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L Levinger

Publications and source records attributed to L Levinger.

At least 19 recordsLinked to original sources
PubMed1999

The 3' end CCA of mature tRNA is an antideterminant for eukaryotic 3'-tRNase.

Cytoplasmic tRNAs undergo posttranscriptional 5' and 3' end processing in the eukaryotic nucleus, and CCA (which forms the mature 3' end of all tRNAs) must be added by tRNA nucleotidyl transferase before tRNA can be aminoacylated and utilized in translation. Eukaryotic 3'-tRNase can endonucleolytically remove a 3' end trailer by cleaving on the 3' side of the discriminator base (the unpaired nucleotide 3' of the last base pair of the acceptor stem). This reaction proceeds despite a wide range in length and sequence of the 3' end trailer, except that mature tRNA containing the 3' terminal CCA is not a substrate for mouse 3'-tRNase (Nashimoto, 1997, Nucleic Acids Res 25:1148-1154). Herein, we extend this result with Drosophila and pig 3'-tRNase, using Drosophila melanogaster tRNAHis as substrate. Mature tRNA is thus prevented from recycling through 3' end processing. We also tested a series of tRNAs ending at the discriminator base (-), with one C added (+C), two Cs added (+CC), and CCA added (+CCA) as 3'-tRNase inhibitors. Inhibition was competitive with both Drosophila and pig 3'-tRNase. The product of the 3'-tRNase reaction (-) is a good 3'-tRNase inhibitor, with a KI approximately two times KM for the normal 3'-tRNase substrate. KI increases with each nucleotide added beyond the discriminator base, until when tRNA+CCA is used as inhibitor, KI is approximately forty times the substrate KM. The 3'-tRNase can thus remain free to process precursors with 3' end trailers because it is barely inhibited by tRNA+CCA, ensuring that tRNA can progress to aminoacylation. The active site of 3'-tRNase may have evolved to make an especially poor fit with tRNA+CCA.

Animals↗
PubMed1998

Matrices of paired substitutions show the effects of tRNA D/T loop sequence on Drosophila RNase P and 3'-tRNase processing.

Drosophila RNase P and 3'-tRNase endonucleolytically process the 5' and 3' ends of tRNA precursors. We examined the processing kinetics of normal substrates and the inhibitory effect of the tRNA product on both processing reactions. The product is not a good RNase P inhibitor, with a KI approximately 7 times greater than the substrate KM of approximately 200 nM and is a better inhibitor of 3'-tRNase, with a KI approximately two times the KM of approximately 80 nM. We generated matrices of substitutions at positions G18/U55 and G19/C56 (two contiguous universally conserved D/T loop base pairs) in Drosophila tRNAHis precursors. More than half the variants display a significant reduction in their ability to be processed by RNase P and 3'-tRNase. Minimal substrates with deleted D and anticodon stems could be processed by RNase P and 3'-tRNase much like full-length substrates, indicating that D/T loop contacts and D arm/enzyme contacts are not required by either enzyme. Selected tRNAs that were poor substrates for one or both enzymes were further analyzed using Michaelis-Menten kinetics and by structure probing. Processing reductions arise principally due to an increase in KM with relatively little change in Vmax, consistent with the remote location of the sequence and structure changes from the processing site for both enzymes. Local changes in variant tRNA susceptibility to RNase T1 and RNase A did not coincide with processing disabilities.

Animals↗
PubMed1995

Sequence and structure requirements for Drosophila tRNA 5'- and 3'-end processing.

Eukaryotic tRNAs are processed at their 5'- and 3'- ends by endonucleases RNase P and 3'-tRNase, respectively. We have prepared substrates for both enzymes, separated the activities from a Drosophila extract, and designed variant tRNAs to assess the effects of sequence and structure on processing. Mutations affect these reactions in similar ways; thus, RNase P and 3'-tRNase probably require similar substrate structures to maintain the catalytic fit. RNase P is more sensitive to substrate substitutions than 3'-tRNase. In three of the four stems, one substitution prevents both processing reactions while the opposite one has less effect; anticodon stem substitutions hardly affect processing, and double substitution intended to restore base pairing also restore processing to the wild type rate. Structure probing suggests that tRNA misfolding sometimes coincides with reduced processing. In other cases, processing inhibition probably results from specific unfavorable stem appositions leading to local helix deformation. A single T loop substitution disrupts the tertiary D-T loop interaction and reduces processing. We have thus begun mapping tRNA processing determinants on the global, local, and tertiary structure levels.

