosis viruses have been shown to be causative of tumors in a variety of avian species. The major structural protein of these non-genetically transmitted viruses is demonstrated to possess antigenic determinants common to those of all known mammalian type C viruses. These findings establish a mammalian origin for this oncogenic avian retrovirus group. None of the known mammalian type C virus groups demonstrated a closer immunological relationship to avian reticuloendotheliosis viruses. These results suggest that reticuloendotheliosis viruses have been non-genetically transmitted for a long period of evolution or that these viruses may have arisen by relatively recent infection of birds with an as yet undiscovered mammalian type C retrovirus.     

Nucleotide sequences in the RNA of mammalian leukemia and sarcoma viruses.

The nucleotide sequences in viral RNA from purified murine sarcoma and hamster leukemia viruses (S+H+) from HTG-1 cells and Rauscher leukemia virus (RLV) from JLS-V 9 cells have been examined by polynucleotide agarose affinity chromatography. There is at least one copy of poly(A) sequences per genomic viral RNA molecule. After heat denaturation of genomic viral RNA (S+H+), there are two types of viral subunits for 34S and 28S species: one that contains poly(A) sequences and one that does not. There are no detectable poly(U) tracts in the viral RNA. However, poly(C) sequences and poly(G) tracts were detected in viral RNA, although less poly(G) than poly(C) tracts were observed. In addition, heat-denatured genomic viral RNA has a greater affinity for poly(G) agarose column than native genomic viral RNA.     

Evolutionary growth process of highly conserved sequences in vertebrate genomes

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage.     

新城疫病毒非编码序列的遗传演化趋势

【目的】探讨新城疫病毒全基因序列中非编码序列的分子演化规律。【方法】结合本研究室2012年自产蛋下降鸭群中分离测序的一株鸭源新城疫病毒全序列,从GenBank下载35株不同基因型新城疫病毒全长cDNA序列,获取非编码序列,分别绘制引导序列、尾随序列、F-HN及HN-L基因间隔序列(IGS)的遗传进化树,比较编码基因内5’及3’UTR序列核苷酸序列替代特点。【结果】非编码序列的长度及位置高度保守,而其核苷酸基因序列在不断发生变异,且变异趋势与编码基因序列相一致。【结论】新城疫病毒在整个基因组上编码和非编码序列同步发生变异。