Ching-Hong Yang
Ching-Hong Yang
Associate Professor
Genomics, Functional Genomics and Host-Microbe Interactions

Ph. D. University of California, Riverside

Postdoctoral fellow
University of California, Riverside
University of California, Davis

Office: Lapham 131D
Phone: 414-229-6331
FAX: 414-229-3926

Research Interests

1) Application of functional genomic tools to investigate microbial gene expression in different environments
With the availability of the complete sequences of the genomes of different microorganisms, functional genomic tools provide a powerful approach for identifying microbial genes that are expressed during association of bacteria with hosts and or in response to various environmental factors. In my current research, I am working on a project to sequence the complete genome of Dickeya dadantii 3937 (formally named Erwinia chrysanthemi). D. dadantii is a common colonist of aerial plant surfaces and causes soft-rot, wilts and blight diseases on a wide range of plant species. Infection of plants by D. dadantii serves as a model for studying the mechanism of bacterial infection. My students and I are using complementary approaches to look at gene expression in this model organism. The first involves a custom designed microarray for D. dadantii that will enable us to look at sets of genes that are regulated over time during the infection process. Secondly, we are using in vivo expression techniques (IVET) to investigate specific genes of D. dadantii that are regulated in plant hosts. Thirdly, by reporter combining with fluorescence-activated cell sorter, we explore genes of D. dadantii 3937 that are involved in type III secretion regulon and pathogenesis. Using bioinformatic tools, the T3SS regulated genes identified in our study are used as a training set for a genomewide identification of potential virulence genes in D. dadantii.

fig1 Jan_2_2009

2) Developing T3SS inhibitors

The type III secretion system (T3SS) is a highly specialized protein secretion system that is essential to the virulence of many plant, animal, and human pathogens. The T3SS is an attractive target for development of antimicrobial compounds since it is present mainly in pathogenic gram-negative bacteria and is often required for virulence by these species. Several components of the T3SS are conserved among different pathogens, suggesting that an inhibitor targeted against such a component could be effective against a broad range of gram-negative pathogens, but not to affect normal microbial flora. A high throughput flow cytometry system combined with a green fluorescent protein-reporter has been established to screen potential T3SS inducers and inhibitors in our lab. My students and I identified two novel plant phenolic compounds, o-coumaric acid (OCA) and t-cinnamic acid (TCA), that induced the expression of T3SS genes in D. dadantii 3937. In addition, several analogs and isomers derived from OCA and TCA were selected and screened to identify compounds that inhibit the T3SS of the bacterium. An inhibitory phenolic compound, p-coumaric acid, which blocks the T3SS pathway, was discovered. This is the first time that inducers and inhibitors of this system have been discovered in phytobacteria (Bacteria that are pathogenic to plants). Our goal is to investigate the structure-activity relationship in depth, to identify the active site(s) of the identified inhibitors, and ultimately to discover novel, potent, selective inhibitors of T3SS.

3) Developing novel approaches for microbial diversity profiling

The quantitative description of microbial communities is one of the most promising areas of research in microbial ecology. Classical culture based techniques recover only a small proportion of microorganisms from environmental samples, but have provided us with a wide array of products that have benefited humanity. New techniques in molecular ecology have now opened the door for a revolutionary advance in our understanding of microbial communities in nature and identification of new microorganisms and microbial products that can be harnessed for biotechnology. My students and I have been especially interested in developing novel approaches to analyze microbial diversity that is associated with plants. Going beyond these initial descriptions of microbial communities, my most recent work has begun to focus on interactions between plants and microorganisms using genome profiling. In addition, I would like to further explore how plant pathogens are influenced by the microbial communities with which they are associated and how gene expression is modified by environmental factors that influence both the pathogen and leaf bacterial communities. This research may lead to improved understanding of disease and methods for biocontrol by promoting disease suppressive bacterial communities on plant leaf surfaces.

