1
|
Crabtree AM, Kizer EA, Hunter SS, Van Leuven JT, New DD, Fagnan MW, Rowley PA. A Rapid Method for Sequencing Double-Stranded RNAs Purified from Yeasts and the Identification of a Potent K1 Killer Toxin Isolated from Saccharomyces cerevisiae. Viruses 2019; 11:v11010070. [PMID: 30654470 PMCID: PMC6356530 DOI: 10.3390/v11010070] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/13/2022] Open
Abstract
Mycoviruses infect a large number of diverse fungal species, but considering their prevalence, relatively few high-quality genome sequences have been determined. Many mycoviruses have linear double-stranded RNA genomes, which makes it technically challenging to ascertain their nucleotide sequence using conventional sequencing methods. Different specialist methodologies have been developed for the extraction of double-stranded RNAs from fungi and the subsequent synthesis of cDNAs for cloning and sequencing. However, these methods are often labor-intensive, time-consuming, and can require several days to produce cDNAs from double-stranded RNAs. Here, we describe a comprehensive method for the rapid extraction and sequencing of dsRNAs derived from yeasts, using short-read next generation sequencing. This method optimizes the extraction of high-quality double-stranded RNAs from yeasts and 3′ polyadenylation for the initiation of cDNA synthesis for next-generation sequencing. We have used this method to determine the sequence of two mycoviruses and a double-stranded RNA satellite present within a single strain of the model yeast Saccharomyces cerevisiae. The quality and depth of coverage was sufficient to detect fixed and polymorphic mutations within viral populations extracted from a clonal yeast population. This method was also able to identify two fixed mutations within the alpha-domain of a variant K1 killer toxin encoded on a satellite double-stranded RNA. Relative to the canonical K1 toxin, these newly reported mutations increased the cytotoxicity of the K1 toxin against a specific species of yeast.
Collapse
Affiliation(s)
- Angela M Crabtree
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Emily A Kizer
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Samuel S Hunter
- IBEST Genomics Core, University of Idaho, Moscow, ID 83843, USA.
| | - James T Van Leuven
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Daniel D New
- IBEST Genomics Core, University of Idaho, Moscow, ID 83843, USA.
| | - Matthew W Fagnan
- IBEST Genomics Core, University of Idaho, Moscow, ID 83843, USA.
| | - Paul A Rowley
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| |
Collapse
|
2
|
18S Ribosomal RNA Evaluation as Preanalytical Quality Control for Animal DNA. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6104323. [PMID: 27672657 PMCID: PMC5031817 DOI: 10.1155/2016/6104323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/18/2016] [Indexed: 01/20/2023]
Abstract
The 18S ribosomal RNA (rRNA) gene is present in all eukaryotic cells. In this study, we evaluated the use of this gene to verify the presence of PCR-amplifiable host (animal) DNA as an indicator of sufficient sample quality for quantitative real-time PCR (qPCR) analysis. We compared (i) samples from various animal species, tissues, and sample types, including swabs; (ii) multiple DNA extraction methods; and (iii) both fresh and formalin-fixed paraffin-embedded (FFPE) samples. Results showed that 18S ribosomal RNA gene amplification was possible from all tissue samples evaluated, including avian, reptile, and FFPE samples and most swab samples. A single swine rectal swab, which showed sufficient DNA quantity and the demonstrated lack of PCR inhibitors, nonetheless was negative by 18S qPCR. Such a sample specifically illustrates the improvement of determination of sample integrity afforded by inclusion of 18S rRNA gene qPCR analysis in addition to spectrophotometric analysis and the use of internal controls for PCR inhibition. Other possible applications for the described 18S rRNA qPCR are preselection of optimal tissue specimens for studies or preliminary screening of archived samples prior to acceptance for biobanking projects.
Collapse
|
3
|
Affiliation(s)
- R. A. McIntosh
- University of Sydney; Plant Breeding Institute; Castle Hill, N.S.W. Australia
| | - Jane E. Cusick
- University of Sydney; Plant Breeding Institute; Castle Hill, N.S.W. Australia
| |
Collapse
|
4
|
Sequencing of the 3'-terminal region of a 16S rRNA gene from Zea mays chloroplast reveals homology with E. coli 16S rRNA. Nature 2014; 279:520-2. [PMID: 25522437 DOI: 10.1038/279520a0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
5
|
Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol 2012; 13:R60. [PMID: 22759449 PMCID: PMC4053730 DOI: 10.1186/gb-2012-13-7-r60] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/03/2012] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic microorganisms are important but understudied components of the human microbiome. Here we present a pipeline for analysis of deep sequencing data on single cell eukaryotes. We designed a new 18S rRNA gene-specific PCR primer set and compared a published rRNA gene internal transcribed spacer (ITS) gene primer set. Amplicons were tested against 24 specimens from defined eukaryotes and eight well-characterized human stool samples. A software pipeline https://sourceforge.net/projects/brocc/ was developed for taxonomic attribution, validated against simulated data, and tested on pyrosequence data. This study provides a well-characterized tool kit for sequence-based enumeration of eukaryotic organisms in human microbiome samples.
Collapse
|
6
|
Subramaniam S, Sanyal A, Mohapatra JK, Hemadri D, Pattnaik B. Comparative complete genome analysis of Indian type A foot-and-mouth disease virus field isolates. Virus Genes 2011; 43:224-33. [PMID: 21604149 DOI: 10.1007/s11262-011-0622-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 05/07/2011] [Indexed: 11/30/2022]
Abstract
Comparative complete genome analysis of 17 serotype A Indian field isolates representing different genotypes and sub-lineages is presented in this report. Overall 79% of amino acids were invariant in the coding region. Chunk deletion of nucleotide was observed in S and L fragment of 5'-UTR. More variability which is comparable to that of capsid coding region was found in L and 3A region. Functional motifs and residues critical for virus biology were conserved most. Polyprotein cleavage sites accepted few changes. Many sites were detected to be under positive selection in L, P1, 2C, 3A, 3C, and 3D region and of which some are functionally important and antigenically critical. Genotype/lineage specific signature residues could be identified which implies evolution under different selection pressure. Transmembrane domain could be predicted in 2B, 2C, 3A, and 3C proteins in agreement with their membrane binding properties. Phylogenetic analysis at complete coding region placed the isolates in genotype IV, VI, and VII and two broad clusters comprising VP3(59)-deletion and non-deletion group within genotypes VII. The VP3(59)-deletion group has diversified genetically with time giving rise to three lineages. Incongruence in tree topology observed for different non structural protein coding region and UTRs-based phylogeny indicate suspected recombination.
Collapse
Affiliation(s)
- Saravanan Subramaniam
- Project Directorate on Foot-and-mouth disease, Mukteswar-Kumaon, Nainital 263138, Uttarakhand, India
| | | | | | | | | |
Collapse
|
7
|
Herzog M, Maroteaux L. Dinoflagellate 17S rRNA sequence inferred from the gene sequence: Evolutionary implications. Proc Natl Acad Sci U S A 2010; 83:8644-8. [PMID: 16578795 PMCID: PMC386987 DOI: 10.1073/pnas.83.22.8644] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present the complete sequence of the nuclear-encoded small-ribosomal-subunit RNA inferred from the cloned gene sequence of the dinoflagellate Prorocentrum micans. The dinoflagellate 17S rRNA sequence of 1798 nucleotides is contained in a family of 200 tandemly repeated genes per haploid genome. A tentative model of the secondary structure of P. micans 17S rRNA is presented. This sequence is compared with the small-ribosomal-subunit rRNA of Xenopus laevis (Animalia), Saccharomyces cerevisiae (Fungi), Zea mays (Planta), Dictyostelium discoideum (Protoctista), and Halobacterium volcanii (Monera). Although the secondary structure of the dinoflagellate 17S rRNA presents most of the eukaryotic characteristics, it contains sufficient archaeobacterial-like structural features to reinforce the view that dinoflagellates branch off very early from the eukaryotic lineage.
