Isolation and partial purification of the major abundant class rat seminal vesicle poly(A+)-messenger RNA

Total poly(A(+))-RNA (poly(A(+))-RNA(tot)) was isolated from rat seminal vesicle and its size distribution determined by 70% formamide 5-25% sucrose density analysis. One major peak was resolved in the 10-13 S region and accounted for approximately 35% of the total poly(A(+))-RNA applied. Preparative 1% SDS, 5-20% linear sucrose density gradients also resolved a single major peak in the 11S region (poly(A(+))(11S). Analysis of poly(A(+))-RNA(tot) and poly(A(+))-RNA(11S) under denaturing conditions on 2% agarose gel electrophoresis demonstrated two major components in both poly(A(+))-RNA populations. Size estimations for these components are 620 and 540 NT respectively. (3)H-cDNA was made to both poly(A(+))-RNA(tot) and poly(A(+))-RNA(11S). Back-hybridization of poly(A(+))-RNA(tot) and poly(A(+))-RNA(11S) to their respective (3)H-cDNA revealed a highly abundant class representing 41% and 85% of the sequences in their respective (3)H-cDNA's. The highly abundant class corresponded to 3-5 sequences present in 30,000-50,000 copies/cell. Invitro translation of poly(A(+))-RNA(11S) resulted in two major polypeptides coded for by the 620 NT long and 540 NT long poly(A(+))-RNA respectively.Images     

Isolation and characterization of monoacetyldiglycerides from bovine udder

Monoacetyldiglycerides (MADGs) were isolated from an animal tissue, bovine udder, by solvent extraction and silica gel column chromatography. Monoacetyldiglyceride structures were identified using a variety of 1-D and 2-D NMR techniques and collision-induced dissociation (CID) tandem mass spectrometry coupled with fast atom bombardment. CID of sodium-adducted molecular ions ([M+ Na](+)) generated numerous types of product ions providing information on the double bond position of fatty acyl groups as well as fatty acid compositions. Structural analysis led to the classification of the MADGs isolated from bovine udder as 1-palmitoyl-2-lauroyl-3-acetyl-rac-glycerol, 1, 2-dimyristoyl-3-acetyl-rac-glycerol, 1-palmitoyl-2-myristoyl-3-acetyl-rac-glycerol, 1-oleoyl-2-myristoyl-3-acetyl-rac-glycerol, 1-palmitoyl-2-palmitoleoyl-3-acetyl-rac-glycerol, 1, 2-dipalmitoyl-3-acetyl-rac-glycerol, 1-linoleoyl-2-palmitoyl-3-acetyl-rac-glycerol, 1-oleoyl-2-palmitoleoyl-3-acetyl-rac-glycerol, 1-oleoyl-2-palmitoyl-3-acetyl-rac-glycerol, 1-stearoyl-2-palmitoyl-3-acetyl-rac-glycerol, 1-oleoyl-2-linoleoyl-3-acetyl-rac-glycerol, 1, 2-dioleoyl-3-acetyl-rac-glycerol, and 1-stearoyl-2-oleoyl-3-acetyl-rac-glycerol.     

Template activity of poly(A+) and poly(A-) messenger RNA of pathogenic arenaviruses

The total RNA from cells infected with Machupo and Lassa viruses as well as poly(A+) and poly(A-) fractions of the RNA were translated in the cell-free protein synthesizing system from rabbit reticulocytes. The translated products were treated with specific antibodies and analyzed in polyacrylamide gel electrophoresis. Only poly(A-) fraction of RNA coded for the synthesis of NP protein in vitro. The mRNAs for NP protein of Machupo and Lassa viruses are supposed to contain no poly(A) sequences at 3'end, or if they really do, the size of the sequences is not adequate for binding with oligo(dT)-cellulose.     

Complexity of poly(A+) and poly(A-) polysomal RNA in mouse liver and cultured mouse fibroblasts.