Animals↗
PubMed1994

Point mutations distal to the processing site affect Drosophila pre-5 S RNA processing. Long range cooperation and a breathing model.

Drosophila pre-5 S RNA, which consists of five conserved stem-loop domains and a 15-nucleotide 3' tail, is 3'-end processed to 120 nucleotide mature 5 S RNA before ribosome assembly. Large deletions in stems II and III, all of stems IV and V, and loop C prohibit Drosophila 5 S RNA processing; deletion of stem IV and half of V does not (Preiser, P. R., and Levinger, L. (1991a) J. Biol. Chem. 266, 7509-7516). Several point mutations in stem I reduce, while certain neighboring sequence changes stimulate, processing (Levinger, L., Vasisht, V., Greene, V., and Arjun, I. (1992) J. Biol. Chem. 267, 23683-23687). Herein we extend this 5 S RNA fine structure analysis to regions farther from the processing site. Most point mutations in loop B, stem III, and loop C severely inhibit processing. One loop C substitution stimulates processing; when combined with stimulatory sequence changes in stem I and loop A, these dispersed mutations improve processing manyfold, perhaps by stabilizing a required conformation or strengthening a protein-binding site. Central stem II sequence changes inhibit processing; several adjacent sequence substitutions which weaken base pairing improve processing. Combining these results with earlier work from stem I and loop A, we hypothesize that slight reduction in base pairing may improve groove access of polypeptide chains to essential contact positions.

Animals↗
PubMed1993

Poly(U)-binding protein inhibits Drosophila pre-5 S RNA 3'-exonuclease digestion.

A approximately 50-kDa protein binds specifically to the 3' terminus of 135-nucleotide Drosophila pre-5 S RNA. Unlabeled poly(U) competes out protein binding and stimulates the activity of a 3'-exonuclease, which eventually degrades the substrate to 120 nucleotides, the size of mature 5 S RNA. In its RNA binding and UV cross-linking properties, the endogenous poly(U)-binding protein resembles human La, an autoantigen that binds the U > 3 3' ends of vertebrate RNA polymerase III primary transcripts. This protein appears to inhibit a 3' exonuclease and could protect 5 S RNA for faithful processing and transport.

Animals↗
PubMed1992

The effects of stem I and loop A on the processing of 5 S rRNA from Drosophila melanogaster.

The 135-nucleotide Drosophila melanogaster 5 S RNA precursor is processed by removal of 15 nucleotides from its 3' end before incorporation into the large ribosomal subunit. Mature 5 S RNA consists of five helical stem-loops; stem IV and part of V are dispensable, whereas stem III and the 1/118 G-C base pair closest to the processing site at nucleotide 120 are required for processing (Preiser, P., and Levinger, L. (1991) J. Biol. Chem. 266, 7509-7516; Preiser, P., and Levinger, L. (1991) J. Biol. Chem. 266, 23602-23605). We have investigated the effects of stem I and loop A transversions, transitions, selected additions and deletions on 5 S RNA processing. Stem I single substitutions generally prevent processing, whereas compensatory double substitutions restore a range of processing rates. Proximal to the processing site, stem I double substitutions inhibit processing. In the distal portion of stem I and loop A, the processing effect of paired sequence changes varies widely in an irregular pattern. The 7/112 GU pair and nucleotide 13A least tolerate sequence changes; several mutations clustered close to the stem I-loop A boundary stimulate processing. We interpret these results in terms of the RNA helix path and possible RNA-protein contacts.

Animals↗
PubMed1986

Group meetings for parents and spouses of bone marrow transplant patients.

To reduce the stress and social isolation of being the parent or spouse of a patient hospitalized for bone marrow transplantation (BMT), a support group for family members was established. Sharing the common experience of the BMT procedure was valuable to family members despite differences in patient's age or disease, relationship to the patient, or socio-economic status. Recommendations are made to include similar groups in planning to meet the psychosocial needs of family members at other centers where patients are treated with high-risk, high intensity procedures.

Adolescent↗
PubMed1985

Nucleosomal structure of two Drosophila melanogaster simple satellites.