Learning and Research Opportunities for Students
Undergraduate students with an interest in microbiology are welcome to enroll in an independent research study (BioSci290, BioSci689) in my lab. Research stipends are available to qualified undergraduate and graduate students.

Selected Publications

Yamazaki, A., J. Li, Q. Zeng, D. Khokhani, W. C. Hutchins, A. C. Yost, E. Biddle, E. J. Toone, X. Chen, C.-H. Yang. Derivatives of plant phenolic compound affect the type III secretion system of Pseudomonas aeruginosa via a GacS/GacA two component signal transduction system. Antimicrob. Agents Chemother. (in press)

Zeng Q., M. D. Laiosa, D. A. Steeber, E. M. Biddle, Q. Peng, and C.-H. Yang. Cell individuality: the bistable gene expression of T3SS in Dickeya dadantii 3937. Mol. Plant-Microbe Interact. (in press).

Li, Y. R., Y. Z. Che, H. S. Zou, Y. P. Cui, W. Guo, L. F. Zou, E. Biddle, C. H. Yang*, and G. Y. Chen*. 2011. Hpa2 required by HrpF to translocate Xanthomonas oryzae transcriptional activator-like effectors into rice for pathogenicity. Appl. Environ. Microbiol. 77: 3809-3818. (* coresponding authors)

Ma, J, A. M. Ibekwe, X. Yi, H. Wang, A. Yamazaki, D. E. Crowley, and C.-H. Yang. 2011. Persistence of Escherichia coli O157:H7 and Its Mutants in Soils. PLoS ONE 6(8): e23191.

Glasner, J. D., C. H. Yang, S. Reverchon, N. Hugouvieux-Cotte-Pattat, G. Condemine, J. P. Bohin, F. Van Gijsegem, S. Yang, T. Franza, D. Expert, G. Plunkett, 3rd, M. J. San Francisco, A. O. Charkowski, B. Py, K. Bell, L. Rauscher, P. Rodriguez-Palenzuela, A. Toussaint, M. C. Holeva, S. Y. He, V. Douet, M. Boccara, C. Blanco, I. Toth, B. D. Anderson, B. S. Biehl, B. Mau, S. M. Flynn, F. Barras, M. Lindeberg, P. R. Birch, S. Tsuyumu, X. Shi, M. Hibbing, M. N. Yap, M. Carpentier, E. Dassa, M. Umehara, J. F. Kim, M. Rusch, P. Soni, G. F. Mayhew, D. E. Fouts, S. R. Gill, F. R. Blattner, N. T. Keen, and N. T. Perna. 2011. Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937. J. Bacteriol. 193: 2076-2077.

Yamazaki, A., J. Li, W. C. Hutchins, L. Wang, J. Ma, A. M. Ibekwe, and C.-H. Yang. 2011. Commensal effect of pectate lyases secreted from Dickeya dadantii on the proliferation of Escherichia coli O157:H7 EDL933 on lettuce leaves. Appl. Environ. Microbiol. 77:156-162.

Yang, S., Q. Peng, Q. Zhang, L. Zou, Y. Li, C. Robert, L. Pritchard, H. Liu, R. Hovey, Q. Wang, P. Birch, I. K. Toth, and C.-H. Yang. 2010. Genome-wide identification of HrpL-regulated genes in the necrotrophic phytopathogen Dickeya dadantii 3937. PLoS ONE 5(10): e13472.

Zeng, Q., A. M. Ibekwe, E. Biddle, and C.-H. Yang. 2010. Regulatory mechanisms of exoribonuclease PNPase and regulatory small RNA on T3SS of Dickeya dadantii. Mol. Plant-Microbe Interact. 23: 1345-1355.

Yi, X., A. Yamazaki, E. Biddle, Q. Zeng, and C.-H. Yang. 2010. Genetic analysis of two phosphodiesterases reveals cyclic diguanylate regulation of virulence factors in Dickeya dadantii. Mol. Microbiol. 77:787-800.

