scholarly journals Quantitative Proteomics Reveals the Defense Response of Wheat against Puccinia striiformis f. sp. tritici

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Yuheng Yang ◽  
Yang Yu ◽  
Chaowei Bi ◽  
Zhensheng Kang
Keyword(s):  
Quantitative Proteomics ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Puccinia Striiformis ◽  
Post Inoculation ◽  
Control Groups ◽  
Stimulus Response ◽  
Wheat Gene ◽  
Related Proteins ◽  
And Control

Abstract Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is considered one of the most aggressive diseases to wheat production. In this study, we used an iTRAQ-based approach for the quantitative proteomic comparison of the incompatible Pst race CYR23 in infected and non-infected leaves of the wheat cultivar Suwon11. A total of 3,475 unique proteins were identified from three key stages of interaction (12, 24, and 48 h post-inoculation) and control groups. Quantitative analysis showed that 530 proteins were differentially accumulated by Pst infection (fold changes >1.5, p < 0.05). Among these proteins, 10.54% was classified as involved in the immune system process and stimulus response. Intriguingly, bioinformatics analysis revealed that a set of reactive oxygen species metabolism-related proteins, peptidyl–prolyl cis–trans isomerases (PPIases), RNA-binding proteins (RBPs), and chaperonins was involved in the response to Pst infection. Our results were the first to show that PPIases, RBPs, and chaperonins participated in the regulation of the immune response in wheat and even in plants. This study aimed to provide novel routes to reveal wheat gene functionality and better understand the early events in wheat–Pst incompatible interactions.

scholarly journals Quantitative proteomics indicate a strong correlation of mitotic phospho-/dephosphorylation with non-structured regions of substrates

2019 ◽  
Author(s):  
Hiroya Yamazaki ◽  
Hidetaka Kosako ◽  
Shige H. Yoshimura
Keyword(s):  
Protein Phosphorylation ◽  
Quantitative Proteomics ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Amino Acid Sequences ◽  
Mass Spectrometry Analysis ◽  
Order Structure ◽  
Ontology Term ◽  
Related Proteins

AbstractProtein phosphorylation plays a critical role in the regulation and progression of mitosis. More than 10,000 phosphorylated residues and the associated kinases have been identified to date via proteomic analyses. Although some of these phosphosites are associated with regulation of either protein-protein interactions or the catalytic activity of the substrate protein, the roles of most mitotic phosphosites remain unclear. In this study, we examined structural properties of mitotic phosphosites and neighboring residues to understand the role of heavy phosphorylation in non-structured domains. Quantitative mass spectrometry analysis of mitosis-arrested and non-arrested HeLa cells revealed >4,100 and >2,200 residues either significantly phosphorylated or dephosphorylated, respectively, at mitotic entry. The calculated disorder scores of amino acid sequences of neighboring individual phosphosites revealed that >70% of dephosphorylated phosphosites exist in disordered regions, whereas 50% of phosphorylated sites exist in non-structured domains. A clear inverse correlation was observed between probability of phosphorylation in non-structured domain and increment of phosphorylation in mitosis. These results indicate that at entry to mitosis, a significant number of phosphate groups are removed from non-structured domains and transferred to more-structured domains. Gene ontology term analysis revealed that mitosis-related proteins are heavily phosphorylated, whereas RNA-related proteins are both dephosphorylated and phosphorylated, suggesting that heavy phosphorylation/dephosphorylation in non-structured domains of RNA-binding proteins plays a role in dynamic rearrangement of RNA-containing organelles, as well as other intracellular environments.Significance StatementProgression of mitosis is tightly regulated by protein phosphorylation/dephosphorylation. Although proteomic studies have identified tens of thousands of phosphosites in mitotic cells, the roles of them remain to be answered. We approached this question from the viewpoint of the higher-order structure of phosphosites. Quantitative proteomics and bioinformatic analyses revealed that more than 70% of mitotic dephosphorylation events occurred in non-structured regions. Non-structured regions of cellular proteins are attracting considerable attention in terms of their involvement in dynamic rearrangements of intracellular membrane-less organelles and protein assembly/disassembly processes. Our results suggest the possibility that a vast amount of mitosis-associated dephosphorylation/phosphorylation at non-structured regions plays a role in regulating the dynamic assembly/disassembly of intracellular architectures and organelles such as chromosomes and nucleolus.

