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Falaleeva MV, Chetverina HV, Ugarov VI, Uzlova EA, Chetverin AB. Factors influencing RNA degradation by Thermus thermophilus polynucleotide phosphorylase. FEBS J 2008; 275:2214-26. [PMID: 18397327 DOI: 10.1111/j.1742-4658.2008.06374.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
At the optimal temperature (65 degrees C), Thermus thermophilus polynucleotide phosphorylase (Tth PNPase), produced in Escherichia coli cells and isolated to functional homogeneity, completely destroys RNAs that possess even a very stable intramolecular secondary structure, but leaves intact RNAs whose 3' end is protected by chemical modification or by hybridization with a complementary oligonucleotide. This allows individual RNAs to be isolated from heterogeneous populations by degrading unprotected species. If oligonucleotide is hybridized to an internal RNA segment, the Tth PNPase stalls eight nucleotides downstream of that segment. This allows any arbitrary 5'-terminal fragment of RNA to be prepared with a precision similar to that of run-off transcription, but without the need for a restriction site. In contrast to the high Mg(2+) requirements of mesophilic PNPases, Tth PNPase retains significant activity when the free Mg(2+) concentration is in the micromolar range. This allows minimization of the Mg(2+)-catalysed nonenzymatic hydrolysis of RNA when phosphorolysis is performed at a high temperature. This capability of Tth PNPase for fully controlled RNA phosphorolysis could be utilized in a variety of research and practical applications.
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Affiliation(s)
- Marina V Falaleeva
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Affiliation(s)
- S N Cohen
- Department of Genetics, Stanford University School of Medicine, California 94305
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Xu F, Cohen SN. RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation. Nature 1995; 374:180-3. [PMID: 7533264 DOI: 10.1038/374180a0] [Citation(s) in RCA: 159] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Although polyadenylation has commonly been regarded as a special feature of eukaryotic messenger RNA, there are many reports of polyA tails on bacterial RNA (for example, refs 3-8). In Escherichia coli, adenylation mediated by the pcnB gene greatly accelerates decay of RNA I, an antisense repressor of replication of ColE1 type plasmids that resembles highly structured transfer RNA but shows the rapid turnover characteristic of mRNA. Here we report that both 3' adenylation and 5' phosphorylation affect the rate of digestion of RNA I by the 3' exonuclease, polynucleotide phosphorylase; conversely, mutation of the polynucleotide phosphorylase-encoding pnp gene affects ribonuclease acting at the 5' end. Together these findings indicate that enzymes attacking RNA I at its separate termini can interact functionally. Additionally, our discovery that adenylation-mediated degradation by polynucleotide phosphorylase imparts an mRNA-like half-like to RNA I suggests a possible mechanism to account for the rapid decay of mRNA in E. coli.
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Affiliation(s)
- F Xu
- Department of Genetics, Stanford University School of Medicine, California 94305
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4
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Simanov AL. High-performance liquid chromatographic analysis of low-molecular-mass products synthesized by polynucleotide phosphorylase in polymerization reaction. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)00639-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Nilsson L, Rigler R, Laggner P. Structural variability of tRNA: small-angle x-ray scattering of the yeast tRNAphe-Escherichia coli tRNAGlu2 complex. Proc Natl Acad Sci U S A 1982; 79:5891-5. [PMID: 6764532 PMCID: PMC347016 DOI: 10.1073/pnas.79.19.5891] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The structure of the complex formed in solution between yeast tRNAPhe and Escherichia coli tRNAGlu2 has been studied by small-angle x-ray scattering. The complex has a radius of gyration of 4.0 nm and an electron-pair distance distribution that is incompatible with a model composed to two tRNAs joined at their complementary anticodons and exhibiting the L shape seen in the crystal. Instead a model in which the two tRNAs, still bound via the anticodons, assume a conformation with the acceptor arms folded toward the anticodon arms agrees with the observed scattering curves.
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6
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Thomas BR. The structural basis of biological systems -- on the structures of transfer RNA and DNA and on some biological consequences. Med Hypotheses 1981; 7:467-79. [PMID: 7289903 DOI: 10.1016/0306-9877(81)90033-5] [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: 01/24/2023]
Abstract
Tetrahelix polynucleotide structure is important in biological systems. Though it is disputed there is firm evidence that transfer RNA has a tetrahelix structure and has the form of a simple cylinder. There is overwhelming chemical, biochemical and sequence evidence and the structure satisfies the constraints of the unit cell lattice. Tetrahelix structure also occurs in DNA and appears to be the most stable form and in many cases the naturally occurring form under physiological conditions. The consequences of tetrahelix structure clarify some longstanding problems such as the physical basis of supertwisting and of compact structure.
