An Efficient Method to Identify Conditionally Activated Transcription Factors and their Corresponding Signal Transduction Pathway Segments

A signal transduction pathway (STP) is a cascade composed of a series of signal transferring steps, which often activate one or more transcription factors (TFs) to control the transcription of target genes. Understanding signaling pathways is important to our understanding of the molecular mechanisms of disease. Many condition-annotated pathways have been deposited in public databases. However, condition-annotated pathways are far from complete, considering the large number of possible conditions. Computational methods to assist in the identification of conditionally activated pathways are greatly needed. In this paper, we propose an efficient method to identify conditionally activated pathway segments starting from the identification of conditionally activated TFs, by incorporating protein-DNA binding data, gene expression data and protein interaction data. Applying our methods on several microarray datasets, we have discovered many significantly activated TFs and their corresponding pathway segments, which are supported by evidence in the literature.

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Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.190309197 ◽

2000 ◽

Vol 97 (21) ◽

pp. 11632-11637 ◽

Cited By ~ 768

Author(s):

Y. Uno ◽

T. Furihata ◽

H. Abe ◽

R. Yoshida ◽

K. Shinozaki ◽

...

Keyword(s):

Signal Transduction ◽

Transcription Factors ◽

Abscisic Acid ◽

Leucine Zipper ◽

High Salinity ◽

Signal Transduction Pathway ◽

Transduction Pathway ◽

Basic Leucine Zipper ◽

Dependent Signal

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Transcription factors as potential participants in the signal transduction pathway of boron deficiency

Plant Signaling & Behavior ◽

10.4161/psb.26114 ◽

2013 ◽

Vol 8 (11) ◽

pp. e26114 ◽

Cited By ~ 12

Author(s):

Agustín González-Fontes ◽

Jesús Rexach ◽

Carlos Quiles-Pando ◽

M Begoña Herrera-Rodríguez ◽

Juan J Camacho-Cristóbal ◽

...

Keyword(s):

Signal Transduction ◽

Transcription Factors ◽

Signal Transduction Pathway ◽

Boron Deficiency ◽

Transduction Pathway

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Copper Response Element and Crr1-Dependent Ni2+-Responsive Promoter for Induced, Reversible Gene Expression in Chlamydomonas reinhardtii

Eukaryotic Cell ◽

10.1128/ec.2.5.995-1002.2003 ◽

2003 ◽

Vol 2 (5) ◽

pp. 995-1002 ◽

Cited By ~ 42

Author(s):

Jeanette M. Quinn ◽

Janette Kropat ◽

Sabeeha Merchant

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Chlamydomonas Reinhardtii ◽

Target Genes ◽

Response Regulator ◽

Signal Transduction Pathway ◽

Transduction Pathway ◽

Nickel Ions ◽

Cobalt Ions ◽

Inducible Gene

ABSTRACT The Cpx1 and Cyc6 genes of Chlamydomonas reinhardtii are activated in copper-deficient cells via a signal transduction pathway that requires copper response elements (CuREs) and a copper response regulator defined by the CRR1 locus. The two genes can also be activated by provision of nickel or cobalt ions in the medium. The response to nickel ions requires at least one CuRE and also CRR1 function, suggesting that nickel interferes with a component in the nutritional copper signal transduction pathway. Nickel does not act by preventing copper uptake/utilization because (i) holoplastocyanin formation is unaffected in Ni2+-treated cells and (ii) provision of excess copper cannot reverse the Ni-dependent activation of the target genes. The CuRE is sufficient for conferring Ni-responsive expression to a reporter gene, which suggests that the system has practical application as a vehicle for inducible gene expression. The inducer can be removed either by replacing the medium or by chelating the inducer with excess EDTA, either of which treatments reverses the activation of the target genes.

