scholarly journals In planta expression screens of candidate effector proteins from the wheat yellow rust fungus reveal processing bodies as a pathogen-targeted plant cell compartment

2015 ◽  
Author(s):  
Benjamin Petre ◽  
Diane GO Saunders ◽  
Jan Sklenar ◽  
Cecile Lorrain ◽  
Ksenia V Krasileva ◽  
...  
Keyword(s):  
Plant Cell ◽  
Molecular Mechanisms ◽  
Puccinia Striiformis ◽  
Yellow Rust ◽  
In Planta ◽  
Cell Compartment ◽  
Processing Bodies ◽  
Subcellular Compartment ◽  
Mrna Decapping ◽  
P Bodies

Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. Our work identifies P-bodies as a novel plant cell compartment targeted by pathogen effectors.

Transcriptomic analysis reveals the molecular mechanisms of wheat seedling resistance to Puccinia striiformis f. sp. tritici

2020 ◽  
Author(s):  
Rong Liu ◽  
Jing Lu ◽  
Mei Du ◽  
Min Zhou ◽  
Mingxiu Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Puccinia Striiformis ◽  
Lignin Content ◽  
Yellow Rust ◽  
Gene Pyramiding ◽  
Mapk Signaling ◽  
Wheat Breeding ◽  
Fine Tuning ◽  
Seedling Resistance

Abstract Background: Stripe rust or yellow rust (Yr), caused by Puccinia striiformis f. sp. Tritici (Pst), is one of the most globally devastating fungal disease that significantly reduces yield and quality in wheat (Triticum aestivum). Although some Yr genes have been successfully used in wheat breeding and a little number of them have been cloned, large of the regulating networks and the molecular mechanisms of Pst resistance remains unknown. In this study, a pair of Yr-gene pyramiding line L58 and its background parent cv. Chuanyu12 (CY12) were used to study the transcriptome profiles after inoculated with Pst physiological race CYR34. Results: The results revealed that the different expression genes (DEGs) were significantly enriched in phenylpropanoid biosynthesis, phenylalanine metabolism, plant-pathogen interaction and MAPK signaling pathways after Pst-CYR34 inoculation. Compared with CY12, L58 showed greater up-regulated DEGs in those pathways by Pst infection at 24hpi. However, these DEGs became lower expression in L58 and opposite expression in CY12 at 7dpi. Besides, the activities of enzymes (PAL, POD) and products of phenylpropanoid pathway (lignin content) were significantly increased in both CY12 and L58, and the increase was greater and faster in the resistant line L58. Some candidate genes and transcription factors (TFs) associated with Pst resistance were identified, including LRR receptor-like serine/threonine protein kinase, disease resistance protein, MYB, NAC and WRKY transcription factors involved in the fine-tuning of Pst infection responses. Conclusions: Our results give insights into the regulating networks of Pst resistance and pave the way for durable resistant breeding in bread wheat.

scholarly journals Protection of specific maternal messenger RNAs by the P body protein CGH-1 (Dhh1/RCK) during Caenorhabditis elegans oogenesis

2008 ◽  
Vol 182 (3) ◽  
pp. 543-557 ◽  
Author(s):  
Peter R. Boag ◽  
Arzu Atalay ◽  
Stacey Robida ◽  
Valerie Reinke ◽  
T. Keith Blackwell
Keyword(s):  
Caenorhabditis Elegans ◽  
Messenger Rnas ◽  
Processing Bodies ◽  
Body Protein ◽  
Translation Inhibition ◽  
Mrna Decapping ◽  
P Bodies ◽  
Somatic Tissues ◽  
Translational Regulators ◽  
Dependent Mechanism

During oogenesis, numerous messenger RNAs (mRNAs) are maintained in a translationally silenced state. In eukaryotic cells, various translation inhibition and mRNA degradation mechanisms congregate in cytoplasmic processing bodies (P bodies). The P body protein Dhh1 inhibits translation and promotes decapping-mediated mRNA decay together with Pat1 in yeast, and has been implicated in mRNA storage in metazoan oocytes. Here, we have investigated in Caenorhabditis elegans whether Dhh1 and Pat1 generally function together, and how they influence mRNA sequestration during oogenesis. We show that in somatic tissues, the Dhh1 orthologue (CGH-1) forms Pat1 (patr-1)-dependent P bodies that are involved in mRNA decapping. In contrast, during oogenesis, CGH-1 forms patr-1–independent mRNA storage bodies. CGH-1 then associates with translational regulators and a specific set of maternal mRNAs, and prevents those mRNAs from being degraded. Our results identify somatic and germ cell CGH-1 functions that are distinguished by the involvement of PATR-1, and reveal that during oogenesis, numerous translationally regulated mRNAs are specifically protected by a CGH-1–dependent mechanism.

