PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation
Abstract
Here, the Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of gamma-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5'-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the "active site" in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic.-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, (S)-4-amino-5-fluoropentanoic acid (AFPA), was used as a molecular probe to examine the reactivity of PLP in both GabR and a homologous aspartate aminotransferase (Asp-AT) from Escherichia coli as a control. A comparison between the structures of the Eb/O-PLP-AFPA complex and Asp-AT-PLP-AFPA complex revealed that GabR is incapable of facilitating further steps of the transamination reaction after the formation of the external aldimine. Results of in vitro and in vivo assays using full-length GabR support the conclusion that AFPA is an agonistic ligand capable of triggering GabR-mediated transcription activation via formation of an external aldimine with PLP.
- Authors:
-
- Loyola Univ. Chicago, Chicago, IL (United States); Weill Cornell Medical College, New York, NY (United States)
- Argonne National Lab. (ANL), Lemont, IL (United States)
- Tufts Univ. School of Medicine, Boston, MA (United States)
- Northwestern Univ., Evanston, IL (United States)
- Northwestern Univ., Evanston, IL (United States); Univ. of Mississippi School of Pharmacy, University, MS (United States)
- Brandeis Univ., Waltham, MA (United States); Columbia Univ., New York, NY (United States)
- Loyola Univ. Chicago, Chicago, IL (United States)
- Brandeis Univ., Waltham, MA (United States); Weill Cornell Medical College, New York, NY (United States)
- Brandeis Univ., Waltham, MA (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1373733
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Volume: 114; Journal Issue: 15; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences, Washington, DC (United States)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; MocR; GabR; PLP; external aldimine; transcription activation
Citation Formats
Wu, Rui, Sanishvili, Ruslan, Belitsky, Boris R., Juncosa, Jose I., Le, Hoang V., Lehrer, Helaina J. S., Farley, Michael, Silverman, Richard B., Petsko, Gregory A., Ringe, Dagmar, and Liu, Dali. PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation. United States: N. p., 2017.
Web. doi:10.1073/pnas.1703019114.
Wu, Rui, Sanishvili, Ruslan, Belitsky, Boris R., Juncosa, Jose I., Le, Hoang V., Lehrer, Helaina J. S., Farley, Michael, Silverman, Richard B., Petsko, Gregory A., Ringe, Dagmar, & Liu, Dali. PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation. United States. doi:10.1073/pnas.1703019114.
Wu, Rui, Sanishvili, Ruslan, Belitsky, Boris R., Juncosa, Jose I., Le, Hoang V., Lehrer, Helaina J. S., Farley, Michael, Silverman, Richard B., Petsko, Gregory A., Ringe, Dagmar, and Liu, Dali. Mon .
"PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation". United States. doi:10.1073/pnas.1703019114. https://www.osti.gov/servlets/purl/1373733.
@article{osti_1373733,
title = {PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation},
author = {Wu, Rui and Sanishvili, Ruslan and Belitsky, Boris R. and Juncosa, Jose I. and Le, Hoang V. and Lehrer, Helaina J. S. and Farley, Michael and Silverman, Richard B. and Petsko, Gregory A. and Ringe, Dagmar and Liu, Dali},
abstractNote = {Here, the Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of gamma-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5'-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the "active site" in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic.-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, (S)-4-amino-5-fluoropentanoic acid (AFPA), was used as a molecular probe to examine the reactivity of PLP in both GabR and a homologous aspartate aminotransferase (Asp-AT) from Escherichia coli as a control. A comparison between the structures of the Eb/O-PLP-AFPA complex and Asp-AT-PLP-AFPA complex revealed that GabR is incapable of facilitating further steps of the transamination reaction after the formation of the external aldimine. Results of in vitro and in vivo assays using full-length GabR support the conclusion that AFPA is an agonistic ligand capable of triggering GabR-mediated transcription activation via formation of an external aldimine with PLP.},
doi = {10.1073/pnas.1703019114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 15,
volume = 114,
place = {United States},
year = {2017},
month = {3}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 4 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Molecular mechanism of PdxR - a transcriptional activator involved in the regulation of vitamin B 6 biosynthesis in the probiotic bacterium Bacillus clausii
journal, June 2015
- Tramonti, Angela; Fiascarelli, Alessio; Milano, Teresa
- FEBS Journal, Vol. 282, Issue 15
A new member of MocR/GabR-type PLP-binding regulator of d -alanyl- d -alanine ligase in Brevibacillus brevis
journal, September 2015
- Takenaka, Takashi; Ito, Tomokazu; Miyahara, Ikuko
- FEBS Journal, Vol. 282, Issue 21
Chiral Discrimination among Aminotransferases: Inactivation by 4-Amino-4,5-dihydrothiophenecarboxylic Acid
journal, April 2010
- Lepore, Bryan W.; Liu, Dali; Peng, Ying
- Biochemistry, Vol. 49, Issue 14
Role of PdxR in the activation of vitamin B 6 biosynthesis in L isteria monocytogenes : Regulation of vitamin B
journal, May 2014
- Belitsky, Boris R.
