scholarly journals A Novel Strategy to Uncover Specific Go Terms/phosphorylation Pathways in Phosphoproteomic Data in Arabidopsis Thaliana

2021 ◽  
Author(s):  
Denise S. Arico ◽  
Paula Beati ◽  
Diego L. Wengier ◽  
María Agustina Mazzella
Keyword(s):  
Experimental Data ◽  
Arabidopsis Thaliana ◽  
Biological Significance ◽  
Mrna Splicing ◽  
Biological Processes ◽  
Cytoplasmic Microtubule ◽  
Reference Set ◽  
Protein Prediction ◽  
Novel Strategy ◽  
Go Terms

Abstract Background. Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to an experimental query from a list of phosphoproteins. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance. Yet, this comparison assumes that GO term distribution between the phosphoproteome and the genome are identical. However, this hypothesis has not been tested due to the lack of a comprehensive phosphoproteome database.Results. In this study, we test this hypothesis by constructing three phosphoproteome databases in Arabidopsis thaliana: one based in experimental data (ExpRS), another based in in silico phosphorylation protein prediction (PredRS) and a third that is the union of both (UnRS). Our results show that the three phosphoproteome reference sets show default enrichment of several GO terms compared to GenRS, indicating that GO term distribution in the phosphoproteomes does not match that of the genome. Moreover, these differences overshadow the identification of GO terms that are specifically enriched in a particular condition. To overcome this limitation, we present an additional comparison of the sample of interest with UnRS to uncover GO terms specifically enriched in a particular phosphoproteome experiment. Using this strategy, we found that mRNA splicing and cytoplasmic microtubule compounds are important processes specifically enriched in the phosphoproteome of dark-grown Arabidopsis seedlings. Conclusions. This study provides a novel strategy to uncover GO specific terms in phosphoproteome data of Arabidopsis that could be applied to any other organism. We also highlight the importance of specific phosphorylation pathways that take place during dark-grown Arabidopsis development.

scholarly journals A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Denise S. Arico ◽  
Paula Beati ◽  
Diego L. Wengier ◽  
Maria Agustina Mazzella
Keyword(s):  
Experimental Data ◽  
Arabidopsis Thaliana ◽  
Biological Significance ◽  
Mrna Splicing ◽  
Biological Processes ◽  
Cytoplasmic Microtubule ◽  
Reference Set ◽  
Protein Prediction ◽  
Novel Strategy ◽  
Go Terms

Abstract Background Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to an experimental query from a list of phosphoproteins. Comparison of the frequency distribution of GO (Gene Ontology) terms in a given phosphoproteome set with that observed in the genome reference set (GenRS) is the most widely used tool to infer biological significance. Yet, this comparison assumes that GO term distribution between the phosphoproteome and the genome are identical. However, this hypothesis has not been tested due to the lack of a comprehensive phosphoproteome database. Results In this study, we test this hypothesis by constructing three phosphoproteome databases in Arabidopsis thaliana: one based in experimental data (ExpRS), another based in in silico phosphorylation protein prediction (PredRS) and a third that is the union of both (UnRS). Our results show that the three phosphoproteome reference sets show default enrichment of several GO terms compared to GenRS, indicating that GO term distribution in the phosphoproteomes does not match that of the genome. Moreover, these differences overshadow the identification of GO terms that are specifically enriched in a particular condition. To overcome this limitation, we present an additional comparison of the sample of interest with UnRS to uncover GO terms specifically enriched in a particular phosphoproteome experiment. Using this strategy, we found that mRNA splicing and cytoplasmic microtubule compounds are important processes specifically enriched in the phosphoproteome of dark-grown Arabidopsis seedlings. Conclusions This study provides a novel strategy to uncover GO specific terms in phosphoproteome data of Arabidopsis that could be applied to any other organism. We also highlight the importance of specific phosphorylation pathways that take place during dark-grown Arabidopsis development.

scholarly journals A family of pathogen-induced cysteine-rich transmembrane proteins is involved in plant disease resistance

Planta ◽  
2021 ◽  
Vol 253 (5) ◽  
Author(s):  
Marciel Pereira Mendes ◽  
Richard Hickman ◽  
Marcel C. Van Verk ◽  
Nicole M. Nieuwendijk ◽  
Anja Reinstädler ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plasma Membrane ◽  
Disease Resistance ◽  
Plant Disease Resistance ◽  
Transmembrane Proteins ◽  
Series Data ◽  
Immune Gene ◽  
Biological Processes ◽  
Hypocotyl Growth ◽  
Enhanced Resistance

