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PubMed2004

Molecular phylogeny of songbirds (Passeriformes) inferred from mitochondrial 16S ribosomal RNA gene sequences.

Phylogenetic relationships among the families of passerine birds have been the subject of many debates. These relationships have been investigated by using a number of different character sets, including morphology, proteins, DNA-DNA hybridization, and mitochondrial DNA gene sequences. Our objective was to examine the phylogenetic relationships of a set of passerine songbirds (Oscines) and to test the taxonomic relationships proposed by. We sequenced 1403 aligned bases encompassing the mitochondrial transfer-RNA-Valine and 16S ribosomal RNA genes in 27 species from 14 families (including a Suboscine outgroup). Our results differ in significant ways from the superfamily designations of Sibley and Ahlquist by questioning the monophyly of the Sylvioidea and by placing the Regulidae in the Corvoidea.

Animals↗
PubMed1998

Armored RNA technology for production of ribonuclease-resistant viral RNA controls and standards.

The widespread use of sensitive assays for the detection of viral and cellular RNA sequences has created a need for stable, well-characterized controls and standards. We describe the development of a versatile, novel system for creating RNase-resistant RNA. "Armored RNA" is a complex of MS2 bacteriophage coat protein and RNA produced in Escherichia coli by the induction of an expression plasmid that encodes the coat protein and an RNA standard sequence. The RNA sequences are completely protected from RNase digestion within the bacteriophage-like complexes. As a prototype, a 172-base consensus sequence from a portion of the human immunodeficiency virus type 1 (HIV-1) gag gene was synthesized and cloned into the packaging vector used to produce the bacteriophage-like particles. After production and purification, the resulting HIV-1 Armored RNA particles were shown to be resistant to degradation in human plasma and produced reproducible results in the Amplicor HIV-1 Monitor assay for 180 days when stored at -20 degreesC or for 60 days at 4 degreesC. Additionally, Armored RNA preparations are homogeneous and noninfectious.

HIV-1↗
PubMed1985

Detection of measles virus RNA in lymphocytes from peripheral-blood and brain perivascular infiltrates of patients with subacute sclerosing panencephalitis.

To clarify the relation between lymphocytes and measles virus in subacute sclerosing panencephalitis, we used in situ hybridization and a cloned measles virus DNA probe, specific for nucleocapsid protein, to detect measles virus RNA sequences in circulating lymphocytes and brain perivascular cuffs of patients with subacute sclerosing panencephalitis. Seventy to 90 per cent of peripheral mononuclear cells from three such patients were found to contain measles virus RNA sequences. In contrast, only a few infected cells were observed in four seropositive adults (0.1 to 5 per cent) and three age-matched children (10 to 15 per cent) used as controls. In one sample of brain tissue from a patient with subacute sclerosing panencephalitis, viral RNA sequences were also detected in nerve cells and in numerous cells from the perivascular infiltrates. In contrast, no hybridization was observed in brain tissue from a patient with herpetic encephalitis and from a patient with postlymphoma encephalitis. We conclude that measles virus has a strong tropism for lymphocytes and nerve cells in subacute sclerosing panencephalitis and that lymphocytes may be involved in the pathogenesis of the disease.

Adult↗
PubMed1978

Age-dependent relaxation of gene repression: increase of endogenous murine leukemia virus-related and globin-related RNA in brain and liver of mice.

A progressive loss in the ability of cells to maintain their normal specialized states of differentiation could be the common denominator underlying much of the physiology and pathology associated with the mammalian aging process. We investigated this possibility by searching for an age-dependent derepression of endogenous genes in tissues in which they are not normally expected to be expressed. Complementary DNA (cDNA) probes to globin genes and to the murine leukemia type C RNA virus (MuLV) genome were used to detect the presence of RNA complementary to these genes in RNA extracted from brain and liver in young and old mice. Significant amounts of globin RNA were found in brain nuclei and cytoplasm. No age difference was found in the globin RNA sequences present, but the number of globin RNA molecules increased from about 15 in 6-month to 34 in 27-month-old animals for nuclei and 280 in 6-month to 500 in 27-month-old animals for cytoplasm. Similar results were found for liver. RNA complementary to the MuLV cDNA probe was also found but, in contrast to globin, the different RNA sequences increased in both brain and liver nuclei from about 45% of the MuLV genome in 6-month to 72% in 27-month-old animals. The number of MuLV-related RNA molecules remained constant at about 22 and 38 per nuclei for brain and liver, respectively. Derepression of genes of this magnitude could result in a time-dependent increase in virus-related diseases and a general deterioration of the organism.