- Molecular Microbiology, Vol. 92, Issue 5
GabR, a member of a novel protein family, regulates the utilization of gamma-aminobutyrate in Bacillus subtilis
journal, July 2002
- Belitsky, Boris R.; Sonenshein, Abraham L.
- Molecular Microbiology, Vol. 45, Issue 2
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997
- Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
Bacillus subtilis GabR, a Protein with DNA-binding and Aminotransferase Domains, is a PLP-dependent Transcriptional Regulator
journal, July 2004
- Belitsky, Boris R.
- Journal of Molecular Biology, Vol. 340, Issue 4
The GntR-Like Regulator TauR Activates Expression of Taurine Utilization Genes in Rhodobacter capsulatus
journal, November 2007
- Wiethaus, J.; Schubert, B.; Pfander, Y.
- Journal of Bacteriology, Vol. 190, Issue 2
Genomic distribution and heterogeneity of MocR-like transcriptional factors containing a domain belonging to the superfamily of the pyridoxal-5′-phosphate dependent enzymes of fold type I
journal, November 2011
- Bramucci, E.; Milano, T.; Pascarella, S.
- Biochemical and Biophysical Research Communications, Vol. 415, Issue 1
Coot model-building tools for molecular graphics
journal, November 2004
- Emsley, Paul; Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
Molecular and genetic characterization of the rhizopine catabolism (mocABRC) genes of Rhizobium meliloti L5-30
journal, January 1994
- Rossbach, Silvia; Kulpa, Deanna A.; Rossbach, Uwe
- Molecular and General Genetics MGG, Vol. 245, Issue 1
X-Ray Crystallographic Study of Pyridoxamine 5'-Phosphate-Type Aspartate Aminotransferases from Escherichia coli in Three Forms1
journal, November 1994
- Miyahara, Ikuko; Hirotsu, Ken; Hayashi, Hideyuki
- The Journal of Biochemistry, Vol. 116, Issue 5
Mechanism of Inactivation of Escherichia coli Aspartate Aminotransferase by ( S )-4-Amino-4,5-dihydro-2-furancarboxylic Acid,
journal, December 2010
- Liu, Dali; Pozharski, Edwin; Fu, Mengmeng
- Biochemistry, Vol. 49, Issue 49
Crystal Structures of Aspartate Aminotransferase Reconstituted with 1-Deazapyridoxal 5′-Phosphate: Internal Aldimine and Stable l -Aspartate External Aldimine
journal, July 2011
- Griswold, Wait R.; Fisher, Andrew J.; Toney, Michael D.
- Biochemistry, Vol. 50, Issue 26
Activation of gab cluster transcription in Bacillus thuringiensis by γ-aminobutyric acid or succinic semialdehyde is mediated by the Sigma 54-dependent transcriptional activator GabR
journal, December 2014
- Peng, Qi; Yang, Min; Wang, Wei
- BMC Microbiology, Vol. 14, Issue 1
Positive transcriptional control of the pyridoxal phosphate biosynthesis genes pdxST by the MocR-type regulator PdxR of Corynebacterium glutamicum ATCC 13032
journal, September 2010
- Jochmann, N.; Gotker, S.; Tauch, A.
- Microbiology, Vol. 157, Issue 1
Structures of γ-Aminobutyric Acid (GABA) Aminotransferase, a Pyridoxal 5′-Phosphate, and [2Fe-2S] Cluster-containing Enzyme, Complexed with γ-Ethynyl-GABA and with the Antiepilepsy Drug Vigabatrin
journal, October 2003
- Storici, Paola; De Biase, Daniela; Bossa, Francesco
- Journal of Biological Chemistry, Vol. 279, Issue 1
Ground-State Electronic Destabilization via Hyperconjugation in Aspartate Aminotransferase
journal, May 2012
- Griswold, Wait R.; Castro, Joan Nieto; Fisher, Andrew J.
- Journal of the American Chemical Society, Vol. 134, Issue 20
Crystal Structures of Unbound and Aminooxyacetate-Bound Escherichia coli γ-Aminobutyrate Aminotransferase †
journal, August 2004
- Liu, Wenshe; Peterson, Peter E.; Carter, Richard J.
- Biochemistry, Vol. 43, Issue 34
A new family of bacterial regulatory proteins
journal, April 1991
- Haydon, David J.; Guest, John R.
- FEMS Microbiology Letters, Vol. 79, Issue 2-3
Pyridoxal Phosphate Enzymes: Mechanistic, Structural, and Evolutionary Considerations
journal, June 2004
- Eliot, Andrew C.; Kirsch, Jack F.
- Annual Review of Biochemistry, Vol. 73, Issue 1
PHENIX : building new software for automated crystallographic structure determination
journal, October 2002
- Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei
- Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11
Kinetic and Crystallographic Analysis of Active Site Mutants of Escherichia coli γ-Aminobutyrate Aminotransferase †
journal, March 2005
- Liu, Wenshe; Peterson, Peter E.; Langston, James A.