Nucleosomes have been fractionated on nondenaturing polyacrylamide gels, and nucleosome subtypes containing the Drosophila melanogaster specific protein D1 and ubiquitinated core histone H2A were identified by solubility in 0.1 M NaCl before nucleoprotein gel electrophoresis. Nucleosomes which contain DNA complementary to the 1.672 density simple satellite (sequence-AATAT-) bind protein D1, as demonstrated by two-dimensional hybridization mapping. This hybridization pattern allows the identification of D1 dinucleosomes, which, like D1 mononucleosomes, are reduced in mobility on the first dimension (nucleoprotein) gel by the addition of D1, an AT sequence-specific DNA-binding protein. The 1.705 density simple satellite (sequence-AAGAG-) is also found in nucleosomes, in a radically different subset from those of the -AATAT- DNA sequence. -AAGAG- nucleosomes do not contain D1 protein, but appear to be enriched in ubiquitinated core histone H2A. One-dimensional hybridization patterns suggest that -AAGAG- nucleosomal DNA is rapidly trimmed to a shorter DNA length than either bulk or -AATAT- nucleosomes.

Animals↗
PubMed1982

On the chromatin structure of the amplified, transcriptionally active gene for dihydrofolate reductase in mouse cells.

The method for two-dimensional hybridization mapping of nucleosomes (Levinger, L., Barsoum, J., and Varshavsky, A. (1981) J. Mol. Biol. 146, 287-304) was used to analyze chromatin structure of the gene for dihydrofolate reductase (DHF reductase; 5,6,7,8-tetrahydrofolate:NADP+ oxidoreductase (EC 1.5.1.3)) in L5178Y-R mouse cells. The DHF reductase gene in these cells is amplified about 350-fold as a result of selection for resistance to methotrexate. Dramatic overproduction of DHF reductase mRNA in L5178Y-R cells suggests that most of the DHF reductase genes in these cells are transcribed. We report that all major mononucleosomal species resolvable by two-dimensional fractionation are detected by both DHF reductase- and satellite DNA-specific hybridization probes. Although the DHF reductase and satellite hybridization patterns differ somewhat from each other and from the total mononucleosomal pattern, their overall similarity is very high. In particular, no large differences in the abundance of mononucleosomes containing high mobility group non-histone proteins (HMG) 14 and 17 are seen between the DHF reductase and satellite chromatin regions under a wide variety of conditions for chromatin isolation, digestion, and fractionation. Possible interpretations of the apparent lack of selectivity of HMG-chromatin interactions in this system are discussed. We also found that the amplified DHF reductase genes possess a wide range of nucleosomal repeat lengths close to that in the bulk chromatin. In contrast, the range of nucleosomal repeat lengths in the satellite chromatin is much narrower than in both DHF reductase and bulk chromatin.

Animals↗
PubMed1982

Selective arrangement of ubiquitinated and D1 protein-containing nucleosomes within the Drosophila genome.

We have a new approach, two-dimensional hybridization mapping of nucleosomes, to compare the structures of mononucleosomes from different regions of the Drosophila melanogaster genome. Approximately one in two nucleosomes of the transcribed copia and heat-shock 70 (hsp 70) genes in nonshocked cultured cells contains ubiquitin-H2A (uH2A) semihistone, a covalent conjugate of histone H2A and a small protein, ubiquitin. In striking contrast, less than one in 25 nucleosomes of tandemly repeated, nontranscribed 1.688 satellite DNA contains uH2A, suggesting that most of the nucleosomal uH2A is located in transcribed genes. Approximately 25% of all nucleosomes are ubiquitinated in nonsynchronized cultured Drosophila cells. The hsp 70 genes in nonshocked cells occur in nucleosomes, are greatly enriched in uH2A and are not digested preferentially by staphylococcal nuclease. In contrast, the same genes in chromatin from heat-shocked cells are highly sensitive to staphylococcal nuclease and no longer possess nucleosomal organization recognizable with this probe. Histone ubiquitination in transcribed nucleosomes may prevent formation of higher order chromosomal structures by modifying nucleosome-nucleosome interactions. The observed loss of nucleosomal organization in very actively transcribed genes, such as the hsp 70 genes in shocked cells, may be related to the recent finding that ubiquitin conjugates are substrates for the cytoplasmic ATP-dependent proteolytic system. We have also found that 1.688 satellite mononucleotomes contain a specific approximately 50,000 dalton nonhistone protein, D1, in addition to being extremely under-ubiquitinated. D1 may be involved in formation of the highly compact structure of satellite heterochromatin.