scholarly journals Genome Sequence Resources for the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) and the Barley Stripe Rust Pathogen (Puccinia striiformis f. sp. hordei)

2018 ◽  
Vol 31 (11) ◽  
pp. 1117-1120 ◽  
Author(s):  
Chongjing Xia ◽  
Meinan Wang ◽  
Chuntao Yin ◽  
Omar E. Cornejo ◽  
Scot H. Hulbert ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Molecular Mechanisms ◽  
Puccinia Striiformis ◽  
Yellow Rust ◽  
Rapid Evolution ◽  
Host Adaptation ◽  
Rust Pathogen ◽  
Structural Differences ◽  
Barley Stripe Rust ◽  
Genomic Basis

Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.

scholarly journals Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance in sensory neurons

2021 ◽  
Author(s):  
Patrick R Smith ◽  
Sarah Loerch ◽  
Nikesh Kunder ◽  
Alexander D Stanowick ◽  
Tzu-Fang Lou ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Sensory Neurons ◽  
Molecular Mechanisms ◽  
Acceptor Site ◽  
Processing Bodies ◽  
P Bodies ◽  
Cryo Electron Microscopy ◽  
Coordinate Control ◽  
Eef2 Kinase

Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible for coordinate control of the two processes are unclear. Here, we uncover key roles for eEF2 kinase (eEF2K) in the control of ribosome availability and p-body abundance. eEF2K acts on a sole known substrate, eEF2, to inhibit translation. We find that the eEF2K agonist nelfinavir abolishes p-bodies specifically in sensory neurons and impairs translation. To probe the latter, we used cryo-electron microscopy. Nelfinavir stabilizes vacant 80S ribosomes. They contain SERBP1 in place of mRNA and eEF2 in the acceptor site. Phosphorylated eEF2 associates with inactive ribosomes that resist splitting in vitro. Collectively, the data suggest that eEF2 phosphorylation defines a population of inactive ribosomes resistant to recycling and protected from degradation. Thus, eEF2K activity is central to both p-body abundance and ribosome availability in sensory neurons.

scholarly journals Analysis of P-Body Assembly in Saccharomyces cerevisiae

2007 ◽  
Vol 18 (6) ◽  
pp. 2274-2287 ◽  
Author(s):  
Daniela Teixeira ◽  
Roy Parker
Keyword(s):  
Deletion Mutants ◽  
Processing Bodies ◽  
Mrna Decapping ◽  
P Bodies ◽  
Translation Repression ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Body Component ◽  
Rate Limiting ◽  
Insight Into

Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), that contain untranslating mRNAs in conjunction with proteins involved in translation repression and mRNA decapping and degradation. However, the order of protein assembly into P-bodies and the interactions that promote P-body assembly are unknown. To gain insight into how yeast P-bodies assemble, we examined the P-body accumulation of Dcp1p, Dcp2p, Edc3p, Dhh1p, Pat1p, Lsm1p, Xrn1p, Ccr4p, and Pop2p in deletion mutants lacking one or more P-body component. These experiments revealed that Dcp2p and Pat1p are required for recruitment of Dcp1p and of the Lsm1-7p complex to P-bodies, respectively. We also demonstrate that P-body assembly is redundant and no single known component of P-bodies is required for P-body assembly, although both Dcp2p and Pat1p contribute to P-body assembly. In addition, our results indicate that Pat1p can be a nuclear-cytoplasmic shuttling protein and acts early in P-body assembly. In contrast, the Lsm1-7p complex appears to primarily function in a rate limiting step after P-body assembly in triggering decapping. Taken together, these results provide insight both into the function of individual proteins involved in mRNA degradation and the mechanisms by which yeast P-bodies assemble.

