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Polevoda B, Joseph R, Friedman AE, Bennett RP, Greiner R, De Zoysa T, Stewart RA, Smith HC. DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315. J Biol Chem 2017; 292:8642-8656. [PMID: 28381554 DOI: 10.1074/jbc.m116.767889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/04/2017] [Indexed: 12/23/2022] Open
Abstract
APOBEC3G (A3G) belongs to the AID/APOBEC protein family of cytidine deaminases (CDA) that bind to nucleic acids. A3G mutates the HIV genome by deamination of dC to dU, leading to accumulation of virus-inactivating mutations. Binding to cellular RNAs inhibits A3G binding to substrate single-stranded (ss) DNA and CDA activity. Bulk RNA and substrate ssDNA bind to the same three A3G tryptic peptides (amino acids 181-194, 314-320, and 345-374) that form parts of a continuously exposed protein surface extending from the catalytic domain in the C terminus of A3G to its N terminus. We show here that the A3G tyrosines 181 and 315 directly cross-linked ssDNA. Binding experiments showed that a Y315A mutation alone significantly reduced A3G binding to both ssDNA and RNA, whereas Y181A and Y182A mutations only moderately affected A3G nucleic acid binding. Consistent with these findings, the Y315A mutant exhibited little to no deaminase activity in an Escherichia coli DNA mutator reporter, whereas Y181A and Y182A mutants retained ∼50% of wild-type A3G activity. The Y315A mutant also showed a markedly reduced ability to assemble into viral particles and had reduced antiviral activity. In uninfected cells, the impaired RNA-binding capacity of Y315A was evident by a shift of A3G from high-molecular-mass ribonucleoprotein complexes to low-molecular-mass complexes. We conclude that Tyr-315 is essential for coordinating ssDNA interaction with or entry to the deaminase domain and hypothesize that RNA bound to Tyr-315 may be sufficient to competitively inhibit ssDNA deaminase-dependent antiviral activity.
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Affiliation(s)
- Bogdan Polevoda
- From the Departments of Biochemistry and Biophysics and.,Center for RNA Biology, and
| | | | | | | | | | | | | | - Harold C Smith
- From the Departments of Biochemistry and Biophysics and .,Center for RNA Biology, and.,OyaGen, Inc., Rochester, New York 14623.,Center for AIDS Research, University of Rochester Medical Center, Rochester, New York 14642 and
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2
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Smith CC, Hollenstein M, Leumann CJ. The synthesis and application of a diazirine-modified uridine analogue for investigating RNA–protein interactions. RSC Adv 2014. [DOI: 10.1039/c4ra08682a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A uridine analogue equipped with a photoactive diazirine unit was generated and incorporated into RNA either syntheticallyviaphosphoramidite chemistry or by enzymatic polymerization. The new analogue was developed to identify and investigate RNA–protein interactions.
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Affiliation(s)
- Christine C. Smith
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
| | - Marcel Hollenstein
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
| | - Christian J. Leumann
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern, Switzerland
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3
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Woo HH, Zhou Y, Yi X, David CL, Zheng W, Gilmore-Hebert M, Kluger HM, Ulukus EC, Baker T, Stoffer JB, Chambers SK. Regulation of non-AU-rich element containing c-fms proto-oncogene expression by HuR in breast cancer. Oncogene 2009; 28:1176-86. [PMID: 19151756 DOI: 10.1038/onc.2008.469] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The role of RNA-binding proteins in cancer biology is recognized increasingly. The nucleocytoplasmic shuttling and AU-rich RNA-binding protein HuR stabilizes several cancer-related target mRNAs. The proto-oncogene c-fms, whose 3'untranslated region (3'UTR) is not AU-rich, is associated with poor prognosis in breast cancer. Using a large breast-cancer tissue array (N=670), we found nuclear HuR expression to be associated with nodal metastasis and independently with poor survival (P=0.03, RR 1.45), as well as to be co-expressed with c-fms in the breast tumors (P=0.0007). We described c-fms mRNA as a direct target of HuR in vivo, and that HuR bound specifically to a 69-nt region containing 'CUU' motifs in 3'UTR c-fms RNA. Overexpressing or silencing HuR significantly up- or down-regulated c-fms RNA expression, respectively. We also found that known glucocorticoid stimulation of c-fms RNA and protein is largely dependent on the presence of HuR. HuR, by binding to the 69-nt wild type, but not mutant, c-fms sequence can regulate reporter gene expression post-transcriptionally. We are the first to describe that HuR can regulate gene expression by binding non-AU-rich sequences in 3'UTR c-fms RNA. Collectively, our findings suggest that HuR plays a supportive role for c-fms in breast cancer progression by binding a 69-nt element in its 3'UTR, thus regulating its expression.
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Affiliation(s)
- H-H Woo
- Arizona Cancer Center, University of Arizona, Tucson, AZ 85724-5024, USA
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4
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Micura R, Höbartner C, Rieder R, Kreutz C, Puffer B, Lang K, Moroder H. Preparation of 2'-deoxy-2'-methylseleno-modified phosphoramidites and RNA. ACTA ACUST UNITED AC 2008; Chapter 1:Unit 1.15. [PMID: 18428963 DOI: 10.1002/0471142700.nc0115s27] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The derivatization of nucleic acids with selenium is a useful approach to facilitate phase determination during three-dimensional structural analysis by X-ray crystallography. This unit describes (1) the synthesis and characterization of 2'-deoxy-2'-methylseleno (2'-Se-methyl) nucleosides and their corresponding 3'-O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite derivatives, (2) the site-specific incorporation of 2'-Se-methyl ribonucleosides into oligoribonucleotides by chemical RNA solid-phase synthesis, and (3) the enzymatic ligation of Se-containing RNA oligonucleotides to produce a biologically relevant RNA sequence.