Collapse
Affiliation(s)
- M Herzog
- Laboratoire Arago, Paris VI University, Centre National de la Recherche Scientifique UA 117, 66650 Banyuls sur Mer, France
| | | |
Collapse
|
8
|
Richter U, Kühn K, Okada S, Brennicke A, Weihe A, Börner T. A mitochondrial rRNA dimethyladenosine methyltransferase in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:558-69. [PMID: 19929881 PMCID: PMC2860759 DOI: 10.1111/j.1365-313x.2009.04079.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
S-adenosyl-L-methionine-dependent rRNA dimethylases mediate the methylation of two conserved adenosines near the 3' end of the rRNA in the small ribosomal subunits of bacteria, archaea and eukaryotes. Proteins related to this family of dimethylases play an essential role as transcription factors (mtTFBs) in fungal and animal mitochondria. Human mitochondrial rRNA is methylated and human mitochondria contain two related mtTFBs, one proposed to act as rRNA dimethylase, the other as transcription factor. The nuclear genome of Arabidopsis thaliana encodes three dimethylase/mtTFB-like proteins, one of which, Dim1B, is shown here to be imported into mitochondria. Transcription initiation by mitochondrial RNA polymerases appears not to be stimulated by Dim1B in vitro. In line with this finding, phylogenetic analyses revealed Dim1B to be more closely related to a group of eukaryotic non-mitochondrial rRNA dimethylases (Dim1s) than to fungal and animal mtTFBs. We found that Dim1B was capable of substituting the E. coli rRNA dimethylase activity of KsgA. Moreover, we observed methylation of the conserved adenines in the 18S rRNA of Arabidopsis mitochondria; this modification was not detectable in a mutant lacking Dim1B. These data provide evidence: (i) for rRNA methylation in Arabidopsis mitochondria; and (ii) that Dim1B is the enzyme catalyzing this process.
Collapse
Affiliation(s)
- Uwe Richter
- Institut für Biologie/Genetik, Humboldt-UniversitätChausseestr. 117, 10115 Berlin, Germany
| | - Kristina Kühn
- Institut für Biologie/Genetik, Humboldt-UniversitätChausseestr. 117, 10115 Berlin, Germany
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western AustraliaCrawley 6009, WA, Australia
| | - Sachiko Okada
- Molekulare Botanik, Universität Ulm89069 Ulm, Germany
| | | | - Andreas Weihe
- Institut für Biologie/Genetik, Humboldt-UniversitätChausseestr. 117, 10115 Berlin, Germany
| | - Thomas Börner
- Institut für Biologie/Genetik, Humboldt-UniversitätChausseestr. 117, 10115 Berlin, Germany
- *(fax +49 302 093 8141; e-mail )
| |
Collapse
|
9
|
Comparative analysis of the large fragment of the 5' untranslated region (LF-5' UTR) of serotype A foot-and-mouth disease virus field isolates from India. Virus Genes 2009; 39:81-9. [PMID: 19444600 DOI: 10.1007/s11262-009-0366-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 04/29/2009] [Indexed: 12/18/2022]
Abstract
India is endemic for foot-and-mouth disease (FMD) and in recent years a unique group within serotype A, carrying a codon deletion at an antigenically critical site in capsid protein VP3 has emerged (VP3(59)-deletion group). This tempted us to analyze the noncoding region, which is an under represented area, though critically associated with virus biology and pathogenesis. Analysis of the large fragment of 5' untranslated region (LF-5' UTR) of type A FMD virus revealed discrepancy in the overall tree topology between LF-5' UTR and 1D region possibly due to independent evolution of coding and noncoding regions. The VP3(59)-deletion group maintained its phylogenetic distinctness even at the LF-5' UTR. Eighteen lineage specific signatures detected here support independent evolutionary paths for the lineages. Extensive deletions of 45 and 89 nucleotides corresponding to the pseudoknot region were noticed. Conservation pattern in the 'A(253)AACA' motif in the cre/bus stem-loop indicates the importance of first three 'A' residues in VPg uridylylation. Of the three polypyrimidine tract binding protein (PTB) binding sites mapped on the internal ribosome entry site (IRES), the pyrimidine tract (Py tract) in the loop of domain 2 was found to be maximally conserved and it might be the major PTB binding site. Strikingly, a deletion group lineage specific transversion was noticed in the Py tract at the 3' end of IRES without significantly affecting its in vitro infectious titer. Hence, we presume that for efficient cap-independent viral translation, either a minimum number of pyrimidine residues rather than a complete Py tract or a Py tract tolerating transversions only at specific locations and a core motif 'CUUU' within the Py tract is essential.
Collapse
|
10
|
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. J Mol Biol 2009; 388:271-82. [PMID: 19285505 DOI: 10.1016/j.jmb.2009.02.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 01/16/2009] [Accepted: 02/28/2009] [Indexed: 11/21/2022]
Abstract
Posttranscriptional modification of ribosomal RNA (rRNA) occurs in all kingdoms of life. The S-adenosyl-L-methionine-dependent methyltransferase KsgA introduces the most highly conserved rRNA modification, the dimethylation of A1518 and A1519 of 16S rRNA. Loss of this dimethylation confers resistance to the antibiotic kasugamycin. Here, we report biochemical studies and high-resolution crystal structures of KsgA from Thermus thermophilus. Methylation of 30S ribosomal subunits by T. thermophilus KsgA is more efficient at low concentrations of magnesium ions, suggesting that partially unfolded RNA is the preferred substrate. The overall structure is similar to that of other methyltransferases but contains an additional alpha-helix in a novel N-terminal extension. Comparison of the apoenzyme with complex structures with 5'-methylthioadenosine or adenosine bound in the cofactor-binding site reveals novel features when compared with related enzymes. Several mobile loop regions that restrict access to the cofactor-binding site are observed. In addition, the orientation of residues in the substrate-binding site indicates that conformational changes are required for binding two adjacent residues of the substrate rRNA.
Collapse
|
11
|
Xing C, Bitzer DL, Alexander WE, Vouk MA, Stomp AM. Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation. Nucleic Acids Res 2008; 37:591-601. [PMID: 19073698 PMCID: PMC2632891 DOI: 10.1093/nar/gkn917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3′-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3′-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3′-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences.
Collapse
Affiliation(s)
- Chuanhua Xing
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695-7911, USA.
| | | | | | | | | |
Collapse
|
12
|
Comparative genomics of serotype Asia 1 foot-and-mouth disease virus isolates from India sampled over the last two decades. Virus Res 2008; 136:16-29. [DOI: 10.1016/j.virusres.2008.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/03/2008] [Accepted: 04/11/2008] [Indexed: 11/21/2022]
|
13
|
Abstract
The ribosome is a dynamic machine that undergoes many conformational rearrangements during the initiation of protein synthesis. Significant differences exist between the process of protein synthesis initiation in eubacteria and eukaryotes. In particular, the initiation of eukaryotic protein synthesis requires roughly an order of magnitude more initiation factors to promote efficient mRNA recruitment and ribosomal recognition of the start codon than are needed for eubacterial initiation. The mechanisms by which these initiation factors promote ribosome conformational changes during stages of initiation have been studied using cross-linking, footprinting, site-directed probing, cryo-electron microscopy, X-ray crystallography, fluorescence spectroscopy and single-molecule techniques. Here, we review how the results of these different approaches have begun to converge to yield a detailed molecular understanding of the dynamic motions that the eukaryotic ribosome cycles through during the initiation of protein synthesis.
Collapse
|
14
|
Xing C, Bitzer DL, Alexander WE, Stomp AM, Vouk MA. Free energy analysis on the coding region of the individual genes of Saccharomyces cerevisiae. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2008; 2006:4225-8. [PMID: 17947071 DOI: 10.1109/iembs.2006.259972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Two methods, power spectrum density analysis (PSD) and synchronization signal approximation, were investigated to determine if underlying periodic, free energy signals could be detected for the individual genes in this paper. These signals could be revealed assuming Watson-Crick type hybridization between the eight, 3'-terminal nucleotides of the 18S rRNA and pre- and mature-mRNA sequences in Saccharomyces cerevisiae in a manner similar to that used to analyze coding region sequences in prokaryotic genes. Using PSD, a periodic signal could only be detected in 35 of 106 genes tested; using the synchronization signal approximation, 91 of 106 genes showed linearly increasing magnitude and phase, characteristics consistent with the presence of an underlying periodic signal with an assumed frequency of one-third. The majority of introns did not show magnitude and phase behavior consistent with an underlying non-periodic signal. The periodicity property for the free energy on the protein-coding regions can contribute to finding the approximate boundaries of the exons (protein coding regions) and the introns, which provides a foundation for future studies in identifying the exact positions of the splice sites, especially for the higher eukaryotic genes.
