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Ganesh RB, Maerkl SJ. Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications. Front Bioeng Biotechnol 2022; 10:918659. [PMID: 35845409 PMCID: PMC9283866 DOI: 10.3389/fbioe.2022.918659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of transcription and translation steps to decode genetic information. Aminoacyl tRNA synthetases (AARSs) and tRNAs are key components involved in translation and thus protein synthesis. This review provides information on AARSs and tRNA biochemistry, their role in the translation process, summarizes progress in cell-free engineering of tRNAs and AARSs, and discusses prospects and challenges lying ahead in cell-free engineering.
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Uzan M. RNA processing and decay in bacteriophage T4. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 85:43-89. [PMID: 19215770 DOI: 10.1016/s0079-6603(08)00802-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteriophage T4 is the archetype of virulent phage. It has evolved very efficient strategies to subvert host functions to its benefit and to impose the expression of its genome. T4 utilizes a combination of host and phage-encoded RNases and factors to degrade its mRNAs in a stage-dependent manner. The host endonuclease RNase E is used throughout the phage development. The sequence-specific, T4-encoded RegB endoribonuclease functions in association with the ribosomal protein S1 to functionally inactivate early transcripts and expedite their degradation. T4 polynucleotide kinase plays a role in this process. Later, the viral factor Dmd protects middle and late mRNAs from degradation by the host RNase LS. T4 codes for a set of eight tRNAs and two small, stable RNA of unknown function that may contribute to phage virulence. Their maturation is assured by host enzymes, but one phage factor, Cef, is required for the biogenesis of some of them. The tRNA gene cluster also codes for a homing DNA endonuclease, SegB, responsible for spreading the tRNA genes to other T4-related phage.
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Affiliation(s)
- Marc Uzan
- Institut Jacques Monod, CNRS-Universites Paris, Paris, France
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3
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Bacteriophage T4 infection mechanisms. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/b978-0-444-80400-6.50013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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5
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Goldfarb A, Daniel V. Transcriptional control of two gene subclusters in the tRNA operon of bacteriophage T4. Nature 1980; 286:418-20. [PMID: 7402325 DOI: 10.1038/286418a0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In bacteriophage T4 DNA, transcription units recognized in vitro by host RNA polymerase consist of promotor-proximal 'immediate early' (IE) genes and promotor-distal 'delayed early' (DE) genes separated from each other by rho-dependent transcription terminators. In vivo, the transition from IE to DE transcription requires phage-specific protein synthesis and can be prevented by chloramphenicol (CAM). Most of the information about IE/DE transition has been obtained by hybridizaton analyses of mixtures of RNA species synthesized simultaneously on several T4 transcription units (for review see ref. 3). A useful model for the study of T4 gene expression at the level of primary transcripts and individual gene products is provided by the T4 tRNA operon, a cluster of genes coding for eight T4-specific transfer RNAs and two stable RNAs (species 1 and 2) of unknown function (Fig. 1). The 10 genes of the tRNA operon are arranged in two subclusters (I and II) with a promotor located about 1 kilobase pair upstream. The primary transcripts and the final gene products of this region have been identified and isolated. Moreover, this genetic region was recently cloned and a part of it sequenced. We describe here the expression of T4 tRNA genes in vivo and in vitro in terms of the IE/DE concept and demonstrate that the two subclusters of the tRNA operon are subject to different modes of control.
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6
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Goldfarb A, Seaman E, Daniel V. In vitro transcription and isolation of a polycistronic RNA product of the T4 tRNA operon. Nature 1978; 273:562-4. [PMID: 661965 DOI: 10.1038/273562a0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Mazzara G, Seidman J, McClain W, Yesian H, Abelson J, Guthrie C. Nucleotide sequence of an arginine transfer ribonucleic acid from bacteriophage T4. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40963-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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8
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Kitamura N, Ikeda H, Yamada Y, Ishikura H. Processing by ribonuclease II of the tRNATyr precursor of Escherichia coli synthesized in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 73:297-306. [PMID: 320007 DOI: 10.1111/j.1432-1033.1977.tb11319.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: 12/14/2022]
Abstract
The tRNATyr precursor molecule, synthesized from phi 80 psu3+ DNA (containing a single tRNA gene) by DNA-dependent RNA polymerase and q factor, was about 205 nucleotides long. The main product of its digestion with a ribonuclease tii preparation from Escherichia coli showed the same electrophoretic mobility as tRNAtyr precursor isolated in vivo and was found to be identical to it when analysed using fingerprint techniques. This intermediate precursor synthesized in vitro was converted further by processing with ribonuclease P into an RNA identical size to mature tRNATyr. It was concluded that the initiation of transcription of the tRNATyr gene in vitro occurs at the same site as that of transcription in vivo and a termination occurs at about 80 nucleotides beyond the CCA end of tRNATyr.
