Cope et al. 2022 Comput. Struct. Biotechnol. J.

Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus

Kevin R. Cope, Erica R. Prates, John I. Miller, Omar Demerdash, Manesh Shah, David Kainer, Ashley Cliff, Kyle Sullivan, Mikaela Cashman, Matthew Lane, Anna Matthiadis, Jesse Labbé, Timonthy J. Tschaplinski, Daniel A. Jacobson, and Udaya C. Kalluri
December 31, 2022, Computational and Structural Biotechnology Journal; DOI: 10.1016/j.csbj.2022.12.052

Abstract

For plants, distinguishing between mutualistic and pathogenic microbes is a matter of survival. All microbes contain microbe-associated molecular patterns (MAMPs) that are perceived by plant pattern recognition receptors (PRRs). Lysin motif receptor-like kinases (LysM-RLKs) are PRRs attuned for binding and triggering a response to specific MAMPs, including chitin oligomers (COs) in fungi, lipo-chitooligosaccharides (LCOs), which are produced by mycorrhizal fungi and nitrogen-fixing rhizobial bacteria and peptidoglycan in bacteria. The identification and characterization of LysM-RLKs in candidate bioenergy crops including Populus are limited compared to other model plant species, thus inhibiting our ability to both understand and engineer microbe-mediated gains in plant productivity. As such, we performed a sequence analysis of LysM-RLKs in the Populus genome and predicted their function based on phylogenetic analysis with known LysM-RLKs. Then, using predicted models, molecular dynamics simulations, and comparative structural analysis with previously characterized CO and LCO plant receptors, we identified probable ligand-binding sites in Populus LysM-RLKs. Using several machine learning models, we predicted remarkably consistent binding affinity rankings of Populus proteins to CO. In addition, we used a modified Random Walk with Restart network-topology based approach to identify a subset of Populus LysM-RLKs that are functionally related and propose a corresponding signal transduction cascade. Our findings provide the first look into the role of LysM-RLKs in Populus-microbe interactions and establish a crucial jumping-off point for future research efforts to understand specificity and redundancy in microbial perception mechanisms.

Citation

Cope KR, Prates ET, Miller JI, Demerdash O, Shah M, Kainer D, Cliff A, Sullivan K, Cashman M, Lane M, Matthiadis A, Labbé J, Tschaplinski TJ, Jacobson DA, and Kalluri UC (2022). Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus.” Computational and Structural Biotechnology Journal, In Press. https://doi.org/10.1016/j.csbj.2022.12.052.