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Transcriptome and phytochemical analyses provide new insights into long non-coding RNAs and characteristic secondary metabolites of oolong tea (Camellia sinensis) in solar-withering

10.21203/rs.2.11183/v1 ◽

2019 ◽

Author(s):

Chen Zhu ◽

Shuting Zhang ◽

Haifeng Fu ◽

Chengzhe Zhou ◽

Lan Chen ◽

...

Keyword(s):

Signal Transduction ◽

Secondary Metabolites ◽

Metabolic Pathway ◽

Target Genes ◽

Expression Profiles ◽

Signal Transduction Pathway ◽

Total Flavonoid ◽

Transduction Pathway ◽

Oolong Tea ◽

Non Coding Rnas

Abstract Background Oolong tea, a semi-fermented tea, was deeply loved by consumers. Among tea processing, withering is the first indispensable process for improving the unique flavor. However, the roles of long non-coding RNAs (lncRNAs) and characteristic secondary metabolites in withering of oolong tea remain unknown. Results Using phytochemical analyses, the total flavonoid, total catechins, EGC, CG, GCG, ECG, and EGCG were all present at significantly lower levels in solar-withered leaves (SW) than in fresh leaves (FL) and indoor-withered leaves (IW). However, terpenoid, JA, and MeJA were present at a higher level in SW than FL and IW. By analyzing the transcriptome data, we obtained a total of 32,036 lncRNAs. On the basis of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, flavonoid metabolic pathway, terpenoid metabolic pathway, and JA/MeJA biosynthesis and signal transduction pathway were the representative pathways in this study. And a total of 63 differentially expressed-lncRNAs (DE-lncRNAs) and 23 target genes were identified in the 3 pathways. Analysis of the expression profiles of DE-lncRNAs and their target genes in SW compared with IW, we found that 4 up-regulated genes (FLS, CCR, CAD, and HCT), 7 up-regulated lncRNAs, 4 down-regulated genes (4CL, CHI, F3H, and F3'H), and 3 down-regulated lncRNAs in flavonoid metabolism; 9 up-regulated genes (DXS, CMK, HDS, HDR, AACT, MVK, PMK, GGPPS, and TPS), 3 up-regulated lncRNAs, 6 down-regulated lncRNAs in terpenoid metabolism; 6 up-regulated genes (LOX, AOS, AOC, OPR, ACX, and MFP2), 4 up-regulated lncRNAs, and 3 down-regulated lncRNAs in JA/MeJA biosynthesis and signal transduction pathway. Conclusions These results suggested that the expression of DE-lncRNAs and their targets involved in the 3 pathways maybe related to the low content of total flavonoid, total catechins, EGC, CG, GCG, ECG, and EGCG, and high content of terpenoid in SW. Moreover, solar light, high content of JA and MeJA, and the endogenous target mimics (eTMs) regulatory mechanism in SW were also crucial factors in increasing the terpenoid. These findings provide new insights into the view of "Kàn qīng shài qīng" that the solar-withering is more contribute to the high quality flavor of oolong tea compared to the indoor-withering.

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pygopusencodes a nuclear protein essential for Wingless/Wnt signaling

Development ◽

10.1242/dev.129.17.4089 ◽

2002 ◽

Vol 129 (17) ◽

pp. 4089-4101 ◽

Cited By ~ 2

Author(s):

Tatyana Y. Belenkaya ◽

Chun Han ◽

Henrietta J. Standley ◽

Xinda Lin ◽

Douglas W. Houston ◽

...

