scholarly journals Structural genomic applied on the rust fungus Melampsora larici-populina reveals two candidate effector proteins adopting cystine-knot and nuclear transport factor 2-like protein folds

2019 ◽  
Author(s):  
Karine de Guillen ◽  
Cécile Lorrain ◽  
Pascale Tsan ◽  
Philippe Barthe ◽  
Benjamin Petre ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Nuclear Transport ◽  
Sequence Similarity ◽  
Rust Fungus ◽  
Parasitic Infection ◽  
Effector Proteins ◽  
Host Cells ◽  
Dimensional Structure ◽  
Structural Genomic ◽  
Transport Factor

ABSTRACTRust fungi are plant pathogens that secrete an arsenal of effector proteins interfering with plant functions and promoting parasitic infection. Effectors are often species-specific, evolve rapidly, and display low sequence similarities with known proteins or domains. How rust fungal effectors function in host cells remains elusive, and biochemical and structural approaches have been scarcely used to tackle this question. In this study, we used a strategy based on recombinant protein production in Escherichia coli to study eleven candidate effectors of the leaf rust fungus Melampsora larici-populina. We successfully purified and solved the three-dimensional structure of two proteins, MLP124266 and MLP124017, using NMR spectroscopy. Although both proteins show no sequence similarity with known proteins, they exhibit structural similarities to knottin and nuclear transport factor 2-like proteins, respectively. Altogether, our findings show that sequence-unrelated effectors can adopt folds similar to known proteins, and encourage the use of biochemical and structural approaches to functionally characterize rust effector candidates.

scholarly journals Structural genomics applied to the rust fungus Melampsora larici-populina reveals two candidate effector proteins adopting cystine knot and NTF2-like protein folds

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Karine de Guillen ◽  
Cécile Lorrain ◽  
Pascale Tsan ◽  
Philippe Barthe ◽  
Benjamin Petre ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Sequence Similarity ◽  
Rust Fungus ◽  
Parasitic Infection ◽  
Three Dimensional ◽  
Effector Proteins ◽  
Host Cells ◽  
Dimensional Structure ◽  
Small Proteins ◽  
Wide Range

AbstractRust fungi are plant pathogens that secrete an arsenal of effector proteins interfering with plant functions and promoting parasitic infection. Effectors are often species-specific, evolve rapidly, and display low sequence similarities with known proteins. How rust fungal effectors function in host cells remains elusive, and biochemical and structural approaches have been scarcely used to tackle this question. In this study, we produced recombinant proteins of eleven candidate effectors of the leaf rust fungus Melampsora larici-populina in Escherichia coli. We successfully purified and solved the three-dimensional structure of two proteins, MLP124266 and MLP124017, using NMR spectroscopy. Although both MLP124266 and MLP124017 show no sequence similarity with known proteins, they exhibit structural similarities to knottins, which are disulfide-rich small proteins characterized by intricate disulfide bridges, and to nuclear transport factor 2-like proteins, which are molecular containers involved in a wide range of functions, respectively. Interestingly, such structural folds have not been reported so far in pathogen effectors, indicating that MLP124266 and MLP124017 may bear novel functions related to pathogenicity. Our findings show that sequence-unrelated effectors can adopt folds similar to known proteins, and encourage the use of biochemical and structural approaches to functionally characterize effector candidates.

scholarly journals Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity

2017 ◽  
Vol 81 (2) ◽  
Author(s):  
Marina Franceschetti ◽  
Abbas Maqbool ◽  
Maximiliano J. Jiménez-Dalmaroni ◽  
Helen G. Pennington ◽  
Sophien Kamoun ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Structural Integrity ◽  
Sequence Similarity ◽  
Large Fraction ◽  
Parasitic Infection ◽  
Effector Proteins ◽  
Host Cells ◽  
Effector Genes ◽  
Filamentous Microorganisms ◽  
Domain Integration

SUMMARY Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.

scholarly journals Candidate Effector Proteins of the Rust Pathogen Melampsora larici-populina Target Diverse Plant Cell Compartments

2015 ◽  
Vol 28 (6) ◽  
pp. 689-700 ◽  
Author(s):  
Benjamin Petre ◽  
Diane G. O. Saunders ◽  
Jan Sklenar ◽  
Cécile Lorrain ◽  
Joe Win ◽  
...  
Keyword(s):  
Rust Fungus ◽  
Effector Proteins ◽  
Host Cells ◽  
Plant Proteins ◽  
In Planta ◽  
Biologically Relevant ◽  
Heterologous System ◽  
Biotrophic Pathogens ◽  
Small Set ◽  
Clone And Express