Li, Y., A. Yamazaki, L. Zou, E. Biddle, Q. Zeng, Y. Wang, H. Lin, Q. Wang, and C.-H. Yang. 2010. ClpXP protease regulates the Type III Secretion System of Dickeya dadantii 3937 and is essential for the bacterial virulence. Mol. Plant-Microbe Interact. 23:871-878.

Ibekwe, A. M., Papiernik, S. K., and C.-H. Yang. 2010. Influence of soil fumigation by methyl bromide and methyl iodide on rhizosphere and phyllosphere microbial community structure. J. Environ. Sci. Health B 45: 427-436.

Ibekwe, A. M., Papiernik, S. K., Grieve, C. M., and C.-H. Yang. 2010. Influence of fumigants on soil microbial diversity and survival of E. coli O157:H7. J. Environ. Sci. Health B 45: 416-426.

Ibekwe, A M., S. Papiernik, C. Grieve, and C.-H. Yang. 2009. Persistence of Escherichia coli O157:H7 on the rhizosphere and phyllosphere of lettuce. Lett. Appl. Microbiol. 49:784-790.

Wang, S., L.-Y. Chang, Y.-J. Wang, Q. Wang, C.-H. Yang, and R.-H. Mei. 2009. Nanoparticles affect the survival of bacteria on leaf surfaces. FEMS Microbiol. Ecol. 28: 182-191.

Li, Y., Q. Peng, D. Selimi, Q. Wang, A. O. Charkowski, X. Chen, and C.-H. Yang. 2009. The plant phenolic compound p-coumaric acid represses the Dickeya dadantii type III secretion system. Appl. Environ. Microbiol. 75:1223-1228.

Yang, S., Q. Peng, M. San Francisco, Y. Wang, Q. Zeng, and C.-H. Yang. 2008. Type III secretion system genes of Dickeya dadantii 3937 are induced by plant phenolic acids. PLoS ONE 3(8): e2973.

Glasner, J. D., M. Marquez-Villavicencio, H.-S. Kim, C. E. Jahn, B. Ma, B. S. Biehl, A. I. Rissman, B. Mole, X. Yi, C.-H. Yang, J. L. Dangl, S. R. Grant, N. T. Perna1, A. O. Charkowski. 2008. Niche-specificity and the variable fraction of the Pectobacterium pan-genome. Mol. Plant-Microbe Interact. 21:1549-60.

Yap, M.-N., C. Rojas, C.-H. Yang, and A. O. Charkowski. 2008. The response regulator HrpY of Dickeya dadantii 3937 regulates virulence genes not linked to the hrp cluster. Mol. Plant-Microbe Interact. 21: 304-314.

Yang, S., Q. Peng, Q. Zhang, X. Yi, C. J. Choi, R. M. Reedy, A. O. Charkowski, and C.-H. Yang. 2008. Dynamic regulation of GacA in type III secretion system, pectinase gene expression, pellicle formation, and pathogenicity of Dickeya dadantii. Mol. Plant-Microbe Interact. 21:133-142.

Yang L., C.-H. Yang, and J. Li. 2008. Adhesion and Retention of a Bacterial Phytopathogen Erwinia Chrysanthemi in Biofilm-Coated Porous Media. Environ. Sci. Technol. 42: 159–165.

Wang, Y.; H. Wang, C.-H. Yang, Q. Wang, and R. Mei. 2007. Two distinct manganese-containing superoxide dismutase genes in Bacillus cereus: their physiological characterizations and roles in surviving in wheat rhizosphere. FEMS Microbiol. Lett. 272:206-213.

Yang, S., Q. Zhang, J. Guo, A. O. Charkowski, B. R. Glick, A. M. Ibekwe, D. A. Cooksey, and C.-H. Yang. 2007. Global effect of Indole-3-acetic acid (IAA) biosynthesis on multiple virulence factors of Erwinia chrysanthemi 3937. Appl. Environ. Microbiol. 73: 1079-1088.

