scholarly journals 454 Genome Sequencing of Pseudoperonospora cubensis Reveals Effector Proteins with a QXLR Translocation Motif

2011 ◽  
Vol 24 (5) ◽  
pp. 543-553 ◽  
Author(s):  
Miaoying Tian ◽  
Joe Win ◽  
Elizabeth Savory ◽  
Alyssa Burkhardt ◽  
Michael Held ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Effector Proteins ◽  
Pseudoperonospora Cubensis ◽  
Sequence Information ◽  
Rxlr Effectors ◽  
Rxlr Effector ◽  
Pathogen Fitness ◽  
Oomycete Pathogen ◽  
Bona Fide ◽  
Secreted Peptides

Pseudoperonospora cubensis is a biotrophic oomycete pathogen that causes downy mildew of cucurbits, a devastating foliar disease threatening cucurbit production worldwide. We sequenced P. cubensis genomic DNA using 454 pyrosequencing and obtained random genomic sequences covering approximately 14% of the genome, thus providing the first set of useful genomic sequence information for P. cubensis. Using bioinformatics approaches, we identified 32 putative RXLR effector proteins. Interestingly, we also identified 29 secreted peptides with high similarity to RXLR effectors at the N-terminal translocation domain, yet containing an R-to-Q substitution in the first residue of the translocation motif. Among these, a family of QXLR-containing proteins, designated as PcQNE, was confirmed to have a functional signal peptide and was further characterized as being localized in the plant nucleus. Internalization of secreted PcQNE into plant cells requires the QXLR-EER motif. This family has a large number of near-identical copies within the P. cubensis genome, is under diversifying selection at the C-terminal domain, and is upregulated during infection of plants, all of which are common characteristics of characterized oomycete effectors. Taken together, the data suggest that PcQNE are bona fide effector proteins with a QXLR translocation motif, and QXLR effectors are prevalent in P. cubensis. Furthermore, the massive duplication of PcQNE suggests that they might play pivotal roles in pathogen fitness and pathogenicity.

scholarly journals Recent Progress in RXLR Effector Research

2015 ◽  
Vol 28 (10) ◽  
pp. 1063-1072 ◽  
Author(s):  
Ryan G. Anderson ◽  
Devdutta Deb ◽  
Kevin Fedkenheuer ◽  
John M. McDowell
Keyword(s):  
Comparative Genomics ◽  
Effector Proteins ◽  
Host Protein ◽  
Protein Targets ◽  
Major Function ◽  
Functional Studies ◽  
Rxlr Effectors ◽  
Cell Compartments ◽  
Rxlr Effector ◽  
Bacteria And Fungi

Some of the most devastating oomycete pathogens deploy effector proteins, with the signature amino acid motif RXLR, that enter plant cells to promote virulence. Research on the function and evolution of RXLR effectors has been very active over the decade that has transpired since their discovery. Comparative genomics indicate that RXLR genes play a major role in virulence for Phytophthora and downy mildew species. Importantly, gene-for-gene resistance against these oomycete lineages is based on recognition of RXLR proteins. Comparative genomics have revealed several mechanisms through which this resistance can be broken, most notably involving epigenetic control of RXLR gene expression. Structural studies have revealed a core fold that is present in the majority of RXLR proteins, providing a foundation for detailed mechanistic understanding of virulence and avirulence functions. Finally, functional studies have demonstrated that suppression of host immunity is a major function for RXLR proteins. Host protein targets are being identified in a variety of plant cell compartments. Some targets comprise hubs that are also manipulated by bacteria and fungi, thereby revealing key points of vulnerability in the plant immune network.

scholarly journals Downy Mildew effector HaRxL21 interacts with the transcriptional repressor TOPLESS to promote pathogen susceptibility

2020 ◽  
Author(s):  
Sarah Harvey ◽  
Priyanka Kumari ◽  
Dmitry Lapin ◽  
Thomas Griebel ◽  
Richard Hickman ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Transcriptional Repression ◽  
Plant Immunity ◽  
Effector Proteins ◽  
Host Susceptibility ◽  
Close Relative ◽  
C Terminus ◽  
Rxlr Effector ◽  
Oomycete Pathogen ◽  
Hyaloperonospora Arabidopsidis

