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PubMed2005

Spam1-associated transmission ratio distortion in mice: elucidating the mechanism.

BACKGROUND: While transmission ratio distortion, TRD, (a deviation from Mendelian ratio) is extensive in humans and well-documented in mice, the underlying mechanisms are unknown. Our earlier studies on carriers of spontaneous mutations of mouse Sperm Adhesion Molecule 1 (Spam1) suggested that TRD results from biochemically different sperm, due to a lack of transcript sharing through the intercellular cytoplasmic bridges of spermatids. These bridges usually allow transcript sharing among genetically different spermatids which develop into biochemically and functionally equivalent sperm. OBJECTIVES: The goals of the study were to provide support for the lack of sharing (LOS) hypothesis, using transgene and null carriers of Spam1, and to determine the mechanism of Spam1-associated TRD. METHODS: Carriers of Spam1-Hyal5 BAC transgenes were mated with wild-type female mice and the progeny analyzed for TRD by PCR genotyping. Sperm from transgene and Spam1 null carriers were analyzed using flow cytometry and immunocytochemistry to detect quantities of Spam1 and/or Hyal5. Transgene-bearing sperm with Spam1 overexpression were detected by fluorescence in situ hybridization. In wild-type animals, EM studies of in situ transcript hybridization of testis sections and Northern analysis of biochemically fractionated testicular RNA were performed to localize Spam1 transcript. Finally, AU-rich motifs identified in the 3' UTR of Spam1 RNA were assayed by UV cross-linking to determine their ability to interact with testicular RNA binding proteins. RESULTS: The Tg8 line of transgene carriers had a significant (P < 0.001) TRD, due to reduced fertilizing ability of transgene-bearing sperm. These sperm retained large cytoplasmic droplets engorged with overexpressed Spam1 or Hyal5 protein. Caudal sperm from transgene carriers and caput sperm of null carriers showed a bimodal distribution of Spam1, indicating that the sperm in a male were biochemically different with respect to Spam1 quantities. Spam1 RNA was absent from the bridges, associated exclusively with the ER, and was shown to be anchored to the cytoskeleton. This compartmentalization of the transcript, mediated by cytoskeletal binding, occurs via protein interactions with 3' UTR AU-rich sequences that are likely involved in its stabilization. CONCLUSION: We provide strong support for the LOS hypothesis, and have elucidated the mechanism of Spam1-associated TRD.

Alleles↗
PubMed1985

Human parainfluenza virus 3: purification and characterization of subviral components, viral proteins and viral RNA.

A simple method was established that allowed large quantities of human parainfluenza 3 (PF3) virions to be isolated from tissue culture cells. The purity of the virus was sufficient for biochemical analysis of virion proteins. The density of PF3 virions was 1.18-1.20. Purified virions contained seven viral proteins with estimated molecular weights of: L, 180 000; P, 83 000; HN, 69 000; NP, 66 000; F0, 60 000; F1, 51 000; and M, 38 000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions. There were three phosphoproteins, P, NP and M, and two glycoproteins, HN and F (includes F0 and F1). F1.2, the activated, cleaved, fusion glycoprotein (60 000 Da), consisting of two disulfide-linked subunits, F1 and F2, was seen only under nonreducing conditions. Because of its small size (approximately 9000 Da) F2 could be seen only on gels with high acrylamide concentrations. As in other enveloped viruses, cellular actin (43 000 Da) was present in purified virions. Several minor bands migrating between NP and M represented breakdown products of NP. Solubilization of the virion membrane in low salt buffer with non-ionic detergent resulted in the loss of HN and F. In high salt buffer, the M protein was also removed. Nucleocapsids isolated by CsCl centrifugation contained L, P, NP and small amounts of M. Nucleocapsids isolated in the presence of the ionic detergent, sarcosyl, contained only the NP protein. The density of nucleocapsids was 1.29-1.30. Genomic 50S RNA isolated from nucleocapsids had an estimated molecular weight of 5 X 10(6).

Animals↗
PubMed1994

Enhancement of in vitro transcription by addition of cloned, overexpressed major sigma factor of Chlamydia psittaci 6BC.

