1
|
Dasgupta R, Ahlquist P, Kaesberg P. Sequence of the 3' untranslated region of brome mosaic virus coat protein messenger RNA. Virology 2008; 104:339-46. [PMID: 18631666 DOI: 10.1016/0042-6822(80)90338-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/1980] [Indexed: 10/26/2022]
Abstract
The 3' terminal 337 bases of BMV (brome mosaic virus) coat protein mRNA (BMV RNA4) are presented. This sequence includes the terminal portion of the coat protein cistron and the complete 300-base 3' noncoding sequence. The 3' noncoding sequence displays significant complementarity to the 5' terminal sequence of BMV RNA3 but not to the 5' terminal sequence of BMV RNA4.
Collapse
Affiliation(s)
- R Dasgupta
- Biophysics Laboratory of the Graduate School and Biochemistry Department of the College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | |
Collapse
|
2
|
Xu H, Nie J. Identification, Characterization, and Molecular Detection of Alfalfa mosaic virus in Potato. PHYTOPATHOLOGY 2006; 96:1237-1242. [PMID: 18943961 DOI: 10.1094/phyto-96-1237] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Alfalfa mosaic virus (AMV) was detected in potato fields in several provinces in Canada and characterized by bioassay, enzyme-linked immunosorbent assay, and reverse-transcription polymerase chain reaction (RT-PCR). The identity of eight Canadian potato AMV isolates was confirmed by sequence analysis of their coat protein (CP) gene. Sequence and phylogenetic analysis indicated that these eight AMV potato isolates fell into one strain group, whereas a slight difference between Ca175 and the other Canadian AMV isolates was revealed. The Canadian AMV isolates, except Ca175, clustered together among other strains based on alignment of the CP gene sequence. To detect the virus, a pair of primers, AMV-F and AMV-R, specific to the AMV CP gene, was designed based on the nucleotide sequence alignment of known AMV strains. Evaluations showed that RT-PCR using this primer set was specific and sensitive for detecting AMV in potato leaf and tuber samples. AMV RNAs were easily detected in composite samples of 400 to 800 potato leaves or 200 to 400 tubers. Restriction analysis of PCR amplicons with SacI was a simple method for the confirmation of PCR tests. Thus, RT-PCR followed by restriction fragment length polymorphism analysis may be a useful approach for screening potato samples on a large scale for the presence of AMV.
Collapse
|
3
|
Localisation of a high affinity binding site for coat protein on the 3′-terminal part of RNA 4 of alfalfa mosaic virus. FEBS Lett 2001. [DOI: 10.1016/0014-5793(80)81279-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
4
|
Ansel-McKinney P, Gehrke L. RNA determinants of a specific RNA-coat protein peptide interaction in alfalfa mosaic virus: conservation of homologous features in ilarvirus RNAs. J Mol Biol 1998; 278:767-85. [PMID: 9614941 DOI: 10.1006/jmbi.1998.1656] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Alfalfa mosaic virus (AMV) coat protein and tobacco streak virus (TSV) coat protein bind specifically to the 3' untranslated regions of the viral RNAs and are required with the genomic RNAs to initiate virus replication. A combination of nucleotide substitutions, hydroxyl radical footprinting, and ethylation and chemical modification interference analysis has been used to define the RNA determinants important for the specific binding of the 3'-terminal 39 nucleotides of AMV RNA 3/4 (AMV843-881) to an amino-terminal coat protein peptide (CP26). The results demonstrate that potential phosphate and base-specific contacts as well as ribose moieties protected upon peptide binding cluster in lower hairpin stems and flanking AUGC sequences of the viral RNA, without direct involvement of loop nucleotides. Nucleotides identified in the modification-interference analyses as important for RNA-protein interactions are highly conserved among AMV and the ilarvirus RNAs. This RNA sequence homology, coupled with the recent identification of an RNA binding consensus sequence for AMV and ilarvirus coat proteins, provides a framework for understanding the functional equivalence of AMV and TSV coat proteins in binding RNA and activating virus replication and may explain why heterologous AMV and ilarvirus coat protein-RNA mixtures are infectious.