AbstractHyaloperonospora arabidopsidis (Hpa) is an oomycete pathogen causing Arabidopsis downy mildew. Effector proteins secreted from the pathogen into the plant play key roles in promoting infection by suppressing plant immunity and manipulating the host to the pathogen’s advantage. One class of oomycete effectors share a conserved ‘RxLR’ motif critical for their translocation into the host cell. Here we characterize the interaction between an RxLR effector, HaRxL21 (RxL21), and the Arabidopsis transcriptional co-repressor Topless (TPL). We establish that RxL21 and TPL interact via an EAR motif at the C-terminus of the effector, mimicking the host plant mechanism for recruiting TPL to sites of transcriptional repression. We show that this motif, and hence interaction with TPL, is necessary for the virulence function of the effector. Furthermore, we provide evidence that RxL21 uses the interaction with TPL, and its close relative TPL-related 1, to repress plant immunity and enhance host susceptibility to both biotrophic and necrotrophic pathogens.

scholarly journals Expression of several Phytophthora cinnamomi putative RxLRs provides evidence for virulence roles in avocado

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254645
Author(s):  
Melissa Joubert ◽  
Robert Backer ◽  
Juanita Engelbrecht ◽  
Noëlani van den Berg
Keyword(s):  
Phytophthora Cinnamomi ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Effector Proteins ◽  
Virulence Determinants ◽  
In Planta ◽  
Phytophthora Root Rot ◽  
Host Immune Responses ◽  
Rxlr Effectors ◽  
Pathogen Fitness

Phytophthora cinnamomi is a plant pathogenic oomycete that causes Phytophthora root rot of avocado (PRR). Currently, there is a limited understanding of the molecular interactions underlying this disease. Other Phytophthora species employ an arsenal of effector proteins to manipulate host physiology, of which the RxLR effectors contribute to virulence by interfering with host immune responses. The aim of this study was to identify candidate RxLR effectors in P. cinnamomi that play a role in establishing PRR, and to infer possible functions for these effectors. We identified 61 candidate RxLR genes which were expressed during infection of a susceptible avocado rootstock. Several of these genes were present in multiple copies in the P. cinnamomi genome, suggesting that they may contribute to pathogen fitness. Phylogenetic analysis of the manually predicted RxLR protein sequences revealed 12 P. cinnamomi RxLRs that were related to characterised effectors in other Phytophthora spp., providing clues to their functions in planta. Expression profiles of nine more RxLRs point to possible virulence roles in avocado–highlighting a way forward for studies of this interaction. This study represents the first investigation of the expression of P. cinnamomi RxLR genes during the course of avocado infection, and puts forward a pipeline to pinpoint effector genes with potential as virulence determinants, providing a foundation for the future functional characterization of RxLRs that contribute to P. cinnamomi virulence in avocado.

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 A Recent Expansion of the RXLR Effector Gene Avrblb2 Is Maintained in Global Populations of Phytophthora infestans Indicating Different Contributions to Virulence

2015 ◽  
Vol 28 (8) ◽  
pp. 901-912 ◽  
Author(s):  
Ricardo F. Oliva ◽  
Liliana M. Cano ◽  
Sylvain Raffaele ◽  
Joe Win ◽  
Tolga O. Bozkurt ◽  
...  
Keyword(s):  
Phytophthora Infestans ◽  
Amino Acid Position ◽  
Single Copy ◽  
Solanum Bulbocastanum ◽  
Rxlr Effector ◽  
Genes Encoding ◽  
Pathogen Fitness ◽  
History Of ◽  
Oomycete Pathogen ◽  
Pathogen Populations

The introgression of disease resistance (R) genes encoding immunoreceptors with broad-spectrum recognition into cultivated potato appears to be the most promising approach to achieve sustainable management of late blight caused by the oomycete pathogen Phytophthora infestans. Rpi-blb2 from Solanum bulbocastanum shows great potential for use in agriculture based on preliminary potato disease trials. Rpi-blb2 confers immunity by recognizing the P. infestans avirulence effector protein AVRblb2 after it is translocated inside the plant cell. This effector belongs to the RXLR class of effectors and is under strong positive selection. Structure-function analyses revealed a key polymorphic amino acid (position 69) in AVRblb2 effector that is critical for activation of Rpi-blb2. In this study, we reconstructed the evolutionary history of the Avrblb2 gene family and further characterized its genetic structure in worldwide populations. Our data indicate that Avrblb2 evolved as a single-copy gene in a putative ancestral species of P. infestans and has recently expanded in the Phytophthora spp. that infect solanaceous hosts. As a consequence, at least four variants of AVRblb2 arose in P. infestans. One of these variants, with a Phe residue at position 69, evades recognition by the cognate resistance gene. Surprisingly, all Avrblb2 variants are maintained in pathogen populations. This suggests a potential benefit for the pathogen in preserving duplicated versions of AVRblb2, possibly because the variants may have different contributions to pathogen fitness in a diversified solanaceous host environment.