Keyword(s):

Signal Transduction ◽

Target Genes ◽

Nuclear Protein ◽

Signal Transduction Pathway ◽

Transduction Pathway ◽

Phd Finger ◽

Nuclear Function ◽

Evolutionarily Conserved ◽

Wnt Signal

The Wingless (Wg)/Wnt signal transduction pathway regulates many developmental processes through a complex of Armadillo(Arm)/β-catenin and the HMG-box transcription factors of the Tcf family. We report the identification of a new component, Pygopus (Pygo), that plays an essential role in the Wg/Wnt signal transduction pathway. We show that Wg signaling is diminished during embryogenesis and imaginal disc development in the absence of pygo activity. Pygo acts downstream or in parallel with Arm to regulate the nuclear function of Arm protein. pygo encodes a novel and evolutionarily conserved nuclear protein bearing a PHD finger that is essential for its activity. We further show that Pygo can form a complex with Arm in vivo and possesses a transcription activation domain(s). Finally, we have isolated a Xenopus homolog of pygo (Xpygo). Depletion of maternal Xpygo by antisense deoxyoligonucleotides leads to ventralized embryonic defects and a reduction of the expression of Wnt target genes. Together, these findings demonstrate that Pygo is an essential component in the Wg/Wnt signal transduction pathway and is likely to act as a transcription co-activator required for the nuclear function of Arm/β-catenin.

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The Dorsal-related immunity factor (Dif) can define the dorsal-ventral axis of polarity in the Drosophila embryo

Development ◽

10.1242/dev.125.11.2159 ◽

1998 ◽

Vol 125 (11) ◽

pp. 2159-2169 ◽

Cited By ~ 2

Author(s):

D. Stein ◽

J.S. Goltz ◽

J. Jurcsak ◽

L. Stevens

Keyword(s):

Signal Transduction ◽

Target Genes ◽

Signal Transduction Pathway ◽

Drosophila Embryo ◽

Transduction Pathway ◽

Homologous Proteins ◽

Helix Loop Helix ◽

Ability To Act ◽

Egg Shell ◽

Drosophila Embryos

In Drosophila embryos, dorsal-ventral polarity is defined by a signal transduction pathway that regulates nuclear import of the Dorsal protein. Dorsal protein's ability to act as a transcriptional activator of some zygotic genes and a repressor of others defines structure along the dorsal-ventral axis. Dorsal is a member of a group of proteins, the Rel-homologous proteins, whose activity is regulated at the level of nuclear localization. Dif, a more recently identified Drosophila Rel-homologue, has been proposed to act as a mediator of the immune response in Drosophila. In an effort to understand the function and regulation of Rel-homologous proteins in Drosophila, we have expressed Dif protein in Drosophila embryos derived from dorsal mutant mothers. We found that the Dif protein was capable of restoring embryonic dorsal-ventral pattern elements and was able to define polarity correctly with respect to the orientation of the egg shell. This, together with the observation that the ability of Dif to restore a dorsal-ventral axis depended on the signal transduction pathway that normally regulates Dorsal, suggests that Dif protein formed a nuclear concentration gradient similar to that seen for Dorsal. By studying the expression of Dorsal target genes we found that Dif could activate the zygotic genes that Dorsal activates and repress the genes repressed by Dorsal. Differences in the expression of these target genes, as well as the results from interaction studies carried out in yeast, suggest that Dif is not capable of synergizing with the basic helix-loop-helix transcription factors with which Dorsal normally interacts, and thereby lacks an important component of Dorsal-mediated pattern formation.

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An absolute requirement for Cubitus interruptus in Hedgehog signaling

Development ◽

10.1242/dev.128.5.733 ◽

2001 ◽

Vol 128 (5) ◽

pp. 733-742 ◽

Cited By ~ 4

Author(s):