Collapse
Affiliation(s)
- P Ansel-McKinney
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | |
Collapse
|
5
|
Houser-Scott F, Baer ML, Liem KF, Cai JM, Gehrke L. Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3' untranslated region of alfalfa mosaic virus RNA 4. J Virol 1994; 68:2194-205. [PMID: 8139004 PMCID: PMC236695 DOI: 10.1128/jvi.68.4.2194-2205.1994] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The specific binding of alfalfa mosaic virus coat protein to viral RNA requires determinants in the 3' untranslated region (UTR). Coat protein and peptide binding sites in the 3' UTR of alfalfa mosaic virus RNA 4 have been analyzed by hydroxyl radical footprinting, deletion mapping, and site-directed mutagenesis experiments. The 3' UTR has several stable hairpins that are flanked by single-stranded (A/U)UGC sequences. Hydroxyl radical footprinting data show that five sites in the 3' UTR of alfalfa mosaic virus RNA 4 are protected by coat protein, and four of the five protected regions contain AUGC or UUGC. Electrophoretic mobility band shift results suggest four coat protein binding sites in the 3' UTR. A 3'-terminal 39-nucleotide RNA fragment containing four AUGC repeats bound coat protein and coat protein peptides with high affinity; however, coat protein bound poorly to antisense 3' UTR transcripts and poly(AUGC)10. Site-directed mutagenesis of AUGC865-868 resulted in a loss of coat protein binding and peptide binding by the RNA fragment. Alignment of alfalfa mosaic RNA sequences with those from several closely related ilarviruses demonstrates that AUGC865-868 is perfectly conserved; moreover, the RNAs are predicted to form similar 3'-terminal secondary structures. The data strongly suggest that alfalfa mosaic virus coat protein and ilavirus coat proteins recognize invariant AUGC sequences in the context of conserved structural elements.
Collapse
Affiliation(s)
- F Houser-Scott
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge 02139
| | | | | | | | | |
Collapse
|
6
|
Gehrke L. Preparation of mRNA transcripts for secondary structure analysis using SP6 polymerase, guanylyltransferase, and preparative gel electrophoresis. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0735-0651(86)90005-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
7
|
Ravelonandro M, Pinck M, Pinck L. Complete nucleotide sequence of RNA 3 from alfalfa mosaic virus, strain S. Biochimie 1984; 66:395-402. [PMID: 6205697 DOI: 10.1016/0300-9084(84)90023-3] [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: 01/19/2023]
Abstract
We report the sequence of RNA 3 from strain S of Alfalfa mosaic virus (2,055 nucleotides). This RNA codes for a 32.4 kd protein (P3) and for the 24 kd coat protein (P4). The largest part of the sequence was established using RNA sequencing methods. The completion of the sequence in the region coding for P3 was achieved with cloned cDNA synthesized after priming at internal sites of RNA 3. Comparison of the RNA sequences coding P3 and P4 proteins in strain S with those reported in the literature for strain 425 revealed a higher amino acid substitution rate (3%) for P3 than for P4 (congruent to 1%) despite a similar average base substitution of 3-4% in these regions. In P3, two out of nine amino acid changes occur in hydrophilic regions. The amino acid changes in P4 do not modify the local hydrophilicity distribution. The intercistronic region displays a low degree of base substitution (2%) when compared with the untranslated 3'-end region (3.6%) or the 5'-end leader region (8%), the average substitution rate being 3.2%.
