Molecular plant-microbe interactions: the immunity of plants

ETS: Effector-Triggered

Susceptibility Despite the fact that PTI inhibits infection, successful pathogens have developed strategies to defeat PTI by secreting virulence factors known as effectors to lead effector-triggered susceptibility (Kawamura et al.; Kawamura et al. 2009b) and pathogen virulence (Fig. 1.2B). Extensive work on function of effectors has been done on bacterial effectors where several were found to suppress or disrupt PTI, ETI, or both (Guo et al. 2009), but remarkable advances have also been made in Cladosporium fulvum and oomycetes. In C. fulvum, the A VR2 effector inhibits at least four tomato cysteine proteases that are believed to be crucial in the basal ho st defense (Rooney et al. 2005), while a chitin-binding protein A VR4 protects fungi from the Iytic activity of plant chitinases (Van den Burg et al. 2006). Another effector from C. fulvum, ECP6, is believed to be involved in the chitin fragments scavenging activity that are secreted during infection from fungal cell walls, hence preventing them from functioning as P AMP triggering molecules (Bolton et al. 2008).

In oomycete species of the genus Phytophthora, elicitins such as INFI triggers a range of defense responses, including programmed cell death in diverse plant species, and are thus considered as P AMPs (Kawamura et al. 2009a). Recently, the P. infestans A VR3a effector has been shown to interact with and stabilize ho st U-box E3 ligase CMPG l, which is required for the triggering of INF I-dependent cell death (Bos et al. 2010). Another oomycete effector from Hyaloperonospora arabidopsidis, ATR13, has been shown to suppress callose deposition, a presumed basal defense response (Sohn et al. 2007). There is ample evidence now that one function of effectors is to suppress PTI through interaction with pattern recognition receptors (PRR) and processes downstrearn of PRR and rnitogenactivated protein kinase (MAPK) cascades (Block et al. 2008). Upon pathogen attack, pathogen-associated molecular patterns (PAMPs) activate patternrecognition receptors (PRRs) in the host, resulting in a downstream signaling cascade that leads to PAMP-triggered immunity (PTI). B) Virulent pathogens have acquired effectors (purple stars) that suppress PTI, resulting in effector-triggered suseeptibility (Kawamura et al. 2009). C) ln tum, plants have acquired resistanee (R) proteins that recognize these attacker specifie effectors, resulting in a seeondary immune response called effeetor-triggered immunity (Kunjeti et al. 2016).

ETI: Effector-triggered immunity Luckily, the plant has an additional defense layer through which these effectors can be directly or indirectly be recognized by the plant defense system. This second layer is called Effector triggered immunity, and involves mostly intracellular receptors that are the products of the c\assically defined resistance R proteins (Fig. 1.2C) (FIor 1971). These receptors recognize the presence of effectors of the pathogen by direct binding or indirectly by detecting their activity in the ho st cells, leading to a faster and stronger version defense response th an PT! (Bolier and He 2009). ET! is extremely specific to a race or strain of pathogen as it recognizes a virulence determinant or its effect (Mur et al. 2008). The outcome of ET! is usually the programmed cell death response called the hypersensitive response (HR) at the site of pathogen infection, which is thought to limit the spread of the pathogen from the infection site (FIor 1971).

Natural selection drives pathogens to suppress ET! again, either through diversifying their effector repertoire or by acquiring new effectors. Nevertheless, natural selection also drives plants to modify their R proteins arsenal or acquire new ones, so that the pathogen effectors can be recognized and, again, the ET! can be triggered (hence the zig-zag model). Several proteins secreted in apoplast or xylem sap during colonization of tomato have been identified in C. fulvum or F. oxysporum f. sp. lycopersici, respectively (Huitema et al. 2004; Thomma et al. 2005), most of which are also avirulence genes that match corresponding resistance genes (Rep et al. 2004; Stergiopoulos and de Wit 2009). In the flax rust fungus Melampsora fini, ail the identified A vr small secreted proteins are expressed in haustoria (Catanzariti et al. 2006; Dodds and Rathjen 2010), however to this date their virulence target are unknown. Similarly, avirulence genes originally isolated from oomycete pathogens encode small secreted proteins, of which transient expression in the ho st cytoplasm leads to R-gene-dependent cell death (Allen et al. 2004; Armstrong et al. 2005; Rehmany et al. 2005; Shan et al. 2008).

