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Matson MEH, Liang Q, Lonardi S, Judelson HS. Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly. PLoS Pathog 2022; 18:e1010869. [PMID: 36215336 PMCID: PMC9584435 DOI: 10.1371/journal.ppat.1010869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/20/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.
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Affiliation(s)
- Michael E. H. Matson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
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2
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Tasak M, Phizicky EM. Initiator tRNA lacking 1-methyladenosine is targeted by the rapid tRNA decay pathway in evolutionarily distant yeast species. PLoS Genet 2022; 18:e1010215. [PMID: 35901126 PMCID: PMC9362929 DOI: 10.1371/journal.pgen.1010215] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/09/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
All tRNAs have numerous modifications, lack of which often results in growth defects in the budding yeast Saccharomyces cerevisiae and neurological or other disorders in humans. In S. cerevisiae, lack of tRNA body modifications can lead to impaired tRNA stability and decay of a subset of the hypomodified tRNAs. Mutants lacking 7-methylguanosine at G46 (m7G46), N2,N2-dimethylguanosine (m2,2G26), or 4-acetylcytidine (ac4C12), in combination with other body modification mutants, target certain mature hypomodified tRNAs to the rapid tRNA decay (RTD) pathway, catalyzed by 5’-3’ exonucleases Xrn1 and Rat1, and regulated by Met22. The RTD pathway is conserved in the phylogenetically distant fission yeast Schizosaccharomyces pombe for mutants lacking m7G46. In contrast, S. cerevisiae trm6/gcd10 mutants with reduced 1-methyladenosine (m1A58) specifically target pre-tRNAiMet(CAU) to the nuclear surveillance pathway for 3’-5’ exonucleolytic decay by the TRAMP complex and nuclear exosome. We show here that the RTD pathway has an unexpected major role in the biology of m1A58 and tRNAiMet(CAU) in both S. pombe and S. cerevisiae. We find that S. pombe trm6Δ mutants lacking m1A58 are temperature sensitive due to decay of tRNAiMet(CAU) by the RTD pathway. Thus, trm6Δ mutants had reduced levels of tRNAiMet(CAU) and not of eight other tested tRNAs, overexpression of tRNAiMet(CAU) restored growth, and spontaneous suppressors that restored tRNAiMet(CAU) levels had mutations in dhp1/RAT1 or tol1/MET22. In addition, deletion of cid14/TRF4 in the nuclear surveillance pathway did not restore growth. Furthermore, re-examination of S. cerevisiae trm6 mutants revealed a major role of the RTD pathway in maintaining tRNAiMet(CAU) levels, in addition to the known role of the nuclear surveillance pathway. These findings provide evidence for the importance of m1A58 in the biology of tRNAiMet(CAU) throughout eukaryotes, and fuel speculation that the RTD pathway has a major role in quality control of body modification mutants throughout fungi and other eukaryotes.
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Affiliation(s)
- Monika Tasak
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, United States of America
- * E-mail:
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3
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Blewett NH, Maraia RJ. La involvement in tRNA and other RNA processing events including differences among yeast and other eukaryotes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:361-372. [PMID: 29397330 DOI: 10.1016/j.bbagrm.2018.01.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 10/25/2022]
Abstract
The conserved nuclear RNA-binding factor known as La protein arose in an ancient eukaryote, phylogenetically associated with another eukaryotic hallmark, synthesis of tRNA by RNA polymerase III (RNAP III). Because 3'-oligo(U) is the sequence-specific signal for transcription termination by RNAP III as well as the high affinity binding site for La, the latter is linked to the intranuclear posttranscriptional processing of eukaryotic precursor-tRNAs. The pre-tRNA processing pathway must accommodate a variety of substrates that are destined for both common steps as well as tRNA-specific events. The order of intranuclear pre-tRNA processing steps is mediated in part by three activities derived from interaction with La protein: 3'-end protection from untimely decay by 3' exonucleases, nuclear retention and chaperone activity that helps prevent pre-tRNA misfolding and mischanneling into offline pathways. A focus of this perspective will be on differences between yeast and mammals in the subcellular partitioning of pre-tRNA intermediates and differential interactions with La. We review how this is most relevant to pre-tRNA splicing which occurs in the cytoplasm of yeasts but in nuclei of higher eukaryotes. Also divergent is La architecture, comprised of three RNA-binding domains in organisms in all examined branches of the eukaryal tree except yeast, which have lost the C-terminal RNA recognition motif-2α (RRM2α) domain. We also review emerging data that suggest mammalian La interacts with nuclear pre-tRNA splicing intermediates and may impact this branch of the tRNA maturation pathway. Finally, because La is involved in intranuclear tRNA biogenesis we review relevant aspects of tRNA-associated neurodegenerative diseases. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Commissioned Corps, U.S. Public Health Service, Rockville, MD, USA.
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4
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Rijal K, Maraia RJ, Arimbasseri AG. A methods review on use of nonsense suppression to study 3' end formation and other aspects of tRNA biogenesis. Gene 2014; 556:35-50. [PMID: 25447915 DOI: 10.1016/j.gene.2014.11.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 12/26/2022]
Abstract
Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to Schizosaccharomyces pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5' and 3' processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3' oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3' oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a 'technical approaches' section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses.
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Affiliation(s)
- Keshab Rijal
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Richard J Maraia
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Aneeshkumar G Arimbasseri
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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5
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Saito Y, Takeda J, Adachi K, Nobe Y, Kobayashi J, Hirota K, Oliveira DV, Taoka M, Isobe T. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway. PLoS One 2014; 9:e112488. [PMID: 25401760 PMCID: PMC4234475 DOI: 10.1371/journal.pone.0112488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/17/2014] [Indexed: 01/07/2023] Open
Abstract
Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNASer-Met. To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNASer-Met, suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry–based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute “Domain 1” in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.
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Affiliation(s)
- Yuichiro Saito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Jun Takeda
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Kousuke Adachi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Yuko Nobe
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Junya Kobayashi
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Douglas V. Oliveira
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan
- * E-mail:
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6
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Hottinger H, Leupold U. Putative frameshift suppressors in Schizosaccharomyces pombe. Curr Genet 2013; 3:133-43. [PMID: 24190059 DOI: 10.1007/bf00365717] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/1981] [Indexed: 10/26/2022]
Abstract
Nine genetically distinct suppressors of ICR-170-induced ade6 and ade7 mutations have been identified in Schizosaccharomyces pombe. The nine suppressors of ICR-170-induced and spontaneous origin have been assigned to the three chromosomes by haploidization and meiotic analysis. They do not suppress missense or nonsense mutations and are therefore likely to be frameshift suppressors. Based on the spectrum of suppression, the nine suppressors fall into two mutually exclusive groups. Group I comprises the two dominant suppressors sufl and suf11. Group II consists of the seven dominant suppressors suf2 through suf8. The suppressors of both groups are inefficient and all lead to a marked reduction of growth rate. Within suppressor groups, combinations of suppressors lead to drastic reductions of growth rates and to an increased efficiency of suppression. Freely segregating modifiers of suppression increasing and decreasing the efficiency of supression have been found for all the suppressors. The two omnipotent suppressors sup1 and sup2 increase the efficiency of suppression of some frameshift suppressors. The suf5 locus is unstable and reverts at very high frequency both meiotically and mitotically.
