Targeting of the rice transcriptome by TAL effectors of Xanthomonas oryzae

Authors: NINO-LIU, DAVID - Iowa State University; BANCROFT, TIMOTHY - Iowa State University; RAJARAM, MISHA - Iowa State University; MOSCOU, MATTHEW - Iowa State University; CALDO, RICO - Iowa State University; SCHMIDT, CLARICE - Iowa State University; DORMAN, KARIN - Iowa State University; YANG, BING - Iowa State University; PATIL, PRABHU - Iowa State University; SZUREK, BORIS - Colorado State University; KOEBNIK, RALF - Colorado State University; VAN SLUYS, MARIE-ANNE - Colorado State University; LEACH, JAN - Colorado State University; SALZBERG, STEVEN - University Of Maryland; WHITE, FRANK - Kansas State University; NETTLETON, DAN - Iowa State University; Wise, Roger; BOGDANOVE, ADAM - Iowa State University

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 1/28/2010
Publication Date: 8/2/2017
Citation: Nino-Liu, D.O., Bancroft, T., Rajaram, M.L., Moscou, M., Caldo, R., Schmidt, C., Dorman, K., Yang, B., Patil, P., Szurek, B., Koebnik, R., Van Sluys, M., Leach, J.E., Salzberg, S.L., White, F.F., Nettleton, D., Wise, R.P., Bogdanove, A.J. 2017. Targeting of the rice transcriptome by TAL effectors of Xanthomonas oryzae. In: Wolpert, T., Shiraishi T., Collmer A., Akimitsu K., and Glazebrook J., editors. Genome-Enabled Analysis of Plant-Pathogen Interactions. St. Paul, Minnesota: American Phytopathological Society Press. p.193-206. https://doi.org/10.1094/9780890544983.021.
DOI: https://doi.org/10.1094/9780890544983.021

Interpretive Summary: Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc), is emerging in importance in many rice-growing areas of the world, particularly in the tropics and subtropics of Asia. Despite some effort, no effective R-gene mediated resistance for this disease has been identified in rice, though quantitative resistance loci have been characterized, and a maize gene has been cloned that confers resistance as a transgene. Bacterial blight of rice, caused by X. oryzae pv. oryzae (Xoo), is one of the most important rice diseases worldwide. In contrast to bacterial leaf streak, however, nearly 30 R genes for bacterial blight have been identified. Xoc and Xoo colonize rice plants in different ways. Xoc colonizes the mesophyll apoplast, whereas, Xoo invades the xylem. The basis for these differences is unknown. This research centers on the molecular basis for bacterial plant pathogenesis and plant disease resistance. We use pathogen and host genome-enabled approaches to identify pathogenicity factors and their targets, with particular attention to candidate determinants of host and tissue specificity. Knowledge from this research will impact how plant breeders engineer and select for disease resistance, one of the most important traits that affect crop yield, and thus food security.

Technical Abstract: This research focuses on bacterial leaf streak and bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo), respectively. In this chapter, we describe results of several studies directed toward identification of pathogenicity factors and their targets, with particular attention to candidate determinants of host and tissue specificity. Several approaches were used to attain these goals: 1) sequencing and comparison of Xoc and Xoo genomes 2) comparative transcript profiling of rice undergoing infection with Xoc vs. Xoo, 3) analyses of the role of the transcription activator-like (TAL) class of type III effectors in shaping rice transcriptional responses, and 4) a deciphering of the DNA binding specificity of TAL effectors. From these studies, differences in TAL effector-mediated modulation of the rice “transcriptome,” i.e., levels of transcripts across the genome, emerge as a major discriminating factor between bacterial leaf streak and bacterial blight, and the effectors and their targets emerge as strong candidate determinants of host and tissue specificity. Our elucidation of the basis for DNA targeting by different TAL effectors enables a new approach to rapidly identify host genes important in disease, and suggests novel strategies for generating varieties of rice, and other crops affected by Xanthomonas spp., that have broad-spectrum and durable resistance.