Transfer RNA processing in archaea: Unusual pathways and enzymes

Heinemann, Ilka U.; Söll, Dieter; Randau, Lennart

doi:10.1016/j.febslet.2009.10.067

Cited by 32 publications

(27 citation statements)

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“…On the other hand, the eukaryotic intron does not have such a motif and is thought to be recognized by splicing machinery through the ''ruler mechanism'' to measure the distance between the cleavage sites and the body of mature tRNA (Abelson et al 1998). Recently, noncanonical introns that interrupt other parts of tRNAs were discovered in various archaea and certain eukaryotes (for review, see Heinemann et al 2010). In extreme cases, three introns are inserted in a tRNAPro UGG gene of Pyrobaculum islandicum, and split tRNA transcripts are joined to form a mature tRNA by a splicinglike mechanism through base-pairing between their appended segments (Sugahara et al 2007;Fujishima et al 2009).…”

Section: Introductionmentioning

confidence: 99%

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The intron of tRNA-Trp_CCA is dispensable for growth and translation of Saccharomyces cerevisiae

Mori¹,

Kajita²,

Endo³

et al. 2011

RNA

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A part of eukaryotic tRNA genes harbor an intron at one nucleotide 39 to the anticodon, so that removal of the intron is an essential processing step for tRNA maturation. While some tRNA introns have important roles in modification of certain nucleotides, essentiality of the tRNA intron in eukaryotes has not been tested extensively. This is partly because most of the eukaryotic genomes have multiple genes encoding an isoacceptor tRNA. Here, we examined whether the intron of tRNA-Trp CCA genes, six copies of which are scattered on the genome of yeast, Saccharomyces cerevisiae, is essential for growth or translation of the yeast in vivo. We devised a procedure to remove all of the tRNA introns from the yeast genome iteratively with marker cassettes containing both positive and negative markers. Using this procedure, we removed all the introns from the six tRNATrp CCA genes, and found that the intronless strain grew normally and expressed tRNA-Trp CCA in an amount similar to that of the wild-type genes. Neither incorporation of 35 S-labeled amino acids into a TCA-insoluble fraction nor the major protein pattern on SDS-PAGE/2D gel were affected by complete removal of the intron, while expression levels of some proteins were marginally affected. Therefore, the tRNA-Trp CCA intron is dispensable for growth and bulk translation of the yeast. This raises the possibility that some mechanism other than selective pressure from translational efficiency maintains the tRNA intron on the yeast genome.

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Section: Introductionmentioning

confidence: 99%

“…Some tRNAs are encoded by genes with an intron. The canonical tRNA intron, in eukaryotes and archaea, is located at one nucleotide 39 to the anticodon (Abelson et al 1998;Heinemann et al 2010). In archaeal tRNA genes, typical splice sites consist of the bulge-helix-bulge motif that is formed between the anticodon loop and intron.…”

Section: Introductionmentioning

confidence: 99%

The intron of tRNA-Trp_CCA is dispensable for growth and translation of Saccharomyces cerevisiae

Mori¹,

Kajita²,

Endo³

et al. 2011

RNA

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“…Removal of introns from pre‐tRNAs in eukaryotes and Archaea is a protein catalyzed process whereas in bacteria and organelles intron removal proceeds via a group I self‐splicing reaction (Review: [30] and references therein). Pre‐tRNA splicing has been thoroughly characterized in budding yeast where it has been shown to be a three‐step process.…”

Section: Pre‐trna Splicing – Different Subcellular Organization Amongmentioning

confidence: 99%

Cellular dynamics of tRNAs and their genes

2009

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Edited by Manuel SantosKeywords: tRNA transcription tRNA processing tRNA modification Nucleolus tRNA nuclear export tRNA retrograde movement tRNA turnover a b s t r a c t This discussion focuses on the cellular dynamics of tRNA transcription, processing, and turnover. Early tRNA biosynthesis steps are shared among most tRNAs, while later ones are often individualized for specific tRNAs. In yeast, tRNA transcription and early processing occur coordinately in the nucleolus, requiring topological arrangement of 300 tRNA genes and early processing enzymes to this site; later processing events occur in the nucleoplasm or cytoplasm. tRNA nuclear export requires multiple exporters which function in parallel and the export process is coupled with other cellular events. Nuclear-cytoplasmic tRNA subcellular movement is not unidirectional as a retrograde pathway delivers mature cytoplasmic tRNAs to the nucleus. Despite the long half-lives, there are multiple pathways to turnover damaged tRNAs or normal tRNAs upon cellular stress.

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“…Mechanistically, it is closely related to tRNA splicing in Eukarya. A specific endonuclease recognizes and cleaves the so-called bulge-helix-bulge (BHB) structure, Figure 1; a specific ligase then joins the exons and circularizes the intron [12][13][14][15]. The prime example of BHB splicing is the removal of tRNA introns.…”

Section: Introductionmentioning

confidence: 99%

Processed Small RNAs in Archaea and BHB Elements

Berkemer

Siederdissen

Amman

et al. 2015

Genomics Comput Biol

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Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piecewise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.

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Transfer RNA processing in archaea: Unusual pathways and enzymes

Cited by 32 publications

References 50 publications

The intron of tRNA-Trp_CCA is dispensable for growth and translation of Saccharomyces cerevisiae

The intron of tRNA-Trp_CCA is dispensable for growth and translation of Saccharomyces cerevisiae

Cellular dynamics of tRNAs and their genes

Processed Small RNAs in Archaea and BHB Elements

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Transfer RNA processing in archaea: Unusual pathways and enzymes

Cited by 32 publications

References 50 publications

The intron of tRNA-TrpCCA is dispensable for growth and translation of Saccharomyces cerevisiae

The intron of tRNA-TrpCCA is dispensable for growth and translation of Saccharomyces cerevisiae

Cellular dynamics of tRNAs and their genes

Processed Small RNAs in Archaea and BHB Elements

Contact Info

Product

Resources

About

The intron of tRNA-Trp_CCA is dispensable for growth and translation of Saccharomyces cerevisiae

The intron of tRNA-Trp_CCA is dispensable for growth and translation of Saccharomyces cerevisiae