scholarly journals What the Wild Things Do: Mechanisms of Plant Host Manipulation by Bacterial Type III-Secreted Effector Proteins

2021 ◽  
Vol 9 (5) ◽  
pp. 1029
Author(s):  
Karl J. Schreiber ◽  
Ilea J. Chau-Ly ◽  
Jennifer D. Lewis
Keyword(s):  
Pseudomonas Syringae ◽  
Structural Data ◽  
Enzymatic Activities ◽  
Effector Proteins ◽  
Host Recognition ◽  
Plant Host ◽  
Type Iii ◽  
Xanthomonas Species ◽  
Pathogen Fitness ◽  
Enzymatic Mechanisms

Phytopathogenic bacteria possess an arsenal of effector proteins that enable them to subvert host recognition and manipulate the host to promote pathogen fitness. The type III secretion system (T3SS) delivers type III-secreted effector proteins (T3SEs) from bacterial pathogens such as Pseudomonas syringae, Ralstonia solanacearum, and various Xanthomonas species. These T3SEs interact with and modify a range of intracellular host targets to alter their activity and thereby attenuate host immune signaling. Pathogens have evolved T3SEs with diverse biochemical activities, which can be difficult to predict in the absence of structural data. Interestingly, several T3SEs are activated following injection into the host cell. Here, we review T3SEs with documented enzymatic activities, as well as T3SEs that facilitate virulence-promoting processes either indirectly or through non-enzymatic mechanisms. We discuss the mechanisms by which T3SEs are activated in the cell, as well as how T3SEs modify host targets to promote virulence or trigger immunity. These mechanisms may suggest common enzymatic activities and convergent targets that could be manipulated to protect crop plants from infection.

scholarly journals FDA oversight of NSIGHT genomic research: the need for an integrated systems approach to regulation

2019 ◽  
Author(s):  
Laura V. Milko ◽  
Flavia Chen ◽  
Kee Chan ◽  
Amy M. Brower ◽  
Pankaj B. Agrawal ◽  
...  
Keyword(s):  
Clinical Research ◽  
Systems Approach ◽  
Genomic Sequence ◽  
Clinical Investigation ◽  
Risk Assessments ◽  
Genomic Research ◽  
Institutional Review Boards ◽  
Sequence Information ◽  
Genomic Technologies ◽  
Challenges And Opportunities

ABSTRACTThe National Institutes of Health (NIH) funded the Newborn Sequencing In Genomic medicine and public HealTh (NSIGHT) Consortium to investigate the implications, challenges and opportunities associated with the possible use of genomic sequence information in the newborn period. Following announcement of the NSIGHT awardees in 2013, the Food and Drug Administration (FDA) contacted investigators and requested that pre-submissions to investigational device exemptions (IDE) be submitted for the use of genomic sequencing under Title 21 of the Code of Federal Regulations (21 CFR) part 812. IDE regulation permits clinical investigation of medical devices that have not been approved by the FDA. To our knowledge, this marked the first time the FDA determined that NIH-funded clinical genomic research projects are subject to IDE regulation. Here we review the history of and rationale behind FDA oversight of clinical research and the NSIGHT Consortium’s experiences in navigating the IDE process. Overall, NSIGHT investigators found that FDA’s application of existing IDE regulations and medical device definitions aligned imprecisely with the aims of publicly funded exploratory clinical research protocols. IDE risk assessments by the FDA were similar to, but distinct from, protocol risk assessments conducted by local Institutional Review Boards (IRBs), and had the potential to reflect novel oversight of emerging genomic technologies. However, the pre-IDE and IDE process delayed the start of NSIGHT research studies by an average of 10 months, and significantly limited the scope of investigation in two of the four NIH approved projects. Based on the experience of the NSIGHT Consortium, we conclude that policies and practices governing the development and use of novel genomic technologies in clinical research urgently need clarification in order to mitigate potentially conflicting or redundant oversight by IRBs, NIH, FDA, and state authorities.

scholarly journals Insights into Xylan Degradation and Haloalkaline Adaptation through Whole-Genome Analysis of Alkalitalea saponilacus, an Anaerobic Haloalkaliphilic Bacterium Capable of Secreting Novel Halostable Xylanase

