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1.
J Biol Chem ; 293(39): 15021-15032, 2018 09 28.
Article in English | MEDLINE | ID: mdl-30087118

ABSTRACT

N-Formylation of the Met-tRNAMet by the nuclearly encoded mitochondrial methionyl-tRNA formyltransferase (MTFMT) has been found to be a key determinant of protein synthesis initiation in mitochondria. In humans, mutations in the MTFMT gene result in Leigh syndrome, a progressive and severe neurometabolic disorder. However, the absolute requirement of formylation of Met-tRNAMet for protein synthesis in mammalian mitochondria is still debated. Here, we generated a Mtfmt-KO mouse fibroblast cell line and demonstrated that N-formylation of the first methionine via fMet-tRNAMet by MTFMT is not an absolute requirement for initiation of protein synthesis. However, it differentially affected the efficiency of synthesis of mtDNA-coded polypeptides. Lack of methionine N-formylation did not compromise the stability of these individual subunits but had a marked effect on the assembly and stability of the OXPHOS complexes I and IV and on their supercomplexes. In summary, N-formylation is not essential for mitochondrial protein synthesis but is critical for efficient synthesis of several mitochondrially encoded peptides and for OXPHOS complex stability and assembly into supercomplexes.


Subject(s)
Hydroxymethyl and Formyl Transferases/genetics , Methionine/genetics , Mitochondria/genetics , Protein Biosynthesis/genetics , Animals , DNA, Mitochondrial/genetics , Fibroblasts/metabolism , Humans , Mice , Mice, Knockout , Mitochondrial Proteins/biosynthesis , Mitochondrial Proteins/genetics , Mutation , Oxidative Phosphorylation , RNA, Transfer, Amino Acyl/genetics
2.
mBio ; 7(6)2016 11 08.
Article in English | MEDLINE | ID: mdl-27834201

ABSTRACT

YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3' end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology. Using a bacterial two-hybrid system, we identified several proteins that interact with YbeY, including ribosomal protein S11, the ribosome-associated GTPases Era and Der, YbeZ, and SpoT. In particular, the interaction of YbeY with S11 and Era provides insight into YbeY's involvement in the 16S rRNA maturation process. The three-way association between YbeY, S11, and Era suggests that YbeY is recruited to the ribosome where it could cleave the 17S rRNA precursor endonucleolytically at or near the 3' end maturation site. Analysis of YbeY missense mutants shows that a highly conserved beta-sheet in YbeY-and not amino acids known to be important for YbeY's RNase activity-functions as the interface between YbeY and S11. This protein-interacting interface of YbeY is needed for correct rRNA maturation and stress regulation, as missense mutants show significant phenotypic defects. Additionally, structure-based in silico prediction of putative interactions between YbeY and the Era-30S complex through protein docking agrees well with the in vivo results. IMPORTANCE: Ribosomes are ribonucleoprotein complexes responsible for a key cellular function, protein synthesis. Their assembly is a highly coordinated process of RNA cleavage, RNA posttranscriptional modification, RNA conformational changes, and protein-binding events. Many open questions remain after almost 5 decades of study, including which RNase is responsible for final processing of the 16S rRNA 3' end. The highly conserved RNase YbeY, belonging to a core set of RNases essential in many bacteria, was previously shown to participate in 16S rRNA processing and ribosome quality control. However, detailed mechanistic insight into YbeY's ribosome-associated function has remained elusive. This work provides the first evidence that YbeY is recruited to the ribosome through interaction with proteins involved in ribosome biogenesis (i.e., ribosomal protein S11, Era). In addition, we identified key residues of YbeY involved in the interaction with S11 and propose a possible binding mode of YbeY to the ribosome using in silico docking.


Subject(s)
Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Escherichia coli/physiology , Metalloproteins/genetics , Metalloproteins/metabolism , RNA Processing, Post-Transcriptional , RNA, Ribosomal, 16S/metabolism , Ribosomes/metabolism , Stress, Physiological , Escherichia coli/genetics , Escherichia coli Proteins/isolation & purification , GTP-Binding Proteins/genetics , GTP-Binding Proteins/isolation & purification , GTP-Binding Proteins/metabolism , Gene Expression Regulation, Bacterial , Molecular Docking Simulation , Mutation, Missense , Protein Binding , RNA, Bacterial/genetics , RNA, Bacterial/isolation & purification , RNA, Bacterial/metabolism , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/isolation & purification , RNA-Binding Proteins/genetics , RNA-Binding Proteins/isolation & purification , RNA-Binding Proteins/metabolism , Ribosomal Proteins/genetics , Ribosomal Proteins/metabolism
4.
Mol Microbiol ; 98(6): 1199-221, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26337258

