This project aims to address a number of structural aspects related to key elements of the plant immune system and its pathogen interactors using a combined approach intricating experimental and computational steps. To this end we intend to build on our previous results in the field and further develop experimental, bioinformatics and molecular modeling methods appropriate for solving the specific problems implied by this proposal.
This project aims to address a number of structural aspects related to key elements of the plant immune system and its pathogen interactors using a combined approach intricating experimental and computational steps. To this end we intend to build on our previous results in the field and further develop experimental, bioinformatics and molecular modeling methods appropriate for solving the specific problems implied by this proposal.
Despite the massive investment in structural biology, results on plant molecular system are scarce. There are not many groups with consistent and systematic interest in structural plant biology. This makes computational techniques very useful but at the same time extremely challenging given the small number of known structures which translates into a very low level or absence of homology.
Over a decade ago we started a long standing collaboration with plant biologists form Wageningen. This led us, in time, to tackle increasingly complex problems related to protein families of the first and second layer of immunity and their pathogen interactors in studies in which we progressively started to intricate computation and experiment, mainly mutational analysis. Such combined strategies allowed us to significantly reduce the dimensionality of the tackled problems but on the other hand it allowed us to validate our computational models. In the end this strategy equates to a structure guided investigation of protein families involved in plant pathogen interaction. Gradually more groups started to show interest in our approach which led nowaday to an extended network of colaborations all over the Europe, Israel & US; and an increasing spread of this approach in the last couple of years.
The paucity of structural data in the field pose significant problems in computational modelling of these systems. This led us to improve and develop de-novo remote homology and ab-initio modelling workflows that we used to generate the first ever R-protein LRR and CC models improved NB models; and also models of some important effectors.
The present proposal intends to further build upon the experience we get in the field by addressing some new systems and new methodology challenges.
Head of Department
Andrei heads the Department of Bioinformatics since 1999. He developed computational assisted work relevant in many fields of molecular life sciences reflected by a large web of collaborations with groups from Oxford, Yale, Berkeley, Wageningen and many other advanced research centers. More...
We aim here to address new aspects related to the molecular structure, interactions and functioning of two major protein classes of plant immune system: (-a) R-gene products and (-b) the constitutive tandems formed as a first layer of plant immunity in tomato by cell surface receptor-like kinases (RLKs) and receptor like proteins (RLPs), in an attempt to understanding their functioning.
Related to (-a) we intend to further build upon results obtained on the structrue of CC-, NB- and LRR- domains and their interactions, by adressing new problems, as follows:
Related to (-b) we intend to combine our experience in glycobiology and biocomputing in aiming to:
| Principal Investigator | Andrei-J Petrescu - IBAR |
| Senior Researcher | Adina Milac - IBAR |
| PostDoc Researcher | Marius Micluta - IBAR |
| PostDoc Researcher | Marius Surleac - IBAR |
| PostDoc Researcher | Cristian A Munteanu - IBAR |
| PhD Student | Eliza Martin - IBAR |
| PhD Student | Laura Georgiana Manica - IBAR |
Results 2017 - 2018
In implementing STRASSIST, during the period 2017 - 2019, we addressed a number of specific problems related to the overall goals of the project concerning the domain structure of resitance gene products and pattern-recognition receptors (PRR) investigated.
Hence, so far:
Along the first line of the proposed research: (a1) quantifying the structural diversiy of LRR domains identified at genome level - we had developed prediction tools for LRR sequence identification (a) with fast local and global classifires based on conditional probabilities/motif densities and (b) more precise machine learning LRR motif identification based on Support Vector Machine and Multi-Layer Perceptron combined with various artificial resampling techniques given the small dimension of the learning set. These tools were used to scan large sequence databases for LRR identification, build a LRR database and cluster the LRRs in the structure propensity space and assess the phylogenetic diversity of this protein architecture. Both methods prove also able to discriminate between very closely related classes of solenoidic proteins. This was instrumental in modelling other solenoidic domains such as neurofibrin CTD domain or protoRAG2 in protoRAG1-RAG2 complex, see references.
On the second line of our proposal: (a2) predicting the structure, dynamics and interactions of the RGA-CC domains - we have generated so far the starting structural models of the coiled-coil domain of RGA protein consistent with known experimental and bioinformatic data. The detalied analysis of the CC structure allowed us to identify general folding, flexibility and interaction rules for CC domains pertinent to Plant Resistance proteins in general - work published in Plant Physiology; PLoS Biology and more recently Plant Journal - accepted for publication (2019), see references.
