Plant Protect. Sci., 2024, 60(3):229-240 | DOI: 10.17221/127/2023-PPS

TIR-NBS-LRR genes play a role in plant defense against biotic stress in Solanum lycopersicumOriginal Paper

Namo Dubey1,2, Anjali Chaudhary1,2, Kunal Singh ORCID...1,2
1 CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
2 Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India

Among the many biotic factors with adverse effects on Solanum lycopersicum (tomato), diseases caused by fungi, viruses and nematodes are notable. Since the genome of S. lycopersicum became available, efforts have continued to identify the genes and proteins associated with the plant defence activity. One such gene family belongs to TIR-NBS-LRR (TNL), a subfamily of larger NBS-LRR genes. In total, 27 full-length TNLs were identified via genome wide analysis. Four pairs of segmental duplication events were observed involving different pairs of chromosomes, except the pairing of Solyc02g082050-Solyc02g032650, which were both present on chromosome 2. More than twenty nine percent (29.63%) of the genes were localised on chromosome 1 alone. Hormone-mediated biotic stress-responsive cis-regulatory elements were detected for methyl-jasmonate, salicylic acid (TCA motif) and ethylene (ERE motif). Differential gene expression was observed for many genes under different plant tissues and biotic stresses. The upregulation of many genes including SlBS4 was observed against Alternaria solani attacks in the disease tolerant varieties. Altogether, the results suggested that TNLs play a significant role in plant defence under biotic stress.

Keywords: Solanum lycopersicum, TIR-NBS-LRR genes, biotic stress, early blight disease

Received: December 2, 2023; Revised: February 26, 2024; Accepted: February 27, 2024; Prepublished online: May 10, 2024; Published: July 9, 2024  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
Dubey N, Chaudhary A, Singh K. TIR-NBS-LRR genes play a role in plant defense against biotic stress in Solanum lycopersicum. Plant Protect. Sci. 2024;60(3):229-240. doi: 10.17221/127/2023-PPS.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    Supplementary files:

    Download file127-2023-PPS-ESM.pdf

    File size: 967.05 kB

    References

    1. Adhikari P., Oh Y., Panthee D.R. (2017): current status of early blight resistance in tomato: An update. International Journal of Molecular Sciences, 18: 2019. Go to original source... Go to PubMed...
    2. Andolfo G., Sanseverino W., Rombauts S., Van de Peer Y., Bradeen J.M., Carputo D., Frusciante L., Ercolano M.R. (2013): Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. New Phytologist, 197: 223-237. Go to original source... Go to PubMed...
    3. Andolfo G., Jupe F., Witek K., Etherington G.J., Ercolano M.R., Jones J.D. (2014): Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq. BMC Plant Biology, 14: 1-2. Go to original source... Go to PubMed...
    4. Bailey T.L., Boden M., Buske F.A., Frith M., Grant C.E., Clementi L., Ren J., Li W.W., et al. (2009): MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research, 37: W202-208. Go to original source... Go to PubMed...
    5. Ballvora A., Pierre M., van den Ackerveken G., Schornack S., Rossier O., Ganal M., Lahaye T., Bonas U. (2001): Genetic mapping and functional analysis of the tomato Bs4 locus governing recognition of the Xanthomonas campestris pv. vesicatoria AvrBs4 protein. Molecular Plant-Microbe Interactions, 14: 629-638. Go to original source... Go to PubMed...
    6. Bashir S., Rehman N., Fakhar Zaman F., Naeem M.K., Jamal A., Tellier A., Llyas M., Silva Arias G.A., et al. (2022): Genome-wide characterization of the NLR gene family in tomato (Solanum lycopersicum) and their relatedness to disease resistance. Frontiers in Genetics, 13: 931580. Go to original source... Go to PubMed...
    7. Bassetti N., Caarls L., Bouwmeester K., Verbaarschot P., van Eijden E., Zwaan B.J., Bonnema G., Schranz M.E., et al. (2023): A butterfly egg-killing hypersensitive response in Brassica nigra is controlled by a single locus, PEK, containing a cluster of TIR-NBS-LRR receptor genes. Plant, Cell & Environment, 4: 1009-1022. Go to original source... Go to PubMed...
    8. Chen C., Chen H., Zhang Y., Thomas H.R., Frank M.H., He Y., Xia R. (2020): TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13: 1194-1202. Go to original source... Go to PubMed...
    9. Chen S.L., Yu H., Luo H.M., Wu Q., Li C.F., Steinmetz A. (2016): Conservation and sustainable use of medicinal plants: problems, progress, and prospects. Chinese medicine, 11: 37. doi: 10.1186/s13020-016-0108-7 Go to original source... Go to PubMed...
    10. Dubey N., Chaudhary A., Singh K. (2022): Genome-wide analysis of TIR-NBS-LRR gene family in potato identified StTNLC7G2 inducing reactive oxygen species in presence of Alternaria solani. Frontiers in Genetics, 12: 791055. Go to original source... Go to PubMed...
    11. Dubey N., Singh K. (2018): Role of NBS-LRR proteins in plant defense. In: Singh A., Singh I., (eds): Molecular Aspects of Plant-Pathogen Interaction. Springer, Singapore: 115-138. Go to original source...
    12. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A. (2005): Protein identification and analysis tools on the ExPASy Server. In: Walker J.M. (eds): The Proteomics Protocols Handbook. Humana Press, New York: 571-607. Go to original source...
    13. Ikeda C., Taku K., Miyazaki T., Shirai R., Nelson R.S., Nyunoya H., Matsushita Y., Sasaki N. (2021): Cooperative roles of intron 1 and 2 of tobacco resistance gene N in enhanced N transcript expression and antiviral defense responses. Scientific Reports, 11: 15424. Go to original source... Go to PubMed...
    14. Kissoudis C., Sunarti S., Van De Wiel C., Visser R.G., van der Linden C.G., Bai Y. (2016): Responses to combined abiotic and biotic stress in tomato are governed by stress intensity and resistance mechanism. Journal of Experimental Botany, 67: 5119-5132. Go to original source... Go to PubMed...
    15. Kopec P.M., Mikolajczyk K., Jajor E., Perek A., Nowakowska J., Obermeier C., Chawla H.S., Korbas M., et al. (2021): Local duplication of TIR-NBS-LRR gene marks clubroot resistance in Brassica napus cv. Tosca. Frontiers in Plant Science, 12: 639631. Go to original source... Go to PubMed...
    16. Kumar S., Stecher G., Tamura K. (2016): MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33: 1870-1874. Go to original source... Go to PubMed...
    17. Kumar T. R., Praveen Kumar M. (2019): Survey and screening of Tomato varieties against Early Blight (Alternaria solani) under field condition. Indian Journal of Pure & Applied Biosciences, 7: 629-635. Go to original source...
    18. Lescot M., Déhais P., Thijs G., Marchal K., Moreau Y., Van de Peer Y., Rouzé P., Rombauts S. (2002): PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30: 325-327. Go to original source... Go to PubMed...
    19. Lupas A., Van Dyke M., Stock J. (1991): Predicting coiled coils from protein sequences. Science, 252: 1162-1164. Go to original source... Go to PubMed...
    20. Mei S., Song Y., Zhang Z., Cui H., Hou S., Miao W., Rong W. (2024): WRR4B contributes to a broad-spectrum disease resistance against powdery mildew in Arabidopsis. Molecular Plant Pathology, 25: 13415. Go to original source... Go to PubMed...
    21. Prigigallo M.I., Križnik M., De Paola D., Catalano D., Gruden K., Finetti-Sialer M.M., Cillo F. (2019): Potato virus Y infection alters small RNA metabolism and immune response in tomato. Viruses, 11: 1100. Go to original source... Go to PubMed...
    22. Qian L.H., Zhou G.C., Sun X.Q., Lei Z., Zhang Y.M., Xue J.Y., Hang Y.Y. (2017): Distinct patterns of gene gain and loss: diverse evolutionary modes of NBS-encoding genes in three Solanaceae crop species. G3: Genes, Genomes, Genetics, 7: 1577-1585. Go to original source... Go to PubMed...
    23. Salmeron J.M., Oldroyd G.E., Rommens C.M., Scofield S.R., Kim H.S., Lavelle D.T., Dahlbeck D., Staskawicz B.J. (1996): 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, 86: 123-133. Go to original source... Go to PubMed...
    24. Song J., Chen F., Lv B., Guo C., Yang J., Huang L., Guo J., Xiang, F. (2023): Genome-wide identification and expression analysis of the TIR-NBS-LRR gene family and its response to fungal disease in rose (Rosa chinensis). Biology, 12: 426. Go to original source... Go to PubMed...
    25. Wolfe D., Dudek S., Ritchie M.D., Pendergrass S.A. (2013): Visualizing genomic information across chromosomes with PhenoGram. BioData Mining, 6: 1-2. Go to original source... Go to PubMed...
    26. Yeon J., Lee Y., Kang B., Lim J., Yi H. (2023): TIR Domains in Arabidopsis thaliana duppressor of npr1-1, constitutive 1 and its closely related disease resistance proteins form intricate interaction networks. Journal of Plant Biology, 66: 439-453. Go to original source...
    27. Zhang C., Liu L., Wang X., Vossen J., Li G., Li T., Zheng Z., Gao J., et al. (2014): The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theoretical and Applied Genetics, 127: 1353-1364. Go to original source... Go to PubMed...
    28. Zhao W., Li Z., Fan J., Hu C., Yang R., Qi X., Chen H., Zhao F., Wang S. (2015): Identification of jasmonic acid-associated microRNAs and characterization of the regulatory roles of the miR319/TCP4 module under root-knot nematode stress in tomato. Journal of Experimental Botany, 66: 4653-4667. Go to original source... Go to PubMed...
    29. Zhao Y., Weng Q., Song J., Ma H., Yuan J., Dong Z., Liu Y. (2016): Bioinformatics analysis of NBS-LRR encoding resistance genes in Setaria italica. Biochemical Genetics, 54: 232-248. Go to original source... Go to PubMed...
    30. Zhou L., Deng S., Xuan H., Fan X., Sun R., Zhao J., Wang H., Guo N., et al. (2022): A novel TIR-NBS-LRR gene regulates immune response to Phytophthora root rot in soybean. The Crop Journal, 10: 1644-1653. Go to original source...
    31. Zhu H., Deng M., Yang Z., Mao L., Jiang S., Yue Y., Zhao K. (2021): Two tomato (Solanum lycopersicum) thaumatin-like protein genes confer enhanced resistance to late blight (Phytophthora infestancs). Phytopathology, 111: 1790-1799. Go to original source... Go to PubMed...

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content