Research

Since 2001, my group studies the molecular and biochemical mechanisms underlying disease -resistance and -susceptibility in plants. We want to understand how the immune system of a plant allows it to recognise a pathogen and mount effective defence responses. Furthermore, we want to elucidate how pathogens manipulate their hosts and manage to evade its immune system. 

As model crop, we use tomato because of its great genetic tools and its importance for Dutch agriculture. Tomato has many natural enemies and one of them is the root-invading soil-borne pathogen Fusarium oxysporum, the causal agent of Fusarium wilt disease. Resistance to fusarium can be conferred by Resistance genes. These genes encode immune receptors that recognize specific proteins secreted by the fungus. Our aim is to understand how NLR-type immune receptors function in disease resistance. Biochemically we have shown that these proteins act as nucleotide-operated molecular switches. In collaboration with the Cann laboratory (Durham UK) we found that these proteins can bind and bend DNA in vivo, and that in planta they bind DNA once activated. In an NWO funded VICI project we studied the role of DNA binding by NLR proteins in plant immunity. Using our knowledge of immune receptors we now aim to adjust their recognition specificity to allow them to recognise newly emerging pathogens. For this reserach we focus on NLR receptors from solanacea recognising fungal, viral and bacterial pathogens.  

Although Fusarium oxysporum is infamous for being a devastating pathogen, many strains are actually endophytes that enhance plant resilience to biotic and abiotic stresses. Current research aims at resolving how endophytes evade host resistance while boosting plant immunity, and to elucidate how endophytes differ from pathogens. 

Disease resistance can also be conferred by a lack of compatibility with a given pathogen. To unravel this mechanism, we focus on the identification of compatibility/susceptibility genes of the host by screening for protein targets that are manipulated by a pathogen. Upon infection Fusarium oxysporum secretes many small proteins in the xylem sap of the host. Many of these Six (Secreted In Xylem) proteins, such as Six3, Six5 and Six6, are important for disease development, like.  We use these Six proteins to identify their plant targets and identified genes whose knockout result in increased disease resistance. Identification of these susceptibility genes increases our understanding on how a pathogen manipulates its host and providing new leads to combat diseases 

Group members

Current members of the research team. 

Machiel Cligge PhD student - "Virus induced genome editing in crops to facilitate precision breeding", TKI Topsector AGri& Food

Margarita Simkovicova PhD student - "Combating Vascular Diseases: Identifying the Guardians of the Xylem Sap", Collaboration with ENZA zaden, funding by ENZA and NWO-VICI program

Thomas Aalders PhD Student- TOPLESS a novel S gene: Unravelling the manipulation of Topless by a conserved effector from Fusarium oxysporum", funding by NWO talent program: 

Dr Daniel Zendler Postdoc - “Integrated research program towards sustainable resistance against the Tospovirus-thrips pathosystem in crops”. Topsector T&U project LWV20.105

Babette Vlieger PhD student -" A leap into the unknown: understanding host-jumping by Fusarium oxysporum in cucurbits" NWO talent program

Jo Gomila technician -"Precision genome editing to alter disease resistance specificities in plants" TKI Topsector AGri& Food

Dr Isidre 'd Hooghvorst - -"Precision genome editing to alter disease resistance specificities in plants" TKI Topsector AGri& Food

Former lab members

Dr Mila Blekemolen,  PhD student - NWO VICI program and UvA: Elucidating the molecular mechanism underlying the virulence and avirulence functions of the Fusarium Avr2/Six5 effector pair

Dr Nico Tintor Postdoc - ENZA project: effector-uptake mediated plant  immunity

Dr Marijn Knip, Postdoc - VICI project: Linking plant immunity and DNA damage. 

Dr Manon Richard, Postdoc - VICI project: Linking DNA binding of plant NLR proteins to plant immunity.

Machiel Beijaert, Technician - VICI project: supporting the VICI project in various ways.

Dr Francisco de Lamo Ruiz, PhD student - ETN Horizon2020 : How do endophytes evade host resistance while enhancing immunity?

Dr Maria Constantin, PhD student - ETN Horizon202: How do endophytes differ from pathogens? 

Dr Lingxue Cao, PhD student - CSC grant: Elucidating the molecular mechanism underlying the virulence and avirulence functions of the Fusarium Avr2/Six5 effector pair,

Dr Xiaotang Di, PhD student - CSC grant : The Avr2 effector protein from Fusarium as a guide to unravel plant innate immunity.

Dirk-Jan Valkenburg,  Technician: involved in various ongoing projects in the group.

