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Bommisetti P, Bandarian V. Site-Specific Profiling of 4-Thiouridine Across Transfer RNA Genes in Escherichia coli. ACS OMEGA 2022; 7:4011-4025. [PMID: 35155896 PMCID: PMC8829951 DOI: 10.1021/acsomega.1c05071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The transfer RNA (tRNA) modification 4-thiouridine (s4U) acts as a near-ultraviolet (UVA) radiation sensor in Escherichia coli (E. coli), where it induces a growth delay upon exposure to the UVA radiation (∼310-400 nm). Herein, we report sequencing methodology for site-specific profiling of s4U modification in E. coli tRNAs. Upon the addition of iodoacetamide (IA) or iodoacetyl-PEG2-biotin (BIA), the nucleophilic sulfur of s4U forms a reaction product that is extensively characterized by liquid chromatography-mass spectrometry (LC-MS/MS) analysis. This method is readily applied to the alkylation of natively occurring s4U on E. coli tRNA. Next-generation sequencing of BIA-treated tRNA from E. coli revealed misincorporations at position 8 in 19 of the 20 amino acid tRNA species. Alternatively, tRNA from the ΔthiI strain, which cannot introduce the s4U modification, does not exhibit any misincorporation at the corresponding positions, directly linking the base transitions and the tRNA modification. Independently, the s4U modification on E. coli tRNA was further validated by LC-MS/MS sequencing. Nuclease digestion of wild-type and deletion strains E. coli tRNA with RNase T1 generated smaller s4U/U containing fragments that could be analyzed by MS/MS analysis for modification assignment. Furthermore, RNase T1 digestion of tRNAs treated either with IA or BIA showed the specificity of iodoacetamide reagents toward s4U in the context of complex tRNA modifications. Overall, these results demonstrate the utility of the alkylation of s4U in the site-specific profiling of the modified base in native cellular tRNA.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112, United States
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2
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Shigi N. Recent Advances in Our Understanding of the Biosynthesis of Sulfur Modifications in tRNAs. Front Microbiol 2018; 9:2679. [PMID: 30450093 PMCID: PMC6225789 DOI: 10.3389/fmicb.2018.02679] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Sulfur is an essential element in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, introduced post-transcriptionally, that function to ensure proper codon recognition or stabilization of tRNA structure, thereby enabling accurate and efficient translation. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems that are closely related to cellular sulfur metabolism, and “modification enzymes” that incorporate sulfur atoms into tRNA. Herein, recent biochemical and structural characterization of the biosynthesis of sulfur modifications in tRNA is reviewed, with special emphasis on the reaction mechanisms of modification enzymes. It was recently revealed that TtuA/Ncs6-type 2-thiouridylases from thermophilic bacteria/archaea/eukaryotes are oxygen-sensitive iron-sulfur proteins that utilize a quite different mechanism from other 2-thiouridylase subtypes lacking iron-sulfur clusters such as bacterial MnmA. The various reaction mechanisms of RNA sulfurtransferases are also discussed, including tRNA methylthiotransferase MiaB (a radical S-adenosylmethionine-type iron-sulfur enzyme) and other sulfurtransferases involved in both primary and secondary sulfur-containing metabolites.
