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Hussain A, Khan AA, Aslam MQ, Nazar A, Zaman N, Amin A, Mahmood MA, Mukhtar MS, Rahman HUU, Farooq M, Saeed M, Amin I, Mansoor S. Comparative analysis, diversification, and functional validation of plant nucleotide-binding site domain genes. Sci Rep 2024; 14:11930. [PMID: 38789717 PMCID: PMC11126693 DOI: 10.1038/s41598-024-62876-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 05/22/2024] [Indexed: 05/26/2024] Open
Abstract
Nucleotide-binding site (NBS) domain genes are one of the superfamily of resistance genes involved in plant responses to pathogens. The current study identified 12,820 NBS-domain-containing genes across 34 species covering from mosses to monocots and dicots. These identified genes are classified into 168 classes with several novel domain architecture patterns encompassing significant diversity among plant species. Several classical (NBS, NBS-LRR, TIR-NBS, TIR-NBS-LRR, etc.) and species-specific structural patterns (TIR-NBS-TIR-Cupin_1-Cupin_1, TIR-NBS-Prenyltransf, Sugar_tr-NBS etc.) were discovered. We observed 603 orthogroups (OGs) with some core (most common orthogroups; OG0, OG1, OG2, etc.) and unique (highly specific to species; OG80, OG82, etc.) OGs with tandem duplications. The expression profiling presented the putative upregulation of OG2, OG6, and OG15 in different tissues under various biotic and abiotic stresses in susceptible and tolerant plants to cotton leaf curl disease (CLCuD). The genetic variation between susceptible (Coker 312) and tolerant (Mac7) Gossypium hirsutum accessions identified several unique variants in NBS genes of Mac7 (6583 variants) and Coker312 (5173 variants). The protein-ligand and proteins-protein interaction showed a strong interaction of some putative NBS proteins with ADP/ATP and different core proteins of the cotton leaf curl disease virus. The silencing of GaNBS (OG2) in resistant cotton through virus-induced gene silencing (VIGS) demonstrated its putative role in virus tittering. The presented study will be further helpful in understanding the plant adaptation mechanism.
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Affiliation(s)
- Athar Hussain
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
- School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54000, Pakistan.
| | - Aqsa Anwer Khan
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Muhammad Qasim Aslam
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan
| | - Aquib Nazar
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Nadir Zaman
- Department of Life Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Ayesha Amin
- Department of Biological Sciences, Superior University, Lahore, 54000, Pakistan
| | - Muhammad Arslan Mahmood
- Plant Science Division, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - M Shahid Mukhtar
- Biosystems Research Complex, Department of Genetics & Biochemistry, Clemson University, Clemson, SC, 29634, USA
| | - Hafiz Ubaid Ur Rahman
- School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Muhammed Farooq
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan
| | - Muhammed Saeed
- Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau Abteilung Phytopathologie, Paul-Ehrlich-Straße 22, 67653, Kaiserslautern, Germany
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.
- Jamil ur Rehman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 74000, Pakistan.
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2
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Melepat B, Li T, Vinkler M. Natural selection directing molecular evolution in vertebrate viral sensors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105147. [PMID: 38325501 DOI: 10.1016/j.dci.2024.105147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 12/30/2023] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.
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Affiliation(s)
- Balraj Melepat
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Tao Li
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic
| | - Michal Vinkler
- Charles University, Faculty of Science, Department of Zoology, Viničná 7, 128 43, Prague, EU, Czech Republic.
