气候变化领域集成服务门户(CCPortal): Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa

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DOI	10.1073/pnas.1708842114
	Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa
	Ortega D.R.; Fleetwood A.D.; Krell T.; Harwood C.S.; Jensen G.J.; Zhulin I.B.
发表日期	2017
ISSN	0027-8424
起始页码	12809
结束页码	12814
卷号	114 期号:48
英文摘要	In contrast to Escherichia coli, a model organism for chemotaxis that has 5 chemoreceptors and a single chemosensory pathway, Pseudomonas aeruginosa PAO1 has a much more complex chemosensory network, which consists of 26 chemoreceptors feeding into four chemosensory pathways. While several chemoreceptors were rigorously linked to specific pathways in a series of experimental studies, for most of them this information is not available. Thus, we addressed the problem computationally. Protein–protein interaction network prediction, coexpression data mining, and phylogenetic profiling all produced incomplete and uncertain assignments of chemoreceptors to pathways. However, comparative sequence analysis specifically targeting chemoreceptor regions involved in pathway interactions revealed conserved sequence patterns that enabled us to unambiguously link all 26 chemoreceptors to four pathways. Placing computational evidence in the context of experimental data allowed us to conclude that three chemosensory pathways in P. aeruginosa utilize one chemoreceptor per pathway, whereas the fourth pathway, which is the main system controlling chemotaxis, utilizes the other 23 chemoreceptors. Our results show that while only a very few amino acid positions in receptors, kinases, and adaptors determine their pathway specificity, assigning receptors to pathways computationally is possible. This requires substantial knowledge about interacting partners on a molecular level and focusing comparative sequence analysis on the pathway-specific regions. This general principle should be applicable to resolving many other receptor–pathway interactions. © 2017, National Academy of Sciences. All rights reserved.
英文关键词	Chemotaxis; Computational prediction; Protein–protein interactions; Signal transduction
语种	英语
scopus关键词	Article; chemoreceptor; chemotaxis; conserved sequence; controlled study; data mining; nonhuman; phylogeny; prediction; priority journal; protein protein interaction; Pseudomonas aeruginosa; sequence analysis; alpha helix; amino acid sequence; beta sheet; binding site; biology; chemistry; classification; gene expression regulation; gene regulatory network; genetics; metabolism; procedures; protein analysis; protein domain; Pseudomonas aeruginosa; sequence alignment; sequence homology; signal transduction; statistics and numerical data; bacterial protein; cell surface receptor; chemotactic factor; ligand; protein binding; Amino Acid Sequence; Bacterial Proteins; Binding Sites; Chemotactic Factors; Chemotaxis; Computational Biology; Data Mining; Gene Expression Regulation, Bacterial; Gene Regulatory Networks; Ligands; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Pseudomonas aeruginosa; Receptors, Cell Surface; Sequence Alignment; Sequence Homology, Amino Acid; Signal Transduction
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/160571
作者单位	Ortega, D.R., Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Fleetwood, A.D., Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States, Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States, College of Medicine, University of Tennessee Health Sciences Center, Memphis, TN 38163, United States; Krell, T., Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, 18008, Spain; Harwood, C.S., Department of Microbiology, University of Washington, Seattle, WA 98195, United States; Jensen, G.J., Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, United States; Zhulin, I.B., Computational Sciences and Engineering D...
推荐引用方式 GB/T 7714	Ortega D.R.,Fleetwood A.D.,Krell T.,et al. Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa[J],2017,114(48).
APA	Ortega D.R.,Fleetwood A.D.,Krell T.,Harwood C.S.,Jensen G.J.,&Zhulin I.B..(2017).Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa.Proceedings of the National Academy of Sciences of the United States of America,114(48).
MLA	Ortega D.R.,et al."Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa".Proceedings of the National Academy of Sciences of the United States of America 114.48(2017).