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Bidart GN, Gharabli H, Welner DH. Functional characterization of the phosphotransferase system in Parageobacillus thermoglucosidasius. Sci Rep 2023; 13:7131. [PMID: 37130962 PMCID: PMC10154347 DOI: 10.1038/s41598-023-33918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium characterized by rapid growth, low nutrient requirements, and amenability to genetic manipulation. These characteristics along with its ability to ferment a broad range of carbohydrates make P. thermoglucosidasius a potential workhorse in whole-cell biocatalysis. The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates and sugar derivatives in bacteria, making it important for their physiological characterization. In this study, the role of PTS elements on the catabolism of PTS and non-PTS substrates was investigated for P. thermoglucosidasius DSM 2542. Knockout of the common enzyme I, part of all PTSs, showed that arbutin, cellobiose, fructose, glucose, glycerol, mannitol, mannose, N-acetylglucosamine, N-acetylmuramic acid, sorbitol, salicin, sucrose, and trehalose were PTS-dependent on translocation and coupled to phosphorylation. The role of each putative PTS was investigated and six PTS-deletion variants could not grow on arbutin, mannitol, N-acetylglucosamine, sorbitol, and trehalose as the main carbon source, or showed diminished growth on N-acetylmuramic acid. We concluded that PTS is a pivotal factor in the sugar metabolism of P. thermoglucosidasius and established six PTS variants important for the translocation of specific carbohydrates. This study lays the groundwork for engineering efforts with P. thermoglucosidasius towards efficient utilization of diverse carbon substrates for whole-cell biocatalysis.
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Affiliation(s)
- Gonzalo N Bidart
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Hani Gharabli
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Ditte Hededam Welner
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark.
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Teze D, Coines J, Fredslund F, Dubey KD, Bidart GN, Adams PD, Dueber JE, Svensson B, Rovira C, Welner DH. O-/N-/S-Specificity in Glycosyltransferase Catalysis: From Mechanistic Understanding to Engineering. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04171] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Joan Coines
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Folmer Fredslund
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kshatresh D. Dubey
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Gonzalo N. Bidart
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Paul D. Adams
- Department of Bioengineering, University of California, Berkeley, California 94704, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, California 94704, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Carme Rovira
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08018, Spain
| | - Ditte H. Welner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Bidart GN, Rodríguez-Díaz J, Palomino-Schätzlein M, Monedero V, Yebra MJ. Human milk and mucosal lacto- and galacto-N-biose synthesis by transgalactosylation and their prebiotic potential in Lactobacillus species. Appl Microbiol Biotechnol 2016; 101:205-215. [DOI: 10.1007/s00253-016-7882-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 09/07/2016] [Accepted: 09/20/2016] [Indexed: 12/14/2022]
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Bidart GN, Rodríguez-Díaz J, Monedero V, Yebra MJ. A unique gene cluster for the utilization of the mucosal and human milk-associated glycans galacto-N-biose and lacto-N-biose in Lactobacillus casei. Mol Microbiol 2014; 93:521-38. [PMID: 24942885 DOI: 10.1111/mmi.12678] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2014] [Indexed: 12/20/2022]
Abstract
The probiotic Lactobacillus casei catabolizes galacto-N-biose (GNB) and lacto-N-biose (LNB) by using a transport system and metabolic routes different from those of Bifidobacterium. L. casei contains a gene cluster, gnbREFGBCDA, involved in the metabolism of GNB, LNB and also N-acetylgalactosamine. Inactivation of gnbC (EIIC) or ptsI (Enzyme I) of the phosphoenolpyruvate : sugar phosphotransferase system (PTS) prevented the growth on those three carbohydrates, indicating that they are transported and phosphorylated by the same PTS(Gnb) . Enzyme activities and growth analysis with knockout mutants showed that GnbG (phospho-β-galactosidase) hydrolyses both disaccharides. However, GnbF (N-acetylgalactosamine-6P deacetylase) and GnbE (galactosamine-6P isomerase/deaminase) are involved in GNB but not in LNB fermentation. The utilization of LNB depends on nagA (N-acetylglucosamine-6P deacetylase), showing that the N-acetylhexosamine moieties of GNB and LNB follow different catabolic routes. A lacAB mutant (galactose-6P isomerase) was impaired in GNB and LNB utilization, indicating that their galactose moiety is channelled through the tagatose-6P pathway. Transcriptional analysis showed that the gnb operon is regulated by substrate-specific induction mediated by the transcriptional repressor GnbR, which binds to a 26 bp DNA region containing inverted repeats exhibiting a 2T/2A conserved core. The data represent the first characterization of novel metabolic pathways for human milk oligosaccharides and glycoconjugate structures in Firmicutes.
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Affiliation(s)
- Gonzalo N Bidart
- Laboratorio de Bacterias Lácticas y Probióticos, Departamento de Biotecnología de Alimentos, IATA-CSIC, Valencia, Spain; Instituto de Investigaciones Biotecnológicas 'Dr. Rodolfo A. Ugalde', Universidad Nacional de San Martín, Buenos Aires, Argentina
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Ruiz JA, de Almeida A, Godoy MS, Mezzina MP, Bidart GN, Méndez BS, Pettinari MJ, Nikel PI. Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals. Comput Struct Biotechnol J 2013; 3:e201210019. [PMID: 24688679 PMCID: PMC3962086 DOI: 10.5936/csbj.201210019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 12/09/2012] [Accepted: 12/13/2012] [Indexed: 11/23/2022] Open
Abstract
Bioprocesses conducted under conditions with restricted O2 supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative aerobe Escherichia coli, the microbial cell factory par excellence, has elaborate sensing and signal transduction mechanisms that respond to the availability of electron acceptors and alternative carbon sources in the surrounding environment. In particular, the ArcBA and CreBC two-component signal transduction systems are largely responsible for the metabolic regulation of redox control in response to O2 availability and carbon source utilization, respectively. Significant advances in the understanding of the biochemical, genetic, and physiological duties of these regulatory systems have been achieved in recent years. This situation allowed to rationally-design novel engineering approaches that ensure optimal carbon and energy flows within central metabolism, as well as to manipulate redox homeostasis, in order to optimize the production of industrially-relevant metabolites. In particular, metabolic flux analysis provided new clues to understand the metabolic regulation mediated by the ArcBA and CreBC systems. Genetic manipulation of these regulators proved useful for designing microbial cells factories tailored for the synthesis of reduced biochemicals with added value, such as poly(3-hydroxybutyrate), under conditions with restricted O2 supply. This network-wide strategy is in contrast with traditional metabolic engineering approaches, that entail direct modification of the pathway(s) at stake, and opens new avenues for the targeted modulation of central catabolic pathways at the transcriptional level.
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Affiliation(s)
- Jimena A Ruiz
- Departamento de Química Biológica (IQUIBICEN-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina ; Instituto de Biociencias Agrícolas y Ambientales (INBA-CONICET), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandra de Almeida
- Departamento de Química Biológica (IQUIBICEN-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Manuel S Godoy
- Departamento de Química Biológica (IQUIBICEN-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariela P Mezzina
- Departamento de Química Biológica (IQUIBICEN-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gonzalo N Bidart
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde" (IIB-CONICET), Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Beatriz S Méndez
- Departamento de Química Biológica (IQUIBICEN-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M Julia Pettinari
- Departamento de Química Biológica (IQUIBICEN-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo I Nikel
- Departamento de Química Biológica (IQUIBICEN-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina ; Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde" (IIB-CONICET), Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
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