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Casas-Román A, Lorite MJ, Werner M, Muñoz S, Gallegos MT, Sanjuán J. The gap gene of Rhizobium etli is required for both free life and symbiosis with common beans. Microbiol Res 2024; 284:127737. [PMID: 38705080 DOI: 10.1016/j.micres.2024.127737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 05/07/2024]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH or Gap) is a ubiquitous enzyme essential for carbon and energy metabolism in most organisms. Despite its primary role in sugar metabolism, GAPDH is recognized for its involvement in diverse cellular processes, being considered a paradigm among multifunctional/moonlighting proteins. Besides its canonical cytoplasmic location, GAPDH has been detected on cell surfaces or as a secreted protein in prokaryotes, yet little is known about its possible roles in plant symbiotic bacteria. Here we report that Rhizobium etli, a nitrogen-fixing symbiont of common beans, carries a single gap gene responsible for both GAPDH glycolytic and gluconeogenic activities. An active Gap protein is required throughout all stages of the symbiosis between R. etli and its host plant Phaseolus vulgaris. Both glycolytic and gluconeogenic Gap metabolic activities likely contribute to bacterial fitness during early and intermediate stages of the interaction, whereas GAPDH gluconeogenic activity seems critical for nodule invasion and nitrogen fixation. Although the R. etli Gap protein is secreted in a c-di-GMP related manner, no involvement of the R. etli gap gene in c-di-GMP related phenotypes, such as flocculation, biofilm formation or EPS production, was observed. Notably, the R. etli gap gene fully complemented a double gap1/gap2 mutant of Pseudomonas syringae for free life growth, albeit only partially in planta, suggesting potential specific roles for each type of Gap protein. Nevertheless, further research is required to unravel additional functions of the R. etli Gap protein beyond its essential metabolic roles.
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Affiliation(s)
- Ariana Casas-Román
- Departmento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - María-José Lorite
- Departmento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Mariana Werner
- Departmento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Socorro Muñoz
- Departmento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Departmento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín (CSIC), Granada, Spain.
| | - Juan Sanjuán
- Departmento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín (CSIC), Granada, Spain.
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Casas-Román A, Lorite MJ, Sanjuán J, Gallegos MT. Two glyceraldehyde-3-phosphate dehydrogenases with distinctive roles in Pseudomonas syringae pv. tomato DC3000. Microbiol Res 2024; 278:127530. [PMID: 37890268 DOI: 10.1016/j.micres.2023.127530] [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: 08/23/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH or Gap) is a ubiquitously distributed enzyme that plays an essential role in the glycolytic and gluconeogenic pathways. However, additional roles have been described unrelated to its enzymatic function in diverse organisms, often linked to its presence in the cell surface or as a secreted protein. Despite being a paradigm among multifunctional/moonlighting proteins, little is known about its possible roles in phytopathogenic bacteria. In the present work we have studied three putative gap paralogous genes identified in the genome of Pseudomonas syringae pv. tomato (Pto) DC3000, an important model in molecular plant pathology, with the aim of determining their physiological and possible non-canonical roles in this bacterium and in the plant infection process. We have established that the Gap1 protein has a predominantly glycolytic activity, whereas the NADPH-dependent Gap2 main activity is gluconeogenic. The third paralogue lacks GAPDH activity in Pto but is indispensable for vitamin B6 metabolism and displays erythrose-4-phosphate dehydrogenase activity, thus referred as epd. Both Gap enzymes exhibit distinct functional characteristics depending on the bacterium physiological state, with Gap1 presenting a substantial role in motility, biosurfactant production and biofilm formation. On the other hand, solely Gap2 appears to be essential for growth on tomato plant. Furthermore, Gap1 and Gap2 present a distinctive transcriptional regulation and both have been identified exported outside the cells with different definite media compositions. This serves as compelling evidence of additional roles beyond their central metabolic functions.
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Affiliation(s)
- Ariana Casas-Román
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-José Lorite
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Juan Sanjuán
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain.
| | - María-Trinidad Gallegos
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain.