ABSTRACT

Threonylcarbamoyladenosine (t(6)A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t(6)A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t(6)A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNA(Ile)-lysidine synthetase. We confirm that t(6)A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t(6)A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t(6)A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t(6)A(-) D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t(6)A in tRNAs. Thus, although t(6)A is universally conserved in tRNAs, its role in translation might vary greatly between organisms.


Subject(s)
Adenosine/analogs & derivatives , Deinococcus/genetics , Escherichia coli/genetics , RNA, Transfer/genetics , RNA, Transfer/metabolism , Adenosine/genetics , Adenosine/metabolism , Amino Acid Sequence , Amino Acyl-tRNA Synthetases/genetics , Amino Acyl-tRNA Synthetases/metabolism , Aminoacylation/genetics , Conserved Sequence , Deinococcus/metabolism , Escherichia coli/metabolism , Molecular Sequence Data , Prokaryotic Cells , Proteomics , RNA, Bacterial/genetics , RNA, Bacterial/metabolism , Saccharomyces cerevisiae/genetics
5.
Nat Commun ; 6: 7520, 2015 Jul 03.
Article in English | MEDLINE | ID: mdl-26138142

ABSTRACT

Dominant mutations in five tRNA synthetases cause Charcot-Marie-Tooth (CMT) neuropathy, suggesting that altered aminoacylation function underlies the disease. However, previous studies showed that loss of aminoacylation activity is not required to cause CMT. Here we present a Drosophila model for CMT with mutations in glycyl-tRNA synthetase (GARS). Expression of three CMT-mutant GARS proteins induces defects in motor performance and motor and sensory neuron morphology, and shortens lifespan. Mutant GARS proteins display normal subcellular localization but markedly reduce global protein synthesis in motor and sensory neurons, or when ubiquitously expressed in adults, as revealed by FUNCAT and BONCAT. Translational slowdown is not attributable to altered tRNA(Gly) aminoacylation, and cannot be rescued by Drosophila Gars overexpression, indicating a gain-of-toxic-function mechanism. Expression of CMT-mutant tyrosyl-tRNA synthetase also impairs translation, suggesting a common pathogenic mechanism. Finally, genetic reduction of translation is sufficient to induce CMT-like phenotypes, indicating a causal contribution of translational slowdown to CMT.


Subject(s)
Charcot-Marie-Tooth Disease/genetics , Glycine-tRNA Ligase/genetics , Motor Neurons/metabolism , Movement , Protein Biosynthesis/genetics , Sensory Receptor Cells/metabolism , Tyrosine-tRNA Ligase/genetics , Animals , Animals, Genetically Modified , Disease Models, Animal , Drosophila , Humans , Life Expectancy , Motor Neurons/pathology , Mutagenesis, Site-Directed , Mutation , Neuromuscular Junction/pathology , Phenotype , Sensory Receptor Cells/pathology
6.
Proc Natl Acad Sci U S A ; 112(19): 6015-20, 2015 May 12.
Article in English | MEDLINE | ID: mdl-25918386

ABSTRACT

Bacterial strains carrying nonsense suppressor tRNA genes played a crucial role in early work on bacterial and bacterial viral genetics. In eukaryotes as well, suppressor tRNAs have played important roles in the genetic analysis of yeast and worms. Surprisingly, little is known about genetic suppression in archaea, and there has been no characterization of suppressor tRNAs or identification of nonsense mutations in any of the archaeal genes. Here, we show, using the ß-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the serine and tyrosine tRNAs of the archaeon Haloferax volcanii are active in suppression of their corresponding stop codons. Using a promoter for tRNA expression regulated by tryptophan, we also show inducible and regulatable suppression of all three stop codons in H. volcanii. Additionally, transformation of a ΔpyrE2 H. volcanii strain with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on agar plates lacking uracil. Thus, an auxotrophic amber mutation in the pyrE2 gene can be complemented by expression of the amber suppressor tRNA. These results pave the way for generating archaeal strains carrying inducible suppressor tRNA genes on the chromosome and their use in archaeal and archaeviral genetics. We also provide possible explanations for why suppressor tRNAs have not been identified in archaea.