Dr Hanna Richter, Technician: involved in all ongoing projects in the group.

ir. Lisong Ma, PhD student: Analysing the intrinsic functions of Avr2 and its perceival by the resistance protein I-2.  

Dr Fleur Gawehns, PhD student - CBSG2012: Functional characterisation of Fusarium secreted effector proteins in disease and resistance

Dr ir. Ewa Lukasik,  PhD student -Bioexploit: "Role of the ATPase activity of the NBS domain of R proteins and the identification of interacting proteins.

drs Vladimir Krasikov, Postdoc -UvA:  Identifying the role of the Xsp10 protein for resistance and disease to Fusarium oxysporum.

dr. ir. Harrold van den Burg, Postdoc, NWO Veni: Eludidating  the role of SUMO modification in plant defence signalling.

ing Marianne de Vroomen Technician, involved in most ongoing projects.

Drs Mobien Kasiem  PhD student: PhD student: Structure and function of tomato disease resistance proteins.

Dr Gerben van Ooijen  PhD student -NWO open program: Structure and function of tomato disease resistance proteins. 

Dr Klaas Jan de Vries, Postdoc - CBSG 2008:  Targeted proteomics of signalosomes mediating pathogen resistance. 

Dr Wladimir Tameling  PhD student: Disease resistance proteins of the NBS-LRR class, molecular switches of plant defence.

Dr Sergio de la Fuente van Bentem  PhD student: Unfolding plant disease resistance, the involvement of HSP90 and its co-chaperone  PP5 in I-2 mediated signalling.

Dr Jack Vossen, Postdoc: Characterisation of the I-2 signalosome.

Dr Sandra Elzinga,  Postdoc: Characterisation of the Mi-1 signalosome.

