Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity

Paukstelis, Paul J.; Lambowitz, Alan M.

doi:10.1073/pnas.0801722105

Cited by 26 publications

(76 citation statements)

References 30 publications

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“…These ribozymes have been well characterized in biochemical and structural studies; and although they do not require a protein cofactor for activity in vitro, they require RNA binding proteins to act as chaperones to correctly fold the RNA into the active intermediate structure in vivo. Different strategies have been used in different organisms, based on recruiting and adapting preexisting proteins, (for example tyrosyl-tRNA synthetase (30)(31)(32), cbp2 protein (33-35), Mrs1 protein (36), and other maturases in fungal mitochondria). None of these proteins is endowed with nuclease and ligase activity.…”

Section: Resultsmentioning

confidence: 99%

“…A typical example concerns enzymes responsible for modification of bases, as in the case of pre-tRNA Trp . The Neurospora crassa mitochondrial genome group I introns self-splice but the ribozyme structure needs to be stabilized by tyrosyl-tRNA synthetase to be efficient (30,31). The crystallographic structure of the enzyme complexed with its substrates demonstrates how the interaction with the intron motif takes place on the opposite face of the enzyme with respect to the tRNA recognition site (32) and how a new specific binding site has been selected through evolution.…”

Section: Resultsmentioning

confidence: 99%

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Evolution of introns in the archaeal world

Tocchini-Valentini

Fruscoloni

Tocchini‐Valentini

2011

Proc. Natl. Acad. Sci. U.S.A.

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The self-splicing group I introns are removed by an autocatalytic mechanism that involves a series of transesterification reactions. They require RNA binding proteins to act as chaperones to correctly fold the RNA into an active intermediate structure in vivo. Pre-tRNA introns in Bacteria and in higher eukaryote plastids are typical examples of self-splicing group I introns. By contrast, two striking features characterize RNA splicing in the archaeal world. First, self-splicing group I introns cannot be found, to this date, in that kingdom. Second, the RNA splicing scenario in Archaea is uniform: All introns, whether in pre-tRNA or elsewhere, are removed by tRNA splicing endonucleases. We suggest that in Archaea, the protein recruited for splicing is the preexisting tRNA splicing endonuclease and that this enzyme, together with the ligase, takes over the task of intron removal in a more efficient fashion than the ribozyme. The extinction of group I introns in Archaea would then be a consequence of recruitment of the tRNA splicing endonuclease. We deal here with comparative genome analysis, focusing specifically on the integration of introns into genes coding for 23S rRNA molecules, and how this newly acquired intron has to be removed to regenerate a functional RNA molecule. We show that all known oligomeric structures of the endonuclease can recognize and cleave a ribosomal intron, even when the endonuclease derives from a strain lacking rRNA introns. The persistance of group I introns in mitochondria and chloroplasts would be explained by the inaccessibility of these introns to the endonuclease. molecular evolution | RNA-protein interactions I n bacterial, bacteriophage, archaeal, eukaryotic, and organelle genomes, RNAs of very different function (tRNAs, rRNAs, and mRNAs) often contain introns. The correct removal of the introns has been shown to proceed by mechanisms that fall into four classes.1. Group I self-splicing introns are removed by an autocatalytic mechanism that involves a series of transesterification reactions involving an external guanosine-5′-triphosphate (GTP). For example, pre-tRNA introns in bacteria and in higher eukaryote plastids are self-splicing group I introns. They fold into ribozymally active tertiary structures and, in several cases, contain genes coding for maturase and reverse transcriptase (1, 2). 2. Group II self-splicing introns, and their sibling group III introns, are also autocatalytically removed, but the excision does not require free GTP, and the reaction involves the formation of an intermediate lariat (3). 3. Nuclear pre-mRNA introns in eukaryotes are removed by the spliceosome (4, 5), postulated to have evolved from the group II self-splicing introns on the basis of the formation of a lariat intermediate, and of the conserved similarities of the small nuclear ribonucleoproteins U6/U2 RNA moieties with domain V of group II ribozymes (6-11). 4. The pre-tRNA intron excision mechanism in Eukaryotes is shared with Archaea. In Eukarya, tRNA introns are small and they invariab...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Evolution of introns in the archaeal world

Tocchini-Valentini

Fruscoloni

Tocchini‐Valentini

2011

Proc. Natl. Acad. Sci. U.S.A.

