Identification of genes encoding receptor-like protein kinases as possible targets of pathogen- and salicylic acid-induced WRKY DNA-binding proteins in Arabidopsis

2000 ◽  
Vol 24 (6) ◽  
pp. 837-847 ◽  
Author(s):  
Liqun Du ◽  
Zhixiang Chen
Keyword(s):  
Salicylic Acid ◽  
Dna Binding ◽  
Protein Kinases ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Genes Encoding

scholarly journals Off-Target Gene Regulation Mediated by Transcriptional Repressors of Antimicrobial Efflux Pump Genes in Neisseria gonorrhoeae

2011 ◽  
Vol 55 (6) ◽  
pp. 2559-2565 ◽  
Author(s):  
Paul J. T. Johnson ◽  
Virginia A. Stringer ◽  
William M. Shafer
Keyword(s):  
Dna Binding ◽  
Neisseria Gonorrhoeae ◽  
Binding Proteins ◽  
Efflux Pump ◽  
Dna Binding Proteins ◽  
Transcriptional Repressors ◽  
Content Type ◽  
Genes Encoding ◽  
Encoding Gene ◽  
Microarray Studies

ABSTRACTDNA-binding proteins that control expression of drug efflux pump genes have been termed “local regulators” as their encoding gene is often located adjacent to the gene(s) that they regulate. However, results from recent studies indicate that they can control genes outside efflux pump-encoding loci, which we term as being “off target.” For example, the MtrR repressor was initially recognized for its ability to repress transcription of themtrCDE-encoded efflux pump operon in the strict human pathogenNeisseria gonorrhoeae, but recent results from genetic and microarray studies have shown that it can control expression of nearly 70 genes scattered throughout the chromosome. One of the off-target MtrR-repressed genes isglnA, which encodes glutamine synthetase. Herein, we confirm the capacity of MtrR to repressglnAexpression and provide evidence that such repression is due to its ability to negatively influence the binding of a second DNA-binding protein (FarR), which activatesglnA. FarR was previously recognized as a transcriptional repressor of thefarAB-encoded efflux pump operon. Thus, two DNA-binding proteins previously characterized as repressors of genes encoding efflux pumps that contribute to gonococcal resistance to antimicrobials can act in an opposing manner to modulate expression of a gene involved in basic metabolism.

Experimental Strategies for Cloning or Identifying Genes Encoding DNA-Binding Proteins

2012 ◽  
Vol 2012 (2) ◽  
pp. pdb.top067900-pdb.top067900
Author(s):  
M. F. Carey ◽  
C. L. Peterson ◽  
S. T. Smale
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Genes Encoding ◽  
Experimental Strategies

scholarly journals Genetic selection for genes encoding sequence-specific DNA-binding proteins.

1989 ◽  
Vol 86 (10) ◽  
pp. 3689-3693 ◽  
Author(s):  
S. J. Elledge ◽  
P. Sugiono ◽  
L. Guarente ◽  
R. W. Davis
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Genetic Selection ◽  
Dna Binding Proteins ◽  
Genes Encoding ◽  
Selection For

DBP-PSSM: Combination of evolutionary profiles with the XGBoost algorithm to improve the identification of DNA-binding proteins

2020 ◽  
Vol 23 ◽  
Author(s):  
Yanping Zhang ◽  
Pengcheng Chen ◽  
Ya Gao ◽  
Jianwei Ni ◽  
Xiaosheng Wang
Keyword(s):  
Logistic Regression ◽  
Protein Structure ◽  
Dna Binding ◽  
Molecular Biology ◽  
Binding Proteins ◽  
Protein Sequences ◽  
Low Complexity ◽  
Dna Binding Proteins ◽  
Position Information ◽  
Position Representation

Aim and Objective:: Given the rapidly increasing number of molecular biology data available, computational methods of low complexity are necessary to infer protein structure, function, and evolution. Method:: In the work, we proposed a novel mthod, FermatS, which based on the global position information and local position representation from the curve and normalized moments of inertia, respectively, to extract features information of protein sequences. Furthermore, we use the generated features by FermatS method to analyze the similarity/dissimilarity of nine ND5 proteins and establish the prediction model of DNA-binding proteins based on logistic regression with 5-fold crossvalidation. Results:: In the similarity/dissimilarity analysis of nine ND5 proteins, the results are consistent with evolutionary theory. Moreover, this method can effectively predict the DNA-binding proteins in realistic situations. Conclusion:: The findings demonstrate that the proposed method is effective for comparing, recognizing and predicting protein sequences. The main code and datasets can download from https://github.com/GaoYa1122/FermatS.

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