Effectors: concepts and definitions

Pathogens have developed strategies to avoid the different levels of host physical and chemical barriers to modify ho st structures and physiology, transforming plant tissues into a suitable niche to obtain the necessary nutrients for their development and ensure the completion of their lifecycle (Gaulin 2017). One of the well-known strategies of pathogens is to secrete an arsenal of molecules called « Effectors » who se various functions aim to promote the success of the infection (Hogenhout et al. 2009; Win et al. 2012). Though the term « effector » is broadly used in the studies of plant-microbe interaction, its definition varies. Kamoun (2003) and Huitema et al. (2004) defined effectors as « molecules that alter the structure and function of ho st cells, thereby facilitating infection (virulence factors or toxins) and triggering defense response (avirulence factors or elicitors). » In another definition Birch and colleagues (2014) referred to effectors in plant-pathogen interactions as « any protein synthesized by a pathogen that is exported to a potential host, which has the effect of making the host environment beneficial to the pathogen ». The widely accepted hallmarks of effectors include; small secreted proteins (SSPs) having a N-terminal signal peptide with low sequence homology across species, no conserved host-targeting signal and capable of manipulating and reprograming host metabolism and immunity (Hogenhout et al. 2009). Most of the described effectors are proteins; however, non-protein effectors have also been described such as metabolites, toxins (Amselem et al. 2011; Arias et al. 2012; Collemare and Lebrun 2011) or small interfering RNAs (Weiberg et al. 2013).

Host-protein targets of effectors

It is now weIl established that the pathogen effectors directly target host proteins and manipulate host targets for their benefit (Rovenich et al. 2014; Win et al. 2012). The first host-targets of plant-pathogen effector proteins to be identified were of bacterial type III effector (T3Es), many of which target positive regulators of immunity in order to inhibit their activity (Des landes and Rivas 2012). One particularly notable example of a ho st target is the A. tha/iana RPMI-interacting prote in RIN4 (Win et al. 2012). Sorne bacterial effectors are enzymes, such as sorne of T3SS delivered effectors which biochemically alter host molecules, such as HopZla which has been reported to physically interact with GmHIDl (2-hydroxyisoflavone). The interaction ofHopZla and GmHID 1 leads to degradation of GmHID 1 and thereby leads to enhanced bacterial multiplication (Cunnac et al. 2009; Deslandes and Rivas 2012). Few effectors do not con vey enzymatic activity; however, they bind to host proteins to alter host cellular functions. In addition to this, many such effectors prevent plant enzymes activity (kinases, glucanases, peroxidases, and proteases) (Song et al. 2009; Tian et al. 2004; Tian et al. 2007). Other groups of bacterial effectors bind nucleic acids and regulate gene expression, for example, Xanthomonas Transcription Activator-Like (TAL) effectors directly bind to promoter motifs of ho st genes to modify host transcription (Boch et al. 2009; Gu et al. 2005; Yang et al. 2006).

SWEET sugar transporters are one of the host susceptibility genes which are induced by TAL effectors (Li et al. 2013). Identification of the effector targets in the host cell remains challenging because of a large number of uncharacterized or unidentified effectors from the diverse group of pathogens, microbes and symbionts. For the same reason, the biochemical mechanisms of how effectors manipulate their ho st target are also poorly understood. Regardless of the specific target of effectors, now it has been reported that a single effector can target multiple plant proteins or can disturb diverse cellular processes in the host (Fig. 1.4) (Win et al. 2012). For example, the P. syringae type-III effectors AvrPto and AvrPtoB in tomato and A rabidopsis, directly bind to several immune receptor kinases to abrogate their function and impede PTI signaling pathways (Abramovitch et al. 2006; GimenezIbanez et al. 2009; Shan et al. 2008; Xiang et al. 2008; Zheng et al. 2012). The HopMl effector, degrades several plant proteins, including AtMin7 (Nomura et al. 2006). Similarly, secreted A Y-WB Protein Il (SAP Il), a phytoplasma effector, binds to both class 1 and II of Teosinte branched lICycloidea/Proliferating (TCP) transcription factors (TF), but subverts the class II type TCP TF (Sugio et al. 2011); hence one of the main function of effectors is the suppression of immunity.

