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Xiao Z, Connor AJ, Worland AM, Tang YJ, Zha RH, Koffas M. Silk fibroin production in Escherichia coli is limited by a positive feedback loop between metabolic burden and toxicity stress. Metab Eng 2023; 77:231-241. [PMID: 37024071 DOI: 10.1016/j.ymben.2023.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/11/2023] [Accepted: 03/25/2023] [Indexed: 04/08/2023]
Abstract
To investigate the metabolic elasticity and production bottlenecks for recombinant silk proteins in Escherichia coli, we performed a comprehensive characterization of one elastin-like peptide strain (ELP) and two silk protein strains (A5 4mer, A5 16mer). Our approach included 13C metabolic flux analysis, genome-scale modeling, transcription analysis, and 13C-assisted media optimization experiments. Three engineered strains maintained their central flux network during growth, while measurable metabolic flux redistributions (such as the Entner-Doudoroff pathway) were detected. Under metabolic burdens, the reduced TCA fluxes forced the engineered strain to rely more on substrate-level phosphorylation for ATP production, which increased acetate overflow. Acetate (as low as 10 mM) in the media was highly toxic to silk-producing strains, which reduced 4mer production by 43% and 16mer by 84%, respectively. Due to the high toxicity of large-size silk proteins, 16mer's productivity was limited, particularly in the minimal medium. Therefore, metabolic burden, overflow acetate, and toxicity of silk proteins may form a vicious positive feedback loop that fractures the metabolic network. Three solutions could be applied: 1) addition of building block supplements (i.e., eight key amino acids: His, Ile, Phe, Pro, Tyr, Lys, Met, Glu) to reduce metabolic burden; 2) disengagement of growth and production; and 3) use of non-glucose based substrate to reduce acetate overflow. Other reported strategies were also discussed in light of decoupling this positive feedback loop.
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Affiliation(s)
- Zhengyang Xiao
- Department of Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Alexander J Connor
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Alyssa M Worland
- Department of Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Yinjie J Tang
- Department of Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - R Helen Zha
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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Niedzwiedzki DM, Magdaong NCM, Su X, Adir N, Keren N, Liu H. Mass spectrometry and spectroscopic characterization of a tetrameric photosystem I supercomplex from Leptolyngbya ohadii, a desiccation-tolerant cyanobacterium. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148955. [PMID: 36708912 DOI: 10.1016/j.bbabio.2023.148955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
Cyanobacteria inhabiting desert biological soil crusts face the harsh conditions of the desert. They evolved a suite of strategies toward desiccation-hydration cycles mixed with high light irradiations, etc. In this study we purified and characterized the structure and function of Photosystem I (PSI) from Leptolyngbya ohadii, a desiccation-tolerant desert cyanobacterium. We discovered that PSI forms tetrameric (PSI-Tet) aggregate. We investigated it by using sucrose density gradient centrifugation, clear native PAGE, high performance liquid chromatography, mass spectrometry (MS), time-resolved fluorescence (TRF) and time-resolved transient absorption (TA) spectroscopy. MS analysis identified the presence of two PsaB and two PsaL proteins in PSI-Tet and uniquely revealed that PsaLs are N-terminally acetylated in contrast to non-modified PsaL in the trimeric PSI from Synechocystis sp. PCC 6803. Chlorophyll (Chl) a fluorescence decay profiles of the PSI-Tet performed at 77 K revealed two emission bands at ∼690 nm and 725 nm with the former appearing only at early delay time. The main fluorescence emission peak, associated with emission from the low energy Chls a, decays within a few nanoseconds. TA studies demonstrated that the 725 nm emission band is associated with low energy Chls a with absorption band clearly resolved at ∼710 nm at 77 K. In summary, our work suggests that the heterogenous composition of PsaBs and PsaL in PSI-Tet is related with the adaptation mechanisms needed to cope with stressful conditions under which this bacterium naturally grows.