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Smith JD. Transcription and processing of transfer RNA precursors. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1976; 16:25-73. [PMID: 766079 DOI: 10.1016/s0079-6603(08)60755-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Küpper H, Contreras R, Landy A, Khorana HG. Promoter-dependent transcription of tRNAITyr genes using DNA fragments produced by restriction enzymes. Proc Natl Acad Sci U S A 1975; 72:4754-8. [PMID: 1107999 PMCID: PMC388809 DOI: 10.1073/pnas.72.12.4754] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Two DNA fragments prepared from the transducing bacteriophage strains ø80psuIII+ and ø80hpsuIII+,- by digestion with restriction enzymes contain one tyrosine tRNA gene (suIII+) and two tyrosine tRNA genes (suIII+, su-) in tandem, respectively, a single promoter in both cases, and some additional DNA regions at the two ends of both. Using these fragments, we have studied characteristics of the promoter-dependent transcription of the tyrosine tRNA genes. The promoter-dependent transcripts were shown to correspond to the expected tRNA precursors. Exposure of the transcript from the single gene fragment to an S100 extract from Escherichia coli gave, via intermediates, 4S material which was active in enzymatically accepting tyrosine and contained some modified bases.
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11
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Bikoff EK, Gefter ML. In vitro synthesis of transfer RNA. I. Purification of required components. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41057-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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12
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13
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14
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Cleavage of Nonglucosylated Bacteriophage T4 deoxyribonucleic acid by Restriction Endonuclease Eco RI. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41730-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Kaplan DA, Nierlich DP. Initiation and transcription of a set of transfer ribonucleic acid genes in vitro. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41874-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Biswas BB, Ganguly A, Das A. Eukaryotic RNA polymerases and the factors that control them. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1975; 15:145-84. [PMID: 166413 DOI: 10.1016/s0079-6603(08)60119-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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MESH Headings
- Autoradiography
- Base Sequence
- Coliphages/metabolism
- DNA, Viral
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/metabolism
- Genes
- Genetic Linkage
- Mutation
- Phosphorus Radioisotopes
- RNA, Bacterial/analysis
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/metabolism
- RNA, Transfer/analysis
- RNA, Transfer/biosynthesis
- RNA, Transfer/metabolism
- Recombination, Genetic
- Ribonucleases/metabolism
- Suppression, Genetic
- Transcription, Genetic
- Transduction, Genetic
- Tyrosine
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Sakano H, Shimura Y, Ozeki H. Studies on T4-tRNA biosynthesis: accumulation of precursor tRNA molecules in a temperature sensitive mutant of Escherichia coli. FEBS Lett 1974; 40:312-6. [PMID: 4605179 DOI: 10.1016/0014-5793(74)80252-8] [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: 01/11/2023]
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19
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Sakano H, Yamada S, Ikemura T, Shimura Y, Ozeki H. Temperature sensitive mutants of Escherichia coli for tRNA synthesis. Nucleic Acids Res 1974; 1:355-71. [PMID: 10793671 PMCID: PMC344021 DOI: 10.1093/nar/1.3.355] [Citation(s) in RCA: 88] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An efficient method was devised to isolate temperature sensitive mutants of E. coli defective in tRNA biosynthesis. Mutants were selected for their inability to express suppressor activity after su3(+)-transducing phage infection. In virtually all the mutants tested, temperature sensitive synthesis of tRNA(Tyr) was demonstrated. Electrophoretic fractionation of (32)P labeled RNA synthesized at high temperature showed in some mutants changes in mobility of the main tRNA band and the appearance of slow migrating new species of RNA. Temperature