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Affiliation(s)
- Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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3
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Shigematsu M, Kirino Y. 5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves. RNA (NEW YORK, N.Y.) 2017; 23:161-168. [PMID: 27879434 PMCID: PMC5238791 DOI: 10.1261/rna.058024.116] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source of tRNA-derived noncoding RNAs that play important roles in various biological processes beyond translation. Among all species of tRNAs, tRNAHisGUG has been known to uniquely contain an additional guanosine residue at the -1 position (G-1) of its 5'-end. To analyze this -1 nucleotide in detail, we developed a TaqMan qRT-PCR method that can distinctively quantify human mature cytoplasmic tRNAHisGUG containing G-1, U-1, A-1, or C-1 or lacking the -1 nucleotide (starting from G1). Application of this method to the mature tRNA fraction of BT-474 breast cancer cells revealed the presence of tRNAHisGUG containing U-1 as well as the one containing G-1 Moreover, tRNA lacking the -1 nucleotide was also detected, thus indicating the heterogeneous expression of 5'-tRNAHisGUG variants. A sequence library of sex hormone-induced 5'-tRNA halves (5'-SHOT-RNAs), identified via cP-RNA-seq of a BT-474 small RNA fraction, also demonstrated the expression of 5'-tRNAHisGUG halves containing G-1, U-1, or G1 as 5'-terminal nucleotides. Although the detected 5'-nucleotide species were identical, the relative abundances differed widely between mature tRNA and 5'-half from the same BT-474 cells. The majority of mature tRNAs contained the -1 nucleotide, whereas the majority of 5'-halves lacked this nucleotide, which was biochemically confirmed using a primer extension assay. These results reveal the novel identities of tRNAHisGUG molecules and provide insights into tRNAHisGUG maturation and the regulation of tRNA half production.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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4
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Fromant M, Plateau P, Blanquet S. Function of the extra 5'-phosphate carried by histidine tRNA. Biochemistry 2000; 39:4062-7. [PMID: 10747795 DOI: 10.1021/bi9923297] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among elongator tRNAs, tRNA specific for histidine has the peculiarity to possess one extra nucleotide at position -1. This nucleotide is believed to be responsible for recognition by histidyl-tRNA synthetase. Here, we show that, in fact, it is the phosphate 5' to the extra nucleotide which mainly supports the efficiency of the tRNA aminoacylation reaction catalyzed by Escherichia coli histidyl-tRNA synthetase. In the case of the reaction of E. coli peptidyl-tRNA hydrolase, this atypical phosphate is dispensable. Instead, peptidyl-tRNA hydrolase recognizes the phosphate of the phosphodiester bond between residues -1 and +1 of tRNA(His). Recognition of the +1 phosphate of tRNA(His) by peptidyl-tRNA hydrolase resembles, therefore, that of the 5'-terminal phosphate of other elongator tRNAs.
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Affiliation(s)
- M Fromant
- Laboratoire de Biochimie, Unité Mixte de Recherche No. 7654, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France
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Abstract
Histidyl-tRNA synthetase (HisRS) is responsible for the synthesis of histidyl-transfer RNA, which is essential for the incorporation of histidine into proteins. This amino acid has uniquely moderate basic properties and is an important group in many catalytic functions of enzymes. A compilation of currently known primary structures of HisRS shows that the subunits of these homo-dimeric enzymes consist of 420-550 amino acid residues. This represents a relatively short chain length among aminoacyl-tRNA synthetases (aaRS), whose peptide chain sizes range from about 300 to 1100 amino acid residues. The crystal structures of HisRS from two organisms and their complexes with histidine, histidyl-adenylate and histidinol with ATP have been solved. HisRS from Escherichia coli and Thermus thermophilus are very similar dimeric enzymes consisting of three domains: the N-terminal catalytic domain containing the six-stranded antiparallel beta-sheet and the three motifs characteristic of class II aaRS, a HisRS-specific helical domain inserted between motifs 2 and 3 that may contact the acceptor stem of the tRNA, and a C-terminal alpha/beta domain that may be involved in the recognition of the anticodon stem and loop of tRNA(His). The aminoacylation reaction follows the standard two-step mechanism. HisRS also belongs to the group of aaRS that can rapidly synthesize diadenosine tetraphosphate, a compound that is suspected to be involved in several regulatory mechanisms of cell metabolism. Many analogs of histidine have been tested for their properties as substrates or inhibitors of HisRS, leading to the elucidation of structure-activity relationships concerning configuration, importance of the carboxy and amino group, and the nature of the side chain. HisRS has been found to act as a particularly important antigen in autoimmune diseases such as rheumatic arthritis or myositis. Successful attempts have been made to identify epitopes responsible for the complexation with such auto-antibodies.