scholarly journals A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay

2005 ◽  
Vol 170 (6) ◽  
pp. 913-924 ◽  
Author(s):  
Maria A. Ferraiuolo ◽  
Sanjukta Basak ◽  
Josee Dostie ◽  
Elizabeth L. Murray ◽  
Daniel R. Schoenberg ◽  
...  
Keyword(s):  
Mrna Decay ◽  
Binding Protein ◽  
Initiation Factor ◽  
Binding Motif ◽  
Processing Bodies ◽  
Mrna Decapping ◽  
P Bodies ◽  
Eukaryotic Initiation Factor 4E ◽  
Messenger Ribonucleoprotein ◽  
Bona Fide

4E-transporter (4E-T) is one of several proteins that bind the mRNA 5′cap-binding protein, eukaryotic initiation factor 4E (eIF4E), through a conserved binding motif. We previously showed that 4E-T is a nucleocytoplasmic shuttling protein, which mediates the import of eIF4E into the nucleus. At steady state, 4E-T is predominantly cytoplasmic and is concentrated in bodies that conspicuously resemble the recently described processing bodies (P-bodies), which are believed to be sites of mRNA decay. In this paper, we demonstrate that 4E-T colocalizes with mRNA decapping factors in bona fide P-bodies. Moreover, 4E-T controls mRNA half-life, because its depletion from cells using short interfering RNA increases mRNA stability. The 4E-T binding partner, eIF4E, also is localized in P-bodies. 4E-T interaction with eIF4E represses translation, which is believed to be a prerequisite for targeting of mRNAs to P-bodies. Collectively, these data suggest that 4E-T interaction with eIF4E is a priming event in inducing messenger ribonucleoprotein rearrangement and transition from translation to decay.

scholarly journals IP6K1 upregulates the formation of processing bodies by promoting proteome remodeling on the mRNA cap

2020 ◽  
Author(s):  
Akruti Shah ◽  
Rashna Bhandari
Keyword(s):  
Protein Interactions ◽  
Inositol Phosphate ◽  
Binding Protein ◽  
Mrna Translation ◽  
Rna Helicase ◽  
Scaffolding Protein ◽  
Processing Bodies ◽  
Activator Proteins ◽  
Mrna Decapping ◽  
P Bodies

AbstractInositol hexakisphosphate kinases (IP6Ks) are ubiquitously expressed small molecule kinases that catalyze the conversion of the inositol phosphate IP6 to 5-IP7. IP6Ks have been reported to influence cellular functions by protein-protein interactions independent of their enzymatic activity. Here, we show that IP6K1 regulates the formation of processing bodies (P-bodies), which are cytoplasmic ribonucleoprotein granules that serve as sites for storage of translationally repressed mRNA. Cells with reduced levels of IP6K1 display a dramatic reduction in the number of P-bodies, which can be restored by the expression of active or catalytically inactive IP6K1. IP6K1 does not localize to P-bodies, but instead facilitates the formation of P-bodies by promoting translation suppression. We demonstrate that IP6K1 is present on ribosomes, where it interacts with proteins that constitute the mRNA decapping complex – the scaffold protein EDC4, activator proteins DCP1A/B, and the decapping enzyme DCP2. IP6K1 also interacts with components of the eIF4F translation initiation complex – the scaffolding protein eIF4G1, the RNA helicase eIF4A2, and the cap binding protein eIF4E. The RNA helicase DDX6 and the eIF4E binding protein 4E-T are known to promote translation suppression to facilitate P-body formation. We show that IP6K1 binds to DDX6 and promotes the interaction of DDX6 and 4E-T with the cap binding protein eIF4E, and also enhances the binding between DDX6 and EDC4, thus acting to suppress mRNA translation and promote mRNA decapping. Our findings unveil IP6K1 as a novel facilitator of proteome remodelling on the mRNA cap, tipping the balance in favour of translation repression over initiation, and thus leading to the formation of P-bodies.

scholarly journals IP6K1 upregulates the formation of processing bodies by influencing protein-protein interactions on the mRNA cap

2021 ◽  
Author(s):  
Akruti Shah ◽  
Rashna Bhandari
Keyword(s):  
Protein Interactions ◽  
Inositol Phosphate ◽  
Translational Repression ◽  
Protein Protein Interactions ◽  
Processing Bodies ◽  
Activator Proteins ◽  
Mrna Decapping ◽  
P Bodies ◽  
Decapping Enzyme ◽  
Translational Suppression

