scholarly journals In Silico Phylogenetic and Structural Analyses of Plant Endogenous Danger Signaling Molecules upon Stress

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Athanasia Pavlopoulou ◽  
Ezgi Karaca ◽  
Alma Balestrazzi ◽  
Alexandros G. Georgakilas
Keyword(s):  
In Silico ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Conservation Status ◽  
Downstream Signaling ◽  
Protein Protein Interaction ◽  
Effector Triggered Immunity ◽  
Molecular Patterns ◽  
Dying Cells ◽  
Diverse Plant Species

The plant innate immune system has two major branches, the pathogen-triggered immunity and the effector-triggered immunity (ETI). The effectors are molecules released by plant attackers to evade host immunity. In addition to the foreign intruders, plants possess endogenous instigators produced in response to general cellular injury termed as damage-associated molecular patterns (DAMPs). In plants, DAMPs or alarmins are released by damaged, stressed, or dying cells following abiotic stress such as radiation, oxidative and drought stresses. In turn, a cascade of downstream signaling events is initiated leading to the upregulation of defense or response-related genes. In the present study, we have investigated more thoroughly the conservation status of the molecular mechanisms implicated in the danger signaling primarily in plants. Towards this direction, we have performed in silico phylogenetic and structural analyses of the associated biomolecules in taxonomically diverse plant species. On the basis of our results, the defense mechanisms appear to be largely conserved within the plant kingdom. Of note, the sequence and/or function of several components of these mechanisms was found to be conserved in animals, as well. At the same time, the molecules involved in plant defense were found to form a dense protein-protein interaction (PPi) network, suggesting a crosstalk between the various defense mechanisms to a variety of stresses, like oxidative stress.

scholarly journals In Silico Phylogenetic and Structural Analysis of Plant Damps

2018 ◽  
Author(s):  
Athanasia pavlopoulou ◽  
Ezgi Karaca ◽  
Alma Balestrazzi ◽  
Alexandros Georgakilas
Keyword(s):  
In Silico ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Conservation Status ◽  
Biological Molecules ◽  
Downstream Signaling ◽  
Molecular Patterns ◽  
Dying Cells ◽  
Diverse Plant Species ◽  
Damage Associated Molecular Patterns

In plants and animals, endogenous biological molecules, termed damage-associated molecular patterns (DAMPs) or alarmins, are released by damaged, stressed or dying cells following abiotic stress such as radiation and drought stress. In turn, a cascade of downstream signaling events is initiated leading to the up-regulation of defense-related genes. In the present study, in an effort to investigate the conservation status of the molecular mechanisms implicated in the danger signaling, thorough in silico phylogenetic and structural analyses of the effector biomolecules were performed in taxonomically diverse plant species. On the basis of our results, the defense mechanisms appear to be largely conserved within the plant kingdom. Of note is our finding that the sequence and/or function of several components of these mechanisms were found to be conserved in animals, as well.

Molecular mechanisms of action and physiological effects of the proinsulin C-peptide (a systematic review)

2020 ◽  
Vol 66 (3) ◽  
pp. 196-207
Author(s):  
O.N. Poteryaeva ◽  
I.F. Usynin
Keyword(s):  
Intracellular Signaling ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Therapeutic Potential ◽  
Experimental Models ◽  
Physiological Effects ◽  
C Peptide ◽  
Downstream Signaling ◽  
Blood Microcirculation ◽  
Patients With Diabetes

The C-peptide is a fragment of proinsulin, the cleavage of which forms active insulin. In recent years, new information has appeared on the physiological effects of the C-peptide, indicating its positive effect on many organs and tissues, including the kidneys, nervous system, heart, vascular endothelium and blood microcirculation. Studies on experimental models of diabetes mellitus in animals, as well as clinical trials in patients with diabetes, have shown that the C-peptide has an important regulatory effect on the early stages of functional and structural disorders caused by this disease. The C-peptide exhibits its effects through binding to a specific receptor on the cell membrane and activation of downstream signaling pathways. Intracellular signaling involves G-proteins and Ca2+-dependent pathways, resulting in activation and increased expression of endothelial nitric oxide synthase, Na+/K+-ATPase and important transcription factors involved in apoptosis, anti-inflammatory and other intracellular defense mechanisms. This review gives an idea of the C-peptide as a bioactive endogenous peptide that has its own biological activity and therapeutic potential.