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Host-protein helpers of effectors

Regardless of the proteins used as effectors target, some plant proteins act as a co-factor for effector function or post-translationally modify effectors in the cytoplasm and are required for the maturation or trafficking of effector prote in to their final subcellular destination within the ho st cell (Win et al. 2012). Therefore, ho st proteins that facilitate effectors maturation or activity, are known as effectors helper proteins (Fig. 1.5A-B) (Win et al. 2012). Several host effector helpers have been identified. Classic examples of helper protein are the cyclophilin (a chaperone) CYP 1. A vrRpt2, a cysteine protease is secreted as an inactive form by P. syringae, but as soon as it is inside the host cell, it interacts with cyclophilin. The association of A vrRpt2-cyclophilin accelerates folding of the effector and cyclophilin activates self-processing of AvrRpt2, aggravating the breakdown of RPMI Interacting Protein 4 (RIN4), the target prote in of AvrRpt2 (Coaker et al. 2005). Another P. syringe type-III effector, HopZla, is activated by cellular phytic acid from the host to become a functional acetyltransferase that acetylates tubulin, a plant target of HopZla (Lee et al. 2012).

Other type-III effectors require host-mediated biochemical modifications, like myristoylation and phosphorylation, to become functional. Myristoyl transferase is an example which myristoylates the A vrPto T3SS secreted effector of Pseudomonas syringae. Myristoylation of A vrPto and A vrRpm 1 is necessary for their avirulence and virulence activities, suggesting that plant N-myristoyl transferase act as a host-cell helper to the effector (Anderson et al. 2006; Nimchuk et al. 2000). The plant protein importin-a is an another well-studied helper protein that mediates nuclear trafficking and is exploited by several pathogen effectors, including SAP 11, T AL and Crinklers (Bai et al. 2009; Schomack et al. 2010; Szurek et al. 2001). T AL effector A vrBs3 interacts with importin which enables its accumulation in the host-ce Il nucleus where it directly binds to plant DNA harboring a conserved promoter element, which is its « real » target, to activate plant gene expression (Kay et al. 2007; Szurek et al. 2001). Therefore, host proteins can act either as an effector helper or target that are taken or manipulated by the pathogen to enable their effector proteins to function and ultimately, establish a state of effectortriggered host susceptibility. Therefore, conceptually the host proteins used as target or helper for the effectors are ho st susceptibility factors (Win et al. 2012).