Collapse
|
8
|
Cornelissen BJ, Janssen H, Zuidema D, Bol JF. Complete nucleotide sequence of tobacco streak virus RNA 3. Nucleic Acids Res 1984; 12:2427-37. [PMID: 6546793 PMCID: PMC318673 DOI: 10.1093/nar/12.5.2427] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Double-stranded cDNA of in vitro polyadenylated tobacco streak virus (TSV) RNA 3 has been cloned and sequenced. The complete primary structure of 2,205 nucleotides reveals two open reading frames flanked by a leader sequence of 210 bases, an intercistronic region of 123 nucleotides and a 3'-extracistronic sequence of 288 nucleotides. The 5'-terminal open reading frame codes for a Mr 31,742 protein, which probably corresponds to the only in vitro translation product of TSV RNA 3. The 3'-terminal coding region predicts a Mr 26,346 protein, probably the viral coat protein, which is the translation product of the subgenomic messenger, RNA 4. Although the coat proteins of alfalfa mosaic virus (A1MV) and TSV are functionally equivalent in activating their own and each others genomes, no homology between the primary structures of those two proteins is detectable.
Collapse
|
9
|
Barker RF, Jarvis NP, Thompson DV, Loesch-Fries LS, Hall TC. Complete nucleotide sequence of alfalfa mosaic virus RNA3. Nucleic Acids Res 1983; 11:2881-91. [PMID: 6856479 PMCID: PMC325930 DOI: 10.1093/nar/11.9.2881] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A full-length cDNA clone of alfalfa mosaic virus (AMV) RNA3 was prepared and sequenced. The 2,037 base sequence contains two open reading frames of 903 and 666 nucleotides that code for a 32,400 dalton protein (32.4K protein) and the 24,380 dalton coat protein, respectively. A 5'-noncoding sequence of 240 bases preceeding the 32.4K protein contains homologous regions that may have a function in its translation. The intercistronic junction is 49 bases long, the last 36 bases representing the 5'-end of the subgenomic RNA4. The remaining 179 bases comprise the 3'-terminal noncoding sequence.
Collapse
|
10
|
Cornelissen BJ, Brederode FT, Moormann RJ, Bol JF. Complete nucleotide sequence of alfalfa mosaic virus RNA 1. Nucleic Acids Res 1983; 11:1253-65. [PMID: 6298738 PMCID: PMC325794 DOI: 10.1093/nar/11.5.1253] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Double-stranded cDNA of alfalfa mosaic virus (AlMV) RNA 1 has been cloned and sequenced. From clones with overlapping inserts, and other sequence data, the complete primary sequence of the 3644 nucleotides of RNA 1 was deduced: a long open reading frame for a protein of Mr 125,685 is flanked by a 5'-terminal sequence of 100 nucleotides and a 3' noncoding region of 163 nucleotides, including the sequence of 145 nucleotides the three genomic RNAs of AlMV have in common. The two UGA-termination codons halfway RNA 1, that were postulated by Van Tol et al. (FEBS Lett. 118, 67-71, 1980) to account for partial translation of RNA 1 in vitro into Mr 58,000 and Mr 62,000 proteins, were not found in the reading frame of the Mr 125,685 protein.
