Youfu Zhao

Associate Professor

Primary Disciplines

Education

  • PhD. Plant Pathology, Oklahoma State University, 2001

Academic Positions

  • Associate Professor, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 2012-present
  • Assistant Professor, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 2006-2012
  • Research Associate, Department of Plant Pathology, Michigan State University, 2003-2006
  • Postdoc Research Associate, Department of Energy-Plant Research Laboratory, Michigan State University, 2001-2003

Research Interests

  • Erwinia amylovora gene regulatory networks (GRNs) -  Fire blight, caused by Erwinia amylovora, is a particularly devastating disease for the apple and pear fruit industry. Our long-term goal is to comprehensively understand the regulation of virulence factors at both transcriptional and post-transcriptional levels, and to reconstruct gene regulatory networks (GRNs) in E. amylovora, thus allowing a better understanding of the basic mechanisms of pathogenicity and biology of E. amylovora.  
  • Understanding pathogen-host interactions for developing novel control strategies-  Type III secretion system (T3SS) is a universal target for developing novel antibacterial agents -Recent advances in studying bacterial virulence factors provide mounting evidence that, the T3SS system is a potent virulence mechanism shared by a broad spectrum of pathogenic Gram negative bacteria that infect both plant and mammalian hosts by injecting effector proteins into host cells. Thus, the T3SS apparatus is essential for bacteria to evade the host immune defense. Our long-term goal is to comprehensively understand the function and regulation of T3SS and use this knowledge to develop agents to curb bacterial infection.
  • Comparative and functional genomics of Pseudomonas savastanoi pv. glycinea, and identification of new resistance sources of soybean against race 4 Soybean - (Glycine max (L.)), one of the world’s largest providers of protein and oil, is a major crop in the United States, which accounts for about 40% of the soybeans produced in the world. Bacterial blight, caused by Pseudomonas savastanoi pv. glycinea (Psg), is a common bacterial disease of soybean and occurs in most soybean grown areas. Yield losses due to bacterial blight disease of soybean estimated at 4 to 40% in the U.S. Genome link: http://www.ncbi.nlm.nih.gov/nuccore/320326756; http://www.ncbi.nlm.nih.gov/nuccore/320332072; and http://www.pseudomonas-syringae.org/
  • Understanding beneficial microorganism-fungi interactions for disease control.
  • Antibiotic resistance and human health.

Chapters in Books

  • Zhao, Y. F. 2014. Genomics of Erwinia amylovora and related species associated with pome fruit trees. In "Genomics of Plant-Associated Bacteria". Dennis Gross, Ann Lichens-Park and Chittaranjan Kole (eds). Springer
  • Ancona, V., and Zhao, Y. F. 2015. Microbial Associated Molecular Patterns. In "Virulence Mechanisms of Plant Pathogenic Bacteria", APS Press
  • McNally, R. Zhao, Y. F., and Sundin G. W. 2015. Towards understanding fire blight: virulence mechanisms and their regulation in Erwinia amylovora. In "Plant pathogenic bacteria: From basic research through systems biology to disease control". Jesus Murillo et. al. (Eds). Horizon Press.

