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Weeramange C, Menjivar C, O'Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. J Biol Chem 2024; 300:107352. [PMID: 38723750 PMCID: PMC11157272 DOI: 10.1016/j.jbc.2024.107352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/21/2024] Open
Abstract
In Escherichia coli, the master transcription regulator catabolite repressor activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli's central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
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Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Pierce T O'Neil
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Kelly S Harrison
- The Department of Molecular Biosciences, The University of Kansas - Lawrence, Lawrence, Kansas, USA
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cole L Bird
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Aron W Fenton
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - P Scott Hefty
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Jeffrey L Bose
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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Weeramange C, Menjivar C, O’Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571569. [PMID: 38168282 PMCID: PMC10760178 DOI: 10.1101/2023.12.14.571569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In Escherichia coli, the master transcription regulator Catabolite Repressor Activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. The ΔfruK strain also alters biofilm formation. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
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Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, 3901 Rainbow Blvd, MSN 3029, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Pierce T. O’Neil
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Samir El Qaidi
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Kelly S. Harrison
- The Department of Molecular Biosciences, 2034 Haworth Hall, 1200 Sunnyside Avenue, The University of Kansas – Lawrence, Lawrence, Kansas, USA 66045
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Cole L. Bird
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Philip R. Hardwidge
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Aron W. Fenton
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - P. Scott Hefty
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Jeffrey L. Bose
- The Department of Microbiology, Molecular Genetics and Immunology, 3901 Rainbow Blvd, MSN 3029, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
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Neetu N, Mahto JK, Sharma M, Katiki M, Dhaka P, Roy P, Tomar S, Narayan A, Yernool D, Kumar P. Sulisobenzone is a potent inhibitor of the global transcription factor Cra. J Struct Biol 2023; 215:108034. [PMID: 37805153 DOI: 10.1016/j.jsb.2023.108034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Transcription is carried out by the RNA polymerase and is regulated through a series of interactions with transcription factors. Catabolite activator repressor (Cra), a LacI family transcription factor regulates the virulence gene expression in Enterohaemorrhagic Escherichia coli (EHEC) and thus is a promising drug target for the discovery of antivirulence molecules. Here, we report the crystal structure of the effector molecule binding domain of Cra from E. coli (EcCra) in complex with HEPES molecule. Based on the EcCra-HEPES complex structure, ligand screening was performed that identified sulisobenzone as an potential inhibitor of EcCra. The electrophoretic mobility shift assay (EMSA) and in vitro transcription assay validated the sulisobenzone binding to EcCra. Moreover, the isothermal titration calorimetry (ITC) experiments demonstrated a 40-fold higher binding affinity of sulisobenzone (KD 360 nM) compared to the HEPES molecule. Finally, the sulisobenzone bound EcCra complex crystal structure was determined to elucidate the binding mechanism of sulisobenzone to the effector binding pocket of EcCra. Together, this study suggests that sulisobenzone may be a promising candidate that can be studied and developed as an effective antivirulence agent against EHEC.
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Affiliation(s)
- Neetu Neetu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Jai Krishna Mahto
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Monica Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Madhusudhanarao Katiki
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Preeti Dhaka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Partha Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Anoop Narayan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dinesh Yernool
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.
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Yoon CK, Lee SH, Zhang J, Lee HY, Kim MK, Seok YJ. HPr prevents FruR-mediated facilitation of RNA polymerase binding to the fru promoter in Vibrio cholerae. Nucleic Acids Res 2023; 51:5432-5448. [PMID: 36987873 PMCID: PMC10287919 DOI: 10.1093/nar/gkad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/17/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Phosphorylation state-dependent interactions of the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) components with transcription factors play a key role in carbon catabolite repression (CCR) by glucose in bacteria. Glucose inhibits the PTS-dependent transport of fructose and is preferred over fructose in Vibrio cholerae, but the mechanism is unknown. We have recently shown that, contrary to Escherichia coli, the fructose-dependent transcriptional regulator FruR acts as an activator of the fru operon in V. cholerae and binding of the FruR-fructose 1-phosphate (F1P) complex to an operator facilitates RNA polymerase (RNAP) binding to the fru promoter. Here we show that, in the presence of glucose, dephosphorylated HPr, a general PTS component, binds to FruR. Whereas HPr does not affect DNA-binding affinity of FruR, regardless of the presence of F1P, it prevents the FruR-F1P complex from facilitating the binding of RNAP to the fru promoter. Structural and biochemical analyses of the FruR-HPr complex identify key residues responsible for the V. cholerae-specific FruR-HPr interaction not observed in E. coli. Finally, we reveal how the dephosphorylated HPr interacts with FruR in V. cholerae, whereas the phosphorylated HPr binds to CcpA, which is a global regulator of CCR in Bacillus subtilis and shows structural similarity to FruR.
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Affiliation(s)
- Chang-Kyu Yoon
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Seung-Hwan Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
| | - Jing Zhang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Hye-Young Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Science, Seoul National University, Seoul, 08826, Korea
| | - Min-Kyu Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, Korea
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