Related to: (a3) predicting the structure and interactions within Arabidopsis ZAR1/ZED1/avr complexes - we have built the predictive frame models of Zar1 domains in both active and inactive state and Zed1 & avr proteins and probed the complex architecture using the determined constraints and in collaboration with our partners was assessed the role of point mutations in crytical regions of these structures. Part of this work that it is still in progress were recently accepted for publication in Plant Journal, see references.
Finaly related to (b1) the investigation of the first RLN-RNK layer of immunity in tomato - we have characterised the occupancy of glycosylation sites in gf4 and have built the complete predictive models of Cf4/9 & SOBIR1 and docking models of Cf4 - BAK1 and Cf4 - BAK1 - SOBIR1complexes that are now in analysis with our collaborators.
The work on RLN-RNK system formed the basis of the MSc Thesis "Importance for food safety of resistance mechanisms in Licopersicum hirsutum" presented by Eliza Martin at the Faculty of Medicine and Pharmacy Bucharest. This MSc was held in parallel to her ongoing PhD Stage in the Department of Bioinformatics and Structural Biocemistry of IBAR.
Publications on issues related to the structure of R-gene products and their interactors:
1. Wróblewski T, Spiridon L, Martin EC, Petrescu AJ, Cavanaugh K, Jose-Truco M, Xu H, Gozdowski D, Pawłowski K, Michelmore RW, Takken FLW.. "Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity." PLOS Biology 16(12): e2005821 (2018)
doi: https://doi.org/10.1371/journal.pbio.2005821
IF = 8.386 AIS = 5.6
Slootweg EJ, Spiridon LN, Martin EC, Tameling WIL, Townsend PD, Pomp R, Roosien J, Drawska O, Sukarta OCA, Schots A, Borst JW, Joosten MHAJ, Bakker J, Smant G, Cann MJ, Petrescu AJ, Goverse A. "Distinct Roles of Non-Overlapping Surface Regions of the Coiled-Coil Domain in the Potato Immune Receptor Rx1." Plant Physiol. 178(3):1310-1331 (2018)
doi: https://doi.org/10.1104/pp.18.00603
IF = 6.305 AIS = 2.2
Baudin M, Schreiber KJ, Martin EC, Petrescu AJ, Lewis JD "Structure-function analysis of ZAR1 immune receptor reveals key molecular interactions for activity" bioRxiv 592824 (2019) - preprint;
doi: https://doi.org/10.1101/592824
16.09.2019: Mannuscript No. TPJ-00632-2019.R1 acceptat spre publicare în Plant Journal IF = 5.775 AIS = 2.1
Diaz-Granados A, Sterken MG, Persoon J, Overmars H, Pokhare S, Mazur MJ, Martin-Ramirez S, Holterman M, Martin EC, Pomp R, Finkers-Tomczak A, Roosien J, Elashry A, Grundler F, Petrescu AJ, Smant G, Goverse A. "SIZ1 is a nuclear host target of the nematode effector GpRbp1 from Globodera pallida that acts as a negative regulator of basal plant defense to cyst nematodes" bioRxiv 725697 (2019);
doi: https://doi.org/10.1101/725697
15.08.2019: Mannuscript No. TPJ-00946-2019 trimis spre evaluare la Plant Journal
Publications based on methods developped in STRASSIST:
Norris EJ, Jones WD, Surleac MD, Petrescu AJ, Destephanis D, Zhang Q, Hamadeh I, Kneisl J, Livasy CA, Ganapathi RN, Tait DL, Ganapathi MK. "Clonal lineage of high grade serous ovarian cancer in a patient with neurofibromatosis type 1." Gynecol Oncol Rep. 23:41-44 (2018).
doi: https://doi.org/10.1016/j.gore.2018.01.005
IF = 0.59 AIS = –
Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell JD, Pontarotti P, Petrescu AJ, Xu A, Xiong Y, Schatz DG. "Transposon molecular domestication and the evolution of the RAG recombinase.", Nature. 569:79-84 (2019).
doi: https://doi.org/10.1038/s41586-019-1093-7
IF = 43.070 AIS = 22.
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