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Affiliation(s)
- W Freist
- Max-Planck-Institut für experimentelle Medizin, Abteilung Molekulare Biologie Neuronaler Signale, Göttingen, Germany
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6
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Recognition of †RNAs by Aminoacyl-†RNA Synthetases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1991. [DOI: 10.1016/s0079-6603(08)60006-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Kleina LG, Masson JM, Normanly J, Abelson J, Miller JH. Construction of Escherichia coli amber suppressor tRNA genes. II. Synthesis of additional tRNA genes and improvement of suppressor efficiency. J Mol Biol 1990; 213:705-17. [PMID: 2193162 DOI: 10.1016/s0022-2836(05)80257-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using synthetic oligonucleotides, we have constructed 17 tRNA suppressor genes from Escherichia coli representing 13 species of tRNA. We have measured the levels of in vivo suppression resulting from introducing each tRNA gene into E. coli via a plasmid vector. The suppressors function at varying efficiencies. Some synthetic suppressors fail to yield detectable levels of suppression, whereas others insert amino acids with greater than 70% efficiency. Results reported in the accompanying paper demonstrate that some of these suppressors insert the original cognate amino acid, whereas others do not. We have altered some of the synthetic tRNA genes in order to improve the suppressor efficiency of the resulting tRNAs. Both tRNA(CUAHis) and tRNA(CUAGlu) were altered by single base changes, which generated -A-A- following the anticodon, resulting in a markedly improved efficiency of suppression. The tRNA(CUAPro) was inactive, but a hybrid suppressor tRNA consisting of the tRNA(CUAPhe) anticodon stem and loop together with the remainder of the tRNA(Pro) proved highly efficient at suppressing nonsense codons. Protein chemistry results reported in the accompanying paper show that the altered tRNA(CUAHis) and the hybrid tRNA(CUAPro) insert only histidine and proline, respectively, whereas the altered tRNA(CUAGlu) inserts principally glutamic acid but some glutamine. Also, a strain deficient in release factor I was employed to increase the efficiency of weak nonsense suppressors.
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MESH Headings
- Anticodon
- Base Sequence
- Cloning, Molecular
- Escherichia coli/genetics
- Genes, Bacterial
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plasmids
- RNA, Transfer/genetics
- RNA, Transfer, Glu/genetics
- RNA, Transfer, His/genetics
- RNA, Transfer, Pro/genetics
- Suppression, Genetic
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Affiliation(s)
- L G Kleina
- Department of Biology, University of California, Los Angeles 90024
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8
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Yavachev L, Ivanov I. What does the homology between E. coli tRNAs and RNAs controlling ColE1 plasmid replication mean? J Theor Biol 1988; 131:235-41. [PMID: 2457135 DOI: 10.1016/s0022-5193(88)80240-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleotide sequences of E. coli tRNAs and RNA I or RNA II (controlling replication of ColE1 plasmids) were compared using the computer. The homology between some of these molecules is over 60%. The distribution of homologous nucleotides among the functional elements (stems and loops) of either RNA I or RNA II and the tRNAs molecules was studied. It was found that the homologous domains are located mainly in the loop regions of RNA I or RNA II. A consensus sequence, the nonanucleotide AGUUGGUAG, was discovered in loop II of RNA I and in the dihydrouridylic loop of tRNAs showing homology with RNA I. Based on this observation, a hypothesis was drawn for a possible role of the tRNAs in the regulation of plasmid DNA replication.
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Affiliation(s)
- L Yavachev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia
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9
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Ulrich AK, Parker J. Strains overproducing tRNA for histidine. MOLECULAR & GENERAL GENETICS : MGG 1986; 205:540-5. [PMID: 3031431 DOI: 10.1007/bf00338095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hybridization analysis of total genomic DNA indicated that Escherichia coli K12 contains a single copy of the gene encoding the histidine-accepting tRNA. This gene was subcloned onto an inducible expression vector under the control of the tac promoter. Strains carrying the resulting plasmid showed five- to six-fold increased histidine-accepting activity after induction. This overproduction of tRNAHis did not effect the growth rate of the strain or lead to derepression of the histidine biosynthetic enzymes. Neither did it have an effect on mistranslation elicited by histidine starvation. However, in cells starved for histidine by the addition of alpha-methyl histidine, the overproduction of tRNAHis interfered with the ability of the cells to recover from starvation.
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10
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Masson JM, Miller JH. Expression of synthetic suppressor tRNA genes under the control of a synthetic promoter. Gene 1986; 47:179-83. [PMID: 3549453 DOI: 10.1016/0378-1119(86)90061-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A synthetic promoter derived from the Escherichia coli lipoprotein promoter sequence was used to express synthetic suppressor tRNA genes in E. coli. These constructs, cloned into a plasmid of the pEMBL family, gave very high yields of suppressor tRNA in vivo.