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3
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Xiong W, van Workum DJM, Berke L, Bakker LV, Schijlen E, Becker FFM, van de Geest H, Peters S, Michelmore R, van Treuren R, Jeuken M, Smit S, Schranz ME. Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding. G3 (BETHESDA, MD.) 2023; 13:jkad204. [PMID: 37740775 PMCID: PMC10627274 DOI: 10.1093/g3journal/jkad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 09/25/2023]
Abstract
Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x = 2n = 18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicated the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Dirk-Jan M van Workum
- Bioinformatics Group, Wageningen University & Research, P.O. Box 633, Wageningen, 6700 AP, The Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Linda V Bakker
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Elio Schijlen
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Frank F M Becker
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
- Laboratory of Genetics, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Henri van de Geest
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Sander Peters
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Richard Michelmore
- The Genome Center, Genome & Biomedical Sciences Facility, University of California, Davis, 451 East Health Sciences Drive, Davis, CA 95616-8816, USA
| | - Rob van Treuren
- Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Marieke Jeuken
- Plant Breeding Group, Wageningen University & Research, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University & Research, P.O. Box 633, Wageningen, 6700 AP, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
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Rizwan M, Haider SZ, Bakar A, Rani S, Danial M, Sharma V, Mubin M, Serfraz A, Shahnawaz-Ur-Rehman M, Shakoor S, Alkahtani S, Saleem F, Mamoon-Ur-Rehman H, Serfraz S. Evolution of NLR genes in genus Arachis reveals asymmetric expansion of NLRome in wild and domesticated tetraploid species. Sci Rep 2023; 13:9305. [PMID: 37291184 PMCID: PMC10250334 DOI: 10.1038/s41598-023-36302-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023] Open
Abstract
Arachis hypogaea is an allotetraploid crop widely grown in the world. Wild relatives of genus Arachis are the rich source of genetic diversity and high levels of resistance to combat pathogens and climate change. The accurate identification and characterization of plant resistance gene, nucleotide binding site leucine rich repeat receptor (NLRs) substantially contribute to the repertoire of resistances and improve production. In the current study, we have studied the evolution of NLR genes in genus Arachis and performed their comparative genomics among four diploids (A. duranensis, A. ipaensis, A. cardenasii, A. stenosperma) and two tetraploid (wild: A. monticola and domesticated: A. hypogaea) species. In total 521, 354, 284, 794, 654, 290 NLR genes were identified from A. cardenasii, A. stenosperma and A. duranensis, A. hypogaea, A. monticola and A. ipaensis respectively. Phylogenetic analysis and classification of NLRs revealed that they belong to 7 subgroups and specific subgroups have expanded in each genome leading towards divergent evolution. Gene gain and loss, duplication assay reveals that wild and domesticated tetraploids species have shown asymmetric expansion of NLRome in both sub-genome (AA and BB). A-subgenome of A. monticola exhibited significant contraction of NLRome while B-subgenome shows expansion and vice versa in case of A. hypogaea probably due to distinct natural and artificial selection pressure. In addition, diploid species A. cardenasii revealed the largest repertoire of NLR genes due to higher frequency of gene duplication and selection pressure. A. cardenasii and A. monticola can be regarded as putative resistance resources for peanut breeding program for introgression of novel resistance genes. Findings of this study also emphasize the application neo-diploids and polyploids due to higher quantitative expression of NLR genes. To the best of our knowledge, this is the first study that studied the effect of domestication and polyploidy on the evolution of NLR genes in genus Arachis to identify genomic resources for improving resistance of polyploid crop with global importance on economy and food security.
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Affiliation(s)
- Muhammad Rizwan
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Syed Zeeshan Haider
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Abu Bakar
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Shamiza Rani
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Muhammad Danial
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Vikas Sharma
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences 1, IBG1, 52425, Jülich, Germany
| | - Muhammad Mubin
- Virology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ali Serfraz
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
- Department of Plant Pathology, University of Arid Agriculture, Rawalpindi , Pakistan
| | | | - Sidra Shakoor
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Fozia Saleem
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan
| | | | - Saad Serfraz
- Evolutionary Biology Lab, CABB, University of Agriculture, Faisalabad, 38000, Pakistan.
