Agricultural proteomics

Cooper’s mass spectrometry-based proteomics research has vastly added to the understanding of biomolecular systems.  His first application of mass spectrometry was for the identification of an unknown plant virus.  He followed this by discovering more than 2,500 proteins from A. thaliana leaves, 3,000 proteins from Phaseolus vulgaris leaves, and 1,400 proteins from soybean root hairs.  He has resolved hundreds of proteins from plant pathogens Phakopsora pachyrhizi, Uromyces appendiculatus, Phytophthora sojae, and Ustilago maydis.  Using more refined techniques such as cellular fractionation, enrichment and relative quantification, Cooper has identified and compared more than 7,000 soybean leaf proteins, including 300 proteins from nuclei and 800 phosphorylated proteins, and more than 25% of the A. thaliana proteome including 1,300 membrane proteins and 300 phosphorylated proteins.  He has studied 37% of the proteome of Salmonella enterica to determine the system-wide effects of its growth in lettuce wash waters. In 2012, Cooper and collaborators were the first to discover the biochemical regulation of ethylene signal transduction.

Papers:

Disruptive Effects of Resveratrol on a Bacterial Pathogen of Beans (2023). Bret Cooper. Journal of Proteome Research 22, 204-214.  Published on-line before print December 13, 2022.  DOI: 10.1021/acs.jproteome.2c00633 

The Detriment of Salicylic Acid to the Pseudomonas savastanoi pv. phaseolicola Proteome (2022).  Bret Cooper.  Molecular Plant-Microbe Interactions 9, 814-824.  Published on-line before print May 25, 2022.  DOI: 10.1094/MPMI-05-22-0104-R 

Bacterial Immobilization and Toxicity Induced by a Bean Plant Immune System (2021). Bret Cooper, Hunter S. Beard, Ronghui Yang, Wesley M. Garrett, and Kimberly B. Campbell. Journal of Proteome Research 20, 3664-3677. DOI: 10.1021/acs.jproteome.1c00232

Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies (2021). Ashwil Klein, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, and David L. Tabb.  Plants 10, 765. 

The Proteomics of Resistance to Halo Blight in Common Bean (2020). Bret Cooper, Kimberly B. Campbell, Hunter Beard, Wesley M Garrett, and Marcio E. Ferreira.  Molecular Plant-Microbe Interactions 33, 1161-1175.  Published on-line before print July 7, 2020. DOI: 10.1094/MPMI-05-20-0112-R 

Benzothiadiazole Conditions the Bean Proteome for Immunity to Bean Rust (2020). Bret Cooper, Hunter Beard, Wesley M. Garrett, and Kimberly B. Campbell.  Molecular Plant-Microbe Interactions.  Published on-line before print January 30, 2020. DOI: 10.1094/MPMI-09-19-0250-R

Blistering1 Modulates Penicillium expansum Virulence via Vesicle-Mediated Protein Secretion (2019).  Wayne M. Jurick II, Hui Peng, Hunter S. Beard, Wesley M. Garrett, Franz J. Lichtner, Dianiris Luciano-Rosario, Otilia Macarisin, Yingjian Liu, Kari A. Peter, Verneta L. Gaskins, Tianbao Yang, Joseph Mowery, Gary Bauchan, Nancy P. Keller, and Bret Cooper. Molecular and Cellular Proteomics 19, 344-361.  Published on-line before print December 23, 2019.  DOI:10.1074/mcp.RA119.001831.

Quantitative Proteomics Reveals a Role for SERINE/ARGININE-Rich 45 in Regulating RNA Metabolism and Modulating Transcriptional Suppression via the ASAP Complex in Arabidopsis thaliana (2019). Samuel L. Chen, Timothy J. Rooney, Anna R. Hu, Hunter S. Beard, Wesley M. Garrett, Leann M. Mangalath, Jordan J. Powers, Bret Cooper, and Xiao-Ning Zhang. Frontiers in Plant Science 10, 1116.  Published on-line September 19, 2019.  DOI: 10.3389/fpls.2019.01116

Quantitative Proteomic Analysis of Staphylococcus aureus Treated with Punicalagin, a Natural Antibiotic from Pomegranate that Disrupts Iron Homeostasis and Induces SOS (2018). Bret Cooper, Nazrul Islam, Yunfeng Xu, Hunter S. Beard, Wesley M. Garrett, Ganyu Gu, and Xiangwu Nou.  Proteomics 18, 1700461.

A Proteomic Network for Symbiotic Nitrogen Fixation Efficiency in Bradyrhizobium elkanii (2018). Bret Cooper, Kimberly B. Campbell, Hunter Beard, Wesley M Garrett, Joseph Mowery, Gary R. Bauchan, and Patrick Elia.  Molecular Plant-Microbe Interactions 31, 334-343.

Putative Rust Fungal Effector Proteins in Infected Bean and Soybean Leaves (2016). Bret Cooper, Kimberly B Campbell, Hunter S. Beard, Wesley M Garrett, and Nazrul Islam. Phytopathology 106, 491-499. 

Proteomics of Nitrogen Remobilization in Poplar Bark (2015).  Nazrul Islam, Gen Li, Wesley M. Garrett, Rongshuang Lin, Ganesh Sriram, Bret Cooper, and Gary D. Coleman. Journal of Proteome Research 14, 1112-1126. 