Invited speaker

Selection from the last ten years 

• Identification of host targets of Fusarium effector proteins provides insight in disease resistance and susceptibility. 17 June 2022, IBMCP symposium at CSIC-Universitat Politècnica de València, Spain.
• Molecular aspects of endophyte-mediated resistance induced by Fusarium oxysporum. 15 December, 2021 (on line).  Institute Colloquium, ETH,  Zurich, Switzerland
• Molecular aspects of endophyte-mediated resistance induced by Fusarium oxysporum. 26 November 2021 (on line).  Colloquium, Phytopathology, WUR, Wageningen, NL
• Molecular aspects of endophyte-mediated resistance induced by Fusarium oxysporum. VISCEA 4^thInternational Conference “Plant Biotic Stresses & Resistance Mechanisms IV” February 19-20, 2020 Technische Universität Wien, Wien, Austria
• Combatting vascular diseases: identifying the guardians of the xylem. December 9 2019 Invited lecture CRAG, Barcelona, Spain
• Good fungi turning bad – what is the difference between beneficial and pathogenic Fusarium oxysporum strains? 25-28 September 2019, New Zealand Microbial Society Conference. Palmerston North, New Zealand.
• The Fusarium oxysporum effector Six8 manipulates plant immunity via the transcriptional co-repressors TPL and TPR1. 25 September 2019, AgResearch, Palmerston North, New Zealand.
• The good, the bad and the ugly: Unraveling the molecular basis of endophyte mediated resistance in tomato triggered by Fusarium oxysporum.  September 20 2019 Invited lecture Copenhagen University, Copenhagen, Denmark
• The good, the bad and the ugly: Unraveling the molecular basis of endophyte mediated resistance in tomato triggered by Fusarium oxysporum. June 6 2019, Symposium Molecular Plant Pathology; Past and Future, Amsterdam, The Netherlands 
•  The CC domains of NLR-type pathogen receptors play essential roles in oligomerization, network formation and immune signalling. July 14-18 2019, MPMI XVIII, Glasgow, Scotland
• The good, the bad and the ugly : Unraveling the molecular basis of endophyte mediated resistance in tomato triggered by Fusarium oxysporum. March 21 2019, Top Lectures IBL-Leiden, the Netherlands
• The good, the bad and the ugly; unravelling the molecular basis of beneficial, pathogenic and commensal interactions between Fusarium oxysporum and tomato. October 26, 2018. Oxford University, Department of Plant Sciences, UK
• The good, the bad and the ugly; unravelling the molecular basis of beneficial, pathogenic and commensal interactions between Fusarium oxysporum and tomato. October 10th, 2018. "The XXIVth Minisymposium on Plant Biology", Koln, Germany
• The Fusarium oxysporum Avr2-Six5 effector pair alters plasmodesmatal exclusion selectivity facilitating cell-to-cell movement of Avr2.  July 2-3, 2018, 3^rd International Conference “Plant Biotic Stresses & Resistance Mechanisms” Vienna Austria
• The good, the bad and the ugly; unravelling the molecular basis of beneficial, pathogenic and commensal interactions between Fusarium oxysporum and tomato.  June 14, 2018 , KEYS symposium.“Harnessing plant-microbe symbiosis to revolutionize agriculture”, Wageningen, NL
• A tale of two effector proteins -How a pair of fusarium effector proteins manipulates tomato. January 20 2018, Hamburg University. Hamburg, Germany
• The Fusarium oxysporum Avr2-Six5 effector pair alters the exclusion selectivity of plasmodesmata. December 1, 2017. Massey University, Palmerston North New Zealand.
• The good, the bad and the ugly - genetic requirements of beneficial, pathogenic and commensal Fusarium oxysporum strains for colonization of tomato plants. 2-23 Nov 2017. NZSM annual conference 2017: our well-being & our microbes. Auckland, New Zealand
• The Fusarium oxysporum effector Six8 manipulates plant immunity through association with the transcriptional co-repressors TPL and TPR1. 28 August 2017,  Shanghai Center for Plant Stress Biology, Shanghai,  P.R.  China.
• The Fusarium oxysporum Avr2-Six5 effector pair alters the exclusion selectivity of plasmodesmata and targets PTI signaling. 23 August 2017. Nanjing Agricultural University, Lab of Molecular Plant Virology, Nanjing. P.R.  China.
• The Fusarium oxysporum Avr2-Six5 effector pair alters exclusion selectivity of plasmodesmata, 12 July 2017, EMBO Workshop; Intracellular Communication in development and disease, Harnack House, Berlin, Germany 
• Functional analysis of the Fusarium Avr2 effector protein. 24 March 2017, Gregor Mendel Insitute Vienna Austria.
• The role of Fusarium effectors in virulence and NLR-mediated innate immunity. December 1 2016, Institut für Biologie/Genetik Martin-Luther-Universität,  Halle (Saale), Germany
