Article

A cytidine deaminase edits C to U in transfer RNAs in Archaea

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Science (Impact Factor: 31.48). 06/2009; 324(5927):657-9. DOI: 10.1126/science.1170123
Source: PubMed

ABSTRACT All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the "cytidine deaminase-like" superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.

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    • "A large number of orphan genes were identified in the M. kandleri genome, which revealed several unusual enzymes including the topoisomerase V and a two-subunit reverse gyrase (6,7). One orphan gene encodes a unique cytidine deaminase that acts on transfer RNA (tRNA) base 8 (CDAT8) (8). All organisms from all three domains of life contain tRNA genes with a conserved T residue at position 8 and the folding of tRNA molecules involves tertiary interactions between U8 and the equally conserved base A14. "
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    ABSTRACT: The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution.
    Nucleic Acids Research 04/2013; 41(12). DOI:10.1093/nar/gkt317 · 9.11 Impact Factor
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    • "The COG0116 family members Smu472 and YcbY-N possess N-terminal THUMP and FLD domains that are probably the RNA-binding modules. Similar domain arrangement are seen in a thiouridine synthase (PDB ID 2C5S) (52) and a cytidine deaminase (PDB ID 3G8Q) (53), both of which are RNA modification enzymes. The THUMP and FLD domains of YcbY form a continuous channel of β-sheet that might direct the RNA substrate into the catalytic site (Supplementary Figure S7), and these features are conserved on the surfaces of Smu472 and YcbY-N (Supplementary Figure S8). "
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    ABSTRACT: The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.
    Nucleic Acids Research 02/2012; 40(11):5138-48. DOI:10.1093/nar/gks160 · 9.11 Impact Factor
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    • "RlmL has a THUMP domain (55) in its N-terminal region. The THUMP domain is frequently found in various tRNA-modifying enzymes including ThiI (56), CDAT8 (57), Tan1p (58), Pus10 (59) and PAB1281 (60). The THUMP domain is an RNA-binding domain, and, according to a structural study of ThiI, the THUMP domain together with the ancillary N-terminal domain configures the surface for RNA binding (56). "
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    ABSTRACT: Modifications of rRNAs are clustered in functional regions of the ribosome. In Helix 74 of Escherichia coli 23S rRNA, guanosines at positions 2069 and 2445 are modified to 7-methylguanosine(m(7)G) and N(2)-methylguanosine(m(2)G), respectively. We searched for the gene responsible for m(7)G2069 formation, and identified rlmL, which encodes the methyltransferase for m(2)G2445, as responsible for the biogenesis of m(7)G2069. In vitro methylation of rRNA revealed that rlmL encodes a fused methyltransferase responsible for forming both m(7)G2069 and m(2)G2445. We renamed the gene rlmKL. The N-terminal RlmL activity for m(2)G2445 formation was significantly enhanced by the C-terminal RlmK. Moreover, RlmKL had an unwinding activity of Helix 74, facilitating cooperative methylations of m(7)G2069 and m(2)G2445 during biogenesis of 50S subunit. In fact, we observed that RlmKL was involved in the efficient assembly of 50S subunit in a mutant strain lacking an RNA helicase deaD.
    Nucleic Acids Research 12/2011; 40(9):4071-85. DOI:10.1093/nar/gkr1287 · 9.11 Impact Factor
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