Abstract Main conclusion Overexpression of pathogen-induced cysteine-rich transmembrane proteins (PCMs) in Arabidopsis thaliana enhances resistance against biotrophic pathogens and stimulates hypocotyl growth, suggesting a potential role for PCMs in connecting both biological processes. Abstract Plants possess a sophisticated immune system to protect themselves against pathogen attack. The defense hormone salicylic acid (SA) is an important player in the plant immune gene regulatory network. Using RNA-seq time series data of Arabidopsis thaliana leaves treated with SA, we identified a largely uncharacterized SA-responsive gene family of eight members that are all activated in response to various pathogens or their immune elicitors and encode small proteins with cysteine-rich transmembrane domains. Based on their nucleotide similarity and chromosomal position, the designated Pathogen-induced Cysteine-rich transMembrane protein (PCM) genes were subdivided into three subgroups consisting of PCM1-3 (subgroup I), PCM4-6 (subgroup II), and PCM7-8 (subgroup III). Of the PCM genes, only PCM4 (also known as PCC1) has previously been implicated in plant immunity. Transient expression assays in Nicotiana benthamiana indicated that most PCM proteins localize to the plasma membrane. Ectopic overexpression of the PCMs in Arabidopsis thaliana resulted in all eight cases in enhanced resistance against the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Additionally, overexpression of PCM subgroup I genes conferred enhanced resistance to the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato DC3000. The PCM-overexpression lines were found to be also affected in the expression of genes related to light signaling and development, and accordingly, PCM-overexpressing seedlings displayed elongated hypocotyl growth. These results point to a function of PCMs in both disease resistance and photomorphogenesis, connecting both biological processes, possibly via effects on membrane structure or activity of interacting proteins at the plasma membrane.

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

scholarly journals Theoretical Basis for the Measurement of Small Differences in the Length of the Cell Cycle between Two Cell Populations

2009 ◽  
Vol 2 (1) ◽  
pp. 95-100
Author(s):  
Juan Sebastian Yakisich
Keyword(s):  
Experimental Data ◽  
Cell Cycle ◽  
Theoretical Basis ◽  
Cycle Length ◽  
Cell Populations ◽  
Experimental Variability ◽  
Cell Strains ◽  
Novel Strategy ◽  
Cell Cycle Length

The length of the cell cycle (TC) is a tight regulated process and is important for proper development and homeostasis. Although several methods are available for estimating the duration of the cell cycle, it is difficult to determinate small differences of TC between two different cell populations due to biological and/or experimental variability. A novel strategy based in co-cultivation of two cell strains followed by a series of dilution and propagation of the culture will allow the quantification of very small differences in the length of two cell populations at resolution levels not possible at present with current methods. This is achieved by a separation of the endpoint variable measured to compare between two cell populations. The theoretical basis of this approach is discussed in the context of published experimental data and simulation of idealized experiments using virtual strains of different cell cycle length.

Cell-specific, activation-dependent regulation of neutrophil CD32A ligand-binding function

Blood ◽  
2000 ◽  
Vol 95 (3) ◽  
pp. 1069-1077 ◽  
Author(s):  
Shanmugam Nagarajan ◽  
Kala Venkiteswaran ◽  
Michael Anderson ◽  
Umar Sayed ◽  
Cheng Zhu ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Chinese Hamster Ovary Cells ◽  
Biological Significance ◽  
Chinese Hamster ◽  
Phosphatidyl Inositol ◽  
Ovary Cells ◽  
Binding Function ◽  
Affinity Modulation ◽  
Activated Neutrophils ◽  
Novel Strategy

Neutrophils express 2 low-affinity FcγR, FcγRIIIB (CD16B), and FcγRIIA (CD32A). CD16B is a glycosyl-phosphatidyl inositol-anchored molecule, whereas CD32A is a polypeptide-anchored molecule. These 2 receptors also differ in their signaling. The biological significance of coexpression of 2 FcγRs with distinct membrane anchors and signaling capacities is not clearly understood. Using neutrophils from a CD16B-deficient donor and normal neutrophils treated with anti-CD16 monoclonal antibodies, the authors demonstrated that affinity modulation of CD32A is one of the mechanisms by which neutrophils regulate their FcγR-dependent functions. Neutrophils isolated from a CD16B− donor rosetted poorly with sheep erythrocytes opsonized with rabbit IgG (EA) (12% ± 2% versus 80% ± 6% for control) and were unable to mediate immunophagocytosis. However, activation of CD16B−neutrophils with fMLP, a bacterial chemotactic peptide, increased the CD32A-dependent EA rosetting to 58%. The CD32A-dependent rosetting of fMLP-activated normal neutrophils also increased nearly 5-fold, but there was no increase in CD32A expression. The CD32A-dependent immune complex (IC) binding was also increased in activated neutrophils. This affinity regulation was not observed with CD32A expressed on Chinese hamster ovary cells. These results suggest that in resting neutrophils CD32A is in a low-affinity state and that these cells primarily engage CD16B for IC binding. However, once the neutrophils are activated, the CD32A is converted to a high-affinity state that leads to CD32A-dependent ligand binding and signaling. These results suggest that neutrophils adopt a novel strategy to engage the 2 different FcγR selectively during physiologic and pathologic conditions to carry out their functions efficiently.

