scholarly journals Plant defense responses against viral and bacterial pathogen infections. Focus on RNA-binding proteins (RBPs)

2015 ◽  
Vol 60 (4) ◽  
pp. 60-73
Author(s):  
Musidlak Oskar ◽  
Waldemar Buchwald ◽  
Robert Nawrot
Keyword(s):  
Medicinal Plants ◽  
Defense Mechanisms ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Plant Immunity ◽  
Bacterial Pathogen ◽  
Defense Responses ◽  
Chelidonium Majus

SummaryPlants have developed intricate defense mechanisms against pathogen infections. Immune system of medicinal plants is well developed. The molecular mechanisms of their ability to protect themselves are not fully understood. Little is known about RNA-binding proteins (RBPs) present in medicinal plants. However, CmGRP1 is an RBP found in the milky sap of medicinal plant Chelidonium majus L. what implies possible importance of RBPs in plant immunity. In this review recent insights into the role of plant RBPs in antiviral and antibacterial defense responses are discussed.

scholarly journals The Arabidopsis homolog of human G3BP1 is a key regulator of stomatal and apoplastic immunity

2018 ◽  
Vol 1 (2) ◽  
pp. e201800046 ◽  
Author(s):  
Aala A Abulfaraj ◽  
Kiruthiga Mariappan ◽  
Jean Bigeard ◽  
Prabhu Manickam ◽  
Ikram Blilou ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Plant Immunity ◽  
Bacterial Pathogen ◽  
Defense Responses ◽  
Pathogen Resistance ◽  
Negative Regulator ◽  
Multifunctional Protein

Mammalian Ras-GTPase–activating protein SH3-domain–binding proteins (G3BPs) are a highly conserved family of RNA-binding proteins that link kinase receptor-mediated signaling to RNA metabolism. Mammalian G3BP1 is a multifunctional protein that functions in viral immunity. Here, we show that the Arabidopsis thaliana homolog of human G3BP1 negatively regulates plant immunity. Arabidopsis g3bp1 mutants showed enhanced resistance to the virulent bacterial pathogen Pseudomonas syringae pv. tomato. Pathogen resistance was mediated in Atg3bp1 mutants by altered stomatal and apoplastic immunity. Atg3bp1 mutants restricted pathogen entry into stomates showing insensitivity to bacterial coronatine–mediated stomatal reopening. AtG3BP1 was identified as a negative regulator of defense responses, which correlated with moderate up-regulation of salicylic acid biosynthesis and signaling without growth penalty.

scholarly journals A novel Phytophthora sojae effector PsFYVE1 modulates transcription and alternative splicing of immunity related genes by targeting host RZ-1A protein

2021 ◽  
Author(s):  
Xinyu Lu ◽  
Zitong Yang ◽  
Wen Song ◽  
Jierui Si ◽  
Zhiyuan Yin ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Plant Immunity ◽  
Phytophthora Sojae ◽  
Protein Family ◽  
Plant Interactions ◽  
Fyve Domain