scholarly journals TRA2A-induced upregulation of LINC00662 regulates blood-brain barrier permeability by affecting ELK4 mRNA stability in Alzheimer's microenvironment

2019 ◽  
Author(s):  
Qianshuo Liu ◽  
Lu Zhu ◽  
Xiaobai Liu ◽  
Jian Zheng ◽  
Yunhui Liu ◽  
...  
Keyword(s):  
Tight Junction ◽  
Blood Brain Barrier ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Brain Barrier ◽  
Blood Brain ◽  
Bbb Permeability ◽  
Novel Target ◽  
Related Proteins

Abstract The blood-brain barrier (BBB) plays a pivotal role in maintenance and regulation of the neural microenvironment. The occurrence of BBB disruption is the pathological change of early Alzheimer’s disease (AD). RNA-binding proteins and long non-coding RNAs are involved in the regulation of BBB permeability. Our study was performed to demonstrate TRA2A/LINC00662/ELK4 axis in regulating BBB permeability in AD microenvironment. In Aβ1-42-incubated microvascular endothelial cells (ECs) of BBB model in vitro, TRA2A and LINC00662 were enriched. TRA2A increased the stability of LINC00662 by binding with it. The knockdown of either TRA2A or LINC00662 decreased the BBB permeability via upregulating the expressions of tight junction-related proteins. ELK4 was lower expressed in BBB model in vitro in AD microenvironment. LINC00662 mediated the degradation of ELK4 mRNA by SMD pathway. The downregulated ELK4 increased the permeability of BTB by increasing the tight junction-related proteins expressions. TRA2A/LINC00662/ELK4 axis plays a crucial role in the regulation of BBB permeability in AD microenvironment, which may provide a novel target for the therapy of AD.

scholarly journals Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1

2020 ◽  
Vol 21 (3) ◽  
pp. 1166 ◽  
Author(s):  
Marian Scherer ◽  
Michal Levin ◽  
Falk Butter ◽  
Marion Scheibe
Keyword(s):  
Quantitative Proteomics ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Full Length ◽  
Interacting Proteins ◽  
Non Coding Rna ◽  
Nuclear Rna ◽  
Long Non Coding Rna ◽  
Shed Light

The long non-coding RNA Malat1 has been implicated in several human cancers, while the mechanism of action is not completely understood. As RNAs in cells function together with RNA-binding proteins (RBPs), the composition of their RBP complex can shed light on their functionality. We here performed quantitative interactomics of 14 non-overlapping fragments covering the full length of Malat1 to identify possible nuclear interacting proteins. Overall, we identified 35 candidates including 14 already known binders, which are able to interact with Malat1 in the nucleus. Furthermore, the use of fragments along the full-length RNA allowed us to reveal two hotspots for protein binding, one in the 5′-region and one in the 3′-region of Malat1. Our results provide confirmation on previous RNA-protein interaction studies and suggest new candidates for functional investigations.

scholarly journals RNA Binding Protein Sex-Lethal (Sxl) and Control of Drosophila Sex Determination and Dosage Compensation

2003 ◽  
Vol 67 (3) ◽  
pp. 343-359 ◽  
Author(s):  
Luiz O. F. Penalva ◽  
Lucas Sánchez
Keyword(s):  
Sex Determination ◽  
Dosage Compensation ◽  
Target Genes ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulatory Gene ◽  
Sex Lethal ◽  
Male Specific ◽  
Regulatory Functions ◽  
And Control

SUMMARY In the past two decades, scientists have elucidated the molecular mechanisms behind Drosophila sex determination and dosage compensation. These two processes are controlled essentially by two different sets of genes, which have in common a master regulatory gene, Sex-lethal (Sxl). Sxl encodes one of the best-characterized members of the family of RNA binding proteins. The analysis of different mechanisms involved in the regulation of the three identified Sxl target genes (Sex-lethal itself, transformer, and male specific lethal-2) has contributed to a better understanding of translation repression, as well as constitutive and alternative splicing. Studies using the Drosophila system have identified the features of the protein that contribute to its target specificity and regulatory functions. In this article, we review the existing data concerning Sxl protein, its biological functions, and the regulation of its target genes.