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“…Among the best-studied examples of such gain-of-function are the mitochondrial tyrosyl-tRNA synthetases (mtTyrRS) of fungi belonging to the subphylum Pezizomycotina, which evolved to promote the splicing of mitochondrial (mt) group I introns (4). Group I introns are ribozymes that catalyze their own splicing via guanosine-initiated transesterification reactions (5).…”

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confidence: 99%

“…Although some self-splice in vitro, most have acquired mutations that impair self-splicing and have thus become dependent upon intron-encoded or cellular proteins to promote formation of the catalytically active ribozyme structure (6). The Pezizomycotina mtTyrRS 2 evolved to function in splicing via a series structural adaptations, which occurred during or after the divergence of Pezizomycotina from Saccharomycotina and resulted in a new group I intron binding surface distinct from that which binds tRNA Tyr (4,7). These structural adaptations included acquisition of a longer N-terminal extension and several small insertions (insertions (Ins) [1][2][3][4][5] resulting from the expansion of flexible terminal or loop regions (4).…”

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confidence: 99%

Structural Divergence of the Group I Intron Binding Surface in Fungal Mitochondrial Tyrosyl-tRNA Synthetases That Function in RNA Splicing

Lamech

Saoji

Paukstelis

et al. 2016

Journal of Biological Chemistry

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The mitochondrial tyrosyl-tRNA synthetases (mtTyrRSs) of Pezizomycotina fungi, a subphylum that includes many pathogenic species, are bifunctional proteins that both charge mitochondrial tRNA Tyr and act as splicing cofactors for autocatalytic group I introns. Previous studies showed that one of these proteins, Neurospora crassa CYT-18, binds group I introns by using both its N-terminal catalytic and C-terminal anticodon binding domains and that the catalytic domain uses a newly evolved group I intron binding surface that includes an N-terminal extension and two small insertions (insertions 1 and 2) with distinctive features not found in non-splicing mtTyrRSs. To explore how this RNA binding surface diverged to accommodate different group I introns in other Pezizomycotina fungi, we determined x-ray crystal structures of C-terminally truncated Aspergillus nidulans and Coccidioides posadasii mtTyrRSs. Comparisons with previous N. crassa CYT-18 structures and a structural model of the Aspergillus fumigatus mtTyrRS showed that the overall topology of the group I intron binding surface is conserved but with variations in key intron binding regions, particularly the Pezizomycotina-specific insertions. These insertions, which arose by expansion of flexible termini or internal loops, show greater variation in structure and amino acids potentially involved in group I intron binding than do neighboring protein core regions, which also function in intron binding but may be more constrained to preserve mtTyrRS activity. Our results suggest a structural basis for the intron specificity of different Pezizomycotina mtTyrRSs, highlight flexible terminal and loop regions as major sites for enzyme diversification, and identify targets for therapeutic intervention by disrupting an essential RNA-protein interaction in pathogenic fungi.Aminoacyl-tRNA synthetases are a class of ancient, essential enzymes that catalyze the ligation of amino acids onto cognate tRNAs. In addition to this essential role, many aminoacyl-tRNA synthetases have evolved secondary functions, frequently by the acquisition of new domains or sequence expansions (1-3).Among the best-studied examples of such gain-of-function are the mitochondrial tyrosyl-tRNA synthetases (mtTyrRS) of fungi belonging to the subphylum Pezizomycotina, which evolved to promote the splicing of mitochondrial (mt) group I introns (4). Group I introns are ribozymes that catalyze their own splicing via guanosine-initiated transesterification reactions (5). Although some self-splice in vitro, most have acquired mutations that impair self-splicing and have thus become dependent upon intron-encoded or cellular proteins to promote formation of the catalytically active ribozyme structure (6). The Pezizomycotina mtTyrRS 2 evolved to function in splicing via a series structural adaptations, which occurred during or after the divergence of Pezizomycotina from Saccharomycotina and resulted in a new group I intron binding surface distinct from that which binds tRNA Tyr (4, 7). These structural adapta...

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“…This includes aiding splicing of group I introns in the mitochondria, which is essential to certain lower eukaryotes. Two fungal mitochondrial aminoacyl tRNA-synthetases, leucyl-tRNA synthetase (LeuRS or NAM2p) (4 -6) and tyrosyl-tRNA synthetase (TyrRS or CYT-18p) (7,8), are required protein splicing factors to facilitate splicing of group I introns in Saccharomyces cerevisiae and Neurospora crassa, respectively (2).…”

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confidence: 99%