Rust fungi are devastating crop pathogens that deliver effector proteins into infected tissues to modulate plant functions and promote parasitic growth. The genome of the poplar leaf rust fungus Melampsora larici-populina revealed a large catalog of secreted proteins, some of which have been considered candidate effectors. Unraveling how these proteins function in host cells is a key to understanding pathogenicity mechanisms and developing resistant plants. In this study, we used an effectoromics pipeline to select, clone, and express 20 candidate effectors in Nicotiana benthamiana leaf cells to determine their subcellular localization and identify the plant proteins they interact with. Confocal microscopy revealed that six candidate effectors target the nucleus, nucleoli, chloroplasts, mitochondria, and discrete cellular bodies. We also used coimmunoprecipitation (coIP) and mass spectrometry to identify 606 N. benthamiana proteins that associate with the candidate effectors. Five candidate effectors specifically associated with a small set of plant proteins that may represent biologically relevant interactors. We confirmed the interaction between the candidate effector MLP124017 and TOPLESS-related protein 4 from poplar by in planta coIP. Altogether, our data enable us to validate effector proteins from M. larici-populina and reveal that these proteins may target multiple compartments and processes in plant cells. It also shows that N. benthamiana can be a powerful heterologous system to study effectors of obligate biotrophic pathogens.

scholarly journals In situ structural analysis of the Yersinia enterocolitica injectisome

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Mikhail Kudryashev ◽  
Marco Stenta ◽  
Stefan Schmelz ◽  
Marlise Amstutz ◽  
Ulrich Wiesand ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Yersinia Enterocolitica ◽  
Pathogenic Bacteria ◽  
Protein Complexes ◽  
Shigella Flexneri ◽  
Effector Proteins ◽  
Host Cells ◽  
Dimensional Structure ◽  
Bacterial Cells

Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the first three-dimensional structure of Yersinia enterocolitica and Shigella flexneri injectisomes in situ and the first structural analysis of the Yersinia injectisome. Unexpectedly, basal bodies of injectisomes inside the bacterial cells showed length variations of 20%. The in situ structures of the Y. enterocolitica and S. flexneri injectisomes had similar dimensions and were significantly longer than the isolated structures of related injectisomes. The crystal structure of the inner membrane injectisome component YscD appeared elongated compared to a homologous protein, and molecular dynamics simulations documented its elongation elasticity. The ring-shaped secretin YscC at the outer membrane was stretched by 30–40% in situ, compared to its isolated liposome-embedded conformation. We suggest that elasticity is critical for some two-membrane spanning protein complexes to cope with variations in the intermembrane distance.

scholarly journals YopJ Family Effectors Promote Bacterial Infection through a Unique Acetyltransferase Activity

2016 ◽  
Vol 80 (4) ◽  
pp. 1011-1027 ◽  
Author(s):  
Ka-Wai Ma ◽  
Wenbo Ma
Keyword(s):  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Bacterial Species ◽  
Cysteine Proteases ◽  
Catalytic Triad ◽  
Effector Proteins ◽  
Host Cells ◽  
Target Proteins ◽  
Acetyltransferase Activity ◽  
Type Iii

SUMMARYGram-negative bacterial pathogens rely on the type III secretion system to inject virulence proteins into host cells. These type III secreted “effector” proteins directly manipulate cellular processes to cause disease. Although the effector repertoires in different bacterial species are highly variable, theYersiniaouter protein J (YopJ) effector family is unique in that its members are produced by diverse animal and plant pathogens as well as a nonpathogenic microsymbiont. All YopJ family effectors share a conserved catalytic triad that is identical to that of the C55 family of cysteine proteases. However, an accumulating body of evidence demonstrates that many YopJ effectors modify their target proteins in hosts by acetylating specific serine, threonine, and/or lysine residues. This unique acetyltransferase activity allows the YopJ family effectors to affect the function and/or stability of their targets, thereby dampening innate immunity. Here, we summarize the current understanding of this prevalent and evolutionarily conserved type III effector family by describing their enzymatic activities and virulence functions in animals and plants. In particular, the molecular mechanisms by which representative YopJ family effectors subvert host immunity through posttranslational modification of their target proteins are discussed.

scholarly journals Visualizing the Translocation and Localization of Bacterial Type III Effector Proteins by Using a Genetically Encoded Reporter System