Selected Articles in Journals

  • Zhao, Y. F., Damicone, J. P., Demezas, D., and Bender, C. 2000. Bacterial leaf spot diseases of leafy crucifers in Oklahoma caused by pathovars of Xanthomonas campestris. Plant Dis. 84:1008-1014.
  • Zhao, Y. F., Damicone, J. P., Demezas, D., Rangaswamy, V., and Bender, C. 2000. Bacterial leaf spot of leafy crucifers in Oklahoma caused by Pseudomonas syringae pv. maculicola. Plant Dis. 84:1015-1020.
  • Jones, W. T., Harvey, D., Zhao, Y. F., Mitchell, R., Bender, C. L., and Reynolds, P. H. S. 2001. Monoclonal antibody-based immunoassays for the phytotoxin coronatine. Food Agric. Immunol. 13:19-32.
  • Zhao, Y. F., Jones, W. T., Sutherland, P., Palmer, D. A., Mitchell, R. E., Reynolds, P. H. S., Damicone, J. P., and Bender, C. L. 2001. Detection of the phytotoxin coronatine by ELISA and immunolocalization in infected plant tissue. Physiol. Mol. Plant Path. 58:247-258.
  • Zhao, Y. F., Damicone, J. P., and Bender, C. 2002. Detection, survival, and sources of inoculum for bacterial diseases of leafy crucifers in Oklahoma. Plant Dis. 86:883-888.
  • Alarcon-Chaidez, F. J., Lisa, K., Zhao, Y. F., and Bender, C. L. 2003. RpoN (σ54) is required for plasmid-encoded coronatine biosynthesis in Pseudomonas syringae. Plasmid 49:106-117.
  • Zhao, Y. F., Thilmony, R., Bender, C. L., Schaller, A., He, S. Y., and Howe, G. A. 2003.Virulence systems of Pseudomonas syringae pv. tomato promotes bacterial speck disease in tomato by targeting the jasmonate signaling pathway. Plant J. 36:485-499.
  • Li, L, Zhao, Y. F., McCaig, B.,Wingerd, B., Wang, J., Whalon, M., Pichersky, E., and Howe, G. A. 2004. The Tomato homolog of CORONATINE-INSENSITIVE1 is required for the maternal control of seed maturation, jasmonate-signaled defense responses, and glandular trichome development. Plant Cell 16:126-143.
  • Sundin, G. W., Mayfield, C. T., Zhao, Y. F., Gunasekera, T. S., Foster, G. L., and Ullrich, M. S. 2004. Complete nucleotide sequence and analysis of pPSR1 (72,601 bp), a pPT23A family plasmid from Pseudomonas syringae pv. syringae A2. Mol. Genet. Genomics. 270:462-475.
  • Zhao, Y. F., Ma, Z., and Sundin, G. W. 2005. Comparative genomic analysis of the pPT23A plasmid family of Pseudomonas syringae. J. Bacteriol. 187:2113-2126.
  • Zhao, Y. F., Blumer, S. E., and Sundin, G. W. 2005. Identification of Erwinia amylovora genes induced during infection of immature pear tissue. J. Bacteriol. 187:8088-8103.
  • Zhao, Y. F., He, S. Y., and Sundin, G. W. 2006. The Erwinia amylovora avrRpt2EA gene contributes to virulence on pear and AvrRpt2EA is recognized by Arabidopsis RPS2 when expressed in Pseudomonas syringae. Mol. Plant-Microbe Interact.9:644-654.
  • Triplett, L., Zhao, Y. F., and Sundin, G. W. 2006. Genetic differences among blight-causing Erwinia species with differing host specificities identified by suppression subtractive hybridization. Appl. Environ. Microbiol. 72:7359-7364.
  • Ma, Z., Smith, J. J., Zhao, Y. F., Jackson, R., Arnold, D., Murillo, J., and Sundin, G. W. 2007. Phylogenetic analysis of the pPT23A plasmid family of Pseudomonas syringae. Appl. Environ. Microbiol. 73:1287-1295.
  • Perez-Martinez, I., Zhao, Y. F., Murillo, J., Sundin, G. W., and Ramos, C. 2008. Global genomic analysis of Pseudomonas savastanoi pv. savastanoi plasmids. J. Bacteriol. 190:625-635.
  • Wise, K. A., Zhao, Y. F., and Bradley, C. A. 2008. First report of pink seed of pea caused by Erwinia rhapontici in North Dakota. Plant Dis. 92:315
