scholarly journals Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

2019 ◽  
Author(s):  
Mark Zander ◽  
Mathew G. Lewsey ◽  
Natalie M. Clark ◽  
Lingling Yin ◽  
Anna Bartlett ◽  
...  
Keyword(s):  
Jasmonic Acid ◽  
Signaling Pathways ◽  
Network Models ◽  
Cellular Functions ◽  
Transcriptional Responses ◽  
Plant Behavior ◽  
Proteomic Data ◽  
Gene Regulatory ◽  
Integrated Time Series ◽  
Insight Into

AbstractUnderstanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigate the signaling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA that spans from the activity of master and secondary-regulatory transcription factors, through gene expression outputs and alternative splicing to protein abundance changes, protein phosphorylation and chromatin remodeling. We integrated time series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enable us to predict previously unknown points of crosstalk from JA to other signaling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behavior, the general principles of which provide a framework for analysis of cross-regulation between other hormone and stress signaling pathways.

scholarly journals New Insights into LINC00346 and its Role in Disease

2022 ◽  
Vol 9 ◽  
Author(s):  
Juan Lu ◽  
Zhaoying Xiao ◽  
Mengqiu Xu ◽  
Lanjuan Li
Keyword(s):  
Signaling Pathways ◽  
Tumor Size ◽  
Clinical Utility ◽  
Histological Grade ◽  
Expression Level ◽  
Cellular Functions ◽  
Protein Coding ◽  
Potential Clinical Utility ◽  
Insight Into

Accumulating evidence has shown that long intergenic non-protein-coding RNA 346 (LINC00346) functions as an oncogene in the tumorigenesis of several cancers. The expression level of LINC00346 has been shown to be obviously correlated with prognosis, lymphoma metastasis, histological grade, TNM stage, tumor size and pathologic stage. LINC00346 has been found to regulate specific cellular functions by interacting with several molecules and signaling pathways. In this review, we summarize recent evidence concerning the role of LINC00346 in the occurrence and development of diseases. We also discuss the potential clinical utility of LINC00346, thereby providing new insight into the diagnosis and treatment of diseases. In addition, we further discuss the potential clinical utility of LINC00346 in the diagnosis, prognostication, and treatment of diseases.

scholarly journals Mapping the Germline and Somatic Mutation Interaction Landscape in Indolent and Aggressive Prostate Cancers

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Tarun Karthik Kumar Mamidi ◽  
Jiande Wu ◽  
Chindo Hicks
Keyword(s):  
Signaling Pathways ◽  
Somatic Mutation ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Somatic Mutations ◽  
Multiple Gene ◽  
Gene Regulatory ◽  
Aggressive Tumors ◽  
Prostate Cancers ◽  
Mutation Information

Background. A majority of prostate cancers (PCas) are indolent and cause no harm even without treatment. However, a significant proportion of patients with PCa have aggressive tumors that progress rapidly to metastatic disease and are often lethal. PCa develops through somatic mutagenesis, but emerging evidence suggests that germline genetic variation can markedly contribute to tumorigenesis. However, the causal association between genetic susceptibility and tumorigenesis has not been well characterized. The objective of this study was to map the germline and somatic mutation interaction landscape in indolent and aggressive tumors and to discover signatures of mutated genes associated with each type and distinguishing the two types of PCa. Materials and Methods. We integrated germline mutation information from genome-wide association studies (GWAS) with somatic mutation information from The Cancer Genome Atlas (TCGA) using gene expression data from TCGA on indolent and aggressive PCas as the intermediate phenotypes. Germline and somatic mutated genes associated with each type of PCa were functionally characterized using network and pathway analysis. Results. We discovered gene signatures containing germline and somatic mutations associated with each type and distinguishing the two types of PCa. We discovered multiple gene regulatory networks and signaling pathways enriched with germline and somatic mutations including axon guidance, RAR, WINT, MSP-RON, STAT3, PI3K, TR/RxR, and molecular mechanisms of cancer, NF-kB, prostate cancer, GP6, androgen, and VEGF signaling pathways for indolent PCa and MSP-RON, axon guidance, RAR, adipogenesis, and molecular mechanisms of cancer and NF-kB signaling pathways for aggressive PCa. Conclusion. The investigation revealed germline and somatic mutated genes associated with indolent and aggressive PCas and distinguishing the two types of PCa. The study revealed multiple gene regulatory networks and signaling pathways dysregulated by germline and somatic alterations. Integrative analysis combining germline and somatic mutations is a powerful approach to mapping germline and somatic mutation interaction landscape.