scholarly journals Calcium-signaling proteins mediate the plant transcriptomic response during a well-established Xanthomonas campestris pv. campestris infection

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Maria Tortosa ◽  
Maria E. Cartea ◽  
Pablo Velasco ◽  
Pilar Soengas ◽  
Victor M. Rodriguez
Keyword(s):  
Calcium Signaling ◽  
Defense Mechanisms ◽  
Xanthomonas Campestris ◽  
Signaling Proteins ◽  
Transcriptomic Response ◽  
Expression Of Genes ◽  
Knockout Mutants ◽  
Effector Triggered Immunity ◽  
Plant Transcriptome ◽  
Molecular Patterns

Abstract The plant immune system is divided into two branches; one branch is based on the recognition of pathogen-associated molecular patterns (PAMP-triggered immunity), and the other relies on pathogenic effector detection (effector-triggered immunity). Despite each branch being involved in different complex mechanisms, both lead to transcription reprogramming and, thus, changes in plant metabolism. To study the defense mechanisms involved in the Brassica oleracea–Xanthomonas campestris pv. campestris (Xcc) interaction, we analyzed the plant transcriptome dynamics at 3 and 12 days postinoculation (dpi) by using massive analysis of 3′-cDNA ends. We identified more induced than repressed transcripts at both 3 and 12 dpi, although the response was greater at 12 dpi. Changes in the expression of genes related to the early infection stages were only detected at 12 dpi, suggesting that the timing of triggered defenses is crucial to plant survival. qPCR analyses in susceptible and resistant plants allowed us to highlight the potential role of two calcium-signaling proteins, CBP60g and SARD1, in the resistance against Xcc. This role was subsequently confirmed using Arabidopsis knockout mutants.

scholarly journals Evolution of Disease Defense Genes and Their Regulators in Plants

2019 ◽  
Vol 20 (2) ◽  
pp. 335 ◽  
Author(s):  
Rongzhi Zhang ◽  
Fengya Zheng ◽  
Shugen Wei ◽  
Shujuan Zhang ◽  
Genying Li ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Plant Diseases ◽  
Regulation System ◽  
Defense Genes ◽  
Biotic Stresses ◽  
Microbial Infections ◽  
Effector Triggered Immunity ◽  
Plant Pathogen Interactions ◽  
Molecular Patterns ◽  
New Generation

Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race of plant–pathogen interactions. The complicated defense systems include pathogen-associated molecular patterns (PAMP) triggered immunity (PTI), effector triggered immunity (ETI), and the exosome-mediated cross-kingdom RNA interference (CKRI) system. Furthermore, plants have evolved a classical regulation system mediated by miRNAs to regulate these defense genes. Most of the genes/small RNAs or their regulators that involve in the defense pathways can have very rapid evolutionary rates in the longitudinal and horizontal co-evolution with pathogens. According to these internal defense mechanisms, some strategies such as molecular switch for the disease resistance genes, host-induced gene silencing (HIGS), and the new generation of RNA-based fungicides, have been developed to control multiple plant diseases. These broadly applicable new strategies by transgene or spraying ds/sRNA may lead to reduced application of pesticides and improved crop yield.

scholarly journals Plant Virus Interaction: Layers of Plant Antiviral Immunity

2019 ◽  
pp. 89-94
Author(s):  
Pedro Filho Noronha Souza
Keyword(s):  
Plant Virus ◽  
Defense Mechanisms ◽  
Second Line ◽  
Basal Resistance ◽  
Double Stranded Rna ◽  
Effector Triggered Immunity ◽  
Virus Interaction ◽  
Two Phases ◽  
Molecular Patterns ◽  
Damage Associated Molecular Patterns