  • Berry, M., McGhee, G. C., Zhao, Y. F., and Sundin, G. W. 2009. Effect of a waaL mutation on lipopolysaccharide composition, oxidative stress survival, and virulence in Erwinia amylovora. FEMS Microbiol. Lett. 291:80-87.
  • Wang, D. P., Korban, S. S., and Zhao, Y. F. 2009. The Rcs phosphorelay system is essential for pathogenicity in Erwinia amylovora. Mol. Plant Pathol. 10:277-290.
  • Di, C., Zhang, Q., Li. M., Zhao, Y. F., and Hartman, G. 2009. Detection of soybean rust using a multispectral image sensor. Sensing and Instrumentation for Food Quality and Safety. 3:49-56.
  • Zhao, Y. F., Sundin, G. W., and Wang, D. P. 2009. Construction and analysis of pathogenicity island deletion mutants in Erwinia amylovora. Can. J. Microbiol. 55:457-464.
  • Li, X., Nie, J., Ward, L., Madani, M., Hsiang, T., Zhao, Y. F., De Boer, S. 2009. Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola. J. Appl. Microbiol. 107:717-726.
  • Zhao, Y. F., Wang, D., Nakka, S., Sundin, G. W., and Korban, S. S. 2009. Systems level analysis of two-component signal transduction systems in Erwinia amylovora: Role in virulence, regulation of amylovoran biosynthesis and swarming motility. BMC Genomics. 10:245. (http://www.biomedcentral.com/content/pdf/1471-2164-10-245.pdf)
  • Koczan, J. M., McGrath, M., Zhao, Y. F., and Sundin, G. W. 2009. The contribution of the exopolysaccharide amylovoran and levan to biofilm formation: Implication in pathogenicity. Phytopathology 99:1237-1244.
  • Nakka, S., Qi, M., and Zhao, Y. F. 2010. The PmrAB system in Erwinia amylovora renders the pathogen more susceptible to polymyxin B and more resistance to excess iron. Res. Microbiol. 161:153-157.
  • Wang, D., Korban, S. S., and Zhao, Y. F. 2010. Molecular signature of differential virulence in natural isolates of Erwinia amylovora. Phytopathology 100:192-198.
  • Qi, M., Sun, F., Caetano-Anolles, G., and Zhao, Y. F. 2010. Comparative genomic and phylogenetic analyses reveal the evolution of core two-component signal transduction systems in enterobacteria. J. Mol. Evol. 70: 167-180.
  • Nakka, S., Qi, M., and Zhao, Y. F. 2010. The Erwinia amylovora PhoPQ system is involved in resistance to antimicrobial peptide and suppresses gene expression of two novel type III secretion systems. Microbiol. Res. 165:665-673.
  • Di, C., Zhang, Q., Li. M., Hartman, G., and Zhao, Y. F. 2010. Image processing methods for quantitatively detecting soybean rust from multispectral images. Biosystems Engineering 107:186-193.
  • Oh, M., Wang, X., Wu, X., Zhao, Y. F., Clouse, S. D., and Huber, S. C. 2010. Phosphorylation of Tyr-610 in the receptor kinase BAK1 plays a role in brassinosteroid signaling and affects basal defense gene expression. Proc. Natl. Acad. Sci. USA. 107: 17827-17832.
  • Qi, M., Wang, D., Bradley, C., and Zhao, Y. F. 2011. Genome sequence analyses of Pseudomonas savastanoi pv. glycinea and in silico subtractive hybridization-based comparative genomics with nine phytopathogenic pseudomonads. PLoS ONE 6:e16451.(http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0016451&representation=PDF)
  • Wang, D., Korban, S. S., Pusey, L., and Zhao, Y. F. 2011. Characterization of the RcsC sensor kinase from Erwinia amylovora and other enterobacteria. Phytopathology 101:710-717.
  • Zhao, Y. F., and Qi, M. S. 2011. Comparative genomics of Erwinia amylovora and related Erwinia species - what do we learn? Genes 2: 627-639 -- Special Issue [Genes and Genomes of Plant Pathogenic Bacteria]. (Invited review)