Obligate parasitic bacteria of the genus Chlamydia possess a developmental cycle that takes place entirely within eucaryotic host cells. Because standard methods of genetic analysis are not available for chlamydiae, an in vitro transcription system has been developed to elucidate the mechanisms by which chlamydiae regulate gene expression. The in vitro system is specific for chlamydial promoters but is inefficient, presumably because the RNA polymerase is not saturated with sigma factor. Therefore, we prepared recombinant Chlamydia psittaci 6BC major sigma factor to enhance transcription in the in vitro system. The gene encoding the major sigma factor (sigA) was identified by using an rpoD box oligonucleotide and was subsequently cloned and sequenced. It was found to encode a potential 571-amino-acid protein (sigma 66) that is greater than 90% identical to the previously identified major sigma factors from the L2 and MoPn strains of Chlamydia trachomatis. sigA was recloned into a T7 RNA polymerase expression system to produce large quantities of sigma 66 in Escherichia coli. Overexpressed sigma 66 was identified by immunoblot by using monoclonal antibodies 2G10 (reactive) and 2F8 (nonreactive) generated against E. coli sigma 70. After purification by polyacrylamide gel electrophoresis, the recombinant protein was found to stimulate, by 10-fold or more, promoter-specific in vitro transcription by C. psittaci 6BC and C. trachomatis L2 RNA polymerases. Transcription was dependent on added chlamydial sigma 66, rather than on potentially contaminating E. coli sigma 70 or other fortuitous activators, since the monoclonal antibody 2G10, and not 2F8, inhibited transcription initiation. Recombinant omega(66) had no effect on transcription by E. coli core polymerase. The addition of recombinant omega(66) to the in vitro system should be useful for distinguishing omega(66)-dependent transcription of developmentally regulated chlamydial genes from omega(66)-independent transcription.

Amino Acid Sequence↗
PubMed2005

A rapid and efficient method for purifying high quality total RNA from peaches (Prunus persica) for functional genomics analyses.

Prunus persica has been proposed as a genomic model for deciduous trees and the Rosaceae family. Optimized protocols for RNA isolation are necessary to further advance studies in this model species such that functional genomics analyses may be performed. Here we present an optimized protocol to rapidly and efficiently purify high quality total RNA from peach fruits (Prunus persica). Isolating high-quality RNA from fruit tissue is often difficult due to large quantities of polysaccharides and polyphenolic compounds that accumulate in this tissue and co-purify with the RNA. Here we demonstrate that a modified version of the method used to isolate RNA from pine trees and the woody plant Cinnamomun tenuipilum is ideal for isolating high quality RNA from the fruits of Prunus persica. This RNA may be used for many functional genomic based experiments such as RT-PCR and the construction of large-insert cDNA libraries.

DNA, Complementary↗
PubMed2002

Persistence of human immunodeficiency virus (HIV) type 1 DNA in peripheral blood despite prolonged suppression of plasma HIV-1 RNA in children.

Human immunodeficiency virus (HIV) type 1 DNA in peripheral blood mononuclear cells (PBMC) was quantified in 31 children who received efavirenz, nelfinavir, and 1 or 2 nucleoside reverse-transcriptase inhibitors for > or =2 years and in whom undetectable plasma HIV-1 RNA levels (< 50 copies/mL) were sustained, to determine the usefulness of HIV-1 DNA as a marker of virus suppression. The median baseline HIV-1 DNA level was 750 copies/10(6) PBMC. After initiation of highly active antiretroviral therapy (HAART), HIV-1 DNA levels decreased gradually, reaching a plateau from week 80 through week 104 (median HIV-1 DNA level, 263 copies/10(6) PBMC). Children who had plasma HIV-1 RNA levels < 50 copies/mL after receiving HAART for 8 weeks (n=16) had persistently lower quantities of intracellular HIV-1 DNA than children whose HIV-1 RNA levels reached < 50 copies/mL after 8 weeks of HAART (n=15). The median half-life for intracellular HIV-1 DNA was 60 weeks. Thus, despite prolonged maintenance of undetectable levels of plasma HIV-1 RNA, HIV-1 DNA remains detectable in PBMC of children and may be a useful marker of further virus suppression.

Adolescent↗
PubMed1992

Biochemical and genetic dissection of the Saccharomyces cerevisiae RNA polymerase C53 subunit through the analysis of a mitochondrially mis-sorted mutant construct.