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11
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Hsu LM, Klee HJ, Zagorski J, Fournier MJ. Structure of an Escherichia coli tRNA operon containing linked genes for arginine, histidine, leucine, and proline tRNAs. J Bacteriol 1984; 158:934-42. [PMID: 6327651 PMCID: PMC215531 DOI: 10.1128/jb.158.3.934-942.1984] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A plasmid containing a gene for the most abundant Escherichia coli leucine isoacceptor tRNA, tRNALeu1 (anticodon CAG) was isolated from the Clarke-Carbon bank of cloned E. coli DNA. The clone contains a 12.3-kilobase DNA insert which was mapped by F' DNA hybridization analysis to the region 82 to 89 min on the chromosome. The cloned tDNALeu corresponds to the minor of two chromosomal regions containing different amounts of DNA complementary to tRNALeuCAG . Sequencing of the tDNA region revealed it to contain a multimeric transcription unit consisting of four different tRNA genes. The genes are in the arrangement 5'-leader- tRNAArgCCG -57 base pairs- tRNAHisGUG -20 base pairs- tRNALeuCAG -42 base pairs- tRNAProUGG -3'. Coordinate expression of the component tRNAs in vivo and the absence of intercistronic promoters indicated that all four tDNAs reside in the same operon. The tDNA sequence is bounded by a promoter element showing good agreement with the procaryotic consensus sequence and a GC-rich stem-loop element that corresponds to a rho-independent terminator. The promoter region contains a GC-rich sequence that agrees with a suggested consensus stringency control element and two domains possessing dyad symmetry which flank the Pribnow box and include the putative stringency control region.
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12
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Sugita M, Kato A, Shimada H, Sugiura M. Sequence analysis of the junctions between a large inverted repeat and single-copy regions in tobacco chloroplast DNA. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00383517] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Bossi L. The hisR locus of Salmonella: nucleotide sequence and expression. MOLECULAR & GENERAL GENETICS : MGG 1983; 192:163-70. [PMID: 6358794 DOI: 10.1007/bf00327662] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In S. typhimurium, the hisR locus is defined by mutations causing reduced levels of the histidine transfer RNA. As a preliminary step in the analysis of the hisR mutants, a 972 bp DNA fragment containing the histidine tRNA gene from wild-type Salmonella was cloned and completely sequenced. This analysis revealed the existence of a tRNA gene cluster which, in addition to the tRNAHis gene, includes the genes for tRNALeu1, tRNAPro1 and a tentative tRNAArgCGG. All four tRNA genes are present as single copies and are separated by spacer sequences ranging from 20 to 53 bp in length. The gene cluster is efficiently transcribed in vitro by E. coli RNA polymerase and yields a transcript, approximately 480 nucleotides long, which contains all four tRNA sequences. This tetrameric precursor can be processed to 4S RNA in vitro with a wild-type Salmonella extract, but not with an extract prepared from a hisU (RNase P) mutant. Using portions of the tRNA gene cluster as specific hybridization probes, various processing intermediates were shown to accumulate in vivo in the hisU mutant. Most of these RNAs are monomeric precursors only a few nucleotides longer than the respective mature tRNA species.
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14
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15
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Brown WM, Prager EM, Wang A, Wilson AC. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 1982; 18:225-39. [PMID: 6284948 DOI: 10.1007/bf01734101] [Citation(s) in RCA: 812] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We cloned and sequenced a segment of mitochondrial DNA from human, chimpanzee, gorilla, orangutan, and gibbon. This segment is 896 bp in length, contains the genes for three transfer RNAs and parts of two proteins, and is homologous in all 5 primates. The 5 sequences differ from one another by base substitutions at 283 positions and by a deletion of one base pair. The sequence differences range from 9 to 19% among species, in agreement with estimates from cleavage map comparisons, thus confirming that the rate of mtDNA evolution in primates is 5 to 10 times higher than in nuclear DNA. The most striking new finding to emerge from these comparisons is that transitions greatly outnumber transversions. Ninety-two percent of the differences among the most closely related species (human, chimpanzee, and gorilla) are transitions. For pairs of species with longer divergence times, the observed percentage of transitions falls until, in the case of comparisons between primates and non-primates, it reaches a value of 45. The time dependence is probably due to obliteration of the record of transitions by multiple substitutions at the same nucleotide site. This finding illustrates the importance of choosing closely related species for analysis of evolutionary process. The remarkable bias toward transitions in mtDNA evolution necessitates the revision of equations that correct for multiple substitutions at the same site. With revised equations, we calculated the incidence of silent and replacement substitutions in the two protein-coding genes. The silent substitution rate is 4 to 6 times higher than the replacement rate, indicating strong functional constraints at replacement sites. Moreover, the silent rate for these two genes is about 10% per million years, a value 10 times higher than the silent rate for the nuclear genes studied so far. In addition, the mean substitution rate in the three mitochondrial tRNA genes is at least 100 times higher than in nuclear tRNA genes. Finally, genealogical analysis of the sequence differences supports the view that the human lineage branched off only slightly before the gorilla and chimpanzee lineages diverged and strengthens the hypothesis that humans are more related to gorillas and chimpanzees than is the orangutan.