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5
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Puffer B, Moroder H, Aigner M, Micura R. 2'-Methylseleno-modified oligoribonucleotides for X-ray crystallography synthesized by the ACE RNA solid-phase approach. Nucleic Acids Res 2008; 36:970-83. [PMID: 18096613 PMCID: PMC2241898 DOI: 10.1093/nar/gkm880] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 10/01/2007] [Accepted: 10/01/2007] [Indexed: 11/15/2022] Open
Abstract
Site-specifically modified 2'-methylseleno RNA represents a valuable derivative for phasing of X-ray crystallographic data. Several successful applications in three-dimensional structure determination of nucleic acids, such as the Diels-Alder ribozyme, have relied on this modification. Here, we introduce synthetic routes to 2'-methylseleno phosphoramidite building blocks of all four standard nucleosides, adenosine, cytidine, guanosine and uridine, that are tailored for 2'-O-bis(acetoxyethoxy)methyl (ACE) RNA solid-phase synthesis. We additionally report on their incorporation into oligoribonucleotides including deprotection and purification. The methodological expansion of 2'-methylseleno labeling via ACE RNA chemistry is a major step to make Se-RNA generally accessible and to receive broad dissemination of the Se-approach for crystallographic studies on RNA. Thus far, preparation of 2'-methylseleno-modified oligoribonucleotides has been restricted to the 2'-O-[(triisopropylsilyl)oxy]methyl (TOM) and 2'-O-tert-butyldimethylsilyl (TBDMS) RNA synthesis methods.
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Affiliation(s)
| | | | | | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens University, Innrain 52a, 6020 Innsbruck, Austria
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6
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Norris CL, Meisenheimer KM, Koch TH. Mechanistic Studies Relevant to Bromouridine-Enhanced Nucleoprotein Photocrosslinking: Possible Involvement of an Excited Tyrosine Residue of the Protein. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1997.tb08546.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Banerjee H, Singh R. A simple crosslinking method, CLAMP, to map the sites of RNA-contacting domains within a protein. Methods Mol Biol 2008; 488:181-90. [PMID: 18982291 DOI: 10.1007/978-1-60327-475-3_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A large number of proteins contain multiple RNA recognition motifs (RRMs). How multiple RRMs contribute to RNA recognition in solution is, however, poorly understood. Here, we describe a simple biochemical approach called CLAMP (crosslinking and mapping of protein domain) to identify an RRM that is crosslinked to a specific nucleotide in RNA. It involves site-specific incorporation of a chromophore, photochemical RNA-protein crosslinking, and site-specific chemical cleavage of the protein. This technique is suitable for numerous other RNA binding proteins that have multiple RNA binding domains.
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Affiliation(s)
- Hiren Banerjee
- Department of Molecular, University of Colorado at Boulder, Boulder, Colorado, USA
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8
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Sheflyan GY, Kubareva EA, Gromova ES. Methods for the covalent attachment of nucleic acids and their derivatives to proteins. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1996v065n08abeh000277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Tang Y, Chen Y, Lichti CF, Hall RA, Raney KD, Jennings SF. CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysis. BMC Bioinformatics 2005; 6 Suppl 2:S9. [PMID: 16026606 PMCID: PMC1637035 DOI: 10.1186/1471-2105-6-s2-s9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these interactions. Combining this technique with chemical crosslinking, it is possible to identify the sites of interactions within these complexes. Due to the complexities of the mass spectrometric data of crosslinked proteins, new software is required to analyze the resulting products of these studies. Result We designed a Cross-Linked Peptide Mapping (CLPM) algorithm which takes advantage of all of the information available in the experiment including the amino acid sequence from each protein, the identity of the crosslinker, the identity of the digesting enzyme, the level of missed cleavage, and possible chemical modifications. The algorithm does in silico digestion and crosslinking, calculates all possible mass values and matches the theoretical data to the actual experimental data provided by the mass spectrometry analysis to identify the crosslinked peptides. Conclusion Identifying peptides by their masses can be an efficient starting point for direct sequence confirmation. The CLPM algorithm provides a powerful tool in identifying these potential interaction sites in combination with chemical crosslinking and mass spectrometry. Through this cost-effective approach, subsequent efforts can quickly focus attention on investigating these specific interaction sites.
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Affiliation(s)
- Yong Tang
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
- MidSouth Bioinformatics Center, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Yingfeng Chen
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Cheryl F Lichti
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Roger A Hall
- MidSouth Bioinformatics Center, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Steven F Jennings
- Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
- MidSouth Bioinformatics Center, University of Arkansas at Little Rock, Little Rock, Arkansas 72204
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10
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Kimoto M, Endo M, Mitsui T, Okuni T, Hirao I, Yokoyama S. Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs. ACTA ACUST UNITED AC 2004; 11:47-55. [PMID: 15112994 DOI: 10.1016/j.chembiol.2003.12.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2003] [Revised: 10/20/2003] [Accepted: 10/22/2003] [Indexed: 11/20/2022]
Abstract
A photo-sensitive ribonucleotide of 5-iodo-2-oxo(1H) pyridine (Iy) capable of site-specific incorporation into transcripts was developed. The site-specific Iy incorporation into RNA was achieved by T7 transcription mediated by unnatural base pairing between Iy and its partner, 2-amino-6-(2-thienyl)purine (s). By this specific transcription, Iy was incorporated into an anti(Raf-1) RNA aptamer, which binds to human Raf-1 and inhibits the interaction between Raf-1 and Ras. Protein-dependent photo-dimerization of the aptamer was observed when Iy was located at specific positions in the aptamer, showing that the site-specific incorporation of the photo-sensitive component into RNA achieves highly specific crosslinking. This specific transcription mediated by the unnatural base pair would be a powerful tool for generating high-affinity RNA ligands and for analyzing RNA-RNA and RNA-protein interactions, as well as for constructing RNA-based nanostructures.
