The Archaeal sRNA Binding Protein L7Ae has a 3D Structure Very Similar to that of its Eukaryal Counterpart While Having a Broader RNA-binding Specificity

Charron, Christophe; Manival, Xavier; Cléry, Antoine; Senty-Ségault, Veronique; Charpentier, Bruno; Marmier‐Gourrier, Nathalie; Branlant, Christiane; Aubry, A.

doi:10.1016/j.jmb.2004.07.046

Cited by 50 publications

(64 citation statements)

References 47 publications

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“…This loop nucleotide also engages in hydrophobic interactions and backbone recognition. Chemical/enzymatic probing and gel-shift assays validate the importance of this U (30,35), because mutating it to C weakens RNA binding, a result easily rationalized by the absence of an O4 carbonyl in C. Collectively, this knowledge of the L7Ae-K-turn interface helped us to design Mma L7Ae and RPR mutants.…”

Section: Resultsmentioning

confidence: 82%

“…L7Ae and its homologs are part of a protein family associated with both archaeal and eukaryal RNPs and bind an RNA motif called the K-turn (22,23,(30)(31)(32)(33)(34)(35)(36)(37)(38). Although thematic variations exist, most K-turns contain two helical stems separated by an asym- Fig.…”

Section: Resultsmentioning

confidence: 99%

“…To better understand the structure-function relationships of L7Ae in Mma RNase P catalysis, we used as a framework the strikingly similar RNA-protein interface revealed by four different high-resolution structures of L7Ae and its homologs bound to their respective K-turn-containing cognate RNA ligands (e.g., C/D box snoRNA, U4 snRNA) (23,30,31,33). In all these cases, a highly conserved NExxK motif in L7Ae homologs permits exquisite structure-specific recognition of the NC stem through H-bonding interactions between the N, E, K side chains and the Gs in the two GA bps.…”

Section: Resultsmentioning

confidence: 99%

“…There has been a shift from L7Ae, which plays multiple roles in archaea, to diverse and distinctive eukaryal L7Ae homologs, each of which play specific biological roles as part of RNase P, snoRNPs, and snRNPs (34,36). The driving force for these changes might be the finer regulation and stringent recognition specificity demanded by the complexity of the eukaryotic cell (30,34,36).…”

Section: Discussionmentioning

confidence: 99%

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Ribosomal protein L7Ae is a subunit of archaeal RNase P

Cho

Lai

Susanti

et al. 2010

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

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To the mounting evidence of nonribosomal functions for ribosomal proteins, we now add L7Ae as a subunit of archaeal RNase P, a ribonucleoprotein (RNP) that catalyzes 5′-maturation of precursor tRNAs (pre-tRNAs). We first demonstrate that L7Ae coelutes with partially purified Methanococcus maripaludis (Mma) RNase P activity. After establishing in vitro reconstitution of the single RNA with four previously known protein subunits (POP5, RPP21, RPP29, and RPP30), we show that addition of L7Ae to this RNase P complex increases the optimal reaction temperature and k cat ∕K m (by ∼360-fold) for pre-tRNA cleavage to those observed with partially purified native Mma RNase P. We identify in the Mma RNase P RNA a putative kink-turn (K-turn), the structural motif recognized by L7Ae. The large stimulatory effect of Mma L7Ae on RNase P activity decreases to ≤4% of wild type upon mutating either the conserved nucleotides in this K-turn or amino acids in L7Ae shown to be essential for K-turn binding. The critical, multifunctional role of archaeal L7Ae in RNPs acting in tRNA processing (RNase P), RNA modification (H/ACA, C/D snoRNPs), and translation (ribosomes), especially by employing the same RNA-recognition surface, suggests coevolution of various translation-related functions, presumably to facilitate their coordinate regulation.pre-tRNA processing | RPP38 | protein-aided RNA catalysis R Nase P is a Mg 2þ -dependent endoribonuclease that is primarily responsible for catalyzing the removal of the 5′ leaders of precursor-tRNAs (pre-tRNAs) (1-3). Except for some unique organellar variants, RNase P functions in all three domains of life as a ribonucleoprotein (RNP) (1, 2). Although catalysis rests with the essential RNase P RNA (RPR) in all three domains of life (4-6), the RNase P protein (RPP) cofactors play essential roles. In the simple one RPR-one RPP bacterial RNase P, the RPP aids RPR catalysis by enhancing cleavage efficiency and affinity for substrate and Mg 2þ (7-9). The bacterial RPP has not been found in any archaeal or eukaryal genome (10). Eukaryal (nuclear) RNase P, which comprises an RPR and 9 or 10 RPPs (11, 12), has not been reconstituted from recombinant subunits, thus thwarting efforts to uncover the individual functions of eukaryal RPPs. Archaeal RNase P, with an RPR and four RPPs (all homologous to eukaryal RPPs), has therefore been explored as an experimental surrogate for its so-far-intractable eukaryal cousin (13-16). Although native archaeal RNase P has not been characterized, Western analysis and immunoprecipitation validated these four RPPs (POP5, RPP21, RPP29, and RPP30) as being associated with partially purified Methanothermobacter thermautotrophicus (Mth) RNase P activity (14). Subsequent structural and biochemical reconstitution studies using recombinant subunits have proven the utility of archaeal RNase P as a model system to dissect the role of multiple protein cofactors in facilitating RNA catalysis (16).Besides POP5, RPP21, RPP29, and RPP30, weak homologies are evident in the archaeal genomes...