Collapse
Affiliation(s)
- Chuanhua Xing
- Dept. of Electr. & Comput. Eng., North Carolina State Univ., Raleigh, NC 27695, USA.
| | | | | | | | | |
Collapse
|
15
|
Osada Y, Saito R, Tomita M. Comparative analysis of base correlations in 5' untranslated regions of various species. Gene 2006; 375:80-6. [PMID: 16618531 DOI: 10.1016/j.gene.2006.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 02/16/2006] [Indexed: 11/29/2022]
Abstract
Translational initiation signals, such as Shine-Dalgarno (SD) sequences in bacteria and Kozak consensus sequences in vertebrates, direct ribosomes to initiate protein synthesis from mRNAs. Investigating sequence characteristics of these signals is important, particularly to infer translational initiation mechanisms. Although various statistical analyses of translational initiation signals have been done, few have focused on base correlations that assess base dependencies in the signal sequences. We used relative entropy and mutual information to analyze base conservation and correlation, respectively, in the 5' UTRs of various species. In eukaryotes, we found peaks of relative entropy at -3 from the translational start site but no peak of mutual information at that position, indicating that the base at that position (known as the core base of the Kozak sequence) is well conserved but not correlated with neighboring bases and thus functions as a single base. We observed unexpected peaks of mutual information between positions -2 and -1 in most eukaryotes. Surprisingly these base correlation also occurred in some bacteria and archaea, although there were no base preferences at neither position. Various dinucleotide patterns existed at these positions, and the correlation between bases at -2 and -1 may be relevant to the context of translational initiation. Because dinucleotide patterns of correlated pairs of nucleotides at -2 and -1 were not unique within respective organisms, the correlation could not be found when analyzing single-nucleotide conservation. Therefore, mutual information allowed us to discover signals that were not found by simply analyzing base conservation.
Collapse
Affiliation(s)
- Yuko Osada
- Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa, 252-8520, Japan
| | | | | |
Collapse
|
16
|
Espinha LM, Gaspar JO, Ward RJ, Ruller R, Camargo LEA. Caracterização da região 5'-terminal de um isolado brasileiro do Southern bean mosaic virus . ACTA ACUST UNITED AC 2004. [DOI: 10.1590/s0100-41582004000300018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
O presente trabalho caracteriza a região 5'-terminal de um isolado do Southern bean mosaic virus encontrado no Estado de São Paulo (SBMV-SP). O RNA foi extraído de partículas virais purificadas e submetido a RT-PCR usando oligonucleotídeos desenhados para amplificar cerca de 590 nt da região 5'-terminal do RNA viral. Foi obtido um fragmento de tamanho esperado que, após clonagem e seqüenciamento, mostrou a existência de uma região não codificadora com 92 nt e a primeira ORF, começando no primeiro AUG (posição 93) e terminando no códon UGA na posição 534. Na região não codificadora foi detectado um segmento parcialmente complementar ao RNA ribossomal 18S. A ORF1 codifica uma proteína de 147 aminoácidos com massa molecular estimada de 17080 Da. A extremidade 3' da ORF1 sobrepõe a extremidade 5' da ORF2 em 34 nucleotídeos. Os resultados obtidos indicam que a região 5'-terminal do RNA do SBMV-SP é similar ao isolado Arkansas (SBMV-ARK) descrito na América do Norte.
Collapse
|
17
|
Zeiner GM, Sturm NR, Campbell DA. The Leishmania tarentolae spliced leader contains determinants for association with polysomes. J Biol Chem 2003; 278:38269-75. [PMID: 12878606 DOI: 10.1074/jbc.m304295200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In kinetoplastids, every nuclear-derived mRNA contains an identical 39-nucleotide (nt) spliced leader at its 5'-terminus. The spliced leader is derived from substrate spliced leader RNA and joined to pre-mRNA by trans-splicing, thus providing mature mRNAs with an m7G cap and additional methylations referred to as cap 4. It was shown previously that mutations spanning nucleotides 10-39 of the spliced leader did not affect substrate spliced leader RNA transcription or trans-splicing in Leishmania tarentolae (Saito, R. M., Elgort, M. G., and Campbell, D. A. (1994) EMBO J. 13, 5460-5469). In this study we examined these sequences for a possible role in translation by assaying the association of mRNAs, which possess mutated spliced leaders, with polysomes. For the nt 28-39 mutated spliced leaders, both the substrate spliced leader RNA and the spliced leader demonstrated a wild-type methylation pattern; spliced nt 28-39 mRNA was found in polysomes. Thus, the nt 28-39 region conserved primary sequence is not a determinant of polysome association. An undermethylated cap 4 structure was present on substrate and mRNA spliced leaders in nt 20-29 mutated exons; nt 20-29 mRNA was not present in polysomes. A differential pattern of cap 4 methylation was seen between the nt 10-19 substrate spliced leader RNA and the nt 10-19 spliced leaders found in the poly(A)+ population of RNA; the nt 10-19 mRNA was not seen in polysomes. Undermethylated spliced leaders did not associate efficiently with polysomes, suggesting a requirement for the cap 4 and/or primary sequence of the spliced leader in translation. This is the first report demonstrating that the spliced leader contains critical structural or sequence determinants for association with polysomes and, hence, translation.
Collapse
Affiliation(s)
- Gusti M Zeiner
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90095-1489, USA
| | | | | |
Collapse
|
18
|
Kweon CH, Ko YJ, Kim WI, Kwon BJ, Hyun BH, Sohn HJ, Choi KS, Shin JH. Molecular characterization of foot-and-mouth disease virus O/SKR/2000. Virus Res 2002; 90:15-22. [PMID: 12457959 DOI: 10.1016/s0168-1702(02)00139-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Molecular cloning and sequencing of the genome of foot-and-mouth disease virus (FMDV) O/SKR/2000, one of PanAsia strain, were performed from FMDV infected cattle. From the poly (C) tract of the 5' nontranslated region (NTR) to the 3' NTR including 14 base pairs (bp) of poly (A) tail, 7813 bp sequences comprising approximately 95% of the whole genome were obtained by reverse transcription polymerase reaction (RT-PCR). The deduced amino acid sequences of the structural and nonstructural proteins (NSP) of the O/SKR/2000 virus were analyzed for the sequence similarity among type O strains. Comparison between FMDV O/SKR/2000 and other strains indicates that overall the number of amino acids appears to be conserved without any deletion in either NSP or capsid proteins, thus, suggesting that O/SKR/2000 evolved with minor difference from preexisting strains.
Collapse
Affiliation(s)
- Chang Hee Kweon
- Virology Research Division, National Veterinary Research and Quarantine Service, Ministry of Agriculture and Forestry, Anyang, South Korea.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
Ribosomal RNAs (rRNAs) from all sources contain modified nucleosides, whose numbers range from a few in mitochondrial rRNA to more than 200 in the complete rRNAs of some higher eukaryotes. In eukaryotic rRNA the great majority of modified nucleosides are 2'-O-methylated nucleosides or pseudouridines. The locations of most of the 2'-O-methylated nucleosides in rRNA from some representative eukaryotes are known from studies whose aim was full characterization of rRNA methylation. More recently, and particularly in connection with the discovery of methylation guide RNAs, it is often required to check for the presence or absence of 2'-O-methyl nucleosides at specified locations within rRNA. Three methods that can be applied for such "local" objectives are reviewed. Two of the methods are based on primer extension by reverse transcriptase. They exploit, respectively, a tendency of 2'-O-methyl groups to impede reverse transcriptase at low dNTP concentrations, or the resistance of phosphodiester bonds adjacent to 2'-O-methyl groups to alkaline hydrolysis. Examples of these methods are summarized. Although the two methods are relatively straightforward, they suffer from various experimental limitations, as discussed. The third method is technically more sophisticated but is capable of overcoming the limitations of the first two methods. It is based on the resistance of a target 2'-O-methylated site to cleavage by RNase H when the site is hybridized to an appropriate chimeric oligonucleotide. An overview of the approaches and methods now available for the complete mapping of 2'-O-methyl groups in rRNA is presented.
Collapse
Affiliation(s)
- B E Maden
- School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
| |
Collapse
|
20
|
Mat-Arip Y, Garver K, Chen C, Sheng S, Shao Z, Guo P. Three-dimensional interaction of Phi29 pRNA dimer probed by chemical modification interference, cryo-AFM, and cross-linking. J Biol Chem 2001; 276:32575-84. [PMID: 11371551 DOI: 10.1074/jbc.m100045200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Six pRNAs (p for packaging) of bacterial virus phi29 form a hexamer complex that is an essential component of the viral DNA translocating motor. Dimers, the building block of pRNA hexamer, assemble in the order of dimer --> tetramer --> hexamer. The two-dimensional structure of the pRNA monomer has been investigated extensively; however, the three-dimensional structure concerning the distance constraints of the three stems and loops are unknown. In this report, we probed the three-dimensional structure of pRNA monomer and dimer by photo affinity cross-linking with azidophenacyl. Bases 75-81 of the left stem were found to be oriented toward the head loop and proximate to bases 26-31 in a parallel orientation. Chemical modification interference indicates the involvement of bases 45-71 and 82-91 in dimer formation. Dimer was formed via hand-in-hand contact, a novel RNA dimerization that in some aspects is similar to the kissing loops of the human immunodeficiency virus. The covalently linked dimers were found to be biologically active. Both the native dimer and the covalently linked dimer were found by cryo-atomic force microscopy to be similar in global conformation and size.
