A protein extension to shorten RNA: elongated elongation factor-Tu recognizes the D-arm of T-armless tRNAs in nematode mitochondria.
Nematode mitochondria possess extremely truncated tRNAs. Of 22 tRNAs, 20 lack the entire T-arm. The T-arm is necessary for the binding of canonical tRNAs and EF (elongation factor)-Tu (thermo-unstable). The nematode mitochondrial translation system employs two different EF-Tu factors named EF-Tu1 and EF-Tu2. Our previous study showed that nematode Caenorhabditis elegans EF-Tu1 binds specifically to T-armless tRNA. C. elegans EF-Tu1 has a 57-amino acid C-terminal extension that is absent from canonical EF-Tu, and the T-arm-binding residues of canonical EF-Tu are not conserved. In this study, the recognition mechanism of T-armless tRNA by EF-Tu1 was investigated. Both modification interference assays and primer extension analysis of cross-linked ternary complexes revealed that EF-Tu1 interacts not only with the tRNA acceptor stem but also with the D-arm. This is the first example of an EF-Tu recognizing the D-arm of a tRNA. The binding activity of EF-Tu1 was impaired by deletion of only 14 residues from the C-terminus, indicating that the C-terminus of EF-Tu1 is required for its binding to T-armless tRNA. These results suggest that C. elegans EF-Tu1 recognizes the D-arm instead of the T-arm by a mechanism involving its C-terminal region. This study sheds light on the co-evolution of RNA and RNA-binding proteins in nematode mitochondria.
Sakurai
Masayuki
M
Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
Watanabe
Yoh-ichi
Y
Watanabe
Kimitsuna
K
Ohtsuki
Takashi
T
D000595:Amino Acid Sequence; D000818:Animals; D017165:Ascaris suum / Q000166:cytology / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000378:metabolism; D003432:Cross-Linking Reagents; D005038:Ethylnitrosourea; D008928:Mitochondria / Q000235:genetics* / Q000378:metabolism*; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010444:Peptide Elongation Factor Tu / Q000737:chemistry / Q000378:metabolism*; D018510:RNA, Helminth / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012358:RNA, Transfer, Met / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D017384:Sequence Deletion
D003432:Cross-Linking Reagents; D050505:Mutant Proteins; D018510:RNA, Helminth; D012358:RNA, Transfer, Met; D010444:Peptide Elongation Factor Tu; D005038:Ethylnitrosourea