Collapse
|
11
|
Nassuth A, Bol JF. Altered balance of the synthesis of plus- and minus-strand RNAs induced by RNAs 1 and 2 of alfalfa mosaic virus in the absence of RNA 3. Virology 1983; 124:75-85. [DOI: 10.1016/0042-6822(83)90291-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/1982] [Accepted: 08/09/1982] [Indexed: 11/29/2022]
|
12
|
Houwing CJ, Jaspars EM. Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA 4. Biochemistry 1982; 21:3408-14. [PMID: 6810924 DOI: 10.1021/bi00257a025] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The subgenomic coat protein messenger RNA 4 of alfalfa mosaic virus forms complexes with one and three coat protein dimers, which are designated complexes I and III, respectively. These complexes were separated, subjected to digestion with ribonuclease T1, and filtered onto Millipore filters. Phenol extracts of the filters contained specific fragments of RNA 4, which were sequenced after electrophoretic separation on nondenaturing and denaturing polyacrylamide gels. Complex I yielded only a 68-nucleotide fragment including the 3' terminus [fragment 814-881 according to the numbering of Brederode, F. Th., Koper-Zwarthoff, E. C., & Bol, J. F. (1980) Nucleic Acids Res. 8, 2213-2223]. Complex III yielded in addition to the former fragment also other, mostly extracistronic, fragments from the 3'-terminal region, as well as fragments from an intracistronic region, comprising positions 425-474, in the middle of RNA 4. The 3'-terminal region was subdivided by small gaps into three coat protein binding sites: 799-881, 759-787, and 667-753, designated sites 1, 2, and 3, respectively, and possibly representing the sites occupied by the three coat protein dimers. A similarity may exist between the secondary structure of sites 1 and 3, which both may have three hairpins, two of which flanked at their 3' side by an AUGC sequence. Furthermore, a complementarity was noted between the loop of a large hairpin which can be drawn in the intracistronic site and the upper part of one of the three hairpins in the 3'-terminal site 1. These binding features have been combined in a model structure for the complex of RNA 4 with three coat protein dimers.
Collapse
|
13
|
Ursi D, Vandenberghe A, De Wachter R. The sequence of the 5.8 S ribosomal RNA of the crustacean Artemia salina. With a proposal for a general secondary structure model for 5.8 S ribosomal RNA. Nucleic Acids Res 1982; 10:3517-30. [PMID: 7099966 PMCID: PMC320728 DOI: 10.1093/nar/10.11.3517] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report the primary structure of 5.8 S rRNA from the crustacean Artemia salina. The preparation shows length heterogeneity at the 5'-terminus, but consists of uninterrupted RNA chains, in contrast to some insect 5.8 S rRNAs, which consist of two chains of unequal length separated in the gene by a short spacer. The sequence was aligned with those of 11 other 5.8 S rRNAs and a general secondary structure model derived. It has four helical regions in common with the model of Nazar et al. (J. Biol. Chem. 250, 8591-8597 (1975)), but for a fifth helix a different base pairing scheme was found preferable, and the terminal sequences are presumed to bind to 28 S rRNA instead of binding to each other. In the case of yeast, where both the 5.8 S and 26 S rRNA sequences are known, the existence of five helices in 5.8 S rRNA is shown to be compatible with a 5.8 S - 26 S rRNA interaction model.
Collapse
|
14
|
Srinivasan S, Jaspars EM. Alterations of the conformation of the RNAs of alfalfa mosaic virus upon binding of a few coat protein molecules. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 696:260-6. [PMID: 7066325 DOI: 10.1016/0167-4781(82)90056-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structural changes in the single-stranded genome RNAs (RNAs 1, 2 and 3) and the subgenomic coat protein messenger (RNA 4) of alfalfa mosaic virus upon addition of a few coat protein molecules of the virus were investigated by measuring the fluorescent intensity of bound ethidium bromide and by circular dichroism. No effect could be observed in the case of the genome RNAs. However, in RNA 4, which is of much less complexity than the genome RNAs, a reduction of the ethidium bromide binding by 30% was found, whereas the positive molar ellipticity at 265 nm was reduced by 9% upon binding of the coat protein. Both changes point to a reduction of the ordered structure of the RNA. Since the protein is known to bind first at the 3'-terminus of RNA 4 and probably also of the genome RNAs, the conformational changes observed could be those thought to be necessary for replicase recognition in this positive-stranded RNa virus which needs the coat protein for starting an infection cycle.