scholarly journals Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

2017 ◽  
Vol 29 (9) ◽  
pp. 2086-2105 ◽  
Author(s):  
Richard Hickman ◽  
Marcel C. Van Verk ◽  
Anja J.H. Van Dijken ◽  
Marciel Pereira Mendes ◽  
Irene A. Vroegop-Vos ◽  
...  
Keyword(s):  
Jasmonic Acid ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Gene Regulatory

scholarly journals Gene regulatory network models in response to sugars in the plant circadian system

2018 ◽  
Vol 457 ◽  
pp. 137-151 ◽  
Author(s):  
Takayuki Ohara ◽  
Timothy J. Hearn ◽  
Alex A.R. Webb ◽  
Akiko Satake
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Network Models ◽  
Circadian System ◽  
Gene Regulatory

scholarly journals 3D micro-environment regulates NF–κβ dependent adhesion to induce monocyte differentiation

2018 ◽  
Author(s):  
Anindita Bhattacharya ◽  
Mahesh Agarwal ◽  
Rachita Mukherjee ◽  
Prosenjit Sen ◽  
Deepak Kumar Sinha
Keyword(s):  
Positive Feedback ◽  
Feedback Loop ◽  
The Novel ◽  
Monocyte Adhesion ◽  
Cellular Functions ◽  
Monocyte Differentiation ◽  
Summary Statement ◽  
Necessary And Sufficient ◽  
Multiple Signaling ◽  
Insight Into

AbstractDifferentiation of monocytes entails their relocation from blood to the tissue, hence accompanied by an altered physicochemical micro-environment. While the mechanism by which the biochemical make-up of the micro-environment induces differentiation is known, the fluid-like to gel-like transition in the physical micro-environment is not well understood. Monocytes maintain non-adherent state to prevent differentiation. We establish that irrespective of the chemical makeup, a 3D gel-like micro-environment induces a positive-feedback loop of adhesion-MAPK-NF-κβ activation to facilitate differentiation. In 2D fluid-like micro-environment, adhesion alone is capable of inducing differentiation via the same positive-feedback signalling. Chemical inducer treatment in fluid-like micro-environment, increases the propensity of monocyte adhesion via a brief pulse of p-MAPK. The adhesion subsequently elicit differentiation, establishing that adhesion is both necessary and sufficient to induce differentiation in 2D/3D micro-environment. Our findings challenge the notion that adhesion is a result of monocyte differentiation. Rather it’s the adhesion which triggers the differentiation of monocytes. MAPK, and NF-κβ being key molecules of multiple signaling pathways, we hypothesize that biochemically inert 3D gel-like micro-environment would also influence other cellular functions.Summary statementThis article brings out a new insight into the novel mechanisms of monocyte differentiation solely driven by physical micro-environment and adhesion.

scholarly journals Computational design of orthogonal membrane receptor-effector switches for rewiring signaling pathways

2018 ◽  
Vol 115 (27) ◽  
pp. 7051-7056 ◽  
Author(s):  
M. Young ◽  
T. Dahoun ◽  
B. Sokrat ◽  
C. Arber ◽  
K. M. Chen ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
G Protein ◽  
Dopamine D2 Receptor ◽  
D2 Receptor ◽  
High Specificity ◽  
Computational Design ◽  
Membrane Receptor ◽  
Membrane Receptors ◽  
Cellular Functions ◽  
Hierarchical Code

Membrane receptors regulate numerous intracellular functions. However, the molecular underpinnings remain poorly understood because most receptors initiate multiple signaling pathways through distinct interaction interfaces that are structurally uncharacterized. We present an integrated computational and experimental approach to model and rationally engineer membrane receptor-intracellular protein systems signaling with novel pathway selectivity. We targeted the dopamine D2 receptor (D2), a G-protein–coupled receptor (GPCR), which primarily signals through Gi, but triggers also the Gq and beta-arrestin pathways. Using this approach, we designed orthogonal D2–Gi complexes, which coupled with high specificity and triggered exclusively the Gi-dependent signaling pathway. We also engineered an orthogonal chimeric D2–Gs/i complex that rewired D2 signaling from a Gi-mediated inhibitory into a Gs-dependent activating pathway. Reinterpreting the evolutionary history of GPCRs in light of the designed proteins, we uncovered an unforeseen hierarchical code of GPCR–G-protein coupling selectivity determinants. The results demonstrate that membrane receptor–cytosolic protein systems can be rationally engineered to regulate mammalian cellular functions. The method should prove useful for creating orthogonal molecular switches that redirect signals at the cell surface for cell-engineering applications.