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7
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Ramstein J, Buckingham RH. Tritium exchange on transfer RNA: slowly exchanging protons sensitive to a change in the dihydrouridine stem. Proc Natl Acad Sci U S A 1981; 78:1567-71. [PMID: 7015338 PMCID: PMC319172 DOI: 10.1073/pnas.78.3.1567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Measurements of tritium exchange on tRNA were made for periods from 0.5 min to 8 hr after separation from labeled solvent. The exchange curve was analysed in terms of three kinetic classes of exchanging protons with half-lives of 5 hr (12 protons), 0.54 hr (37 protons) and about 3.5 min (58 protons) at 0 degrees C in 0.14 M K+/10 mM Mg2+. The behaviour under varying ionic conditions of protons in the slowest exchange class and of some protons in the intermediate class suggests that they are dependent on the tertiary structure of the molecule. Moreover, in the same range of exchange times characteristic of these latter protons, about 9 more protons were observed in the case of a mutant form of tRNA Trp, the UGA-suppressor species, than in the wild-type tRNATrp. These two species differ only in base 24 in the dihydrouridine stem. This dynamic difference between the wild-type and suppressor species may be related to a functionally important difference in coupling between the conformation of the molecule and interactions at the anticodon.
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Lefevre JF, Ehrlich R, Kilhoffer MC, Remy P. Mutual adaptation of yeast tRNAPhe and phenylalanyl-tRNA synthetase: Possible role of tryptophan residues and long range interactions. FEBS Lett 1980; 114:219-24. [PMID: 6993228 DOI: 10.1016/0014-5793(80)81118-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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9
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Ehrenberg M, Rigler R, Wintermeyer W. On the structure and conformational dynamics of yeast phenylalanine-accepting transfer ribonucleic acid in solution. Biochemistry 1979; 18:4588-99. [PMID: 387074 DOI: 10.1021/bi00588a020] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The solution structure of yeast tRNAPhe was investigated by using ethidium as a fluorescent probe in the D loop and the anticodon loop. For this purpose the dihydrouracils in position 16/17 and wybutine in position 37 were substituted by ethidium. The lifetimes and the time-dependent anisotropy of ethidium fluorescence were measured by pulsed nanosecond fluorometry. The kinetics of the transitions between different states of the tRNAPheEtd derivatives were determined by chemical relaxation measurements. It was found that the ethidium label irrespective of its position exhibits three different states called T1, T2 and T3 characterized by lifetimes tau 1 = 30 ns, tau 2 = 12 ns, and tau 3 = 3 ns. The lifetime differences are due to different accessibilities of ethidium for solvent quenching in the three states. Thus, there are three different defined structural environments of the ethidium in both the anticodon and the D loop. The distribution of the three states was measured as a function of Mg2+ concentration and temperature; it was found that state T3 is favored over states T2 and T1 by both increasing Mg2+ concentration and increasing temperature. The chemical relaxation kinetics exhibit a fast transition between T1 and T2 (10--100 ms) and a slow transition between T2 and T3 (100--1000 ms). The rates of both transitions depend likewise on Mg2+ concentration and temperature. The equilibrium and kinetic data clearly show the presence of strong and weak interactions between Mg2+ and tRNA. A cooperative model accounting for this behavior is developed. The ethidium probe behaves identically when located in different regions of the tRNA regarding both its distribution of states and its transition kinetics. This suggests that the different spectroscopic states report different conformations of the tRNA structure. The dependence of the three states on Mg2+ and spermine indicates that conformation T3 is closely related to or identical with the crystal structure. The rotational diffusion constants indicate that of all three states T3 is most extended while T2 is most compact. The thermodynamic analysis reveals that the strongly bound Mg2+ ions reduce both the activation entropy and enthalpy of all transitions. The weakly bound Mg2+ ions increase both the activation enthalpy and entropy of the slow transition between T2 and T3. It is suggested that the breaking of several intramolecular bonds, e.g., hydrogen bonds, is involved in this transition.
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Sprinzl M, Cramer F. The -C-C-A end of tRNA and its role in protein biosynthesis. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1979; 22:1-69. [PMID: 392600 DOI: 10.1016/s0079-6603(08)60798-9] [Citation(s) in RCA: 127] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Rigler R, Ehrenberg M, Wintermeyer W. Structural dynamics of tRNA. A fluorescence relaxation study of tRNA Phe yeast. MOLECULAR BIOLOGY, BIOCHEMISTRY, AND BIOPHYSICS 1977; 24:219-44. [PMID: 333269 DOI: 10.1007/978-3-642-81117-3_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Kinscherf TG, Apirion D. Polynucleotide phosphorylase can participate in decay of mRNA in Escherichia coli in the absence of ribonuclease II. MOLECULAR & GENERAL GENETICS : MGG 1975; 139:357-62. [PMID: 1102947 DOI: 10.1007/bf00267975] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In a mutant strain defective in polynucleotide phosphorylase, under conditions where the enzyme becomes limiting, it is possible to demonstrate that chemical as well as functional half lives of mRNA become longer if the strain is also missing ribonuclease II. These results allow to unify in a simple model a variety of observations about turnover of RNA in a variety of bacteria.