Collapse
Affiliation(s)
- Y Mat-Arip
- Department of Pathobiology, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | | | | | |
Collapse
|
21
|
Hoffman MA, Banerjee AK. Precise mapping of the replication and transcription promoters of human parainfluenza virus type 3. Virology 2000; 269:201-11. [PMID: 10725212 DOI: 10.1006/viro.2000.0223] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The terminal RNA regions of the genomic and antigenomic RNAs of the paramyxoviruses and rhabdoviruses are known to contain sequences essential for directing RNA replication and transcription. The 3' terminus (leader region) of the negative-sense, genomic RNA of the rhabdoviruses and paramyxoviruses is known as the leader (Le) promoter and directs synthesis of positive-sense replication and transcription products. The 3' terminus of the antigenome is termed the trailer complementary (TrC) promoter and directs the synthesis of genomic RNA. By creating mutations in the corresponding regions of an HPIV3 minireplicon in which the viral protein coding sequences were replaced by the luciferase gene, we were able to precisely define the elements of the leader promoter involved in directing positive-strand replication of HPIV3. Nucleotides 1 through 12 (from the terminus) formed a domain critical for replication. The region from nucleotides 13 through 55 was important but not crucial for replication, while G residues at positions 79, 85, and 91 comprised another domain critical for replication. It was also shown that the TrC promoter is similar, though not identical, to the Le promoter. Nucleotides 1 through 12 of the TrC promoter were critical for synthesis of genomic RNA, though specific positions behaved differently from the corresponding positions of the Le promoter. While many of these mutations could not be analyzed for transcription because they completely abrogated genomic RNA synthesis (the template for transcription), we were surprised to find that no mutations in the leader promoter which decreased replication had any significant effect on transcription. However, mutations in the intergenic sequence and gene start signal following the leader and preceding the luciferase message severely decreased transcription, but not replication.
Collapse
MESH Headings
- Base Sequence
- Gene Expression Regulation, Viral/genetics
- Genes, Reporter/genetics
- Genome, Viral
- HeLa Cells
- Humans
- Mutation/genetics
- Parainfluenza Virus 3, Human/genetics
- Physical Chromosome Mapping
- Promoter Regions, Genetic/genetics
- RNA, Complementary/analysis
- RNA, Complementary/biosynthesis
- RNA, Complementary/genetics
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/analysis
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Replication Origin/genetics
- Replicon
- Sequence Alignment
- Templates, Genetic
- Transcription, Genetic/genetics
- Transfection
Collapse
Affiliation(s)
- M A Hoffman
- Department of Virology, Lerner Research Institute, Cleveland, OH 44195, USA
| | | |
Collapse
|
22
|
Garver K, Guo P. Mapping the inter-RNA interaction of bacterial virus phi29 packaging RNA by site-specific photoaffinity cross-linking. J Biol Chem 2000; 275:2817-24. [PMID: 10644747 DOI: 10.1074/jbc.275.4.2817] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During replication, the lengthy genome of double-stranded DNA viruses is translocated with remarkable velocity into a limited space within the procapsid. The question of how this fascinating task is accomplished has long been a puzzle. Our recent investigation suggests that phi29 DNA packaging is accomplished by a mechanism similar to the driving of a bolt with a hex nut and that six packaging RNAs (pRNAs) form a hexagonal complex to gear the DNA-translocating machine (Chen, C., and Guo, P. (1997) J. Virol. 71, 3864-3871; Zhang, F., Lemieux, S., Wu, X., St.-Arnaud, S., McMurray, C. T., Major, F., and Anderson, D. (1998) Mol. Cell 2, 141-147; Guo, P., Zhang, C., Chen, C., Garver, K., and Trottier, M., (1998) Mol. Cell 2, 149-155). In the current study, circularly permuted pRNAs were used to position an azidophenacyl photoreactive cross-linking agent specifically at a strategic site that was predicted to be involved in pRNA-pRNA interaction. Cross-linked pRNA dimers were isolated, and the sites of cross-link were mapped by primer extension. The cross-linked pRNA dimer retained full activity in phi29 procapsid binding and genomic DNA translocation, indicating that the cross-link distance constraints identified in dimer formation reflect the native pRNA complex. Both cross-linked dimers either containing or not containing the interlocking loops for programmed hexamer formation bound procapsid equally well; however, only the one containing the interlocking loops programmed for hexamer formation was active in phi29 DNA packaging. The cross-linked pRNA dimers were also identified as the minimum binding unit necessary for procapsid binding. Primer extension of the purified cross-linked pRNA dimers revealed that base G(82) was cross-linked to bases G(39), G(40), A(41), C(49), G(62), C(63), and C(64), which contribute to the formation of the three-way junction, suggesting that these bases are proximate in the formation of pRNA tertiary structure. Interestingly, the photoaffinity agent in the left interacting loop did not cross-link directly to the right loop as expected but cross-linked to bases adjacent to the right loop. These data provide a background for future modeling of pRNA tertiary structure.
Collapse
Affiliation(s)
- K Garver
- Department of Pathobiology, Purdue University, West Lafayette, Indiana 47907, USA
| | | |
Collapse
|
23
|
Falk JD, Vargiu P, Foye PE, Usui H, Perez J, Danielson PE, Lerner DL, Bernal J, Sutcliffe JG. Rhes: A striatal-specific Ras homolog related to Dexras1. J Neurosci Res 1999. [DOI: 10.1002/(sici)1097-4547(19990915)57:6%3c782::aid-jnr3%3e3.0.co;2-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
24
|
Falk JD, Vargiu P, Foye PE, Usui H, Perez J, Danielson PE, Lerner DL, Bernal J, Sutcliffe JG. Rhes: A striatal-specific Ras homolog related to Dexras1. J Neurosci Res 1999. [DOI: 10.1002/(sici)1097-4547(19990915)57:6<782::aid-jnr3>3.0.co;2-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
25
|
|
26
|
Azad AA, Failla P, Hanna PJ. Inhibition of ribosomal subunit association and protein synthesis by oligonucleotides corresponding to defined regions of 18S rRNA and 5S rRNA. Biochem Biophys Res Commun 1998; 248:51-6. [PMID: 9675084 DOI: 10.1006/bbrc.1998.8778] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strong complementarity between a conserved sequence near the 3' end of 18S (16S) rRNA of the small ribosomal subunit and a conserved sequence in the 5S rRNA of the large ribosomal subunit supported the suggestion that base-paired interaction between the two RNA molecules could be responsible for the reversible association of ribosomal subunits during protein synthesis. If this were true then oligonucleotides corresponding to defined regions of the 18S and 5S rRNAs should have profound effects on the association of ribosomal subunits and protein synthesis. In this report we show that oligonucleotides, corresponding to a defined region of eukaryotic 18S rRNA, when bound to wheat embryo 60S ribosomal subunits, inhibited association with 40S ribosomal subunits and also inhibited in vitro protein synthesis. Similarly oligonucleotides corresponding to a defined region of 5S rRNA when bound to 40S ribosomal subunits also inhibited the formation of 80S ribosomes and in vitro protein synthesis. The minimum sequences responsible for the inhibition of ribosomal subunit association and in vitro protein synthesis corresponded to the 5' strand of the m2(6)A m2(6)A hairpin structure near the 3' end of 18S rRNA and nucleotides 91-100 of 5S rRNA which are complementary to each other. Sequences at identical positions of Escherichia coli 16S and 5S rRNAs are also complementary to each other.
Collapse
Affiliation(s)
- A A Azad
- Division of Molecular Science, CSIRO, Parkville, Victoria, Australia
| | | | | |
Collapse
|
27
|
Genicot S, Rentier-Delrue F, Edwards D, VanBeeumen J, Gerday C. Trypsin and trypsinogen from an Antarctic fish: molecular basis of cold adaptation. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1298:45-57. [PMID: 8948488 DOI: 10.1016/s0167-4838(96)00095-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Trypsin from Antarctic fish Paranotothenia magellanica displays molecular and kinetic properties typical of enzymes produced by psychrophilic organisms. The enzyme has a high catalytic efficiency at low and moderate temperatures and is rapidly inactivated at temperatures higher than 30 degrees C. The nucleotide sequence was determined after mRNA extraction and cDNA synthesis. The cDNA encodes a pretrypsinogen which includes a seven residue activation peptide containing only three acidic residues preceeding the 222 amino-acid mature enzyme. A three-dimensional model of the enzyme was built. Structural parameters possibly involved in the adaptation to cold have been derived from comparison with the three-dimensional structure of the bovine enzyme. Among them are the lack of Tyr-151 in the substrate binding pocket, an overall decrease in the number of salt bridges and hydrophobicity and the increase in the surface hydrophilicity.
