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 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 Positively selected effector genes and their contribution to virulence in the smut fungus Sporisorium reilianum

2017 ◽  
Author(s):  
Gabriel Schweizer ◽  
Karin Münch ◽  
Gertrud Mannhaupt ◽  
Jan Schirawski ◽  
Regine Kahmann ◽  
...  
Keyword(s):  
Positive Selection ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Large Fraction ◽  
Gene Families ◽  
Effector Proteins ◽  
Smut Fungi ◽  
Formae Speciales ◽  
Effector Genes ◽  
Sporisorium Reilianum

AbstractPlants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example are secreted fungal effector proteins and their host targets, which play an important role in pathogenic interactions. Biotrophic smut fungi (Basidiomycota) are well-suited to investigate the evolution of plant pathogens, because several reference genomes and genetic tools are available for these species. Here, we used the genomes of Sporisorium reilianum f. sp. zeae and S. reilianum f. sp. reilianum, two closely related formae speciales infecting maize and sorghum, respectively, together with the genomes of Ustilago hordei, Ustilago maydis and Sporisorium scitamineum to identify and characterize genes displaying signatures of positive selection. We identified 154 gene families having undergone positive selection during species divergence in at least one lineage, among which 77% were identified in the two investigated formae speciales of S. reilianum. Remarkably, only 29% of positively selected genes encode predicted secreted proteins. We assessed the contribution to virulence of nine of these candidate effector genes in S. reilianum f. sp. zeae by deleting individual genes, including a homologue of the effector gene pit2 previously characterized in U. maydis. Only the pit2 deletion mutant was found to be strongly reduced in virulence. Additional experiments are required to understand the molecular mechanisms underlying the selection forces acting on the other candidate effector genes, as well as the large fraction of positively selected genes encoding predicted cytoplasmic proteins.

scholarly journals roles Hrp-dependent effector proteins and hrp gene regulation as determinants of virulence and host-specificity in Erwinia stewartii and E. herbicola pvs. gypsophilae and betae

2005 ◽  
Author(s):  
David L. Coplin ◽  
Shulamit Manulis ◽  
Isaac Barash
Keyword(s):  
Gene Expression ◽  
Host Specificity ◽  
Pathogenic Bacteria ◽  
Effector Proteins ◽  
Host Cells ◽  
Secretion Systems ◽  
Gram Negative ◽  
Regulatory Cascade ◽  
Effector Genes ◽  
Erwinia Stewartii

Gram-negative plant pathogenic bacteria employ specialized type-III secretion systems (TTSS) to deliver an arsenal of pathogenicity proteins directly into host cells. These secretion systems are encoded by hrp genes (for hypersensitive response and pathogenicity) and the effector proteins by so-called dsp or avr genes. The functions of effectors are to enable bacterial multiplication by damaging host cells and/or by blocking host defenses. We characterized essential hrp gene clusters in the Stewart's Wilt of maize pathogen, Pantoea stewartii subsp. stewartii (Pnss; formerly Erwinia stewartii) and the gall-forming bacterium, Pantoea agglomerans (formerly Erwinia herbicola) pvs. gypsophilae (Pag) and betae (Pab). We proposed that the virulence and host specificity of these pathogens is a function of a) the perception of specific host signals resulting in bacterial hrp gene expression and b) the action of specialized signal proteins (i.e. Hrp effectors) delivered into the plant cell. The specific objectives of the proposal were: 1) How is the expression of the hrp and effector genes regulated in response to host cell contact and the apoplastic environment? 2) What additional effector proteins are involved in pathogenicity? 3) Do the presently known Pantoea effector proteins enter host cells? 4) What host proteins interact with these effectors? We characterized the components of the hrp regulatory cascade (HrpXY ->7 HrpS ->7 HrpL ->7 hrp promoters), showed that they are conserved in both Pnss and Fag, and discovered that the regulation of the hrpS promoter (hrpSp) may be a key point in integrating apoplastic signals. We also analyzed the promoters recognized by HrpL and demonstrated the relationship between their composition and efficiency. Moreover, we showed that promoter strength can influence disease expression. In Pnss, we found that the HrpXY two-component signal system may sense the metabolic status of the bacterium and is required for full hrp gene expression in planta. In both species, acyl-homoserine lactone-mediated quorum sensing may also regulate epiphytic fitness and/or pathogenicity. A common Hrp effector protein, DspE/WtsE, is conserved and required for virulence of both species. When introduced into corn cells, Pnss WtsE protein caused water-soaked lesions. In other plants, it either caused cell death or acted as an Avr determinant. Using a yeast- two-hybrid system, WtsE was shown to interact with a number of maize signal transduction proteins that are likely to have roles in either programmed cell death or disease resistance. In Pag and Pab, we have characterized the effector proteins HsvG, HsvB and PthG. HsvG and HsvB are homologous proteins that determine host specificity of Pag and Pab on gypsophila and beet, respectively. Both possess a transcriptional activation domain that functions in yeast. PthG was found to act as an Avr determinant on multiple beet species, but was required for virulence on gypsophila. In addition, we demonstrated that PthG acts within the host cell. Additional effector genes have been characterized on the pathogenicity plasmid, pPATHₚₐg, in Pag. A screen for HrpL- regulated genes in Pnsspointed up 18 candidate effector proteins and four of these were required for full virulence. It is now well established that the virulence of Gram-negative plant pathogenic bacteria is governed by Hrp-dependent effector proteins. However; the mode of action of many effectors is still unresolved. This BARD supported research will significantly contribute to the understanding of how Hrp effectors operate in Pantoea spp. and how they control host specificity and affect symptom production. This may lead to novel approaches for genetically engineering plants resistant to a wide range of bacterial pathogens by inactivating the Hrp effectors with "plantabodies" or modifying their receptors, thereby blocking the induction of the susceptible response. Alternatively, innovative technologies could be used to interfere with the Hrp regulatory cascade by blocking a critical step or mimicking plant or quorum sensing signals.   