RPC53 has previously been shown to encode an essential subunit required for tRNA gene transcription by RNA polymerase C in vivo (Mann, C., Micouin, J.-Y., Chiannilkulchai, N., Treich, I., Buhler, J.-M., and Sentenac, A. (1992) Mol. Cell. Biol. 12, in press). In this paper, we have determined that an unusual rho+ lethality associated with the rpc53::HIS3-1 disruption mutation is due to the inadvertent formation of a Pet56-C53 fusion protein. This fusion protein is missorted to mitochondria, thereby reducing the quantity of the C53 subunit available for RNA polymerase C assembly. We show that the carboxyl-terminal region of C53 contains the essential functional domain of the subunit and that a mutant RNA polymerase containing only this domain is thermolabile for its function in vivo and in vitro. The thermolability of the carboxyl-terminal C53 domain is suppressed by five different genes on multicopy plasmids, including RPC160, encoding the largest subunit of RNA polymerase C and SSD1/SRK1, which has been implicated in the activity of protein phosphatases.

Alleles↗
PubMed1982

Correlation between activation of quiescent 3T3 cells by retinoic acid and increases in uridine phosphorylation and cellular RNA synthesis.

Short exposure of cultured quiescent cells to micromolar quantities of beta-all-trans-retinoic acid (RA) has been reported to potentiate the effects of phorbol myristate acetate in promoting the transition from the resting to growing states of these cells. Longer periods of exposure to RA result in substantial inhibition of cellular proliferation. We now show that short-term treatment of quiescent Swiss 3T3 cells with RA yields marked increases in uridine phosphorylation and total cellular RNA synthesis as well as 2-deoxyglucose uptake. Upon subsequent treatment of the cells with phorbol myristate acetate, a direct correlation between the comitogenic activity of RA and its stimulation of uridine phosphorylation and RNA synthesis is apparent. The increases in 2-deoxyglucose uptake persist after long-term exposure of the cells to RA when the growth-inhibitory effects of this agent are observed.

Animals↗
PubMed1987

Duck hepatitis B virus replicates in the yolk sac of developing embryos.

Duck hepatitis B virus (DHBV) is the only member of the hepadnavirus family in which nearly 100% vertical transmission from carrier mother to embryo has been reported. Large quantities of maternally transmitted virus particles are present in the yolk prior to incubation of the eggs, and replicative forms of DHBV DNA are detectable in the liver at 6 days of incubation. Since the yolk sac is similar to the liver in its production of serum proteins, we examined the yolk sacs of developing embryos for signs of viral replication. We detected the supercoiled form of DHBV DNA, DHBV RNA transcripts similar to those in the virus-replicating liver, and DNA polymerase activity and viral DNA in corelike particles in extracts of yolk sac tissue of naturally infected eggs. DHBV core antigen was strongly stained in only the endodermal layer of the yolk sac by immunofluorescence. DHBV RNA was detectable in the yolk sac from 4 days of incubation until hatching, and a larger quantity of DHBV RNA was present in the yolk sac than in the liver during all the stages of embryogenesis. Our data indicate that DHBV replicates actively in the yolk sac from an earlier stage than that previously reported in studies of embryonic liver and that replication is limited to the endodermal cell layer, which is ontogenetically and functionally related to the liver. The yolk sac may support the vertical transmission of DHBV.

Animals↗
PubMed1991

First large scale chemical synthesis of the 72 amino acid HIV-1 nucleocapsid protein NCp7 in an active form.

The nucleocapsid protein (NC) of the human immunodeficiency virus type 1 plays a crucial role in the formation of infectious viral particles and therefore should be a major target for the development of antiviral agents. This requires an investigation of NC protein structure and of its interactions with both primer tRNA(Lys,3) and genomic RNA. Nucleocapsid protein NCp7, which results from the maturation of NCp15, contains two zinc fingers flanked by sequences rich in basic and proline residues. Here we report the first synthesis of large quantities of NCp7 able to activate HIV-1 RNA dimerization and replication primer tRNA(Lys,3) annealing to the initiation site of reverse transcription. In addition UV spectroscopic analyses performed to characterize the Co2+ binding properties of each zinc finger suggest that the two fingers probably interact in NCp7.

Amino Acid Sequence↗
PubMed1977

Phosphorylation of yeast DNA-dependent RNA polymerases in vivo and in vitro. Isolation of enzymes and identification of phosphorylated subunits.