Plant defense mechanisms are divided into two phases; (1) the Pathogen-Triggered Immunity (PTI), which is basal resistance and; (2) Effector-Triggered Immunity (ETI) or induced resistance, the second line of defense of plants [1,2]. The PTI response is rapidly active by plants after recognizing pathogens effectors, which could be MAMPS or PAMPs (Microbe/pathogen-associated molecular patterns, e.g., bacterial flagellin), DAMPs (Damage-associated molecular patterns, e.g., fungal haustorium), and VAMPs (Viral-associated molecular patterns, e.g., double-stranded RNA of viruses). The recognition of pathogens effectors is performed by Pattern Recognition Receptors (PRR) [3-6].

Resolution-Associated Molecular Patterns (RAMPs) as Endogenous Regulators of Glia Functions in Neuroinflammatory Disease

2020 ◽  
Vol 19 (7) ◽  
pp. 483-494
Author(s):  
Tyler J. Wenzel ◽  
Evan Kwong ◽  
Ekta Bajwa ◽  
Andis Klegeris
Keyword(s):  
Molecular Mechanisms ◽  
Inflammatory Responses ◽  
Bioactive Lipids ◽  
Prothymosin Α ◽  
Neuroinflammatory Disease ◽  
Cellular Debris ◽  
Αb Crystallin ◽  
Endogenous Regulators ◽  
The Central Nervous System ◽  
Molecular Patterns

: Glial cells, including microglia and astrocytes, facilitate the survival and health of all cells within the Central Nervous System (CNS) by secreting a range of growth factors and contributing to tissue and synaptic remodeling. Microglia and astrocytes can also secrete cytotoxins in response to specific stimuli, such as exogenous Pathogen-Associated Molecular Patterns (PAMPs), or endogenous Damage-Associated Molecular Patterns (DAMPs). Excessive cytotoxic secretions can induce the death of neurons and contribute to the progression of neurodegenerative disorders, such as Alzheimer’s disease (AD). The transition between various activation states of glia, which include beneficial and detrimental modes, is regulated by endogenous molecules that include DAMPs, cytokines, neurotransmitters, and bioactive lipids, as well as a diverse group of mediators sometimes collectively referred to as Resolution-Associated Molecular Patterns (RAMPs). RAMPs are released by damaged or dying CNS cells into the extracellular space where they can induce signals in autocrine and paracrine fashions by interacting with glial cell receptors. While the complete range of their effects on glia has not been described yet, it is believed that their overall function is to inhibit adverse CNS inflammatory responses, facilitate tissue remodeling and cellular debris removal. This article summarizes the available evidence implicating the following RAMPs in CNS physiological processes and neurodegenerative diseases: cardiolipin (CL), prothymosin α (ProTα), binding immunoglobulin protein (BiP), heat shock protein (HSP) 10, HSP 27, and αB-crystallin. Studies on the molecular mechanisms engaged by RAMPs could identify novel glial targets for development of therapeutic agents that effectively slow down neuroinflammatory disorders including AD.

scholarly journals A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max)

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Arun Kumaran Anguraj Vadivel ◽  
Tim McDowell ◽  
Justin B. Renaud ◽  
Sangeeta Dhaubhadel
Keyword(s):  
Transcription Factor ◽  
Hairy Roots ◽  
Defense Mechanisms ◽  
Biosynthetic Pathway ◽  
Bzip Transcription Factor ◽  
Myb Transcription Factor ◽  
In Planta ◽  
Rnai Silencing ◽  
Protein Protein Interaction ◽  
Soybean Roots

