Nova Biologica Reperta

Detection and amplification of LysM effector genes in F. oxysporum f. sp. lycopersici

Authors

Farhad Shokouhifar 1
Elahe Rabiei-Motlagh 2
Nahid Abbaspour 1
Sahba Toosi 1

1 Research Center for Plant Sciences, Ferdowsi University of Mashhad, Mashhad, Iran

2 Plant Pathology Department, College of Agriculture, Ferdowsi University of Mashhad. Mashhad, Iran

https://doi.org/10.21859/acadpub.nbr.2.4.235
Abstract
During the infection- while the xylem is colonized by the F. oxysporum f. sp. Lycopersici (Fol)- several effector proteins have been secreted into the xylem that suppress the plant’s defense response and enable parasitic colonization. So far, 14 effector proteins have been reported in Fol. However, there are no identified domains in their sequences. LysM effector proteins were identified in some plant pathogenic fungi and involved in sequestering chitin oligosaccharides. Here, considering the role of LysM effector proteins in plant-pathogen interactions, we searched for candidate effector proteins possessed Lysin (LysM) domains in the genome of FOL. Hence, the LysM domain was searched in the WGS data bank of Fol using Pfam tool and 17 proteins were identified. Two proteins, Fol-LysM1 and Fol-LysM3, were selected based on low molecular weight and present of signal peptide in their sequences. Prediction of the gene structures preformed using FGENESH tools and domain structures and effector characters including signal peptide, number and position of cysteine residues, disulfide bond connectivity and molecular weight of proteins were predicted. The entire nucleotide sequences of the coding region of their genes were determined by PCR and phylogeny of lysM effector proteins was studied. Furthermore, the domain organization of these proteins was compared with that of other lysM effector proteins. This is a first report of detection of lysM effector genes in Fol.

Keywords

plant-microbe interaction
secreted protein
vascular wilt disease
امینی، ج.،کاظمی، م.، عبداله زاده، ج. و درویش نیا، م. 1392. شناسایی و بیماری‌زایی گونه‌های فوزاریوم مرتبط با ریشه و طوقه گوجه فرنگی در منطقه مرودشت. - مجلۀ دانش گیاه‌پزشکی ایران 44: 80-71.
اعتباریان، ح.ر. 1371. بررسی بیماری پژمردگی فوزاریومی گوجه‌فرنگی و مبارزه شیمیایی با آندر منطقه ورامین. - مجلۀ علوم کشاورزی ایران 23: 14-1.
حیدرزاده، ن.، روحانی،ح.، فلاحتی رستگار،م. و مهدیخانی مقدم، ع. 1392. شناسایی آنزیم ‌توماتیناز با تکنیک کروماتوگرافی لایه نازک در جدایه‌های نژاد 1 قارچ Fusarium oxysporum f. sp lycopersici عامل پژمردگی آوندی گوجه‌فرنگی در استان‌های خراسان شمالی و رضوی. - نشریۀ حفاظت گیاهان (علوم و صنایع کشاورزی) 27: 191- 185.

خرسندی، س.، بابای اهری، ا.، رضایی، س. و محمدی پور، م. 1388. شناسایی عوامل بیماریزای قارچی پوسیدگی ریشه و طوقۀ گوجه-فرنگی در استان آذربایجان شرقی. - مجلۀ علمی-پژوهشی علوم کشاورزی دانشگاه آزاد اسلامی واحد تبریز 3: 93 –79.
فصیحانی، ع. 1368. نژاد فیزیولوژیک فوزاریوم عامل پژمردگی گوجه‌فرنگی در استان هرمزگان. - خلاصه مقالات نهمین کنگرۀ گیاه پزشکی ایران. دانشگاه فردوسی مشهد.