Collapse
Affiliation(s)
- S Genicot
- Laboratory of Biochemistry, University of Liège, Belgium
| | | | | | | | | |
Collapse
|
28
|
Ghadessy FJ, Chen D, Kini RM, Chung MC, Jeyaseelan K, Khoo HE, Yuen R. Stonustoxin is a novel lethal factor from stonefish (Synanceja horrida) venom. cDNA cloning and characterization. J Biol Chem 1996; 271:25575-81. [PMID: 8810331 DOI: 10.1074/jbc.271.41.25575] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Stonustoxin (SNTX) is a multifunctional lethal protein isolated from venom elaborated by the stonefish, Synanceja horrida. It comprises two subunits, termed alpha and beta, which have respective molecular masses of 71 and 79 kDa. SNTX elicits an array of biological responses both in vitro and in vivo, particularly a potent hypotension that appears to be mediated by the nitric oxide pathway. As a prelude to structure-function studies, we have isolated and sequenced cDNA clones encoding the alpha- and beta-subunits of SNTX from a venom gland cDNA library. The deduced amino acid sequence of neither subunit shows significant homology with any known protein. Protein sequence alignment does, however, show the subunits to be 50% homologous to each other and implies that they may have arisen from a common ancestor. The subunits of this novel toxin lack typical N-terminal signal sequences commonly found in proteins that are secreted via the endoplasmic reticulum-Golgi apparatus pathway, indicating the possibility of its being secreted by a non-classical pathway, which is not clearly understood. The SNTX subunits have been expressed in Escherichia coli as cleavable fusion proteins that cross-react with antibodies raised against the native toxin. To the best of our knowledge, this is the first complete sequence of a fish-derived protein toxin to be reported.
Collapse
Affiliation(s)
- F J Ghadessy
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, USA
| | | | | | | | | | | | | |
Collapse
|
29
|
Shin JT, Opalenik SR, Wehby JN, Mahesh VK, Jackson A, Tarantini F, Maciag T, Thompson JA. Serum-starvation induces the extracellular appearance of FGF-1. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1312:27-38. [PMID: 8679713 DOI: 10.1016/0167-4889(96)00013-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Autocrine/paracrine stimulation of cell growth by members of the fibroblast growth factor (FGF) family of polypeptides is dependent upon extracellular interactions with specific high affinity receptors at the cell surface. Acidic FGF (FGF-1) lacks a classical signal sequence for secretion, suggesting that intrinsic levels of this mitogen may not stimulate cell growth and utilizes a non-classical pathway to gain access to the extracellular compartment. To evaluate the biological potential of intracellular FGF-1 more rigorously, human cDNA sequences for the growth factor were introduced into primary murine embryonic fibroblasts using retrovirally mediated gene transfer. Heparin affinity, Western analysis, mitogenic assays, in situ immunohistochemical techniques, induction of tyrosine phosphorylation and antibody inhibition studies were used to demonstrate functionality of the FGF-1 transgene in this experimental model. Under normal culture conditions, cells constitutively expressing intracellular FGF-1 exhibited a slight growth advantage. In contrast, when maintained in reduced serum, these cells adopted a transformed phenotype and demonstrated an enhanced growth potential, induction of FGF-specific phosphotyrosyl proteins and the nuclear association of the growth factor. Analysis of the conditioned media from these stressed cells indicated that serum starvation induces the secretion of FGF-1 as latent high molecular mass complexes requiring reducing agents to activate its full biological potential.
Collapse
Affiliation(s)
- J T Shin
- Department of Surgery, School of Medicine, University of Alabama at Birmingham 35294, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Opalenik SR, Shin JT, Wehby JN, Mahesh VK, Thompson JA. The HIV-1 TAT protein induces the expression and extracellular appearance of acidic fibroblast growth factor. J Biol Chem 1995; 270:17457-67. [PMID: 7542239 DOI: 10.1074/jbc.270.29.17457] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Mounting experimental evidence suggests that the TAT protein, released from human immunodeficiency virus-1 (HIV-1)-infected inflammatory cells, may genetically reprogram targeted cells within a localized environment to develop highly vascularized tumors of mesenchymal origin. The fibroblast growth factor (FGF) family of polypeptides has gained general acceptance as initiators of angiogenesis and functions as potent mitogens for mesoderm-derived cells. To evaluate a potential biological relationship between TAT and acidic FGF (FGF-1), primary murine embryonic fibroblasts either were transfected with the viral transactivator or were transduced (retrovirally mediated) with a secreted, chimeric form of the human polypeptide growth factor, human stomach tumor/Kaposi's sarcoma (hst/KS)FGF-1. Reverse transcriptase-polymerase chain reaction, Western blotting, in situ immunohistochemical, heparin affinity, DNA synthesis, and transient transfection techniques were used to confirm expression, localization, and functionality of the transgenes. Both transfected and transduced cells constitutively expressing either TAT or (hst/KS)FGF-1 adopted a transformed phenotype, maintained aggressive growth behavior, and demonstrated both induction of FGF-specific phosphotyrosyl proteins and nuclear association of FGF-1 and FGF-1 receptor. Increased levels of endogenous, murine FGF-1 mRNA (reverse transcriptase-polymerase chain reaction) and protein (immunoblot analysis) were apparent in both (hst/KS)FGF-1- and TAT-transformed cells. Medium conditioned by (hst/KS)FGF-1-transduced cells contained steady-state levels of biologically active FGF-1 which exhibited a representative molecular weight. Limited sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of the conditioned medium from TAT-transformed cells demonstrated the appearance of FGF-1 as latent, high molecular weight complexes requiring reducing agents to activate full biological activity. Collectively, these results suggest that TAT induces the expression and secretion of FGF-1, which may be potentially relevant to the pathophysiological development of AIDS-Kaposi's sarcoma.
Collapse
Affiliation(s)
- S R Opalenik
- Department of Surgery, School of Medicine, University of Alabama at Birmingham 35294, USA
| | | | | | | | | |
Collapse
|
31
|
Ajuh PM, Maden EB. Chemical secondary structure probing of two highly methylated regions in Xenopus laevis 28S ribosomal RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1219:89-97. [PMID: 8086482 DOI: 10.1016/0167-4781(94)90250-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The large ribosomal subunit (LSU) RNA or 28S rRNA of vertebrates is characterized by two highly conserved and methylated regions towards the 3' end of the molecule that extend from domains IV to V of the molecule. In this report we describe the probing of the secondary structure of these two highly methylated regions in Xenopus laevis LSU RNA by chemical modification using the single-strand nucleotide specific probes; dimethyl sulphate (DMS) and 1-cyclo-hexyl-3-(2-morpholinoethyl-carbodiimide metho-p-toluene sulphonate (CMCT) followed by primer extension. The same regions in in vitro synthesized unmethylated X. laevis 28S rRNA were also probed for comparison. Our results in general tend to support the theoretically determined secondary structure model for the probed domains. From the results obtained, methylated cellular LSU RNA appears to be relatively more reactive than the in vitro transcript to the chemical probes. Accessibility to the probes was found to be similar at most sites for cellular and in vitro transcript LSU RNAs. This implies that structural destabilization due to 2'-O-methylations in cellular LSU RNA is not significant.
Collapse
Affiliation(s)
- P M Ajuh
- Department of Biochemistry, University of Liverpool, UK
| | | |
Collapse
|
32
|
Sun S, Sugane K. Complete structure of the gene encoding an immunodominant antigen of Dirofilaria immitis and larva-specific synthesis of primary transcript. J Helminthol 1994; 68:259-64. [PMID: 7829848 DOI: 10.1017/s0022149x00014449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The complete gene encoding an immunodominant antigen of Dirofilaria immitis was isolated from a Charomid 9-36 genomic DNA library. This genomic DNA clone termed 'Dg2' was characterized by restriction mapping, DNA sequencing of the 5' flanking region, the exon/intron boundaries and the polyadenylation addition site. The Dg2 with 4872 bp in length consisted of five exons interspersed with four introns. These exons reveal a single open reading frame followed by a long 3' non-coding region of 1383 bp. The open reading frame of 969 bp encodes a polypeptide of 322 amino acids with a molecular weight of 34,400. The ATG translation initiation codon starts 22 nucleotides downstream from the 5' end of the first exon. The polyadenylation signal sequence. AATAAA, is located at the 3' end of the last exon. The transcription initiation site was determined by primer extension technique. S1 nuclease mapping analysis demonstrated that the primary transcript derived from Dg2 is synthesized in microfilariae but not in male or female adult worms. The result suggests that the stage-specific expression of Dg2 is regulated at the level of primary transcript.