• Functional analysis of the Fusarium Avr2 effector protein. October 26  016, Sainsbury Laboratory, Norwich United Kingdom
• Gene-for-gene resistance - old dogma’s new insights: NLR’s, sentinels of plant immunity. TSL Summer School: Plant Microbe Interactions. 17-28 August 2015. TSL Norwich, United Kingdom
• The Fusarium oxysporum effector Six8 manipulates plant immunity through association with the transcriptional co-repressors TPL and TPR1. Annual Conference of the SUSTAIN COST Action (FA1208)   17-19 February 2016 Banyuls, France 
• The role of Fusarium effectors in virulence and NLR-mediated innate immunity.  New Phytologist workshop; “The apoplast as battleground for plant-microbe interactions”. 9 ^th– 10 ^st July 2015, Castle Rauischholzhausen, Gießen, Germany
• The Fusarium oxysporum effector Six8 manipulates plant immunity through association with the transcriptional co-repressors TPL and TPR1. International Conference on “Plant Biotic Stresses & Resistance Mechanisms II” July 2 - 4, 2015 Vienna, Austria
• The NLR immune receptors I-2 and Rx1 are DNA deforming proteins. 13-14 April 2015 De Wereld, Lunteren, The Netherlands
• The NLR immune receptors I-2 and Rx1 are DNA deforming proteins. MPI symposium ‘NLR Biology in Plants and Animals’, May 3-6, 2015 Schloss Ringberg Munich, Germany
• The NLR immune receptors I-2 and Rx1 are DNA deforming proteins. 15 Jan 2015 University of Copenhagen Copenhagen, Denmark
• The Fusarium oxysporum effector Six8 manipulates plant immunity through association with the transcriptional co-repressors TPL and TPR1. MINI-SYMPOSIUM: Wageningen University 24 Nov 2014, Wageningen Campus - Netherlands
• The tomato-fusarium pathosystem: a game of hide and seek, 16th IS-MPMI July 2014 Rhodos Greece
• The Fusarium oxysporum effector Six8 manipulates plant immunity through association with the transcriptional co-repressors TPL and TPR1. COST WORKSHOP: Structure-guided investigation of effector function, action and recognition. 10 – 12 Sept 2014, Bucharest, Romania
• De wapenwedloop tussen planten en hun belagers, een strijd om leven en dood.  5 March 2014  Spui lezing Amsterdam
• The role of Fusarium effectors in NLR-mediated innate immunity. XV International Congress on Molecular Plant-Microbe Interactions (IS-MPMI) July 29-August 2, 2012, Kyoto, Japan
• How to build a pathogen detector; structural basis of NB-LRR function. EMBO practical course 18-29 june 2012 TSL, Norwich, UK
• The role of Fusarium effectors in NLR-mediated plant innate immunity. 9 April 2012, Plant Biology Department, University of Fribourg, Fribourg Switzerland.
• The role of pathogen effectors in NLR-mediated plant innate immunity. International Meeting of the Collaborative Research Center SFB 648  "Communication in Plants and their Responsesto the Environment" May 19-22, 2011, Halle (Saale), Germany 
• Molecular co-evolution in the tomato-Fusarium pathosystem. October 8, 2010, Justus Liebig University , Giessen, Germany
• Functional analysis of Fusarium oxysporum f.sp. lycopersici effector proteins. DFG funded colloquium: 'Microbial reprogramming of plant cell development' priority project SPP1212 'Plant-Micro' June 2010,  Freising, Germany
• The arms race between effectors of Fusarium oxysporum and resistance proteins of tomato. Seminar series School of Biological and Biomedical Sciences, May 2010. Durham University, Durham, UK
• How to resist a resistance protein? British Society for Plant Pathology, Presidential Meeting, 2009, Oxford, UK
• How to resist tomato resistance proteins? XIV International Congress on Molecular Plant-Microbe Interactions. July 19-23, 2009, Quebec, Canada.
• Resistance proteins: scouts of the plant innateimmune system. 18th EUCARPIA congress, "Modern Variety Breeding for Present and Future Needs" 9-12 September 2008, Valencia, Spain
• Structure-function analysis of plant NB-LRR disease resistance proteins. SFB 670 " Structure Function and Evolution of Innate immunity" 22-23 September 2008, Max-Planck-Institut für Züchtungsforschung, Koln, Germany
• Resistance proteins: scouts of the plant innate immune system. EPS/Bioexploit Summerschool "On the evolution of plant-pathogen interactions: from principles to practices" 18-20 June 2008, Wageningen, the Netherlands.
• Resistance proteins: scouts of the plant innate immune system.  4th EPSO Conference, 22-26 June 2008 , Presqu'ile de Giens (Côte d'Azur), France
•  Molecular aspects of I-2 mediated resistanceto Fusarium oxysporum . Seminar series. May 2008, Max-Planck-Institut für Züchtungsforschung, Koln, Germany
• Function of the Nucleotide Binding Domain for R Proteins. Keystone Symposium on Plant Innate Immunity, Feb 2008 Keystone Resort,  Keystone, Colorado, USA