Animals↗
PubMed1982

Protein D1 preferentially binds A + T-rich DNA in vitro and is a component of Drosophila melanogaster nucleosomes containing A + T-rich satellite DNA.

Our previous work [Levinger, L. & Varshavsky, A. (1982) Cell 28, 375-385] has shown that D1, a 50-kilodalton chromosomal protein of Drosophila melanogaster, is specifically associated with isolated nucleosomes that contain a complex A + T-rich satellite DNA with buoyant density of 1.688 g/ml. We show here that D1 is also a component of nucleosomes containing a simple-sequence, pure A + T satellite DNA, buoyant density 1.672 g/ml. Furthermore, using a modification of a protein blotting technique in which proteins are not exposed to dodecyl sulfate denaturation, we have found that D1 preferentially binds to A + T-rich double-stranded DNA in vitro, and it is apparently the only abundant nuclear protein in cultured D. melanogaster cells that possesses this property. Synthetic poly[d(A-T)].poly[d(A-T)] and poly(dA).poly(dT) duplexes effectively compete in vitro with A + T-rich D. melanogaster satellite DNAs for binding to D1, whereas total Escherichia coli DNA is an extremely poor competitor. These findings strongly suggest that D1 is a specific component of A + T-rich, tandemly repeated, heterochromatic regions, which constitute up to 15-20% of the total D. melanogaster genome. Possible functions of D1 protein include compaction of A + T-rich heterochromatin and participation in microtubule-centromere interactions in mitosis. In addition, D1 may prevent nonspecific binding to A + T-rich satellite DNA of other nuclear proteins that have a preference for AT-DNA, such as RNA polymerase or regulatory proteins, and may also participate in the higher-order chromatin organization outside tandemly repetitive regions by binding to nonrandomly positioned stretches of A + T-rich DNA.

Adenine Nucleotides↗
PubMed1981

Heat-shock proteins of Drosophila are associated with nuclease-resistant, high-salt-resistant nuclear structures.

Proteins produced in cultured Drosophila cells during the heat-shock response (HSPs) were recently shown by autoradiography to be confined in large measure to the cell nucleus. We report here that nuclear HSPs are not associated with nucleosomes solubilizes by treatment with staphylococcal nuclease at low ionic strength nor are HSPs released by extraction with high salt, which solubilized most of the remaining histones and DNA. Possible functions of nuclear HSPs are discussed.

Animals↗
PubMed1980

High-resolution fractionation of nucleosomes: minor particles, "whiskers," and separation of mononucleosomes containing and lacking A24 semihistone.

Staphyloccal nuclease digests of HeLa chromatin fractionated on low ionic strength nucleoprotein gels have been further analyzed by second-dimension DNA and protein gel electrophoresis. In vivo radioactive labeling of chromatin components and use of longer gels allowed a higher sensitivity and resolution than has been previously reported for this approach. A number of nonhistone protein spots and about 20 DNA spots can be detected in the mononucleosomal region of the second-dimension gel. In particular, there are three DNA spots identical in DNA size that correspond to three discrete kinds of core mononucleosomes resolved on the first-dimension nucleoprotein gel. Analysis of protein composition shows that the most rapidly migrating particle contains all four core histones but no A24 semihistone (A24 is a covalent conjugate of histone H2A and a specific nonhistone protein, ubiquitin), whereas the other two core mononucleosomes contain A24 semihistone. Thus, one can now quantitatively separate the A24-lacking core mononucleosomes from those containing A24, making it possible to directly address the question of whether A24 is associated with nucleosomes containing a specific subset of DNA sequences. Additional features of two-dimensional nucleoprotein-DNA patterns are "whiskers," which run slower than core mononucleosomes in the nucleoprotein dimension and both faster and slower than core-length DNA in the DNA dimension. In more extensive digests, "secondary whiskers" are observed, which run faster than core mononucleosomes in both dimensions and appear to coincide with previously described subnucleosomal particles SN7 and SN8 [Bakayev, V., Bakayeva, T. & Varshavsky, A. (1977) Cell 11, 619-629]. Possible mechanisms of whisker formation are discussed.

Base Sequence↗