Amini, J. 2009. Physiological race of Fusarium oxysporum f. sp. lycopersici in Kurdistan province of Iran and reaction of some tomato cultivars to race 1 of pathogen. – Plant Pathology Journal 8: 68-73.
Baroncelli, R., Sreenivasaprasad, S., Sukno, S.A., Thon, M.R. and Holub, E. 2014. Draft genome sequence of Colletotrichum acutatum sensu lato (Colletotrichum fioriniae). – Genome Announc. 2:e00112-14.
Bolton, M.D., Esse, H.P., Vossen, J.H., Jonge, R.J., Stergiopoulos, I., Stulemeijer, I.J.E., Van den Berg, G.C.M., Borrás-Hidalgo, O., Dekke, H.L., Koster, C.G.K., Wit, P.J.G.M., Joosten, M.H.A.J. and Thomma, B.P.H.J. 2008. The novel Cladosporium fulvum lysin motif effecter Ecp6 is a virulence factor with orthologues in other fungal species. – Molecular Microbiology 69: 19-136.
Brefort, T., Tanaka, S., Neidig, N., Doehlemann, G. and Vincon, V. 2014. Characterization of the largest effector gene cluster of ustilago maydis. – PLoS Pathology 10: e1003866.
Broad Institute of MIT and Harvard, Fusarium Comparative Database. 2007. http://www. broadinstitute org/annotation/genome/ fusarium group/ MultiHome.html
Condon, B.J., Leng, Y., Wu, D., Bushley, K.E. and Ohm, R.A. 2013. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. – PLoS Genetics 9: e1003233.
Finn, R.D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Heger, A., Hetherington, K., Holm, L., Mistry, J., Sonnhammer, E.L.L., Tate, J. and Punta, M. 2014. Pfam: the protein families’ database. – Nucleic Acids Research 42: D222-D230.
Ferre, F. and Clote, P. 2005. DiANNA: a web server for disulfide connectivity prediction. – Nucleic Acids Research 33: 230-232.
Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D. and Bairoch, A. 2005. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook. – Humana Press. pp. 571-607.
Garvey, K.J. Saedi, M.S. and Ito, J. 1986. Nucleotide sequence of Bacillus phage phi 29 genes 14 and 15: homology of gene 15 with other phage lysozymes. –Nucleic Acids Research 14: 10001-10008.
Houterman, P.M., Ma, L., VanOoijen, G., DeVroomen, M.J., Cornelissen, B.J.C., Takken, F.L.W. and Rep, M. 2009. The effector protein Avr2 of the xylem-colonizing fungus Fusarium oxysporum activates the tomato resistance protein I-2 intracellularly. – The Plant Journal 58: 970-978.
Houterman, P.M., Cornelissen, B.J.C. and Rep, M. 2008. Suppression of plant resistance gene-based immunity by a fungal effector. Plos Pathog. doi: 10.1371/journal.ppat.1000061.
Jones, J. and Dangl, J. 2006. The plant immune system. – Nature 444: 323-329.
Jonge, R. and Thomma, B.H.J. 2009. Fungal LysM effectors: extinguishers of host immunity? – Trends in Microbiology 4: 151-157.
Kombrink, A. and Thomma, B.P.H.J. 2013. LysM effectors: secreted proteins supporting fungal Life. –PLOS Pathogens 9: e1003769.
Knogge, W. and Scheel, D. 2006. LysM receptors recognize friend and foe. – Proceedings of the National Academy of Sciences of the United States of America 103: 10829-10830.
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. 2007. Clustal W and Clustal X version 2.0. – Bioinformatics 23: 2947-2948.
Letunic, I., Copley, R., Schmid, S., Ciccarelli, F., Doerks, T. and Schuitz, J. 2004. SMART 4.0: towards genomic data integration. – Nucleic Acids Research 32: 142-143.
Marshall, R., Kombrink, A., Motteram, J. Loza-Reyes, L., Lucas, J., Hammond-Kosack, K.E., Thomma, B.H.J. and Rudd, J.J. 2011. Analysis of two in planta expressed LysM effectors homolog’s from the fungus Mycosphaerella graminicola reveals novel functional properties and varying contributions to virulence on Wheat. – Plant Physiology 156: 756-769.
Mentlak, T.A., Shinya, T., Ryder, L.S., Otomo, I., Saitoh, H., Kombrink, A., Nishizawa, Y., Shibuya, N., Thomma, B.H.J. and Talbot, N.J. 2012. Effector-mediated suppression of chitin- triggered immunity by Magnaporthe oryzae is necessary for rice blast disease. – The Plant Cell 24: 322-335.
Ohm, R.A., Feau, F., Henrissat, B., Schoch, C.L., Horwitz, B.A., Barry, K.W., Condon, B.J., Copeland, A.C., Dhillon, B. and Glaser, F. 2012. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideo mycetes fungi. –PLoS Pathogens 8:e1003037.
Petersen, T.N., Brunak, S., Heijne, G. and Nielsen, H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. – Nature Methods 8: 785-786.
Rep, M. 2005. Small proteins of plant-pathogenic fungi secreted during host colonization. – FEMS Microbiol Lett 253: 19-27.
Rouxel, T., Grandaubert, J., Hane, J.K., Hoede and C van de Wouw, A.P. 2001. Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations. – Natuter Communcation 2: 1-10.
Solovyev, V., Kosarev, P., Seledsov, I., Vorobyev, D. 2006. Automatic annotation of eukaryotic genes, pseudogenes and promoters. – Genome Biology 7: 10.1-10.12.
Swindell, S.R. and Plasterer, T.N. 1997. SEQMAN. – Methods In Molecular Medicine 70: 75-89.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. – Molecular Biology and Evolution 28: 2731-2739.
Thomma, B.H.J., Nurnberger T. and Joosten, M.H.A.J. 2011. Of PAMPs and effectors: tThe blurred PTI-ETI dichotomy. – The Plant Cell 23: 4-15.
Vleeshouwers, V.G.A.A. and Oliver, R.P. 2014. Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens. – Molecular Plant-Microbe Interactions 27: 196-206.
Zhang, X.C., Wu, X., Findley, S., Wan, J., Libault, M., Nguyen, H.T., Cannon, S.B. and Stacey, G. 2007. Molecular evolution of lysin motif-type receptor-like kinases in plants. – Plant Physiol. 144: 623-663.
Nova Biologica Reperta
Volume 2, Issue 4 - Serial Number 6
Autumn 2015
Pages 235-249

  • Receive Date 08 June 2026
  • Publish Date 08 June 2026

Home

Guide for Authors

Submit Manuscript

Reviewers

Contact Us