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1. The Tomato U-Box Type E3 Ligase PUB13 Acts With Group III Ubiquitin E2 Enzymes to Modulate FLS2-Mediated Immune Signaling

   https://doi.org/10.3389/fpls.2018.00615  

   Zhou, Bangjun; Zeng, Lirong (May 2018, Frontiers in Plant Science)
2. RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development

   https://doi.org/10.12688/f1000research.25750.1  

   Ivanchenko, Maria G; Ozguc, Olivia R; Bollmann, Stephanie R; Fraser, Valerie N; Megraw, Molly (January 2020, F1000Research)

   Cyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (‘Ailsa Craig’) anddgttissues from three spatially separated developmental stages of the tomato root tip, with three replicates for each tissue and genotype. We also identify differentially expressed genes, provide an initial comparison of genes affected in each genotype and tissue, and provide the pipeline used to analyze the data. Further analysis of this dataset can be used to gain insight into the effects of DGT on various root developmental pathways in tomato. 

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3. Comparison between slow anisotropic LE4PD fluctuations and the principal component analysis modes of ubiquitin

   https://doi.org/10.1063/5.0041211  

   Beyerle, E. R.; Guenza, M. G. (March 2021, The Journal of Chemical Physics)
4. Ubiquitylome analysis reveals a central role for the ubiquitin-proteasome system in plant innate immunity

   https://doi.org/10.1093/plphys/kiab011  

   Ma, Xiyu; Zhang, Chao; Kim, Do Young; Huang, Yanyan; Chatt, Elizabeth; He, Ping; Vierstra, Richard D; Shan, Libo (January 2021, Plant Physiology)

   null (Ed.)

   Abstract Protein ubiquitylation profoundly expands proteome functionality and diversifies cellular signaling processes, with recent studies providing ample evidence for its importance to plant immunity. To gain a proteome-wide appreciation of ubiquitylome dynamics during immune recognition, we employed a two-step affinity enrichment protocol based on a 6His-tagged ubiquitin (Ub) variant coupled with high sensitivity mass spectrometry to identify Arabidopsis proteins rapidly ubiquitylated upon plant perception of the microbe-associated molecular pattern (MAMP) peptide flg22. The catalog from 2-week-old seedlings treated for 30 min with flg22 contained 690 conjugates, 64 Ub footprints, and all seven types of Ub linkages, and included previously uncharacterized conjugates of immune components. In vivo ubiquitylation assays confirmed modification of several candidates upon immune elicitation, and revealed distinct modification patterns and dynamics for key immune components, including poly- and monoubiquitylation, as well as induced or reduced levels of ubiquitylation. Gene ontology and network analyses of the collection also uncovered rapid modification of the Ub-proteasome system itself, suggesting a critical auto-regulatory loop necessary for an effective MAMP-triggered immune response and subsequent disease resistance. Included targets were UBIQUITIN-CONJUGATING ENZYME 13 (UBC13) and proteasome component REGULATORY PARTICLE NON-ATPASE SUBUNIT 8b (RPN8b), whose subsequent biochemical and genetic analyses implied negative roles in immune elicitation. Collectively, our proteomic analyses further strengthened the connection between ubiquitylation and flg22-based immune signaling, identified components and pathways regulating plant immunity, and increased the database of ubiquitylated substrates in plants. 

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5. Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modes

   https://doi.org/10.1063/1.5123513  

   Beyerle, Eric R.; Guenza, Marina G. (October 2019, The Journal of Chemical Physics)