The crystal structure of type III effector protein XopQ fromXanthomonas oryzaecomplexed with adenosine diphosphate ribose

Abstract

Effector proteins are virulence factors that promote pathogenesis by interfering with various cellular events and are delivered directly into host cells by the secretion systems of many Gram-negative bacteria. Type III effector protein XOO4466 from the plant pathogen Xanthomonas oryzae pv. oryzae (XopQ(Xoo)) and XopQ homologs from other phytopathogens have been predicted to be nucleoside hydrolases based on their sequence similarities. However, despite such similarities, recent structural and functional studies have revealed that XopQ(Xoo) does not exhibit the expected activity of a nucleoside hydrolase. On the basis of the conservation of a Ca(2+) coordination shell of a ribose-binding site and the spacious active site in XopQ(Xoo), we hypothesized that a novel compound containing a ribosyl moiety could serve as a substrate for XopQ(Xoo). Here, we report the crystal structure of XopQ(Xoo) in complex with adenosine diphosphate ribose (ADPR), which is involved in regulating cytoplasmic Ca(2+) concentrations in eukaryotic cells. ADPR is bound to the active site of XopQ(Xoo) with its ribosyl end tethered to the Ca(2+) coordination shell. The binding of ADPR is further stabilized by interactions mediated by hydrophobic residues that undergo ligand-induced conformational changes. These data showed that XopQ(Xoo) is capable of binding a novel chemical bearing a ribosyl moiety, thereby providing the first step toward understanding the functional role of XopQ(Xoo).

Dissecting virulence function from recognition: cell death suppression in Nicotiana benthamiana by XopQ/HopQ1‐family effectors relies on EDS1‐dependent immunity

“…XopQ Xoo folds into an α–β–α‐sandwich domain, similarly to known NHs, and a protruding α‐helical segment not found in NHs (Yu et al ., ). Upon binding of the potential substrate adenosine diphosphate ribose to XopQ Xoo , the protruding segment shifts to the protein center leading to a closed conformation (Yu et al ., ). We wondered if other XopQ/HopQ1‐family members share similar structural features and predicted the structures of HopQ1 Pto , XopQ Xcv and XopQ Xcc using Phyre2 (Kelley et al ., ).…”

“…In a first set of mutants, we deleted the N-terminal region including the 14-3-3-binding site (D2-69), a C-terminal region (D455-462) and introduced substitutions: D116A/N118A, D120A/D122A/D123A, D275A/R277A, N280/ R281/N284A, E308A/Y311F, F319E, Y320A and N396A/398A/ D399A, respectively ( Figure S1a). Substitutions are expected to render XopQ catalytically inactive, as the positions correspond to the substrate binding site and a Ca 2+coordinating motif, respectively, in XopQ Xoo (Yu et al, 2014). However, none of the mutations abolished in planta recognition ( Figure 2).…”

3′-NADP and 3′-NAADP, Two Metabolites Formed by the Bacterial Type III Effector AvrRxo1

“…A curious side note is that structural studies on the type III effector XopQ from X. oryzae pv. oryzae suggested a nucleoside hydrolase activity on the Ca 2+ -mobilizing second messenger cyclic adenosine diphosphate ribose (51). Hence, manipulation of the host cell Ca 2+ signature might not only be performed by AvrRxo1 but could be a common approach of plant pathogens.…”

Structure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ

“…2E). XopQ's specific substrate remains unidentified, but previous studies have shown that XopQ binds ADPR, an important immune signaling molecule in plants, consistent with its immunosuppressive function (19).…”

“…The greatest number of contacts between the PL domain and XopQ are made by a 33 residue loop (aa 1163-1196) that dives into the active site cleft of the effector and positions sidechains in close contact with conserved sites required for ADPR-binding ( Fig. 2D,E) (19). We refer to this loop as the NR loop for its ability to bind residues in XopQ responsible for nucleoside recognition (NR).…”