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Affiliation(s)
- Michiko Kimoto
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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11
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Cho HD, Weiner AM. A single catalytically active subunit in the multimeric Sulfolobus shibatae CCA-adding enzyme can carry out all three steps of CCA addition. J Biol Chem 2004; 279:40130-6. [PMID: 15265870 DOI: 10.1074/jbc.m405518200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The CCA-adding enzyme ATP(CTP):tRNA nucleotidyltransferase builds and repairs the 3'-terminal CCA sequence of tRNA. Although this unusual RNA polymerase has no nucleic acid template, it can construct the CCA sequence one nucleotide at a time using CTP and ATP as substrates. We found previously that tRNA does not translocate along the enzyme during CCA addition (Yue, D., Weiner, A. M., and Maizels, N. (1998) J. Biol. Chem. 273, 29693-29700) and that a single nucleotidyltransferase motif adds all three nucleotides (Shi, P.-Y., Maizels, N., and Weiner, A. M. (1998) EMBO J. 17, 3197-3206). Intriguingly, the CCA-adding enzyme from the archaeon Sulfolobus shibatae is a homodimer that forms a tetramer upon binding two tRNAs. We therefore asked whether the active form of the S. shibatae enzyme might have two quasi-equivalent active sites, one adding CTP and the other ATP. Using an intersubunit complementation approach, we demonstrate that the dimer is active and that a single catalytically active subunit can carry out all three steps of CCA addition. We also locate one UV light-induced tRNA cross-link on the enzyme structure and provide evidence suggesting the location of another. Our data rule out shuttling models in which the 3'-end of the tRNA shuttles from one quasi-equivalent active site to another, demonstrate that tRNA-induced tetramerization is not required for CCA addition, and support a role for the tail domain of the enzyme in tRNA binding.
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Affiliation(s)
- HyunDae D Cho
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, Washington 98195-7350, USA
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12
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Carrasco N, Buzin Y, Tyson E, Halpert E, Huang Z. Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion. Nucleic Acids Res 2004; 32:1638-46. [PMID: 15007109 PMCID: PMC390325 DOI: 10.1093/nar/gkh325] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report here the solid phase synthesis of RNA and DNA oligonucleotides containing the 2'-selenium functionality for X-ray crystallography using multiwavelength anomalous dispersion. We have synthesized the novel 2'-methylseleno cytidine phosphoramidite and improved the accessibility of the 2'-methylseleno uridine phosphoramidite for the synthesis of many selenium-derivatized DNAs and RNAs in large scales. The yields of coupling these Se-nucleoside phosphoramidites into DNA or RNA oligonucleotides were over 99% when 5-(benzylmercapto)-1H-tetrazole was used as the coupling reagent. The UV melting study of A-form dsDNAs indicated that the 2'-selenium derivatization had no effect on the stability of the duplexes with the 3'-endo sugar pucker. Thus, the stems of functional RNA molecules with the same 3'-endo sugar pucker appear to be the ideal sites for the selenium derivatization with 2'-Se-C and 2'-Se-U. Crystallization of the selenium-derivatized oligonucleotides is also reported here. The results demonstrate that this 2'-selenium functionality is suitable for RNA and A-form DNA derivatization in X-ray crystallography.
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Affiliation(s)
- Nicolas Carrasco
- Department of Chemistry, Brooklyn College, and Program of Biochemistry and Chemistry, The Graduate School, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
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13
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Banerjee H, Rahn A, Gawande B, Guth S, Valcarcel J, Singh R. The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro. RNA (NEW YORK, N.Y.) 2004; 10:240-53. [PMID: 14730023 PMCID: PMC1370536 DOI: 10.1261/rna.5153204] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2003] [Accepted: 10/13/2003] [Indexed: 05/09/2023]
Abstract
The general splicing factor U2AF(65) recognizes the polypyrimidine tract (Py tract) that precedes 3' splice sites and has three RNA recognition motifs (RRMs). The C-terminal RRM (RRM3), which is highly conserved, has been proposed to contribute to Py-tract binding and establish protein-protein contacts with splicing factors mBBP/SF1 and SAP155. Unexpectedly, we find that the human RRM3 domain is dispensable for U2AF(65) activity in vitro. However, it has an essential function in Schizosaccharomyces pombe distinct from binding to the Py tract or to mBBP/SF1 and SAP155. First, deletion of RRM3 from the human protein has no effect on Py-tract binding. Second, RRM123 and RRM12 select similar sequences from a random pool of RNA. Third, deletion of RRM3 has no effect on the splicing activity of U2AF(65) in vitro. However, deletion of the RRM3 domain of S. pombe U2AF(59) abolishes U2AF function in vivo. In addition, certain amino acid substitutions on the four-stranded beta-sheet surface of RRM3 compromise U2AF function in vivo without affecting binding to mBBP/SF1 or SAP155 in vitro. We propose that RRM3 has an unrecognized function that is possibly relevant for the splicing of only a subset of cellular introns. We discuss the implications of these observations on previous models of U2AF function.
