Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2002
Publication Date: 5/28/2002
Citation: SCHNEIDER, D.J., PETNICKI-OCWIEJA, T., TAM, V., CHANCEY, S., SHAN, L., JAMIR, Y., SCHECHTER, L., TANG, X., COLLMER, A., ALFANO, J.R. GENOME-WIDE IDENTIFICATION OF PROTEINS SECRETED BY THE HRP TYPE III SECRETION SYSTEM OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2002. Interpretive Summary: Many bacterial pathogens use very similar mechanisms for causing infections in both plants and animals. Despite its critical role in infectious processes, this mechanism, called the type III secretion system, is very poorly understood. In this paper we describe computational methods for analyzing the DNA sequence of Pseudomonas syringae, an important plant pathogen, to identify proteins likely to be secreted by the type III secretory system, as well as laboratory data verifying that some of the candidates are actually secreted. In this paper we increase the total number of proteins proven to be secreted via the type III secretory system in this organism from 2 to 15. The computational methods are applicable to other pathogens as well.
Technical Abstract: The ability of Pseudomonas syringae pv. tomato DC3000 to be pathogenic on plants is dependent on the Hrp type III protein secretion system and, collectively, the effector proteins translocated into plant cells. A genome wide search for Hrp effectors was performed based on patterns in the N terminal 50 residues of Hrp secretion substrates. These rules were applied to a group of proteins recently found downstream of apparent Hrp promoters in the DC3000 genome. Six proteins were found to be secreted in culture from DC3000 or translocated into plants via the Hrp pathway: HopPtoE, HopPtoG, HopPtoH, HopPtoI, HopPtoL and HopPtoS1. HopPtoL shares significant sequence similarities with the Nudix family of hydrolases, a broadly conserved protein class. HopPtoS1 shares sequence similarity with ADP ribosyltransferases, proteins known to be substrates for type III systems of animal pathogens, but not known to travel the Hrp system of bacterial plant pathogens. We also found that five proteins that were similar to Avr proteins in other bacterial plant pathogens were either secreted or translocated by DC3000. These were named HopPtoC (AvrPpiC2 homolog), HopPtoD1 and HopPtoD2 (AvrPphD homologs), HopPtoK (AvrRps4 homolog), and HopPtoJ (AvrXv3 homolog). A computer search identified new candidate effectors containing putative export signals including additional ADP ribosyltransferases, catalase, and glucokinase.