Yeast DNA-dependent RNA polymerases I, II, and III are phosphorylated in vivo. Yeast cells were grown continuously in 32Pi and the RNA polymerases were isolated by a new procedure which allows the simultaneous purification of these enzymes from small quantities (35 to 60 g) of cells. Each of the RNA polymerases was phosphorylated. The following phosphorylated polymerase polypeptides were identified: polymerase I subunits of 185,000, 44,000, 36,000, 24,000, and 20,000 daltons; a polymerase II subunit of 24,000 daltons; and polymerase III subunits of 24,000 and 20,000 daltons. The incorporated 32P was acid-stable but base-labile. Phosphoserine and phosphothreonine were identified after partial acid hydrolysis of purified [32P]polymerase I. A yeast protein kinase that co-purifies with polymerase I during part of the isolation procedure was partially purified and characterized. This protein kinase phosphorylates the subunits of the purified polymerases that are phosphorylated in vivo and, in addition, a polymerase I subunit of 48,000 daltons and a polymerase II subunit of 33,500 daltons. Phosphorylation of the purified enzymes with this protein kinase had no substantial effect on polymerase activity in simple assays using native yeast DNA as a template. Preincubation of purified polymerase I with acid or alkaline phosphatase also had no detectable effect on polymerase activity.

DNA-Directed RNA Polymerases↗
PubMed2000

Expression of human lymphotoxin alpha in Aspergillus niger.

A gene-fusion expression strategy was applied for heterologous expression of human lymphotoxin alpha (LTalpha) in the Aspergillus niger AB1.13 protease-deficient strain. The LTalpha gene was fused with the A. niger glucoamylase GII-form as a carrier-gene, behind its transcription control and secretion signals. Special attention was paid to the influence of different codon usage on secretion of protein. In the case of human tumor necrosis factor alpha (TNFalpha) a dramatic change of secretion has been observed when human cDNA sequence was used instead of synthetic E. coli biased codons. In the case of LTalpha such a change of codon usage brought improvement at the RNA level, however, no increase in the quantity of secreted protein was observed, due to the proteolitic activity of the host organism. The estimated yield of secretion of LTalpha from A. niger into the soya medium was 50 pg l(-1) of culture.

Artificial Gene Fusion↗
PubMed1991

Specific cessation of minus-strand RNA accumulation at an early stage of tobacco mosaic virus infection.

The time course of accumulation of viral plus-strand RNAs (genomic RNA and subgenomic mRNA for the coat protein) and minus-strand RNA in tobacco protoplasts synchronously infected with tobacco mosaic virus (TMV) RNA was examined. In protoplasts infected with the wild-type TMV L RNA, the plus and minus strands accumulated differently not only in quantity but also in the outline of kinetics. The time courses of accumulation of the genomic RNA and coat protein mRNA were similar: they became detectable at 2 or 4 h postinoculation (p.i.), and their accumulation increased until 14 to 18 h p.i. The accumulation rate reached the maximum at about 4 h p.i. and then gradually decreased. In contrast, accumulation of the minus-strand RNA ceased at 6 to 8 h p.i., at which time the plus-strand accumulation was already about 100 times greater and still continued vigorously. This specific halt of minus-strand accumulation was not caused exclusively by encapsidation of the genomic RNA, because a similar halt was observed upon infection with a deletion mutant that lacks the 30K and coat protein genes. Upon infection with a mutant that could not produce the 130K protein (one of the two proteins that are thought to be involved in viral RNA replication), the accumulation levels of both plus and minus strands were lower than that of the parental wild-type virus. Given these observations, possible mechanisms of TMV replication are discussed.

Cell Transformation, Viral↗
PubMed1987

RNA target loss during solid phase hybridization of body fluids--a quantitative study.