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Affiliation(s)
- H Hottinger
- Institute of General Microbiology, University of Bern, Altenbergrain 21, CH-3013, Bern, Switzerland
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7
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Rijal K, Maraia RJ. RNA polymerase III mutants in TFIIFα-like C37 that cause terminator readthrough with no decrease in transcription output. Nucleic Acids Res 2012; 41:139-55. [PMID: 23093604 PMCID: PMC3592421 DOI: 10.1093/nar/gks985] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How eukaryotic RNA polymerases switch from elongation to termination is unknown. Pol III subunits Rpc53 and Rpc37 (C53/37) form a heterodimer homologous to TFIIFβ/α. C53/37 promotes efficient termination and together with C11 also mediates pol III recycling in vitro. We previously developed Schizosaccharomyces pombe strains that report on two pol III termination activities: RNA oligo(U) 3′-end cleavage, and terminator readthrough. We randomly mutagenized C53 and C37 and isolated many C37 mutants with terminator readthrough but no comparable C53 mutants. The majority of C37 mutants have strong phenotypes with up to 40% readthrough and map to a C-terminal tract previously localized near Rpc2p in the pol III active center while a minority represent a distinct class with weaker phenotype, less readthrough and 3′-oligo(U) lengthening. Nascent pre-tRNAs released from a terminator by C37 mutants have shorter 3′-oligo(U) tracts than in cleavage-deficient C11 double mutants indicating RNA 3′-end cleavage during termination. We asked whether termination deficiency affects transcription output in the mutants in vivo both by monitoring intron-containing nascent transcript levels and 14C-uridine incorporation. Surprisingly, multiple termination mutants have no decrease in transcript output relative to controls. These data are discussed in context of current models of pol III transcription.
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Affiliation(s)
- Keshab Rijal
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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8
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Iben JR, Mazeika JK, Hasson S, Rijal K, Arimbasseri AG, Russo AN, Maraia RJ. Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III. Nucleic Acids Res 2011; 39:6100-13. [PMID: 21450810 PMCID: PMC3152337 DOI: 10.1093/nar/gkr182] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl regions of C11 are homologous to domains of the pol II subunit Rpb9p, and the pol II elongation and RNA cleavage factor, TFIIS, respectively. We isolated C11 mutants from Schizosaccharomyces pombe that cause pol III to readthrough terminators in vivo. Mutant RNA confirmed the presence of terminator readthrough transcripts. A predominant mutation site, F32, resides in the C11 Rpb9-like domain. Another mutagenic approach confirmed the F32 mutation and also isolated I34 and Y30 mutants. Modeling Y30, F32 and I34 of C11 in available cryoEM pol III structures predicts a hydrophobic patch that may interface with C53/37. Another termination mutant, Rpc2-T455I, appears to reside internally, near the RNA-DNA hybrid. We show that the Rpb9 and TFIIS homologous mutants of C11 reflect distinct activities, that differentially affect terminator recognition and RNA 3' cleavage. We propose that these C11 domains integrate action at the upper jaw and center of pol III during termination.
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Affiliation(s)
- James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Commissioned Corps, US Public Health Service, Bethesda, MD, USA. 20892
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9
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Marck C, Kachouri-Lafond R, Lafontaine I, Westhof E, Dujon B, Grosjean H. The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res 2006; 34:1816-35. [PMID: 16600899 PMCID: PMC1447645 DOI: 10.1093/nar/gkl085] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 02/03/2006] [Accepted: 03/03/2006] [Indexed: 01/09/2023] Open
Abstract
We present the first comprehensive analysis of RNA polymerase III (Pol III) transcribed genes in ten yeast genomes. This set includes all tRNA genes (tDNA) and genes coding for SNR6 (U6), SNR52, SCR1 and RPR1 RNA in the nine hemiascomycetes Saccharomyces cerevisiae, Saccharomyces castellii, Candida glabrata, Kluyveromyces waltii, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and the archiascomycete Schizosaccharomyces pombe. We systematically analysed sequence specificities of tRNA genes, polymorphism, variability of introns, gene redundancy and gene clustering. Analysis of decoding strategies showed that yeasts close to S.cerevisiae use bacterial decoding rules to read the Leu CUN and Arg CGN codons, in contrast to all other known Eukaryotes. In D.hansenii and C.albicans, we identified a novel tDNA-Leu (AAG), reading the Leu CUU/CUC/CUA codons with an unusual G at position 32. A systematic 'p-distance tree' using the 60 variable positions of the tRNA molecule revealed that most tDNAs cluster into amino acid-specific sub-trees, suggesting that, within hemiascomycetes, orthologous tDNAs are more closely related than paralogs. We finally determined the bipartite A- and B-box sequences recognized by TFIIIC. These minimal sequences are nearly conserved throughout hemiascomycetes and were satisfactorily retrieved at appropriate locations in other Pol III genes.
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MESH Headings
- Ascomycota/enzymology
- Ascomycota/genetics
- Base Sequence
- Codon
- Conserved Sequence
- DNA, Fungal/chemistry
- Evolution, Molecular
- Genes, Fungal
- Genome, Fungal
- Genomics
- Introns
- Molecular Sequence Data
- Multigene Family
- Polymorphism, Genetic
- Promoter Regions, Genetic
- RNA Polymerase III/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Untranslated/genetics
- Transcription Factors, TFIII/metabolism
- Transcription, Genetic
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Affiliation(s)
- Christian Marck
- Service de Biochimie et de Génétique Moléculaire, Bât 144. CEA/Saclay, 91191 Gif-sur-Yvette, France.
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10
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Braglia P, Percudani R, Dieci G. Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem 2005; 280:19551-62. [PMID: 15788403 DOI: 10.1074/jbc.m412238200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic RNA polymerase (Pol) III terminates transcription at short runs of T residues in the coding DNA strand. By genomic analysis, we found that T(5) and T(4) are the shortest Pol III termination signals in yeasts and mammals, respectively, and that, at variance with yeast, oligo(dT) terminators longer than T(5) are very rare in mammals. In Saccharomyces cerevisiae, the strength of T(5) as a terminator was found to be largely influenced by both the upstream and the downstream sequence context. In particular, the CT sequence, which is naturally present downstream of T(5) in the 3'-flank of some tDNAs, was found to act as a terminator-weakening element that facilitates translocation by reducing Pol III pausing at T(5). In contrast, tDNA transcription termination was highly efficient when T(5) was followed by an A or G residue. Surprisingly, however, when a termination-proficient T(5) signal was taken out from the tDNA context and placed downstream of a fragment of the SCR1 gene, its termination activity was compromised, both in vitro and in vivo. Even the T(6) sequence, acting as a strong terminator in tRNA gene contexts, was unexpectedly weak within the SNR52 transcription unit, where it naturally occurs. The observed sequence context effects reflect intrinsic recognition properties of Pol III, because they were still observed in a simplified in vitro transcription system only consisting of purified RNA polymerase and template DNA. Our findings strengthen the notion that termination signal recognition by Pol III is influenced in a complex way by the region surrounding the T cluster and suggest that read-through transcription beyond T clusters might play a significant role in the biogenesis of class III gene products.
