Research

Jump to: Review

Open AccessArticle TrmL and TusA Are Necessary for rpoS and MiaA Is Required for hfq Expression in Escherichia coli

by Joseph I. Aubee, Morenike Olu and Karl M. Thompson

Biomolecules 2017, 7(2), 39; doi:10.3390/biom7020039

Received: 1 January 2017 / Revised: 31 March 2017 / Accepted: 12 April 2017 / Published: 4 May 2017

PDF Full-text (1505 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Previous work demonstrated that efficient RNA Polymerase sigma S-subunit (RpoS) translation requires the N6-isopentenyladenosine i6A37 transfer RNA (tRNA) modification for UUX-Leu decoding. Here we investigate the effect of two additional tRNA modification systems on RpoS translation; the analysis was also extended to another

[...] Read more.

Previous work demonstrated that efficient RNA Polymerase sigma S-subunit (RpoS) translation requires the N6-isopentenyladenosine i6A37 transfer RNA (tRNA) modification for UUX-Leu decoding. Here we investigate the effect of two additional tRNA modification systems on RpoS translation; the analysis was also extended to another High UUX-leucine codon (HULC) protein, Host Factor for phage Qβ (Hfq). One tRNA modification, the addition of the 2’-O-methylcytidine/uridine 34 (C/U34m) tRNA modification by tRNA (cytidine/uridine-2’O)-ribose methyltransferase L (TrmL), requires the presence of the N⁶-isopentenyladenosine 37 (i⁶A37) and therefore it seemed possible that the defect in RpoS translation in the absence of i⁶A37 prenyl transferase (MiaA) was in fact due to the inability to add the C/U34m modification to UUX-Leu tRNAs. The second modification, addition of 2-thiouridine (s²U), part of (mnm⁵s²U34), is dependent on tRNA 2-thiouridine synthesizing protein A (TusA), previously shown to affect RpoS levels. We compared expression of P_BAD-rpoS990-lacZ translational fusions carrying wild-type UUX leucine codons with derivatives in which UUX codons were changed to CUX codons, in the presence and absence of TrmL or TusA. The absence of these proteins, and therefore presumably the modifications they catalyze, both abolished P_BAD-rpoS990-lacZ translation activity. UUX-Leu to CUX-Leu codon mutations in rpoS suppressed the trmL requirement for P_BAD-rpoS990-lacZ expression. Thus, it is likely that the C/U34m and s²U34 tRNA modifications are necessary for full rpoS translation. We also measured P_BAD-hfq306-lacZ translational fusion activity in the absence of C/U34m (trmL) or i⁶A37 (miaA). The absence of i⁶A37 resulted in decreased P_BAD-hfq306-lacZ expression, consistent with a role for i⁶A37 tRNA modification for hfq translation. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessArticle QueF-Like, a Non-Homologous Archaeosine Synthase from the Crenarchaeota

by Adriana Bon Ramos, Lide Bao, Ben Turner, Valérie de Crécy-Lagard and Dirk Iwata-Reuyl

Biomolecules 2017, 7(2), 36; doi:10.3390/biom7020036

Received: 28 February 2017 / Revised: 23 March 2017 / Accepted: 24 March 2017 / Published: 6 April 2017

PDF Full-text (2333 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Archaeosine (G⁺) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and

[...] Read more.

Archaeosine (G⁺) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and location in the tRNA, led to the proposal that it serves a key role in stabilizing tRNA structure. Although G⁺ is limited to the Archaea, it is structurally related to the bacterial modified nucleoside queuosine, and the two share homologous enzymes for the early steps of their biosynthesis. In the Euryarchaeota, the last step of the archaeosine biosynthetic pathway involves the amidation of a nitrile group on an archaeosine precursor to give formamidine, a reaction catalyzed by the enzyme Archaeosine Synthase (ArcS). Most Crenarchaeota lack ArcS, but possess two proteins that inversely distribute with ArcS and each other, and are implicated in G⁺ biosynthesis. Here, we describe biochemical studies of one of these, the protein QueF-like (QueF-L) from Pyrobaculum calidifontis, that demonstrate the catalytic activity of QueF-L, establish where in the pathway QueF-L acts, and identify the source of ammonia in the reaction. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessArticle Protection of the Queuosine Biosynthesis Enzyme QueF from Irreversible Oxidation by a Conserved Intramolecular Disulfide

by Adeba Mohammad, Adriana Bon Ramos, Bobby W. K. Lee, Spencer W. Cohen, Maryam K. Kiani, Dirk Iwata-Reuyl, Boguslaw Stec and Manal A. Swairjo