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16
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Abstract
The structural and conformational features of the "anomeric" DL-trans- and DL-cis-5-(3-hydroxytetrahydrofuran-2-yl)uracils (3a, 4a) and five similar analogues were studied in order to determine their applicability as models of beta- and alpha-pseudouridine. The 270-MHz proton NMR spectra were measured for all analogues to define their ring geometries in solution and to estimate the solution population of model N, S conformers in a two-state dynamic equilibrium treatment. Two sets of calculations were employed to evaluate the relative contributions of these states to the observed vicinal coupling constants related to the C(3')-C(4') fragment. In the first, similar geometries were assumed for each pair of conformers, while in the second, limited to 3, the geometries were those derived from X-ray crystallographic data; both gave comparable results. The cis analogues 4a and 4b are excellent conformational models for alpha-pseudouridine. In the trans series (3a-c), the equilibrium is weighted toward the N conformer (approximately 80%), differing from that found in beta-pseudouridine for which each model conformer is equally populated. Possible implications of the conformational effects upon the pairing properties of pseudouridine in tRNA are discussed.
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17
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Boisnard M, Petrissant G. The nucleotide sequence of sheep liver histidine-tRNA (anticodon Q-U-G). FEBS Lett 1981; 129:180-4. [PMID: 7274464 DOI: 10.1016/0014-5793(81)80785-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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18
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Ray BK, Apirion D. Transfer RNA precursors are accumulated in Escherichia coli in the absence of RNase E. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 114:517-24. [PMID: 6263617 DOI: 10.1111/j.1432-1033.1981.tb05175.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A temperature-sensitive Escherichia coli mutant, which contains a heat-labile RNase E, fails to produce 5-S rRNA at a non-permissive temperature. It accumulates a number of RNA molecules in the 4-12-S range. One of these molecules, a 9-S RNA, is a precursor to 5-S rRNA [Ghora, B. K. and Apirion, D. (1978) Cell, 15, 1055-1056]. These molecules were purified and processed in a cell-free system. Some of these RNA molecules, after processing, give rise to products the size of transfer RNA, but not to 5-S-rRNA. Further characterization of the processed products of one such precursor molecule shows that it contains tRNA1Leu and tRNA1His. RNase E is necessary but not sufficient for the processing of this molecule to mature tRNAs in vitro. The accumulation of such tRNA precursors in an RNase E mutant cell and the obligatory participation of RNase E in its processing indicate that RNase E functions in the maturation of transfer RNAs as well as of 5-S rRNA.
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19
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Cedergren RJ, Sankoff D, LaRue B, Grosjean H. The evolving tRNA molecule. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1981; 11:35-104. [PMID: 7030617 DOI: 10.3109/10409238109108699] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The study of tRNA molecular evolution is crucial to understanding the origin and establishment of the genetic code as well as the differentiation and refinement of the machinery of protein synthesis in prokaryotes, eukaryotes, organelles, and phage systems. The small size of the molecule and its critical involvement in a multiplicity of roles distinguish its study from classical protein molecular evolution with respect to goals and methods. Here, the authors assess available and missing data, existing and needed methodology, and the impact of tRNA studies on current theories both of genetic code evolution and of the evolution of species. They analyze mutational "hot spots", the role of base modification, synthetase recognition, codon-anticodon interactions and the status of organelle tRNA.
