Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements
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ABSTRACT:
ORGANISM(S): Phytophthora infestans
PROVIDER: GSE75282 | GEO | 2016/03/17
SECONDARY ACCESSION(S): PRJNA303083
REPOSITORIES: GEO
Similar Datasets
Project description:The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). The frequencies and sizes of TE-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in control of different TE classes. We further provide evidence for involvement of PiAgo1 in the P. infestans miRNA pathway. Protein-coding genes are likely to be regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing CRN effectors was bound to PiAgo1, implicating this protein in regulation of the expanded CRN gene family. These findings highlight the different roles played by Ago proteins in an economically important plant pathogenic oomyce
2016-03-17 | GSE75281 | GEO
Project description:The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). The frequencies and sizes of TE-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in control of different TE classes. We further provide evidence for involvement of PiAgo1 in the P. infestans miRNA pathway. Protein-coding genes are likely to be regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing CRN effectors was bound to PiAgo1, implicating this protein in regulation of the expanded CRN gene family. These findings highlight the different roles played by Ago proteins in an economically important plant pathogenic oomyce
2016-03-17 | GSE74370 | GEO
Project description:Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements
| PRJNA303083 | ENA
Project description:Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19-40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs.
| S-EPMC3522703 | biostudies-literature
Project description:Phytophthora infestans is a devastating plant pathogen in several crops such as potato (Solanum tuberosum), tomato (Solanum lycopersicum) and Andean fruits such as tree tomato (Solanum betaceum), lulo (Solanum quitoense), uchuva (Physalis peruviana) and wild species in the genus Solanum sp. Despite intense research performed around the world, P. infestans populations from Colombia, South America, are poorly understood. Of particular importance is knowledge about pathogen effector proteins, which are responsible for virulence. The present work was performed with the objective to analyze gene sequences coding for effector proteins of P. infestans from isolates collected from different hosts and geographical regions. Several genetic parameters, phylogenetic analyses and neutrality tests for non-synonymous and synonymous substitutions were calculated. Non-synonymous substitutions were identified for all genes that exhibited polymorphisms at the DNA level. Significant negative selection values were found for two genes (PITG_08994 and PITG_12737) suggesting active coevolution with the corresponding host resistance proteins. Implications for pathogen virulence mechanisms and disease management are discussed.
| S-EPMC7400436 | biostudies-literature
Project description:BackgroundThe oomycete pathogen secretes many effectors into host cells to manipulate host defenses. For the majority of effectors, the mechanisms related to how they alter the expression of host genes and reprogram defenses are not well understood. In order to investigate the molecular mechanisms governing the influence that the Phytophthora infestans RXLR effector Pi04089 has on host immunity, a comparative transcriptome analysis was conducted on Pi04089 stable transgenic and wild-type potato plants.ResultsPotato plants stably expressing Pi04089 were more susceptible to P. infestans. RNA-seq analysis revealed that 658 upregulated genes and 722 downregulated genes were characterized in Pi04089 transgenic lines. A large number of genes involved in the biological process, including many defense-related genes and certain genes that respond to salicylic acid, were suppressed. Moreover, the comparative transcriptome analysis revealed that Pi04089 significantly inhibited the expression of many flg22 (a microbe-associated molecular pattern, PAMP)-inducible genes, including various Avr9/Cf-9 rapidly elicited (ACRE) genes. Four selected differentially expressed genes (StWAT1, StCEVI57, StKTI1, and StP450) were confirmed to be involved in host resistance against P. infestans when they were transiently expressed in Nicotiana benthamiana.ConclusionThe P. infestans effector Pi04089 was shown to suppress the expression of many resistance-related genes in potato plants. Moreover, Pi04089 was found to significantly suppress flg22-triggered defense signaling in potato plants. This research provides new insights into how an oomycete effector perturbs host immune responses at the transcriptome level.
