Transcriptional expression of aminoacyl tRNA synthetase genes of Xanthomonas oryzae pv. oryzae (Xoo) on rice-leaf extract treatment and crystal structure of Xoo glutamyl-tRNA synthetase

2017 ◽  
Vol 68 (5) ◽  
pp. 434
Author(s):  
Thien-Hoang Ho ◽  
Myoung-Ki Hong ◽  
Seunghwan Kim ◽  
Jeong-Gu Kim ◽  
Jongha Lee ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bacterial Blight ◽  
Leaf Extract ◽  
Catalytic Domain ◽  
Trna Synthetase ◽  
Binding Domain ◽  
Xanthomonas Oryzae ◽  
Transcriptional Expression ◽  
Aminoacyl Trna Synthetase ◽  
Rice Leaf

Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight of rice, one of the most devastating rice diseases. We analysed the time-resolved transcriptional expression of aminoacyl-tRNA synthetase (aaRS) genes in Xoo cells treated with rice-leaf extract. Most aaRS genes showed decreased expression in the initial 30 min and recovered or increased expression in the later 30 min. The protein-synthetic machinery of bacterial cells is an important target for developing antibiotic agents; aaRSs play an essential role in peptide synthesis by attaching amino acids onto the corresponding tRNA. In bacteria, glutaminyl-tRNA (Gln-tRNAGln) is synthesised in two steps by glutamyl-tRNA synthetase (GluRS) and tRNA-dependent aminotransferase, the indirect biosynthetic mechanism of which is not present in eukaryotes. We determined the crystal structure of GluRS from Xoo (XoGluRS) at resolution of 3.0 Å, this being the first GluRS structure from a plant pathogen such as Xoo. The XoGluRS structure consists of five domains, which are conserved in other bacterial GluRS structures. In the bacterial GluRS structures, the Rossmann-fold catalytic domain and the stem-contact domain are most conserved in both sequence and structure. The anticodon-binding domain 1 is less conserved in sequence but overall structure is conserved. The connective-polypeptide domain and the anticodon-binding domain 2 show various conformations in structure. The XoGluRS structure could provide useful information to develop a new pesticide against Xoo and bacterial blight.

scholarly journals Crystal structure of GH43 exo-β-1,3-galactanase from the basidiomycete Phanerochaete chrysosporium provides insights into the mechanism of bypassing side chains

2020 ◽  
Author(s):  
Kaori Matsuyama ◽  
Naomi Kishine ◽  
Zui Fujimoto ◽  
Naoki Sunagawa ◽  
Toshihisa Kotake ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Phanerochaete Chrysosporium ◽  
Catalytic Domain ◽  
Interaction Mechanism ◽  
Binding Domain ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Side Chains ◽  
Ligand Interaction

AbstractArabinogalactan proteins (AGPs) are functional plant proteoglycans, but their functions are largely unexplored, mainly because of the complexity of the sugar moieties, which are generally analyzed with the aid of glycoside hydrolases. In this study, we solved the apo and liganded structures of exo-β-1,3-galactanase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. It is composed of a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family (CBM) 35 binding domain. GH43_sub24 lacks the catalytic base Asp that is conserved among other GH43 subfamilies. Crystal structure and kinetic analyses indicated that the tautomerized imidic acid function of Gln263 serves instead as the catalytic base residue. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s. Some of the residues involved in ligand recognition differ from those of galactomannan-binding CBM35, including substitution of Trp for Gly, which affects pyranose stacking, and substitution of Asn for Asp in the lower part of the binding pocket. Pc1,3Gal43A WT and its mutants at residues involved in substrate recognition are expected to be useful tools for structural analysis of AGPs. Our findings should also be helpful in engineering designer enzymes for efficient utilization of various types of biomass.

scholarly journals Arabidopsis seryl‐ tRNA synthetase: the first crystal structure and novel protein interactor of plant aminoacyl‐ tRNA synthetase

FEBS Journal ◽  
2019 ◽  
Vol 286 (3) ◽  
pp. 536-554 ◽  
Author(s):  
Mario Kekez ◽  
Vladimir Zanki ◽  
Ivana Kekez ◽  
Jurica Baranasic ◽  
Vesna Hodnik ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Trna Synthetase ◽  
Aminoacyl Trna Synthetase ◽  
Novel Protein

A chimaeric glutamyl:glutaminyl-tRNA synthetase: implications for evolution

2008 ◽  
Vol 417 (2) ◽  
pp. 449-455 ◽  
Author(s):  
Rajesh Saha ◽  
Saumya Dasgupta ◽  
Gautam Basu ◽  
Siddhartha Roy
Keyword(s):  
Catalytic Domain ◽  
Trna Synthetase ◽  
Binding Domain ◽  
Temperature Sensitive ◽  
Trna Synthetases ◽  
E Coli ◽  
Discrimination Capability ◽  
Binding Domains ◽  
History Of ◽  
Substrate Binding Domain

aaRSs (aminoacyl-tRNA synthetases) are multi-domain proteins that have evolved by domain acquisition. The anti-codon binding domain was added to the more ancient catalytic domain during aaRS evolution. Unlike in eukaryotes, the anti-codon binding domains of GluRS (glutamyl-tRNA synthetase) and GlnRS (glutaminyl-tRNA synthetase) in bacteria are structurally distinct. This originates from the unique evolutionary history of GlnRSs. Starting from the catalytic domain, eukaryotic GluRS evolved by acquiring the archaea/eukaryote-specific anti-codon binding domain after branching away from the eubacteria family. Subsequently, eukaryotic GlnRS evolved from GluRS by gene duplication and horizontally transferred to bacteria. In order to study the properties of the putative ancestral GluRS in eukaryotes, formed immediately after acquiring the anti-codon binding domain, we have designed and constructed a chimaeric protein, cGluGlnRS, consisting of the catalytic domain, Ec GluRS (Escherichia coli GluRS), and the anti-codon binding domain of EcGlnRS (E. coli GlnRS). In contrast to the isolated EcN-GluRS, cGluGlnRS showed detectable activity of glutamylation of E. coli tRNAglu and was capable of complementing an E. coli ts (temperature-sensitive)-GluRS strain at non-permissive temperatures. Both cGluGlnRS and EcN-GluRS were found to bind E. coli tRNAglu with native EcGluRS-like affinity, suggesting that the anticodon-binding domain in cGluGlnRS enhances kcat for glutamylation. This was further confirmed from similar experiments with a chimaera between EcN-GluRS and the substrate-binding domain of EcDnaK (E. coli DnaK). We also show that an extended loop, present in the anticodon-binding domains of GlnRSs, is absent in archaeal GluRS, suggesting that the loop was a later addition, generating additional anti-codon discrimination capability in GlnRS as it evolved from GluRS in eukaryotes.

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