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Affiliation(s)
- Priscilla Braglia
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Italy
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11
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Kruszka K, Barneche F, Guyot R, Ailhas J, Meneau I, Schiffer S, Marchfelder A, Echeverría M. Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. EMBO J 2003; 22:621-32. [PMID: 12554662 PMCID: PMC140725 DOI: 10.1093/emboj/cdg040] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) guiding modifications of ribosomal RNAs and other RNAs display diverse modes of gene organization and expression depending on the eukaryotic system: in animals most are intron encoded, in yeast many are monocistronic genes and in plants most are polycistronic (independent or intronic) genes. Here we report an unprecedented organization: plant dicistronic tRNA-snoRNA genes. In Arabidopsis thaliana we identified a gene family encoding 12 novel box C/D snoRNAs (snoR43) located just downstream from tRNA(Gly) genes. We confirmed that they are transcribed, probably from the tRNA gene promoter, producing dicistronic tRNA(Gly)-snoR43 precursors. Using transgenic lines expressing a tagged tRNA-snoR43.1 gene we show that the dicistronic precursor is accurately processed to both snoR43.1 and tRNA(Gly). In addition, we show that a recombinant RNase Z, the plant tRNA 3' processing enzyme, efficiently cleaves the dicistronic precursor in vitro releasing the snoR43.1 from the tRNA(Gly). Finally, we describe a similar case in rice implicating a tRNA(Met-e) expressed in fusion with a novel C/D snoRNA, showing that this mode of snoRNA expression is found in distant plant species.
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Affiliation(s)
| | - Fredy Barneche
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Romain Guyot
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | | | | | - Steffen Schiffer
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Anita Marchfelder
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
| | - Manuel Echeverría
- Laboratoire Génome et Développement des Plantes, UMR CNRS 5096, Université de Perpignan, 66860 Perpignan cedex, France,
Molecular Biology Department, University of Geneva-Sciences II, 30 Quai Ernest Ansermet, 1211-Geneva, Institut of Plant Biology, University of Zurich, Zollikerstrasse 19, 8008-Zurich, Switzerland and Molekulare Botanik, Universität Ulm, 89069 Ulm, Germany Corresponding author e-mail:
K.Kruszka, F.Barneche and R.Guyot contributed equally to this work
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12
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Feschotte C, Fourrier N, Desmons I, Mouchès C. Birth of a retroposon: the Twin SINE family from the vector mosquito Culex pipiens may have originated from a dimeric tRNA precursor. Mol Biol Evol 2001; 18:74-84. [PMID: 11141194 DOI: 10.1093/oxfordjournals.molbev.a003721] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
SINEs are short interspersed repetitive elements found in many eukaryotic genomes and are believed to propagate by retroposition. Almost all SINEs reported to date have a composite structure made of a 5' tRNA-related region followed by a tRNA-unrelated region. Here, we describe a new type of tRNA-derived SINEs from the genome of the mosquito Culex pipiens. These elements, called TWINs, are approximately 220 bp long and reiterated at approximately 500 copies per haploid genome. TWINs have a unique structure compared with other tRNA-SINEs described so far. They consist of two tRNA(Arg)-related regions separated by a 39-bp spacer. Other tRNA-unrelated sequences include a 5-bp leader preceding the left tRNA-like unit and a short trailer located downstream of the right tRNA-like region. This 3' trailer is a 10-bp sequence that is ended by a TTTT motif and followed by a polyA tract of variable length. The right tRNA-like unit also contains a 16-bp sequence which is absent in the left one and appears to be located in the ancestral anticodon stem precisely at a position expected for a nuclear tRNA intron. According to this singular structure, we hypothesize that the TWIN: SINE family originated from an unprocessed polymerase III transcript containing two tRNA sequences. We suggest that some peculiar properties acquired by this dicistronic transcript, such as a polyA tail and a 3' stem-loop secondary structure, promote its retroposition by increasing its chances of being recognized by a reverse transcriptase encoded elsewhere in the C. pipiens genome.
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Affiliation(s)
- C Feschotte
- Laboratoire Ecologie Moléculaire et Faculté Sciences et Techniques Côte-Basque, Université de Pau et des Pays de l'Adour, Pau, France
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13
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Huang Y, Hamada M, Maraia RJ. Isolation and cloning of four subunits of a fission yeast TFIIIC complex that includes an ortholog of the human regulatory protein TFIIICbeta. J Biol Chem 2000; 275:31480-7. [PMID: 10906331 DOI: 10.1074/jbc.m004635200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic tRNA genes are controlled by proximal and downstream elements that direct transcription by RNA polymerase (pol) III. Transcription factors (TFs) that reside near the initiation site are related in Saccharomyces cerevisiae and humans, while those that reside at or downstream of the B box share no recognizable sequence relatedness. Human TFIIICbeta is a transcriptional regulator that exhibits no homology to S. cerevisiae sequences on its own. We cloned an essential Schizosaccharomyces pombe gene that encodes a protein, Sfc6p, with homology to the S. cerevisiae TFIIIC subunit, TFC6p, that extends to human TFIIICbeta. We also isolated and cloned S. pombe homologs of three other TFIIIC subunits, Sfc3p, Sfc4p, and Sfc1p, the latter two of which are conserved from S. cerevisiae to humans, while the former shares homology with the S. cerevisiae B box-binding homolog only. Sfc6p is a component of a sequence-specific DNA-binding complex that also contains the B box-binding homolog, Sfc3p. Immunoprecipitation of Sfc3p further revealed that Sfc1p, Sfc3p, Sfc4p, and Sfc6p are associated in vivo and that the isolated Sfc3p complex is active for pol III-mediated transcription of a S. pombe tRNA gene in vitro. These results establish a link between the downstream pol III TFs in yeast and humans.
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Affiliation(s)
- Y Huang
- Laboratory of Molecular Growth Regulation, NICHD, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
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14
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Hamada M, Sakulich AL, Koduru SB, Maraia RJ. Transcription termination by RNA polymerase III in fission yeast. A genetic and biochemically tractable model system. J Biol Chem 2000; 275:29076-81. [PMID: 10843998 DOI: 10.1074/jbc.m003980200] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In order for RNA polymerase (pol) III to produce a sufficient quantity of RNAs of appropriate structure, initiation, termination, and reinitiation must be accurate and efficient. Termination-associated factors have been shown to facilitate reinitiation and regulate transcription in some species. Suppressor tRNA genes that differ in the dT(n) termination signal were examined for function in Schizosaccharomyces pombe. We also developed an S. pombe extract that is active for tRNA transcription that is described here for the first time. The ability of this tRNA gene to be transcribed in extracts from different species allowed us to compare termination in three model systems. Although human pol III terminates efficiently at 4 dTs and S. pombe at 5 dTs, Saccharomyces cerevisiae pol III requires 6 dTs to direct comparable but lower termination efficiency and also appears qualitatively distinct. Interestingly, this pattern of sensitivity to a minimal dT(n) termination signal was found to correlate with the sensitivity to alpha-amanitin, as S. pombe was intermediate between human and S. cerevisiae pols III. The results establish that the pols III of S. cerevisiae, S. pombe, and human exhibit distinctive properties and that termination occurs in S. pombe in a manner that is functionally more similar to human than is S. cerevisiae.