Aging↗
PubMed2002

Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya.

The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.

Amino Acid Sequence↗
PubMed2004

RNA-protein interactions in the yeast three-hybrid system: affinity, sensitivity, and enhanced library screening.

The yeast three-hybrid system has become a useful tool in analyzing RNA-protein interactions. An RNA sequence is tested in combination with an RNA-binding protein linked to a transcription activation domain (AD). A productive RNA-protein interaction activates a reporter gene in vivo. The system has been used to test candidate RNA-protein pairs, to isolate mutations in each interacting partner, and to identify proteins that bind a given RNA sequence. However, the relationship between reporter gene activation and in vitro affinity of an RNA-protein interaction has not been examined systematically. This limits interpretation of the data and complicates the development of new strategies. Here, we analyze several key parameters of the three-hybrid system, using as a model the interaction of a PUF protein, FBF-1, with a range of RNA targets. We compare activation of two reporter genes as a function of the in vitro affinity of the interaction. HIS3 and LacZ expression levels are directly related to affinity over a 10-fold range of Kd. Expression of the reporter genes also is directly related to the abundance of the activation domain fusion protein. We describe a new yeast strain, YBZ1, that simplifies screening of cDNA/AD libraries. This strain possesses a tandem, head-to-tail dimer of a high-affinity variant of MS2 coat protein, fused to a monomer of the LexA DNA-binding protein. We show that the use of this strain in cDNA library screens increases the number of genuine, sequence-specific positives detected, and at the same time reduces the background of false, RNA-independent positives.

Adaptor Proteins, Signal Transducing↗
PubMed1999

Molecular phylogenetic studies on Theileria parasites based on small subunit ribosomal RNA gene sequences.

Classification of Theileria parasites of south-east Asian countries is still ambiguous due to the lack of basic studies, especially their molecular genetic information. In this study, we included 6 known species and 14 unclassified Theileria parasite isolates: Theileria annulata, Theileria parva, Theileria taurotragi, Theileria sergenti, Theileria buffeli, Theileria types Sable, Theileria types A, B, B1, B2, C, D, E, F, G, G1, Theileria type Medan (Indonesia), Theileria type Ipoh (Malaysia) and Theileria type Thong Song (Thailand). Small subunit ribosomal RNA (srRNA) nucleotide sequence data were collected by PCR, cloning and dideoxy sequencing. The srRNA nucleotide sequences were aligned and analyzed by distance methods, maximum parsimony algorithms and maximum likelihood methods to construct phylogenetic trees. Bootstrap analysis was used to test the strength of the different phylogenetic reconstructions. The data indicated that all of the tree-building methods gave very similar results. This study identified two groups of Theileria, the pathogenic and benign groups, which are strongly supported by bootstrap analysis. The analysis also indicated that three subgroups (A, B and C) were generated within the benign Theileria group whereas the classification of Theileria type D and Thong Song is questionable. However, more basic information such as life cycle differences, vectors, modes of transmission, virulent and genetic/sexual compatability is essential for clearer taxonomic definition of the benign Theileria parasites.

Animals↗
PubMed1981

Template recognition sequence for RNA primer synthesis by gene 4 protein of bacteriophage T7.

The gene 4 protein of bacteriophage T7 recognizes specific sequences on single-stranded DNA and then catalyzes the synthesis of tetraribonucleotide primers complementary to the template. With phi X174 DNA as a template, the gene 4 protein enables T7 DNA polymerase (deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC 2.7.7.7) to initiate DNA synthesis at 13 major sites. DNA sequence analysis of the 5' termini of the newly synthesized DNA shows the predominant recognition sequences for the gene 4 protein to be 3'-C-T-G-G-G-5' or 3'-C-T-G-G-T-5'; the products of synthesis at these sites are RNA primers having the sequences pppA-C-C-C or pppA-C-C-A. The gene 4 protein can also synthesize primers at the sequences 3'-C-T-G-G-AC-5' and 3'-C-T-G-T-N-5', although these sites are used less than 10% as frequently as the predominant sites. Comparison of the utilization of primer sites suggests that the gene 4 protein binds randomly to single-stranded DNA and then translocates along the DNA in a unidirectional 5'-to-3' direction with regard to the DNA strand in search of recognition sequences. Models are presented for the role of the gene 4 protein in the initiation of lagging-strand synthesis and in the initiation of DNA replication at the origin.