2016 ◽  
Vol 82 (9) ◽  
pp. 2700-2708 ◽  
Author(s):  
Jayde A. Gawthorne ◽  
Laurent Audry ◽  
Claire McQuitty ◽  
Paul Dean ◽  
John M. Christie ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Effector Proteins ◽  
Host Cells ◽  
Dependent Manner ◽  
Virulence Determinants ◽  
Entry Site ◽  
Host Cell Membrane ◽  
Content Type ◽  
Type Iii ◽  
Bacterial Type

ABSTRACTBacterial type III secretion system (T3SS) effector proteins are critical determinants of infection for many animal and plant pathogens. However, monitoring of the translocation and delivery of these important virulence determinants has proved to be technically challenging. Here, we used a genetically engineered LOV (light-oxygen-voltage) sensing domain derivative to monitor the expression, translocation, and localization of bacterial T3SS effectors. We found theEscherichia coliO157:H7 bacterial effector fusion Tir-LOV was functional following its translocation and localized to the host cell membrane in discrete foci, demonstrating that LOV-based reporters can be used to visualize the effector translocation with minimal manipulation and interference. Further evidence for the versatility of the reporter was demonstrated by fusing LOV to the C terminus of theShigella flexnerieffector IpaB. IpaB-LOV localized preferentially at bacterial poles before translocation. We observed the rapid translocation of IpaB-LOV in a T3SS-dependent manner into host cells, where it localized at the bacterial entry site within membrane ruffles.

scholarly journals EffectorO: motif-independent prediction of effectors in oomycete genomes using machine learning and lineage specificity

2021 ◽  
Author(s):  
Munir J Nur ◽  
Kelsey Jordan Wood ◽  
Richard W Michelmore
Keyword(s):  
Machine Learning ◽  
Late Blight ◽  
Downy Mildew ◽  
Plant Pathogens ◽  
Sequence Similarity ◽  
Biochemical Properties ◽  
Effector Proteins ◽  
Evolutionary Divergence ◽  
Lineage Specificity ◽  
Late Blight Of Potato

Oomycete plant pathogens cause a wide variety of diseases, including late blight of potato, sudden oak death, and downy mildew of many plants. These pathogens are major contributors to losses in many food crops. Oomycetes secrete "effector" proteins to manipulate their hosts to the advantage of the pathogen. Plants have evolved to recognize effectors, resulting in an evolutionary cycle of defense and counter-defense in plant-microbe interactions. This selective pressure results in highly diverse effector sequences that can be difficult to computationally identify using sequence similarity. We developed a pipeline, EffectorO, that uses two complementary approaches to predict effectors in oomycete pathogen genomes: (1) a machine learning-based pipeline that predicts effector probability based on the biochemical properties of the N-terminal amino acid sequence of a protein and is trained on experimentally verified oomycete effectors and (2) a pipeline based on lineage-specificity to find proteins that are unique to one species or genus, a sign of evolutionary divergence due to adaptation to the host. We tested EffectorO on Bremia lactucae, which causes lettuce downy mildew, and Phytophthora infestans, which causes late blight of potato and tomato, and predicted many novel effector candidates, while still recovering the majority of known effector candidates. EffectorO will be useful for discovering novel families of oomycete effectors without relying on sequence similarity to known effectors.

scholarly journals Legionella pneumophila S1P-lyase targets host sphingolipid metabolism and restrains autophagy

2016 ◽  
Vol 113 (7) ◽  
pp. 1901-1906 ◽  
Author(s):  
Monica Rolando ◽  
Pedro Escoll ◽  
Tamara Nora ◽  
Joëlle Botti ◽  
Valérie Boitez ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Effector Proteins ◽  
Host Cells ◽  
Sphingolipid Metabolism ◽  
Intracellular Pathogens ◽  
Macrophage Infection ◽  
Independent Manner ◽  
S1p Lyase