RNA excess hybridization experiments were used to measure the complexity of nuclear RNA, poly(A+) mRNA, poly(A-) mRNA, and EDTA-released polysomal RNA sedimenting at less than 80 S in mouse liver and in cultured mouse cells. With both cell types, poly(A-) RNA was found to contain 30-40% of the sequence diversity of total mRNA. In the case of liver this represents 5,700 poly(A-) molecules and 8,600 poly(A+) molecules for a total of approximately 14,300 different mRNAs. Comparison of the complexity of mRNA with that of nuclear RNA revealed that in liver and in cultured cells, mRNA has only 10-20% of the sequence diversity present in nuclear RNA. This latter observation is consistent with existing data on mammalian cells from this and other laboratories.     

Isolation of poly(A)+ RNA by paper affinity chromatography

Poly(A)+ RNA was isolated from in vitro short-term-labeled total cytoplasmic RNA of Ehrlich ascites tumor cells by oligo(dT) cellulose chromatography. This poly(A)+ RNA fraction was compared with a poly(A)+ RNA fraction isolated by a new procedure which involves specific binding of poly(A)+ RNA to messenger affinity paper (mAP) and its release in hot (70 degrees C) water. In typical experiments 10-11 micrograms (2.3%) of poly(A)+ RNA can be retained from 500 micrograms of total cytoplasmic RNA per cm2 of mAP in a quick one-step procedure. The poly(A)+ RNA preparations isolated by the two methods proved to be almost identical with respect to their fraction in total cytoplasmic RNA, specific radioactivities, sucrose gradient profiles, and translation assays. Since the isolation of poly(A)+ RNA by mAP is much less time consuming than that by oligo(dT) column chromatography and since the poly(A)+ RNA can be recovered from mAP in small volumes, which avoids further loss during precipitations, it can be advantageously used for preparative isolation of poly(A)+ RNA.     

Isolation and characterization of individual tRNA Leu 1,2,and 4 from the bovine udder

tRNA-Leu 1, tRNA-Leu 2 and tRNA-Leu 4 were isolated from a lactating cow mammary gland by combination of several chromatographic methods. Chromatography on a Sepharose 4B column with a reverse salt gradient was used as the first step. Individual tRNAsLeu were further purified by RPC-5 column chromatography at pH 4.5 and 7.5. For isolation of tRNA-Leu 2 a RPC-5 column was additionally used at pH 3.3 in the presence of 7 M urea. Using micro-column chromatography of Ti-RNAases digests, it was demonstrated that tRNA-Leu 1 and tRNA-Leu 2+ are similar in their primary structure and differ essentially from tRNA-Leu 4.     

Isolation of poly(A)-containing RNA on synthetic fluorophlogopite (Mica).

Synthetic fluorophlogopite, an aluminosilicate of the same structure as naturally occurring mineral mica in which potassium ions on the basal surface have been replaced by aluminum ions, has the ability to retain polynucleotides irreversibly. This property of Al³⁺-mica was used for irreversible adsorption of poly(U) and subsequent selective adsorption of poly(A)-containing RNA from rabbit reticulocyte polysomes at high salt concentration and its elution by 50% dimethylsulfoxide. The properties of RNA isolated on poly(U)-Al³⁺-mica were studied by sucrose density gradient centrifugation and by stimulation of globin synthesis in an in vitro protein synthesizing system from wheat germ and from Krebs II-ascites cells. The preparation contained 9s RNA species which corresponds to rabbit globin messenger RNA, and under optimal conditions it stimulated protein synthesis more than 100-fold. Polyacrylamide-gel electrophoresis in sodium dodecyl sulfate showed that synthesized product was identical with rabbit globin.     

Caenorhabditis elegans: purification of isocitrate lyase and the isolation and cell-free translation of poly(A+)RNA

