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Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis.

Suzuki T, Nakamura A, Kato K, Söll D, Tanaka I, Sheppard K, Yao M
Proc Natl Acad Sci U S A 112 382-7 (2015)
Cited: 21 times
EuropePMC logo PMID: 25548166

Abstract

Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNA(Asn), and instead synthesize asparagine from tRNA(Asn)-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNA(Asn), and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNA(Asn) to form Asn-tRNA(Asn) for use in protein synthesis. ND-AspRS, GatCAB, and tRNA(Asn) may assemble in an ∼400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNA(Asn). We report the 3.7-Å resolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNA(Asn) molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNA(Asn) formation evolutionarily preceded the direct attachment of Asn to tRNA(Asn), our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.

Reviews - 4wj3 mentioned but not cited (1)

  1. Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs. Tragni V, Primiano G, Tummolo A, Cafferati Beltrame L, La Piana G, Sgobba MN, Cavalluzzi MM, Paterno G, Gorgoglione R, Volpicella M, Guerra L, Marzulli D, Servidei S, De Grassi A, Petrosillo G, Lentini G, Pierri CL. Molecules 27 3494 (2022)

Articles - 4wj3 mentioned but not cited (12)

  1. Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis. Suzuki T, Nakamura A, Kato K, Söll D, Tanaka I, Sheppard K, Yao M. Proc. Natl. Acad. Sci. U.S.A. 112 382-387 (2015)
  2. Potential DNA binding and nuclease functions of ComEC domains characterized in silico. Baker JA, Simkovic F, Taylor HM, Rigden DJ. Proteins 84 1431-1442 (2016)
  3. Rooted tRNAomes and evolution of the genetic code. Pak D, Du N, Kim Y, Sun Y, Burton ZF. Transcription 9 137-151 (2018)
  4. Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells. Nolan LM, Cain AK, Clamens T, Furniss RCD, Manoli E, Sainz-Polo MA, Dougan G, Albesa-Jové D, Parkhill J, Mavridou DAI, Filloux A. Nat Microbiol 6 1199-1210 (2021)
  5. An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. Esquirol L, Peat TS, Wilding M, Liu JW, French NG, Hartley CJ, Onagi H, Nebl T, Easton CJ, Newman J, Scott C. J. Biol. Chem. 293 7880-7891 (2018)
  6. Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine. Johannsson S, Neumann P, Wulf A, Welp LM, Gerber HD, Krull M, Diederichsen U, Urlaub H, Ficner R. Sci Rep 8 8880 (2018)
  7. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Mukai T, Amikura K, Fu X, Söll D, Crnković A. Front Genet 12 794509 (2021)
  8. Bicyclic Schellman Loop Mimics (BSMs): Rigid Synthetic C-Caps for Enforcing Peptide Helicity. Mi T, Nguyen D, Burgess K. ACS Cent Sci 9 300-306 (2023)
  9. Clinically Relevant Mutations of Mycobacterial GatCAB Inform Regulation of Translational Fidelity. Li YY, Cai RJ, Yang JY, Hendrickson TL, Xiang Y, Javid B. mBio 12 e0110021 (2021)
  10. Forward Genetics Reveals a gatC-gatA Fusion Polypeptide Causes Mistranslation and Rifampicin Tolerance in Mycobacterium smegmatis. Cai RJ, Su HW, Li YY, Javid B. Front Microbiol 11 577756 (2020)
  11. Recognition motifs for importin 4 [(L)PPRS(G/P)P] and importin 5 [KP(K/Y)LV] binding, identified by bio-informatic simulation and experimental in vitro validation. Panagiotopoulos AA, Kalyvianaki K, Tsodoulou PK, Darivianaki MN, Dellis D, Notas G, Daskalakis V, Theodoropoulos PA, Panagiotidis CΑ, Castanas E, Kampa M. Comput Struct Biotechnol J 20 5952-5961 (2022)
  12. Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant. Andi B, Soares AS, Shi W, Fuchs MR, McSweeney S, Liu Q. Acta Crystallogr F Struct Biol Commun 75 616-624 (2019)


Reviews citing this publication (1)

  1. Unconventional genetic code systems in archaea. Meng K, Chung CZ, Söll D, Krahn N. Front Microbiol 13 1007832 (2022)

Articles citing this publication (7)

  1. The Bacillus subtilis and Bacillus halodurans Aspartyl-tRNA Synthetases Retain Recognition of tRNA(Asn). Nair N, Raff H, Islam MT, Feen M, Garofalo DM, Sheppard K. J. Mol. Biol. 428 618-630 (2016)
  2. Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNA(Cys) synthesis. Chen M, Nakazawa Y, Kubo Y, Asano N, Kato K, Tanaka I, Yao M. Acta Crystallogr F Struct Biol Commun 72 569-572 (2016)
  3. Cyclic peptides identified by phage display are competitive inhibitors of the tRNA-dependent amidotransferase of Helicobacter pylori. Pham VH, Maaroufi H, Levesque RC, Lapointe J. Peptides 79 8-15 (2016)
  4. Letter Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase. Zhao L, Rathnayake UM, Dewage SW, Wood WN, Veltri AJ, Cisneros GA, Hendrickson TL. FEBS Lett. 590 3122-3132 (2016)
  5. Kidney-Type Glutaminase Inhibitor Hexylselen Selectively Kills Cancer Cells via a Three-Pronged Mechanism. Ruan JJ, Yu Y, Hou W, Chen Z, Fang J, Zhang J, Ni M, Li D, Lu S, Rui J, Wu R, Zhang W, Ruan BH. ACS Pharmacol Transl Sci 2 18-30 (2019)
  6. 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL. F1000Res 8 (2019)
  7. Structural basis for tRNA-dependent cysteine biosynthesis. Chen M, Kato K, Kubo Y, Tanaka Y, Liu Y, Long F, Whitman WB, Lill P, Gatsogiannis C, Raunser S, Shimizu N, Shinoda A, Nakamura A, Tanaka I, Yao M. Nat Commun 8 1521 (2017)


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