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20
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Berlani RE, Pentella C, Macino G, Tzagoloff A. Assembly of the mitochondrial membrane system: isolation of mitochondrial transfer ribonucleic acid mutants and characterization of transfer ribonucleic acid genes of Saccharomyces cerevisiae. J Bacteriol 1980; 141:1086-97. [PMID: 6245059 PMCID: PMC293786 DOI: 10.1128/jb.141.3.1086-1097.1980] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A method is described for isolating cytoplasmic mutants of Saccharomyces cerevisiae with lesions in mitochondrial transfer ribonucleic acids (tRNA's). The mutants were selected for slow growth on glycerol and for restoration of wild-type growth by cytoplasmic "petite" testers that contain regions of mitochondrial deoxyribonucleic acid (DNA) with tRNA genes. The aminoacylated mitochondrial tRNA's of several presumptive tRNA mutants were analyzed by reverse-phase chromatography on RPC-5. Two mutant strains, G76-26 and G76-35, were determined to carry mutations in the cysteine and histidine tRNA genes, respectively. The cysteine tRNA mutant was used to isolate cytoplasmic petite mutants whose retained segments of mitochondrial DNA contain the cysteine tRNA gene. The segment of one such mutant (DS504) was sequenced and shown to have the cysteine, histidine, and threonine tRNA genes. The structures of the three mitochondrial tRNA's were deduced from the DNA sequence.
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21
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Abstract
The major isoacceptor of tRNAHis from sheep liver was purified. Two different methods were described which both took advantage of the presence of the hypermodified Q nucleotide in this tRNA. In the first procedure, CNBr treatment of tRNA which was previously enriched in tRNAHis greatly increased the efficiency of the subsequent chromatographic steps. The tRNAHis obtained by this technique showed a specific activity of 1,690 picomoles of histidine per A260 unit. In the second one, a twenty-fold enrichment in tRNAHis was obtained by fractionation of crude tRNA on acetylated DBAE-cellulose columns. The nucleotide composition of the tRNA obtained by the CNBr procedure was determined. No thymine ribotide could be detected. When this tRNA was submitted to periodate oxidation and tritium borohydride reduction, a radioactive label was introduced in this molecule which was assumed to be located in the Q nucleotide.
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22
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Achberger EC, Kolenbrander PE. Isolation and characterization of morphogenetic mutants of Arthrobacter crystallopoietes. J Bacteriol 1978; 135:595-602. [PMID: 681281 PMCID: PMC222420 DOI: 10.1128/jb.135.2.595-602.1978] [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: 12/24/2022] Open
Abstract
Mutants of Arthrobacter crystallopoietes that exhibited altered ability to undergo the normal sphere-to-rod-to-sphere morphogenetic cycle were isolated. The procedure used to isolate these mutants involved velocity sedimentation in a sterile sucrose gradient to separate morphogenesis-deficient spherical cells from rod-shaped cells capable of normal morphogenesis. Three classes of mutants were obtained: (i) those that cannot form rods, (ii) those that cannot form long rods, and (iii) those that form long rods but exhibit more extensive rudimentary branching than the wild type. The isolation and characterization of these mutants are described, and the use of these mutants in the study of the morphogenetic cycle of arthrobacters is discussed.
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23
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Goddard JP. The structures and functions of transfer RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1978. [DOI: 10.1016/0079-6107(78)90021-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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24
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25
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Kolenbrander PE, Weinberger M. 2-Hydroxypyridine metabolism and pigment formation in three Arthrobacter species. J Bacteriol 1977; 132:51-9. [PMID: 199576 PMCID: PMC221825 DOI: 10.1128/jb.132.1.51-59.1977] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Three species of the genus Arthrobacter, A. crystallopoietes, A. pyridinolis, and A. viridescens, have the capabilities to utilize 2-hydroxypyridine (2-HP) as the sole source of carbon and nitrogen for growth and to produce an extracellular crystalline pigment from this substrate. Degradation of 2-HP by cell-free extracts requires the presence of both reduced nicotinamide adenine dinucleotide and molecular oxygen and is stimulated by flavin mononucleotide, suggesting the presence of a monooxygenase activity in the extract. Loss of the ability to produce pigment at a high spontaneous frequency, 0.26% loss per generation, is observed only with A. crystallopoietes and can be visualized by the presence of sectored and fully nonpigmented colonies on solid media containing 2-HP. Concomitant with the loss of pigment-producing character are both loss of ability to utilize 2-HP for growth and oxidation of 2-HP by cell-free extracts. These three 2-HP-associated characteristics also are lost simultaneously by treating cultures of A. crystallopoietes with curing agents, such as acridine orange and mitomycin C, but are not curable in A. pyridinolis or A. viridescens. All nonpigmented strains of A. crystallopoietes are nonrevertible for these properties. These data suggest that 2-HP-related characteristics are plasmid determined in A. crystallopoietes but not in A. pyridinolis and A. viridescens. A survey for the presence of plasmids in these three species and two physiologically unrelated species, A. globiformis and A. atrocyaneus, revealed plasmid material only in A. globiformis and A. crystallopoietes.