scholarly journals Dietary microRNA—A Novel Functional Component of Food

2019 ◽  
Vol 10 (4) ◽  
pp. 711-721 ◽  
Author(s):  
Lin Zhang ◽  
Ting Chen ◽  
Yulong Yin ◽  
Chen-Yu Zhang ◽  
Yong-Liang Zhang
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Biological Significance ◽  
Circulatory System ◽  
Physiological Effects ◽  
Biological Processes ◽  
Regulate Gene Expression ◽  
Functional Component ◽  
Health And Disease ◽  
Regulate Gene

ABSTRACT MicroRNAs are a class of small RNAs that play essential roles in various biological processes by silencing genes. Evidence emerging in recent years suggests that microRNAs in food can be absorbed into the circulatory system and organs of humans and other animals, where they regulate gene expression and biological processes. These food-derived dietary microRNAs may serve as a novel functional component of food, a role that has been neglected to date. However, a significant amount of evidence challenges this new concept. The absorption, stability, and physiological effects of dietary microRNA in recipients, especially in mammals, are currently under heavy debate. In this review, we summarize our current understanding of the unique characteristics of dietary microRNAs and concerns about both the mechanistic and methodological basis for studying the biological significance of dietary microRNAs. Such efforts will benefit continuing investigations and offer new perspectives for the interpretation of the roles of dietary microRNA with respect to the health and disease of humans and animals.

scholarly journals Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology

2010 ◽  
Vol 74 (4) ◽  
pp. 479-503 ◽  
Author(s):  
Trudy Torto-Alalibo ◽  
Candace W. Collmer ◽  
Michelle Gwinn-Giglio ◽  
Magdalen Lindeberg ◽  
Shaowu Meng ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Effector Proteins ◽  
Biological Processes ◽  
Gene Products ◽  
Host Defenses ◽  
Host Interactions ◽  
Microbial Associations ◽  
Bioinformatic Approaches ◽  
Go Terms ◽  
Diverse Plant

SUMMARY Microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.

scholarly journals Bioinformatic resources for the investigation of proteins and proteomes

Peptidomics ◽  
2016 ◽  
Vol 2 (1) ◽  
Author(s):  
Angelo Facchiano
Keyword(s):  
Experimental Data ◽  
Data Management ◽  
Protein Identification ◽  
Molecular Mechanisms ◽  
Strong Support ◽  
Biological Processes ◽  
Functional Interpretation ◽  
Huge Data ◽  
Protein World ◽  
Protein Functions

AbstractExperimental techniques in omics sciences need strong support of bioinformatics tools for the data management, analysis and interpretation. Scientific community develops continuously new databases and tools. They make it possible the comparison of new experimental data with the existing ones, to gain new knowledge. Bioinformatics assists proteomics scientists for protein identification from experimental data, management of the huge data produced, investigation of molecular mechanisms of protein functions, their roles in biochemical pathways, and functional interpretation of biological processes. This article introduces the main bioinformatics resources for investigation in the protein world, with references to analyses performed by means of free tools available on the net.

scholarly journals A System-Level Investigation into the Mechanisms of Apigenin Against Inflammation

2019 ◽  
Vol 14 (9) ◽  
pp. 1934578X1987860 ◽  
Author(s):  
Ying Xie ◽  
Dongdong Liang ◽  
Qingke Wu ◽  
Xuemei Chen ◽  
Manal Ali Buabeid ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Biological Activities ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Mitogen Activated Protein Kinase ◽  
System Level ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Biological Processes ◽  
Go Terms

Apigenin is a natural flavone that possesses excellent biological activities especially against aging and cancer. However, the underlying mode of its action is not yet revealed. The purpose of this study was to examine the pharmacological mechanisms of apigenin using the knowledge of network pharmacology, protein-protein interaction (PPI) databases and biological processes analysis through Cytoscape. Apigenin targets were retrieved through PASS Prediction and STITCH database and the interactive associations between these targets were studied using STITCH, followed by GO (gene ontology) and pathway enrichment analysis. As a result of target search, 125 protein targets were retrieved. Moreover, 216 GO terms related to various biological processes, 16 GO terms for various molecular processes, 5 GO terms for the cellular components, and 52 Kyoto Encyclopedia of Genes and Genomes pathway terms were achieved by analyzing gene functional annotation clusters and abundance values of these targets. Most of these terms are strongly associated with inflammation through various pathways, for example, FOXO, mammalian target of rapamycin, tumor necrosis factor, p53, AMP-activated protein kinase, p13K-AKT, and mitogen-activated protein kinase, which play an important role in inflammation, aging and cancer. Apigenin can be used to treat inflammation, aging, and cancer with an underlying mechanism of inflammation suppression. This study contributed excellent information for a better understanding of the modes of action of apigenin. However, further studies such as docking and MD simulation are required to understand the therapeutic and toxicological roles of these targets of apigenin.

Sign in / Sign up

Export Citation Format

Share Document