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 Coding sequence-independent homology search identifies highly divergent homopteran putative effector gene family

2021 ◽  
Author(s):  
David Stern ◽  
Clair Han
Keyword(s):  
Sequence Similarity ◽  
Structural Features ◽  
Aphid Species ◽  
Effector Proteins ◽  
Scale Insects ◽  
Homology Search ◽  
Coding Sequence ◽  
Effector Genes ◽  
Expression Studies ◽  
Independent Features

Many genomes contain rapidly evolving and highly divergent genes whose homology to genes of known function often cannot be determined from sequence similarity alone. However, coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of rapidly evolving bicycle aphid effector genes identified many putative bicycle homologs in aphids, phylloxerids, and scale insects, whereas sequence similarity search methods yielded few homologs in most aphids and no homologs in phylloxerids and scale insects. Subsequent examination of sequence features and intron locations supported homology assignments. Differential expression studies of newly-identified bicycle homologs, together with prior proteomic studies, support the hypothesis that BICYCLE proteins act as plant effector proteins in many aphid species and perhaps also in phylloxerids and scale insects.

scholarly journals Effectors with different gears: divergence of Ustilago maydis effector genes is associated with their temporal expression pattern during plant infection

2020 ◽  
Author(s):  
Jasper R.L. Depotter ◽  
Weiliang Zuo ◽  
Maike Hansen ◽  
Boqi Zhang ◽  
Mingliang Xu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Plant Pathogens ◽  
Ustilago Maydis ◽  
Effector Proteins ◽  
Intraspecific Diversity ◽  
Close Relative ◽  
Host Immune System ◽  
Gene Repertoire ◽  
Effector Genes ◽  
Amino Acid Divergence

AbstractPlant pathogens secrete a variety of effector proteins that enable host colonization but are also typical pathogen detection targets for the host immune system. Consequently, effector genes encounter high selection pressures, which typically makes them fast evolving. The corn smut pathogen Ustilago maydis has an effector gene repertoire with a dynamic expression across the different disease stages. We determined the amino acid divergence of U. maydis effector candidates with Sporisorium reilianum orthologs, a close relative of U. maydis. Intriguingly, there are two distinct groups of effector candidates, ones with a respective conserved and diverged protein evolution. Conservatively evolving effector genes especially have their peak expression during the (pre-)penetration stages of the disease cycle. In contrast, expression of divergently evolving effector genes generally peaks during fungal proliferation within the host. To test if this interspecific effector diversity corresponds to intraspecific diversity, we sampled and sequenced a diverse collection of U. maydis strains from the most important maize breeding and production regions in China. Effector candidates with a diverged interspecific evolution had more intraspecific amino acid variation than candidates with a conserved evolution. In conclusion, we highlight diversity in evolution within the U. maydis effector repertoire with dynamically and conservatively evolving members.

scholarly journals Functional analysis of a Phytophthora host-translocated effector using the yeast model system

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12576
Author(s):  
Avery C. Wilson ◽  
William R. Morgan
Keyword(s):  
Amino Acid ◽  
Plant Pathogens ◽  
Bioinformatics Analysis ◽  
Effector Proteins ◽  
Yeast Cells ◽  
Phosphate Homeostasis ◽  
Rxlr Effectors ◽  
Effector Genes ◽  
Rxlr Effector ◽  
Yeast Genes

Background Phytophthora plant pathogens secrete effector proteins that are translocated into host plant cells during infection and collectively contribute to pathogenicity. A subset of these host-translocated effectors can be identified by the amino acid motif RXLR (arginine, any amino acid, leucine, arginine). Bioinformatics analysis has identified hundreds of putative RXLR effector genes in Phytophthora genomes, but the specific molecular function of most remains unknown. Methods Here we describe initial studies to investigate the use of Saccharomyces cerevisiae as a eukaryotic model to explore the function of Phytophthora RXLR effector proteins. Results and Conclusions Expression of individual RXLR effectors in yeast inhibited growth, consistent with perturbation of a highly conserved cellular process. Transcriptome analysis of yeast cells expressing the poorly characterized P. sojae RXLR effector Avh110 identified nearly a dozen yeast genes whose expression levels were altered greater than two-fold compared to control cells. All five of the most down-regulated yeast genes are normally induced under low phosphate conditions via the PHO4 transcription factor, indicating that PsAvh110 perturbs the yeast regulatory network essential for phosphate homeostasis and suggesting likely PsAvh110 targets during P. sojae infection of its soybean host.

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.

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