scholarly journals Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq

2020 ◽  
Vol 48 (11) ◽  
pp. 5859-5872
Author(s):  
Danielle A Adekunle ◽  
Eric T Wang
Keyword(s):  
Sucrose Gradient ◽  
Rna Binding ◽  
Cell Function ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Biological Functions ◽  
New Associations ◽  
Subcellular Organization ◽  
Cellular Compartments ◽  
Related Proteins

Abstract Subcellular organization of RNAs and proteins is critical for cell function, but we still lack global maps and conceptual frameworks for how these molecules are localized in cells and tissues. Here, we introduce ATLAS-Seq, which generates transcriptomes and proteomes from detergent-free tissue lysates fractionated across a sucrose gradient. Proteomic analysis of fractions confirmed separation of subcellular compartments. Unexpectedly, RNAs tended to co-sediment with other RNAs in similar protein complexes, cellular compartments, or with similar biological functions. With the exception of those encoding secreted proteins, most RNAs sedimented differently than their encoded protein counterparts. To identify RNA binding proteins potentially driving these patterns, we correlated their sedimentation profiles to all RNAs, confirming known interactions and predicting new associations. Hundreds of alternative RNA isoforms exhibited distinct sedimentation patterns across the gradient, despite sharing most of their coding sequence. These observations suggest that transcriptomes can be organized into networks of co-segregating mRNAs encoding functionally related proteins and provide insights into the establishment and maintenance of subcellular organization.

scholarly journals Label-Free Quantitative Proteomics Analysis in Susceptible and Resistant Brassica napus Cultivars Infected with Xanthomonas campestris pv. campestris

2021 ◽  
Vol 9 (2) ◽  
pp. 253
Author(s):  
Md Tabibul Islam ◽  
Bok-Rye Lee ◽  
Van Hien La ◽  
Dong-Won Bae ◽  
Woo-Jin Jung ◽  
...  
Keyword(s):  
Innate Immunity ◽  
Brassica Napus ◽  
Quantitative Proteomics ◽  
Xanthomonas Campestris ◽  
Rna Binding ◽  
Protein Profile ◽  
Mitochondrial Outer Membrane ◽  
Ps Ii ◽  
Related Proteins ◽  
Xanthomonas Campestris Pv Campestris

Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the main disease of cruciferous vegetables. To characterize the resistance mechanism in the Brassica napus–Xcc pathosystem, Xcc-responsive proteins in susceptible (cv. Mosa) and resistant (cv. Capitol) cultivars were investigated using gel-free quantitative proteomics and analysis of gene expression. This allowed us to identify 158 and 163 differentially expressed proteins following Xcc infection in cv. Mosa and cv. Capitol, respectively, and to classify them into five major categories including antioxidative systems, proteolysis, photosynthesis, redox, and innate immunity. All proteins involved in protein degradation such as the protease complex, proteasome subunits, and ATP-dependent Clp protease proteolytic subunits, were upregulated only in cv. Mosa, in which higher hydrogen peroxide accumulation concurred with upregulated superoxide dismutase. In cv. Capitol, photosystem II (PS II)-related proteins were downregulated (excepting PS II 22 kDa), whereas the PS I proteins, ATP synthase, and ferredoxin-NADP+ reductase, were upregulated. For redox-related proteins, upregulation of thioredoxin, 2-cys peroxiredoxin, and glutathione S-transferase occurred in cv. Capitol, consistent with higher NADH-, ascorbate-, and glutathione-based reducing potential, whereas the proteins involved in the C2 oxidative cycle and glycolysis were highly activated in cv. Mosa. Most innate immunity-related proteins, including zinc finger domain (ZFD)-containing protein, glycine-rich RNA-binding protein (GRP) and mitochondrial outer membrane porin, were highly enhanced in cv. Capitol, concomitant with enhanced expression of ZFD and GRP genes. Distinguishable differences in the protein profile between the two cultivars deserves higher importance for breeding programs and understanding of disease resistance in the B. napus–Xcc pathosystem.