Collapse
Affiliation(s)
- S Sun
- Department of Parasitology, Shinshu University School of Medicine, Nagano Prefecture, Japan
| | | |
Collapse
|
33
|
Yano K, Sakurai MT, Watabe S, Izumi S, Tomino S. Structure and expression of mRNA for vitellogenin in Bombyx mori. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1218:1-10. [PMID: 8193154 DOI: 10.1016/0167-4781(94)90094-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Vitellogenin, a precursor of major yolk protein of the silkworm, Bombyx mori is a tetramer composed of each two molecules of heavy and light subunits. We cloned mRNA sequence for the B. mori vitellogenin and analyzed its structure. Sequence alignment of several overlapping cDNA clones indicated that the vitellogenin mRNA is approx. 5.7 kb, containing an open reading frame for a peptide with 1782 amino acid residues. By comparing the deduced amino acid sequence with the amino-terminal primary structures of vitellogenin subunits, it is suggested that the heavy and light subunits of the B. mori vitellogenin are encoded by a single contiguous mRNA. The primary translation product of the vitellogenin mRNA was detected in the microsomal fraction prepared from the fat body of vitellogenic females. Northern blot analysis of the fat body RNA demonstrated that the biosynthesis of vitellogenin in B. mori is regulated in a tissue-, sex- and stage-specific manner at the level of mRNA. Possible cause for discrepancy between the present results and our previous proposal (Izumi, S. and Tomino, S. (1983) Insect Biochem. 13, 81-85) on the biosynthesis of B. mori vitellogenin is also discussed.
Collapse
Affiliation(s)
- K Yano
- Department of Biology, Tokyo Metropolitan University, Japan
| | | | | | | | | |
Collapse
|
34
|
Harrod R, Gu Z, Lovett PS. Analysis of the secondary structure that negatively regulates inducible cat translation by use of chemical probing and mutagenesis. Gene 1994; 140:79-83. [PMID: 8125344 DOI: 10.1016/0378-1119(94)90734-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Induction of chloramphenicol (Cm) acetyltransferase-encoding genes (cat) by Cm has been proposed to result from the destabilization of a stem-loop that sequesters the ribosome-binding site for the cat coding sequence. Destabilization is caused by the stalling of a ribosome at a specific site in the leader of cat transcripts that immediately precedes the stem-loop. By use of in vivo dimethylsulfate probing of cat-86 leader mRNA, we demonstrate the existence of the stem-loop structure in cat transcripts isolated from uninduced cells and its release during induction. Leader mutations chosen to provide the mRNA with an alternative folding pattern that destabilizes the stem-loop cause constitutive cat expression. Our results establish the occurrence in vivo of the stem-loop in cat-86 transcripts and its role as a negative regulator of cat expression.
Collapse
Affiliation(s)
- R Harrod
- Department of Biological Sciences, University of Maryland Baltimore County, Catonsville 21228
| | | | | |
Collapse
|
35
|
Ganoza MC, Louis BG. Potential secondary structure at the translational start domain of eukaryotic and prokaryotic mRNAs. Biochimie 1994; 76:428-39. [PMID: 7849110 DOI: 10.1016/0300-9084(94)90120-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In order to identify conserved potential secondary structures within translational start sites, mRNA sequences derived from different species were studied with programs able to depict such features. The potential secondary structure of 71 bases around the initiator AUG or AUGs in the coding sequences of 290 eukaryotic mRNAs was first examined and compared to 290 similarly analyzed regions derived from prokaryotic mRNA sequences (Nucleic Acids Res (1987) 15, 345-360). In both sets of sequences the initiator codon was often found to be in an open potential structure whereas a denser region characterized by nearly-periodic spacings defined the coding regions. Randomization of the sequences obliterated the observed patterns suggesting that the structure of the mRNA may determine these differences. Three sets of eukaryotic and prokaryotic mRNAs of approximately equal length were analyzed and found to preserve an open unpaired non-coding region 5' to the start codon. The start codon was found free of potential secondary structure in over 80% of all the sequences analyzed. These data, and study of mutants that restrict the accessibility of the start codon to the ribosomal initiation complex, suggest that both the prokaryotic and eukaryotic mRNA start sites must occur free of potential secondary structure for efficient initiation. A striking difference of the eukaryotic mRNA sequences analyzed was the high propensity of the coding region vicinal to the start codon to form secondary structures. Certain translation-defective mutants exhibit impaired formation of these secondary structures suggesting that the structure of the coding regions adjacent to the start codons of eukaryotic mRNAs may be an important, thus far unexamined, determinant of initiation. We propose that, for all genes studied, the transition in secondary structure between the coding and non-coding regions may be an important determinant of initiation.
Collapse
Affiliation(s)
- M C Ganoza
- Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada
| | | |
Collapse
|
36
|
Deng R, Brock KV. 5' and 3' untranslated regions of pestivirus genome: primary and secondary structure analyses. Nucleic Acids Res 1993; 21:1949-57. [PMID: 8388102 PMCID: PMC309437 DOI: 10.1093/nar/21.8.1949] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Within the conserved 5' untranslated region (UTR) of the pestivirus genome three highly variable regions were identified. Preceding the polyprotein start codon, multiple cryptic AUG codons and several small open reading frames are characteristic for all the five pestiviruses. Inspection of the context of AUGs revealed that the polyprotein initiation AUG of pestivirus has a weak context for efficient translation initiation. The most favorable context was found in two of the cryptic AUGs. Two oligopyrimidine-rich tracts upstream to the conserved either cryptic or authentic AUG in the 5'-UTR of pestivirus were identified and 83.3% of their nucleotide sequences are complementary to the consensus sequence at the 3' terminus of eucaryotic 18S rRNA. A secondary structure model for the 5'-UTR of pestivirus was predicted. Nucleotide sequence comparison among five pestiviruses led to the identification of a variable region and a conserved region in the 3'-UTR. A deletion of 41 nucleotides was found within the variable region in Osloss. A secondary structure model for the 3'-UTR was also predicted. The structural similarity of the 5'-UTR between pestiviruses and picornaviruses and hepatitis C viruses was demonstrated and the possible implications of features of the 5' and 3'-UTR of pestiviruses are discussed.
Collapse
Affiliation(s)
- R Deng
- Ohio Agricultural Research and Development Center, Food Animal Health Research Program, Wooster 44691
| | | |
Collapse
|
37
|
Matveeva OV, Shabalina SA. Intermolecular mRNA-rRNA hybridization and the distribution of potential interaction regions in murine 18S rRNA. Nucleic Acids Res 1993; 21:1007-11. [PMID: 8451167 PMCID: PMC309236 DOI: 10.1093/nar/21.4.1007] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Intermolecular hybridization experiments show that murine 18S rRNA and 28S rRNA are capable of forming stable hybrid structures with mRNA from genes p53, c-myc and c-mos from the same species. Both 5'-uncoding and coding oncogene p53 mRNA regions contain fragments interacting with rRNA. Computer analysis revealed 18S rRNA fragments complementary to oligonucleotides frequently met in mRNA, which are potential hybridization regions (clinger-fragments). The distribution of clinger-fragments along 18S rRNA sequence is universal at least for one hundred murine mRNA sequences analyzed. Maximal frequencies of oligonucleotides complementary to 18S rRNA clinger-fragments are reliably (2-3 times) higher for mRNA than for intron sequences and randomly generated sequences. The results obtained suggest a possible role of clinger-fragments in translation processes as universal regions of mRNA binding.
Collapse
Affiliation(s)
- O V Matveeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
| | | |
Collapse
|
38
|
Ganoza MC, Farrow NA, An G. Effect of deletions 5' to the translation initiation sequence on the expression of an mRNA in animal cells. Mol Biol Rep 1992; 16:277-84. [PMID: 1454061 DOI: 10.1007/bf00419668] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To learn if an mRNA.18S rRNA interaction or a special secondary structure in the mRNA start region is essential for translation in eukaryotic cells, we constructed recombinant plasmids with the SV40 early promoter 5' to part of the Escherichia coli tufB-lacZ gene. Deletion of bases potentially complementary to the 18S rRNA highly increased the transient beta-galactosidase expressed in transfected CHO cells. Deletion of bases that fostered formation of potential hairpins with the mRNA 5'-terminus or altered the structure of the coding region reduced beta-galactosidase activity suggesting that these features of the mRNA secondary structure may be essential for initiation of translation. Computer aided analysis of the potential structure of 290 mRNAs suggests these are conserved features of the initiation region.