Bacteriophage phi X 174↗
PubMed1998

Evidence for specific RNA/protein interactions in the differential segment of the W sex chromosome in the amphibian Pleurodeles waltl.

Pleurodeles exhibits a ZZ/ZW system of GSD (genotype sex determination). However, the Z and W sex chromosomes appear to be morphologically identical. A short RNA sequence is described that was specifically bound to lampbrush loops in the differential segment of the sexual bivalent IV. The distribution of these labeled loops in experimentally produced ZZ and WW females enabled us to demonstrate that such labeled loops were perfectly correlated with the W chromosome. Therefore, this RNA sequence constitutes an excellent marker for the W differential segment. Furthermore, analysis of the labeled loops under various experimental conditions suggested that their labeling is caused by specific interactions between this RNA sequence and lampbrush loop-associated proteins (RNA/protein interactions). North-western assays revealed that nuclear polypeptide(s) of 65 kDa could be responsible for such binding.

Animals↗
PubMed2005

Clostridium bacteraemia characterised by 16S ribosomal RNA gene sequencing.

BACKGROUND: Owing to problems in accurate species identification of the diverse genus clostridium, the epidemiology and pathogenicity of many species are not fully understood. Moreover, previous studies on clostridium bacteraemia have been limited and relied only on phenotypic species identification. AIMS: To characterise the epidemiology, disease spectrum, and outcome of clostridium bacteraemia using 16S ribosomal RNA (rRNA) gene sequencing. METHOD: During a four year period (1998-2001), all cases of clostridium bacteraemia were prospectively studied and all "non-perfringens" clostridium isolates identified to the species level by 16S rRNA gene sequencing. RESULTS: Fifty one blood culture isolates were identified as Clostridium perfringens and 17 belonged to 11 other clostridium species. The first case of C disporicum infection and two cases of clostridium bacteraemia in children with intussusception were also described. Of the 68 clostridium isolates from 68 different patients, 38 were associated with clinically relevant bacteraemia. The gastrointestinal and hepatobiliary tracts were common sites of both underlying disease and portal of entry in these patients. Clostridium perfringens accounted for 79% of all clinically relevant bacteraemia, with the remainder caused by a diversity of species. The attributable mortality rate of clinically relevant clostridium bacteraemia was 29%. Younger age and underlying gastrointestinal/hepatobiliary tract disease were associated with mortality (p < 0.05). CONCLUSIONS: Patients with clinically relevant clostridium bacteraemia should be investigated for the presence of underlying disease processes in the gastrointestinal or hepatobiliary tracts. 16S rRNA gene analysis will continue to be useful in further understanding the pathogenicity of various clostridium species.

Adult↗
PubMed1990

The gene for Klebsiella bacteriophage K11 RNA polymerase: sequence and comparison with the homologous genes of phages T7, T3, and SP6.

We determined the nucleotide sequence of gene 1 of Klebsiella phage K11, which is a member of the T7 group of phages. The largest open reading frame corresponds to a polypeptide with 906 amino acids and a molecular weight of 100,383 daltons. The deduced amino acid sequence of this polypeptide shows 71% homology to the T7 RNA polymerase (the product of T7 gene 1), 72% homology to the T3 RNA polymerase and 27% homology to the SP6 RNA polymerase. Divergent evolution was clearly most pronounced in the amino-terminal portion.

Amino Acid Sequence↗
PubMed1988

Computer-aided detection and alignment of weakly homologous amino acid sequences of RNA replicase beta (MS2 phage) and DNA polymerases (T7 phage and E. coli).

Alignment of the amino acid (aa) sequences of T7 phage DNA polymerase (DPase), E. coli DNA polymerase I (Pol I) and MS2 phage RNA replicase beta subunit (MS2 Repl) were established by computer-aided methods. The results showed that the entire length (aa's 16-704) of T7 DPase is homologous to Pol I aa's 207-928(C-term) with 21.5% aa identity, and that domains I (aa's-1-311) and II (312-451(C-term] were found to be homologous to each other and to N-terminal region of T7 DPase (aa's 1-250). Thus these enzymes and domains are homologous to one another and must have evolved from a co-ancestral enzyme.

Amino Acid Sequence↗
PubMed2005

On realizing shapes in the theory of RNA neutral networks.

