A novel fungal effector from <i>Puccinia graminis</i> suppressing <scp>RNA</scp> silencing and plant defense responses

Yin, Chuntao; Ramachandran, Sowmya; Zhai, Ying; Bu, Chunya; Pappu, H. R.; Hulbert, Scot H.

doi:10.1111/nph.15676

Cited by 62 publications

(50 citation statements)

References 53 publications

(105 reference statements)

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“…Our study identified 62 Pst Avr candidates through comparative genomics and association analyses. With the identification of more effectors in Puccinia species in recently years [20,25,31,72], functional verification using RNA silencing and transient expression systems should be plausible approaches to identify Pst effectors. Confirmation of the roles of these effector candidates in the future studies is very likely to clone Avr genes in Pst, which should shed light on the mechanisms of interactions between the host and pathogen.…”

Section: Discussionmentioning

confidence: 99%

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

Xia

Wang

et al. 2020

BMC Genomics

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Background: The stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), threats world wheat production. Resistance to Pst is often overcome by pathogen virulence changes, but the mechanisms of variation are not clearly understood. To determine the role of mutation in Pst virulence changes, in previous studies 30 mutant isolates were developed from a least virulent isolate using ethyl methanesulfonate (EMS) mutagenesis and phenotyped for virulence changes. The progenitor isolate was sequenced, assembled and annotated for establishing a high-quality reference genome. In the present study, the 30 mutant isolates were sequenced and compared to the wide-type isolate to determine the genomic variation and identify candidates for avirulence (Avr) genes. Results: The sequence reads of the 30 mutant isolates were mapped to the wild-type reference genome to identify genomic changes. After selecting EMS preferred mutations, 264,630 and 118,913 single nucleotide polymorphism (SNP) sites and 89,078 and 72,513 Indels (Insertion/deletion) were detected among the 30 mutant isolates compared to the primary scaffolds and haplotigs of the wild-type isolate, respectively. Deleterious variants including SNPs and Indels occurred in 1866 genes. Genome wide association analysis identified 754 genes associated with avirulence phenotypes. A total of 62 genes were found significantly associated to 16 avirulence genes after selection through six criteria for putative effectors and degree of association, including 48 genes encoding secreted proteins (SPs) and 14 non-SP genes but with high levels of association (P ≤ 0.001) to avirulence phenotypes. Eight of the SP genes were identified as avirulence-associated effectors with high-confidence as they met five or six criteria used to determine effectors. Conclusions: Genome sequence comparison of the mutant isolates with the progenitor isolate unraveled a large number of mutation sites along the genome and identified high-confidence effector genes as candidates for avirulence genes in Pst. Since the avirulence gene candidates were identified from associated SNPs and Indels caused by artificial mutagenesis, these avirulence gene candidates are valuable resources for elucidating the mechanisms of the pathogen pathogenicity, and will be studied to determine their functions in the interactions between the wheat host and the Pst pathogen.

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Section: Discussionmentioning

confidence: 99%

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

Xia

Wang

et al. 2020

BMC Genomics

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“…Effectors are essential virulence proteins produced by microbial pathogens to defeat host immunity (Dodds and Rathjen, 2010;Dou and Zhou, 2012). Effectors with RNAi suppression activities have been reported in numerous viruses (Burgyán and Havelda, 2011), several species of Phytophthora (Qiao et al, 2013;Xiong et al, 2014;Zhang et al, 2019), and the fungus Puccinia graminis (Yin et al, 2019). The identification of these viral, Phytophthora, or fungal suppressors of RNA silencing supports plant sRNAs as antimicrobial agents in the corresponding pathosystems.…”

Section: The Prevalence Of Trans-species Rnai In Plantsmentioning

confidence: 99%

Exchange of Small Regulatory RNAs between Plants and Their Pests

Hudzik

Hou

et al. 2019

Plant Physiol.

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Regulatory small RNAs are well known as antiviral agents, regulators of gene expression, and defenders of genome integrity in plants. Several studies over the last decade have also shown that some small RNAs are exchanged between plants and their pathogens and parasites. Naturally occurring trans-species small RNAs are used by host plants to silence mRNAs in pathogens. These gene-silencing events are thought to be detrimental to the pathogen and beneficial to the host. Conversely, trans-species small RNAs from pathogens and parasites are deployed to silence host mRNAs; these events are thought to be beneficial for the pests. The natural ability of plants to exchange small RNAs with invading eukaryotic organisms can be exploited to provide disease resistance. This review gives an overview of the current state of trans-species small RNA research in plants and discusses several outstanding questions for future research. SMALL REGULATORY RNA BACKGROUND Small regulatory RNAs (sRNAs) are numerous in plants. They usually range in size from 21 to 24 nucleotides and serve as key regulators of gene expression. sRNAs are involved in myriad processes, including development, cell type designation, responses to abiotic stress, and silencing of repetitive elements. sRNAs are processed from longer precursor RNAs (either the helical stem regions of self-complementary singlestranded RNAs or double-stranded RNAs [dsRNAs]) by endonucleases in the Dicer-like (DCL) protein family. DCL endonucleases produce an initial short duplex RNA. One of the two short RNA strands forms a complex with a protein in the Argonaute (AGO) family. The AGO-sRNA complex then identifies target RNAs based on complementarity between target and sRNA. sRNAs can be categorized based on differences in their biogenesis and differences in their modes of targeting (Fig. 1). MicroRNAs (miRNAs) in plants are processed from RNA polymerase II-transcribed primary RNAs. A region of the primary transcript forms an imperfect hairpin structure that is recognized by the DCL1 endonuclease. DCL1, along with several accessory proteins, liberates a miRNA/miRNA* duplex. The duplex is disassembled, with the mature miRNA becoming bound to an Argonaute (AGO) protein, most frequently AGO1. Once the mature miRNA is bound to an AGO protein, the miRNA* is typically separated from the complex and degraded (for a more detailed review of plant miRNA biogenesis, see Rogers and Chen, 2013). The resulting miRNA/AGO complex directs posttranscriptional regulation of mRNAs and long noncoding RNAs. Target selection is primarily based on complementarity between the miRNA and target RNA

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“…TAL与植物寄主靶基因相互结合是一种特异性的蛋白质与DNA结合方式. 在TAL效应子的应用中, 可以利用分子密码发掘抗病基因和感病基因 [33] , 比如Boch等 [36] . 据预测, 每个疫霉菌种均可编码数百到上千种效应子, 这些效应子在植物宿主体内具有不同的细胞功能 [37] .…”

Section: 菌中的Cfem蛋白进行检测发现 22个cfem分泌蛋白unclassified

Recent developments of plant pathogen effectors

Yang¹,

Zhang²,

Li³

et al. 2020

Sci. Sin.-Vitae

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A novel fungal effector from Puccinia graminis suppressing RNA silencing and plant defense responses

Cited by 62 publications

References 53 publications

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

Exchange of Small Regulatory RNAs between Plants and Their Pests

Recent developments of plant pathogen effectors

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