Subject(s)
Archaea/genetics , Codon, Terminator , Haloferax volcanii/genetics , RNA, Transfer/metabolism , Suppression, Genetic , Archaea/metabolism , Base Sequence , Codon, Nonsense , Escherichia coli/metabolism , Genes, Suppressor , Haloferax volcanii/metabolism , Molecular Sequence Data , Novobiocin/chemistry , Plasmids/metabolism , Promoter Regions, Genetic , Serine/chemistry , Thymidine/chemistry , Tryptophan/chemistry , Uracil/chemistry , beta-Galactosidase/metabolism
7.
J Biol Chem ; 289(47): 32729-41, 2014 Nov 21.
Article in English | MEDLINE | ID: mdl-25288793

ABSTRACT

N-Formylation of initiator methionyl-tRNA (Met-tRNA(Met)) by methionyl-tRNA formyltransferase (MTF) is important for translation initiation in bacteria, mitochondria, and chloroplasts. Unlike all other translation systems, the metazoan mitochondrial system is unique in using a single methionine tRNA (tRNA(Met)) for both initiation and elongation. A portion of Met-tRNA(Met) is formylated for initiation, whereas the remainder is used for elongation. Recently, we showed that compound heterozygous mutations within the nuclear gene encoding human mitochondrial MTF (mt-MTF) significantly reduced mitochondrial translation efficiency, leading to combined oxidative phosphorylation deficiency and Leigh syndrome in two unrelated patients. Patient P1 has a stop codon mutation in one of the MTF genes and an S209L mutation in the other MTF gene. P2 has a S125L mutation in one of the MTF genes and the same S209L mutation as P1 in the other MTF gene. Here, we have investigated the effect of mutations at Ser-125 and Ser-209 on activities of human mt-MTF and of the corresponding mutations, Ala-89 or Ala-172, respectively, on activities of Escherichia coli MTF. The S125L mutant has 653-fold lower activity, whereas the S209L mutant has 36-fold lower activity. Thus, both patients depend upon residual activity of the S209L mutant to support low levels of mitochondrial protein synthesis. We discuss the implications of these and other results for whether the effect of the S209L mutation on mitochondrial translational efficiency is due to reduced activity of the mutant mt-MTF and/or reduced levels of the mutant mt-MTF.


Subject(s)
Hydroxymethyl and Formyl Transferases/genetics , Leigh Disease/genetics , Mitochondrial Proteins/genetics , Mutation , Alanine/genetics , Alanine/metabolism , Amino Acid Sequence , Amino Acid Substitution , Base Sequence , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Humans , Hydroxymethyl and Formyl Transferases/metabolism , Immunoblotting , Leigh Disease/metabolism , Mitochondria/genetics , Mitochondria/metabolism , Mitochondrial Proteins/metabolism , Molecular Sequence Data , Protein Biosynthesis/genetics , RNA, Transfer, Met/genetics , RNA, Transfer, Met/metabolism , Sequence Homology, Amino Acid , Serine/genetics , Serine/metabolism
8.
PLoS Pathog ; 10(6): e1004175, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24901994

ABSTRACT

YbeY, a highly conserved protein, is an RNase in E. coli and plays key roles in both processing of the critical 3' end of 16 S rRNA and in 70 S ribosome quality control under stress. These central roles account for YbeY's inclusion in the postulated minimal bacterial genome. However, YbeY is not essential in E. coli although loss of ybeY severely sensitizes it to multiple physiological stresses. Here, we show that YbeY is an essential endoribonuclease in Vibrio cholerae and is crucial for virulence, stress regulation, RNA processing and ribosome quality control, and is part of a core set of RNases essential in most representative pathogens. To understand its function, we analyzed the rRNA and ribosome profiles of a V. cholerae strain partially depleted for YbeY and other RNase mutants associated with 16 S rRNA processing; our results demonstrate that YbeY is also crucial for 16 S rRNA 3' end maturation in V. cholerae and that its depletion impedes subunit assembly into 70 S ribosomes. YbeY's importance to V. cholerae pathogenesis was demonstrated by the complete loss of mice colonization and biofilm formation, reduced cholera toxin production, and altered expression levels of virulence-associated small RNAs of a V. cholerae strain partially depleted for YbeY. Notably, the ybeY genes of several distantly related pathogens can fully complement an E. coli ΔybeY strain under various stress conditions, demonstrating the high conservation of YbeY's activity in stress regulation. Taken together, this work provides the first comprehensive exploration of YbeY's physiological role in a human pathogen, showing its conserved function across species in essential cellular processes.