AbstractGmMYB176 is an R1 MYB transcription factor that regulates multiple genes in the isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean roots. While GmMYB176 is important for isoflavonoid synthesis, it is not sufficient for the function and requires additional cofactor(s). The aim of this study was to identify the GmMYB176 interactome for the regulation of isoflavonoid biosynthesis in soybean. Here, we demonstrate that a bZIP transcription factor GmbZIP5 co-immunoprecipitates with GmMYB176 and shows protein–protein interaction in planta. RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean hairy roots. Furthermore, co-overexpression of GmMYB176 and GmbZIP5 enhanced the level of multiple isoflavonoid phytoallexins including glyceollin, isowighteone and a unique O-methylhydroxy isoflavone in soybean hairy roots. These findings could be utilized to develop biotechnological strategies to manipulate the metabolite levels either to enhance plant defense mechanisms or for human health benefits in soybean or other economically important crops.

scholarly journals Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods

2021 ◽  
Vol 22 (12) ◽  
pp. 6505
Author(s):  
Jishizhan Chen ◽  
Jia Hua ◽  
Wenhui Song
Keyword(s):  
Stem Cells ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Negative Control ◽  
Gene Set Enrichment Analysis ◽  
Venn Diagram ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Two Samples ◽  
Key Genes

Applying mesenchymal stem cells (MSCs), together with the distraction osteogenesis (DO) process, displayed enhanced bone quality and shorter treatment periods. The DO guides the differentiation of MSCs by providing mechanical clues. However, the underlying key genes and pathways are largely unknown. The aim of this study was to screen and identify hub genes involved in distraction-induced osteogenesis of MSCs and potential molecular mechanisms. Material and Methods: The datasets were downloaded from the ArrayExpress database. Three samples of negative control and two samples subjected to 5% cyclic sinusoidal distraction at 0.25 Hz for 6 h were selected for screening differentially expressed genes (DEGs) and then analysed via bioinformatics methods. The Gene Ontology (GO) terms and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment were investigated. The protein–protein interaction (PPI) network was visualised through the Cytoscape software. Gene set enrichment analysis (GSEA) was conducted to verify the enrichment of a self-defined osteogenic gene sets collection and identify osteogenic hub genes. Results: Three hub genes (IL6, MMP2, and EP300) that were highly associated with distraction-induced osteogenesis of MSCs were identified via the Venn diagram. These hub genes could provide a new understanding of distraction-induced osteogenic differentiation of MSCs and serve as potential gene targets for optimising DO via targeted therapies.

scholarly journals A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yu Zhang ◽  
Christopher D. Kontos ◽  
Brian H. Annex ◽  
Aleksander S. Popel
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Vascular Dysfunction ◽  
Reaction Network ◽  
Vascular Growth ◽  
Downstream Signaling ◽  
Signaling Axis ◽  
Agonistic Activity ◽  
Molecular Regulatory Mechanisms

AbstractThe Ang–Tie signaling pathway is an important vascular signaling pathway regulating vascular growth and stability. Dysregulation in the pathway is associated with vascular dysfunction and numerous diseases that involve abnormal vascular permeability and endothelial cell inflammation. The understanding of the molecular mechanisms of the Ang–Tie pathway has been limited due to the complex reaction network formed by the ligands, receptors, and molecular regulatory mechanisms. In this study, we developed a mechanistic computational model of the Ang–Tie signaling pathway validated against experimental data. The model captures and reproduces the experimentally observed junctional localization and downstream signaling of the Ang–Tie signaling axis, as well as the time-dependent role of receptor Tie1. The model predicts that Tie1 modulates Tie2’s response to the context-dependent agonist Ang2 by junctional interactions. Furthermore, modulation of Tie1’s junctional localization, inhibition of Tie2 extracellular domain cleavage, and inhibition of VE-PTP are identified as potential molecular strategies for potentiating Ang2’s agonistic activity and rescuing Tie2 signaling in inflammatory endothelial cells.

Sign in / Sign up

Export Citation Format

Share Document