Isocitrate lyase (EC 4.1.3.1) from mixed larval populations of Caenorhabditis elegans was stabilized in crude extracts by centrifugation over a 0.2-0.6 M sucrose gradient for 2.5 hr in a vertical rotor (VTi 50) at 210,000g. The peak fractions from this sucrose gradient showed a half-life of 33 hr at 30 C and 225 hr at 4 C in contrast to 2.5 and 52 hr, respectively, for the crude extract. A purification scheme involving (NH4)2SO4 precipitation and chromatography on Sepharose 6B and diethylaminoethyl-cellulose yielded isocitrate lyase that gave one band after electrophoresis in a sodium dodecyl sulfate-gel polymerized from 12% acrylamide. The purified enzyme with a molecular weight of 250,000 and subunit molecular weight of 61,600, had a specific activity of 2 mumoles glyoxylate formed min-1 mg protein-1, and was obtained in a 4% yield. Isocitrate lyase from C. elegans lost 80-85% of its activity in the precipitation by 33-55% (NH4)2SO4, but this step appeared to be necessary for purification to homogeneity. The use of fast protein liquid chromatography appeared to be promising in that it provided an enzyme preparation that was about 50% pure with a specific activity as high as 3 mumoles glyoxylate formed min-1 mg protein-1. Poly(A+)RNA was isolated from C. elegans and translated in wheat germ cell-free system. Analysis on a 10% sodium dodecyl sulfate-polyacrylamide gel showed varied translation products including one or more 60,000-Da polypeptides.     

Characterization of poly(A+)RNA in free messenger ribonucleoprotein and polysomes of mouse Taper ascites cells

Cytoplasmic extracts of mouse Taper ascites cells were centrifuged on sucrose gradients to give 0–80 S, monosome, and polysome fractions. CsCl equilibrium density centrifugation of formaldehyde-fixed material from the 0–80 S fraction demonstrated that the messenger RNA in the 0–80 S fraction was in the form of free ribonucleoprotein. The size of the poly(A⁺)RNA and the size of the poly(A) segments of these molecules were shown to be very similar in both the free mRNP² and polysome fractions. The labeling kinetics of the free mRNP poly(A⁺)RNA was similar to that of the polysomal poly(A⁺)RNA.The free mRNP poly(A⁺)RNA efficiently stimulated protein synthesis in the wheat germ cell-free system, supporting the view that it was mRNA. Two-dimensional gel electrophoresis was used to analyze the proteins whose synthesis was directed by free mRNP and polysomal poly(A⁺)RNA. The free mRNP poly(A⁺)RNA directed the synthesis of a simpler set of abundant protein products than did the polysomal poly(A⁺)RNA. Most of the free mRNP abundant protein products were also present in the polysomal products, though obvious quantitative differences were evident, indicating that each individual mRNA had its own characteristic distribution between polysomes and the translationally inactive RNP form.     

Isolation and characterization of plasma membrane from lactating bovine mammary gland

Plasma membranes were isolated from lactating bovine mammary gland. Two crude membrane fractions; medium/d 1.033 (light membrane) and 1.033/1.053 interfaces (heavy membrane), were obtained by Ficoll density gradient centrifugation of osmotically washed microsomal fraction. Two crude membranes were further purified separately by sucrose density gradient centrifugation. Both light and heavy membranes banded at a sucrose density of 1.14. The purified membranes appeared as heterogeneous smooth membrane vesicles on electron microscopy. The contaminating suborganelles were not detected. The yield of the purified membranes relative to the homogenate was 1.2%. The degree of purity of the membranes was shown by a great increase in the specific activity of 5′-nucleotidase over the homogenate of 20-fold for light membrane and of 16-fold for heavy membrane. The relative activities of Mg²⁺-ATPase, (Na⁺ + K⁺)-ATPase, γ-glutamyl transpeptidase, phosphodiesterase I, akaline phosphatase and xanthine oxidase were also high (12–18-times) and nearly 20% of these enzymes was recovered. The activity of marker enzyme for mitochondria, endoplasmic reticulum and Golgi apparatus was very low, while that of acid phosphatase for lysosome was relatively high (5-times). DNA and RNA contents were very low. The major polypeptides rich in other suborganelles were not detected profoundly in the membrane fraction and the polypeptide compositions in both light and heavy membranes were similar upon SDS-polyacrylamide gel electrophoresis.     

Isolation and translation in vitro of poly(A)+RNA from the free-living nematode Panagrellus silusiae.

