scholarly journals DeepLRR: An Online Webserver for Leucine-Rich-Repeat Containing Protein Characterization Based on Deep Learning

Plants ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 136
Author(s):  
Zhenya Liu ◽  
Zirui Ren ◽  
Lunyi Yan ◽  
Feng Li
Keyword(s):  
Gene Cluster ◽  
Plant Disease Resistance ◽  
Plant Disease ◽  
Evolutionary Relationship ◽  
Chromosome Mapping ◽  
Protein Characterization ◽  
Biological Processes ◽  
Leucine Rich Repeat ◽  
Resistance Proteins ◽  
New Perspective

Members of the leucine-rich repeat (LRR) superfamily play critical roles in multiple biological processes. As the LRR unit sequence is highly variable, accurately predicting the number and location of LRR units in proteins is a highly challenging task in the field of bioinformatics. Existing methods still need to be improved, especially when it comes to similarity-based methods. We introduce our DeepLRR method based on a convolutional neural network (CNN) model and LRR features to predict the number and location of LRR units in proteins. We compared DeepLRR with six existing methods using a dataset containing 572 LRR proteins and it outperformed all of them when it comes to overall F1 score. In addition, DeepLRR has integrated identifying plant disease-resistance proteins (NLR, LRR-RLK, LRR-RLP) and non-canonical domains. With DeepLRR, 223, 191 and 183 LRR-RLK genes in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa ssp. Japonica) and tomato (Solanum lycopersicum) genomes were re-annotated, respectively. Chromosome mapping and gene cluster analysis revealed that 24.2% (54/223), 29.8% (57/191) and 16.9% (31/183) of LRR-RLK genes formed gene cluster structures in Arabidopsis, rice and tomato, respectively. Finally, we explored the evolutionary relationship and domain composition of LRR-RLK genes in each plant and distributions of known receptor and co-receptor pairs. This provides a new perspective for the identification of potential receptors and co-receptors.

scholarly journals Tomato Prf Is a Member of the Leucine-Rich Repeat Class of Plant Disease Resistance Genes and Lies Embedded within the Pto Kinase Gene Cluster

Cell ◽  
1996 ◽  
Vol 86 (1) ◽  
pp. 123-133 ◽  
Author(s):  
John M Salmeron ◽  
Giles E.D Oldroyd ◽  
Caius M.T Rommens ◽  
Steven R Scofield ◽  
Han-Suc Kim ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Gene Cluster ◽  
Resistance Genes ◽  
Plant Disease Resistance ◽  
Plant Disease ◽  
Leucine Rich Repeat ◽  
Kinase Gene ◽  
Repeat Class ◽  
Plant Disease Resistance Genes ◽  
Pto Kinase

scholarly journals N-Terminal Motifs in Some Plant Disease Resistance Proteins Function in Membrane Attachment and Contribute to Disease Resistance

2012 ◽  
Vol 25 (3) ◽  
pp. 379-392 ◽  
Author(s):  
Daigo Takemoto ◽  
Maryam Rafiqi ◽  
Ursula Hurley ◽  
Greg J. Lawrence ◽  
Maud Bernoux ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Disease Resistance ◽  
Golgi Apparatus ◽  
Plant Disease Resistance ◽  
Plant Disease ◽  
Protein Accumulation ◽  
Resistance Proteins ◽  
Membrane Attachment ◽  
Signal Anchor ◽  
Terminal Domains

To investigate the role of N-terminal domains of plant disease resistance proteins in membrane targeting, the N termini of a number of Arabidopsis and flax disease resistance proteins were fused to green fluorescent protein (GFP) and the fusion proteins localized in planta using confocal microscopy. The N termini of the Arabidopsis RPP1-WsB and RPS5 resistance proteins and the PBS1 protein, which is required for RPS5 resistance, targeted GFP to the plasma membrane, and mutation of predicted myristoylation and potential palmitoylation sites resulted in a shift to nucleocytosolic localization. The N-terminal domain of the membrane-attached Arabidopsis RPS2 resistance protein was targeted incompletely to the plasma membrane. In contrast, the N-terminal domains of the Arabidopsis RPP1-WsA and flax L6 and M resistance proteins, which carry predicted signal anchors, were targeted to the endomembrane system, RPP1-WsA to the endoplasmic reticulum and the Golgi apparatus, L6 to the Golgi apparatus, and M to the tonoplast. Full-length L6 was also targeted to the Golgi apparatus. Site-directed mutagenesis of six nonconserved amino acid residues in the signal anchor domains of L6 and M was used to change the localization of the L6 N-terminal fusion protein to that of M and vice versa, showing that these residues control the targeting specificity of the signal anchor. Replacement of the signal anchor domain of L6 by that of M did not affect L6 protein accumulation or resistance against flax rust expressing AvrL567 but removal of the signal anchor domain reduced L6 protein accumulation and L6 resistance, suggesting that membrane attachment is required to stabilize the L6 protein.