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Affiliation(s)
- M Hamada
- Laboratory of Molecular Growth Regulation, NICHHD, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
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15
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Intine RV, Sakulich AL, Koduru SB, Huang Y, Pierstorff E, Goodier JL, Phan L, Maraia RJ. Control of transfer RNA maturation by phosphorylation of the human La antigen on serine 366. Mol Cell 2000; 6:339-48. [PMID: 10983981 DOI: 10.1016/s1097-2765(00)00034-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conversion of a nascent precursor tRNA to a mature functional species is a multipartite process that involves the sequential actions of several processing and modifying enzymes. La is the first protein to interact with pre-tRNAs in eukaryotes. An opal suppressor tRNA served as a functional probe to examine the activities of yeast and human (h)La proteins in this process in fission yeast. An RNA recognition motif and Walker motif in the metazoan-specific C-terminal domain (CTD) of hLa maintain pre-tRNA in an unprocessed state by blocking the 5'-processing site, impeding an early step in the pathway. Faithful phosphorylation of hLa on serine 366 reverses this block and promotes tRNA maturation. The results suggest that regulation of tRNA maturation at the level of RNase P cleavage may occur via phosphorylation of serine 366 of hLa.
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Affiliation(s)
- R V Intine
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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16
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Abstract
Ribonuclease P (RNase P) is the endoribonuclease that generates the mature 5'-ends of tRNA by removal of the 5'-leader elements of precursor-tRNAs. This enzyme has been characterized from representatives of all three domains of life (Archaea, Bacteria, and Eucarya) (1) as well as from mitochondria and chloroplasts. The cellular and mitochondrial RNase Ps are ribonucleoproteins, whereas the most extensively studied chloroplast RNase P (from spinach) is composed solely of protein. Remarkably, the RNA subunit of bacterial RNase P is catalytically active in vitro in the absence of the protein subunit (2). Although RNA-only activity has not been demonstrated for the archael, eucaryal, or mitochondrial RNAs, comparative sequence analysis has established that these RNAs are homologous (of common ancestry) to bacterial RNA. RNase P holoenzymes vary greatly in organizational complexity across the phylogenetic domains, primarily because of differences in the RNase P protein subunits: Mitochondrial, archaeal, and eucaryal holoenzymes contain larger, and perhaps more numerous, protein subunits than do the bacterial holoenzymes. However, that the nonbacterial RNase P RNAs retain significant structural similarity to their catalytically active bacterial counterparts indicates that the RNA remains the catalytic center of the enzyme.
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Affiliation(s)
- D N Frank
- Department of Plant and Microbial Biology, University of California, Berkeley 94720-3102, USA.
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17
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Abstract
Mature tRNAs are remarkably similar in all cells. However, the primary transcripts from tRNA genes can vary considerably due to differences in gene organization. RNase P must be able to recognize the elements that are common to all tRNA precursors to accurately remove the 5'-leader sequences.
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Affiliation(s)
- C J Green
- SRI International, Menlo Park, CA, USA
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18
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Drabkin HJ, Helk B, RajBhandary UL. The role of nucleotides conserved in eukaryotic initiator methionine tRNAs in initiation of protein synthesis. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74591-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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19
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Otter CA, Edqvist J, Stråby KB. Characterization of transcription and processing from plasmids that use polIII and a yeast tRNA gene as promoter to transcribe promoter-deficient downstream DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1131:62-8. [PMID: 1581361 DOI: 10.1016/0167-4781(92)90099-l] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transfer RNA (tRNA) with mutations affecting the internal promoters and thereby causing them to be nontranscribable by polIII (exemplified, e.g., by nematode tDNAPro with large insertions between the two internal promoters) could be transcribed by polIII both in vitro (yeast) and in vivo (oocytes) when cloned behind a yeast tRNAArg gene. PolIII initiated RNA synthesis could also proceed into a downstream structural gene normally read by polIII. the resultant yeast-nematode dimeric tRNA linked in front of mRNA sequences was recognized by processing enzymes to give mature tRNA. Thus, a yeast tRNA gene preceded by its 5' flank can function as a promoter for polIII transcription of any DNA, also of DNA coding for genes that otherwise could not have been expressed either in vitro or in vivo.
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Affiliation(s)
- C A Otter
- Department of Microbiology, University of Umeå, Sweden
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20
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Clustered tRNA genes in Schizosaccharomyces pombe centromeric DNA sequence repeats. Proc Natl Acad Sci U S A 1991; 88:1306-10. [PMID: 1996332 PMCID: PMC51006 DOI: 10.1073/pnas.88.4.1306] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The centromere-associated B' and B DNA sequence repeats of Schizosaccharomyces pombe chromosomes I and II have been found to contain clusters of tRNA genes. The centromere II region (cen2) includes at least 22 tRNA genes distributed among five copies of the B sequence repeat containing genes specifying tRNA(Ile), tRNA(Ala), and tRNA(Val). Individual B repeats are variously associated with other tRNA genes, including those specifying tRNA(Lys), tRNA(Arg), and tRNA(Glu2). The centromere I region (cen1) contains at least six tRNA genes in two copies of the B' repeated element, including genes specifying tRNA(Ile), tRNA(Ala), and tRNA(Glu3). Multiple tandemly arranged clusters of tRNA genes are presumably conserved due to restricted recombination frequencies in the centromere regions.
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21
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Expression and function of a human initiator tRNA gene in the yeast Saccharomyces cerevisiae. Mol Cell Biol 1990. [PMID: 2201892 DOI: 10.1128/mcb.10.9.4486] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We showed previously that the human initiator tRNA gene, in the context of its own 5'- and 3'-flanking sequences, was not expressed in Saccharomyces cerevisiae. Here we show that switching its 5'-flanking sequence with that of a yeast arginine tRNA gene allows its functional expression in yeast cells. The human initiator tRNA coding sequence was either cloned downstream of the yeast arginine tRNA gene, with various lengths of intergenic spacer separating them, or linked directly to the 5'-flanking sequence of the yeast arginine tRNA coding sequence. The human initiator tRNA made in yeast cells can be aminoacylated with methionine, and it was clearly separated from the yeast initiator and elongator methionine tRNAs by RPC-5 column chromatography. It was also functional in yeast cells. Expression of the human initiator tRNA in transformants of a slow-growing mutant yeast strain, in which three of the four endogenous initiator tRNA genes had been inactivated by gene disruption, resulted in enhancement of the growth rate. The degree of growth rate enhancement correlated with the steady-state levels of human tRNA in the transformants. Besides providing a possible assay for in vivo function of mutant human initiator tRNAs, this work represents the only example of the functional expression of a vertebrate RNA polymerase III-transcribed gene in yeast cells.