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Affiliation(s)
- Dariusz M Niedzwiedzki
- Center for Solar Energy and Energy Storage, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Energy Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | | | - Xinyang Su
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Noam Adir
- Schulich Faculty of Chemistry, Technion, Israel Institute of Technology, Hafai, Israel
| | - Nir Keren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Haijun Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Roell GW, Zha J, Carr RR, Koffas MA, Fong SS, Tang YJ. Engineering microbial consortia by division of labor. Microb Cell Fact 2019; 18:35. [PMID: 30736778 PMCID: PMC6368712 DOI: 10.1186/s12934-019-1083-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
During microbial applications, metabolic burdens can lead to a significant drop in cell performance. Novel synthetic biology tools or multi-step bioprocessing (e.g., fermentation followed by chemical conversions) are therefore needed to avoid compromised biochemical productivity from over-burdened cells. A possible solution to address metabolic burden is Division of Labor (DoL) via natural and synthetic microbial consortia. In particular, consolidated bioprocesses and metabolic cooperation for detoxification or cross feeding (e.g., vitamin C fermentation) have shown numerous successes in industrial level applications. However, distributing a metabolic pathway among proper hosts remains an engineering conundrum due to several challenges: complex subpopulation dynamics/interactions with a short time-window for stable production, suboptimal cultivation of microbial communities, proliferation of cheaters or low-producers, intermediate metabolite dilution, transport barriers between species, and breaks in metabolite channeling through biosynthesis pathways. To develop stable consortia, optimization of strain inoculations, nutritional divergence and crossing feeding, evolution of mutualistic growth, cell immobilization, and biosensors may potentially be used to control cell populations. Another opportunity is direct integration of non-bioprocesses (e.g., microbial electrosynthesis) to power cell metabolism and improve carbon efficiency. Additionally, metabolic modeling and 13C-metabolic flux analysis of mixed culture metabolism and cross-feeding offers a computational approach to complement experimental research for improved consortia performance.
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Affiliation(s)
- Garrett W Roell
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO, 63130, USA
| | - Jian Zha
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA
| | - Rhiannon R Carr
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO, 63130, USA
| | - Mattheos A Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY, 12180, USA
| | - Stephen S Fong
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, MO, 63130, USA.
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Fang Z, Jones JA, Zhou J, Koffas MAG. Engineering
Escherichia coli
Co‐Cultures for Production of Curcuminoids From Glucose. Biotechnol J 2017; 13:e1700576. [DOI: 10.1002/biot.201700576] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/09/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Zhen Fang
- Biofuels InstituteSchool of the EnvironmentJiangsu University301 Xuefu RoadZhenjiang 212013Jiangsu ProvinceChina
- Department of Chemical and Biological EngineeringRensselaer Polytechnic InstituteTroyNY 12180USA
| | - John A. Jones
- Department of Chemical and Biological EngineeringRensselaer Polytechnic InstituteTroyNY 12180USA
- Department of Chemical, Paper, and Biomedical EngineeringMiami UniversityOxfordOH 45056USA
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial BiotechnologyMinistry of EducationJiangnan UniversityWuxiJiangsu 214122China
| | - Mattheos A. G. Koffas
- Department of Chemical and Biological EngineeringRensselaer Polytechnic InstituteTroyNY 12180USA
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyNY 12180USA
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Cell-Type Specific Metabolic Flux Analysis: A Challenge for Metabolic Phenotyping and a Potential Solution in Plants. Metabolites 2017; 7:metabo7040059. [PMID: 29137184 PMCID: PMC5746739 DOI: 10.3390/metabo7040059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/22/2022] Open
Abstract
Stable isotope labelling experiments are used routinely in metabolic flux analysis (MFA) to determine the metabolic phenotype of cells and tissues. A complication arises in multicellular systems because single cell measurements of transcriptomes, proteomes and metabolomes in multicellular organisms suggest that the metabolic phenotype will differ between cell types. In silico analysis of simulated metabolite isotopomer datasets shows that cellular heterogeneity confounds conventional MFA because labelling data averaged over multiple cell types does not necessarily yield averaged flux values. A potential solution to this problem—the use of cell-type specific reporter proteins as a source of cell-type specific labelling data—is proposed and the practicality of implementing this strategy in the roots of Arabidopsis thaliana seedlings is explored. A protocol for the immunopurification of ectopically expressed green fluorescent protein (GFP) from Arabidopsis thaliana seedlings using a GFP-binding nanobody is developed, and through GC-MS analysis of protein hydrolysates it is established that constitutively expressed GFP reports accurately on the labelling of total protein in root tissues. It is also demonstrated that the constitutive expression of GFP does not perturb metabolism. The principal obstacle to the implementation of the method in tissues with cell-type specific GFP expression is the sensitivity of the GC-MS system.
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Turon V, Trably E, Fouilland E, Steyer JP. Potentialities of dark fermentation effluents as substrates for microalgae growth: A review. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.03.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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