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Allen JD, Parsons SM. Properties of the 5'-terminus of tRNAHis: kinetics of polynucleotide kinase catalyzed exchange and effect of dephosphorylation on the aminoacylation reaction. Biochem Biophys Res Commun 1977; 78:28-35. [PMID: 199163 DOI: 10.1016/0006-291x(77)91217-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Ikemura T, Nomura M. Expression of spacer tRNA genes in ribosomal RNA transcription units carried by hybrid Col E1 plasmids in E. coli. Cell 1977; 11:779-93. [PMID: 329999 DOI: 10.1016/0092-8674(77)90291-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Bloch JC, Garel JP. Influence of modified nucleosides in E. coli transfer ribonucleic acids on chromatographic mobilities of transfer RNA. J Chromatogr A 1977; 137:93-109. [PMID: 330553 DOI: 10.1016/s0021-9673(00)89244-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Reid BR, Ribeiro NS, McCollum L, Abbate J, Hurd RE. High-resolution nuclear magnetic resonance determination of transfer RNA tertiary base pairs in solution. 1. Species containing a small variable loop. Biochemistry 1977; 16:2086-94. [PMID: 324514 DOI: 10.1021/bi00629a006] [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: 12/14/2022]
Abstract
Eight class I tRNA species have been purified to homogeneity and their proton nuclear magnetic resonance (NMR) spectra in the low-field region (-11 to -15 ppm) have been studied at 360 MHz. The low-field spectra contain only one low-field resonance from each base pair (the ring NH hydrogen bond) and hence directly monitor the number of long-lived secondary and tertiary base pairs in solution. The tRNA species were chosen on the basis of their sequence homology with yeast phenylalanine tRNA in the regions which form tertiary base pairs in the crystal structure of this tRNA. All of the spectra show 26 or 27 low-field resonances approximately 7 of which are derived from tertiary base pairs. These results are contrary to previous claims that the NMR spectra indicate the presence of resonances from secondary base pairs only, as well as more recent claims of only 1-3 tertiary resonances, but are in good agreement with the number of tertiary base pairs expected in solution based on the crystal structure. The tertiary base pair resonances are stable up to at least 46 degrees C. Removal of magnesium ions causes structural changes in the tRNA but does not result in the loss of any secondary or tertiary base pairs.
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Bruni CB, Colantuoni V, Sbordone L, Cortese R, Blasi F. Biochemical and regulatory properties of Escherichia coli K-12 hisT mutants. J Bacteriol 1977; 130:4-10. [PMID: 323237 PMCID: PMC235167 DOI: 10.1128/jb.130.1.4-10.1977] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli K-12 hisT mutants were isolated, and their properties were studied. These mutants are derepressed for the histidine operon, map close to the purF locus at about 49.5 min on the E. coli linkage map, and lack pseudouridylate synthetase activity. The defect in this enzyme leads to the absence of pseudouridines in the anticodon loop of several transfer ribonucleic acid species, as evidenced by the altered elution profile on reversed-phase chromatography and resistance to amino acid analogues. Finally, the hisT mutants studied have a reduced growth rate that appears to be linked to hisT, although it is not known whether it is due to the same mutation. The normal generation time can be restored by supplementing the medium with adenine, uracil, and isoleucine.