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Affiliation(s)
- Hiren Banerjee
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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Abstract
The potential of photoaptamers as proteomic probes was investigated. Photoaptamers are defined as aptamers that bear photocross-linking functionality, in this report, 5-bromo-2'-deoxyuridine. A key question regarding the use of photoaptamer probes is the specificity of the cross-linking reaction. The specificity of three photoaptamers was explored by comparing their reactions with target proteins and non-target proteins. The range of target/non-target specificity varies from 100- to >10(6)-fold with most values >10(4)-fold. The contributions of the initial binding step and the photocross-linking step were evaluated for each reaction. Photocross-linking never degraded specificity and significantly increased aptamer specificity in some cases. The application of photoaptamer technology to proteomics was investigated in microarray format. Immobilized anti-human immunodeficiency virus-gp120 aptamer was able to detect subnanomolar concentrations of target protein in 5% human serum. The levels of sensitivity and specificity displayed by photoaptamers, combined with other advantageous properties of aptamers, should facilitate development of protein chip technology.
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Affiliation(s)
- Drew Smith
- SomaLogic, Inc, Boulder, Colorado 80301, USA.
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15
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Meisenheimer KM, Meisenheimer PL, Koch TH. Nucleoprotein photo-cross-linking using halopyrimidine-substituted RNAs. Methods Enzymol 2001; 318:88-104. [PMID: 10889982 DOI: 10.1016/s0076-6879(00)18046-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- K M Meisenheimer
- Department of Chemistry, Angelo State University, San Angelo, Texas 76909, USA
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16
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Abstract
High sensitivity and specificity of two modified ssDNA aptamers capable of photocross-linking recombinant human basic fibroblast growth factor (bFGF((155))) were demonstrated. The aptamers were identified through a novel, covalent, in vitro selection methodology called photochemical systematic evolution of ligands by exponential enrichment (PhotoSELEX). The aptamers exhibited high sensitivity for bFGF((155)) comparable with commercially available ELISA monoclonal antibodies with an absolute sensitivity of at least 0.058 ppt bFGF((155)) under prevailing test conditions. The aptamers exquisitely distinguished bFGF((155)) from consanguine proteins, vascular endothelial growth factor (VEGF) and platelet derived growth factor (PDGF). A commercially viable diagnostic system incorporating PhotoSELEX-evolved aptamers capable of simultaneous quantification of a large number of analyte molecules is also described. Such a system benefits from covalent bonding of aptamer to target protein allowing vigorous washing with denaturants to improve signal to noise.
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Affiliation(s)
- M C Golden
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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Golden MC, Resing KA, Collins BD, Willis MC, Koch TH. Mass spectral characterization of a protein-nucleic acid photocrosslink. Protein Sci 1999; 8:2806-12. [PMID: 10631998 PMCID: PMC2144224 DOI: 10.1110/ps.8.12.2806] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A photocrosslink between basic fibroblast growth factor (bFGF155) and a high affinity ssDNA oligonucleotide was characterized by positive ion electrospray ionization mass spectrometry (ESIMS). The DNA was a 61-mer oligonucleotide photoaptamer bearing seven bromodeoxyuridines, identified by in vitro selection. Specific photocrosslinking of the protein to the oligonucleotide was achieved by 308 nm XeCl excimer laser excitation. The cross-linked protein nucleic acid complex was proteolyzed with trypsin. The resulting peptide crosslink was purified by PAGE, eluted, and digested by snake venom phosphodiesterase/alkaline phosphatase. Comparison of the oligonucleotide vs. the degraded peptide crosslink by high performance liquid chromatography coupled to an electrospray ionization triple quadrupole mass spectrometer showed a single ion unique to the crosslinked material. Sequencing by collision induced dissociation (MS/MS) on a triple quadrupole mass spectrometer revealed that this ion was the nonapeptide TGQYKLGSK (residues 130-138) crosslinked to a dinucleotide at Tyr133. The MS/MS spectrum indicated sequential fragmentation of the oligonucleotide to uracil covalently attached to the nonapeptide followed by fragmentation of the peptide bonds. Tyr133 is located within the heparin binding pocket, suggesting that the in vitro selection targeted this negative ion binding region of bFGF155.
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Affiliation(s)
- M C Golden
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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18
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Kraemer B, Crittenden S, Gallegos M, Moulder G, Barstead R, Kimble J, Wickens M. NANOS-3 and FBF proteins physically interact to control the sperm-oocyte switch in Caenorhabditis elegans. Curr Biol 1999; 9:1009-18. [PMID: 10508609 DOI: 10.1016/s0960-9822(99)80449-7] [Citation(s) in RCA: 222] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The Caenorhabditis elegans FBF protein and its Drosophila relative, Pumilio, define a large family of eukaryotic RNA-binding proteins. By binding regulatory elements in the 3' untranslated regions (UTRs) of their cognate RNAs, FBF and Pumilio have key post-transcriptional roles in early developmental decisions. In C. elegans, FBF is required for repression of fem-3 mRNA to achieve the hermaphrodite switch from spermatogenesis to oogenesis. RESULTS We report here that FBF and NANOS-3 (NOS-3), one of three C. elegans Nanos homologs, interact with each other in both yeast two-hybrid and in vitro assays. We have delineated the portions of each protein required for this interaction. Worms lacking nanos function were derived either by RNA-mediated interference (nos-1 and nos-2) or by use of a deletion mutant (nos-3). The roles of the three nos genes overlap during germ-line development. In certain nos-deficient animals, the hermaphrodite sperm-oocyte switch was defective, leading to the production of excess sperm and no oocytes. In other nos-deficient animals, the entire germ line died during larval development. This germ-line death did not require CED-3, a protease required for apoptosis. CONCLUSIONS The data suggest that NOS-3 participates in the sperm-oocyte switch through its physical interaction with FBF, forming a regulatory complex that controls fem-3 mRNA. NOS-1 and NOS-2 also function in the switch, but do not interact directly with FBF. The three C. elegans nanos genes, like Drosophila nanos, are also critical for germ-line survival. We propose that this may have been the primitive function of nanos genes.