Subject(s)
Bacterial Proteins/metabolism , Endoribonucleases/metabolism , RNA 3' End Processing , RNA, Bacterial/metabolism , RNA, Ribosomal/metabolism , Stress, Physiological , Vibrio cholerae/enzymology , Amino Acid Sequence , Animals , Animals, Newborn , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Biofilms/growth & development , Cholera/enzymology , Cholera/immunology , Cholera/metabolism , Cholera/microbiology , Cholera Toxin/biosynthesis , Conserved Sequence , Endoribonucleases/chemistry , Endoribonucleases/genetics , Gene Expression Regulation, Bacterial , Immunity, Mucosal , Intestinal Mucosa/growth & development , Intestinal Mucosa/immunology , Intestinal Mucosa/microbiology , Intestinal Mucosa/pathology , Mice , Mutation , Phylogeny , Vibrio cholerae/immunology , Vibrio cholerae/pathogenicity , Vibrio cholerae/physiology , Virulence , Virulence Factors/biosynthesis
9.
Nucleic Acids Res ; 42(3): 1904-15, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24194599

ABSTRACT

Translation of the isoleucine codon AUA in most prokaryotes requires a modified C (lysidine or agmatidine) at the wobble position of tRNA2(Ile) to base pair specifically with the A of the AUA codon but not with the G of AUG. Recently, a Bacillus subtilis strain was isolated in which the essential gene encoding tRNA(Ile)-lysidine synthetase was deleted for the first time. In such a strain, C34 at the wobble position of tRNA2(Ile) is expected to remain unmodified and cells depend on a mutant suppressor tRNA derived from tRNA1(Ile), in which G34 has been changed to U34. An important question, therefore, is how U34 base pairs with A without also base pairing with G. Here, we show (i) that unlike U34 at the wobble position of all B. subtilis tRNAs of known sequence, U34 in the mutant tRNA is not modified, and (ii) that the mutant tRNA binds strongly to the AUA codon on B. subtilis ribosomes but only weakly to AUG. These in vitro data explain why the suppressor strain displays only a low level of misreading AUG codons in vivo and, as shown here, grows at a rate comparable to that of the wild-type strain.


Subject(s)
Bacillus subtilis/genetics , Codon , Isoleucine/metabolism , Protein Biosynthesis , RNA, Transfer, Ile/chemistry , RNA, Transfer, Ile/metabolism , Amino Acyl-tRNA Synthetases/genetics , Bacillus subtilis/growth & development , Gene Deletion , Phenotype , RNA, Transfer, Ile/isolation & purification , Ribosomes/metabolism , Transfer RNA Aminoacylation
10.
RNA ; 20(2): 177-88, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24344322

ABSTRACT

Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2(Ile)) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2(Ile) binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.


Subject(s)
Anticodon/genetics , Haloarcula marismortui/genetics , RNA, Archaeal/genetics , RNA, Transfer, Ile/genetics , Uridine/analogs & derivatives , Base Pairing , Base Sequence , Codon/genetics , Escherichia coli/genetics , Haloferax/genetics , Molecular Structure , Point Mutation , RNA, Archaeal/chemistry , RNA, Archaeal/metabolism , RNA, Bacterial/genetics , RNA, Fungal/genetics , RNA, Transfer, Ile/chemistry , RNA, Transfer, Ile/metabolism , Ribosomes/chemistry , Saccharomyces cerevisiae/genetics , Sulfolobus/genetics , Transfer RNA Aminoacylation , Uridine/chemistry , Uridine/genetics
11.
Nat Struct Mol Biol ; 20(5): 641-3, 2013 May.
Article in English | MEDLINE | ID: mdl-23542153

ABSTRACT

Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA. Here, we report the crystal structure of the archaeal tRNA2(Ile), which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome. The structure illustrates how agmatidine confers codon specificity for AUA over AUG.


