Coordinated regulation of acid resistance in Escherichia coli.

Autor:	Aquino P; Department of Biomedical Engineering, Boston University, Boston, USA.; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Honda B; Department of Biomedical Engineering, Boston University, Boston, USA., Jaini S; Department of Biomedical Engineering, Boston University, Boston, USA., Lyubetskaya A; Bioinformatics program, Boston University, Boston, USA., Hosur K; Department of Biomedical Engineering, Boston University, Boston, USA.; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Chiu JG; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Ekladious I; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Hu D; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Jin L; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Sayeg MK; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Stettner AI; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Wang J; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Wong BG; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Wong WS; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Alexander SL; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Ba C; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Bensussen SI; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Bernstein DB; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Braff D; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Cha S; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Cheng DI; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Cho JH; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Chou K; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Chuang J; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Gastler DE; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Grasso DJ; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Greifenberger JS; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Guo C; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Hawes AK; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Israni DV; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Jain SR; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Kim J; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Lei J; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Li H; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Li D; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Li Q; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Mancuso CP; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Mao N; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Masud SF; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Meisel CL; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Mi J; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Nykyforchyn CS; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Park M; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Peterson HM; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Ramirez AK; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Reynolds DS; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Rim NG; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Saffie JC; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Su H; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Su WR; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Su Y; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Sun M; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Thommes MM; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Tu T; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Varongchayakul N; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Wagner TE; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Weinberg BH; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Yang R; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Yaroslavsky A; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Yoon C; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Zhao Y; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Zollinger AJ; BE605 Course, Biomedical Engineering, Boston University, Boston, USA., Stringer AM; Wadsworth Center, New York State Department of Health, Albany, NY, USA., Foster JW; Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL, 36688, USA., Wade J; Wadsworth Center, New York State Department of Health, Albany, NY, USA.; Department of Biomedical Sciences, University at Albany, Albany, NY, USA., Raman S; Department of Microbiology and Immunology, University of South Alabama College of Medicine, Mobile, AL, 36688, USA., Broude N; Department of Biomedical Engineering, Boston University, Boston, USA., Wong WW; Department of Biomedical Engineering, Boston University, Boston, USA., Galagan JE; Department of Biomedical Engineering, Boston University, Boston, USA. jgalag@bu.edu.; Bioinformatics program, Boston University, Boston, USA. jgalag@bu.edu.; National Emerging Infectious Diseases Laboratory, Boston University, Boston, USA. jgalag@bu.edu.
Jazyk:	angličtina
Zdroj:	BMC systems biology [BMC Syst Biol] 2017 Jan 06; Vol. 11 (1), pp. 1. Date of Electronic Publication: 2017 Jan 06.
DOI:	10.1186/s12918-016-0376-y
Abstrakt:	Background: Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored. Results: We utilized a combination of ChIP-Seq and gene expression analysis to experimentally map the regulatory interactions of four TFs: nac, ntrC, ompR, and csiR. Our data identified all previously in vivo confirmed direct interactions and revealed several others previously inferred from gene expression data. Our data demonstrate that nac and csiR directly modulate AR, and leads to a regulatory network model in which all four TFs participate in coordinating acid resistance, glutamate metabolism, and nitrogen metabolism. This model predicts a novel mechanism for AR1 by which the decarboxylation enzymes of AR2 are used with internally derived glutamate. This hypothesis makes several testable predictions that we confirmed experimentally. Conclusions: Our data suggest that the regulatory network underlying AR is complex and deeply interconnected with the regulation of GABA and glutamate metabolism, nitrogen metabolism. These connections underlie and experimentally validated model of AR1 in which the decarboxylation enzymes of AR2 are used with internally derived glutamate.
Databáze:	MEDLINE
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