Collapse
Affiliation(s)
- M C Ganoza
- C.H. Best Institute, Banting & Best Department of Medical Research, University of Toronto, Ontario, Canada
| | | | | |
Collapse
|
39
|
Tesar M, Harmon SA, Summers DF, Ehrenfeld E. Hepatitis A virus polyprotein synthesis initiates from two alternative AUG codons. Virology 1992; 186:609-18. [PMID: 1310188 DOI: 10.1016/0042-6822(92)90027-m] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The genomic RNA of hepatitis A virus has two potential translation initiation sites for synthesis of a 251-kDa polyprotein. It is not known which of these AUG codons, located at positions 735-737 and 741-743, is used in vitro or in vivo. Site-directed mutagenesis was carried out to eliminate each start codon independently. Transcripts from the unmodified and modified cDNA clones were used either to program an in vitro translation system or for transfection of BS-C-1 cells. In vitro and in vivo translation data revealed preferential usage of the downstream AUG located at position 741 to 743, although either site could be utilized in the absence of the other. Both modified RNAs were able to induce productive infections in BS-C-1 cells. Deletion of almost all of the 5'-untranslated region (5'UTR) of the RNA, however, stimulated selection of AUG 735-737 in vitro resulting in equal utilization of both sites, suggesting a strong influence of the 5'UTR for directing the ribosome to a specific internal initiation site.
Collapse
Affiliation(s)
- M Tesar
- Department of Cellular, Viral, and Molecular Biology, University of Utah School of Medicine, Salt Lake City 84132
| | | | | | | |
Collapse
|
40
|
Pilipenko EV, Gmyl AP, Maslova SV, Svitkin YV, Sinyakov AN, Agol VI. Prokaryotic-like cis elements in the cap-independent internal initiation of translation on picornavirus RNA. Cell 1992; 68:119-31. [PMID: 1310072 DOI: 10.1016/0092-8674(92)90211-t] [Citation(s) in RCA: 233] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Initiation of translation on picornavirus RNAs is accomplished through internal binding of ribosomes to a complex cis-acting element. Here we show that efficient function of this element involves two appropriately spaced smaller elements: UUUCC and an AUG. This conclusion emerged from analysis of the genome structures of spontaneous revertants of mutant polioviruses with extended insertions between the UUUCC and AUG motifs. It was confirmed by the results obtained with specially designed constructs. A similarity to the prokaryotic translation initiation mechanism, which involves the Shine-Dalgarno sequence, is emphasized, but in the picornavirus system the position of the UUUCC must be strictly fixed relative to upstream cis-acting elements, and the AUG may not necessarily serve as an initiation codon.
Collapse
MESH Headings
- Base Sequence
- Chromosome Deletion
- Cloning, Molecular
- Genome, Viral
- Models, Structural
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational
- Plasmids
- Poliovirus/genetics
- Protein Biosynthesis
- RNA Caps/genetics
- RNA, Viral/genetics
- Restriction Mapping
- Ribosomes/metabolism
- Sequence Homology, Nucleic Acid
- Templates, Genetic
- Transcription, Genetic
- Viral Plaque Assay
Collapse
Affiliation(s)
- E V Pilipenko
- Institute of Poliomyelitis and Viral Encephalitides, USSR Academy of Medical Sciences, Moscow
| | | | | | | | | | | |
Collapse
|
41
|
Liesack W, Weyland H, Stackebrandt E. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. MICROBIAL ECOLOGY 1991; 21:191-8. [PMID: 24194210 DOI: 10.1007/bf02539153] [Citation(s) in RCA: 172] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/1990] [Revised: 03/06/1991] [Indexed: 05/27/2023]
Abstract
The 16S rDNA genes of an apparently pure culture of a psychrophilic and strict barophilic bacterium (WHB 46) were studied by PCR-mediated amplification and cloning into phage M13 mp18. Sequence analysis of five individual clones revealed the presence of two different 16S rDNA types. The homology value of 90% indicates that culture WHB 46 is actually composed of two closely related species (WHB 46-1 and 46-2). Both strains are members of the γ-subdivision of proteobacteria. Analysis of a sixth clone (WHB 46-1/2) leads to the conclusion that it represents a 16S rDNA hybrid molecule assembled during the PCR reaction. This hypothesis was confirmed by secondary structure analysis of the chimeric rDNA. The appearance of such hybrid molecules point to a potential risk in studies on the diversity of bacterial populations by analysis of rDNA pattern via PCR-mediated amplification because they suggest the existence of organisms that do not actually exist in the sample investigated.
Collapse
Affiliation(s)
- W Liesack
- Department of Microbiology, University of Queensland, 4072, St. Lucia, Queensland, Australia
| | | | | |
Collapse
|
42
|
Urata H, Kinoshita A, Perez D, Misono K, Bumpus F, Graham R, Husain A. Cloning of the gene and cDNA for human heart chymase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)47355-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
43
|
Smirnyagina EV, Morozov SY, Rodionova NP, Miroshnichenko NA, Solovev AG, Fedorkin ON, Atabekov JG. Translational efficiency and competitive ability of mRNAs with 5'-untranslated alpha beta-leader of potato virus X RNA. Biochimie 1991; 73:587-98. [PMID: 1764504 DOI: 10.1016/0300-9084(91)90027-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 5'-untranslated leader sequence of potato virus X (PVX) RNA (63 nucleotides apart from cap-structure) consists of two sub-sequences referred to as alpha-sequence (41 nucleotides with no G) and beta-sequence (42 nucleotides upstream from the first AUG). Computer-based folding predictions suggest that the 5'-proximal region of alpha beta-leader is unstructured. The second structural feature of alpha beta-leader is the presence of the sequences apparently complementary to the 3'-terminal region of 18S rRNA. The alpha beta-leader has been shown to strongly enhance the translation of the contiguous foreign gene (NPT1) transcripts in cell-free translation systems from rabbit reticulocytes (RRL), wheat germ (WG) and Krebs-2 ascite cell extract (KA). In competitive translation PVX, RNA strongly inhibited tobacco mosaic virus (TMV) RNA, in RRL and WG systems. No competition occurred between PVX and TMV RNAs in KA system. There was no correlation between the translational efficiency and competitive ability of PVX RNA in different cell-free translation systems. The competitive ability did not solely depend on the presence of alpha beta-leader in mRNA. We present evidence to suggest that alpha beta-leader together with about 150 bases of the coding sequence is responsible for the translation competitive ability of PVX RNA.
Collapse
|
44
|
Yamanishi K, Liew FM, Konishi K, Yasuno H, Doi H, Hirano J, Fukushima S. Molecular cloning of human epidermal transglutaminase cDNA from keratinocytes in culture. Biochem Biophys Res Commun 1991; 175:906-13. [PMID: 1673840 DOI: 10.1016/0006-291x(91)91651-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have isolated a cDNA encoding human epidermal transglutaminase, a key enzyme of terminal differentiation of keratinocytes. A cDNA library from cultured human keratinocytes was screened by a PCR-amplified partial cDNA fragment of the enzyme with oligonucleotide primers based on the homology of the transglutaminase family. The cDNA is 2734 bp coding a protein of 817 amino acids. The several regions including the active site cysteine residue are highly conserved among the transglutaminase family. However, the charged N-terminal domain is unique to the epidermal transglutaminse, suggesting that the region is involved in the function of the enzyme in keratinocytes.
Collapse
Affiliation(s)
- K Yamanishi
- Department of Dermatology, Kyoto Prefectural University of Medicine, Japan
| | | | | | | | | | | | | |
Collapse
|
45
|
Stebbins-Boaz B, Gerbi SA. Structural analysis of the peptidyl transferase region in ribosomal RNA of the eukaryote Xenopus laevis. J Mol Biol 1991; 217:93-112. [PMID: 1988683 DOI: 10.1016/0022-2836(91)90614-c] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Accessible single-strand bases in Xenopus laevis 28 S ribosomal RNA (rRNA) Domain V, the peptidyl transferase region, were determined by chemical modification with dimethylsulfate, 1-cyclohexyl-3-(2-morpholinoethyl-carbodiimide metho-p-toluene sulfonate and kethoxal, followed by primer extension. The relative accessibilities of three rRNA substrates were compared: deproteinized 28 S rRNA under non-denaturing conditions (free 28 S rRNA), 60 S subunits and 80 S ribosomes. Overall, our experimental results support the theoretical secondary structure model of Domain V derived by comparative sequence analysis and compensatory base-pair changes, and support some theoretical tertiary interactions previously suggested by covariation. The 60 S subunits and 80 S ribosomes generally show increasing resistance to chemical modification. Bases which are sensitive in free 28 S rRNA but protected in 60 S subunits may be sites for ribosomal protein binding or induced structural rearrangements. Another class of nucleotides is distinguished by its sensitivity in 60 S subunits but protection in 80 S ribosomes; these nucleotides may be involved in subunit-subunit interactions or located at the interface of the ribosome. We found a third class of bases, which is protected in free 28 S rRNA but sensitive in 60 S subunits and/or 80 S ribosomes, suggesting that structural changes occur in Domain V as a result of subunit assembly and ribosome formation. One such region is uniquely hypersensitive in eukaryotic ribosomes but is absent in Escherichia coli ribosomes. Sites that we determined to be accessible on empty 80 S ribosomes could serve as recognition sites for translation components.
