Mechanism, Specificity and General Properties of the Yeast Enzyme Catalysing the Formation of Inosine 34 in the Anticodon of Transfer RNA

Auxilien, Sylvie; Crain, Pamela F.; Trewyn, Ronald W.; Grosjean, Henri

doi:10.1006/jmbi.1996.0527

Cited by 103 publications

(135 citation statements)

References 71 publications

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“…This domain is formed by a string of positively charged amino acids (arginines and lysines) we termed the KR-domain. Due to its overall charge, one could envision possible interactions between the KRdomain and the phosphate backbone of the tRNA, as suggested by Grosjean and coworkers for the yeast enzyme (Auxilien et al 1996). Notably, binding of TbADAT2 alone to either the A 34 -or G 34 -containing tRNA is poor (>3.0mM) (data not shown), despite still harboring a KR-domain, indicating that the KR-domain is necessary but not sufficient to provide functional binding.…”

Section: Discussionmentioning

confidence: 83%

“…Partly due to earlier reports by Grosjean and coworkers on the requirement of a full-length tRNA for activity (Auxilien et al 1996), our group has speculated on the basis for substrate binding by the eukaryal deaminases (Rubio and Alfonzo 2005). Most recently, Huang and coworkers suggested that eukaryotic deaminases have evolved the ability to utilize many different substrates by acquiring RNA binding motifs that are distinct from active site residues (Elias and Huang 2005).…”

Section: Resultsmentioning

confidence: 99%

“…The essential A to I tRNA editing event in bacteria is orchestrated by a homodimeric adenosine deaminase acting on tRNA (ADATa) or an ADAT2/ADAT3 heterodimer in eukarya (Auxilien et al 1996;Gerber and Keller 1999;Wolf et al 2002). While the subunit composition varies between domains of life, the catalytic cores of these enzymes are highly conserved (Gerber and Keller 1999;Wolf et al 2002).…”

Section: Introductionmentioning

confidence: 99%

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The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

Ragone

Spears²,

Wohlgamuth-Benedum³

et al. 2011

RNA

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Adenosine to inosine editing at the wobble position allows decoding of multiple codons by a single tRNA. This reaction is catalyzed by adenosine deaminases acting on tRNA (ADATs) and is essential for viability. In bacteria, the anticodon-specific enzyme is a homodimer that recognizes a single tRNA substrate (tRNA Arg ACG ) and can efficiently deaminate short anticodon stem-loop mimics of this tRNA in vitro. The eukaryal enzyme is composed of two nonidentical subunits, ADAT2 and ADAT3, which upon heterodimerization, recognize seven to eight different tRNAs as substrates, depending on the organism, and require a full-length tRNA for activity. Although crystallographic data have provided clues to why the bacterial deaminase can utilize short substrates, residues that provide substrate binding and recognition with the eukaryotic enzymes are not currently known. In the present study, we have used a combination of mutagenesis, binding studies, and kinetic analysis to explore the contribution of individual residues in Trypanosoma brucei ADAT2 (TbADAT2) to tRNA recognition. We show that deletion of the last 10 amino acids at the C terminus of TbADAT2 abolishes tRNA binding. In addition, single alanine replacements of a string of positively charged amino acids (KRKRK) lead to binding defects that correlate with losses in enzyme activity. This region, which we have termed the KR-domain, provides a first glance at key residues involved in tRNA binding by eukaryotic tRNA editing deaminases.

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Section: Discussionmentioning

confidence: 83%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

Ragone

Spears²,

Wohlgamuth-Benedum³

et al. 2011

RNA

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show abstract

“…The first class includes enzymes that require only the presence of the correct nucleotide at the position to be modified, such as the tRNA adenosine deaminase (Tad2/Tad3 in yeast) that catalyzes I 34 formation (Gerber and Keller 1999). The adenosine deaminase modifies all A 34 -containing tRNAs in the cell (8/8 sequenced tRNAs in yeast), and identity of the tRNA plays a minor role in substrate selection (Auxilien et al 1996). The second class includes enzymes for which the presence of the correct nucleotide alone is not sufficient to specify modification and therefore whose substrate specificity must be determined by additional parameters.…”