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Affiliation(s)
- B Kraemer
- Department of Biochemistry University of Wisconsin-Madison Madison, Wisconsin 53706, USA
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Revers F, Cario M, Cao TL, Cazenave C. Detection of proteins binding to short RNA.DNA hybrids or short antisense oligonucleotides in Xenopus laevis oocytes and human macrophage cell extracts by photoaffinity radiolabeling. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1999; 9:317-31. [PMID: 10463076 DOI: 10.1089/oli.1.1999.9.317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Using a 12 base pair RNA.DNA hybrid, substituted with bromouracil on either the RNA or DNA strand, we have detected by photoaffinity radiolabeling a limited set of proteins able to bind to RNA.DNA hybrids in both Xenopus oocyte extracts and human macrophage extracts. Resulting patterns of crosslinked proteins were highly dependent on the strand (DNA or RNA) that was substituted. With one exception, none of the proteins investigated in competition experiments was found to be absolutely specific for RNA.DNA hybrids, as at least one other nucleic acid, either single-stranded DNA or single-stranded RNA, was found to compete efficiently. None of the proteins detected in this assay correspond to the size expected for RNases H. Using the same methodology, we have detected proteins that bind to short oligodeoxyribonucleotides. Although we have essentially detected in Xenopus oocytes one prominent protein of approximately 75 kDa, corresponding to replication protein A (RPA) whatever the oligonucleotide used, the patterns obtained with extracts of human macrophages were more complex and dependent on the oligonucleotide used. If a protein corresponding to RPA was observed most of the time, other crosslinks of similar or sometimes higher intensity were also detected. Interestingly, among these, one protein of 35 kDa appears paradoxically to bind and crosslink to a dodecamer but not to an octadecamer containing the same sequence placed either at its 3'-end or 5'-end.
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Affiliation(s)
- F Revers
- Laboratoire de Biophysique Moléculaire, INSERM U386, Université Victor Segalen Bordeaux II, France
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20
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Abstract
Derivatization of RNA with heterobifunctional photocrosslinking reagents becomes an increasingly popular method for the analysis of structural properties of ribonucleoprotein complexes. This article describes a simple chemical modification-derivatization strategy used to introduce selected chemical groups at specific internal positions within the RNA ribose backbone. The strategy is based on the coupling of a haloacetyl adduct to a thiol residue in the phosphodiester bond. The use of a number of RNA probes derivatized with several different photoreactive groups can provide invaluable information on the structural distribution of components in complex ribonucleoprotein assemblies.
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Affiliation(s)
- M M Konarska
- Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, New York 10021, USA
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21
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Abstract
Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies. The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.
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Affiliation(s)
- S Verma
- Max-Planck-Institut für Experimentelle Medizin, Göttingen, Germany
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22
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Luyten I, Herdewijn P. Hybridization properties of base-modified oligonucleotides within the double and triple helix motif. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80016-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Chen F, Wilusz J. Auxiliary downstream elements are required for efficient polyadenylation of mammalian pre-mRNAs. Nucleic Acids Res 1998; 26:2891-8. [PMID: 9611233 PMCID: PMC147640 DOI: 10.1093/nar/26.12.2891] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have previously identified a G-rich sequence (GRS) as an auxiliary downstream element (AUX DSE) which influences the processing efficiency of the SV40 late polyadenylation signal. We have now determined that sequences downstream of the core U-rich element (URE) form a fundamental part of mammalian polyadenylation signals. These novel AUX DSEs all influenced the efficiency of 3'-end processing in vitro by stabilizing the assembly of CstF on the core downstream URE. Three possible mechanisms by which AUX DSEs mediate efficient in vitro 3'-end processing have been explored. First, AUX DSEs can promote processing efficiency by maintaining the core elements in an unstructured domain which allows the general polyadenylation factors to efficiently assemble on the RNA substrate. Second, AUX DSEs can enhance processing by forming a stable structure which helps focus binding of CstF to the core downstream URE. Finally, the GRS element, but not the binding site for the bacteriophage R17 coat protein, can substitute for the auxiliary downstream region of the adenovirus L3 polyadenylation signal. This suggests that AUX DSE binding proteins may play an active role in stimulating 3'-end processing by stabilizing the association of CstF with the RNA substrate. AUX DSEs, therefore, serve as a integral part of the polyadenylation signal and can affect signal strength and possibly regulation.