  • Sarowar, S., Zhao, Y. F., Guerra, R., Ali, S., Zheng, D., Wang, D. P., and Korban, S. S. 2011. Expression profiles of differentially regulated genes during early stages of apple flower infection with Erwinia amylovora. J. Exp. Bot. 62:4851-4861.
  • Wang, D. P., Calla, B., Vimolmangkang, S., Wu, X., Korban, S. S., Huber, S. C., Clough, S. J., and Zhao, Y. F. 2011. The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli. PLoS ONE 6:e25293.(DOI:10.1371/journal.pone.0025293)
  • Wang, D. P., Qi, M. S., Calla, B., Korban, S. S., Clough, S. J., Cock, P., Sundin, G. W., Toth, I., and Zhao, Y. F. 2012. Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora. Mol. Plant-Microbe Interact. 25:6-17.
  • McNally, R., Toth, I., Cock, P., Pritchard, L., Hedley, P., Morris, R., Zhao, Y. F., and Sundin, G. W. 2012. Genetic characterization of the HrpL regulon of the fire blight pathogen Erwinia amylovora reveals novel virulence factors. Mol. Plant Pathol. 13:160-173.
  • Khan, M.A., Zhao, Y.F., and Korban, S.S. 2012. Molecular mechanisms of pathogenesis and resistance to the bacterial pathogen Erwinia amylovora, causal agent of fire blight disease in Rosaceae. Plant Mol. Biol. Rep. 30:247-260. (invited review)
  • Khan, M. A., Han, Y., Zhao, Y. F., and Korban, S. S. 2012. A high-throughput apple SNP genotyping platform using the GoldenGate Assay. Gene 494: 196-201.
  • Kim, I., Pusey, L., Zhao, Y. F., Korban, S. S., Choi, H., and Kim, K. 2012. Microencapsulation and controlled release of Pantoea agglomerans E325 for biocontrol of fire blight disease of apple. J. Controlled Release 161:109-115.
  • Wang, D., Korban, S. S., and Pusey, L., and Zhao, Y. F. 2012. AmyR is a novel negative regulator of amylovoran production in Erwinia amylovora. PLoS ONE 7: e45038.
  • Khan, A. M., Han, Y., Zhao, Y. F., Troggio, M., and Korban, S. S. 2012. A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome. PLoS ONE 7:e47864.
  • Wu, X., Vellaichamy, A., Wang, D., Zamdborg, L., Kelleher, N. L., Huber, S. C. and Zhao, Y. F. 2013. Differential lysine acetylation profiles of Erwinia amylovora strains revealed by proteomics. J. Proteomics 79:60-71.
  • Khan, A. M., Zhao, Y. F., and Korban, S. S. 2013. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping. Physiol. Plantarum 148:344-353.
  • Metelev, M., Serebryakova, M., Ghilarov, D., Zhao, Y. F., Severinov, K. 2013. Structure of microcin-B-like compounds produced by Pseudomonas syringae and species specificity of their antibacterial action. J. Bacteriol. 195: 4129-4137.
  • Yang, F., Korban, S.S., Pusey, P. L., Elofsson, M., Sundin, G. W., and Zhao, Y. F. 2014. Small molecule inhibitors suppress the expression of both type III secretion and amylovoran biosynthesis genes in Erwinia amylovora. Mol. Plant Pathol. 15:44-57.
  • Anocona, V., Li, W., and Zhao, Y. F. 2014. Alternative sigma factor RpoN and its modulation protein YhbH are indenpensible for Erwinia amylovora virulence. Mol. Plant Pathol. 15:58-66.
  • Li, W., Anocona, V., and Zhao, Y. F. 2014. Co-regulation of polysaccharide production, motility, and expression of type III secretion genes by EnvZ/OmpR and GrrS/GrrA systems in Erwinia amylovora. Mol. Gen. Genomics 289:63-75.
  • Ancona, V., Lee, J. H., Chatnaparat, T., Oh, J., Hong, J., and Zhao, Y. F. 2015. The bacterial alarmone (p)ppGpp activates type III secretion system in Erwinia amylovora. J. Bacteriol. 197:1433-1443.