Collapse
Affiliation(s)
- B Stebbins-Boaz
- Division of Biology and Medicine, Brown University, Providence, RI 02912
| | | |
Collapse
|
46
|
Abstract
Picornaviruses are small naked icosahedral viruses with a single-stranded RNA genome of positive polarity. According to current taxonomy, the family includes four genera: Enterouirus (polioviruses, coxsackieviruses, echoviruses, and other enteroviruses), Rhinovirus, Curdiouirus [encephalomyocarditis virus (EMCV), mengovirus, Theiler's murine encephalomyelitis virus (TMEV)], and Aphthouirus [foot-and-mouth disease viruses (FMDV)]. There are also some, as yet, unclassified picornaviruses [e.g., hepatitis A virus (HAW] that should certainly be assessed as a separate genus. Studies on the molecular biology of picornaviruses might be divided into two periods: those before and after the first sequencing of the poliovirus genome. The 5'-untranslated region (5-UTR) of the viral genome was one of the unexpected problems. This segment proved to be immensely long: about 750 nucleotides or ∼10% of the genome length. There were also other unusual features (e.g., multiple AUG triplets preceding the single open reading frame (ORF) that encodes the viral polyprotein). This chapter shows that the picornaviral 5-UTRs are not only involved in such essential events as the synthesis of viral proteins and RNAs that could be expected to some extent, although some of the underlying mechanisms appeared to be quite a surprise, but also may determine diverse biological phenotypes from the plaque size or thermosensitivity of reproduction to attenuation of neurovirulence. Furthermore, a close inspection of the 5-UTR structure unravels certain hidden facets of the evolution of the picornaviral genome. Finally, the conclusions drawn from the experiments with the picornaviral5-UTRs provide important clues for understanding the functional capabilities of the eukaryotic ribosomes.
Collapse
Affiliation(s)
- V I Agol
- Institute of Poliomyelitis and Viral Encephalitides, U.S.S.R. Academy of Medical Sciences, Moscow
| |
Collapse
|
47
|
Knap AK, Wesolowski D, Altman S. Protection from chemical modification of nucleotides in complexes of M1 RNA, the catalytic subunit of RNase P from E coli, and tRNA precursors. Biochimie 1990; 72:779-90. [PMID: 1707681 DOI: 10.1016/0300-9084(90)90187-l] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Certain nucleotides in M1 RNA, the catalytic RNA subunit of RNase P from E coli, are protected from chemical modification when M1 RNA forms complexes with tRNA precursor molecules (ES complexes). Many of these nucleotides are important in the formation of the Michaelis complex. In the presence of tRNA precursor molecules, the pattern of protection from chemical modification of a region in M1 RNA that resembles the E site in 23S rRNA is similar to the pattern of protection of the E site in the presence of deacylated tRNA. In the complex with the RNA enzyme, more nucleotides in the substrate become accessible to modification, an indication that the substrate is in an unfolded conformation under these conditions.
Collapse
Affiliation(s)
- A K Knap
- Department of Biology, Yale University, New Haven, CT 06520
| | | | | |
Collapse
|
48
|
Downs WD, Cech TR. An ultraviolet-inducible adenosine-adenosine cross-link reflects the catalytic structure of the Tetrahymena ribozyme. Biochemistry 1990; 29:5605-13. [PMID: 2201409 DOI: 10.1021/bi00475a027] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When a shortened enzymatic version of the Tetrahymena self-splicing intervening sequence (IVS) RNA is placed under catalytic conditions and irradiated at 254 nm, a covalent cross-link forms with high efficiency. The position of the cross-link was mapped by using three independent methods: RNase H digestion, primer extension with reverse transcriptase, and partial hydrolysis of end-labeled RNA. The cross-link is chemically unusual in that it joins two adenosines, A57 and A95. Formation of this cross-link depends upon the identity and concentration of divalent cations present and upon heat-cool renaturation of the IVS in a manner that parallels conditions required for optimal catalytic activity. Furthermore, cross-linking requires the presence of sequences within the core structure, which is conserved among group I intervening sequences and necessary for catalytic activity. Together these correlations suggest that a common folded structure permits cross-linking and catalytic activity. The core can form this structure independent of the presence of P1 and elements at the 3' end of the IVS. The cross-linked RNA loses catalytic activity under destabilizing conditions, presumably due to disruption of the folded structure by the cross-link. One of the nucleotides participating in this cross-link is highly conserved (86%) within the secondary structure of group I intervening sequences. We conclude that A57 and A95 are precisely aligned in a catalytically active conformation of the RNA. A model is presented for the tertiary arrangement in the vicinity of the cross-link.
Collapse
Affiliation(s)
- W D Downs
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Colorado, Boulder 80309-0215
| | | |
Collapse
|
49
|
Dolph PJ, Huang JT, Schneider RJ. Translation by the adenovirus tripartite leader: elements which determine independence from cap-binding protein complex. J Virol 1990; 64:2669-77. [PMID: 1692346 PMCID: PMC249445 DOI: 10.1128/jvi.64.6.2669-2677.1990] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The adenovirus tripartite leader is a 200-nucleotide-long 5' noncoding region which facilitates translation of viral mRNAs at late times after infection. The tripartite leader also confers the ability to initiate translation independent of the requirement for cap-binding protein complex or eIF-4F without any requirement for adenovirus gene products. To elucidate the manner by which the tripartite leader functions, the primary determinants of leader activity were investigated in vivo by testing a series of mutations expressed from transfected plasmids. The results of these experiments indicate that the tripartite leader does not promote internal ribosome binding, at least in a manner recently described for picornavirus mRNAs. In addition, despite an unusual arrangement of sequences complementary to the 3' end of 18S rRNA in the tripartite leader, we could find no evidence for involvement in its translation activity. Instead, our results are consistent with a model in which much of the first leader is maintained in an unstructured conformation which determines the ability of the tripartite leader to facilitate translation and bypass a normal requirement for eIF-4F activity. Several possible translation models are discussed, as well as the implications for translation of late viral mRNAs.
Collapse
Affiliation(s)
- P J Dolph
- Kaplan Cancer Center, New York University Medical Center, New York 10016
| | | | | |
Collapse
|
50
|
Guo PX, Goebel S, Perkus ME, Taylor J, Norton E, Allen G, Languet B, Desmettre P, Paoletti E. Coexpression by vaccinia virus recombinants of equine herpesvirus 1 glycoproteins gp13 and gp14 results in potentiated immunity. J Virol 1990; 64:2399-406. [PMID: 2157895 PMCID: PMC249404 DOI: 10.1128/jvi.64.5.2399-2406.1990] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The equine herpesvirus 1 glycoprotein 14 (EHV-1 gp14) gene was cloned, sequenced, and expressed by vaccinia virus recombinants. Recombinant virus vP613 elicited the production of EHV-1-neutralizing antibodies in guinea pigs and was effective in protecting hamsters from subsequent lethal EHV-1 challenge. Coexpression of EHV-1 gp14 in vaccinia virus recombinant vP634 along with EHV-1 gp13 (P. Guo, S. Goebel, S. Davis, M. E. Perkus, B. Languet, P. Desmettre, G. Allen, and E. Paoletti, J. Virol. 63:4189-4198, 1989) greatly enhanced the protective efficacy in the hamster challenge model over that obtained with single recombinants. The inoculum doses (log10) required for protection of 50% of hamsters were 6.1 (EHV-1 gp13), 5.2 (EHV-1 gp14), and less than 3.6 (vaccinia virus recombinant expressing both EHV-1 glycoproteins [gp13 and gp14]).
Collapse
Affiliation(s)
- P X Guo
- Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany 12201
| | | | | | | | | | | | | | | | | |
Collapse
|