Yang L., C.-H. Yang, and J. Li. 2007. Influence of extracellular polymeric substances (EPS) on Pseudomonas aeruginosa transport and deposition profiles in porous media. Environ. Sci. Technol. 41:198-205.

Ibekwe, A. M., C. M. Grieve, and C.-H. Yang. 2007. Survival of E. coli O157:H7 in soil and on lettuce after soil fumigation. Can. J. Microbiol. 53:623-635.

Ahn, S.-J., C.-H. Yang, and D. A. Cooksey. 2007. Pseudomonas putida 06909 genes expressed during colonization on mycelial surfaces and phenotypic characterization of mutants. J. Appl. Microbiol. 103: 120-132.

Ibekwe, A. M., A. C. Kennedy, J. J. Halvorson, and C.-H. Yang. 2007. Characterization of developing microbial communities in Mount St. Helens pyroclastic substrate. Soil Biol. Biochem. 39:2496-2507.

Peng Q., S. Yang, A. O. Charkowski, M.-N. Yap, D. A. Steeber, N. T. Keen, and C.-H. Yang. 2006. Population behavior analysis of dspE and pelD regulation in Erwinia chrysanthemi 3937. Mol. Plant-Microbe Interact. 19:451-457.

Okinaka, Y., N. T. Perna, S. Yang, N. T. Keen, and C.-H. Yang. 2006. Identification of potential virulence genes in Erwinia chrysanthemi 3937: transposon insertion into plant-upregulated genes J. Gen. Plant Pathology 72: 360-368.

Yap, M.-N., C. Rojas, C.-H., Yang, and A. O. Charkowski. 2006. Harpin mediates cell aggregation in Erwinia chrysanthemi 3937. J. Bacteriol. 188:2280-2284.

Yang, L., Y.-H. Zhaoa, B.-X. Zhang, C.-H. Yang, and X. Zhang. 2005. Isolation and characterization of a chlorpyrifos and 3,5,6-trichloro-2-pyridionol degrading bacterium. FEMS Microbiol. Lett. 251:67-73.

Kawai T., C.-H. Yang, M. R. Matsumoto, D. E. Crowley, and J. D. Sheppard. 2005. Comparison of PCR-DGGE and selective plating methods for monitoring the dynamics of a mixed culture population in synthetic brewery wastewater. Biotechnol. Prog. 21:712–719.

Yap, M.-N., C.-H. Yang, J. D. Barak, and A. O. Charkowski. 2005. The Erwinia chrysanthemi type III secretion system is required for multicellular behavior. J. Bacteriol. 187:639-648.

Yang, S., N. T. Perna, D. A. Cooksey, Y. Okinaka, S. E. Lindow, A. M. Ibekwe, N. T. Keen, and C.-H Yang. 2004. Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array.  Mol. Plant-Microbe Interact. 17:999-1008.

Marschner, P., D. Crowley, and C.-H. Yang. 2004. Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type. Plant and Soil. 261: 199-208.

Ibekwe, A. M., S. K. Papiernik, and C.-H. Yang. 2004. Enrichment and molecular characterization of chloropicrin- and metam-sodium-degrading microbial communities. Appl. Microbiol. Biotechnol. 66:325-332.

Alvey, S., C.-H. Yang, A. Buerkert, and D. E. Crowley. 2003. Cereal/legume rotation effects on rhizosphere bacterial community structure in West African soils. Biol Fert. Soils 37:73-82.

Yang, C.-H., M. Gavilanes-Ruiz, Y. Okinaka, R. Vedel, I. Bethuy, M. Boccara, J. W. Chen, N. T. Perna, and N. T. Keen. 2002. hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. Mol. Plant-Microbe Interact. 15:472-480.

Okinaka, Y., C.-H. Yang, N. T. Perna, and N. T. Keen. 2002. Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection. Mol. Plant-Microbe Interact. 15:619-629.