Autophagy is an essential component of innate immunity, enabling the detection and elimination of intracellular pathogens. Legionella pneumophila, an intracellular pathogen that can cause a severe pneumonia in humans, is able to modulate autophagy through the action of effector proteins that are translocated into the host cell by the pathogen’s Dot/Icm type IV secretion system. Many of these effectors share structural and sequence similarity with eukaryotic proteins. Indeed, phylogenetic analyses have indicated their acquisition by horizontal gene transfer from a eukaryotic host. Here we report that L. pneumophila translocates the effector protein sphingosine-1 phosphate lyase (LpSpl) to target the host sphingosine biosynthesis and to curtail autophagy. Our structural characterization of LpSpl and its comparison with human SPL reveals high structural conservation, thus supporting prior phylogenetic analysis. We show that LpSpl possesses S1P lyase activity that was abrogated by mutation of the catalytic site residues. L. pneumophila triggers the reduction of several sphingolipids critical for macrophage function in an LpSpl-dependent and -independent manner. LpSpl activity alone was sufficient to prevent an increase in sphingosine levels in infected host cells and to inhibit autophagy during macrophage infection. LpSpl was required for efficient infection of A/J mice, highlighting an important virulence role for this effector. Thus, we have uncovered a previously unidentified mechanism used by intracellular pathogens to inhibit autophagy, namely the disruption of host sphingolipid biosynthesis.

scholarly journals ApoplastP: prediction of effectors and plant proteins in the apoplast using machine learning

2017 ◽  
Author(s):  
Jana Sperschneider ◽  
Peter N. Dodds ◽  
Karam B. Singh ◽  
Jennifer M. Taylor
Keyword(s):  
Machine Learning ◽  
Plant Pathogens ◽  
False Positive Rate ◽  
Effector Proteins ◽  
Computational Method ◽  
Host Cells ◽  
Plant Proteins ◽  
Functional Studies ◽  
Positive Rate ◽  
Improving Accuracy

AbstractThe plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no computational method currently exists to discriminate between these localizations. We present ApoplastP, the first method for predicting if an effector or plant protein localizes to the apoplast. ApoplastP uncovers features for apoplastic localization common to both effectors and plant proteins, namely an enrichment in small amino acids and cysteines as well as depletion in glutamic acid. ApoplastP predicts apoplastic localization in effectors with sensitivity of 75% and false positive rate of 5%, improving accuracy of cysteine-rich classifiers by over 13%. ApoplastP does not depend on the presence of a signal peptide and correctly predicts the localization of unconventionally secreted plant and effector proteins. The secretomes of fungal saprophytes, necrotrophic pathogens and extracellular pathogens are enriched for predicted apoplastic proteins. Rust pathogen secretomes have the lowest percentage of apoplastic proteins, but these are highly enriched for predicted effectors. ApoplastP pioneers apoplastic localization prediction using machine learning. It will facilitate functional studies and will be valuable for predicting if an effector localizes to the apoplast or if it enters plant cells. ApoplastP is available at http://apoplastp.csiro.au.

scholarly journals Conserved RxLR Effectors From Oomycetes Hyaloperonospora arabidopsidis and Phytophthora sojae Suppress PAMP- and Effector-Triggered Immunity in Diverse Plants

2018 ◽  
Vol 31 (3) ◽  
pp. 374-385 ◽  
Author(s):  
Devdutta Deb ◽  
Ryan G. Anderson ◽  
Theresa How-Yew-Kin ◽  
Brett M. Tyler ◽  
John M. McDowell
Keyword(s):  
Plant Pathogens ◽  
Phytophthora Species ◽  
Phytophthora Sojae ◽  
Effector Proteins ◽  
Host Cells ◽  
Rxlr Effectors ◽  
Genes Encoding ◽  
Effector Triggered Immunity ◽  
Hyaloperonospora Arabidopsidis ◽  
Diverse Plant

Effector proteins are exported to the interior of host cells by diverse plant pathogens. Many oomycete pathogens maintain large families of candidate effector genes, encoding proteins with a secretory leader followed by an RxLR motif. Although most of these genes are very divergent between oomycete species, several genes are conserved between Phytophthora species and Hyaloperonospora arabidopsidis, suggesting that they play important roles in pathogenicity. We describe a pair of conserved effector candidates, HaRxL23 and PsAvh73, from H. arabidopsidis and P. sojae respectively. We show that HaRxL23 is expressed early during infection of Arabidopsis. HaRxL23 triggers an ecotype-specific defense response in Arabidopsis, suggesting that it is recognized by a host surveillance protein. HaRxL23 and PsAvh73 can suppress pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) in Nicotiana benthamiana and effector-triggered immunity (ETI) in soybean. Transgenic Arabidopsis constitutively expressing HaRxL23 or PsAvh73 exhibit suppression of PTI and enhancement of bacterial and oomycete virulence. Together, our experiments demonstrate that these conserved oomycete RxLR effectors suppress PTI and ETI across diverse plant species.

Sign in / Sign up

Export Citation Format

Share Document