枯草芽孢杆菌GntR型LutR转录因子的计算机表征及比较分析

Q3 Agricultural and Biological Sciences Eurasian Journal of Biosciences Pub Date : 2014-07-01 DOI:10.5053/EJOBIOS.2014.8.0.2
M. Avci, Ç. Yamaner, M. Ayvaz, A. Yazgan-Karatas
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引用次数: 3

摘要

背景:gntr型转录因子LutR(以前称为YvfI)作为过渡状态调节剂,控制枯草芽孢杆菌细胞从指数生长过渡到固定阶段的适应。材料和方法:在本研究中,我们评估了NCBI数据库中来自不同细菌物种的30种LutR蛋白。通过理化分析、结构域分析和系统发育树构建,我们确定了这30个LutR蛋白之间的相似性和差异性。此外,仅对枯草芽孢杆菌168 LutR的引物结构与众所周知的hth型转录因子FadR (PDB ID: 1 HW1,1 HW2,1 HT9)和YvoA (PDB ID: 2WV0)的序列和三维构象情况进行了PyMOL比较。结果:这些分析表明,LutR的dna识别和dna结合关键残基高度保守,构象与FadR和YvoA相同。LutR中第二螺旋的序列(15-SVQALAESF-23)似乎对DNA结合很重要,而Q17-R27-Q47残基可能对DNA识别至关重要。在这里,我们详细描述了枯草芽孢杆菌LutR与来自不同细菌种类的其他LutR蛋白以及其他hth型转录因子之间的异同。结论:这些结果提供了科学基础,可用于先进的硅分析、同源性建模和体外研究,包括dna -蛋白质相互作用分析,如ChIP和EMSA方法。
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In silico characterization and comparative analysis of Bacillus subtilis GntR type LutR transcription factor
Background: The GntR-type transcriptional factor LutR (formerly YvfI) behaves as a transition state regulator, governing adaptations of Bacillus subtilis cells to the transition from exponential growth to stationary phase. Material and Methods: In this study, we evaluated a total of 30 LutR proteins from different bacterial species that were available in the NCBI database. By performing the physicochemical analyses, domain analysis, and phylogenetic tree construction, we identified some similarities and differences among these 30 LutR proteins. Furthermore, only the primer structure of Bacillus subtilis 168 LutR was compared with the sequences and 3D conformational situations of the well-known HTH-type transcriptional factors FadR (PDB ID: 1 HW1,1 HW2,1 HT9) and YvoA (PDB ID: 2WV0) using PyMOL. Results: These analyses revealed that the critical residues for DNA-recognition and DNA-binding of LutR are highly conserved and conformationally correspond to the same positions as those in FadR and YvoA. The sequence (15-SVQALAESF-23) of the second helix in LutR seems to be important for DNA-binding, while the Q17-R27-Q47 residues might be critical for DNA recognition. Here, we provide a detailed description of the similarities and differences between B. subtilis LutR and both the other LutR proteins from different bacterial species and other HTH-type transcriptional factors. Conclusions: These results provide a scientific groundworkbase and can be used for advanced in silico analysis, homology modelling, and in vitro studies, including DNA-protein interaction analysis, such as ChIP and EMSA methods.
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来源期刊
Eurasian Journal of Biosciences
Eurasian Journal of Biosciences Agricultural and Biological Sciences-Agricultural and Biological Sciences (all)
CiteScore
1.20
自引率
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期刊介绍: EurAsian Journal of BioSciences (Abbrev. Eurasia J Biosci or EJOBIOS) is an international, refereed electronic journal. It publishes the results of original research in the field of biological sciences restricted tomorphology, physiology, genetics, taxonomy, ecology and biogeography of both prokaryotic and eucaryotic organisms. The journal encourages submission of manuscripts dealing with plant biology, animal biology, plant physiology, microbiology, hydrobiology, ecology and environmental science, ethnobiology, biodiversity and conservation biology. EurAsian Journal of BioSciences publishes original articles in the following areas: -Agriculture, Fisheries & Food -Anatomy & Morphology -Behavioural Sciences -Biology, Biochemistry and Biotechnology -Biophysics -Biology Education -Cellular Biology and Anatomical Sciences -Ecology, Evolution & Environment -Entomology -Forestry -General Biology -Genetics & Heredity -Life Sciences - Other topics -Microbiology and Immunology -Molecular Biology -Mycology -Palaeontology -Parasitology -Pharmacology & Pharmacy -Physiology and Related Sciences -Plant Sciences -Toxicology -Veterinary Sciences -Virology -Zoology
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