Section: Introductionmentioning

confidence: 99%

Unexpected expansion of tRNA substrate recognition by the yeast m¹G₉methyltransferase Trm10

Swinehart

Henderson

Jackman

2013

RNA

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N-1 Methylation of the nearly invariant purine residue found at position 9 of tRNA is a nucleotide modification found in multiple tRNA species throughout Eukarya and Archaea. First discovered in Saccharomyces cerevisiae, the tRNA methyltransferase Trm10 is a highly conserved protein both necessary and sufficient to catalyze all known instances of m 1 G 9 modification in yeast. Although there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m 1 G 9 in wild-type cells. The elements that allow Trm10 to distinguish between structurally similar tRNA species are not known, and sequences that are shared between all substrate or all nonsubstrate tRNAs have not been identified. Here, we demonstrate that the in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m 1 G 9 methyltransferase activity. Similarly, overexpression of Trm10 in yeast yields m 1 G 9 containing tRNA species that are ordinarily unmodified in vivo. Thus, yeast Trm10 has a significantly broader tRNA substrate specificity than is suggested by the observed pattern of modification in wildtype yeast. These results may shed light onto the suggested involvement of Trm10 in other pathways in other organisms, particularly in higher eukaryotes that contain up to three different genes with sequence similarity to the single TRM10 gene in yeast, and where these other enzymes have been implicated in pathways beyond tRNA processing.

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“…The deamination reaction is catalyzed by two different kinds of enzymes: adenosine deaminases that act on RNA (ADAR) and adenosine deaminases that act on tRNA (ADAT). ADAR specifically acts on dsRNAs [26][27][28][29][30][31], while ADAT is a tRNA-specific adenosine deaminase [32][33][34][35][36].…”

Section: A-to-i Rna Editor Genes: Adar and Adatmentioning

confidence: 99%

ADAR-mediated RNA editing in non-coding RNA sequences

Yang

Zhou

Jin

2013

Sci. China Life Sci.

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Adenosine to inosine (A-to-I) RNA editing is the most abundant editing event in animals. It converts adenosine to inosine in double-stranded RNA regions through the action of the adenosine deaminase acting on RNA (ADAR) proteins. Editing of pre-mRNA coding regions can alter the protein codon and increase functional diversity. However, most of the A-to-I editing sites occur in the non-coding regions of pre-mRNA or mRNA and non-coding RNAs. Untranslated regions (UTRs) and introns are located in pre-mRNA non-coding regions, thus A-to-I editing can influence gene expression by nuclear retention, degradation, alternative splicing, and translation regulation. Non-coding RNAs such as microRNA (miRNA), small interfering RNA (siRNA) and long non-coding RNA (lncRNA) are related to pre-mRNA splicing, translation, and gene regulation. A-to-I editing could therefore affect the stability, biogenesis, and target recognition of non-coding RNAs. Finally, it may influence the function of non-coding RNAs, resulting in regulation of gene expression. This review focuses on the function of ADAR-mediated RNA editing on mRNA non-coding regions (UTRs and introns) and non-coding RNAs (miRNA, siRNA, and lncRNA).

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Mechanism, Specificity and General Properties of the Yeast Enzyme Catalysing the Formation of Inosine 34 in the Anticodon of Transfer RNA

Cited by 103 publications

References 71 publications

The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

Unexpected expansion of tRNA substrate recognition by the yeast m¹G₉methyltransferase Trm10

ADAR-mediated RNA editing in non-coding RNA sequences

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Mechanism, Specificity and General Properties of the Yeast Enzyme Catalysing the Formation of Inosine 34 in the Anticodon of Transfer RNA

Cited by 103 publications

References 71 publications

The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

Unexpected expansion of tRNA substrate recognition by the yeast m1G9methyltransferase Trm10

ADAR-mediated RNA editing in non-coding RNA sequences

Contact Info

Product

Resources

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Unexpected expansion of tRNA substrate recognition by the yeast m¹G₉methyltransferase Trm10