scholarly journals Structure–function analysis of the NB-ARC domain of plant disease resistance proteins

2008 ◽  
Vol 59 (6) ◽  
pp. 1383-1397 ◽  
Author(s):  
Gerben van Ooijen ◽  
Gabriele Mayr ◽  
Mobien M. A. Kasiem ◽  
Mario Albrecht ◽  
Ben J. C. Cornelissen ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Structure Function ◽  
Plant Disease Resistance ◽  
Plant Disease ◽  
Function Analysis ◽  
Resistance Proteins

scholarly journals A cell death assay in barley and wheat protoplasts for identification and validation of matching pathogen AVR effector and plant NLR immune receptors

Plant Methods ◽  
2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Isabel M. L. Saur ◽  
Saskia Bauer ◽  
Xunli Lu ◽  
Paul Schulze-Lefert
Keyword(s):  
Cell Death ◽  
Plant Disease Resistance ◽  
Fungal Pathogen ◽  
Fungal Pathogens ◽  
Plant Disease ◽  
Mesophyll Protoplast ◽  
Leucine Rich Repeat ◽  
Cell Death Assay ◽  
Host Cell Death ◽  
A Cell

Abstract Background Plant disease resistance to host-adapted pathogens is often mediated by host nucleotide-binding and leucine-rich repeat (NLR) receptors that detect matching pathogen avirulence effectors (AVR) inside plant cells. AVR-triggered NLR activation is typically associated with a rapid host cell death at sites of attempted infection and this response constitutes a widely used surrogate for NLR activation. However, it is challenging to assess this cell death in cereal hosts. Results Here we quantify cell death upon NLR-mediated recognition of fungal pathogen AVRs in mesophyll leaf protoplasts of barley and wheat. We provide measurements for the recognition of the fungal AVRs AvrSr50 and AVRa1 by their respective cereal NLRs Sr50 and Mla1 upon overexpression of the AVR and NLR pairs in mesophyll protoplast of both, wheat and barley. Conclusions Our data demonstrate that the here described approach can be effectively used to detect and quantify death of wheat and barley cells induced by overexpression of NLR and AVR effectors or AVR effector candidate genes from diverse fungal pathogens within 24 h.

scholarly journals Recent Advances in Understanding the Function of the PGIP Gene and the Research of Its Proteins for the Disease Resistance of Plants

2021 ◽  
Vol 11 (23) ◽  
pp. 11123
Author(s):  
Siqi Cheng ◽  
Ruonan Li ◽  
Lili Lin ◽  
Haojie Shi ◽  
Xunyan Liu ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Plant Disease Resistance ◽  
Plant Disease ◽  
Resistance Breeding ◽  
Leucine Rich Repeat ◽  
Repeat Structure ◽  
Recent Advances ◽  
Polygalacturonase Inhibiting Protein ◽  
Disease Factor ◽  
Pgip Gene

Polygalacturonase-inhibiting protein (PGIP) is an important plant biochemical anti-disease factor. PGIP has a leucine-rich repeat structure that can selectively bind and inhibit the activity of endo-polygalacturonase (endo-PG) in fungi, playing a key role in plant disease resistance. The regulation of PGIP in plant disease resistance has been well studied, and the effect of PGIP to increase disease resistance is clear. This review summarizes recent advances in understanding the PGIP protein structure, the PGIP mechanism of plant disease resistance, and anti-disease activity by PGIP gene transfer. This overview should contribute to a better understanding of PGIP function and can help guide resistance breeding of PGIP for anti-disease effects.

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