Recent applications of nucleic acid hybridization to the diagnosis of viral infections are limited by the sensitivity of the assay system and, hence, by the amount of target viral nucleic acid in the specimen. In the case of single-stranded RNA viruses, RNase activity in body fluids poses a potential obstacle to optimizing sensitivity. We added radioactively labelled, purified, single-stranded enteroviral RNA to various body fluids and noted significant loss of this 'target' RNA during the course of routine hybridization procedures. We confirmed that RNase activity was responsible for much of the target loss. Further characterization of the RNase activity found it to be rapidly acting (less than 15 s), concentrated (equally active at 10-fold dilution of body fluid) and potent--resulting in RNA breakdown products too small to be retained by any of six commercially available membrane filters. The RNase was active only in solution and was effectively inhibited by treatment of the body fluid with inhibitors prior to contact of the fluid with RNA. In contrast, when RNA within virions was added to body fluids, it was largely retained by membrane filters during the hybridization procedure. We conclude that detection of single-stranded RNA viruses in body fluids will depend upon the quantity of intact virions in the specimen. RNase inhibitors should be immediately added to body fluid specimens after collection to minimize the loss of RNA which will occur if virions are disrupted in transport and handling of the specimen.

Amniotic Fluid↗
PubMed1971

Kinetics of RNA synthesis in toad bladder epithelium: action of aldosterone during the latent period.

Processing of RNA in the toad bladder was analyzed by polyacrylamide-gel electrophoresis to determine whether aldosterone causes any changes in the 1 hr before it potentiates transport of sodium ion. No change was found in the quantity or in the specific activity of bulk RNA labeled with uridine-5-(3)H. In vivo and in vitro with either uridine-5-(3)H or with methionine-(methyl)-(3)H as precursors, processing of RNA was extremely slow. Heterodisperse RNA was obvious after 30 min of continuous labeling, but labeling of the 40S precursor of ribosomal RNA was not apparent for 60 min. Labeling of mature 28S and 18S RNA first became apparent after 8 hr. approximately 7S RNA was the principal fastmigrating species labeled at 30 min, and 4S RNA was not heavily labeled until 1 hr. Aldosterone (5 x 10(-7) mole/liter) produced no changes. If care were not taken to inhibit metabolism of native bacteria colonizing the bladder, bacterial RNA of high specific activity predominated. We conclude that RNA metabolism in the toad bladder is extraordinarily slow, that a major acceleration of de novo synthesis in response to physiologic doses of aldosterone was not demonstrable, and that some reports to the contrary may have been influenced by artifacts from bacterial RNA metabolism. Earlier evidence for obligatory alterations in RNA metabolism during the latent period is not strong.

Aldosterone↗
PubMed2006

Impact of suppressive herpes therapy on genital HIV-1 RNA among women taking antiretroviral therapy: a randomized controlled trial.

OBJECTIVE: To demonstrate a causal relationship between herpes simplex virus 2 (HSV-2) and increased genital HIV-1-RNA shedding in women on HAART. DESIGN: A randomized, double-blind, placebo-controlled trial of herpes-suppressive therapy (valacyclovir 500 mg twice a day) in HIV-1/HSV-2-infected women taking HAART in Burkina Faso. METHODS: Participants were followed for a total of 12 biweekly visits before and after randomization. The presence and frequency of genital and plasma HIV-1 RNA, and of genital HSV-2 were assessed using summary measures, adjusting for baseline values. Random effect linear regression models were used to assess the impact of treatment on genital and plasma viral loads among visits with detectable virus. RESULTS: Sixty women were enrolled into the trial. Their median CD4 lymphocyte count was 228 cells/mul, and 83% had undetectable plasma HIV-1 RNA at baseline. Valacyclovir reduced the proportion of visits with detectable genital HSV-2 DNA [odds ratio (OR) 0.37, 95% confidence interval (CI) 0.13, 1.05], but had no significant impact on the frequency (OR 0.90, 95% CI 0.31, 2.62) or quantity (reduction of 0.33 log copies/ml, 95% CI -0.81, 0.16) of genital HIV-1 RNA. However, according to pre-defined secondary analyses restricted to women who shed HIV-1 at least once in the baseline phase, valacyclovir reduced both the proportion of visits with detectable HIV-1 shedding (OR 0.27, 95% CI 0.07, 0.99) and the quantity of genital HIV-1 RNA during these visits (-0.71 log10 copies/ml, 95% CI -1.27, -0.14). CONCLUSION: HSV-2 facilitates residual genital HIV-1 replication among dually infected women taking HAART despite HIV-1 suppression at the systemic level.

Acyclovir↗
PubMed1981

Poly(adenylic acid) in small amounts, free or covalently linked to substrate, protects RNA from hydrolysis by ribonuclease.