AbstractOomycete pathogens secrete many effectors to manipulate plant immunity and promote infection. However, relatively few effector types have been well characterized. In this study, members of a FYVE domain-containing protein family that is highly expanded in oomycetes were systematically identified, and one secreted protein, PsFYVE1, was selected for further study. PsFYVE1 enhanced Phytophthora infection in Nicotiana benthamiana and was necessary for P. sojae virulence. The FYVE domain of PsFYVE1 had PI3P-binding activity that depended on four conservative amino acid residues. Furthermore, PsFYVE1 targeted RNA-binding proteins RZ-1A/1B/1C in N. benthamiana and soybean, and silencing of NbRZ-1A/1B/1C genes attenuates plant immunity. NbRZ-1A was associated with spliceosome that included three important components, NbGRP7, NbGRP8, and NbU1-70K. Notably, PsFYVE1 could disrupt NbRZ-1A–NbGRP7 interaction. RNA-seq and subsequent experimental analysis demonstrated that PsFYVE1 and NbRZ-1A not only co-regulated transcription of NbHCT, NbEIN2, and NbSUS4 genes but also modulated pre-mRNA alternative splicing (AS) of the NbNSL1 gene, which participated in plant immunity. Collectively, these findings indicate that the FYVE domain-containing protein family includes potential new effector types and also highlight that plant pathogen effectors can regulate plant immunity related genes at both transcription and AS levels to promote disease.Author summaryMany plant pathogenic oomycetes secrete effector proteins into plants to facilitate infection. Discovering potential repertoire of novel effectors and corresponding molecular mechanisms are major themes in the study of oomycete–plant interactions. Here, we characterized a FYVE domain-containing protein (PsFYVE1) in P. sojae. PsFYVE1 carries a functional secretory signal peptide and is a virulence-essential effector for P. sojae infection. We demonstrated that PsFYVE1 interacted with a class of plant RNA-binding proteins, including soybean GmRZ-1A/1B/1C and N. benthamiana NbRZ-1A/1B/1C. Silencing of NbRZ-1A/1B/1C proteins increased Phytophthora infection and suppressed plant defense. Furthermore, NbRZ-1A interacted with the spliceosome components, and PsFYVE1 disrupted association between NbRZ-1A and spliceosome component NbGRP7. We examined the global transcription and alternative splicing (AS) changes regulated by PsFYVE1 and NbRZ-1A, which indicated that PsFYVE1 and NbRZ-1A co-regulated transcription and pre-mRNA AS of immunity-related genes. Thus, this study identifies a novel virulence-related effector from P. sojae and a class of positive regulators of plant immunity, and reveals a detailed mechanism of effector-medicated transcription and AS regulation during pathogen–plant interactions.

The expanding world of metabolic enzymes moonlighting as RNA binding proteins

2021 ◽  
Author(s):  
Nicole J. Curtis ◽  
Constance J. Jeffery
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Molecular Structures ◽  
Intermediary Metabolism ◽  
The Many ◽  
And Function

RNA binding proteins play key roles in many aspects of RNA metabolism and function, including splicing, transport, translation, localization, stability and degradation. Within the past few years, proteomics studies have identified dozens of enzymes in intermediary metabolism that bind to RNA. The wide occurrence and conservation of RNA binding ability across distant branches of the evolutionary tree suggest that these moonlighting enzymes are involved in connections between intermediary metabolism and gene expression that comprise far more extensive regulatory networks than previously thought. There are many outstanding questions about the molecular structures and mechanisms involved, the effects of these interactions on enzyme and RNA functions, and the factors that regulate the interactions. The effects on RNA function are likely to be wider than regulation of translation, and some enzyme–RNA interactions have been found to regulate the enzyme's catalytic activity. Several enzyme–RNA interactions have been shown to be affected by cellular factors that change under different intracellular and environmental conditions, including concentrations of substrates and cofactors. Understanding the molecular mechanisms involved in the interactions between the enzymes and RNA, the factors involved in regulation, and the effects of the enzyme–RNA interactions on both the enzyme and RNA functions will lead to a better understanding of the role of the many newly identified enzyme–RNA interactions in connecting intermediary metabolism and gene expression.

scholarly journals First Identification of RNA-Binding Proteins That Regulate Alternative Exons in the Dystrophin Gene

2020 ◽  
Vol 21 (20) ◽  
pp. 7803
Author(s):  
Julie Miro ◽  
Anne-Laure Bougé ◽  
Eva Murauer ◽  
Emmanuelle Beyne ◽  
Dylan Da Cunha ◽  
...  
Keyword(s):  
Large Scale ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Dystrophin Gene ◽  
Rna Seq ◽  
Spatio Temporal ◽  
Dmd Gene ◽  
Shed Light