Polysomal RNA was isolated from the free-living nematode Panagrellus silusiae. Passage of this RNA through a cellulose column resulted in the fractionation of the input RNA into poly(A)-RNA (ca. 97.5% of the total) and poly(A)+ RNA (ca. 2.5% of the total). RNase digestion, followed by polyacrylamide gel electrophoresis, revealed that the poly(A)+ RNA contained poly(A) tracts that ranged from 75 to 104 nucleotides in length with a mean value of about 90 residues. There was no evidence of poly(A) sequences in the poly(A)- RNA fraction. Poly(A)+ RNA gave a 25- to 50-fold stimulation (over background) of amino acid incorporation in the wheat germ cell-free protein-synthesizing system. At least 26 proteins were evident after electrophoresis in cylindrical sodium dodecyl sulfate-polyacrylamide gels. Poly(A)-RNA was capable of stimulating protein synthesis in vitro with about five discrete proteins being produced. In summary, the properties of mRNA from a simple organism such as P. silusiae are very similar to those of more complex eukaryotes.     

Distribution of cytoplasmic poly(A+)RNA sequences in free messenger ribonucleoprotein and polysomes of mouse ascites cells

The cytoplasmic non-polysomal poly(A⁺)mRNA found in the free messenger ribonucleoprotein of mouse Taper ascites cells was demonstrated by nucleic acid hybridization to contain only about 400 different mRNA sequences, in contrast to the greater than the 8000 sequences of the total cytoplasm. Approximately 50% by mass of the free RNP³-mRNA was shown to consist of only 15 different mRNA sequences and the other 50% to represent 400 different mRNA sequences. The abundant free mRNP sequences were also present in the polysomes at one-tenth of their concentration in the free mRNP. The 400 less abundant free RNP-mRNAs were found to be in the middle abundant class of total cytoplasmic sequences. The 400 less abundant free RNP-mRNA sequences were also found on the polysomes: 50% of these sequences were at similar concentrations in the polysomes as in the free mRNP, while 50% were found in the polysomes at reduced concentrations. Thus it is concluded that these mouse tumor cells maintain a highly polarized distribution of certain subsets of mRNA species between the functioning (polysomes) and non-functioning (free mRNP) compartments of the cytoplasm.     

Isolation of genomic and cDNA clones encoding bovine poly(A) binding protein II.

cDNA clones for bovine poly(A) binding protein II (PAB II) were isolated. Their sequence predicts a protein of 32.8 kDa, revising earlier estimates of molecular mass. The protein contains one putative RNA-binding domain of the RNP type, an acidic N-terminal and a basic C-terminal domain. Analyses of authentic PAB II were in good agreement with all predictions from the cDNA sequence except that a number of arginine residues appeared to be post-translationally modified. Poly(A) binding protein II expressed in Escherichia coli was active in poly(A) binding and reconstitution of processive polyadenylation, including poly(A) tail length control. The cDNA clones showed a number of potential PAB II binding sites in the 3' untranslated sequence. Bovine poly(A)+RNA contained two mRNAs hybridizing to a PAB II-specific probe. Analysis of a genomic clone revealed six introns in the coding sequence. The revised molecular mass led to a demonstration of PAB II oligomer formation and a reinterpretation of earlier data concerning the protein's binding to poly(A).     

Uptake of free plasma amino acids by the lactating cow''s udder and amino acid composition of udder lymph

1. Total α-amino N and the amounts of 24 ninhydrin-positive substances were determined in several samples of plasma and lymph from the cow's udder. The arteriovenous differences of these substances across the mammary glands were measured in several experiments performed on lactating cows and in one experiment on a `dry' cow. Udder lymph obtained from live lactating cows by a lymph fistula and taken after killing lactating cows was analysed. 2. The concentrations of the individual free amino acids in udder lymph obtained from the live cow were similar to those found in cow's plasma. The concentrations of many amino acids in udder lymph taken immediately after death were two- to four-fold higher than those of the corresponding amino acids in udder lymph obtained from the live cow. 3. Most amino acids of the blood showed a considerable decrease in concentration by passage across the lactating mammary gland. Ornithine, a non-casein amino acid, showed arteriovenous differences of up to 60% of the arterial plasma concentration. No substantial amino acid uptake by the udder could be demonstrated in the experiment on the non-lactating cow. 4. The arteriovenous differences obtained for arginine, glutamine, isoleucine, leucine, lysine, valine, threonine and histidine were probably large enough to provide all the respective amino acid residues in milk protein. 5. The uptake of aspartic acid, asparagine, glutamic acid, serine and proline by the lactating cow's udder was not sufficient to account for all these respective amino acid residues found in milk protein.     