Publications arising from my PhD and Postdoc period, for recent papers see Tab "publications"

Papers <2002

• C. F. de Jong, F. L. W. Takken , X. Cai, P. J. G. M. de Wit and M. H. A.J. Joosten (2002)Attenuation of Cf -mediated defenseresponses atelevated temperatures correlates withadecrease in elicitor-binding sites.Molecular Plant-Microbe Interactions 15: 10. 1040-9.
• P. J. G. M. de Wit, B. F. Brandwagt, H. A. Van den Burg, X. Cai, R. A. L. Van der Hoorn, C.F. De Jong, J. van 't Klooster, M. J. D. de Kock, M. Kruijt, W. H. Lindhout, R. Luderer, F. L. W. Takken , N. Westerink, J.J. M. vervoort and M. H. A. J. Joosten (2002) The molecular basis of co-evolution between Cladosporium fulvum  and tomato. Antonie vanLeeuwenhoek 81: 409-412
• R. Luderer, F. L. W. Takken , P.J. G.m.Witand M. H. A. J. Joosten (2002) Cladosporiumfulvum overcomes Cf-2 -mediated resistance by producing truncated AVR2 elicitor proteins. Molecular Microbiology 45: 3. 875-84.
• W. I. L. Tameling, S.D. Elzinga,P.S. Darmin, J. H. Vossen, F. L. W. Takken , M.A.Haring and B. J. C. Cornelissen (2002) The tomato R gene products I-2 and Mi-1 are functional ATP binding proteins withATPase activity. Plant Cell 14: 11. 2929-39.
• X. Cai, F. L. W. Takken , M. H. A. J. Joosten and P.J. G. M. De Wit(2001) Specific recognition of Avr4 and Avr9 result in distinct patternsof hypersensitive cell death in tomato, but similar patterns ofdefence-related geneepxression. Molecular Plant Pathology 2: 2. 77-86
• B. F. Brandwagt, L. A.Mesbah, F. L. W. Takken , P. L. Laurent, T. J. A. Kneppers, J. Hille and H. J. J. Nijkamp (2000) A longevity assurance gene homolog of tomatomediates resistanceto Alternaria alternata f. sp. lycopersici toxins and fumonisin B1. Proc Natl Acad Sci USA 97:9.4961-6.
• F.L. W.Takken and M. H. A. J.Joosten (2000) Plant resistance genes: their structure, function and evolution. European Journal of Plant Pathology 106: 8. 699-713
• F. L. W. Takken, R. Luderer, S. H. E. J. Gabriëls, N.Westerink, R. Lu, P.J.G. M. de Wit and M.H.A.J.Joosten (2000) A functional cloning strategy, based on a binaryPVX-expression vector, toisolate HR-inducing cDNAsof plant pathogens. The Plant Journal 24: 2). 275-283
• L. A.Mesbah, T.J. A. Kneppers, F. L. W. Takken, P. Laurent,J.Hille and H. J. J. Nijkamp (1999) Geneticand physical analysis of aYAC contig spanning the fungal diseaseresistancelocus Asc of tomato ( Lycopersicon esculentum ). Molecular and General Genetics 261 (1): 50-57
• F.L. W. Takken , M. Thomas, M.H. A. J. Joosten, C. Golstein, N.Westerink, J. Hille, H. J. J. Nijkamp, P. J. G. M. DeWit and J. D. G. Jones (1999) A second gene at the tomato Cf-4 locus confers resistance to Cladosporium fulvum through recognition of anovel avirulence determinant. The Plant Journal 20: 3. 279-288
• F.L. W. Takken , D. Schipper, H. J. J. Nijkamp and J.Hille (1998)Identification and Ds-tagged isolation of a new gene at the Cf-4 locus of tomato involved in disease resistance to Cladosporium fulvum race 5. The Plant Journal 14: 401-411

patent applications

• Takken, F.L.W., &Wit, P.J.G.M.de (10-01-2002). Elicitor from Cladosporium . no WO02/02787.
• Turk, S.C.H.J., Takken, F.L.W., Jong, C.F. de, Joosten, M.H.A.J.,& Wit, P.J.G.M. de (02-01-2003). Nucleotide sequences involved in plantdisease resistance.no01202420.4./ WO03000930  
• Joosten, M.H.A.J., Jong, C.F. de, Wit, P.J.G.M. de, Takken, F.L.W., & Turk, S.C.H.J. (17-03-2004). Nucleotide sequences involved in plantresistance. no EP1397515

Biography

Frank Takken (1969) is interested in how plants defend themselves against pathogens. Plants are able to sense the presence of invading microbes. Recognition subsequently results in activation of the plant innate immune system. In this process, resistance proteins play a key role as they mediate pathogen recognition and trigger the activation of downstream signaling cascades that halt the pathogen and thereby prevent disease. An example of a succesfull immune response is shown in the figure below where the tomato  Immunity-2 ( I-2) gene halts ingress of the pathogenic fungus Fusarium oxysporum.

Resistance genes come in different flavors, but the majority encodes intracellular tri-partite proteins that contain a central nucleotide-binding domain. One of Frank's major research interests is the role the distinct domains in these proteins have for their function. Structure-function analysis in combination with 3D modeling of the different subdomain is used to predict mutations that will have specific effects on the activity of these proteins. These mutants are subsequently analyzed for altered biochemical properties, differences in inter- and intramolecular interactions as well as for their effect on disease resistance.

To examine how resistance proteins activate downstream signaling it is essential to know their interacting partners. Using various screens, candidate interacting proteins, and recently also DNA, have been identified and these interactors are analyzed for their involvement in plant defense. Part of this research is funded by an NWO VICI grant that was awarded in 2015. Besides resistance genes, I also have a long standing interest to resolve the molecular basis of host susceptibility and the induced resistance responses triggered by biocontrol fungi.

Frank is appointed as Associate professor in the Molecular Plant Pathology group at the Swammerdam Institute for Life Sciences and was from 2012-2019 Scientific Advisor for Scienza Biotechnology. Previously he worked as postdoc at the Phytopathology group at Wageningen University. During this time he worked on a self-written project at the biotech company Keygene NV in Wageningen. In that project he focused on the identification of genes that are transcriptionally regulated during the onset of plant defense signaling. He received his PhD in 1999 from the Free University of Amsterdam for his pioneering work on the isolation of resistance genes from tomato.