Subject(s)
Archaea/genetics , Codon , Isoleucine/genetics , Protein Biosynthesis , RNA, Transfer, Ile/chemistry , Ribosomes/chemistry , Archaea/chemistry , Archaea/metabolism , Isoleucine/metabolism , Models, Molecular , Nucleic Acid Conformation , RNA, Transfer, Ile/metabolism , Ribosomes/metabolism
13.
Cell Metab ; 14(3): 428-34, 2011 Sep 07.
Article in English | MEDLINE | ID: mdl-21907147

ABSTRACT

The metazoan mitochondrial translation machinery is unusual in having a single tRNA(Met) that fulfills the dual role of the initiator and elongator tRNA(Met). A portion of the Met-tRNA(Met) pool is formylated by mitochondrial methionyl-tRNA formyltransferase (MTFMT) to generate N-formylmethionine-tRNA(Met) (fMet-tRNA(met)), which is used for translation initiation; however, the requirement of formylation for initiation in human mitochondria is still under debate. Using targeted sequencing of the mtDNA and nuclear exons encoding the mitochondrial proteome (MitoExome), we identified compound heterozygous mutations in MTFMT in two unrelated children presenting with Leigh syndrome and combined OXPHOS deficiency. Patient fibroblasts exhibit severe defects in mitochondrial translation that can be rescued by exogenous expression of MTFMT. Furthermore, patient fibroblasts have dramatically reduced fMet-tRNA(Met) levels and an abnormal formylation profile of mitochondrially translated COX1. Our findings demonstrate that MTFMT is critical for efficient human mitochondrial translation and reveal a human disorder of Met-tRNA(Met) formylation.


Subject(s)
Cyclooxygenase 1/metabolism , DNA, Mitochondrial/chemistry , Fibroblasts/metabolism , Leigh Disease/genetics , Mitochondria/genetics , Mitochondrial Proteins/genetics , Protein Biosynthesis , RNA, Transfer, Met/metabolism , Cells, Cultured , Child , Cyclooxygenase 1/genetics , DNA, Mitochondrial/genetics , Fibroblasts/pathology , Heterozygote , Humans , Hydroxymethyl and Formyl Transferases , Immunoblotting , Leigh Disease/metabolism , Leigh Disease/pathology , Lentivirus , Mitochondria/metabolism , Mitochondrial Proteins/metabolism , Mutation , Protein Biosynthesis/genetics , Sequence Analysis, DNA , Transduction, Genetic , Virion
14.
Mol Microbiol ; 78(2): 506-18, 2010 Oct.
Article in English | MEDLINE | ID: mdl-20807199

ABSTRACT

The UPF0054 protein family is highly conserved with homologues present in nearly every sequenced bacterium. In some bacteria, the respective gene is essential, while in others its loss results in a highly pleiotropic phenotype. Despite detailed structural studies, a cellular role for this protein family has remained unknown. We report here that deletion of the Escherichia coli homologue, YbeY, causes striking defects that affect ribosome activity, translational fidelity and ribosome assembly. Mapping of 16S, 23S and 5S rRNA termini reveals that YbeY influences the maturation of all three rRNAs, with a particularly strong effect on maturation at both the 5'- and 3'-ends of 16S rRNA as well as maturation of the 5'-termini of 23S and 5S rRNAs. Furthermore, we demonstrate strong genetic interactions between ybeY and rnc (encoding RNase III), ybeY and rnr (encoding RNase R), and ybeY and pnp (encoding PNPase), further suggesting a role for YbeY in rRNA maturation. Mutation of highly conserved amino acids in YbeY, allowed the identification of two residues (H114, R59) that were found to have a significant effect in vivo. We discuss the implications of these findings for rRNA maturation and ribosome assembly in bacteria.


Subject(s)
Escherichia coli Proteins/metabolism , Metalloproteins/metabolism , RNA, Bacterial/metabolism , RNA, Ribosomal/metabolism , Amino Acid Sequence , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Gene Deletion , Metalloproteins/genetics , Molecular Sequence Data , Prokaryotic Initiation Factors/metabolism , Protein Binding , Ribosomes/metabolism , Sequence Alignment
15.
Proc Natl Acad Sci U S A ; 107(7): 2872-7, 2010 Feb 16.
Article in English | MEDLINE | ID: mdl-20133752