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22
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Francis MA, Rajbhandary UL. Expression and function of a human initiator tRNA gene in the yeast Saccharomyces cerevisiae. Mol Cell Biol 1990; 10:4486-94. [PMID: 2201892 PMCID: PMC361035 DOI: 10.1128/mcb.10.9.4486-4494.1990] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We showed previously that the human initiator tRNA gene, in the context of its own 5'- and 3'-flanking sequences, was not expressed in Saccharomyces cerevisiae. Here we show that switching its 5'-flanking sequence with that of a yeast arginine tRNA gene allows its functional expression in yeast cells. The human initiator tRNA coding sequence was either cloned downstream of the yeast arginine tRNA gene, with various lengths of intergenic spacer separating them, or linked directly to the 5'-flanking sequence of the yeast arginine tRNA coding sequence. The human initiator tRNA made in yeast cells can be aminoacylated with methionine, and it was clearly separated from the yeast initiator and elongator methionine tRNAs by RPC-5 column chromatography. It was also functional in yeast cells. Expression of the human initiator tRNA in transformants of a slow-growing mutant yeast strain, in which three of the four endogenous initiator tRNA genes had been inactivated by gene disruption, resulted in enhancement of the growth rate. The degree of growth rate enhancement correlated with the steady-state levels of human tRNA in the transformants. Besides providing a possible assay for in vivo function of mutant human initiator tRNAs, this work represents the only example of the functional expression of a vertebrate RNA polymerase III-transcribed gene in yeast cells.
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Affiliation(s)
- M A Francis
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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23
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Chapter 1 Synthesis and Function of Modified Nucleosides in tRNA. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0301-4770(08)61487-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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24
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Interaction of yeast transcription factor IIIC with dimeric Schizosaccharomyces pombe tRNASer-tRNAMet genes. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)47290-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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25
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Nichols M, Bell J, Klekamp MS, Weil PA, Söll D. Multiple Mutations of the First Gene of a Dimeric tRNA Gene Abolish in Vitro tRNA Gene Transcription. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)71462-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Piper PW, Stråby KB. Processing of transcripts of a dimeric tRNA gene in yeast uses the nuclease responsible for maturation of the 3' termini upon 5 S and 37 S precursor rRNAs. FEBS Lett 1989; 250:311-6. [PMID: 2666158 DOI: 10.1016/0014-5793(89)80745-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The rna82 mutation of Saccharomyces cerevisiae inactivates an RNA processing activity responsible for maturation of 3'-terminal sequences upon 5 S and 37 S ribosomal RNA precursors. This study describes a difference in the processing of transcripts of an S. cerevisiae dimeric tRNA gene (tRNA(arg)-tRNA(Asp) in RNA polymerase III in vitro transcription extracts prepared from rna82 and wild-type cells. The mutant extract accumulated additional processing intermediates containing tRNA(Arg) sequences as compared to the extract from wild-type cells. The structure of these intermediates revealed a defect in removal of the 10 nucleotides left 3' to the tRNA(Arg) sequence by the RNase P cleavage immediately 5' to tRNA(Asp). This is the first demonstration of a mutational defect affecting maturation of 3' sequences upon a eukaryotic tRNA precursor.
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Affiliation(s)
- P W Piper
- Department of Biochemistry, University College London, England
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27
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Dingermann T, Amon-Böhm E, Bertling W, Marschalek R, Nerke K. A family of non-allelic tRNA(ValGUU) genes from the cellular slime mold Dictyostelium discoideum. Gene 1988; 73:373-84. [PMID: 3072263 DOI: 10.1016/0378-1119(88)90502-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A haploid genome of the cellular slime mold Dictyostelium discoideum contains at least 14 non-allelic gene copies coding for a tRNA(ValGUU). The structure, genomic organization, and expression of these genes have been analyzed in relation to stages of the developmental cycle. So far, 13 tRNA(ValGUU) genes have been isolated and characterized. All genes contain identical mature tRNA-coding regions, and consequently identical gene internal promoter elements. However, different genes differ with respect to their 5'- and 3'-flanking regions, although a certain degree of sequence conservation seems apparent. Different members of this tRNA gene family appear to be randomly dispersed along the seven D. discoideum chromosomes, and not clustered at any one genomic location. In vivo expression of individual genes was studied in yeast. All but one tRNA(ValGUU) gene are actively transcribed, though with different efficiencies. There is also evidence that not all of these tRNA genes are constitutively transcribed in Dictyostelium throughout the developmental cycle. One characteristic primary transcript can only be detected in cells of the late preaggregation phase, whereas growing cells, cells in the stationary phase or cells harvested 4 h after the onset of development do not seem to carry this transcript. This product seems to be transcribed from a gene of an unusual structure. Although this particular gene has not yet been isolated, it can be predicted from the sequence of the cDNA synthesized from primary transcription products of this putative gene, that it is composed of nt 1-54 of a 3'-truncated tRNA(ValGUU) gene linked to a bona fide tRNA(ValGUU) gene.
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Affiliation(s)
- T Dingermann
- Institut für Biochemie der Medizinischen Fakultät, Universität Erlangen-Nürnberg, F.R.G
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28
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Szekely E, Belford HG, Greer CL. Intron sequence and structure requirements for tRNA splicing in Saccharomyces cerevisiae. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68320-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Reddy PS, Padayatty JD. Effects of 5' flanking sequences and changes in the 5' internal control region on the transcription of rice tRNA % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaqcKbay-haafaqabe% GabaaabaGaae4raiaabYgacaqG5baabaGaae4raiaaboeacaqGdbaa% aaaa!3CC7!\[\begin{array}{*{20}c} {{\text{Gly}}} \\ {{\text{GCC}}} \\ \end{array} \]. PLANT MOLECULAR BIOLOGY 1988; 11:575-583. [PMID: 24272491 DOI: 10.1007/bf00017457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/1988] [Accepted: 08/10/1988] [Indexed: 06/02/2023]
Abstract
A stretch of 71 nucleotides in a 1.2 kilobase pair Pst I fragment of rice DNA was identified as tRNA% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaqcaauaauaabeqace% aaaeaacaqGhbGaaeiBaiaabccacaqG5baabaGaae4raiaaboeacaqG% dbaaaaaa!3BE7!\[\begin{array}{*{20}c} {{\text{Gl y}}} \\ {{\text{GCC}}} \\ \end{array} \] gene by hybridization and nucleotide sequence analyses. The hybridization of genomic DNA with the tRNA gene showed that there are about 10 glycine tRNA genes per diploid rice genome. The 3' and 5' internal control regions, where RNA polymerase III and transcription factors bind, were found to be present in the coding sequence. The gene was transcribed into a 4S product in an yeast cell-free extract. The substitution of 5' internal control region with analogous sequences from either M13mp19 or M13mp18 DNA did not affect the transcription of the gene in vitro. The changes in three highly conserved nucleotides in the consensus 5' internal control region (RGYNNARYGG; R = purine, Y = pyrimidine, N = any nucleotide) did not affect transcription showing that these nucleotides are not essential for promotion of transcription. There were two 16 base pair repeats, 'TGTTTGTTTCAGCTTA' at -130 and -375 positions upstream from the start of the gene. Deletion of 5' flanking sequences including the 16 base pair repeat at -375 showed increased transcription indicating that these sequences negatively modulate the expression of the gene.
