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      NLR receptors in plant immunity: making sense of the alphabet soup

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          Abstract

          Plants coordinately use cell‐surface and intracellular immune receptors to perceive pathogens and mount an immune response. Intracellular events of pathogen recognition are largely mediated by immune receptors of the nucleotide binding and leucine rich‐repeat (NLR) classes. Upon pathogen perception, NLRs trigger a potent broad‐spectrum immune reaction, usually accompanied by a form of programmed cell death termed the hypersensitive response. Some plant NLRs act as multifunctional singleton receptors which combine pathogen detection and immune signaling. However, NLRs can also function in higher order pairs and networks of functionally specialized interconnected receptors. In this article, we cover the basic aspects of plant NLR biology with an emphasis on NLR networks. We highlight some of the recent advances in NLR structure, function, and activation and discuss emerging topics such as modulator NLRs, pathogen suppression of NLRs, and NLR bioengineering. Multi‐disciplinary approaches are required to disentangle how these NLR immune receptor pairs and networks function and evolve. Answering these questions holds the potential to deepen our understanding of the plant immune system and unlock a new era of disease resistance breeding.

          Abstract

          Pathogen recognition in plants is largely mediated by immune receptors of the nucleotide binding and leucine rich‐repeat (NLR) classes. This review covers basic aspects of NLR biology and networks and highlights recent advances in NLR structure, function, and activation.

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          Most cited references231

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

            The Interactive Tree Of Life ( https://itol.embl.de ) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new dataset type has been added (MEME motifs), while annotation options have been expanded for several existing ones. Node metadata display options have been extended and now also support non-numerical categorical values, as well as multiple values per node. Direct manual annotation is now available, providing a set of basic drawing and labeling tools, allowing users to draw shapes, labels and other features by hand directly onto the trees. Support for tree and dataset scales has been extended, providing fine control over line and label styles. Unrooted tree displays can now use the equal-daylight algorithm, proving a much greater display clarity. The user account system has been streamlined and expanded with new navigation options and currently handles >1 million trees from >70 000 individual users. Graphical Abstract iTOL: an online tool for the tree display and annotation.
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              CD-HIT: accelerated for clustering the next-generation sequencing data

              Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions. Availability: http://cd-hit.org. Contact: liwz@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                mauricio.contreras@tsl.ac.uk
                sophien.kamoun@tsl.ac.uk
                Journal
                EMBO Rep
                EMBO Rep
                10.1002/(ISSN)1469-3178
                EMBR
                embor
                EMBO Reports
                John Wiley and Sons Inc. (Hoboken )
                1469-221X
                1469-3178
                21 August 2023
                October 2023
                21 August 2023
                : 24
                : 10 ( doiID: 10.1002/embr.v24.10 )
                : e57495
                Affiliations
                [ 1 ] The Sainsbury Laboratory University of East Anglia Norwich UK
                Author notes
                [*] [* ] Corresponding author. E‐mail: mauricio.contreras@ 123456tsl.ac.uk

                Corresponding author. E‐mail: sophien.kamoun@ 123456tsl.ac.uk

                Author information
                https://orcid.org/0000-0001-6002-0730
                https://orcid.org/0000-0002-7284-6131
                https://orcid.org/0000-0002-0644-699X
                https://orcid.org/0000-0002-0290-0315
                Article
                EMBR202357495
                10.15252/embr.202357495
                10561179
                37602936
                155353b6-4781-4f7f-bdb0-7f2877dfa255
                © 2023 The Authors. Published under the terms of the CC BY 4.0 license

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 22 July 2023
                : 16 May 2023
                : 03 August 2023
                Page count
                Figures: 5, Tables: 1, Pages: 24, Words: 28033
                Funding
                Funded by: Deutsche Forschungsgemeinschaft (DFG)
                Award ID: 464864389
                Funded by: EC | ERC | HORIZON EUROPE European Research Council (ERC)
                Award ID: 743165
                Funded by: UKRI | Biotechnology and Biological Sciences Research Council (BBSRC) , doi 10.13039/501100000268;
                Award ID: BB/P012574
                Award ID: BBS/E/J/000PR9795
                Award ID: BBS/E/J/000PR9796
                Award ID: BBS/E/J/000PR9797
                Award ID: BBS/E/J/000PR9798
                Award ID: BB/V002937/1
                Categories
                Review
                Reviews
                Custom metadata
                2.0
                09 October 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.4 mode:remove_FC converted:09.10.2023

                Molecular biology
                bioengineering,immunology,nb‐lrr,nbs‐lrr,nod,microbiology, virology & host pathogen interaction,signal transduction

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