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Asif J, Qureshi F, Zain M, Nawaz H, Naz E, Fareed S, Bibi A, Nawaz S, Saleem F, Shafique M, Tabasum S, Maqsood U, Serfraz S, Alkahtani S. Investigation of Resistance Genes in Genus Vigna Reveals Highly Variable NLRome in Parallel Domesticated Member Species. Genes (Basel) 2023; 14:1129. [PMID: 37372309 DOI: 10.3390/genes14061129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
Vigna is a unique genus that consist of multiple crop species that are domesticated in parallel fashion between 7-10 thousand years ago. Here we studied the evolution of nucleotide-binding site leucine-rich repeat receptor (NLR) genes across five crop species of genus Vigna. In total identified 286, 350, 234, 250, 108 and 161 NLR genes were from Phaseolous vulgaris, Vigna. unguiculata, Vigna mungo, Vigna radiata, Vigna angularis and Vigna umbellata respectively. Comprehensive phylogenetic and clusterization analysis reveals the presence of seven subgroups of Coiled coil like NLRs (CC-NLR) genes and four distinct lineages of Toll interleukin receptor like NLRs (TIR-NLR). Subgroup CCG10-NLR shows large scale diversification among Vigna species suggesting genus specific distinct duplication pattern in Vigna species. Mainly birth of new NLR gene families and higher rate of terminal duplication is the major determinants for expansion of NLRome in genus Vigna. Recent expansion of NLRome in V. anguiculata and V. radiata was also observed which might suggest that domestication have supported their duplication of lineage specific NLR genes. In short, large scale difference in the architecture of NLRome were observed in diploid plant species. Our findings allowed us to hypothesized that independent parallel domestication is the major drivers of highly divergent evolution of NLRome in genus Vigna.
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Affiliation(s)
- Jehanzaib Asif
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Fatima Qureshi
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Zain
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Hamza Nawaz
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Effat Naz
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shahid Fareed
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Aqsa Bibi
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Sehar Nawaz
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Fozia Saleem
- Metabolomics Innovative Institute, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | | | - Saba Tabasum
- Department of Plant Breeding and Genetics, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | - Umer Maqsood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan, Institute of Engineering and Applied Sciences, Faisalabad 38000, Pakistan
| | - Saad Serfraz
- Evolutionary Biology Lab, Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Shen Z, Ding X, Cheng J, Wu F, Yin H, Wang M. Phylogenetic studies of magnoliids: Advances and perspectives. FRONTIERS IN PLANT SCIENCE 2023; 13:1100302. [PMID: 36726671 PMCID: PMC9885158 DOI: 10.3389/fpls.2022.1100302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Magnoliids are the largest flowering plant clades outside of the eudicots and monocots, which are distributed worldwide and have high economic, ornamental and ecological values. Eudicots, monocots and magnoliids are the three major clades of Mesangiospermae, and their phylogenetic relationship is one of the most interesting issues. In recent years, with the continuous accumulation of genomic information, the evolutionary status of magnoliids has become a hot spot in plant phylogenetic research. Although great efforts have been made to study the evolution of magnoliids using molecular data from several representative species such as nuclear genome, plastid genome, mitochondrial genome, and transcriptome, the results of current studies on the phylogenetic status of magnoliids are inconsistent. Here, we systematically describe the current understanding of the molecular research on magnoliid phylogeny and review the differences in the evolutionary state of magnoliids. Understanding the research approaches and limitations of magnoliid phylogeny can guide research strategies to further improve the study of the phylogenetic evolution of magnoliids.
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Affiliation(s)
- Zhiguo Shen
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Xin Ding
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Jianming Cheng
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Fangfang Wu
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Minyan Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
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Bashir S, Rehman N, Fakhar Zaman F, Naeem MK, Jamal A, Tellier A, Ilyas M, Silva Arias GA, Khan MR. Genome-wide characterization of the NLR gene family in tomato ( Solanum lycopersicum) and their relatedness to disease resistance. Front Genet 2022; 13:931580. [PMID: 36544493 PMCID: PMC9760929 DOI: 10.3389/fgene.2022.931580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Nucleotide-binding leucine-rich-repeat receptors (NLR), the largest group of genes associated with plant disease resistance (R), have attracted attention due to their crucial role in protecting plants from pathogens. Genome-wide studies of NLRs have revealed conserved domains in the annotated tomato genome. The 321 NLR genes identified in the tomato genome have been randomly mapped to 12 chromosomes. Phylogenetic analysis and classification of NLRs have revealed that 211 genes share full-length domains categorized into three major clades (CNL, TNL, and RNL); the remaining 110 NLRs share partial domains and are classified in CN, TN, and N according to their motifs and gene structures. The cis-regulatory elements of NLRs exhibit the maximum number of these elements and are involved in response to biotic and abiotic stresses, pathogen recognition, and resistance. Analysis of the phylogenetic relationship between tomato NLRs and orthologs in other species has shown conservation among Solanaceae members and variation with A. thaliana. Synteny and Ka/Ks analyses of Solanum lycopersicum and Solanum tuberosum orthologs have underscored the importance of NLR conservation and diversification from ancestral species millions of years ago. RNA-seq data and qPCR analysis of early and late blight diseases in tomatoes revealed consistent NLR expression patterns, including upregulation in infected compared to control plants (with some exceptions), suggesting the role of NLRs as key regulators in early blight resistance. Moreover, the expression levels of NLRs associated with late blight resistance (Solyc04g007060 [NRC4] and Solyc10g008240 [RIB12]) suggested that they regulate S. lycopersicum resistance to P. infestans. These findings provide important fundamental knowledge for understanding NLR evolution and diversity and will empower the broader characterization of disease resistance genes for pyramiding through speed cloning to develop disease-tolerant varieties.
