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Berard A, Kroeker A, McQueen P, Coombs KM. Methods and approaches to disease mechanisms using systems kinomics. Synth Syst Biotechnol 2018; 3:34-43. [PMID: 29911197 PMCID: PMC5884222 DOI: 10.1016/j.synbio.2017.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 02/06/2023] Open
Abstract
All cellular functions, ranging from regular cell maintenance and homeostasis, specialized functions specific to cellular types, or generating responses due to external stimulus, are mediated by proteins within the cell. Regulation of these proteins allows the cell to alter its behavior under different circumstances. A major mechanism of protein regulation is utilizing protein kinases and phosphatases; enzymes that catalyze the transfer of phosphates between substrates [1]. Proteins involved in phosphate signaling are well studied and include kinases and phosphatases that catalyze opposing reactions regulating both structure and function of the cell. Kinomics is the study of kinases, phosphatases and their targets, and has been used to study the functional changes in numerous diseases and infectious diseases with aims to delineate the cellular functions affected. Identifying the phosphate signaling pathways changed by certain diseases or infections can lead to novel therapeutic targets. However, a daunting 518 putative protein kinase genes have been identified [2], indicating that this protein family is very large and complex. Identifying which enzymes are specific to a particular disease can be a laborious task. In this review, we will provide information on large-scale systems biology methodologies that allow global screening of the kinome to more efficiently identify which kinase pathways are pertinent for further study.
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Affiliation(s)
- Alicia Berard
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | | | - Peter McQueen
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Canada
| | - Kevin M. Coombs
- Department of Medical Microbiology, University of Manitoba, Winnipeg, R3E 0J9, Canada
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Li TG, Zhang DD, Zhou L, Kong ZQ, Hussaini AS, Wang D, Li JJ, Short DPG, Dhar N, Klosterman SJ, Wang BL, Yin CM, Subbarao KV, Chen JY, Dai XF. Genome-Wide Identification and Functional Analyses of the CRK Gene Family in Cotton Reveals GbCRK18 Confers Verticillium Wilt Resistance in Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2018; 9:1266. [PMID: 30254650 PMCID: PMC6141769 DOI: 10.3389/fpls.2018.01266] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/10/2018] [Indexed: 05/07/2023]
Abstract
Cysteine-rich receptor-like kinases (CRKs) are a large subfamily of plant receptor-like kinases that play a critical role in disease resistance in plants. However, knowledge about the CRK gene family in cotton and its function against Verticillium wilt (VW), a destructive disease caused by Verticillium dahliae that significantly reduces cotton yields is lacking. In this study, we identified a total of 30 typical CRKs in a Gossypium barbadense genome (GbCRKs). Eleven of these (>30%) are located on the A06 and D06 chromosomes, and 18 consisted of 9 paralogous pairs encoded in the A and D subgenomes. Phylogenetic analysis showed that the GbCRKs could be classified into four broad groups, the expansion of which has probably been driven by tandem duplication. Gene expression profiling of the GbCRKs in resistant and susceptible cotton cultivars revealed that a phylogenetic cluster of nine of the GbCRK genes were up-regulated in response to V. dahliae infection. Virus-induced gene silencing of each of these nine GbCRKs independently revealed that the silencing of GbCRK18 was sufficient to compromise VW resistance in G. barbadense. GbCRK18 expression could be induced by V. dahliae infection or jasmonic acid, and displayed plasma membrane localization. Therefore, our expression analyses indicated that the CRK gene family is differentially regulated in response to Verticillium infection, while gene silencing experiments revealed that GbCRK18 in particular confers VW resistance in G. barbadense.
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Affiliation(s)
- Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Adamu S. Hussaini
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun-Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dylan P. G. Short
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- U.S. Agricultural Research Station, Salinas, CA, United States
| | - Nikhilesh Dhar
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- U.S. Agricultural Research Station, Salinas, CA, United States
| | - Steven J. Klosterman
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA, United States
| | - Bao-Li Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun-Mei Yin
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- U.S. Agricultural Research Station, Salinas, CA, United States
- *Correspondence: Krishna V. Subbarao, Jie-Yin Chen, Xiao-Feng Dai,
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Krishna V. Subbarao, Jie-Yin Chen, Xiao-Feng Dai,
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Krishna V. Subbarao, Jie-Yin Chen, Xiao-Feng Dai,
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Kim NY, Jang YJ, Park OK. AP2/ERF Family Transcription Factors ORA59 and RAP2.3 Interact in the Nucleus and Function Together in Ethylene Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:1675. [PMID: 30510560 PMCID: PMC6254012 DOI: 10.3389/fpls.2018.01675] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/26/2018] [Indexed: 05/19/2023]
Abstract
The gaseous plant hormone ethylene is a key signaling molecule regulating plant growth, development, and defense against pathogens. Octadecanoid-responsive arabidopsis 59 (ORA59) is an ethylene response factor (ERF) transcription factor and has been suggested to integrate ethylene and jasmonic acid signaling and regulate resistance to necrotrophic pathogens. Here we screened for ORA59 interactors using the yeast two-hybrid system to elucidate the molecular function of ORA59. This led to the identification of RELATED TO AP2.3 (RAP2.3), another ERF transcription factor belonging to the group VII ERF family. In binding assays, ORA59 and RAP2.3 interacted in the nucleus and showed ethylene-dependent nuclear localization. ORA59 played a positive role in ethylene-regulated responses, including the triple response, featured by short, thick hypocotyl and root, and exaggerated apical hook in dark-grown seedlings, and resistance to the necrotrophic pathogen Pectobacterium carotovorum, as shown by the increased and decreased ethylene sensitivity and disease resistance in ORA59-overexpressing (ORA59OE) and null mutant (ora59) plants, respectively. In genetic crosses, ORA59OE rap2.3 crossed lines lost ORA59-mediated positive effects and behaved like rap2.3 mutant. These results suggest that ORA59 physically interacts with RAP2.3 and that this interaction is important for the regulatory roles of ORA59 in ethylene responses.
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