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High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove.

Suddala KC, Zhang J
Nat Struct Mol Biol 26 1114-1122 (2019)
Cited: 24 times
EuropePMC logo PMID: 31792448

Abstract

T-box riboswitches are modular bacterial noncoding RNAs that sense and regulate amino acid availability through direct interactions with tRNAs. Between the 5' anticodon-binding stem I domain and the 3' amino acid sensing domains of most T-boxes lies the stem II domain of unknown structure and function. Here, we report a 2.8-Å cocrystal structure of the Nocardia farcinica ileS T-box in complex with its cognate tRNAIle. The structure reveals a perpendicularly arranged ultrashort stem I containing a K-turn and an elongated stem II bearing an S-turn. Both stems rest against a compact pseudoknot, dock via an extended ribose zipper and jointly create a binding groove specific to the anticodon of its cognate tRNA. Contrary to proposed distal contacts to the tRNA elbow region, stem II locally reinforces the codon-anticodon interactions between stem I and tRNA, achieving low-nanomolar affinity. This study illustrates how mRNA junctions can create specific binding sites for interacting RNAs of prescribed sequence and structure.

Reviews - 6ufm mentioned but not cited (1)

  1. Unboxing the T-box riboswitches-A glimpse into multivalent and multimodal RNA-RNA interactions. Zhang J. Wiley Interdiscip Rev RNA 11 e1600 (2020)

Articles - 6ufm mentioned but not cited (6)

  1. Geometric deep learning of RNA structure. Townshend RJL, Eismann S, Watkins AM, Rangan R, Karelina M, Das R, Dror RO. Science 373 1047-1051 (2021)
  2. High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove. Suddala KC, Zhang J. Nat Struct Mol Biol 26 1114-1122 (2019)
  3. Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble. Suddala KC, Yoo J, Fan L, Zuo X, Wang YX, Chung HS, Zhang J. Nat Commun 14 5438 (2023)
  4. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. Banna HA, Das NK, Ojha M, Koirala D. BBA Adv 4 100101 (2023)
  5. Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch. Niu X, Xu Z, Zhang Y, Zuo X, Chen C, Fang X. Nat Commun 14 7394 (2023)
  6. De novo prediction of RNA 3D structures with deep generative models. Ramakers J, Blum CF, König S, Harmeling S, Kollmann M. PLoS One 19 e0297105 (2024)


Reviews citing this publication (10)

  1. Advances in RNA 3D Structure Modeling Using Experimental Data. Li B, Cao Y, Westhof E, Miao Z. Front Genet 11 574485 (2020)
  2. Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Bou-Nader C, Zhang J. Molecules 25 E2881 (2020)
  3. Interplay between Host tRNAs and HIV-1: A Structural Perspective. Zhang J. Viruses 13 1819 (2021)
  4. Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions. Skeparnias I, Zhang J. Noncoding RNA 7 81 (2021)
  5. The diverse structural modes of tRNA binding and recognition. Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. J Biol Chem 299 104966 (2023)
  6. A Riboswitch-Driven Era of New Antibacterials. Giarimoglou N, Kouvela A, Maniatis A, Papakyriakou A, Zhang J, Stamatopoulou V, Stathopoulos C. Antibiotics (Basel) 11 1243 (2022)
  7. Engineering the Translational Machinery for Biotechnology Applications. Wang T, Liang C, An Y, Xiao S, Xu H, Zheng M, Liu L, Wang G, Nie L. Mol Biotechnol 62 219-227 (2020)
  8. Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond. Gilmer O, Quignon E, Jousset AC, Paillart JC, Marquet R, Vivet-Boudou V. Viruses 13 1894 (2021)
  9. Incorporation of nonstandard amino acids into proteins: principles and applications. Wang T, Liang C, Xu H, An Y, Xiao S, Zheng M, Liu L, Nie L. World J Microbiol Biotechnol 36 60 (2020)
  10. Recognition of the tRNA structure: Everything everywhere but not all at once. Zhang J. Cell Chem Biol 31 36-52 (2024)

Articles citing this publication (7)

  1. TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs. Marchand JA, Pierson Smela MD, Jordan THH, Narasimhan K, Church GM, Church GM. Nucleic Acids Res 49 D229-D235 (2021)
  2. Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay. Wencker FDR, Marincola G, Schoenfelder SMK, Maaß S, Becher D, Ziebuhr W. Nucleic Acids Res 49 2192-2212 (2021)
  3. T-box RNA gets boxed. Weaver JW, Serganov A. Nat Struct Mol Biol 26 1081-1083 (2019)
  4. Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action. Giarimoglou N, Kouvela A, Patsi I, Zhang J, Stamatopoulou V, Stathopoulos C. Nucleic Acids Res 50 5834-5849 (2022)
  5. Improving RNA Crystal Diffraction Quality by Postcrystallization Treatment. Zhang J, Ferré-D'Amaré AR. Methods Mol Biol 2323 25-37 (2021)
  6. Rational engineering enables co-crystallization and structural determination of the HIV-1 matrix-tRNA complex. Bou-Nader C, Zhang J. STAR Protoc 3 101056 (2022)
  7. Research Support, N.I.H., Intramural The long and short of it: long noncoding RNAs in neural development and diseases. Zhang J. Front Biosci (Landmark Ed) 26 258-261 (2021)


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