Genes ◽  
2018 ◽  
Vol 10 (1) ◽  
pp. 1 ◽  
Author(s):  
Ziya Liao ◽  
Mark Holtzapple ◽  
Yanchun Yan ◽  
Haisheng Wang ◽  
Jun Li ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genomic Sequence ◽  
Carbon Sources ◽  
Compatible Solutes ◽  
Tween 20 ◽  
Sequence Information ◽  
Ph Homeostasis ◽  
Whole Genome Analysis ◽  
Xylanase Production ◽  
Xylan Degradation

The obligately anaerobic haloalkaliphilic bacterium Alkalitalea saponilacus can use xylan as the sole carbon source and produce propionate as the main fermentation product. Using mixed carbon sources of 0.4% (w/v) sucrose and 0.1% (w/v) birch xylan, xylanase production from A. saponilacus was 3.2-fold greater than that of individual carbon sources of 0.5% (w/v) sucrose or 0.5% (w/v) birch xylan. The xylanse is halostable and exhibits optimal activity over a broad salt concentration (2–6% NaCl). Its activity increased approximately 1.16-fold by adding 0.2% (v/v) Tween 20. To understand the potential genetic mechanisms of xylan degradation and molecular adaptation to saline-alkali extremes, the complete genome sequence of A. saponilacus was performed with the pacBio single-molecule real-time (SMRT) and Illumina Misseq platforms. The genome contained one chromosome with a total size of 4,775,573 bps, and a G+C genomic content of 39.27%. Ten genes relating to the pathway for complete xylan degradation were systematically identified. Furthermore, various genes were predicted to be involved in isosmotic cytoplasm via the “compatible-solutes strategy” and cytoplasmic pH homeostasis though the “influx of hydrogen ions”. The halostable xylanase from A. saponilacus and its genomic sequence information provide some insight for potential applications in industry under double extreme conditions.

scholarly journals Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

2015 ◽  
Vol 28 (3) ◽  
pp. 298-309 ◽  
Author(s):  
Alyssa Burkhardt ◽  
Alex Buchanan ◽  
Jason S. Cumbie ◽  
Elizabeth A. Savory ◽  
Jeff H. Chang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Draft Genome ◽  
Pseudoperonospora Cubensis ◽  
Rna Seq ◽  
Transcriptome Regulation ◽  
Oomycete Pathogen ◽  
Alternatively Spliced ◽  
Genome Annotations ◽  
Obligate Pathogen

Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing during different stages of its development. Almost half of the original gene annotations were improved and nearly 4,000 previously unannotated genes were identified. We also demonstrated that approximately 24% of the expressed genome and nearly 55% of the intron-containing genes from P. cubensis had evidence for alternative splicing. Our analyses revealed that intron retention is the predominant alternative splicing type in P. cubensis, with alternative 5′- and alternative 3′-splice sites occurring at lower frequencies. Representatives of the newly identified genes and predicted alternatively spliced transcripts were experimentally validated. The results presented herein highlight the utility of RNA-Seq for improving draft genome annotations and, through this approach, we demonstrate that alternative splicing occurs more frequently than previously predicted. In total, the current study provides evidence that alternative splicing plays a key role in transcriptome regulation and proteome diversification in plant-pathogenic oomycetes.

scholarly journals Saudi Arabian SARS-CoV-2 genomes implicate a mutant Nucleocapsid protein in modulating host interactions and increased viral load in COVID-19 patients

2021 ◽  
Author(s):  
Tobias Mourier ◽  
Muhammad Shuaib ◽  
Sharif Hala ◽  
Sara Mfarrej ◽  
Fadwa Alofi ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Viral Load ◽  
Nucleocapsid Protein ◽  
Rna Binding ◽  
Genomic Sequence ◽  
Mass Spectrometry Analysis ◽  
Interferon Response ◽  
Sequence Information ◽  
Effective Population ◽  
N Protein

Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. The availability of patient hospital records is crucial for linking the genomic sequence information to virus function during the course of infections. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. From the assembled sequences, we estimate the SARS-CoV-2 effective population size and infection rate and outline the epidemiological dynamics of import and transmission events during this period in Saudi Arabia. We show that two consecutive mutations (R203K/G204R) in the SARS-CoV-2 nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein by mass-spectrometry analysis. Furthermore, analysis of the host cell transcriptome suggests that the mutant N protein results in dysregulated interferon response genes. We provide crucial information in linking the R203K/G204R mutations in the N protein as a major modulator of host-virus interactions and increased viral load and underline the potential of the nucleocapsid protein as a drug target during infection.

Sign in / Sign up

Export Citation Format

Share Document