sensitive function of mutant cells was also evident in tRNA synthes: directed by virulent phage T4 and BF23. We conclude that although the mutants show individual differences, many are temperature sensitive in tRNA maturation functions. In spite of much information on the structure and function of transfer RNA (tRNA), our knowledge concerning the biosynthesis of tRNA is relatively poor. It is generally assumed that complete tRNA molecules are made via a series of processing steps from the original transcription products of tRNA genes which are presumably unmodified and longer than mature tRNA molecules. In the case of tyrosine suppressor tRNA of su3(+), an unmodified precursor RNA carrying additional residues at the 3' and 5' ends has been isolated (1,2), and an endonuclease cleaving at the 5' side of this precursor has been identified in E. coli (3). In the case of T4 encoded tRNA, a large precursor molecule for several tRNA's has been reported (4). Some enzymes that catalyze the modifications have also been described (5). However, the over-all picture and the precise mechanisms of tRNA maturation are as yet largely unkown. For study of tRNA biosynthesis in E. coli, a genetic approach may prove useful, as has been the case in other biosynthetic pathways. In order to obtain mutants blocked in any of the intermediary steps of tRNA synthesis, we have developed an efficient selection system that enriches these mutants. Since any mutational block in tRNA biosynthesis might well be lethal, we looked for conditional lethal mutants in which the defect in tRNA synthesis occurs only at high temperature. In this selection system, the su3 gene carried by a temperate phage was newly introduced into cells(su(-)) and those cells incapable of synthesizing su3(+) tRNA at high temperature were selected. Such mutants were easily enriched by using conditions in which cells expressing suppressor activity were killed by two virulent phages. In this communication, we report the method for isolation of mutants and some characterization of tRNA synthesis in these mutants. Recently, Schedl and Primakoff (6) have independently isolated thermosensitive mutants of E. coli defective in tRNA synthesis which may or may not be different types from ours.
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21
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Lamfrom H, Sarabhai A, Nierlich DP, Abelson J. Synthesis of tRNA in cell-free extracts. NATURE: NEW BIOLOGY 1973; 246:11-2. [PMID: 4586116 DOI: 10.1038/newbio246011a0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Guthrie C, Seidman JG, Altman S, Barrell BG, Smith JD, McClain WH. Identification of tRNA precursor molecules made by phage T4. NATURE: NEW BIOLOGY 1973; 246:6-11. [PMID: 4519024 DOI: 10.1038/newbio246006a0] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
MESH Headings
- Base Sequence
- Chromatography, Thin Layer
- Coliphages/analysis
- Coliphages/metabolism
- Electrophoresis, Polyacrylamide Gel
- Genes
- Hydrolysis
- Lysogeny
- Mutation
- Oligonucleotides/analysis
- Phosphorus Radioisotopes
- Proline
- RNA, Transfer/analysis
- RNA, Transfer/biosynthesis
- RNA, Transfer/isolation & purification
- RNA, Viral/analysis
- RNA, Viral/biosynthesis
- RNA, Viral/metabolism
- RNA, Viral/toxicity
- Ribonucleases
- Serine
- Transcription, Genetic
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23
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Chen GS, Siddiqui MA. Biosynthesis of transfer RNA: in vitro conversion of transfer RNA precursors from Bombyx mori to 4S RNA by Escherichia coli enzymes. Proc Natl Acad Sci U S A 1973; 70:2610-3. [PMID: 4582191 PMCID: PMC427066 DOI: 10.1073/pnas.70.9.2610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Evidence for the presence of rapidly labeled short-lived RNA species, presumed to be precursors to transfer RNA (tRNA), in the silk glands of Bombyx mori is presented. These precursors, which migrate between 4S and 5S markers on acrylamide gels, can be converted in vitro into molecules indistinguishable in size from tRNA. The conversion is also catalyzed by a crude enzyme fraction isolated from ribosomes of E. coli. Since a similar enzyme preparation cleaves the suppressor tRNA(Tyr) sequence of E. coli from its precursor molecule, it would appear that the precursor to E. coli tRNA(Tyr) and the precursors to silk-gland tRNAs share common structural features.
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