Properties of H. volcanii tRNA Intron Endonuclease Reveal a Relationship between the Archaeal and Eucaryal tRNA Intron Processing Systems

Kleman-Leyer, Karen; Armbruster, David W.; Daniels, Charles J.

doi:10.1016/s0092-8674(00)80269-x

Cited by 94 publications

(90 citation statements)

References 41 publications

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“…It is evident from this analysis and the published work of others that the known tRNA endonucleases of Archaea can take one of two forms: (i) a homotetramer in which two of the subunits play a structural role and two contain the catalytic sites or (ii) a homodimer, each of whose subunits, twice the length of the METJA class, contains a structural part and a catalytic part (7,8,18,19). The bioinformatic analysis suggests that the latter enzyme arose from a gene duplication͞fusion event, followed by a few mutations that allow for subfunctionalization of the two regions of the protein.…”

Section: Resultsmentioning

confidence: 84%

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Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization

Tocchini-Valentini

Fruscoloni

Tocchini‐Valentini

2005

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

104

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We have detected two paralogs of the tRNA endonuclease gene of Methanocaldococcus jannaschii in the genome of the crenarchaeote Sulfolobus solfataricus. This finding has led to the discovery of a previously unrecognized oligomeric form of the enzyme. The two genes code for two different subunits, both of which are required for cleavage of the pre-tRNA substrate. Thus, there are now three forms of tRNA endonuclease in the Archaea: a homotetramer in some Euryarchaea, a homodimer in other Euryarchaea, and a heterotetramer in the Crenarchaea and the Nanoarchaea. The last-named enzyme, arising most likely by gene duplication and subsequent ''subfunctionalization,'' requires the products of both genes to be active. molecular evolution ͉ RNA-protein interactions ͉ tRNA splicing G ene duplication is the primary source of new genes. The ''subfunctionalization'' hypothesis argues that duplicate genes experience degenerate mutations that divide the activity encoded by a single ancestral gene among its descendants (1). Here, we report a striking example of subfunctionalization.In Archaea, the tRNA endonuclease plays a key role in assuring the correct removal of the intron from pre-tRNAs and pre-rRNA (2-6), which constitute the core of the translation machinery. Crystal structures of the tRNA endonucleases from Methanocaldococcus jannaschii (METJA) and Archaeoglobus fulgidus (ARCFU), both belonging to the phylum Euryarchaeota, are available (7,8). These structures differ in a remarkable way. The structure of the homotetrameric endonuclease from METJA reveals two different functional roles for the monomeric units. The METJA endonuclease is organized as a dimer of dimers, with one subunit from each dimer participating in the catalytic cleavage reaction (the catalytic subunit) and the other (structural) subunit acting to place the two catalytic subunits correctly in space.The crystal structure of the ARCFU endonuclease, by contrast, shows it to be a homodimer. Each subunit contains two similar repeating domains that are homologous to the subunit structure of the homotetrameric enzyme from METJA; the C-terminal repeat (CR) is the active domain, and the N-terminal repeat (NR) acts to stabilize the dimer.The overall shape and size of the homodimeric ARCFU endonuclease resembles that of the homotetrameric METJA enzyme.Both METJA and ARCFU belong to the Euryarchaeota. Nothing is known about the tRNA endonuclease of Crenarchaeota, the other main family of Archaea. To determine the properties of a crenarchaeal endonuclease, we searched the genome sequence of Sulfolobus solfataricus (SULSO) for homologs of the METJA endonuclease and found two candidate sequences.Characterization of the two gene products reveals that both are required for tRNA endonuclease activity, each presumably functioning like one-half of the ARCFU enzyme. Detailed analysis of the amino acid sequences of the two proteins supports the idea that they evolved by the process called subfunctionalization (1, 9, 10). Materials and MethodsIdentification of the Homologs. Th...

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Section: Resultsmentioning

confidence: 84%

“…We reasoned that the second gene could code for a second subunit of the endonuclease. The METJA enzyme is a homotetramer, whereas the ARCFU enzyme is assembled as a homodimer with the monomeric unit resulting from duplication and fusion of a METJA-like monomer (18). We named the second SULSO protein ␤ SULSO.…”

Section: Resultsmentioning

confidence: 99%

Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization

Tocchini-Valentini

Fruscoloni

Tocchini‐Valentini

2005

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

104

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“…The yeast proteins of the heterotetramer are: Sen2, Sen34, Sen15, and Sen54 (Trotta et al 1997;Phizicky and Hopper 2010). Sen2 and Sen34 are conserved from Archaea to humans (Kleman-Leyer et al 1997;Trotta et al 1997;Paushkin et al 2004); however, the archaeal endonucleases are composed of a2 homodimers, a4 homotetramers, or (ab)2 heterodimers (reviewed in Abelson et al 1998). Sen15 and Sen54 are poorly conserved between yeast and vertebrate cells (Paushkin et al 2004) and are absent from the archaeal genomes.…”