The Duchenne muscular dystrophy (DMD) gene has a complex expression pattern regulated by multiple tissue-specific promoters and by alternative splicing (AS) of the resulting transcripts. Here, we used an RNAi-based approach coupled with DMD-targeted RNA-seq to identify RNA-binding proteins (RBPs) that regulate splicing of its skeletal muscle isoform (Dp427m) in a human muscular cell line. A total of 16 RBPs comprising the major regulators of muscle-specific splicing events were tested. We show that distinct combinations of RBPs maintain the correct inclusion in the Dp427m of exons that undergo spatio-temporal AS in other dystrophin isoforms. In particular, our findings revealed the complex networks of RBPs contributing to the splicing of the two short DMD exons 71 and 78, the inclusion of exon 78 in the adult Dp427m isoform being crucial for muscle function. Among the RBPs tested, QKI and DDX5/DDX17 proteins are important determinants of DMD exon inclusion. This is the first large-scale study to determine which RBP proteins act on the physiological splicing of the DMD gene. Our data shed light on molecular mechanisms contributing to the expression of the different dystrophin isoforms, which could be influenced by a change in the function or expression level of the identified RBPs.

A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity

Nature ◽  
2007 ◽  
Vol 447 (7142) ◽  
pp. 284-288 ◽  
Author(s):  
Zheng Qing Fu ◽  
Ming Guo ◽  
Byeong-ryool Jeong ◽  
Fang Tian ◽  
Thomas E. Elthon ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Plant Immunity ◽  
Type Iii Effector ◽  
Type Iii

scholarly journals Circular RNAs: Biogenesis, Mechanism, and Function in Human Cancers

2019 ◽  
Vol 20 (16) ◽  
pp. 3926 ◽  
Author(s):  
Xing Zhao ◽  
Yujie Cai ◽  
Jianzhen Xu
Keyword(s):  
Noncoding Rna ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cancer Development ◽  
Circular Rnas ◽  
Open Questions ◽  
Circular Configuration ◽  
And Function

CircRNAs are a class of noncoding RNA species with a circular configuration that is formed by either typical spliceosome-mediated or lariat-type splicing. The expression of circRNAs is usually abnormal in many cancers. Several circRNAs have been demonstrated to play important roles in carcinogenesis. In this review, we will first provide an introduction of circRNAs biogenesis, especially the regulation of circRNA by RNA-binding proteins, then we will focus on the recent findings of circRNA molecular mechanisms and functions in cancer development. Finally, some open questions are also discussed.

scholarly journals In heart failure reactivation of RNA-binding proteins drives the transcriptome into a fetal state

2021 ◽  
Author(s):  
Matteo D'Antonio ◽  
Jennifer P. Nguyen ◽  
Timothy D. Arthur ◽  
Hiroko Matsui ◽  
Margaret K.R. Donovan ◽  
...  
Keyword(s):  
Heart Failure ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Healthy Adult ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Fetal Tissue ◽  
Cellular Heterogeneity ◽  
Rna Seq

Transcriptome-wide expression changes occur during heart failure, including reactivation of fetal-specific isoforms. However, the underlying molecular mechanisms and the extent to which a fetal gene program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal and adult (healthy and diseased) stages have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that RNA-binding proteins (RBPs) are highly overexpressed in fetal-like compared with healthy adult and are reactivated in heart failure, which results in expression of thousands fetal-specific isoforms. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms are more likely to bind RBPs, have canonical sequences at their splice sites and encode proteins with more functions. Our findings suggest targeting RBP fetal-specific isoforms could result in novel therapeutics for heart failure.

scholarly journals Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 591 ◽  
Author(s):  
Daria Mordovkina ◽  
Dmitry N. Lyabin ◽  
Egor A. Smolin ◽  
Ekaterina M. Sogorina ◽  
Lev P. Ovchinnikov ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Translation ◽  
Large Family ◽  
Stability Control ◽  
Mrna Stabilization ◽  
Cell Tissue ◽  
Structural Peculiarities

Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.

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