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Conversion of mammalian cell culture media waste to microbial fermentation feed efficiently supports production of recombinant protein by Escherichia coli. PLoS One 2022; 17:e0266921. [PMID: 35507546 PMCID: PMC9067682 DOI: 10.1371/journal.pone.0266921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/29/2022] [Indexed: 11/19/2022] Open
Abstract
Deriving new value from waste streams through secondary processes is a central aim of the circular bioeconomy. In this study we investigate whether chemically defined spent media (CDSM) waste from cell culture bioprocess can be recycled and used as a feed in secondary microbial fermentation to produce new recombinant protein products. Our results show that CDSM supplemented with 2% glycerol supported a specific growth rate of E. coli cultures equivalent to that achieved using a nutritionally rich microbiological media (LB). The titre of recombinant protein produced following induction in a 4-hour expression screen was approximately equivalent in the CDSM fed cultures to that of baseline, and this was maintained in a 16-hr preparative fermentation. To understand the protein production achieved in CDSM fed culture we performed a quantitative analysis of proteome changes in the E. coli using mass spectrometry. This analysis revealed significant upregulation of protein synthesis machinery enzymes and significant downregulation of carbohydrate metabolism enzymes. We conclude that spent cell culture media, which represents 100s of millions of litres of waste generated by the bioprocessing industry annually, may be valorized as a feed resource for the production of recombinant proteins in secondary microbial fermentations. Data is available via ProteomeXchange with identifier PXD026884.
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McGauran G, Dorris E, Borza R, Morgan N, Shields DC, Matallanas D, Wilson AG, O'Connell DJ. Resolving the Interactome of the Human Macrophage Immunometabolism Regulator (MACIR) with Enhanced Membrane Protein Preparation and Affinity Proteomics. Proteomics 2020; 20:e2000062. [PMID: 32864787 DOI: 10.1002/pmic.202000062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/17/2020] [Indexed: 11/10/2022]
Abstract
Expression of the macrophage immunometabolism regulator gene (MACIR) is associated with severity of autoimmune disease pathology and with the regulation of macrophage biology through unknown mechanisms. The encoded 206 amino acid protein lacks homology to any characterized protein sequence and is a disordered protein according to structure prediction algorithms. To identify interactions of MACIR with proteins from all subcellular compartments, a membrane solubilization buffer is employed, that together with a high affinity EF hand based pull down method, increases the resolution of quantitative mass spectrometry analysis with significant enrichment of interactions from membrane bound nuclear and mitochondrial compartments compared to samples prepared with radioimmunoprecipitation assay buffer. A total of 63 significant interacting proteins are identified and interaction with the nuclear transport receptor TNPO1 and the trafficking proteins UNC119 homolog A and B are validated by immunoprecipitation. Mutational analysis in two candidate nuclear localization signal motifs in the MACIR amino acid sequence shows the interaction with TNPO1 is likely via a non-classical proline/tyrosine-nuclear localization signal motif (aa98-117). It is shown that employing a highly specific and high affinity pull down method that performs efficiently in this glycerol and detergent rich buffer is a powerful approach for the analysis of uncharacterized protein interactomes.
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Affiliation(s)
- Gavin McGauran
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Emma Dorris
- School of Medicine, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Razvan Borza
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Niamh Morgan
- School of Medicine, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Denis C Shields
- School of Medicine, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - David Matallanas
- School of Medicine, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland.,Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - Anthony G Wilson
- School of Medicine, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
| | - David J O'Connell
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,BiOrbic Bioeconomy Research Centre, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
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