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Affiliation(s)
- Sehrish Bashir
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan,*Correspondence: Nazia Rehman, ; Muhammad Ramzan Khan,
| | - Fabia Fakhar Zaman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Atif Jamal
- Crop Disease Research Institute, National Agricultural Research Center, Islamabad, Pakistan
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Muhammad Ilyas
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Gustavo Adolfo Silva Arias
- Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,PARC Institute for Advanced Studies in Agriculture, NARC, Islamabad, Pakistan,*Correspondence: Nazia Rehman, ; Muhammad Ramzan Khan,
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Martin EC, Ion CF, Ifrimescu F, Spiridon L, Bakker J, Goverse A, Petrescu AJ. NLRscape: an atlas of plant NLR proteins. Nucleic Acids Res 2022; 51:D1470-D1482. [PMID: 36350627 PMCID: PMC9825502 DOI: 10.1093/nar/gkac1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
NLRscape is a webserver that curates a collection of over 80 000 plant protein sequences identified in UniProtKB to contain NOD-like receptor signatures, and hosts in addition a number of tools aimed at the exploration of the complex sequence landscape of this class of plant proteins. Each entry gathers sequence information, domain and motif annotations from multiple third-party sources but also in-house advanced annotations aimed at addressing caveats of the existing broad-based annotations. NLRscape provides a top-down perspective of the NLR sequence landscape but also services for assisting a bottom-up approach starting from a given input sequence. Sequences are clustered by their domain organization layout, global homology and taxonomic spread-in order to allow analysis of how particular traits of an NLR family are scattered within the plant kingdom. Tools are provided for users to locate their own protein of interest in the overall NLR landscape, generate custom clusters centered around it and perform a large number of sequence and structural analyses using included interactive online instruments. Amongst these, we mention: taxonomy distribution plots, homology cluster graphs, identity matrices and interactive MSA synchronizing secondary structure and motif predictions. NLRscape can be found at: https://nlrscape.biochim.ro/.
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Affiliation(s)
- Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Catalin F Ion
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Florin Ifrimescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Jaap Bakker
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
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Lapin D, Johanndrees O, Wu Z, Li X, Parker JE. Molecular innovations in plant TIR-based immunity signaling. THE PLANT CELL 2022; 34:1479-1496. [PMID: 35143666 PMCID: PMC9153377 DOI: 10.1093/plcell/koac035] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/27/2022] [Indexed: 05/19/2023]
Abstract
A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes and eukaryotes. Here, we present an overview of TIR evolution and the molecular versatility of TIR domains in different protein architectures for host protection against microbial attack. Plant TIR-based signaling emerges as being central to the potentiation and effectiveness of host defenses triggered by intracellular and cell-surface immune receptors. Equally relevant for plant fitness are mechanisms that limit potent TIR signaling in healthy tissues but maintain preparedness for infection. We propose that seed plants evolved a specialized protein module to selectively translate TIR enzymatic activities to defense outputs, overlaying a more general function of TIRs.
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Affiliation(s)
- Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
- Author for correspondence: (D.L.), (J.E.P.)
| | - Oliver Johanndrees
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Zhongshou Wu
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Duesseldorf 40225, Germany
- Author for correspondence: (D.L.), (J.E.P.)
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