It is known (Reidys et al., 1997b. Bull. Math. Biol. 59(2), 339-397) that for any two secondary structures S,S' there exists an RNA sequence compatible with both, and that this result does not extend to more than two secondary structures. Indeed, a simple formula for the number of RNA sequences compatible with secondary structures S,S' plays a role in the algorithms of Flamm et al. (2001. RNA 7, 254-265) and of Abfalter et al. (2003. Proceedings of the German Conference on Bioinformatics, ) to design an RNA switch. Here we show that a natural extension of this problem is NP-complete. Unless P=NP, there is no polynomial time algorithm, which when given secondary structures S1,...,S(k), for k4, determines the least number of positions, such that after removal of all base pairs incident to these positions there exists an RNA nucleotide sequence compatible with the given secondary structures. We also consider a restricted version of this problem with a "fixed maximum" number of possible stars and show that it has a simple polynomial time solution.

Algorithms↗
PubMed1991

Characterization of the aldose reductase-encoding gene family in rat.

Although the enzyme aldose reductase (AR) is implicated in the development of tissue pathology in diabetes, the exact mechanism of this involvement remains unclear. To better understand the role that expression of the aldose reductase-encoding gene (ALR) may play in diabetic complications, we have begun to analyze the gene and its regulatory regions, and we present here the sequence of four ALR genes in the rat. The putative functional gene is 14.1 kb long, has ten exons which show perfect sequence identity to the rat lens AR RNA sequence, and nine introns with classical splice-site consensus sequences. Potential regulatory elements in the 5'-flanking region of this gene include a TATA box and two CCAAT boxes. Probing rat genomic Southern blots with a fragment from the first intron indicates that there is probably only one copy of this gene in the rat genome. The other three genes are processed pseudogenes which show approx. 90% identity to the rat lens AR RNA sequence, contain no introns, and have poly(A) regions at their 3' ends. Chromosomal localization studies show the presence of ALR genes on chromosomes 3, 4 and 6 in the rat with the putative functional gene mapped on chromosome 4.

Aldehyde Reductase↗
PubMed2000

Phylogenetic and biogeographic relationships of eastern Asian and eastern North American disjunct Suillus species (fungi) as inferred from nuclear ribosomal RNA ITS sequences.

Species of Suillus produce fleshy, pored mushrooms. They are important symbiotic (ectomycorrhizal) partners of many coniferous trees. The genus includes several putative eastern Asian and eastern North American disjunct species, i.e., the S. americanus-S. sibiricus and S. decipiens-S. spraguei complexes. Phylogenetic relationships among the groups were determined to further understand the biogeographic pattern. Analyses were based on 40 sequences of the ITS region of the nuclear ribosomal RNA tandem repeats, representing 18 distinct species/populations. Our phylogenetic analyses suggested that: (1) Chinese and United States' (U.S.) S. spraguei plus S. decipiens form a strongly supported monophyletic group, with North American S. decipiens and Chinese S. spraguei being sister taxa; (2) S. americanus, Asian and U.S. S. sibiricus, plus S. umbonatus form a clade supported by a high bootstrap value; and (3) little ITS sequence divergence exists within the latter group compared to the S. decipiens-S. spraguei clade. Phylogenetic patterns revealed by this study imply a close phylogenetic relationship between eastern Asian and eastern North American disjunct population/species of Suillus. These fungi display relatively high host fidelity (at least to the host subgenus level), suggesting potential coevolutionary/comigratory trends.

Agaricales↗
PubMed1978

Characterization of the poly(adenylic acid) sequences in RNA synthesized in vitro by mouse myeloma nuclei.

The size and quantity of poly(A)sequences made by mouse myeloma nuclei in vitro are dependent on the concentration of KCI, ATP, other ribonucleoside triphosphates, as well as the nature of the divalent cation in the reaction medium. Reduction of the KC1 concentration from 120 mM to 5 mM, for example, stimulates poly(A) synthesis 10- to 20-fold. These poly (A) sequences are similar in size to cellular nuclear poly(A), but the RNA molecules to which they are attached are much shorter than poly(A) containing RNA molecules made at 120 mM KC1. Presence of Mn2+ in the medium led to a much more heterogenous population of poly(A) sequences. From such observations we have found reaction conditions in which nuclei synthesize molecules that resemble native nuclear poly(A) + RNA. Not only are the lengths and amounts of the poly(A) sequences similar, but they also undergo a terminal turnover like that of the poly(A) in hnRNA. An oligo(A) sequence that resembles the oligo(A) found in non-poly(A) containing hnRNA of mouse myeloma and HeLa cells is also synthesized in vitro. These observations suggest that some processing functions are retained during the in vitro incubation of these nuclei.

Base Sequence↗
PubMed1994

Mixed cryoglobulinemia and hepatitis C virus.