ABSTRACT

Modification of the cytidine in the first anticodon position of the AUA decoding tRNA(Ile) (tRNA2(Ile)) of bacteria and archaea is essential for this tRNA to read the isoleucine codon AUA and to differentiate between AUA and the methionine codon AUG. To identify the modified cytidine in archaea, we have purified this tRNA species from Haloarcula marismortui, established its codon reading properties, used liquid chromatography-mass spectrometry (LC-MS) to map RNase A and T1 digestion products onto the tRNA, and used LC-MS/MS to sequence the oligonucleotides in RNase A digests. These analyses revealed that the modification of cytidine in the anticodon of tRNA2(Ile) adds 112 mass units to its molecular mass and makes the glycosidic bond unusually labile during mass spectral analyses. Accurate mass LC-MS and LC-MS/MS analysis of total nucleoside digests of the tRNA2(Ile) demonstrated the absence in the modified cytidine of the C2-oxo group and its replacement by agmatine (decarboxy-arginine) through a secondary amine linkage. We propose the name agmatidine, abbreviation C(+), for this modified cytidine. Agmatidine is also present in Methanococcus maripaludis tRNA2(Ile) and in Sulfolobus solfataricus total tRNA, indicating its probable occurrence in the AUA decoding tRNA(Ile) of euryarchaea and crenarchaea. The identification of agmatidine shows that bacteria and archaea have developed very similar strategies for reading the isoleucine codon AUA while discriminating against the methionine codon AUG.


Subject(s)
Anticodon/genetics , Base Pairing/genetics , Cytidine/chemistry , Haloarcula marismortui/chemistry , RNA, Transfer, Ile/chemistry , Agmatine/chemistry , Chromatography, Liquid , Methanococcus/chemistry , Molecular Structure , RNA, Transfer, Ile/genetics , Sulfolobus solfataricus/chemistry , Tandem Mass Spectrometry
16.
Mol Cell ; 35(2): 181-90, 2009 Jul 31.
Article in English | MEDLINE | ID: mdl-19647515

ABSTRACT

Translation initiation of the second ORF of insect dicistrovirus RNA depends on an internal ribosomal entry site (IRES) in its intergenic region (IGR) and is exceptional in using a codon other than AUG and in not using the canonical initiator methionine tRNA. Studies in vitro suggest that pseudoknot I (PKI) immediately preceding the initiation codon occupies the ribosomal P site and that an elongator tRNA initiates translation from the ribosomal A site. Using dicistronic reporters carrying mutations in the initiation codon of the second ORF and mutant elongator or initiator tRNAs capable of reading these codons, we provide direct evidence for initiation from the A site in mammalian cells and, under certain conditions, also from the P site. Initiation from the A but not the P site requires PKI. Thus, PKI structure may be dynamic, and optimal IGR IRES-mediated translation of dicistroviral RNAs may require trans-acting factors to stabilize PKI.


Subject(s)
Picornaviridae/genetics , Protein Biosynthesis/physiology , Ribosomes/chemistry , Codon, Initiator , Codon, Terminator , Genes, Reporter , Humans , Luciferases/genetics , Luciferases/metabolism , Mutation , Open Reading Frames , RNA, Transfer/genetics , RNA, Transfer/metabolism , RNA, Transfer/physiology , RNA, Transfer, Met , Ribosomes/physiology , Transfection , Untranslated Regions , Viral Proteins/genetics , Viral Proteins/metabolism
18.
Methods ; 44(2): 129-38, 2008 Feb.
Article in English | MEDLINE | ID: mdl-18241794

ABSTRACT

Here we describe the many applications of acid urea polyacrylamide gel electrophoresis (acid urea PAGE) followed by Northern blot analysis to studies of tRNAs and aminoacyl-tRNA synthetases. Acid urea PAGE allows the electrophoretic separation of different forms of a tRNA, discriminated by changes in bulk, charge, and/or conformation that are brought about by aminoacylation, formylation, or modification of a tRNA. Among the examples described are (i) analysis of the effect of mutations in the Escherichia coli initiator tRNA on its aminoacylation and formylation; (ii) evidence of orthogonality of suppressor tRNAs in mammalian cells and yeast; (iii) analysis of aminoacylation specificity of an archaeal prolyl-tRNA synthetase that can aminoacylate archaeal tRNA(Pro) with cysteine, but does not aminoacylate archaeal tRNA(Cys) with cysteine; (iv) identification and characterization of the AUA-decoding minor tRNA(Ile) in archaea; and (v) evidence that the archaeal minor tRNA(Ile) contains a modified base in the wobble position different from lysidine found in the corresponding eubacterial tRNA.