Okinaka, Y., C.-H. Yang, E. Herman, A. Kinney, and N. T. Keen. 2002. The P34 elicitor interacts with a soybean photorespiration enzyme, NADH-dependent hydroxypyruvate reductase. Mol. Plant-Microbe Interact. 15:1213-1218.

Ibekwe A. M., A. C. Kennedy, P. S. Frohne, S. K. Papiernik, C.-H. Yang, and D. E. Crowley. 2002. Microbial diversity along a transect of agronomic zones. FEMS Microbial. Ecol. 39:183-191.

Luepromchai, E., A. C. Singer, C.-H. Yang, and D. E. Crowley. 2002. Interactions of earthworms with indigenous and bioaugmented PCB-degrading bacteria. FEMS Microbial. Ecol. 41:191-197.

Yang, C.-H., D. E. Crowley, J., Borneman, and N. T. Keen. 2001. Microbial phyllosphere populations are more complex than previously realized. Proc. Natl. Acad. Sci. USA 98:3889-3894.

Yang, C.-H., D. E. Crowley, and J. A. Mange. 2001. 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and phytophthora infected avocado roots. FEMS Microbial. Ecol. 35:129-136.

Marschner, P., C.-H. Yang, R. Lieberei, D. E. Crowley. 2001. Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol. Biochem. 33:1437-1445.

Ibekwe A. M., S. K. Papiernik, J. Gan, S. R. Yate, D. E. Crowley, and C.-H. Yang. 2001. Microcosm enrichment of 1, 3-Dichloropropene-degrading microbial communities. J. of Appl. Microbiol. 91:668-676.

Ibekwe A. M., S. K. Papiernik, J. Gan, S. R. Yate, C.-H. Yang, and D. E. Crowley. 2001. Impact of fumigants on soil microbial community. Appl. Environ. Microbiol. 67:3245-3257.

Yang, C.-H., D. E. Crowley, G. H. Anthony, and N. T. Keen. 2000. Strain level identification of Pseudomonas using denaturing gradient gel electrophoresis of 16S-23S spacer region rDNA. J. Gen. Plant Pathology 66:225-233.

Yang, C.-H., and D. E. Crowley. 2000. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl. Environ. Microbiol. 66:345-351.

Yang, C.-H., H. R. Azad, and D. A. Cooksey. 1996. A chromosomal locus required for copper resistance, competitive fitness, and cytochrome c biogenesis in Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 93:7315-7320.

Yang, C.-H., J. A. Menge, and D. A. Cooksey. 1994. Mutation affecting hyphal colonization and pyoverdine production in pseudomonads toward Phytophthora parasitica. Appl. Environ. Microbiol. 60:473-481.

Yang, C.-H., J. A. Menge, and D. A. Cooksey. 1993. Role of copper resistance in competitive survival of Pseudomonas fluorescens in soil. Appl. Environ. Microboil. 59:580-584.

Book Chapters:
Yang, C.-H. and S.-H. Yang. Managing bacterial plant diseases by modulating quorum sensing and Type III secretory systems. 2008. In: Z.K. Punja, S.H. De Boer and H. Sanfacon (eds.) Biotechnology and Plant Disease Management. CABI Publishing. Oxfordshire. UK. P. 16-57.

Crowley, D.E., E. S. Gilbert, A. Singer, D. Newcombe, and C.-H. Yang. 1999. Bioremediation of organic contaminants using repeated applications of xenobiotic degrading bacteria. In: R. Fass, Y Flashner, and S. Reuveny (eds.) Novel Methods for Bioremediation of Organic Pollution. Plenum Press. NY. p. 273-284.

Keen, N. T., C. K. Dumenyo, C.-H. Yang, and D. A Cooksey. 2000. From rags to riches: insights from the first genomic sequence of a plant pathogenic bacterium. Genome Biology 1: 1019.1-1019.4.

Keen, N. T. and C.-H. Yang. 1999. Functional genomics: Plant-Microbe interactions gingerly puts a foot in the water. Physiol. and Mol. Plant Pathology 55:313-315.