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
{"title":"枯草芽孢杆菌GntR型LutR转录因子的计算机表征及比较分析","authors":"M. Avci, Ç. Yamaner, M. Ayvaz, A. Yazgan-Karatas","doi":"10.5053/EJOBIOS.2014.8.0.2","DOIUrl":null,"url":null,"abstract":"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. \nMaterial 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 \nHTH-type transcriptional factors FadR (PDB ID: 1 HW1,1 HW2,1 HT9) and YvoA (PDB ID: 2WV0) using PyMOL. \nResults: 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. \nConclusions: 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.","PeriodicalId":11848,"journal":{"name":"Eurasian Journal of Biosciences","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5053/EJOBIOS.2014.8.0.2","citationCount":"3","resultStr":"{\"title\":\"In silico characterization and comparative analysis of Bacillus subtilis GntR type LutR transcription factor\",\"authors\":\"M. Avci, Ç. Yamaner, M. Ayvaz, A. Yazgan-Karatas\",\"doi\":\"10.5053/EJOBIOS.2014.8.0.2\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"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. \\nMaterial 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 \\nHTH-type transcriptional factors FadR (PDB ID: 1 HW1,1 HW2,1 HT9) and YvoA (PDB ID: 2WV0) using PyMOL. \\nResults: 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. \\nConclusions: 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.\",\"PeriodicalId\":11848,\"journal\":{\"name\":\"Eurasian Journal of Biosciences\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2014-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.5053/EJOBIOS.2014.8.0.2\",\"citationCount\":\"3\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Eurasian Journal of Biosciences\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.5053/EJOBIOS.2014.8.0.2\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Eurasian Journal of Biosciences","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.5053/EJOBIOS.2014.8.0.2","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
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.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
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
0.00%
发文量
0
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
期刊最新文献
Clean and Healthy Lifestyle Behaviors and Healthy Housing Influenced the Incident of Acute Respiratory Infection in Childhood Sustainable strategy of charcoal (Panglong Arang) management in the Bengkalis Regency Histological evidence of the heart and ovarian vessels in the short mackerel, Rastrelliger brachysoma An investigation on determining heavy metal accumulation in plants growing at Kumalar Mountain in Turkey Diversity and distribution of macrofungi in the Eastern Himalayan ecosystem
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1