Inositol hexakisphosphate kinase 1 (IP6K1) is a small molecule kinase that catalyzes the conversion of the inositol phosphate IP6 to 5-IP7. We show that IP6K1 acts independent of its catalytic activity to upregulate the formation of processing bodies (P-bodies), which are cytoplasmic ribonucleoprotein granules that store translationally repressed mRNA. IP6K1 does not localize to P-bodies, but instead binds to ribosomes, where it interacts with the mRNA decapping complex - the scaffold protein EDC4, activator proteins DCP1A/B, decapping enzyme DCP2, and RNA helicase DDX6. Along with its partner 4E-T, DDX6 is known to nucleate protein-protein interactions on the 5’ mRNA cap to facilitate P-body formation. IP6K1 binds the translation initiation complex eIF4F on the mRNA cap, augmenting the interaction of DDX6 with 4E-T and the cap binding protein eIF4E. Cells with reduced IP6K1 show downregulated microRNA-mediated translational suppression and increased stability of DCP2-regulated transcripts. Our findings unveil IP6K1 as a novel facilitator of proteome remodelling on the mRNA cap, tipping the balance in favour of translational repression over initiation, thus leading to P-body assembly.

scholarly journals Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Patrick R. Smith ◽  
Sarah Loerch ◽  
Nikesh Kunder ◽  
Alexander D. Stanowick ◽  
Tzu-Fang Lou ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Sensory Neurons ◽  
Molecular Mechanisms ◽  
Acceptor Site ◽  
Processing Bodies ◽  
P Bodies ◽  
Cryo Electron Microscopy ◽  
Coordinate Control ◽  
Eef2 Kinase

AbstractProcessing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible for coordinate control of the two processes are unclear. Here, we uncover key roles for eEF2 kinase (eEF2K) in the control of ribosome availability and p-body abundance. eEF2K acts on a sole known substrate, eEF2, to inhibit translation. We find that the eEF2K agonist nelfinavir abolishes p-bodies in sensory neurons and impairs translation. To probe the latter, we used cryo-electron microscopy. Nelfinavir stabilizes vacant 80S ribosomes. They contain SERBP1 in place of mRNA and eEF2 in the acceptor site. Phosphorylated eEF2 associates with inactive ribosomes that resist splitting in vitro. Collectively, the data suggest that eEF2K defines a population of inactive ribosomes resistant to recycling and protected from degradation. Thus, eEF2K activity is central to both p-body abundance and ribosome availability in sensory neurons.

scholarly journals Human Pat1b Connects Deadenylation with mRNA Decapping and Controls the Assembly of Processing Bodies

2010 ◽  
Vol 30 (17) ◽  
pp. 4308-4323 ◽  
Author(s):  
Sevim Ozgur ◽  
Marina Chekulaeva ◽  
Georg Stoecklin
Keyword(s):  
Rna Helicase ◽  
Rna Decay ◽  
Eukaryotic Cells ◽  
Central Component ◽  
Processing Bodies ◽  
Mrna Decapping ◽  
P Bodies ◽  
Amino Terminal ◽  
Acidic Domain ◽  
Reporter Mrna

ABSTRACT In eukaryotic cells, degradation of many mRNAs is initiated by removal of the poly(A) tail followed by decapping and 5′-3′ exonucleolytic decay. Although the order of these events is well established, we are still lacking a mechanistic understanding of how deadenylation and decapping are linked. In this report we identify human Pat1b as a protein that is tightly associated with the Ccr4-Caf1-Not deadenylation complex as well as with the Dcp1-Dcp2 decapping complex. In addition, the RNA helicase Rck and Lsm1 proteins interact with human Pat1b. These interactions are mediated via at least three independent domains within Pat1b, suggesting that Pat1b serves as a scaffold protein. By tethering Pat1b to a reporter mRNA, we further provide evidence that Pat1b is also functionally linked to both deadenylation and decapping. Finally, we report that Pat1b strongly induces the formation of processing (P) bodies, cytoplasmic foci that contain most enzymes of the RNA decay machinery. An amino-terminal region within Pat1b serves as an aggregation-prone domain that nucleates P bodies, whereas an acidic domain controls the size of P bodies. Taken together, these findings provide evidence that human Pat1b is a central component of the RNA decay machinery by physically connecting deadenylation with decapping.

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