Short lengths (18 residues) of poly(A), covalently linked to the 3'-termini of Escherichia coli 5 S rRNA, induce powerful inhibitions (38-87%) of the activities of RNAases (ribonucleases) from Citrobacter sp., Enterobacter sp., bovine pancreas, human spleen and human plasma. As the polypurine chain length is extended, enzyme activity declines. Furthermore, poly(A) sequences, present only on a small subpopulation of RNA, and accounting for less than 1% of total RNA, serve to protect all RNA, polyadenylated or not, from enzyme-catalysed degradation. The quantity of 3'-terminal adenylic acid residues, relative to the amount of substrate, determines enzyme activity. The exact distribution of a fixed amount of poly(A) residues on the 3'-termini of substrate molecules is unimportant in this respect. Comparison of the efficacies of inhibition of RNAase activity, by using linked poly(A) and similar quantities of free poly(A), revealed that although the free polypurine inhibits RNAase activity, covalent linkage of poly(A) to RNA is more advantageous to the stability of an RNA substrate. However, the ratio of inhibited activities obtained by using linked or free poly(A) may change considerably with alterations in either substrate concentration or polyadenylic acid segment length.

Animals↗
PubMed2002

Fatty acid and lipid biosynthetic genes are expressed at constant molar ratios but different absolute levels during embryogenesis.

In plants, fatty acid and complex lipid synthesis requires the correct spatial and temporal activity of many gene products. Quantitative northern analysis showed that mRNA for the biotin carboxylase subunit of heteromeric acetyl-coenzyme A carboxylase, fatty acid synthase components (3-oxoacyl-acyl carrier protein [ACP] reductase, enoyl-ACP reductase, and acyl-ACP thioesterase), and stearoyl-ACP desaturase accumulate in a coordinate manner during Brassica napus embryogenesis. The mRNAs were present in a constant molar stoichiometric ratio. Transcript abundance of mRNAs for the catalytic proteins was found to be similar, whereas the number of ACP transcripts was approximately 7-fold higher. The peak of mRNA accumulation of all products was between 20 and 29 d after flowering; by 42 d after flowering, the steady-state levels of all transcripts fell to about 5% of their peak levels, which suggests that the mRNAs have similar stability and kinetics of synthesis. Biotin carboxylase was found to accumulate to a maximum of 59 fmol mg(-1) total RNA in embryos, which is in general agreement with the value of 170 fmol mg(-1) determined for Arabidopsis siliques (J.S. Ke, T.N. Wen, B.J. Nikolau, E.S. Wurtele [2000] Plant Physiol 122: 1057-1071). Embryos accumulated between 3- and 15-fold more transcripts per unit total RNA than young leaf tissue; the lower quantity of leaf 3-oxoacyl-ACP reductase mRNA was confirmed by reverse transcriptase-polymerase chain reaction. This is in conflict with analysis of B. napus transcripts using an Arabidopsis microarray (T. Girke, J. Todd, S. Ruuska, J. White, C. Benning, J. Ohlrogge [2000] Plant Physiol 124: 1570-1581) where similar leaf to seed levels of fatty acid synthase component mRNAs were reported.

3-Oxoacyl-(Acyl-Carrier-Protein) Reductase↗
PubMed2002

Effect of dietary protein quantity and quality on the brain protein synthesis rate in ovariectomized female rats.

The purpose of this study was to determine whether the quantity and quality of dietary protein affected the rate of brain protein synthesis in ovariectomized female rats. Two experiments were conducted on the ovariectomized female rats (12 weeks old) given diets containing 20%, 5%, or 0% casein (experiment 1) and 20% casein, 20% soy protein, 20% gluten, or 20% gelatin (experiment 2) for 10 d, respectively. The fractional rates of protein synthesis in the brain declined with a decrease of the quantity and quality of dietary protein. In the brain, the RNA activity [g of protein synthesized/((g of RNA) d)] was significantly correlated with the fractional rate of protein synthesis. The RNA concentration (mg of RNA/g of protein) was not related to the fractional rate of protein synthesis in any organ. The results suggest that the rate of protein synthesis in the brain declines with the decrease of the quantity and quality of dietary protein in ovariectomized female rats, and that RNA activity is at least partly related to the fractional rate of brain protein synthesis.

Animals↗