scholarly journals TRA2A-induced upregulation of LINC00662 regulates blood-brain barrier permeability by affecting ELK4 mRNA stability in Alzheimer's microenvironment

2019 ◽  
Author(s):  
Qianshuo Liu ◽  
Lu Zhu ◽  
Xiaobai Liu ◽  
Jian Zheng ◽  
Yunhui Liu ◽  
...  
Keyword(s):  
Tight Junction ◽  
Blood Brain Barrier ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Brain Barrier ◽  
Blood Brain ◽  
Bbb Permeability ◽  
Novel Target ◽  
Related Proteins

Abstract The blood-brain barrier (BBB) plays a pivotal role in maintenance and regulation of the neural microenvironment. The occurrence of BBB disruption is the pathological change of early Alzheimer’s disease (AD). RNA-binding proteins and long non-coding RNAs are involved in the regulation of BBB permeability. Our study was performed to demonstrate TRA2A/LINC00662/ELK4 axis in regulating BBB permeability in AD microenvironment. In Aβ1-42-incubated microvascular endothelial cells (ECs) of BBB model in vitro, TRA2A and LINC00662 were enriched. TRA2A increased the stability of LINC00662 by binding with it. The knockdown of either TRA2A or LINC00662 decreased the BBB permeability via upregulating the expressions of tight junction-related proteins. ELK4 was lower expressed in BBB model in vitro in AD microenvironment. LINC00662 mediated the degradation of ELK4 mRNA by SMD pathway. The downregulated ELK4 increased the permeability of BTB by increasing the tight junction-related proteins expressions. TRA2A/LINC00662/ELK4 axis plays a crucial role in the regulation of BBB permeability in AD microenvironment, which may provide a novel target for the therapy of AD.

scholarly journals Hsp40 Affinity to Identify Proteins Destabilized by Cellular Toxicant Exposure

2021 ◽  
Author(s):  
Guy M Quanrud ◽  
Maureen R Montoya ◽  
Liangyong Mei ◽  
Mohammad R Awad ◽  
Joseph C Genereux
Keyword(s):  
Quantitative Proteomics ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Pyruvate Dehydrogenase Complex ◽  
Limited Proteolysis ◽  
Environmental Toxins ◽  
Reaction Monitoring ◽  
Toxicant Exposure ◽  
Protein Targets ◽  
Parallel Reaction Monitoring

Environmental toxins and toxicants can damage proteins and threaten cellular proteostasis. Most current methodologies to identify misfolded proteins in cells survey the entire proteome for sites of changed reactivity. We describe and apply a quantitative proteomics methodology to identify destabilized proteins based on their binding to the human Hsp40 chaperone DNAJB8. These protein targets are validated by an orthogonal limited proteolysis assay using parallel reaction monitoring. We find that brief exposure of HEK293T cells to meta-arsenite increases the affinity of two dozen proteins to DNAJB8, including known arsenite-sensitive proteins. In particular, arsenite treatment destabilizes both the pyruvate dehydrogenase complex E1 subunit and several RNA-binding proteins. This platform can be used to explore how environmental toxins impact cellular proteostasis, and to identify the susceptible proteome.

RNA binding proteins and the pathological cascade in ALS/FTD neurodegeneration

2017 ◽  
Vol 9 (415) ◽  
pp. eaah5436 ◽  
Author(s):  
Daisuke Ito ◽  
Mami Hatano ◽  
Norihiro Suzuki
Keyword(s):  
Quality Control ◽  
Amyotrophic Lateral Sclerosis ◽  
Molecular Basis ◽  
Binding Proteins ◽  
Rna Binding ◽  
Protein Quality ◽  
Rna Binding Proteins ◽  
Therapeutic Strategies ◽  
Related Proteins ◽  
Lateral Sclerosis

Advanced genetic approaches have accelerated the identification of causative genes linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Most of the disease-related proteins encoded by these genes form aggregates in the cellular machineries that regulate RNA and protein quality control in cells. Cross-talk among the signaling pathways governing these machineries leads to pathological cascades mediated by the accumulation of mutant RNA binding proteins. We outline the molecular basis of ALS and FTD pathogenesis and discuss the prospects for therapeutic strategies to treat these diseases.

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