  • Ancona, V., Chatnaparat, T., and Zhao, Y. F. 2015. Conserved aspartate and lysine residues of RcsB are required for amylovoran biosynthesis, virulence, and DNA binding in Erwinia amylovora. Mol. Gen. Genomics 290: 1265-1276.
  • Chatnaparat, T., Li, Z., Korban, S. S., and Zhao, Y. F. 2015. The stringent response mediated by (p)ppGpp is required for virulence of Pseudomonas syringae pv. tomato and its survival on tomato. Mol. Plant-Microbe Interact. 28:776-789.
  • Chatnaparat, T., Li, Z., Korban, S. S., and Zhao, Y. F. 2015. The bacterial alarmone (p)ppGpp is required for virulence and controls cell size and survival of Pseudomonas syringae on plants. Environ. Microbiol. 17:4253-4270.
  • Lee, J. H., and Zhao, Y. F. 2016. Integration host factor is required for RpoN-dependent hrpL gene expression and controls motility by positively regulating rsmB sRNA in Erwinia amylovora. Phytopathology 106:29-36.
  • Lee, J. H., Sundin, G. W., and Zhao, Y. F. 2016. Identification of the HrpS binding site in the hrpLpromoter and effect of the RpoN binding site of HrpS in regulation of the type III secretion system in Erwinia amylovora. Mol. Plant Pathol.17: 691-702.
  • Sundin, W. G., Wang, N., Charkowski, A. O., Castiblanco, L. F., and Zhao, Y. F. 2016. Perspectives on the transition from bacterial phytopathogen genomics studies to applications enhancing disease management: from promise to practice. Phytopathology (special issue) 106:1071-1082.
  • Ancona, V., Lee, J. H., and Zhao, Y. F. 2016. The RNA binding protein CsrA plays a central role in positively regulating virulence factors in Erwinia amylovora. Sci. Rep . 6:37195.
  • Tian, Y., Zhao, Y. Q., Cui, Z., Hu, B. S., and Zhao, Y. F. 2017. Type VI secretion systems of Erwinia amylovora contribute to bacterial competition, virulence, and exopolysaccharide production. Phytopathology 107: 654-661.
  • Bartho, J. D., Bellini, D., Wuerges, J., Demitri, N., Toccafondi, M., Schmitt, A. O., Zhao, Y. F., Walsh, M. A., and Benini, S. 2017. The crystal structure of Erwinia amylovora AmyR, a member of the YbjN family, shows similarity to type III chaperones but suggests different cellular functions. PLoS ONE 12:e0176049.
  • Lee, J. H., Ancona, V., and Zhao, Y. F. 2017. Lon protease modulates virulence traits in Erwinia amylovora by directly monitoring major regulators and indirectly through the Rcs and Gac-Csr regulatory systems. Mol Plant Pathol. DOI: 10.1111/mpp.12566.
  • Zhao, Y. F., and Sundin, G. W. 2017. Exploring linear and cyclic (di)nucleotides as messengers for regulation of T3SS and biofilm formation in Erwinia amylovora. J. Plant Pathol. (in press).
  • Smits, T. H. M., Duffy, B., Sundin, G. W., Zhao, Y. F., and Rezzonico, F. 2017. Erwinia amylovora in the genomics era: from genomes to pathogen virulence, regulation and disease control strategies. J. Plant Pathol. (in press).
  • Singh, V., Perraki, A., Kim, S. Y., Shrivastava, S., Lee, J. H., Zhao, Y. F., Schwessinger, B., Oh, M., Marshall-Colon, A., Zipfel, C. and Huber, S. 2017. Tyrosine-610 in the receptor kinase BAK1 does not play a major role in brassinosteroid signaling or innate immunity. Frontiers Plant Physiol. (accepted)
  • Lee, J. H. and Zhao, Y. F. 2017. ClpXP-depdendent RpoS degradation enables full activation of type III secretion system, amylovoran production and motility in Erwinia amylovora. Phytopathology (accepted).