Subject(s)
Amino Acyl-tRNA Synthetases/analysis , Electrophoresis, Polyacrylamide Gel/methods , RNA, Transfer/analysis , Animals , Archaea/metabolism , Blotting, Northern/methods , Humans , Hydrogen-Ion Concentration , Lysine/analogs & derivatives , Lysine/biosynthesis , Protein Engineering/methods , Pyrimidine Nucleosides/biosynthesis , RNA, Bacterial/isolation & purification , RNA, Transfer/isolation & purification , RNA, Transfer, Cys/biosynthesis , RNA, Transfer, Ile/metabolism , RNA, Transfer, Met/metabolism , Urea
19.
Mol Microbiol ; 67(5): 1012-26, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18221266

ABSTRACT

Despite its importance in post-transcriptional regulation of polycistronic operons in Escherichia coli, little is known about the mechanism of translation re-initiation, which occurs when the same ribosome used to translate an upstream open reading frame (ORF) also translates a downstream ORF. To investigate translation re-initiation in Escherichia coli, we constructed a di-cistronic reporter in which a firefly luciferase gene was linked to a chloramphenicol acetyltransferase gene using a segment of the translationally coupled geneV-geneVII intercistronic region from M13 phage. With this reporter and mutant initiator tRNAs, we show that two of the unique properties of E. coli initiator tRNA - formylation of the amino acid attached to the tRNA and binding of the tRNA to the ribosomal P-site - are as important for re-initiation as for de novo initiation. Overexpression of IF2 or increasing the affinity of mutant initiator tRNA for IF2 enhanced re-initiation efficiency, suggesting that IF2 is required for efficient re-initiation. In contrast, overexpression of IF3 led to a marked decrease in re-initiation efficiency, suggesting that a 30S ribosome and not a 70S ribosome is used for translation re-initiation. Strikingly, overexpression of IF3 also blocked E. coli from acting as a host for propagation of M13 phage.


Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Peptide Chain Initiation, Translational , Prokaryotic Initiation Factor-2/metabolism , Prokaryotic Initiation Factor-3/metabolism , RNA, Transfer, Met/metabolism , Bacteriophage M13/growth & development , Base Sequence , Chloramphenicol O-Acetyltransferase/genetics , Chloramphenicol O-Acetyltransferase/metabolism , Escherichia coli/virology , Escherichia coli Proteins/genetics , Gene Expression Regulation, Bacterial , Genes, Reporter , Luciferases, Firefly/genetics , Luciferases, Firefly/metabolism , Molecular Sequence Data , Nucleic Acid Conformation , Prokaryotic Initiation Factor-2/genetics , Prokaryotic Initiation Factor-3/genetics , RNA, Transfer, Met/chemistry , RNA, Transfer, Met/genetics , Ribosomes/metabolism
20.
RNA ; 14(1): 117-26, 2008 Jan.
Article in English | MEDLINE | ID: mdl-17998287

ABSTRACT

Annotation of the complete genome of the extreme halophilic archaeon Haloarcula marismortui does not include a tRNA for translation of AUA, the rare codon for isoleucine. This is a situation typical for most archaeal genomes sequenced to date. Based on computational analysis, it has been proposed recently that a single intron-containing tRNA gene produces two very similar but functionally different tRNAs by means of alternative splicing; a UGG-decoding tRNA(TrpCCA) and an AUA-decoding tRNA(IleUAU). Through analysis of tRNAs from H. marismortui, we have confirmed the presence of tRNA(TrpCCA), but found no evidence for the presence of tRNA(IleUAU). Instead, we have shown that a tRNA, currently annotated as elongator methionine tRNA and containing CAU as the anticodon, is aminoacylated with isoleucine in vivo and that this tRNA represents the missing isoleucine tRNA. Interestingly, this tRNA carries a base modification of C34 in the anticodon different from the well-known lysidine found in eubacteria, which switches the amino acid identity of the tRNA from methionine to isoleucine and its decoding specificity from AUG to AUA. The methods described in this work for the identification of individual tRNAs present in H. marismortui provide the tools necessary for experimentally confirming the presence of any tRNA in a cell and, thereby, to test computational predictions of tRNA genes.


Subject(s)
Codon , Haloarcula marismortui/genetics , RNA, Transfer/genetics , Acetylation , Anticodon , Base Sequence , Molecular Sequence Data , Nucleic Acid Conformation , Nucleic Acid Hybridization , RNA, Transfer/chemistry
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