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31
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Lamy D, Jonard G, Guilley H, Hirth L. Comparison between the 3'OH end RNA sequence of two strains of tobacco mosaic virus (TMV) which may be aminoacylated. FEBS Lett 1975; 60:202-4. [PMID: 1227955 DOI: 10.1016/0014-5793(75)80451-0] [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: 12/26/2022]
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32
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Yaniv M, Folk WR. The nucleotide sequences of the two glutamine transfer ribonucleic acids from Escherichia coli. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41506-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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33
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Kuntzel B, Weissenbach J, Dirheimer G. [Primary structure of tRNA Arg/III of brewer's yeast. 2-Partial hydrolysis of tRNA Arg/III by pancreatic and T1 ribonucleases and determination of their complete primary structure]. Biochimie 1974; 56:1069-87. [PMID: 4614865 DOI: 10.1016/s0300-9084(74)80096-9] [Citation(s) in RCA: 13] [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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34
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35
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Nauheimer U, Hedgcoth C. Activation of several tRNAs of Escherichia coli by the phenoxyacetyl derivative of N-hydroxysuccinimide. Arch Biochem Biophys 1974; 160:631-42. [PMID: 4598621 DOI: 10.1016/0003-9861(74)90440-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Cortese R, Kammen HO, Spengler SJ, Ames BN. Biosynthesis of Pseudouridine in Transfer Ribonucleic Acid. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42947-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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37
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Straus DS, Wyche JH. Histidine regulation in Salmonella typhimurium. XV. Procedure for the selection of mutants unable to derepress the histidine operon. J Bacteriol 1974; 117:116-25. [PMID: 4587601 PMCID: PMC246532 DOI: 10.1128/jb.117.1.116-125.1974] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A general search has been made for mutants defective in their ability to derepress the histidine operon. The procedure was to select for mutants with an increased sensitivity to the false feedback inhibitor, 2-thiazolealanine. Five mutant strains defective in derepression have been isolated. All five strains are unable to derepress normally because of mutations located in the operator-promoter region of the histidine operon.
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Hill C, Combriato G, Steinhart W, Riddle DL, Carbon J. The Nucleotide Sequence of the GGG-specific Glycine Transfer Ribonucleic Acid of Escherichia coli and of Salmonella typhimurium. J Biol Chem 1973. [DOI: 10.1016/s0021-9258(19)43765-4] [Citation(s) in RCA: 23] [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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40
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Beauchemin N, Larue B, Cedergren RJ. The characterization of the RNAs and aminoacyl-tRNA synthetases of the blue-green alga, Anacystis nidulans. Arch Biochem Biophys 1973; 156:17-25. [PMID: 4199781 DOI: 10.1016/0003-9861(73)90336-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Affiliation(s)
- Y Yamada
- Biology Division, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
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43
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Weissenbach J, Martin R, Dirheimer G. Nucleotide sequence of tRNA(Arg)(II) from brewer's yeast. FEBS Lett 1972; 28:353-355. [PMID: 11946894 DOI: 10.1016/0014-5793(72)80748-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- J Weissenbach
- Laboratoire de Toxicologie et de Biologie moléculaires, U.E.R. de Sciences pharmaceutiques, Université Louis Pasteur, 67083, Strasbourg, France
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44
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Allaudeen HS, Yang SK, Söll D. Leucine tRNA(1) from HisT mutant of Salmonella typhimurium lacks two pseudouridines. FEBS Lett 1972; 28:205-208. [PMID: 11946859 DOI: 10.1016/0014-5793(72)80713-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- H S. Allaudeen
- Department of Molecular Biophysics and Biochemistry, Yale University, 06520, New Haven, Connecticut, USA
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45
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Brenner M, Lewis JA, Straus DS, De Lorenzo F, Ames BN. Histidine Regulation in Salmonella typhimurium. J Biol Chem 1972. [DOI: 10.1016/s0021-9258(19)45080-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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46
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Keith G, Roy A, Ebel JP, Dirheimer G. The primary structure of tryptophan transfer ribonucleic acid from brewer's yeast. II. Partial digestion with pancreatic ribonuclease and derivation of complete sequence. Biochimie 1972; 54:1417-26. [PMID: 4350483 DOI: 10.1016/s0300-9084(72)80083-x] [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: 01/10/2023]
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