Section: Removal Of 59 Leader and 39 Trailer Sequences From Pre-trnasmentioning

confidence: 99%

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

2013

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Transfer RNAs (tRNAs) are essential for protein synthesis. In eukaryotes, tRNA biosynthesis employs a specialized RNA polymerase that generates initial transcripts that must be subsequently altered via a multitude of post-transcriptional steps before the tRNAs beome mature molecules that function in protein synthesis. Genetic, genomic, biochemical, and cell biological approaches possible in the powerful Saccharomyces cerevisiae system have led to exciting advances in our understandings of tRNA post-transcriptional processing as well as to novel insights into tRNA turnover and tRNA subcellular dynamics. tRNA processing steps include removal of transcribed leader and trailer sequences, addition of CCA to the 39 mature sequence and, for tRNA His , addition of a 59 G. About 20% of yeast tRNAs are encoded by intron-containing genes. The three-step splicing process to remove the introns surprisingly occurs in the cytoplasm in yeast and each of the splicing enzymes appears to moonlight in functions in addition to tRNA splicing. There are 25 different nucleoside modifications that are added post-transcriptionally, creating tRNAs in which 15% of the residues are nucleosides other than A, G, U, or C. These modified nucleosides serve numerous important functions including tRNA discrimination, translation fidelity, and tRNA quality control. Mature tRNAs are very stable, but nevertheless yeast cells possess multiple pathways to degrade inappropriately processed or folded tRNAs. Mature tRNAs are also dynamic in cells, moving from the cytoplasm to the nucleus and back again to the cytoplasm; the mechanism and function of this retrograde process is poorly understood. Here, the state of knowledge for tRNA post-transcriptional processing, turnover, and subcellular dynamics is addressed, highlighting the questions that remain. TABLE OF CONTENTS Abstract 43Introduction 44

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“…These enzymes remove the intron by making two independent endonucleolytic cleavages. It is generally accepted that the archaeal enzymes act without any reference to the mature domain but instead recognize specific structures that define the intron-exon boundaries (6)(7)(8). By contrast, the eukaryal enzyme normally acts in a mature-domain-dependent mode (3,4).…”

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confidence: 99%

The dawn of dominance by the mature domain in tRNA splicing

Tocchini-Valentini

Fruscoloni

Tocchini‐Valentini

2007

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

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The relationship between enzyme architecture and substrate specificity among archaeal pre-tRNA splicing endonucleases has been investigated more deeply, by using biochemical assays and model building. The enzyme from Archeoglobus fulgidus (AF) is particularly interesting: it cleaves the bulge-helix-bulge target without requiring the mature tRNA domain, but, when the target is a bulge-helix-loop, the mature domain is required. A model of AF based on its electrostatic potential shows three polar patches interacting with the pre-tRNA substrate. A simple deletion mutant of the AF endonuclease lacking two of the three polar patches no longer cleaves the bulge-helix-loop substrate with or without the mature domain. This single deletion shows a possible path for the evolution of eukaryal splicing endonucleases from the archaeal enzyme. molecular evolution ͉ RNA-protein interactions ͉ tRNA endonucleases A ccuracy in tRNA splicing is essential for the formation of functional tRNAs and therefore for gene expression. In Bacteria, pre-tRNA introns are self-splicing group I introns, and the splicing mechanism is autocatalytic. In Eukarya, tRNA introns are small and invariably interrupt the anticodon loop one base 3Ј to the anticodon. In Archaea, the introns are also small and often reside in the same location as eukaryal tRNA introns, but not always (1, 2). In both Eukarya and Archaea, the specificity for recognition of the pre-tRNA resides in the endonucleases (3-5). These enzymes remove the intron by making two independent endonucleolytic cleavages. It is generally accepted that the archaeal enzymes act without any reference to the mature domain but instead recognize specific structures that define the intron-exon boundaries (6-8). By contrast, the eukaryal enzyme normally acts in a mature-domain-dependent mode (3, 4).The exact way in which the eukaryal endonucleases recognize the precursors has yet to be determined, but many RNA-protein interactions are presumably required. Previous studies have shown the role of the three-dimensional structure and of specific invariant bases of the mature domain in recognition and binding by the enzyme (3, 4). The importance of structural regularities in the precursors suggested an anchor-and-measure mechanism in which the endonuclease binds to one or more reference sites in the mature domain, which are common to all pre-tRNAs, and measures the distance to the equivalently positioned intron-exon junctions. This hypothesis was supported by experiments that involved the engineering of changes in the distance that separate the mature domain from the splice sites. These alterations changed the size of the intron in a predictable way: the insertion of 1 bp in the anticodon stem increased the size of the intron by two bases, one at each end, and the insertion of 2 bp in the anticodon stem increased the size of the intron by 4 nt (3, 4). These striking results, which had been observed in specific instances, were generalized and taken to mean that there are no important recognition elements at t...

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Properties of H. volcanii tRNA Intron Endonuclease Reveal a Relationship between the Archaeal and Eucaryal tRNA Intron Processing Systems

Cited by 94 publications

References 41 publications

Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization

Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

The dawn of dominance by the mature domain in tRNA splicing

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