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Okada S, Gregg CM, Allen RS, Menon A, Hussain D, Gillespie V, Johnston E, Byrne K, Colgrave ML, Wood CC. A Synthetic Biology Workflow Reveals Variation in Processing and Solubility of Nitrogenase Proteins Targeted to Plant Mitochondria, and Differing Tolerance of Targeting Sequences in a Bacterial Nitrogenase Assay. FRONTIERS IN PLANT SCIENCE 2020; 11:552160. [PMID: 33013970 PMCID: PMC7511584 DOI: 10.3389/fpls.2020.552160] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/21/2020] [Indexed: 05/13/2023]
Abstract
While industrial nitrogen fertilizer is intrinsic to modern agriculture, it is expensive and environmentally harmful. One approach to reduce fertilizer usage is to engineer the bacterial nitrogenase enzyme complex within plant mitochondria, a location that may support enzyme function. Our current strategy involves fusing a mitochondrial targeting peptide (MTP) to nitrogenase (Nif) proteins, enabling their import to the mitochondrial matrix. However, the process of import modifies the N-terminus of each Nif protein and may impact nitrogenase assembly and function. Here we present our workflow assessing the mitochondrial processing, solubility and relative abundance of 16 Klebsiella oxytoca Nif proteins targeted to the mitochondrial matrix in Nicotiana benthamiana leaf. We found that processing and abundance of MTP::Nif proteins varied considerably, despite using the same constitutive promoter and MTP across all Nif proteins tested. Assessment of the solubility for all MTP::Nif proteins when targeted to plant mitochondria found NifF, M, N, S, U, W, X, Y, and Z were soluble, while NifB, E, H, J, K, Q, and V were mostly insoluble. The functional consequence of the N-terminal modifications required for mitochondrial targeting of Nif proteins was tested using a bacterial nitrogenase assay. With the exception of NifM, the Nif proteins generally tolerated the N-terminal extension. Proteomic analysis of Nif proteins expressed in bacteria found that the relative abundance of NifM with an N-terminal extension was increased ~50-fold, while that of the other Nif proteins was not influenced by the N-terminal extension. Based on the solubility, processing and functional assessments, our workflow identified that K. oxytoca NifF, N, S, U, W, Y, and Z successfully met these criteria. For the remaining Nif proteins, their limitations will need to be addressed before proceeding towards assembly of a complete set of plant-ready Nif proteins for reconstituting nitrogenase in plant mitochondria.
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Affiliation(s)
- Shoko Okada
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Christina M. Gregg
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Robert Silas Allen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Amratha Menon
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Dawar Hussain
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Vanessa Gillespie
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Ema Johnston
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Keren Byrne
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
| | - Michelle Lisa Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, QLD, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Queensland Biosciences Precinct, St. Lucia, QLD, Australia
| | - Craig C. Wood
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
- *Correspondence: Craig C. Wood,
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Tatli M, Hebert AS, Coon JJ, Amador-Noguez D. Genome Wide Phosphoproteome Analysis of Zymomonas mobilis Under Anaerobic, Aerobic, and N 2-Fixing Conditions. Front Microbiol 2019; 10:1986. [PMID: 31551951 PMCID: PMC6737584 DOI: 10.3389/fmicb.2019.01986] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/13/2019] [Indexed: 11/29/2022] Open
Abstract
Protein phosphorylation is a post-translational modification with widespread regulatory roles in both eukaryotes and prokaryotes. Using mass spectrometry, we performed a genome wide investigation of protein phosphorylation in the non-model organism and biofuel producer Zymomonas mobilis under anaerobic, aerobic, and N2-fixing conditions. Our phosphoproteome analysis revealed 125 unique phosphorylated proteins, belonging to major pathways such as glycolysis, TCA cycle, electron transport, nitrogen metabolism, and protein synthesis. Quantitative analysis revealed significant and widespread changes in protein phosphorylation across growth conditions. For example, we observed increased phosphorylation of nearly all glycolytic enzymes and a large fraction of ribosomal proteins during aerobic and N2-fixing conditions. We also observed substantial changes in the phosphorylation status of enzymes and regulatory proteins involved in nitrogen fixation and ammonia assimilation during N2-fixing conditions, including nitrogenase, the Rnf electron transport complex, the transcription factor NifA, GS-GOGAT cycle enzymes, and the PII regulatory protein. This suggested that protein phosphorylation may play an important role at regulating all aspects of nitrogen metabolism in Z. mobilis. This study provides new knowledge regarding the specific pathways and cellular processes that may be regulated by protein phosphorylation in this important industrial organism and provides a useful road map for future experiments that investigate the physiological role of specific phosphorylation events in Z. mobilis.
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Affiliation(s)
- Mehmet Tatli
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Alexander S Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Genome Center of Wisconsin, Madison, WI, United States
| | - Joshua J Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States.,Morgridge Institute for Research, Madison, WI, United States
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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