Biomolecules 2017, 7(1), 30; doi:10.3390/biom7010030

Received: 10 January 2017 / Revised: 7 March 2017 / Accepted: 10 March 2017 / Published: 16 March 2017

PDF Full-text (6107 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ₀) to 7-aminomethyl-7-deazaguanine (preQ₁) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF-catalyzed reaction includes formation of a covalent thioimide

[...] Read more.

QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ₀) to 7-aminomethyl-7-deazaguanine (preQ₁) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF-catalyzed reaction includes formation of a covalent thioimide intermediate with a conserved active site cysteine that is prone to oxidation in vivo. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide formed between the catalytic Cys55 and a conserved Cys99 located near the active site. This structure is more symmetric than the substrate-bound structure and exhibits major rearrangement of the loops responsible for substrate binding. Mutation of Cys99 to Ala/Ser does not compromise enzyme activity, indicating that the disulfide does not play a catalytic role. Peroxide-induced inactivation of the wild-type enzyme is reversible with thioredoxin, while such inactivation of the Cys99Ala/Ser mutants is irreversible, consistent with protection of Cys55 from irreversible oxidation by disulfide formation with Cys99. Conservation of the cysteine pair, and the reported in vivo interaction of QueF with the thioredoxin-like hydroperoxide reductase AhpC in Escherichia coli suggest that regulation by the thioredoxin disulfide-thiol exchange system may constitute a general mechanism for protection of QueF from oxidative stress in vivo. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessArticle Modulation of the Proteostasis Machinery to Overcome Stress Caused by Diminished Levels of t6A‐Modified tRNAs in Drosophila

by Diego Rojas‐Benítez, Cristián Eggers and Alvaro Glavic

Biomolecules 2017, 7(1), 25; doi:10.3390/biom7010025

Received: 30 November 2016 / Accepted: 28 February 2017 / Published: 6 March 2017

PDF Full-text (5999 KB) | HTML Full-text | XML Full-text

Abstract

Transfer RNAs (tRNAs) harbor a subset of post‐transcriptional modifications required for structural stability or decoding function. N6‐threonylcarbamoyladenosine (t6A) is a universally conserved modification found at position 37 in tRNA that pair A‐starting codons (ANN) and is required for proper translation initiation and to

[...] Read more.

Transfer RNAs (tRNAs) harbor a subset of post‐transcriptional modifications required for structural stability or decoding function. N6‐threonylcarbamoyladenosine (t6A) is a universally conserved modification found at position 37 in tRNA that pair A‐starting codons (ANN) and is required for proper translation initiation and to prevent frame shift during elongation. In its absence, the synthesis of aberrant proteins is likely, evidenced by the formation of protein aggregates. In this work, our aim was to study the relationship between t6A‐modified tRNAs and protein synthesis homeostasis machinery using Drosophila melanogaster. We used the Gal4/UAS system to knockdown genes required for t6A synthesis in a tissue and time specific manner and in vivo reporters of unfolded protein response (UPR) activation. Our results suggest that t6A‐modified tRNAs, synthetized by the threonyl‐carbamoyl transferase complex (TCTC), are required for organismal growth and imaginal cell survival, and is most likely to support proper protein synthesis. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessArticle Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation

by Virginie Marchand, Florian Pichot, Kathrin Thüring, Lilia Ayadi, Isabel Freund, Alexander Dalpke, Mark Helm and Yuri Motorin

Biomolecules 2017, 7(1), 13; doi:10.3390/biom7010013

Received: 29 December 2016 / Accepted: 2 February 2017 / Published: 9 February 2017

Cited by 1 | PDF Full-text (2429 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Analysis of RNA modifications by traditional physico‐chemical approaches is labor intensive, requires substantial amounts of input material and only allows site‐by‐site measurements. The recent development of qualitative and quantitative approaches based on next‐generation sequencing (NGS) opens new perspectives for the analysis of various

[...] Read more.

