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http://dx.doi.org/10.14348/molcells.2018.0403

A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems  

Kim, Hanhae (Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University)
Joe, Anna (Department of Plant Pathology and the Genome Center, University of California)
Lee, Muyoung (Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University)
Yang, Sunmo (Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University)
Ma, Xiaozhi (Rice Research Institute, Guangdong Academy of Agricultural Sciences)
Ronald, Pamela C. (Department of Plant Pathology and the Genome Center, University of California)
Lee, Insuk (Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University)
Publication Information
Molecules and Cells / v.42, no.2, 2019 , pp. 166-174 More about this Journal
Abstract
Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.
Keywords
co-functional network; plant bacterial pathogen; Xanthomonas oryzae pv. oryzae;
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