Collapse
|
15
|
Littauer UZ, Soreq H. The regulatory function of poly(A) and adjacent 3' sequences in translated RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1982; 27:53-83. [PMID: 7048421 DOI: 10.1016/s0079-6603(08)60597-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
16
|
Diels L, De Baere R, Vandenberghe A, De Wachter R. The sequence of 5S ribosomal RNA of the crustacean Artemia salina. Nucleic Acids Res 1981; 9:5141-4. [PMID: 7312626 PMCID: PMC327504 DOI: 10.1093/nar/9.19.5141] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The primary structure of the 5 S rRNA isolated from the cryptobiotic cysts of the brine shrimp Artemia salina is pACCAACGGCCAUACCACGUUGAAAGUACCCAGUCUCGUCAGAUCCUGGAAGUCACACAACGUCGGGCCCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGGGUGCUGUUGGCAU (OH).
Collapse
|
17
|
Smit C, Roosien J, Van Vloten-Doting L, Jaspars E. Evidence that alfalfa mosaic virus infection starts with three RNA-protein complexes. Virology 1981; 112:169-73. [DOI: 10.1016/0042-6822(81)90622-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/1981] [Indexed: 11/30/2022]
|
18
|
Limited sequence variation in the leader sequence of RNA 4 from several strains of alfalfa mosaic virus. Virology 1980; 106:145-7. [DOI: 10.1016/0042-6822(80)90230-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/1980] [Indexed: 11/20/2022]
|
19
|
Koper-Zwarthoff EC, Bol JF. Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus. Nucleic Acids Res 1980; 8:3307-18. [PMID: 6160470 PMCID: PMC324154 DOI: 10.1093/nar/8.15.3307] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The sequence of the 3'-terminal 180 and 140 nucleotides of RNAs 2 and 3, respectively, of tobacco streak virus (TSV) was deduced by reverse transcription in the presence of a specific primer and chain terminators. Homology between the two RNAs was found to be restricted to a 3-terminal region of about 45 nucleotides. The data were compared with the sequence of the homologous region of 145 nucleotides occurring at the 3'-termini of the alfalfa mosaic virus (A1MV) RNAs, which contains the specific binding site for coat protein (Koper-Zwarthoff et al., Nucleic Acids Res. 7, 1887-1900 (1979); Houwing and Jaspars, Biochemistry 17, 2927-2933 (1978)). This was done because of the evidence that the RNAs of A1MV and TSV contain specific binding sites for their own as well as each others coat protein, and that binding of coat protein to these sites is required to initiate infection (Van Vloten-Doting, Virology 65, 215-225 (1975)). The 3'-terminal homologous regions of A1MV and TSV have two features in common: the presence of several stable hairpins and the multiple occurrence of the tetranucleotide sequence AUGC. The hairpins cause the linear array of tandemly repeated AUGC-boxes. It is postulated that the primary interaction of coat protein molecules with the RNAs of AlMV and TSV is a cooperative process involving several binding sites each being composed of a hairpin flanked at its 3'-side by an AUGC-sequence.
Collapse
|
20
|
Smit C, Jaspars E. Activation of the genome of alfalfa mosaic virus is enhanced by the presence of the coat protein on all three genome parts. Virology 1980; 104:454-61. [DOI: 10.1016/0042-6822(80)90347-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/1980] [Indexed: 10/26/2022]
|
21
|
Brederode FT, Koper-Zwarthoff EC, Bol JF. Complete nucleotide sequence of alfalfa mosaic virus RNA 4. Nucleic Acids Res 1980; 8:2213-23. [PMID: 7433090 PMCID: PMC324073 DOI: 10.1093/nar/8.10.2213] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Alfalfa mosaic virus RNA 4, the subgenomic messenger for viral coat protein, was partially digested with RNase T1 or RNase A and the sequence of a number of fragments was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. From overlapping fragments, the complete primary sequence of the 881 nucleotides of RNA 4 was constructed: the coding region of 660 nucleotides (not including the initiation and termination codon) is flanked by a 5' noncoding region of 39 nucleotides and a 3' noncoding region of 182 nucleotides. The RNA sequencing data completely confirm the amino acid sequence of the coat protein as deduced by Van Beynum et al. (Fur.J. Biochem. 72, 63-78, 1977).
Collapse
|