- Biochemistry, Vol. 44, Issue 8
The Vitamin B6 Biosynthesis Pathway in Streptococcus pneumoniae Is Controlled by Pyridoxal 5'-Phosphate and the Transcription Factor PdxR and Has an Impact on Ear Infection
journal, March 2013
- El Qaidi, S.; Yang, J.; Zhang, J. -R.
- Journal of Bacteriology, Vol. 195, Issue 10
Insight into the induction mechanism of the GntR/HutC bacterial transcription regulator YvoA
journal, January 2010
- Resch, Marcus; Schiltz, Emile; Titgemeyer, Fritz
- Nucleic Acids Research, Vol. 38, Issue 7
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995
- Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
- Journal of Biomolecular NMR, Vol. 6, Issue 3
Mechanism of inactivation of .gamma.-aminobutyric acid-.alpha.-ketoglutaric acid aminotransferase by 4-amino-5-halopentanoic acids
journal, March 1981
- Silverman, Richard B.; Levy, Mark A.
- Biochemistry, Vol. 20, Issue 5
Identification and Spectral Characterization of the External Aldimine of the O-Acetylserine Sulfhydrylase Reaction
journal, September 1995
- Schnackerz, Klaus D.; Tai, Chia-Hui; Simmons, James W. III
- Biochemistry, Vol. 34, Issue 38
Redesign of the substrate specificity of escherichia coli aspartate aminotransferase to that of escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis
journal, September 1995
- Onuffer, James J.; Kirsch, Jack F.
- Protein Science, Vol. 4, Issue 9
Role of the aminotransferase domain in B acillus subtilis GabR, a pyridoxal 5′-phosphate-dependent transcriptional regulator : Aminotransferase domain of GabR
journal, December 2014
- Okuda, Keita; Kato, Shiro; Ito, Tomokazu
- Molecular Microbiology, Vol. 95, Issue 2
Role of the Pyridine Nitrogen in Pyridoxal 5′-Phosphate Catalysis: Activity of Three Classes of PLP Enzymes Reconstituted with Deazapyridoxal 5′-Phosphate
journal, September 2011
- Griswold, Wait R.; Toney, Michael D.
- Journal of the American Chemical Society, Vol. 133, Issue 37
Mechanistic Crystallography. Mechanism of Inactivation of γ-Aminobutyric Acid Aminotransferase by (1 R ,3 S ,4 S )-3-Amino-4-fluorocyclopentane-1-carboxylic Acid As Elucidated by Crystallography †
journal, November 2004
- Storici, Paola; Qiu, Jian; Schirmer, Tilman
- Biochemistry, Vol. 43, Issue 44
The CCP4 suite programs for protein crystallography
journal, September 1994
- ,
- Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763
3-Alkyl-4-aminobutyric acids: the first class of anticonvulsant agents that activates L-glutamic acid decarboxylase
journal, July 1991
- Silverman, Richard B.; Andruszkiewicz, Ryszard; Nanavati, Shrenik M.
- Journal of Medicinal Chemistry, Vol. 34, Issue 7
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
Inactivation of Escherichia coli l -Aspartate Aminotransferase by ( S )-4-Amino-4,5-dihydro-2-thiophenecarboxylic Acid Reveals “A Tale of Two Mechanisms” † , ‡
journal, September 2007
- Liu, Dali; Pozharski, Edwin; Lepore, Bryan W.
- Biochemistry, Vol. 46, Issue 37
Subdivision of the Helix-Turn-Helix GntR Family of Bacterial Regulators in the FadR, HutC, MocR, and YtrA Subfamilies
journal, December 2001
- Rigali, Sébastien; Derouaux, Adeline; Giannotta, Fabrizio
- Journal of Biological Chemistry, Vol. 277, Issue 15
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT
journal, October 2013
- Edayathumangalam, R.; Wu, R.; Garcia, R.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 44
Works referencing / citing this record:
GABA attenuates ETEC-induced intestinal epithelial cell apoptosis involving GABA A R signaling and the AMPK-autophagy pathway
journal, January 2019
- Xia, Yaoyao; Chen, Siyuan; Zhao, Yuanyuan
- Food & Function, Vol. 10, Issue 11
The demise of catalysis, but new functions arise: pseudoenzymes as the phoenixes of the protein world
journal, February 2019
- Jeffery, Constance J.
- Biochemical Society Transactions, Vol. 47, Issue 1
The MocR‐like transcription factors: pyridoxal 5′‐phosphate‐dependent regulators of bacterial metabolism
journal, July 2018
- Tramonti, Angela; Nardella, Caterina; Salvo, Martino L.
- The FEBS Journal, Vol. 285, Issue 21
A Survey of Pyridoxal 5′-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis
journal, May 2019
- Richts, Björn; Rosenberg, Jonathan; Commichau, Fabian M.
- Frontiers in Molecular Biosciences, Vol. 6
Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis
journal, March 2018
- Czech, Laura; Hermann, Lucas; Stöveken, Nadine
- Genes, Vol. 9, Issue 4