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Affiliation(s)
- P S Reddy
- Department of Biochemistry, Indian Institute of Science, 560 012, Bangalore, India
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30
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Joyce PB, Spencer DF, Bonen L, Gray MW. Genes for tRNA(Asp), tRNA (Pro), tRNA (Tyr) and two tRNAs (Ser) in wheat mitochondrial DNA. PLANT MOLECULAR BIOLOGY 1988; 10:251-262. [PMID: 24277519 DOI: 10.1007/bf00027402] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/1987] [Accepted: 11/13/1987] [Indexed: 06/02/2023]
Abstract
We have begun a systematic search for potential tRNA genes in wheat mtDNA, and present here the sequences of regions of the wheat mitochondrial genome that encode genes for tRNA(Asp) (anticodon GUC), tRNA(Pro) (UGG), tRNA(Tyr) (GUA), and two tRNAs(Ser) (UGA and GCU). These genes are all solitary, not immediately adjacent to other tRNA or known protein coding genes. Each of the encoded tRNAs can assume a secondary structure that conforms to the standard cloverleaf model, and that displays none of the structural aberrations peculiar to some of the corresponding mitochondrial tRNAs from other eukaryotes. The wheat mitochondrial tRNA sequences are, on average, substantially more similar to their eubacterial and chloroplast counterparts than to their homologues in fungal and animal mitochondria. However, an analysis of regions ∼ 150 nucleotides upstream and ∼ 100 nucleotides downstream of the tRNA coding regions has revealed no obvious conserved sequences that resemble the promoter and terminator motifs that regulate the expression of eubacterial and some chloroplast tRNA genes. When restriction digests of wheat mtDNA are probed with (32)P-labelled wheat mitochondrial tRNAs, <20 hybridizing bands are detected, whether enzymes with 4 bp or 6 bp recognition sites are used. This suggests that the wheat mitochondrial genome, despite its large size, may carry a relatively small number of tRNA genes.
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Affiliation(s)
- P B Joyce
- Department of Biochemistry, Dalhousie University, B3H 4H7, Halifax, Nova Scotia, Canada
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31
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Stråby KB. A yeast tRNA(Arg) gene can act as promoter for a 5' flank deficient, non-transcribable tRNA(SUP)6 gene to produce biologically active suppressor tRNA. Nucleic Acids Res 1988; 16:2841-57. [PMID: 3285324 PMCID: PMC336436 DOI: 10.1093/nar/16.7.2841] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In S. cerevisiae most tRNA genes are located and expressed as single entities. The tDNA(Arg)-tDNA(Asp) pair, however, is transcribed into a dimeric precursor before being processed into two mature tRNA species. The second gene of this pair, tDNA(Asp), is totally dependent on the first gene, tDNA(Arg), and its promoter components, for homologous in vitro transcription. The second gene in the pair is now replaced by the ochre suppressor tDNA(SUP)6-o, which, by itself, cannot be transcribed because of a nonfunctional 5' flanking region. The tDNA(Arg)-tDNA(SUP)6-o was transcribed into a dimeric precursor which was processed to mature tRNA molecules as judged in vitro by electrophoretic separation, and in vivo by their ability to suppress ochre but not amber yeast mutations. Mutations in the internal promoter of the first gene decreased transcription, both in vitro and in vivo, of the second-tRNA(SUP)6-o-gene. Thus tDNA(Arg) with its 5' flanking region can act as an external promoter for other RNA polymerase III-read genes that are by themselves inactive due to impaired promoter/modulator regions.
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MESH Headings
- Base Sequence
- Genes, Fungal
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Regulatory Sequences, Nucleic Acid
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Suppression, Genetic
- Transcription, Genetic
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Affiliation(s)
- K B Stråby
- Department of Microbiology, University of Umeå, Sweden
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32
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Hariharan N, Reddy PS, Padayatty JD. 5S-rRNA genes in rice embryos. PLANT MOLECULAR BIOLOGY 1987; 9:443-451. [PMID: 24277131 DOI: 10.1007/bf00015876] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/1986] [Accepted: 07/03/1987] [Indexed: 06/02/2023]
Abstract
The 5S-rRNA from the ungerminated and 48-h-germinated rice embryos differs from the wheat, rye and maize by two nucleotides. The 48-h-germinated embryos contain another species of 5S-rRNA which differs by 3 nucleotides from the ungerminated embryos, thereby showing the expression of two 5S-rRNA genes during germination. The 5S-rRNA genes are present in tandem repeats of a 0.3-kb sequence with some length heterogeneity in the rice genome. The 5S-rRNA gene that was sequenced is identical to that of wheat and maize, except for two nucleotides, C and T, which are interchanged at positions 107 and 117. The insert of continuous 5S-rRNA gene in pBR322 was transcribed in vitro much more efficiently than the discontinuous gene. There was no homology between the 184-bp spacer sequence of 5S-rRNA genes in rice and other systems except the presence of the oligo(T) transcription terminator sequence.
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Affiliation(s)
- N Hariharan
- Department of Biochemistry, Indian Institute of Science, 560 012, Bangalore, India
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33
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Mutational analysis of the coordinate expression of the yeast tRNAArg-tRNAAsp gene tandem. Mol Cell Biol 1987. [PMID: 3537719 DOI: 10.1128/mcb.6.7.2436] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
tRNA genes occur in the yeast genome as highly dispersed and independent transcriptional units. The 5'-tRNAArg-tRNAAsp-3' gene tandem, separated by a 10-base-pair spacer sequence, thus represents a rare case of tight clustering. Previous in vitro studies did not reveal any primary transcript from the tRNAAsp gene, but rather a dimeric precursor containing both gene sequences plus spacer, which undergoes a series of maturation steps. This seems anomalous since the tRNAAsp gene contains the sequences necessary for its own transcription. We found that site-directed mutation of the highly conserved C at position 56 to a G in the tRNAArg gene suppresses all transcription and does not activate the tRNAAsp gene. Precise deletion of the entire tRNAArg gene gives a similar result. Rescue of tRNAAsp gene transcription is effected either by the precise deletion of both the tRNAArg gene and spacer or by the precise deletion of this gene with concomitant introduction of an artificial RNA polymerase III start site in the spacer. This artificial start site is ineffective if the tRNAArg gene is present upstream.
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34
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Abstract
A new approach has been proposed for predicting the kinetic ensemble of the RNA secondary structures during chain growth. It is based on an analysis of time intervals in structural reconstruction. The Markov chain employed for describing structural reconstruction was modelled on the Monte Carlo method. A calculation was made of possible secondary structures formed during transcription. An algorithm has also been suggested for the search of a helix with a bulge type defect in which a cooperative effect is retained. Kinetic ensembles of the SD-sites and initiation regions of the polycistronic mRNA transcribed from ATP operon E. coli were calculated. A correlation between the secondary structures of these mRNA regions and the relative cistronic expression was established.
