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Disturbance of Arabidopsis thaliana microRNA-regulated pathways by Xcc bacterial effector proteins

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Abstract

Plants are continuously subjected to infection by pathogens, including bacteria and viruses. Bacteria can inject a variety of effector proteins into the host to reprogram host defense mechanism. It is known that microRNAs participate in plant disease resistance to bacterial pathogens and previous studies have suggested that some bacterial effectors have evolved to disturb the host’s microRNA-regulated pathways; and so enabling infection. In this study, the inter-species interaction between an Xanthomonas campestris pv campestris (Xcc) pathogen effector and Arabidopsis thaliana microRNA transcription promoter was investigated using three methods: (1) interolog, (2) alignment based on using transcription factor binding site profile matrix, and (3) the web-based binding site prediction tool, PATSER. Furthermore, we integrated another two data sets from our previous study into the present web-based system. These are (1) microRNA target genes and their downstream effects mediated by protein–protein interaction (PPI), and (2) the Xcc–Arabidopsis PPI information. This present work is probably the first comprehensive study of constructing pathways that comprises effector, microRNA, target genes and PPI for the study of pathogen–host interactions. It is expected that this study may help to elucidate the role of pathogen–host interplay in a plant’s immune system. The database is freely accessible at: http://ppi.bioinfo.asia.edu.tw/EDMRP.

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Acknowledgments

The work of Ka-Lok Ng and Nilubon Kurubanjerdjit is supported by the National Science Council of Taiwan, under the grants of NSC 100-2221-E-468-013, and NSC 101-2221-E-468 -027. The work of Ka-Lok Ng and Jeffrey J.P. Tsai is supported by the grants of NSC 99-2632-E-468-001-MY3. The work of Chien-Hung Huang is supported by the grants of NSC 101-2221-E-150-088-MY2. Our gratitude goes to Dr. Timothy Williams, Asia University, for his help in proof reading the manuscript.

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Authors and Affiliations

  1. Department of Biomedical Informatics, Asia University, Taichung, 41354, Taiwan

    Nilubon Kurubanjerdjit, Jeffrey J. P. Tsai & Ka-Lok Ng

  2. School of Information Technology, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Nilubon Kurubanjerdjit

  3. Department of Computer Science and Information Engineering, National Formosa University, Huwei, 632, Taiwan

    Chien-Hung Huang

  4. School of Pharmacy, China Medical University, Taichung, 40402, Taiwan

    Ka-Lok Ng

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  1. Nilubon Kurubanjerdjit
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  2. Jeffrey J. P. Tsai
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  3. Chien-Hung Huang
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  4. Ka-Lok Ng
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Correspondence to Ka-Lok Ng.

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Kurubanjerdjit, N., Tsai, J.J.P., Huang, CH. et al. Disturbance of Arabidopsis thaliana microRNA-regulated pathways by Xcc bacterial effector proteins. Amino Acids 46, 953–961 (2014). https://doi.org/10.1007/s00726-013-1646-2

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  • DOI: https://doi.org/10.1007/s00726-013-1646-2

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