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A conserved lysine residue in the crenarchaea-specific loop is important for the crenarchaeal splicing endonuclease activity.

Okuda M, Shiba T, Inaoka DK, Kita K, Kurisu G, Mineki S, Harada S, Watanabe Y, Yoshinari S
J Mol Biol 405 92-104 (2011)
Cited: 12 times
EuropePMC logo PMID: 21050862

Abstract

In Archaea, splicing endonuclease (EndA) recognizes and cleaves precursor RNAs to remove introns. Currently, EndAs are classified into three families according to their subunit structures: homotetramer, homodimer, and heterotetramer. The crenarchaeal heterotetrameric EndAs can be further classified into two subfamilies based on the size of the structural subunit. Subfamily A possesses a structural subunit similar in size to the catalytic subunit, whereas subfamily B possesses a structural subunit significantly smaller than the catalytic subunit. Previously, we solved the crystal structure of an EndA from Pyrobaculum aerophilum. The endonuclease was classified into subfamily B, and the structure revealed that the enzyme lacks an N-terminal subdomain in the structural subunit. However, no structural information is available for crenarchaeal heterotetrameric EndAs that are predicted to belong to subfamily A. Here, we report the crystal structure of the EndA from Aeropyrum pernix, which is predicted to belong to subfamily A. The enzyme possesses the N-terminal subdomain in the structural subunit, revealing that the two subfamilies of heterotetrameric EndAs are structurally distinct. EndA from A. pernix also possesses an extra loop region that is characteristic of crenarchaeal EndAs. Our mutational study revealed that the conserved lysine residue in the loop is important for endonuclease activity. Furthermore, the sequence characteristics of the loops and the positions towards the substrate RNA according to a docking model prompted us to propose that crenarchaea-specific loops and an extra amino acid sequence at the catalytic loop of nanoarchaeal EndA are derived by independent convergent evolution and function for recognizing noncanonical bulge-helix-bulge motif RNAs as substrates.

Reviews - 3ajv mentioned but not cited (2)

  1. Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex. Hayne CK, Lewis TA, Stanley RE. Wiley Interdiscip Rev RNA 13 e1717 (2022)
  2. Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases. Hirata A. Front Genet 10 103 (2019)

Articles - 3ajv mentioned but not cited (1)

  1. Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop. Hirata A, Kitajima T, Hori H. Nucleic Acids Res. 39 9376-9389 (2011)


Reviews citing this publication (2)

  1. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. FEMS Microbiol. Rev. 42 579-613 (2018)
  2. New insights into RNA processing by the eukaryotic tRNA splicing endonuclease. Hayne CK, Sekulovski S, Hurtig JE, Stanley RE, Trowitzsch S, van Hoof A. J Biol Chem 299 105138 (2023)

Articles citing this publication (7)

  1. Discovery of permuted and recently split transfer RNAs in Archaea. Chan PP, Cozen AE, Lowe TM. Genome Biol. 12 R38 (2011)
  2. A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, Kanai A. Nucleic Acids Res. 39 9695-9704 (2011)
  3. Yeast ribosomal protein S3 possesses a β-lyase activity on damaged DNA. Seong KM, Jung SO, Kim HD, Kim HJ, Jung YJ, Choi SY, Kim J. FEBS Lett. 586 356-361 (2012)
  4. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H. Nucleic Acids Res. 40 10554-10566 (2012)
  5. An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Ikeda Y, Okada Y, Sato A, Kanai T, Tomita M, Atomi H, Kanai A. Sci Rep 7 12674 (2017)
  6. Identification of an entire set of tRNA molecules and characterization of cleavage sites of the intron-containing tRNA precursors in acidothermophilic crenarchaeon Sulfolobus tokodaii strain7. Yamazaki S, Yoshinari S, Kita K, Watanabe Y, Kawarabayasi Y. Gene 489 103-110 (2011)
  7. The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity. Kaneta A, Fujishima K, Morikazu W, Hori H, Hirata A. Nucleic Acids Res. 46 1958-1972 (2018)


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