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Affiliation(s)
- A Mironov
- All Union Institute of Genetics and Selection of Microorganisms, Moscow, USSR
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35
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Reyes VM, Newman A, Abelson J. Mutational analysis of the coordinate expression of the yeast tRNAArg-tRNAAsp gene tandem. Mol Cell Biol 1986; 6:2436-42. [PMID: 3537719 PMCID: PMC367797 DOI: 10.1128/mcb.6.7.2436-2442.1986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
tRNA genes occur in the yeast genome as highly dispersed and independent transcriptional units. The 5'-tRNAArg-tRNAAsp-3' gene tandem, separated by a 10-base-pair spacer sequence, thus represents a rare case of tight clustering. Previous in vitro studies did not reveal any primary transcript from the tRNAAsp gene, but rather a dimeric precursor containing both gene sequences plus spacer, which undergoes a series of maturation steps. This seems anomalous since the tRNAAsp gene contains the sequences necessary for its own transcription. We found that site-directed mutation of the highly conserved C at position 56 to a G in the tRNAArg gene suppresses all transcription and does not activate the tRNAAsp gene. Precise deletion of the entire tRNAArg gene gives a similar result. Rescue of tRNAAsp gene transcription is effected either by the precise deletion of both the tRNAArg gene and spacer or by the precise deletion of this gene with concomitant introduction of an artificial RNA polymerase III start site in the spacer. This artificial start site is ineffective if the tRNAArg gene is present upstream.
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36
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Rooney RJ, Harding JD. Processing of mammalian tRNA transcripts in vitro: different pre-tRNAs are processed along alternative pathways that contain a common rate-limiting step. Nucleic Acids Res 1986; 14:4849-64. [PMID: 3725588 PMCID: PMC311496 DOI: 10.1093/nar/14.12.4849] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have analyzed the pathways and kinetics of processing of mouse tRNA gene transcripts in vitro. Different transcripts are processed along two alternative pathways. The 3' trailer sequence of the tRNA His primary transcript is excised before the 5' leader sequence. In contrast, for the tRNA Gly primary transcript, the 5' leader sequence is excised before the 3' trailer sequence, as has been found for other monomeric eukaryotic tRNA gene transcripts. Computerized analysis of the kinetics of processing indicates that tRNA Asp, tRNA Gly, tRNA Glu and tRNA His transcripts are processed in a substrate concentration-dependent manner and also reveals the existence of a common rate-limiting step, the rate constant of which is equivalent for three of the four transcripts tested. The processing of one pre-tRNA transcript can be competitively inhibited by addition of another pre-tRNA transcript to the processing reaction. The common rate-limiting step is associated with the conversion of the primary transcript to an intermediate and is independent of sequence and the particular processing pathway of the transcript.
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37
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Willis I, Frendewey D, Nichols M, Hottinger-Werlen A, Schaack J, Söll D. A single base change in the intron of a serine tRNA affects the rate of RNase P cleavage in vitro and suppressor activity in vivo in Saccharomyces cerevisiae. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)38465-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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38
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Heyer WD, Munz P, Amstutz H, Aebi R, Gysler C, Schuchert P, Szankasi P, Leupold U, Kohli J, Gamulin V. Inactivation of nonsense suppressor transfer RNA genes in Schizosaccharomyces pombe. Intergenic conversion and hot spots of mutation. J Mol Biol 1986; 188:343-53. [PMID: 3735426 DOI: 10.1016/0022-2836(86)90159-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Intergenic conversion is a mechanism for the concerted evolution of repeated DNA sequences. A new approach for the isolation of intergenic convertants of serine tRNA genes in the yeast Schizosaccharomyces pombe is described. Contrary to a previous scheme, the intergenic conversion events studied in this case need not result in functional tRNA genes. The procedure utilizes crosses of strains that are homozygous for an active UGA suppressor tRNA gene, and the resulting progeny spores are screened for loss of suppressor activity. In this way, intergenic convertants of a tRNA gene are identified that inherit varying stretches of DNA sequence from either of two other tRNA genes. The information transferred between genes includes anticodon and intron sequences. Two of the three tRNA genes involved in these information transfers are located on different chromosomes. The results indicate that intergenic conversion is a conservative process. No infidelity is observed in the nucleotide sequence transfers. This provides further evidence for the hypothesis that intergenic conversion and allelic conversion are the result of the same molecular mechanism. The screening procedure for intergenic revertants also yields spontaneous mutations that inactivate the suppressor tRNA gene. Point mutations and insertions of A occur at various sites at low frequency. In contrast, A insertions at one specific site occur with high frequency in each of the three tRNA genes. This new type of mutation hot spot is found also in vegetative cells.
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39
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Mitotic recombination between dispersed but related rRNA genes of Schizosaccharomyces pombe generates a reciprocal translocation. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf00333268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Hottinger-Werlen A, Schaack J, Lapointe J, Mao J, Nichols M, Söll D. Dimeric tRNA gene arrangement in Schizosaccharomyces pombe allows increased expression of the downstream gene. Nucleic Acids Res 1985; 13:8739-47. [PMID: 3936021 PMCID: PMC318948 DOI: 10.1093/nar/13.24.8739] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Three Schizosaccharomyces pombe dimeric tRNA genes, consisting of a tRNASer gene encoding a minor species with an intervening sequence followed by a tRNAMeti gene, have been described [Mao et al. (1980) Cell 21, 509-516; Hottinger et al. (1982) Mol. Gen. Genet. 188, 219-224; Willis et al. (1984) EMBO J. 3, 1573-1580]. We have examined the reason for the dimeric structure by comparing the transcriptional efficiencies and competitive abilities of the genes subcloned from the dimeric arrangement. Both of the subcloned genes are active in vivo in Saccharomyces cerevisiae, but only the tRNASer gene is efficiently transcribed in vitro. The tRNASer gene competes efficiently for transcription factors, while the tRNAMeti gene does so only weakly. Thus, it appears that the dimeric arrangement is required to support expression of the tRNAMeti gene. S. pombe genes encoding major species of tRNASer are transcribed considerably less efficiently than are the minor genes from the dimers, so coupling of the tRNAMeti gene to the minor species genes should lead to efficient production of tRNAMeti.
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41
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Mutations preventing expression of sup3 tRNASer nonsense suppressors of Schizosaccharomyces pombe. Mol Cell Biol 1985. [PMID: 3921825 DOI: 10.1128/mcb.5.4.808] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Suppression of nonsense codons in Schizosaccharomyces pombe by sup3-e tRNASerUGA or sup3-i tRNASerUAA is reduced or abolished by mutations within the suppressor locus. Twenty-five suppressor-inactive sup3-e genes and thirteen mutant sup3-i genes were isolated from S. pombe genomic clone banks by colony hybridization. Sequence analysis of these revertant alleles corroborates genetic evidence for mutational hotspots within the sup3 tRNA gene. Fifteen types of point mutations or insertions were found. Many of these replace bases which are highly or completely conserved in eucaryotic tRNA genes. Transcription of the altered sup3 genes in a Saccharomyces cerevisiae extract enabled the identification of mutations which affect the rate of 5'-end maturation or splicing of the tRNA precursors or both. A total of seven mutations were found which alter transcriptional efficiencies. Of these, five are located outside the internal transcription control regions.