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Thang MN, Buckingham RH, Dondon L. No correlation between native and denatured forms of tRNA(Trp) form Escherichia coli and the resistant and sensitive molecules characterised by phosphorolysis. Two classes of conformation characterised by phosphorolysis in both native and denatured tRNA(Trp). EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 54:93-6. [PMID: 1097252 DOI: 10.1111/j.1432-1033.1975.tb04117.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Some tRNA molecules in solution are sensitive to attack by polynucleotide phosphorylase while others are resistant, even with pure species of tRNA. Further analysis of this behaviour has revealed an underlying microheterogeneity in tRNA structure. In order to clarify the relation between the sensitive and resistant classes of tRNA, and the native and denatured forms with respect to amino acid acceptance, the phosphorolysis of tRNATrp from Escherichia coli has been investigated. Native tRNATrp is similar to species examined previously: resistant and sensitive classes are observed and the sensitive proportion increases with temperature. At 20 degrees C both native and denatured tRNATrp are stable under phosphorolysis conditions, and denaturated tRNATrp is found also to possess resistant and sensitive classes. About 10% of both native and denatured tRNATrp is rapidly phosphorolysed at 20 degrees C, but the rate of conversion of resistant denatured tRNATrp to the sensitive class is about twice as fact as for the native form. Thus it can be concluded that the sensitive molecules of tRNATrp attacked by polynucleotide phosphorylase are not due to denaturation.
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14
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Renaud M, Bollack C, Ebel JP. Interpretation of incomplete aminoacylation of yeast tRNA-Phe: evidence for a phenylalanyl-tRNA synthetase catalyzed transconformation of tRNA-Phe. Biochimie 1974; 56:1203-9. [PMID: 4451674 DOI: 10.1016/s0300-9084(74)80012-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Buckingham RH, Danchin A, Grunberg-Manago M. The effect of an intramolecular cross-link on reversible denaturation in tryptophan transfer ribonucleic acid from Escherichia coli. Biochemistry 1973; 12:5393-9. [PMID: 4586519 DOI: 10.1021/bi00750a023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Bähr W, Faerber P, Scheit KH. The effects of thioketo substitution upon uracil-adenine interactions in polyribonucleotides. Synthesis and properties of poly (2-thiouridylic acid) and poly(2,4-dithiouridylic acid). EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 33:535-44. [PMID: 4348398 DOI: 10.1111/j.1432-1033.1973.tb02713.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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17
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Pongs O, Bald R, Reinwald E. On the structure of yeast tRNA Phe . Complementary-oligonucleotide binding studies. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 32:117-25. [PMID: 4569067 DOI: 10.1111/j.1432-1033.1973.tb02586.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Zachau HG, Streeck RE, Hänggi UJ. Conformational states of transfer ribonucleic acids. BASIC LIFE SCIENCES 1973; 1:217-28. [PMID: 4589680 DOI: 10.1007/978-1-4684-0877-5_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Farkas WR, Hewins S, Welch JW. Effects of plumbous ion on some functions of transfer RNA. Chem Biol Interact 1972; 5:191-200. [PMID: 4558619 DOI: 10.1016/0009-2797(72)90054-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Faerber P, Scheit KH, Sommer H. A new polynucleotide complex poly(s 2 C)-poly(I). EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 27:109-15. [PMID: 5049048 DOI: 10.1111/j.1432-1033.1972.tb01816.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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21
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Danchin A, Thang MN. Multiple states in macromolecules II. Entropic behaviour of tRNA degraded by polynucleotide phosphorylase. FEBS Lett 1972; 19:297-300. [PMID: 11946235 DOI: 10.1016/0014-5793(72)80064-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- A Danchin
- Institut de Biologie Physico-chimique, rue P. Curie, Ve, Paris, France
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Beltchev B, Thang MN, Portier C. Phosphorolysis of the tRNA. Conformations of specific tRNAs and effect of the localized regions on the stability of the structure. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 19:194-9. [PMID: 4928256 DOI: 10.1111/j.1432-1033.1971.tb01304.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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