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Affiliation(s)
- F Chen
- UMDNJ-New Jersey Medical School, Department of Microbiology and Molecular Genetics, 185 South Orange Avenue, Newark, NJ 07103, USA
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24
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25
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26
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Meisenheimer KM, Koch TH. Photocross-linking of nucleic acids to associated proteins. Crit Rev Biochem Mol Biol 1997; 32:101-40. [PMID: 9145285 DOI: 10.3109/10409239709108550] [Citation(s) in RCA: 213] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes. It can be accomplished by one or two photon excitations of wild-type nucleoprotein complexes or by one photon excitation of nucleoprotein complexes bearing one or more substitutions with photoreactive chromophores. Chromophores that have been incorporated into nucleic acids for this purpose include aryl azides, 5-azidouracil, 8-azidoadenine, 8-azidoguanine, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-iodocytosine. The various techniques and chromophores are described and compared, with attention to the photochemical mechanism.
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Affiliation(s)
- K M Meisenheimer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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27
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SenGupta DJ, Zhang B, Kraemer B, Pochart P, Fields S, Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci U S A 1996; 93:8496-501. [PMID: 8710898 PMCID: PMC38700 DOI: 10.1073/pnas.93.16.8496] [Citation(s) in RCA: 387] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
RNA-protein interactions are pivotal in fundamental cellular processes such as translation, mRNA processing, early development, and infection by RNA viruses. However, in spite of the central importance of these interactions, few approaches are available to analyze them rapidly in vivo. We describe a yeast genetic method to detect and analyze RNA-protein interactions in which the binding of a bifunctional RNA to each of two hybrid proteins activates transcription of a reporter gene in vivo. We demonstrate that this three-hybrid system enables the rapid, phenotypic detection of specific RNA-protein interactions. As examples, we use the binding of the iron regulatory protein 1 (IRP1) to the iron response element (IRE), and of HIV trans-activator protein (Tat) to the HIV trans-activation response element (TAR) RNA sequence. The three-hybrid assay we describe relies only on the physical properties of the RNA and protein, and not on their natural biological activities; as a result, it may have broad application in the identification of RNA-binding proteins and RNAs, as well as in the detailed analysis of their interactions.
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Affiliation(s)
- D J SenGupta
- Department of Molecular Genetics and Microbiology, State University of New York, Stony Brook 11794, USA
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28
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Liu Y, Wang Z, Rana TM. Visualizing a specific contact in the HIV-1 Tat protein fragment and trans-activation responsive region RNA complex by photocross-linking. J Biol Chem 1996; 271:10391-6. [PMID: 8626612 DOI: 10.1074/jbc.271.17.10391] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Replication of human immunodeficiency virus type 1 (HIV-1) requires specific interactions of Tat protein with the trans-activation responsive region (TAR) RNA, a stem-loop structure containing two helical stem regions separated by a trinucleotide bulge. The Tat protein contains a basic RNA-binding region (amino acids 49-57) located in the carboxyl-terminal half of the protein, and peptides containing this basic domain of Tat protein can bind TAR RNA with high affinities. We synthesized a 31-amino acid Tat fragment (amino acids 42-72) containing the basic region and part of flanking regulatory core domain that formed a specific complex with TAR RNA. Upon UV irradiation (254 nm), this Tat fragment cross-linked covalently with TAR RNA. Sites of cross-links were determined on both the TAR RNA and Tat protein fragment by RNA and protein sequencing, respectively. These results revealed that guanosine 26 of TAR RNA was cross-linked with tyrosine 47 of the Tat peptide. Our results provide the first physical evidence for a direct amino acid-base contact in Tat-TAR complex. Recently, orientation of the Tat-(42-72) was determined in our laboratory by psoralen.Tat-(42-72) conjugate (Wang, Z., and Rana, T. M. (1995) J. Am. Chem. Soc. 117, 5438-5444). On the basis of our findings, we suggest a model in which Tat binds to TAR RNA by inserting the basic recognition sequence into the major groove with an orientation where lysine 41 in the core domain of Tat contacts the lower stem and Tyr47 is close to G26 of TAR RNA. The knowledge of the orientation of Tat and details of other interactions with TAR RNA in Tat-TAR complex has significant implications for understanding gene regulation in HIV-1.
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Affiliation(s)
- Y Liu
- Department of Pharmacology, Robert Wood Johnson Medical School-University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
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29
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Meisenheimer KM, Meisenheimer PL, Willis MC, Koch TH. High yield photocrosslinking of a 5-iodocytidine (IC) substituted RNA to its associated protein. Nucleic Acids Res 1996; 24:981-2. [PMID: 8600470 PMCID: PMC145727 DOI: 10.1093/nar/24.5.981] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- K M Meisenheimer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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30
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Norris CL, Meisenheimer PL, Koch TH. Mechanistic Studies of the 5-Iodouracil Chromophore Relevant to Its Use in Nucleoprotein Photo-Cross-Linking. J Am Chem Soc 1996. [DOI: 10.1021/ja9607852] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Celewicz L. Photochemical reactions of 5-bromocytosine and its N-1-substituted derivatives with in aqueous solution. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1995. [DOI: 10.1016/1011-1344(95)07176-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Ni CZ, Hettinga BS, Wickersham J, Mitchell RS, Williamson MM, Celikel R, Prangé T, Fourme R, Krapcho KJ, Thulin C. Crystallization of the MS2 translational repressor alone and complexed to bromouridine. Protein Sci 1995; 4:1010-2. [PMID: 7663336 PMCID: PMC2143122 DOI: 10.1002/pro.5560040522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The coat protein from the MS2 bacteriophage plays a dual role by encapsidating viral RNA and also by binding RNA as a translational repressor. In order to study the isolated dimer in a conformation not influenced by capsid interactions, a mutant molecule was crystallized that is defective in capsid assembly but is an active repressor. The unassembled dimer crystallized in the space group P21212 with a = 76.2, b = 55.7, and c = 28.4 A. In these crystals, monomers were related by twofold symmetry. When this dimer was co-crystallized with 5-bromouridine, crystals formed in space group R3 with a = b = 155.9 A, c = 29.9 A, gamma = 120 degrees; the dimer was the asymmetric unit.