Table des matières

ACKNOWLEDGEMENTS
RÉSUMÉ
SUMMARY
LIST OF FIGURES
LIST OF ABBREVIATIONS AND ACRONYMS
CHAPTERI INTRODUCTION
1.1 Plant diseases: major threats to global food security
1.2 Lifestyles of plant microbes and types of interaction
1.3 Molecular plant-microbe interactions: the immunity of plants
1.3.1 PT!: PAMP-triggered immunity
1.3.2 ETS: Effector-Triggered Susceptibility
1.3.3 ET!: Effector-triggered immunity
1.4 Effector biology
1.4.1 Effectors: concepts and definitions
1.4.2 Different types of effectors
1.4.3 Effector dei ivery systems
1.4.4 Host-protein targets of effectors
1.4.5 Host-protein helpers of effectors
1.5 Poplar-Melampsora larici-populina interaction
1.6 Poplar and poplar rust: a model system
1.7 CSEPs from Melampsora larici-populina (Mlp)
1.7.1 Identification and selection
1.7.2 Subcellular localization of M larici-populina effectors
1.7.3 Heterologous system to study effectors
1.8 Research objectives
CHAPTERII VACUOLAR MEMBRANE STRUCTURES AND THEIR ROLES IN PLANT-PATHOGEN INTERACTIONS
2.1 Author contributions
2.2 Résumé de l’article
2.3 Full article in English: Vacuolar membrane structures and their roles in plant-pathogen interactions
Abstract
Introduction
The plant vacuole and its function in the cell
Vacuolar structures
Markers to study the vacuolar structures
Chemical markers
Protein markers
Protein distribution and motility in tonoplast and bulbs
Protein distribution
Protein mobility
The vacuole in plant-pathogen interaction
Secondary metabolites
Hydrolytic enzymes
Defense proteins
Vacuole dynamics
Tonoplast, TVS, and bulbs in plant-pathogen interaction
Conclusions and future perspectives
Acknowledgement
References
CHAPTERIII NEW INSIDE INTO BULB DYNAMICS IN THE VACUOLAR LUMEN OF ARABIDOPSIS CELLS
3.1 Authorcontributions
3.2 Résumé de l’article
3.3 Full article in English: New insight into bulb dynamics in the vacuolar lumen of Arabidopsis cells
Abstract
Introduction
Materials and Methods
Plasmid constructs, transformation, and growth conditions
Confocal laser scanning microscopy
Crosses 65
Fluorescence recovery after the FRAP experiments
Results
The candidate effector Mlp 124357 labels the tonoplast, TVS, and bulbs, enabling bulb speed quantification
Marker proteins are not distributed evenly on the bulb surface
Once bulbs are formed they no longer exchange protein with the tonoplast
Discussion
Acknowledgments
References
Supplementary data
CHAPTERIV A POPLAR RUST EFFECTOR PROTEIN ASSOCIATES WITH PROTEIN DISULFIDE ISOMERASE AND ENHANCE PLANT SUSCEPTIBILITY IN ARABIDOPSIS
4.1 Authors contributions
4.2 Résumé de l’article
4.3 Full text in English: A poplar rust effector protein associates with protein disulfide isomerase and enhance plant susceptibility in Arabidopsis
Abstract
Introduction
Materials and Methods
Plants material and growth conditions
Cloning procedures and plasmid constructs
Expression ofproteins in N. benthamiana and A. thaliana
Pathogen infections assay
Membrane fractionation
Sample preparation for mass spectrometry
LCIES-MSIMS, data processing, and protein identification
Western blot analysis
Confocal Microscopy
Y2H reporter assays
RNA extraction and transcriptome analysis
Molecular modeling of the proteins
Results
Identification/selection and phylogenetic analysis ofMlp124357
Mlp 124357 expression in planta affects the plant susceptibility to bacterial and oomycete pathogens
Mlp124357 possesses a GxxxG motif that is required for the interaction with tonoplast
Immunoprecipitation and mass spectrometry reveal potential plant interactor protein ofMlp124357
Mlp124357 associates with Arabidopsis and poplar protein disulfideIsomerase
Molecular modeling also supports the association of AtPDI-11 and Mlp124357 effector
The Mlp124357-PDI association takes place in an effector-specific manner
Protein disulfide-isomerase act as a helper ofMlp124357
Transcriptome analysis ofMlp124357-expressed Arabidopsis
Discussion
Acknowledgements
References
Supplementary data
CHAPTERV CONCLUSIONS
5.1 Conclusion
5.1.1 Mlp 124357 localize in the tonoplast, TVs, and bulbs of Arabidopsis epidermal cells
5.1.2 Why might Mlp124357 target vacuolar structures?
5.1.3 Marker proteins are not even1y distributed on the bulb membrane
5.1.4 Protein movement does not occur between bulb and tonoplast
5.1.5 Mlp124357 enhance plant susceptibility
5.1.6 GxxxG motif of Mlp 124357 is required to localize in the tonoplast and plant susceptibility
5.1.7 Mlp124357 interact with protein disu1fide isomerase
5.1.8 Protein disulfide isomerase is a helper but not a virulence target of Mlp124357
5.1.9 The Mlp124357 effector affect plant transcriptome
5.2 Perspectives! Outlook
5.2.1 Assessment and confirmation of virulent target ofMlp124357
5.2.2 Structural studies
5.2.3 Host-induced gene silencing (HIGS) of Mlp 124357
5.3 Final Conclusions
REFERENCES

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