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42
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43
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Amstutz H, Munz P, Heyer WD, Leupoid U, Kohli J. Concerted evolution of tRNA genes: intergenic conversion among three unlinked serine tRNA genes in S. pombe. Cell 1985; 40:879-86. [PMID: 3921260 DOI: 10.1016/0092-8674(85)90347-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In many cases the multiple genes coding for one specific tRNA are dispersed throughout the genome. The members of such a gene family nevertheless maintain a common nucleotide sequence during evolution. A major mechanism contributing to this concerted evolution is intergenic conversion. Here we show that it occurs between three tRNA genes of related sequence residing on different chromosomes of Schizosaccharomyces pombe. Sequence analysis of converted genes indicates that blocks of a minimal length of 18-33 bp and of a maximal length of 190 bp can be transferred from one gene to the other. During meiosis the frequency of these transfers lies in the order of 10(-5) per progeny spore. Information transfer between any two members of the gene family occurs in both directions.
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44
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Pearson D, Willis I, Hottinger H, Bell J, Kumar A, Leupold U, Söll D. Mutations preventing expression of sup3 tRNASer nonsense suppressors of Schizosaccharomyces pombe. Mol Cell Biol 1985; 5:808-15. [PMID: 3921825 PMCID: PMC366785 DOI: 10.1128/mcb.5.4.808-815.1985] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Suppression of nonsense codons in Schizosaccharomyces pombe by sup3-e tRNASerUGA or sup3-i tRNASerUAA is reduced or abolished by mutations within the suppressor locus. Twenty-five suppressor-inactive sup3-e genes and thirteen mutant sup3-i genes were isolated from S. pombe genomic clone banks by colony hybridization. Sequence analysis of these revertant alleles corroborates genetic evidence for mutational hotspots within the sup3 tRNA gene. Fifteen types of point mutations or insertions were found. Many of these replace bases which are highly or completely conserved in eucaryotic tRNA genes. Transcription of the altered sup3 genes in a Saccharomyces cerevisiae extract enabled the identification of mutations which affect the rate of 5'-end maturation or splicing of the tRNA precursors or both. A total of seven mutations were found which alter transcriptional efficiencies. Of these, five are located outside the internal transcription control regions.
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45
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Dingermann T, Bertling W, Pistel F, Amon E. Characterisation of a Dictyostelium discoideum DNA fragment coding for a putative tRNAValGUU gene. Evidence for a single transcription unit consisting of two overlapping class III genes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 146:449-58. [PMID: 3967666 DOI: 10.1111/j.1432-1033.1985.tb08672.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A genomic DNA fragment from Dictyostelium discoideum was characterized. This DNA, although 74% d(A + T)-rich, codes for a putative tRNAValGUU. The tRNAVal gene overlaps at its 5' half with another RNA polymerase III transcription unit. This RNA polymerase III transcription unit can be folded into a tRNA-like shape and is comprised of significant amounts of invariant and semi-invariant nucleotides present in all eukaryotic tRNAs. This unit contains the two promoter blocks defined for RNA polymerase III, which are homologous to recently defined promoter elements to the extent of 76-88% (A block) and 86-93% (B block) respectively [Sharp et al. (1981) Proc. Natl Acad. Sci. USA 78, 6657-6661]. Both of the overlapping class III genes are transcribed in germinal vesicle extracts prepared from Xenopus laevis oocytes as a single transcription unit, resulting in an unusually large product compared to primary transcripts of other tRNA genes. The unit is not transcribed in HeLa extracts but it competes very strongly for transcription factor(s) under the conditions of stable transcription complex formation. Although the whole unit is transcribed, it is believed that only one functional product is formed. Therefore we define the tRNA-like structure, coded for on this class III transcription unit, as a putative tRNA 'pseudogene' meaning that, although it is transcribed by RNA polymerase III, it is not likely to mature to a functional tRNA.
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46
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Engelke DR, Gegenheimer P, Abelson J. Nucleolytic processing of a tRNAArg-tRNAAsp dimeric precursor by a homologous component from Saccharomyces cerevisiae. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(20)71239-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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47
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Frendewey D, Dingermann T, Cooley L, Söll D. Processing of precursor tRNAs in Drosophila. Processing of the 3‘ end involves an endonucleolytic cleavage and occurs after 5‘ end maturation. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89752-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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48
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Rogers JH. The origin and evolution of retroposons. INTERNATIONAL REVIEW OF CYTOLOGY 1985; 93:187-279. [PMID: 2409043 DOI: 10.1016/s0074-7696(08)61375-3] [Citation(s) in RCA: 421] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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49
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Sumner-Smith M, Hottinger H, Willis I, Koch TL, Arentzen R, Söll D. The sup8 tRNALeu gene of Schizosaccharomyces pombe has an unusual intervening sequence and reduced pairing in the anticodon stem. MOLECULAR & GENERAL GENETICS : MGG 1984; 197:447-52. [PMID: 6597338 DOI: 10.1007/bf00329941] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have cloned and sequenced the wild-type and suppressor alleles of the S. pombe sup8 tRNA gene. The wild-type allele has a leucine UAA anticodon and the suppressor (sup8-e) carries the opal suppressor anticodon UCA. The gene has a 16 base pair intervening sequence that, in the RNA, is predicted to form a secondary structure which involves base pairing to the 5', rather than the usual 3' side of the 5' splice site. When incubated in Saccharomyces cerevisiae cell-free extracts both alleles are efficiently transcribed, the 5' leader and 3' trailer sequences are removed and CCA is added to the 3' processed end; however, the intervening sequence is not excised. This finding implies that the structural requirements of the splicing endonucleases in the two yeasts have diverged. No other tRNA genes with related sequences were detected in S. pombe DNA by hybridization, suggesting that other UUA isoacceptors may be structurally dissimilar to sup8 or that the UUA codon may be decoded by a UUG leucine isoacceptor.
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50
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Gutierrez-Hartmann A, Lieberburg I, Gardner D, Baxter JD, Cathala GG. Transcription of two classes of rat growth hormone gene-associated repetitive DNA: differences in activity and effects of tandem repeat structure. Nucleic Acids Res 1984; 12:7153-73. [PMID: 6091058 PMCID: PMC320148 DOI: 10.1093/nar/12.18.7153] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The rat growth hormone (rGH) gene contains two classes of repetitive DNA arranged as clusters within intron B and the 3' flanking region. The major family is equivalent to the CHO type 2 DNA. The second ("truncated repeat", TR) is a truncated version of the first and occurs in certain neural-specific transcripts and genes ("identifier" elements, ID). Here we report, using the HeLa cell-free transcription assay, that RNA polymerase III (Pol III) efficiently initiates at internal promoters within a tandem array of rGH gene repetitive DNA monomers and results in a novel organization of overlapping Class III transcription units. Transcription competition studies revealed that the rat type 2 structures share Pol III transcription factors with a tRNA gene, a human Alu repeat, and a mutant VA1 gene. Also, the rGH type 2 but not the TR DNA efficiently promotes Pol III initiation, yet other TR members, which differ only in flanking DNA, are transcribed. Thus, the rGH gene is strikingly enriched with 10 repetitive DNA monomers; multimeric type 2 elements are actively transcribed; rGH-TR sequences are expressed only as part of larger transcripts promoted by type 2 DNA; and, type 2 DNA uses tRNA gene transcription factors. These studies show that flanking sequences, promoter organization and factor competition may all affect rat repetitive DNA expression.
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