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Affiliation(s)
- C Z Ni
- Cancer Research Center, La Jolla Cancer Research Foundation, California 92037, USA
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33
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Affiliation(s)
- S Miyamoto
- Molecular Biology and Virology Laboratory, Salk Institute, San Diego, California 92186, USA
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34
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35
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Willis MC, LeCuyer KA, Meisenheimer KM, Uhlenbeck OC, Koch TH. An RNA-protein contact determined by 5-bromouridine substitution, photocrosslinking and sequencing. Nucleic Acids Res 1994; 22:4947-52. [PMID: 7800485 PMCID: PMC523761 DOI: 10.1093/nar/22.23.4947] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
An analogue of the replicase translational operator of bacteriophage R17, that contains a 5-bromouridine at position -5 (RNA 1), complexes with a dimer of the coat protein and photocrosslinks to the coat protein in high yield upon excitation at 308 nm with a xenon chloride excimer laser. Tryptic digestion of the crosslinked nucleoprotein complex followed by Edman degradation of the tryptic fragment bearing the RNA indicates crosslinking to tyrosine 85 of the coat protein. A control experiment with a Tyr 85 to Ser 85 variant coat protein showed binding but no photocrosslinking at saturating protein concentration. This is consistent with the observation from model compound studies of preferential photocrosslinking of BrU to the electron rich aromatic amino acids tryptophan, tyrosine, and histidine with 308 nm excitation.
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Affiliation(s)
- M C Willis
- Department of Chemistry, University of Colorado, Boulder 80309-0215
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36
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Stockley PG, Stonehouse NJ, Valegård K. Molecular mechanism of RNA phage morphogenesis. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1994; 26:1249-60. [PMID: 7851629 DOI: 10.1016/0020-711x(94)90094-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recent progress on the molecular mechanism of RNA phage morphogenesis is described. Functional studies, both in vivo and in vitro, are correlated with the latest structural studies on phages, their capsids and the assembly initiation RNA stem-loop.
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Affiliation(s)
- P G Stockley
- Department of Genetics, University of Leeds, England
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37
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Grasby JA, Pritchard CE, Gait MJ. Applications of synthetic oligoribonucleotide analogues in studies of RNA structure and function. J CHEM SCI 1994. [DOI: 10.1007/bf02841914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Cao TL, Revers F, Cazenave C. Production of double-stranded RNA during synthesis of bromouracil-substituted RNA by transcription with T7 RNA polymerase. FEBS Lett 1994; 351:253-6. [PMID: 8082775 DOI: 10.1016/0014-5793(94)00870-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using T7 RNA polymerase we synthesized a short oligoribonucleotide containing bromouracil by in vitro transcription of a synthetic DNA template. Whereas the major transcript obtained had the expected size and was apparently homogeneous on a sequencing gel, additional analysis revealed the presence of double-stranded RNA in this preparation. As this was not observed when the same template was transcribed in the presence of uracil, we hypothesize that bromouracil promoted the apparition of double-stranded 'parasitic' RNA presumably by favouring priming for the RNA-dependent RNA synthesis of the T7 RNA polymerase or by facilitating an end-to-end copy mechanism.
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Affiliation(s)
- T L Cao
- Laboratoire de Biophysique Moléculaire, INSERM U386, Université de Bordeaux II, France
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39
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Cazenave C, Uhlenbeck OC. RNA template-directed RNA synthesis by T7 RNA polymerase. Proc Natl Acad Sci U S A 1994; 91:6972-6. [PMID: 7518923 PMCID: PMC44320 DOI: 10.1073/pnas.91.15.6972] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In an attempt to synthesize an oligoribonucleotide by run-off transcription by bacteriophage T7 RNA polymerase, a major transcript was produced that was much longer than expected. Analysis of the reaction indicated that the product resulted from initial DNA-directed run-off transcription followed by RNA template-directed RNA synthesis. This reaction occurred because the RNA made from the DNA template displayed self-complementarity at its 3' end and therefore could form an intra- or intermolecular primed template. In reactions containing only an RNA template, the rate of incorporation of NTPs was quite comparable to DNA-dependent transcription. RNA template-directed RNA synthesis has been found to occur with a great number of oligoribonucleotides, even with primed templates that are only marginally stable. In one instance, we observed a multistep extension reaction converting the oligonucleotide into a final product longer than twice its original length. Presumably, such a process could have generated some of the RNAs found to be efficiently replicated by T7 RNA polymerase.