BACKGROUND: Mixed cryoglobulinemia (MC) is frequently associated with clinical and biological evidence of liver disease and has recently been reported in cases of hepatitis C virus (HCV) infection. The aim of this study was to assess prospectively in a large series of MC patients: (1) the prevalence of HCV markers (anti-HCV antibodies and HCV RNA in serum and cryoprecipitate); (2) the main clinical, biologic and liver histologic features in patients with or without HCV infection. PATIENTS: One hundred fifteen consecutive unselected MC patients were studied: 45% had well-defined underlying diseases ("nonessential" MC). Fifty-five percent with no cause of MC were considered to have "essential" MC and were subjected to in-depth examination. METHODS: Patients were considered to have MC if two successive determinations of their serum cryoglobulin level were above 0.05 g/L. Anti-HCV antibodies (Ab) were detected in all patients by second-generation tests (ELISA, RIBA). We also looked for HCV RNA sequences amplified by polymerase chain reaction (PCR) in the sera and cryoprecipitates of 39 patients; HBs antigen, anti-HBs Ab and anti-HBc Ab in all patients; and HBV DNA in 20 sera and 17 cryoprecipitates. Quantitative HCV Ab and RNA studies were performed on whole serum, cryoprecipitates, and supernatants. Clinical features were recorded retrospectively for each patient. Liver biopsies from 23 anti-HCV Ab-positive and 7 anti-HCV Ab-negative patients were examined histologically, with qualitative and quantitative analysis. RESULTS: Anti-HCV Ab were found in 47/115 (41%) patients by ELISA and RIBA: 33/63 (52%) essential MC and 14/52 (27%) nonessential MC. Among the 63 essential MC patients, the 33 anti-HCV Ab-positive (Group 1) were compared to the 30 anti-HCV Ab-negative patients (Group 2). Group 1 patients had more cutaneous involvement (Raynaud's phenomenon, purpura, livedo, distal ulcers, or gangrenous changes) (17 versus 5: p = 0.004), higher alanine aminotransferase levels (110 +/- 22 versus 41 +/- 10 IU; p < 0.005), higher serum cryoglobulin levels (0.35 +/- 0.07 versus 0.12 +/- 0.04 g/L; p = 0.01), lower CH50 (28 +/- 3 versus 44 +/- 2 CH50/mL; p = 0.0001) and lower C4 levels (0.20 +/- 0.02 versus 0.29 +/- 0.03 g/L; p < 0.04). The prevalence of HBV serum markers was low in both groups, and HBV DNA was never detected in any of the sera and cryoprecipitates tested. HCV RNA sequences were detected in 10/16 (63%) sera and 12/16 (75%) cryoprecipitates from Group 1 patients, whereas they were not in the sera or cryoprecipitates from 23 Group 2 patients. Using quantitative PCR, HCV RNA in cryoprecipitates was concentrated 20 to 100 times despite the absence of significant anti-HCV Ab concentration in these samples. Histologic examination of liver biopsies revealed a spectrum of lesions ranging from chronic active hepatitis to cirrhosis, but Knodell's score did not differ between the groups. CONCLUSION: (1) About 50% of the essential MC patients had anti-HCV Ab, and these patients had more severe cryoglobulinemia-associated clinical and biological signs; (2) HCV RNA sequences were found in the large majority of sera and cryoprecipitates from patients with essential MC and anti-HCV Ab and were more concentrated in cryoprecipitates than in supernatants. These results suggest a role for HCV in the pathogenesis of MC and indicate that many cases of essential MC may be secondary to HCV infection and thus nonessential.

Adult↗
PubMed1980

Nonviral oligonucleotides at the 5' terminus of cytoplasmic influenza viral mRNA deduced from cloned complete genomic sequences.

We obtained influenza viral DNA clones containing sequences derived from cytoplasmic viral mRNA and genomic viral RNA. Sequence analysis of terminal nucleotides of five independentlyisolated viral DNA segments showed that additional oligonucleotides were covalently linked to the 5' terminus of viral mRNA transcripts. The sequences of these additional nucleotides varied among DNA clones of the same gene and of different genes as well. These inserts also varied in length, ranging from 6 to 14 nucleotides. The heterogeneity of these sequences suggests that they were derived originally from cellular RNA molecules. These findings provide evidence that cellular RNA sequences are used to prime influenza viral mRNA transcription in infected cells. In addition, the sequences at both termini of vRNA were fully represented in clone pFV 88, indicating that the cloned DNA contained the complete viral gene coding for the hemagglutinin.

Base Sequence↗