scholarly journals C-terminal tail polyglycylation and polyglutamylation alter microtubule mechanical properties

2019 ◽  
Author(s):  
Kathryn P. Wall ◽  
Harold Hart ◽  
Thomas Lee ◽  
Cynthia Page ◽  
Taviare L. Hawkins ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Molecular Mechanisms ◽  
High Stress ◽  
Resonance Spectroscopy ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Peptide Backbone ◽  
Post Translational Modifications ◽  
Intrinsic Stiffness ◽  
Insight Into

ABSTRACTMicrotubules are biopolymers that perform diverse cellular functions. The regulation of microtubule behavior occurs in part through post-translational modification of both the α- and β- subunits of tubulin. One class of modifications is the heterogeneous addition of glycine and glutamate residues to the disordered C-terminal tails of tubulin. Due to their prevalence in stable, high stress cellular structures such as cilia, we sought to determine if these modifications alter the intrinsic stiffness of microtubules. Here we describe the purification and characterization of differentially-modified pools of tubulin from Tetrahymena thermophila. We found that glycylation on the α-C-terminal tail is a key determinant of microtubule stiffness, but does not affect the number of protofilaments incorporated into microtubules. We measured the dynamics of the tail peptide backbone using nuclear magnetic resonance spectroscopy. We found that the spin-spin relaxation rate (R2) showed a pronounced decreased as a function of distance from the tubulin surface for the α-tubulin tail, indicating that the α-tubulin tail interacts with the dimer surface. This suggests that the interactions of the α-C-terminal tail with the tubulin body contributes to the stiffness of the assembled microtubule, providing insight into the mechanism by which glycylation and glutamylation can alter microtubule mechanical properties.SIGNIFICANCEMicrotubules are regulated in part by post-translational modifications including the heterogeneous addition of glycine and glutamate residues to the C-terminal tails. By producing and characterizing differentially-modified tubulin, this work provides insight into the molecular mechanisms of how these modifications alter intrinsic microtubule properties such as flexibility. These results have broader implications for mechanisms of how ciliary structures are able to function under high stress.

What are Gene Regulatory Networks?

2010 ◽  
pp. 1-27 ◽  
Author(s):  
Alberto de la Fuente
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Network Models ◽  
Transcriptional Regulatory Networks ◽  
Biochemical Processes ◽  
Transcriptional Regulatory ◽  
Biochemical Systems ◽  
Gene Regulatory

This book deals with algorithms for inferring and analyzing Gene Regulatory Networks using mainly gene expression data. What precisely are the Gene Regulatory Networks that are inferred by such algorithms from this type of data? There is still much confusion in the current literature and it is important to start a book about computational methods for Gene Regulatory Networks with a definition that is as unambiguous as possible. In this chapter, I provide a definition and try to clearly explain what Gene Regulatory Networks are in terms of the underlying biochemical processes. To do the latter in a formal way, I will use a linear approximation to the in general non-linear kinetics underlying interactions in biochemical systems and show how a biochemical system can be ‘condensed’ into the more compact description of Gene Regulatory Networks. Important differences between the defined Gene Regulatory Networks and other network models for gene regulation, such as Transcriptional Regulatory Networks and Co-Expression Networks, will be highlighted.

scholarly journals Functions of Jasmonic Acid in Plant Regulation and Response to Abiotic Stress

2020 ◽  
Vol 21 (4) ◽  
pp. 1446 ◽  
Author(s):  
Jia Wang ◽  
Li Song ◽  
Xue Gong ◽  
Jinfan Xu ◽  
Minhui Li
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Jasmonic Acid ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Large Scale ◽  
Higher Plants ◽  
Complex Signal ◽  
Ja Signaling ◽  
Signal Network

Jasmonic acid (JA) is an endogenous growth-regulating substance, initially identified as a stress-related hormone in higher plants. Similarly, the exogenous application of JA also has a regulatory effect on plants. Abiotic stress often causes large-scale plant damage. In this review, we focus on the JA signaling pathways in response to abiotic stresses, including cold, drought, salinity, heavy metals, and light. On the other hand, JA does not play an independent regulatory role, but works in a complex signal network with other phytohormone signaling pathways. In this review, we will discuss transcription factors and genes involved in the regulation of the JA signaling pathway in response to abiotic stress. In this process, the JAZ-MYC module plays a central role in the JA signaling pathway through integration of regulatory transcription factors and related genes. Simultaneously, JA has synergistic and antagonistic effects with abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and other plant hormones in the process of resisting environmental stress.

Sign in / Sign up

Export Citation Format

Share Document