Plant tumour biocontrol agent employs a tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase

Abstract

Leucyl-tRNA synthetases (LeuRSs) have an essential role in translation and are promising targets for antibiotic development. Agrocin 84 is a LeuRS inhibitor produced by the biocontrol agent Agrobacterium radiobacter K84 that targets pathogenic strains of A. tumefaciens, the causative agent of plant tumours. Agrocin 84 acts as a molecular Trojan horse and is processed inside the pathogen into a toxic moiety (TM84). Here we show using crystal structure, thermodynamic and kinetic analyses, that this natural antibiotic employs a unique and previously undescribed mechanism to inhibit LeuRS. TM84 requires tRNA Leu for tight binding to the LeuRS synthetic active site, unlike any previously reported inhibitors. TM84 traps the enzyme-tRNA complex in a novel 'aminoacylation-like' conformation, forming novel interactions with the KMSKS loop and the tRNA 3 0 -end. Our findings reveal an intriguing tRNAdependent inhibition mechanism that may confer a distinct evolutionary advantage in vivo and inform future rational antibiotic design.

Progress and challenges in aminoacyl-tRNA synthetase-based therapeutics

“…The adenylate moiety, a potent LeuRS inhibitor, is referred to as TM84 and features a stable 5-N-acylphosphoramidite bond rather than the standard phosphoanhydride. Interestingly, this molecule does not inhibit the activation reaction and requires the participation of the tRNA for inhibition (100). The agrocin 84 -producing strain carries a protective version of LeuRS (AgnB2) (98,101) that is analogous to the corresponding ARSs encoded in the Pseudomonas and Streptomyces genomes that carry protective alleles providing immunity against pseudomonic acid and borrelidin, respectively.…”

Drugging tRNA aminoacylation

“…Similarly, plant tumor control agent Agrocin 84 has been shown to be processed inside the cell to produce TM84, a Leu-AMP analog that crystal structures show to also bind to the 3 0 terminus of tRNA Leu 84 . This binding interaction traps the aaRS-tRNA complex in an 'aminoacylation-like' conformation, preventing further enzymatic turnover [84].…”

Progress of nitrogen-phosphorus bond biosynthesis study of naturally occurring phosphoramidates

“…84(图1)是一种广泛使用的生防制剂 [3,4] , 其水解产生 的 毒 素 核 心 TM84是 亮 氨 酰 单 磷 酸 腺 苷 酸 (leucyladenosine-5′-monophosphate, Leu-AMP)的类似物, 能 够特异性地抑制亮氨酰tRNA合成酶(leucyl-tRNA synthetases, LeuRSs), 从而抑杀作物的冠瘿瘤病原菌 根癌农杆菌Agrobacterium tumefaciens. 磷酸酰胺天 然产物金属蛋白酶抑制剂FMPI [5,6] , 小菌素Microcin C7 [7] , 磷连氮霉素Fosfazinomycin [8] , FR-900137 [9] , 磷 酸阿米酮Phosphoramidon [10] , 鱼卵毒素Dinogunellins [11] , Phosmidosine [12,13] , 1100-50 [14] , L-(N-phosphonyl) methionine-S-sulfoximinyl-L-alanyl-L-alanine [15] , EM 2487 [16] , Sulphostin [17] , JU-2 [18] 也表现出各种各样的生 物活性(图1).…”