Isolation and characteristics of bovine pituitary secretory granules

Secretory granules containing primarily growth hormone and prolactin were isolated from bovine anterior pituitaries. Marker enzyme analysis and electron microscopy indicated that the secretory granule fraction did not contain measureable amounts of other intracellular organelles. Such isolated granules were resistant to a variety of chemical and physical challenges including variations in osmolarity, ionic strength, EGTA, sonication, boiling, etc. The only treatments that were found to routinely result in granules lysis were alkaline pH and 0.5% SDS. Nonspecific leakage of both growth hormone and prolactin was less than 9% of total hormone pool even after a 60-min incubation. The release of prolactin but not growth hormone could be increased by lowering the free calcium concentration. Conversely, 10(-5) M ionophore A23187 caused a decrease in nonspecific hormone leakage. This raises the possibility that a nonexocytosis secretory pathway might be involved in pituitary hormone release. The initial secretory granule fraction was further purified using discontinuous sucrose gradient ultracentrifugation to yield a subfraction highly enriched in prolactin granules. These granules had the same stability characteristics as the original secretory granule fraction. The use of such granules should prove useful in our efforts to understand how calcium regulates cellular secretion.     

Isolation and characteristics of bovine pituitary secretory granules

Secretory granules containing primarily growth hormone and prolactin were isolated from bovine anterior pituitaries. Marker enzyme analysis and electron microscopy indicated that the secretory granule fraction did not contain measurable amounts of other intracellular organelles. Such isolated granules were resistant to a variety of chemical and physical challenges including variations in osmolarity, ionic strength, EGTA, sonication, boiling, etc. The only treatments that were found to routinely result in granules lysis were alkaline pH and 0.5% SDS. Nonspecific leakage of both groth hormone and prolactin was less than 9% of total hormone pool even after a 60-min incubation. The release of prolactin but not growth hormone could be increased by lowering the free calcium concentration. Conversely, 10⁻⁵ M ionophore A23187 caused a decrease in nonspecific hormone leakage. This raises the possibility that a nonexocytosis secretory pathway might be involved in pituitary hormone release. The initial secretory granule fraction was further purified using discontinuous sucrose gradient ultracentrifugation to yield a subfraction highly enriched in prolactin granules. These granules had the same stability characteristics as the original secretory granule fraction. The use of such granules should prove useful in our efforts to understand how calcium regulates cellular secretion.     

RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex.

The vaccinia virus-encoded heterodimer responsible for poly(A) tail elongation comprises a polyadenylylation catalytic subunit (VP55) and associated processivity factor (VP39). We show that monomeric VP39's affinity for RNA homopolymers follows the hierarchy poly(I) >poly(U) >poly(G) >poly(A) >poly(C), that the heterodimer interacts stably with 40-45 nucleotide nucleic acid segments, and that its homopolymer preference for polyadenylylation priming is comparable to the VP39 affinity hierarchy (above). For oligonucleotide ligands possessing the previously-identified (rU)2-(N)25-rU heterodimer-binding motif, the heterodimer's affinity and base-type preference are mediated via both the (rU)2and rU portions, with the greater contribution coming from (rU)2. VP39's R107 sidechain contributes to specificity at the downstream rU. Substitution of each ribouridylate of the motif with either ribothymidine or 4-thiodeoxythymidine indicated that the downstream rU interacts with both heterodimer subunits, whereas the upstream (rU)2interacts only with VP55. A 'crosslinking SELEX' approach indicated VP39-base proximity around position -10 of a 4-thioribouridine/deoxycytidine ligand pool. Upon incubating the heterodimer with a panel of identical-sequence oligonucleotides derivatized with azidophenacyl bromide at various phosphate positions, those derivatized at positions -11 to -21 photocrosslinked to both subunits in a coordinated manner. This region may therefore pass through a 'cleft' or enclosed 'channel' at the subunit interface.