Phosphothreonine 218 is required for the function of SR45.1 in regulating flower petal development in Arabidopsis (2014).  Xiao-Ning Zhang, Cecilia Mo, Wesley M. Garrett, and Bret Cooper. Plant Signaling & Behavior, 9, e29134.

Separation anxiety:  An analysis of ethylene-induced cleavage of EIN2 (2013).  Bret Cooper. Plant Signaling & Behavior, 8, e24721-1-5.

CTR1 phosphorylates the central regulator EIN2 to control ethylene hormone signaling from the ER membrane to the nucleus in Arabidopsis (2012). Chuanli Ju, Gyeong Mee Yoon, Jennifer M. Shemansky, David Lin, Z. Irene Ying, Jianhong Chang, Wesley M. Garrett, Mareike Kessenbrock, Georg Groth, Mark L. Tucker, Bret Cooper, Joseph J. Kieber and Caren Chang. Proc. Natl. Acad. Sci. USA, 109, 19486-19491.  Published on-line before print Nov. 6, 2012.

Proteomic Pleiotropy of OpgGH, an Operon Necessary for Efficient Growth of Salmonella enterica serovar Typhimurium under Low-osmotic Conditions (2012).  Bret Cooper, Ruiqiang Chen, Wesley M. Garrett, Charles Murphy, Caren Chang, Mark L. Tucker, and Arvind A. Bhagwat. Journal of Proteome Research, 11, 1720-1727.

Proteomic Responses in Arabidopsis thaliana Seedlings Treated with Ethylene (2011).  Ruiqiang Chen, Brad M. Binder, Wesley M. Garrett, Mark L. Tucker, Caren Chang and Bret Cooper.  Molecular BioSystems, 7, 2637-2650.

Nuclear Proteomic Changes Linked to Soybean Rust Resistance (2011).  Bret Cooper, Kimberly B. Campbell, Jian Feng, Wesley M. Garrett and Reid Frederick.  Molecular BioSystems 7, 773-783.  Published on-line before print Dec. 3, 2010.

Relative, Label-free Protein Quantitation: Spectral Counting Error Statistics from Nine Replicate MudPIT Samples (2010).  Bret Cooper, Jian Feng, Wesley M. Garrett.  Journal of the American Society for Mass Spectrometry 21, 1534-1546.  Published on-line before print May 6, 2010.

Establishment of a Protein Reference Map for Soybean Root Hair Cells (2009). Laurent Brechenmacher, Joohyun Lee, Sherri Sachdev, Zhao Song, Tran Hong Nha Nguyen, Trupti Joshi, Nathan Oehrle, Marc Libault, Brian Mooney, Dong Xu, Bret Cooper, and Gary Stacey.  Plant Physiology 149, 670–682.  Published on-line before print November 26, 2008.

Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus (2009).  Joohyun Lee, Kimberly B. Campbell, Brian E. Scheffler, Jian Feng, Daniel Q. Naiman, Wesley M. Garrett, Sandra Thibivilliers, Gary Stacey, Mark L. Tucker, M.A. Pastor-Corrales and Bret Cooper.  Molecular and Cellular Proteomics 8, 19-31.  Published on-line before print August 28, 2008.

Tandem Mass Spectrometry for the Detection of Plant Pathogenic Fungi and the Effects of Database Composition on Protein Inferences (2007).  Neerav D. Padliya, Wesley M. Garrett, Kimberly B. Campbell, David L. Tabb, and Bret Cooper.  Proteomics 7, 3932-3942.

Shotgun Proteomic Analysis of Arabidopsis thaliana Leaves (2007).  Joohyun Lee, Wesley M. Garrett and Bret Cooper.  Journal of Separation Science 30, 2225-2230.  Published on line before print July 25, 2007.  DOI: 10.1002/jssc.200700151.

Protein Accumulation in the Germinating Uromyces appendiculatus Uredospore (2007). Bret Cooper, Anil Neelam, Kimberly B. Campbell, Joohyun Lee, George Liu, Wesley M. Garrett, Brian Scheffler and Mark L. Tucker.  Molecular Plant-Microbe Interactions 20, 857-866.  DOI: 10.1094/MPMI-20-7-0857

Alternative Workflows for Plant Proteomic Analysis (2006).  Joohyun Lee and Bret Cooper.  Molecular BioSystems 2, 621-626, DOI: 10.1039/b612326k. (review)

Mass Spectrometry-Based Proteomics for the Detection of Plant Pathogens (2006).  Neerav D. Padliya and Bret Cooper.  Proteomics 6, 4069-4075. (review)

Shotgun Identification of Proteins from Uredospores of the Bean Rust Uromyces appendiculatus (2006).  Bret Cooper, Wesley M. Garrett and Kimberly B. Campbell.  Proteomics6, 2477-2484.

Investigative Proteomics:  Identification of an Unknown Plant Virus from Infected Plants Using Mass Spectrometry (2003).  Bret Cooper, Donna Eckert, Nancy L. Andon, John R. Yates III and Paul A. Haynes.  Journal of the American Society for Mass Spectrometry 14, 736-741; published online before print May 23, 2003.