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Pavkova I, Kopeckova M, Link M, Vlcak E, Filimonenko V, Lecova L, Zakova J, Laskova P, Sheshko V, Machacek M, Stulik J. Francisella tularensis Glyceraldehyde-3-Phosphate Dehydrogenase Is Relocalized during Intracellular Infection and Reveals Effect on Cytokine Gene Expression and Signaling. Cells 2023; 12:cells12040607. [PMID: 36831274 PMCID: PMC9954481 DOI: 10.3390/cells12040607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is known for its multifunctionality in several pathogenic bacteria. Our previously reported data suggest that the GAPDH homologue of Francisella tularensis, GapA, might also be involved in other processes beyond metabolism. In the present study, we explored GapA's potential implication in pathogenic processes at the host cell level. Using immunoelectron microscopy, we demonstrated the localization of this bacterial protein inside infected macrophages and its peripheral distribution in bacterial cells increasing with infection time. A quantitative proteomic approach based on stable isotope labeling of amino acids in cell culture (SILAC) combined with pull-down assay enabled the identification of several of GapA's potential interacting partners within the host cell proteome. Two of these partners were further confirmed by alternative methods. We also investigated the impact of gapA deletion on the transcription of selected cytokine genes and the activation of the main signaling pathways. Our results show that ∆gapA-induced transcription of genes encoding several cytokines whose expressions were not affected in cells infected with a fully virulent wild-type strain. That might be caused, at least in part, by the detected differences in ERK/MAPK signaling activation. The experimental observations together demonstrate that the F. tularensis GAPDH homologue is directly implicated in multiple host cellular processes and, thereby, that it participates in several molecular mechanisms of pathogenesis.
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Affiliation(s)
- Ivona Pavkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
- Correspondence: ; Tel.: +420-973-255-201
| | - Monika Kopeckova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Marek Link
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Erik Vlcak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Electron Microscopy Core Facility, Videnska 1083, 142 20 Prague, Czech Republic
| | - Vlada Filimonenko
- Institute of Molecular Genetics of the Czech Academy of Sciences, Electron Microscopy Core Facility, Videnska 1083, 142 20 Prague, Czech Republic
- Institute of Molecular Genetics of the Czech Academy of Sciences, Department of Biology of the Cell Nucleus, Videnska 1083, 142 20 Prague, Czech Republic
| | - Lenka Lecova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Jitka Zakova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Pavlina Laskova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Valeria Sheshko
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
| | - Miloslav Machacek
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Akademika Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
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Kopeckova M, Link M, Pavkova I. Identification of Protein Interaction Partners in Bacteria Using Affinity Purification and SILAC Quantitative Proteomics. Methods Mol Biol 2023; 2603:31-42. [PMID: 36370268 DOI: 10.1007/978-1-0716-2863-8_3] [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] [Indexed: 06/16/2023]
Abstract
Affinity purification, combined with mass spectrometry (AP-MS) is considered a pivotal technique in protein-protein interaction studies enabling systematic detection at near physiological conditions. The addition of a quantitative proteomic method, like SILAC metabolic labeling, allows the elimination of non-specifically bound contaminants which greatly increases the confidence of the identified interaction partners. Compared to eukaryotic cells, the SILAC labeling of bacteria has specificities that must be considered. The protocol presented here describes the labeling of bacterial cultures with stable isotope-labeled amino acids, purification of an affinity-tagged protein, and sample preparation for MS measurement. Finally, we discuss the analysis and interpretation of MS data to identify and select the specific partners interacting with the protein of interest. As an example, this workflow is applied to the discovery of potential interaction partners of glyceraldehyde-3-phosphate dehydrogenase in the gram-negative bacterium Francisella tularensis.
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Affiliation(s)
- Monika Kopeckova
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Hradec Kralove, Czech Republic
| | - Marek Link
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Hradec Kralove, Czech Republic
| | - Ivona Pavkova
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Hradec Kralove, Czech Republic.
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