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Section: Resultsmentioning

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Cho

Lai

Susanti

et al. 2010

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

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“…We have been able to thoroughly analyze the effects of RNA binding on the protein structure and compare it with the RNA-bound form (35), other homologues (26,30,36,46,47), and structurally related proteins (27,50,52).…”

Section: Resultsmentioning

confidence: 99%

The Crystal Structure of the Methanocaldococcus jannaschii Multifunctional L7Ae RNA-Binding Protein Reveals an Induced-Fit Interaction with the Box C/D RNAs^,

et al. 2005

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Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal, box H/ACA, and box C/D sRNAs. The crystal structure of Methanocaldococcus jannaschii L7Ae has been determined to 1.45 Å, and L7Ae's amino acid composition, evolutionary conservation, functional characteristics, and structural details have been analyzed. Comparison of the L7Ae structure to those of a number of related proteins with diverse functions has revealed significant structural homology which suggests that this protein fold is an ancient RNA-binding motif. Notably, the free M. jannaschii L7Ae structure is essentially identical to that with RNA bound, suggesting that RNA binding occurs through an induced-fit interaction. Circular dichroism experiments show that box C/D and C′/D′ RNA motifs undergo conformational changes when magnesium or the L7Ae protein is added, corroborating the induced-fit model for L7Ae-box C/D RNA interactions.The most prevalent nucleotide modifications of ribosomal RNA are the methylation of ribose 2′-hydroxyl moieties and the isomerization of uridines to pseudouridines. Although their biological significance is unclear, most of these modifications are relegated to distinct functional regions and thus suggest an important role in ribosome function (1-9). Failure to properly modify rRNA can impair the efficiency of protein synthesis (6, 7). In eukaryotic cells, the small nucleolar RNAs (snoRNAs) 1 guide the 2′-O-methylation of approximately 100 nucleotides and the pseudouridylation of a similar number of nucleotides (10). The mechanisms specifying the target sites for RNA modification are remarkably similar between Archaea and Eucarya (11-13). Comparable snoRNA-like RNAs (sRNA) also guide the 2′-Omethylation and pseudouridylation of RNA in Archaea. It appears that in both kingdoms strong evolutionary pressure has maintained the function of these guide RNAs, which likely have common and thus ancient origins prior to the divergence of eukaryotes and archaea, some 2 billion years ago (1,3,9,12,14).Modification of ribosomal and other RNAs is directed by small nucleolar ribonucleoprotein complexes (RNPs) that consist of a guide RNA bound by a set of RNP core proteins. The box C/D family of guide RNAs specifically targets 2′-O-methylation of both eukaryotic and archaeal RNAs (8,12,[15][16][17][18]. Box C/D RNAs possess C and D box sequences located near their 5′-and 3′-termini, respectively, and often contain sequence-related C′ and D′ boxes located internally (Figure 1) (16,(19)(20)(21)(22)(23). The C/D and C′/D′ boxes are short, conserved nucleotide sequences that fold to form specific core protein-recognition sites. Regions that guide methylation are positioned upstream of boxes D and D′ and are complementary to the target RNA(s) where modification occurs. The target nucleotide of the snoRNA-target duplex positioned five nucleotides upstream of box D or D′ is the substrate nucleotide for 2′-O-methylation (24, 25).The box C/D core motif is positioned at the ter...

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The Box C/D RNP S : Evolutionarily Ancient Nucleotide Modification Complexes

Gagnon

Zhang

Maxwell

2007

RNA and DNA Editing

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The Archaeal sRNA Binding Protein L7Ae has a 3D Structure Very Similar to that of its Eukaryal Counterpart While Having a Broader RNA-binding Specificity

Cited by 50 publications

References 47 publications

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Ribosomal protein L7Ae is a subunit of archaeal RNase P

The Crystal Structure of the Methanocaldococcus jannaschii Multifunctional L7Ae RNA-Binding Protein Reveals an Induced-Fit Interaction with the Box C/D RNAs^,

The Box C/D RNP S : Evolutionarily Ancient Nucleotide Modification Complexes

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The Archaeal sRNA Binding Protein L7Ae has a 3D Structure Very Similar to that of its Eukaryal Counterpart While Having a Broader RNA-binding Specificity

Cited by 50 publications

References 47 publications

Ribosomal protein L7Ae is a subunit of archaeal RNase P

Ribosomal protein L7Ae is a subunit of archaeal RNase P

The Crystal Structure of the Methanocaldococcus jannaschii Multifunctional L7Ae RNA-Binding Protein Reveals an Induced-Fit Interaction with the Box C/D RNAs,

The Box C/D RNP S : Evolutionarily Ancient Nucleotide Modification Complexes

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The Crystal Structure of the Methanocaldococcus jannaschii Multifunctional L7Ae RNA-Binding Protein Reveals an Induced-Fit Interaction with the Box C/D RNAs^,