A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation

Desai, Kevin K.; Cheng, Chin L.; Bingman, C.A.; Phillips, George N.; Raines, Ronald T.

doi:10.1093/nar/gkt1375

Cited by 51 publications

(67 citation statements)

References 38 publications

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“…We had shown previously that RtcB and Archease from P. horikoshii can function in tandem to allow RNA ligation to proceed efficiently with ATP (Desai et al 2014). Yet, in assays with T. thermophilus RtcB and Archease, we were unable to observe RNA ligation using ATP as a cofactor (data not shown), suggesting that dual GTP/ATP cofactor usage by RtcB and Archease might be unique to archaea or perhaps exclusive to P. horikoshii.…”

Section: Resultsmentioning

confidence: 99%

“…Archease proteins across domains of life share low sequence identity; however, the two essential aspartates in the metalbinding site are strictly conserved (Desai et al 2014). To discern if Archease proteins are interchangeable, we determined if Archease from P. horikoshii can activate RtcB from T. thermophilus, despite the Archeases from these two organisms having only 36% sequence identity.…”

Section: Archease Proteins Are Interchangeablementioning

confidence: 99%

“…In many bacteria and archaea, the genes encoding RtcB and Archease are localized in an operon (Desai et al 2014). Archease is a cofactor of RtcB that accelerates RNA ligation and alters the NTP specificity of the Pyrococcus horikoshii enzyme such that ligation proceeds efficiently with both GTP and ATP (Desai et al 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Archease is a cofactor of RtcB that accelerates RNA ligation and alters the NTP specificity of the Pyrococcus horikoshii enzyme such that ligation proceeds efficiently with both GTP and ATP (Desai et al 2014). Like RtcB, Archease is critical for tRNA splicing and XBP1 splicing in metazoa Popow et al 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Archease is a small (∼16 kDa) protein with an anionic surface charge, suggesting that it might bind in the cationic RNA-binding cleft of RtcB. A crystal structure of Archease has revealed a metal-binding site, located on the exterior of the protein, which is essential for its activity (Desai et al 2014). RtcB and Archease are conserved across all three domains of life; though, Archease is not widely distributed in bacteria.…”

Section: Introductionmentioning

confidence: 99%

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Coevolution of RtcB and Archease created a multiple-turnover RNA ligase

Desai

Beltrame

Raines

2015

RNA

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RtcB is a noncanonical RNA ligase that joins either 2 ′ ,3 ′ -cyclic phosphate or 3 ′ -phosphate termini to 5 ′ -hydroxyl termini. The genes encoding RtcB and Archease constitute a tRNA splicing operon in many organisms. Archease is a cofactor of RtcB that accelerates RNA ligation and alters the NTP specificity of the ligase from Pyrococcus horikoshii. Yet, not all organisms that encode RtcB also encode Archease. Here we sought to understand the differences between Archease-dependent and Archease-independent RtcBs so as to illuminate the evolution of Archease and its function. We report on the Archeasedependent RtcB from Thermus thermophilus and the Archease-independent RtcB from Thermobifida fusca. We find that RtcB from T. thermophilus can catalyze multiple turnovers only in the presence of Archease. Remarkably, Archease from P. horikoshii can activate T. thermophilus RtcB, despite low sequence identity between the Archeases from these two organisms. In contrast, RtcB from T. fusca is a single-turnover enzyme that is unable to be converted into a multiple-turnover ligase by Archease from either P. horikoshii or T. thermophilus. Thus, our data indicate that Archease likely evolved to support multiple-turnover activity of RtcB and that coevolution of the two proteins is necessary for a functional interaction.

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Section: Resultsmentioning

confidence: 99%

Section: Archease Proteins Are Interchangeablementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Coevolution of RtcB and Archease created a multiple-turnover RNA ligase

Desai

Beltrame

Raines

2015

RNA

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The role of RNA modifications in the regulation of tRNA cleavage

2018

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Transfer RNA (tRNA) have been harbingers of many paradigms in RNA biology. They are among the first recognized noncoding RNA (ncRNA) playing fundamental roles in RNA metabolism. Although mainly recognized for their role in decoding mRNA and delivering amino acids to the growing polypeptide chain, tRNA also serve as an abundant source of small ncRNA named tRNA fragments. The functional significance of these fragments is only beginning to be uncovered. Early on, tRNA were recognized as heavily post-transcriptionally modified, which aids in proper folding and modulates the tRNA:mRNA anticodon-codon interactions. Emerging data suggest that these modifications play critical roles in the generation and activity of tRNA fragments. Modifications can both protect tRNA from cleavage or promote their cleavage. Modifications to individual fragments may be required for their activity. Recent work has shown that some modifications are critical for stem cell development and that failure to deposit certain modifications has profound effects on disease. This review will discuss how tRNA modifications regulate the generation and activity of tRNA fragments.

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Transfer RNA Synthesis and Regulation

Hori¹,

Hirata²,

Ueda³

et al. 2021

Encyclopedia of Life Sciences

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Transfer ribonucleic acid (tRNA), which is primarily transcribed from tRNA genes by RNA polymerase, matures via several steps: processing, splicing, CCA addition and posttranscriptional modifications. Primary transcripts of tRNA genes contain extra 5′ and 3′ sequences, which are removed by a set of nucleases. In addition, some primary transcripts contain introns, which are spliced out by specific endonucleases or in self‐splicing reactions. The ligation of exons generally requires a tRNA ligase. In some species, the CCA sequences present at the 3′‐termini of all mature tRNAs are not encoded in the tRNA genes but are added posttranscriptionally by a CCA‐adding enzyme. All mature tRNA molecules contain modified nucleotides, generated by specific tRNA modification enzymes or guide RNA systems. Recent studies have revealed that tRNA‐derived fragments act on biological phenomena such as regulation of translation. Furthermore, numerous tRNA‐like small RNAs have been found by genome sequencing. Key Concepts tRNA is transcribed from tRNA genes by RNA polymerase and matures through processing, splicing, CCA addition and posttranscriptional modification. Synthesis of tRNA is regulated by promoter activity and specific factors, depending on the nutrient conditions of the cell. The relative amounts of tRNA are regulated by several factors: copy number of tRNA genes, transcriptional activity and degradation by various nucleases. Primary transcripts of tRNA genes contain extra 5′ and 3′ sequences, which are removed by a set of nucleases. In some cases, tRNA transcripts contain introns, which are spliced out by specific endonuclease or the group I intron reaction. The two resultant fragments are joined by RNA ligase or the self‐splicing reaction. CCA‐adding enzyme regulates the amount of active tRNA by introducing the CCA sequence at the C ‐terminus of tRNA. tRNA possesses a variety of modified nucleotides, which are introduced by specific tRNA modification enzymes. Several modifications of tRNA play important roles in the translation process: promotion, expansion, restriction, and/or alteration of codon–anticodon interactions; stabilisation of tRNA structure; recognition by translation factors and aminoacyl‐tRNA synthetases; etc. Several modified nucleotides in tRNA are involved in RNA quality control systems, regulation of tRNA transport, infection and immune responses. Fragments derived from tRNA are not degradation products of tRNA but function as regulator molecules for translation and gene expression. In living cells, tRNA‐like small RNAs, which are often aminoacylated, have been found and may possess several physiological functions.

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A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation

Cited by 51 publications

References 38 publications

Coevolution of RtcB and Archease created a multiple-turnover RNA ligase

Coevolution of RtcB and Archease created a multiple-turnover RNA ligase

The role of RNA modifications in the regulation of tRNA cleavage

Transfer RNA Synthesis and Regulation

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