Analysis of RNA modifications by traditional physico‐chemical approaches is labor intensive, requires substantial amounts of input material and only allows site‐by‐site measurements. The recent development of qualitative and quantitative approaches based on next‐generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing‐based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2′‐O‐methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally‐important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2′‐O‐methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessArticle The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ₀) Transport

by Rémi Zallot, Yifeng Yuan and Valérie de Crécy-Lagard

Biomolecules 2017, 7(1), 12; doi:10.3390/biom7010012

Received: 22 December 2016 / Revised: 27 January 2017 / Accepted: 30 January 2017 / Published: 8 February 2017

PDF Full-text (5687 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

Queuosine (Q) is a complex modification of the wobble base in tRNAs with GUN anticodons. The full Q biosynthesis pathway has been elucidated in Escherichia coli. FolE, QueD, QueE and QueC are involved in the conversion of guanosine triphosphate (GTP) to 7-cyano-7-deazaguanine

[...] Read more.

Queuosine (Q) is a complex modification of the wobble base in tRNAs with GUN anticodons. The full Q biosynthesis pathway has been elucidated in Escherichia coli. FolE, QueD, QueE and QueC are involved in the conversion of guanosine triphosphate (GTP) to 7-cyano-7-deazaguanine (preQ₀), an intermediate of increasing interest for its central role in tRNA and DNA modification and secondary metabolism. QueF then reduces preQ₀ to 7-aminomethyl-7-deazaguanine (preQ₁). PreQ₁ is inserted into tRNAs by tRNA guanine₍₃₄₎ transglycosylase (TGT). The inserted base preQ₁ is finally matured to Q by two additional steps involving QueA and QueG or QueH. Most Eubacteria harbor the full set of Q synthesis genes and are predicted to synthesize Q de novo. However, some bacteria only encode enzymes involved in the second half of the pathway downstream of preQ₀ synthesis, including the signature enzyme TGT. Different patterns of distribution of the queF, tgt, queA and queG or queH genes are observed, suggesting preQ₀, preQ₁ or even the queuine base being salvaged in specific organisms. Such salvage pathways require the existence of specific 7-deazapurine transporters that have yet to be identified. The COG1738 family was identified as a candidate for a missing preQ₀/preQ₁ transporter in prokaryotes, by comparative genomics analyses. The existence of Q precursor salvage was confirmed for the first time in bacteria, in vivo, through an indirect assay. The involvement of the COG1738 in salvage of a Q precursor was experimentally validated in Escherichia coli, where it was shown that the COG1738 family member YhhQ is essential for preQ₀ transport. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessArticle Role of Pseudouridine Formation by Deg1 for Functionality of Two Glutamine Isoacceptor tRNAs

by Roland Klassen and Raffael Schaffrath

Biomolecules 2017, 7(1), 8; doi:10.3390/biom7010008

Received: 16 December 2016 / Revised: 20 January 2017 / Accepted: 20 January 2017 / Published: 26 January 2017

PDF Full-text (2085 KB) | HTML Full-text | XML Full-text

Abstract

Loss of Deg1/Pus3 and concomitant elimination of pseudouridine in tRNA at positions 38 and 39 (ψ38/39) was shown to specifically impair the function of tRNA^Gln_UUG under conditions of temperature-induced down-regulation of wobble uridine thiolation in budding yeast and is linked to

[...] Read more.

Loss of Deg1/Pus3 and concomitant elimination of pseudouridine in tRNA at positions 38 and 39 (ψ38/39) was shown to specifically impair the function of tRNA^Gln_UUG under conditions of temperature-induced down-regulation of wobble uridine thiolation in budding yeast and is linked to intellectual disability in humans. To further characterize the differential importance of the frequent ψ38/39 modification for tRNAs in yeast, we analyzed the in vivo function of non-sense suppressor tRNAs SUP4 and sup70-65 in the absence of the modifier. In the tRNA^Tyr_GψA variant SUP4, UAA read-through is enabled due to an anticodon mutation (UψA), whereas sup70-65 is a mutant form of tRNA^Gln_CUG (SUP70) that mediates UAG decoding due to a mutation of the anticodon-loop closing base pair (G31:C39 to A31:C39). While SUP4 function is unaltered in deg1/pus3 mutants, the ability of sup70-65 to mediate non-sense suppression and to complement a genomic deletion of the essential SUP70 gene is severely compromised. These results and the differential suppression of growth defects in deg1 mutants by multi-copy SUP70 or tQ(UUG) are consistent with the interpretation that ψ38 is most important for tRNA^Gln_UUG function under heat stress but becomes crucial for tRNA^Gln_CUG as well when the anticodon loop is destabilized by the sup70-65 mutation. Thus, ψ38/39 may protect the anticodon loop configuration from disturbances by loss of other modifications or base changes. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessArticle CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles

by Ralf Hauenschild, Stephan Werner, Lyudmil Tserovski, Andreas Hildebrandt, Yuri Motorin and Mark Helm

Biomolecules 2016, 6(4), 42; doi:10.3390/biom6040042

Received: 29 August 2016 / Revised: 20 October 2016 / Accepted: 21 October 2016 / Published: 10 November 2016

Cited by 3 | PDF Full-text (1122 KB) | HTML Full-text | XML Full-text

Abstract

Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for the detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures

[...] Read more.

Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for the detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures of modified ribonucleotides relying on both sequence-dependent mismatch patterns and reverse transcription arrests. Common alignment viewers lack specialized functionality, such as filtering, tailored visualization, image export and differential analysis. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer (CAn) was developed in response to the demand for a powerful inspection tool. It is freely available for all three main operating systems. With SAM file format as standard input, CAn is an intuitive and user-friendly tool that is generally applicable to the large community of biomedical users, starting from simple visualization of RNA sequencing (RNA-Seq) data, up to sophisticated modification analysis with significance-based modification candidate calling. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Review

Jump to: Research

Open AccessReview tRNA Modifications: Impact on Structure and Thermal Adaptation

by Christian Lorenz, Christina E. Lünse and Mario Mörl

Biomolecules 2017, 7(2), 35; doi:10.3390/biom7020035

Received: 5 March 2017 / Revised: 27 March 2017 / Accepted: 28 March 2017 / Published: 4 April 2017

Cited by 3 | PDF Full-text (6523 KB) | HTML Full-text | XML Full-text

Abstract

Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all

[...] Read more.

Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots—the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

by Chenkang Zheng, Katherine A. Black and Patricia C. Dos Santos

Biomolecules 2017, 7(1), 33; doi:10.3390/biom7010033

Received: 6 February 2017 / Revised: 10 March 2017 / Accepted: 16 March 2017 / Published: 22 March 2017

PDF Full-text (2108 KB) | HTML Full-text | XML Full-text

Abstract

Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all

[...] Read more.

Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Trm5 and TrmD: Two Enzymes from Distinct Origins Catalyze the Identical tRNA Modification, m¹G37

by Sakurako Goto-Ito, Takuhiro Ito and Shigeyuki Yokoyama

Biomolecules 2017, 7(1), 32; doi:10.3390/biom7010032

Received: 13 February 2017 / Revised: 7 March 2017 / Accepted: 16 March 2017 / Published: 21 March 2017

Cited by 1 | PDF Full-text (3515 KB) | HTML Full-text | XML Full-text

Abstract

The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation

[...] Read more.

The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function

by Ville Y. P. Väre, Emily R. Eruysal, Amithi Narendran, Kathryn L. Sarachan and Paul F. Agris

Biomolecules 2017, 7(1), 29; doi:10.3390/biom7010029

Received: 23 January 2017 / Revised: 6 March 2017 / Accepted: 6 March 2017 / Published: 16 March 2017

Cited by 1 | PDF Full-text (3670 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability

[...] Read more.

RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA’s cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Open AccessReview Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways

by Mirela Čavužić and Yuchen Liu

Biomolecules 2017, 7(1), 27; doi:10.3390/biom7010027

Received: 1 February 2017 / Revised: 3 March 2017 / Accepted: 6 March 2017 / Published: 11 March 2017

PDF Full-text (2508 KB) | HTML Full-text | XML Full-text

Abstract

Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s²U)

[...] Read more.

Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s²U) derivatives, 4-thiouridine (s⁴U), 2-thiocytidine (s²C), and 2-methylthioadenosine (ms²A). Their biosynthetic pathways have two major types depending on the requirement of iron–sulfur (Fe–S) clusters. In all cases, the first step in bacteria and eukaryotes is to activate the sulfur atom of free l-cysteine by cysteine desulfurases, generating a persulfide (R-S-SH) group. In some archaea, a cysteine desulfurase is missing. The following steps of the bacterial s²U and s⁴U formation are Fe–S cluster independent, and the activated sulfur is transferred by persulfide-carrier proteins. By contrast, the biosynthesis of bacterial s²C and ms²A require Fe–S cluster dependent enzymes. A recent study shows that the archaeal s⁴U synthetase (ThiI) and the eukaryotic cytosolic 2-thiouridine synthetase (Ncs6) are Fe–S enzymes; this expands the role of Fe–S enzymes in tRNA thiolation to the Archaea and Eukarya domains. The detailed reaction mechanisms of Fe–S cluster depend s²U and s⁴U formation await further investigations. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use

by Richard J. Maraia and Aneeshkumar G. Arimbasseri

Biomolecules 2017, 7(1), 26; doi:10.3390/biom7010026

Received: 9 January 2017 / Accepted: 24 February 2017 / Published: 8 March 2017

PDF Full-text (2327 KB) | HTML Full-text | XML Full-text

Abstract

Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity

[...] Read more.

Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias. Here, we review convergent evidence that suggest that expansion of the eukaryotic tRNAome was supported by its dedicated RNA polymerase III transcription system and coupling to the precursor‐tRNA chaperone, La protein. We also review aspects of eukaryotic tRNAome evolution involving G34/A34 anticodon‐sparing, relation to A34 modification to inosine, biased codon use and regulatory information in the redundancy (synonymous) component of the genetic code. We then review interdependent anticodon loop modifications involving position 37 in eukaryotes. This includes the eukaryote‐specific tRNA modification, 3‐methylcytidine‐32 (m3C32) and the responsible gene, TRM140 and homologs which were duplicated and subspecialized for isoacceptor‐specific substrates and dependence on i6A37 or t6A37. The genetics of tRNA function is relevant to health directly and as disease modifiers. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5‐Formylcytosine Modification in Mitochondrial tRNA^Met

by Lindsey Van Haute, Christopher A. Powell and Michal Minczuk

Biomolecules 2017, 7(1), 24; doi:10.3390/biom7010024

Received: 13 January 2017 / Accepted: 24 February 2017 / Published: 2 March 2017

PDF Full-text (4287 KB) | HTML Full-text | XML Full-text

Abstract

Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt‐tRNAMet) also recognises AUA during translation initiation and elongation. Post‐transcriptional modifications of tRNAs are important for structure, stability,

[...] Read more.

Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt‐tRNAMet) also recognises AUA during translation initiation and elongation. Post‐transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5‐formylcytosine (f5C) modification of position 34 in mt‐tRNAMet has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation. However, the enzymes responsible for the formation of mitochondrial f5C have been identified only recently. The first step of the f5C pathway consists of methylation of cytosine by NSUN3. This is followed by further oxidation by ABH1. Here, we review the role of f5C, the latest breakthroughs in our understanding of the biogenesis of this unique mitochondrial tRNA modification and its involvement in human disease. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Transfer RNA methyltransferases with a SpoU‐TrmD (SPOUT) fold and their modified nucleosides in tRNA

by Hiroyuki Hori

Biomolecules 2017, 7(1), 23; doi:10.3390/biom7010023

Received: 7 January 2017 / Accepted: 23 February 2017 / Published: 28 February 2017

PDF Full-text (1714 KB) | HTML Full-text | XML Full-text | Supplementary Files

Abstract

The existence of SpoU‐TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2’‐Omethylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N1‐methylguanosine at position 37 in tRNA. Although SpoU

[...] Read more.