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Affiliation(s)
- C Cazenave
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215
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40
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Pearson L, Chen CB, Gaynor RP, Sigman DS. Footprinting RNA-protein complexes following gel retardation assays: application to the R-17-procoat-RNA and tat--TAR interactions. Nucleic Acids Res 1994; 22:2255-63. [PMID: 8036153 PMCID: PMC523682 DOI: 10.1093/nar/22.12.2255] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
RNA-protein complexes isolated following a gel retardation assay can be footprinted within the gel matrix using the chemical nuclease activities of 4,7-dimethyl-, 5,6-dimethyl-, and 3,4,7,8-tetramethyl-1,10-phenanthroline-copper. These complexes are more reactive than 1,10-phenanthroline-copper but share its reaction preference for bulges and loops. The interaction of the coat protein of R-17 with its viral RNA target and tat- and tat-derived peptides with HIV TAR RNA have been studied. In both cases, the RNA sequence opposite a 2-3 nucleotide bulge are protected. Tat-derived peptides inhibit cleavage at sites which intact tat does not protect. These results are consistent with transcription studies which have suggested that truncation of tat increases nonspecific binding.
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Affiliation(s)
- L Pearson
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles 90024-1570
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41
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Grasby JA, Gait MJ. Synthetic oligoribonucleotides carrying site-specific modifications for RNA structure-function analysis. Biochimie 1994; 76:1223-34. [PMID: 7538326 DOI: 10.1016/0300-9084(94)90053-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Synthetic oligoribonucleotides have become increasingly valuable in studies of RNA structure and function. A range of nucleotide analogues is available which carry modifications in the base, sugar or phosphate moieties. Such analogues have been incorporated into synthetic RNA structures to eliminate or alter individual functional groups in the RNA which potentially can take part in hydrogen-bonding or other non-covalent interactions. Comparisons of the properties of the modified RNAs with unmodified RNA models allow conclusions to be drawn concerning the importance or otherwise of specific functional groups within the RNA. These methods have been applied to studies of RNA interactions with proteins, RNA catalysis and RNA structure.
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Affiliation(s)
- J A Grasby
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
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42
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Wower J, Rosen KV, Hixson SS, Zimmermann RA. Recombinant photoreactive tRNA molecules as probes for cross-linking studies. Biochimie 1994; 76:1235-46. [PMID: 7538327 DOI: 10.1016/0300-9084(94)90054-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Photoreactive tRNA derivatives have been used extensively for investigating the interaction of tRNA molecules with their ligands and substrates. Recombinant RNA technology facilitates the construction of such tRNA probes through site-specific incorporation of photoreactive nucleosides. The general strategy involves preparation of suitable tRNA fragments and their ligation either to a photoreactive nucleotide or to each other. tRNA fragments can be prepared by site-specific cleavage of native tRNAs, or synthesized by enzymatic and chemical means. A number of photoreactive nucleosides suitable for incorporation into tRNA are presently available. Joining of tRNA fragments is accomplished either by RNA ligase or by DNA ligase in the presence of a DNA splint. The application of this methodology to the study of tRNA binding sites on the ribosome is discussed, and a model of the tRNA-ribosome complex is presented.
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Affiliation(s)
- J Wower
- Department of Biochemistry, University of Massachusetts, Amherst 01003, USA
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43
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Abstract
Female-specific splicing of Drosophila doublesex (dsx) pre-mRNA is regulated by the products of the transformer (tra) and transformer 2 (tra2) genes. In this paper we show that Tra and Tra2 act by recruiting general splicing factors to a regulatory element located downstream of a female-specific 3' splice site. Remarkably, Tra, Tra2, and members of the serine/arginine-rich (SR) family of general splicing factors are sufficient to commit dsx pre-mRNA to female-specific splicing, and individual SR proteins differ significantly in their ability to participate in commitment complex formation. Characterization of the proteins associated with affinity-purified complex formed on dsx pre-mRNA reveals the presence of Tra, Tra2, SR proteins, and additional unidentified components. We conclude that Tra, Tra2, and SR proteins are essential components of a splicing enhancer complex.
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Affiliation(s)
- M Tian
- Harvard University, Department of Biochemistry and Molecular Biology, Cambridge, Massachusetts 02138
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44
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Kempe E, Muhs B, Schäfer M. Gene regulation in Drosophila spermatogenesis: analysis of protein binding at the translational control element TCE. DEVELOPMENTAL GENETICS 1993; 14:449-59. [PMID: 8111973 DOI: 10.1002/dvg.1020140606] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have previously identified a 12 nucleotide long sequence element, the TCE, that was demonstrated to be necessary for translational control of expression in the male germ line of Drosophila melanogaster (Schäfer et al., 1990). It is conserved among all seven members of the Mst(3)CGP gene family, that encode structural proteins of the sperm tail. The TCE is invariably located in the 5' untranslated region (UTR) at position +28 relative to the transcription start site. In this paper we analyse the mode of action of this element. We show that protein binding occurs at the TCE after incubation with testis protein extracts from Drosophila melanogaster. While several proteins are associated with the translational control element in the RNA, only one of these proteins directly crosslinks to the sequence element. The binding activity is exclusively observed with testis protein extracts but can be demonstrated with testis extracts from other Drosophila species as well, indicating that regulatory proteins involved in translational regulation in the male germ line are conserved. Although binding to the TCE can occur independent of its position relative to the transcription start site of the in vitro transcripts, its function in vivo is not exerted when shifted further downstream within the 5' UTR of a fusion gene. In addition to being a translational control element the TCE also functions as a transcriptional regulator. Consequently, a DNA-protein complex is also formed at the TCE. In contrast to the RNA-protein complexes we find DNA-protein complexes with protein extracts of several tissues of Drosophila melanogaster.
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Affiliation(s)
- E Kempe
- Institut für Genetick, Heinrich-Heine-Universität, Düsseldorf, Germany
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