LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors

Bej, Aritra; Sahoo, Bikash R.; Swain, Bichitrananda; Basu, Madhubanti; Jayasankar, P.; Samanta, Mrinal

doi:10.1016/j.compbiomed.2014.07.016

Cited by 36 publications

(39 citation statements)

References 37 publications

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“…70% similarity with each other; moreover, both Pm60 and PmR1 are typical CC‐NB‐LRR proteins (Fig. S5) based on the SMART program (http://smart.embl-heidelberg.de/) (Letunic et al ., ) and the LRRsearch program (http://lrrsearch.com/index.php?page=tool) (Bej et al ., ).…”

Section: Resultsmentioning

confidence: 97%

The NB‐LRR gene Pm60 confers powdery mildew resistance in wheat

et al. 2017

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Powdery mildew is one of the most devastating diseases of wheat. To date, few powdery mildew resistance genes have been cloned from wheat due to the size and complexity of the wheat genome. Triticum urartu is the progenitor of the A genome of wheat and is an important source for powdery mildew resistance genes. Using molecular markers designed from scaffolds of the sequenced T. urartu accession and standard map-based cloning, a powdery mildew resistance locus was mapped to a 356-kb region, which contains two nucleotide-binding and leucine-rich repeat domain (NB-LRR) protein-encoding genes. Virus-induced gene silencing, single-cell transient expression, and stable transformation assays demonstrated that one of these two genes, designated Pm60, confers resistance to powdery mildew. Overexpression of full-length Pm60 and two allelic variants in Nicotiana benthamiana leaves induced hypersensitive cell death response, but expression of the coiled-coil domain alone was insufficient to induce hypersensitive response. Yeast two-hybrid, bimolecular fluorescence complementation and luciferase complementation imaging assays showed that Pm60 protein interacts with its neighboring NB-containing protein, suggesting that they might be functionally related. The identification and cloning of this novel wheat powdery mildew resistance gene will facilitate breeding for disease resistance in wheat.

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Section: Resultsmentioning

confidence: 97%

The NB‐LRR gene Pm60 confers powdery mildew resistance in wheat

et al. 2017

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“…All genes were expressed from the CaMV 35S promoter. were identified using the LRRSearch Tool (Bej, et al, 2014) and adjusted manually. Figure S4.…”

Section: Generation Of Synthetic Ptr1mentioning

confidence: 99%

Ptr1evolved convergently withRPS2andMr5to mediate recognition of AvrRpt2 in diverse solanaceous species

Mazo-Molina

Mainiero

Haefner

et al. 2020

Preprint

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SummaryThe Ptr1 (Pseudomonas tomato race 1) locus in Solanum lycopersicoides confers resistance to strains of Pseudomonas syringae pv. tomato expressing AvrRpt2 and Ralstonia pseudosolanacearum expressing RipBN. Here we describe the identification and phylogenetic analysis of the Ptr1 gene. A single recombinant among 585 F2 plants segregating for the Ptr1 locus was discovered that narrowed the Ptr1 candidates to eight nucleotide-binding leucine-rich repeat protein (NLR)-encoding genes. From analysis of the gene models in the S. lycopersicoides genome sequence and RNA-Seq data, two of the eight genes emerged as the strongest candidates for Ptr1. One of these two candidates was found to encode Ptr1 based on its ability to mediate recognition of AvrRpt2 and RipBN when it was transiently expressed with these effectors in leaves of Nicotiana glutinosa. The ortholog of Ptr1 in tomato and in Solanum pennellii is a pseudogene. However, a functional Ptr1 ortholog exists in N. benthamiana and potato and both mediate recognition of AvrRpt2 and RipBN. In apple and Arabidopsis, recognition of AvrRpt2 is mediated by the Mr5 and RPS2 proteins, respectively. Phylogenetic analysis places Ptr1 in a distinct clade compared to Mr5 and RPS2 and it therefore appears to have arisen by convergent evolution for recognition of AvrRpt2.

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“…Clade support was assessed with posterior probabilities computed with MrBayes. An internet-based platform (http://lrrsearch.com/index.php?page=tool) was used to search for leucine-rich repeats (LRR) (Bej et al 2014) (Supplementary Table 3). Toll/interleukin-1 receptor domains (TIR) were identified using Blast search.…”

Section: Methodsmentioning

confidence: 99%

Embryonic expression of a Long Toll (Loto) gene in the onychophorans Euperipatoides kanangrensis and Cephalofovea clandestina

Janßen

Lionel

2018

Dev Genes Evol

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Recent research has shown that Toll genes, and in particular a newly defined class of Toll genes, the so-called Long Toll Genes (Loto genes), are crucial factors in embryogenesis. In arthropods, they are involved in axis formation via a process called convergent extension (CE). A hallmark of Loto genes is their relatively (compared to other Toll genes) high number of leucine-rich repeat elements (LRRs) coupled with the fact that they are expressed in transverse stripes in all segments, or a subset of segments, patterns that are reminiscent of classical segmentation genes such as the pair-rule genes. Onychophorans represent a close outgroup to the arthropods; however, their embryonic development differs substantially. It is unclear if convergent extension contributes to onychophoran germ band formation and, if so, whether Loto genes are involved in governing this process. This study identifies a single onychophoran Toll gene from a sequenced embryonic transcriptome in two onychophoran species. The identified gene shows sequence and expression pattern characteristics of Loto genes. However, its expression pattern also comprises some general differences to arthropod Loto genes that are involved in CE.Electronic supplementary materialThe online version of this article (10.1007/s00427-018-0609-8) contains supplementary material, which is available to authorized users.

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LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors

Cited by 36 publications

References 37 publications

The NB‐LRR gene Pm60 confers powdery mildew resistance in wheat

The NB‐LRR gene Pm60 confers powdery mildew resistance in wheat

Ptr1evolved convergently withRPS2andMr5to mediate recognition of AvrRpt2 in diverse solanaceous species

Embryonic expression of a Long Toll (Loto) gene in the onychophorans Euperipatoides kanangrensis and Cephalofovea clandestina

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