The existence of SpoU‐TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2’‐Omethylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N1‐methylguanosine at position 37 in tRNA. Although SpoU (TrmH) and TrmD were originally considered to be unrelated, the bioinformatics study suggested that they might share a common evolution origin and form a single superfamily. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil knot in the catalytic domain. In the past decade, the SPOUT RNA methyltransferase superfamily has grown; furthermore, knowledge concerning the functions of their modified nucleosides in tRNA has also increased. Some enzymes are potential targets in the design of antibacterial drugs. In humans, defects in some genes may be related to carcinogenesis. In this review, recent findings on the tRNA methyltransferases with a SPOUT fold and their methylated nucleosides in tRNA, including classification of tRNA methyltransferases with a SPOUT fold; knot structures, domain arrangements, subunit structures and reaction mechanisms; tRNA recognition mechanisms, and functions of modified nucleosides synthesized by this superfamily, are summarized. Lastly, the future perspective for studies on tRNA modification enzymes are considered. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Mapping Post‐Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry

by Robert L. Ross, Xiaoyu Cao and Patrick A. Limbach

Biomolecules 2017, 7(1), 21; doi:10.3390/biom7010021

Received: 30 December 2016 / Accepted: 15 February 2017 / Published: 22 February 2017

PDF Full-text (1644 KB) | HTML Full-text | XML Full-text

Abstract

Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post‐transcriptionally modified transfer ribonucleic acids (tRNAs). Given that the information collected using this platform is entirely determined by the mass of the analyte, it

[...] Read more.

Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post‐transcriptionally modified transfer ribonucleic acids (tRNAs). Given that the information collected using this platform is entirely determined by the mass of the analyte, it has proven to be the gold standard for accurately assigning nucleobases to the sequence. For the past few decades many labs have worked to improve the analysis, contiguous to instrumentation manufacturers developing faster and more sensitive instruments. With biological discoveries relating to ribonucleic acid happening more frequently, mass spectrometry has been invaluable in helping to understand what is happening at the molecular level. Here we present a brief overview of the methods that have been developed and refined for the analysis of modified tRNAs by liquid chromatography tandem mass spectrometry. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview m1A Post‐Transcriptional Modification in tRNAs

by Stephanie Oerum, Clément Dégut, Pierre Barraud and Carine Tisné

Biomolecules 2017, 7(1), 20; doi:10.3390/biom7010020

Received: 16 January 2017 / Accepted: 16 February 2017 / Published: 21 February 2017

Cited by 1 | PDF Full-text (3014 KB) | HTML Full-text | XML Full-text

Abstract

To date, about 90 post‐transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post‐transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on

[...] Read more.

To date, about 90 post‐transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post‐transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2′-OH. The methylation on the N1 atom of adenosine to form 1‐methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs. In some cases, these modifications have been shown to increase tRNA structural stability and induce correct tRNA folding. This review provides an overview of the currently known m1A modifications, the different m1A modification sites, the biological role of each modification, and the enzyme responsible for each methylation in different species. The review further describes, in detail, two enzyme families responsible for formation of m1A at nucleotide position 9 and 58 in tRNA with a focus on the tRNA binding, m1A mechanism, protein domain organisation and overall structures. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Sulfur Modifications of the Wobble U₃₄ in tRNAs and their Intracellular Localization in Eukaryotic Cells

by Yumi Nakai, Masato Nakai and Takato Yano

Biomolecules 2017, 7(1), 17; doi:10.3390/biom7010017

Received: 13 January 2017 / Revised: 8 February 2017 / Accepted: 8 February 2017 / Published: 18 February 2017

PDF Full-text (2716 KB) | HTML Full-text | XML Full-text

Abstract

The wobble uridine (U₃₄) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNA^Lys_UUU, tRNA^Glu_UUC, and tRNA^Gln_UUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of

[...] Read more.

The wobble uridine (U₃₄) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNA^Lys_UUU, tRNA^Glu_UUC, and tRNA^Gln_UUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U₃₄, respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U₃₄ (s²U₃₄) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations. The s²U₃₄ formation in cy-tRNAs involves a sulfur delivery system required for the biosynthesis of iron-sulfur (Fe/S) clusters and certain resultant Fe/S proteins. This review addresses presumed sulfur delivery pathways for the s²U₃₄ formation in distinct intracellular locations, especially that for cy-tRNAs in comparison with that for mt-tRNAs. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification

by Ann E. Ehrenhofer-Murray

Biomolecules 2017, 7(1), 14; doi:10.3390/biom7010014

Received: 19 December 2016 / Revised: 2 February 2017 / Accepted: 2 February 2017 / Published: 10 February 2017

PDF Full-text (1081 KB) | HTML Full-text | XML Full-text

Abstract

Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5

[...] Read more.

Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5’-triphosphate (GTP) by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus

by Gabrielle Bourgeois, Juliette Létoquart, Nhan van Tran and Marc Graille

Biomolecules 2017, 7(1), 7; doi:10.3390/biom7010007

Received: 13 December 2016 / Revised: 16 January 2017 / Accepted: 18 January 2017 / Published: 27 January 2017

PDF Full-text (5048 KB) | HTML Full-text | XML Full-text

Abstract

Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on

[...] Read more.

Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation. The Trm112-Trm9 and Trm112-Trm11 complexes modify tRNAs, while the Trm112-Mtq2 complex targets translation termination factor eRF1, which is a tRNA mimic. The last complex formed between Trm112 and Bud23 proteins modifies 18S rRNA and participates in the 40S biogenesis pathway. In this review, we present the functions of these eukaryotic Trm112-MTase complexes, the molecular bases responsible for complex formation and substrate recognition, as well as their implications in human diseases. Moreover, as Trm112 orthologs are found in bacterial and archaeal genomes, the conservation of this Trm112 network beyond eukaryotic organisms is also discussed. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Critical Minireview: The Fate of tRNA^Cys during Oxidative Stress in Bacillus subtilis

by Juan Campos Guillen, George H. Jones, Carlos Saldaña Gutiérrez, José Luis Hernández-Flores, Julio Alfonso Cruz Medina, José Humberto Valenzuela Soto, Sergio Pacheco Hernández, Sergio Romero Gómez and Verónica Morales Tlalpan

Biomolecules 2017, 7(1), 6; doi:10.3390/biom7010006

Received: 14 November 2016 / Revised: 12 January 2017 / Accepted: 13 January 2017 / Published: 20 January 2017

PDF Full-text (981 KB) | HTML Full-text | XML Full-text

Abstract

Oxidative stress occurs when cells are exposed to elevated levels of reactive oxygen species that can damage biological molecules. One bacterial response to oxidative stress involves disulfide bond formation either between protein thiols or between protein thiols and low-molecular-weight (LMW) thiols. Bacillithiol was

[...] Read more.

Oxidative stress occurs when cells are exposed to elevated levels of reactive oxygen species that can damage biological molecules. One bacterial response to oxidative stress involves disulfide bond formation either between protein thiols or between protein thiols and low-molecular-weight (LMW) thiols. Bacillithiol was recently identified as a major low-molecular-weight thiol in Bacillus subtilis and related Firmicutes. Four genes (bshA, bshB1, bshB2, and bshC) are involved in bacillithiol biosynthesis. The bshA and bshB1 genes are part of a seven-gene operon (ypjD), which includes the essential gene cca, encoding CCA-tRNA nucleotidyltransferase. The inclusion of cca in the operon containing bacillithiol biosynthetic genes suggests that the integrity of the 3′ terminus of tRNAs may also be important in oxidative stress. The addition of the 3′ terminal CCA sequence by CCA-tRNA nucleotidyltransferase to give rise to a mature tRNA and functional molecules ready for aminoacylation plays an essential role during translation and expression of the genetic code. Any defects in these processes, such as the accumulation of shorter and defective tRNAs under oxidative stress, might exert a deleterious effect on cells. This review summarizes the physiological link between tRNA^Cys regulation and oxidative stress in Bacillus. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Open AccessReview Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes

by Silke Leimkühler, Martin Bühning and Lena Beilschmidt

Biomolecules 2017, 7(1), 5; doi:10.3390/biom7010005

Received: 8 December 2016 / Revised: 4 January 2017 / Accepted: 9 January 2017 / Published: 14 January 2017

Cited by 1 | PDF Full-text (5985 KB) | HTML Full-text | XML Full-text

Abstract

Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the

[...] Read more.

Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm⁵s²U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT). Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco) and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes. Full article

(This article belongs to the Special Issue tRNA Modifications: Synthesis, Function and Beyond)

► Figures

Figure 1

Journal Menu

E-Mail Alert

Journal Browser

Special Issue "tRNA Modifications: Synthesis, Function and Beyond"

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (23 papers)

Research

Jump to: Review

Review

Jump to: Research

Journal Contact