N. Methot ◽

K. Basler

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Hedgehog Signaling ◽

Target Gene ◽

Target Genes ◽

Signal Transduction Pathway ◽

Transduction Pathway ◽

Cubitus Interruptus ◽

Target Gene Expression ◽

Hh Signaling

Hedgehog (Hh) proteins play diverse organizing roles in animal development by regulating gene expression in responding cells. Several components of the Hh signal transduction pathway have been identified, yet their precise role in mediating the various outputs of the pathway is still poorly understood. The Gli homolog Cubitus interruptus (Ci) is involved in controlling the transcription of Drosophila Hh target genes and thus represents the most downstream component known in this pathway. We address the question of whether the Hh pathway is distally branched or, in other words, whether the regulation of Ci activity is the sole output of Hh signaling. Putative Ci-independent branches of Hh signaling are explored by analyzing the behavior of cells that lack Ci but have undergone maximal activation of the Hh transduction pathway due to the removal of Patched (Ptc). The analysis of target gene expression and morphogenetic read-outs of Hh in embryonic, larval and adult stages indicates that Ci is absolutely required for all examined aspects of Hh outputs. We interpret this as evidence against the existence of Ci-independent branches in the Hh signal transduction pathway and propose that most cases of apparent Ci/Gli-independent Hh output can be attributed to the derepression of target gene expression in the absence of Ci/Gli repressor function.

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The Mechanism of MAPK Signal Transduction Pathway Involved with Electroacupuncture Treatment for Different Diseases

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2019/8138017 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Weibin Du ◽

Huahui Hu ◽

Jiangsong Zhang ◽

Guanai Bao ◽

Rongliang Chen ◽

...

Keyword(s):

Signal Transduction ◽

Electrical Stimulation ◽

Molecular Mechanisms ◽

Signal Transduction Pathway ◽

Cerebrovascular Diseases ◽

Mitogen Activated Protein Kinase ◽

Signal Pathways ◽

Transduction Pathway ◽

Analgesic Effects ◽

Electroacupuncture Treatment

The mitogen-activated protein kinase (MAPK) signal transduction pathway plays an important role in the regulation of various diseases, such as cardiovascular and cerebrovascular diseases, and takes part in anti-inflammatory effects, analgesic effects, protection against injury, and maintenance of gastrointestinal functions. Electroacupuncture therapy is an external therapy used in traditional Chinese medicine. By adding external electrical stimulation to traditional acupuncture, the stimulus gets doubled and the therapeutic efficacy gets enhanced accordingly. It combines the benefits of both acupuncture and electrical stimulation. In recent years, some studies have explored the molecular mechanisms of MAPK signal pathways involved with electroacupuncture treatment. Based on these recent studies, this article summarizes the mechanisms of MAPK signal transduction pathways involved with electroacupuncture treatment. This adds great value to the studies of molecular mechanisms of electroacupuncture treatment and also provides an effective reference for its clinical use.

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A Mutation in an HSP90 Gene Affects the Sexual Cycle and Suppresses Vegetative Incompatibility in the Fungus Podospora anserina

Genetics ◽

10.1093/genetics/147.2.581 ◽

1997 ◽

Vol 147 (2) ◽

pp. 581-588

Author(s):

Gabriel Loubradou ◽

Joel Bégueret ◽

Béatrice Turcq

Keyword(s):

Signal Transduction ◽

Molecular Mechanisms ◽

Biological Function ◽

Molecular Level ◽

Signal Transduction Pathway ◽

Podospora Anserina ◽

Sexual Cycle ◽

Transduction Pathway ◽

Vegetative Incompatibility ◽

Developmental Defects

Vegetative incompatibility is widespread in fungi but its molecular mechanism and biological function are still poorly understood. A way to study vegetative incompatibility is to investigate the function of genes whose mutations suppress this phenomenon. In Podospora anserina, these genes are known as mod genes. In addition to suppressing vegetative incompatibility, mod mutations cause some developmental defects. This suggests that the molecular mechanisms of vegetative incompatibility and development pathways are interconnected. The mod-E1 mutation was isolated as a suppressor of the developmental defects of the mod-D2 strain. We show here that mod-E1 also partially suppresses vegetative incompatibility, strengthening the link between development and vegetative incompatibility. mod-E1 is the first suppressor of vegetative incompatibility characterized at the molecular level. It encodes a member of the Hsp90 family, suggesting that development and vegetative incompatibility use common steps of a signal transduction pathway. The involvement of mod-E in the sexual cycle has also been further investigated.

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