| S-EPMC8656059 | biostudies-literature
Project description:Potato is the world's fourth largest food crop yet it continues to endure late blight, a devastating disease caused by the Irish famine pathogen Phytophthora infestans. Breeding broad-spectrum disease resistance (R) genes into potato (Solanum tuberosum) is the best strategy for genetically managing late blight but current approaches are slow and inefficient. We used a repertoire of effector genes predicted computationally from the P. infestans genome to accelerate the identification, functional characterization, and cloning of potentially broad-spectrum R genes. An initial set of 54 effectors containing a signal peptide and a RXLR motif was profiled for activation of innate immunity (avirulence or Avr activity) on wild Solanum species and tentative Avr candidates were identified. The RXLR effector family IpiO induced hypersensitive responses (HR) in S. stoloniferum, S. papita and the more distantly related S. bulbocastanum, the source of the R gene Rpi-blb1. Genetic studies with S. stoloniferum showed cosegregation of resistance to P. infestans and response to IpiO. Transient co-expression of IpiO with Rpi-blb1 in a heterologous Nicotiana benthamiana system identified IpiO as Avr-blb1. A candidate gene approach led to the rapid cloning of S. stoloniferum Rpi-sto1 and S. papita Rpi-pta1, which are functionally equivalent to Rpi-blb1. Our findings indicate that effector genomics enables discovery and functional profiling of late blight R genes and Avr genes at an unprecedented rate and promises to accelerate the engineering of late blight resistant potato varieties.
| S-EPMC2483939 | biostudies-literature
Project description:Resistance genes against Phytophthora infestans (Rpi genes), the most important potato pathogen, are still highly valued in the breeding of Solanum spp. for enhanced resistance. The Rpi genes hitherto explored are localized most often in clusters, which are similar between the diverse Solanum genomes. Their distribution is not independent of late maturity traits. This review provides a summary of the most recent important revelations on the genomic position and cloning of Rpi genes, and the structure, associations, mode of action and activity spectrum of Rpi and corresponding avirulence (Avr) proteins. Practical implications for research into and application of Rpi genes are deduced and combined with an outlook on approaches to address remaining issues and interesting questions. It is evident that the potential of Rpi genes has not been exploited fully.
| S-EPMC6638693 | biostudies-literature
Project description:Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Reports suggest that pathogen-derived sRNAs can modulate the expression of plant defense genes. The experiments reported here were designed to shed light on impact of sRNAs in the potato-P. infestans interaction. We used the Argonaute or Ago1 from P. infestans tagged with GFP transformed into the 88069 strain to infect potato cv. Bintje plants. Collected leaf materials were used in co-immunoprecipitation experiments together with P. infestans harboring GFP (control GFP) and P. infestans mycelia grown on media (control mycelia). These three materials were sequenced at a Ion Proton platform. The reads length of 8-38 nt were adaptor-trimmed and mapped to the P. infestans genome and the Solanom tuberosum genome v4.04. Both P. infestans-associated and potato derived sRNAs were identified.
2021-06-30 | GSE119230 | GEO
Project description:Despite intensive breeding efforts, potato late blight, caused by the oomycete pathogen Phytophthora infestans, remains a threat to potato production worldwide because newly evolved pathogen strains have consistently overcome major resistance genes. The potato RB gene, derived from the wild species Solanum bulbocastanum, confers resistance to most P. infestans strains through recognition of members of the pathogen effector family IPI-O. While the majority of IPI-O proteins are recognized by RB to elicit resistance (e.g. IPI-O1, IPI-O2), some family members are able to elude detection (e.g. IPI-O4). In addition, IPI-O4 blocks recognition of IPI-O1, leading to inactivation of RB-mediated programmed cell death. Here, we report results that elucidate molecular mechanisms governing resistance elicitation or suppression of RB by IPI-O. Our data indicate self-association of the RB coiled coil (CC) domain as well as a physical interaction between this domain and the effectors IPI-O4 and IPI-O1. We identified four amino acids within IPI-O that are critical for interaction with the RB CC domain and one of these amino acids, at position 129, determines hypersensitive response (HR) elicitation in planta. IPI-O1 mutant L129P fails to induce HR in presence of RB while IPI-O4 P129L gains the ability to induce an HR. Like IPI-O4, IPI-O1 L129P is also able to suppress the HR mediated by RB, indicating a critical step in the evolution of this gene family. Our results point to a model in which IPI-O effectors can affect RB function through interaction with the RB CC domain.
| S-EPMC3305431 | biostudies-literature