1
|
Schito S, Zuchowski R, Bergen D, Strohmeier D, Wollenhaupt B, Menke P, Seiffarth J, Nöh K, Kohlheyer D, Bott M, Wiechert W, Baumgart M, Noack S. Communities of Niche-optimized Strains (CoNoS) - Design and creation of stable, genome-reduced co-cultures. Metab Eng 2022; 73:91-103. [PMID: 35750243 DOI: 10.1016/j.ymben.2022.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/20/2022] [Accepted: 06/17/2022] [Indexed: 10/18/2022]
Abstract
Current bioprocesses for production of value-added compounds are mainly based on pure cultures that are composed of rationally engineered strains of model organisms with versatile metabolic capacities. However, in the comparably well-defined environment of a bioreactor, metabolic flexibility provided by various highly abundant biosynthetic enzymes is much less required and results in suboptimal use of carbon and energy sources for compound production. In nature, non-model organisms have frequently evolved in communities where genome-reduced, auxotrophic strains cross-feed each other, suggesting that there must be a significant advantage compared to growth without cooperation. To prove this, we started to create and study synthetic communities of niche-optimized strains (CoNoS) that consists of two strains of the same species Corynebacterium glutamicum that are mutually dependent on one amino acid. We used both the wild-type and the genome-reduced C1* chassis for introducing selected amino acid auxotrophies, each based on complete deletion of all required biosynthetic genes. The best candidate strains were used to establish several stably growing CoNoS that were further characterized and optimized by metabolic modelling, microfluidic experiments and rational metabolic engineering to improve amino acid production and exchange. Finally, the engineered CoNoS consisting of an l-leucine and l-arginine auxotroph showed a specific growth rate equivalent to 83% of the wild type in monoculture, making it the fastest co-culture of two auxotrophic C. glutamicum strains to date. Overall, our results are a first promising step towards establishing improved biobased production of value-added compounds using the CoNoS approach.
Collapse
Affiliation(s)
- Simone Schito
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Rico Zuchowski
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Bergen
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Strohmeier
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Bastian Wollenhaupt
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Philipp Menke
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Seiffarth
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Katharina Nöh
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Dietrich Kohlheyer
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Wolfgang Wiechert
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany; Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, D-52074, Aachen, Germany
| | - Meike Baumgart
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany.
| |
Collapse
|
2
|
Yunus IS, Lee TS. Applications of targeted proteomics in metabolic engineering: advances and opportunities. Curr Opin Biotechnol 2022; 75:102709. [DOI: 10.1016/j.copbio.2022.102709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022]
|
3
|
Increased carvone production in Escherichia coli by balancing limonene conversion enzyme expression via targeted quantification concatamer proteome analysis. Sci Rep 2021; 11:22126. [PMID: 34764337 PMCID: PMC8586248 DOI: 10.1038/s41598-021-01469-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 10/27/2021] [Indexed: 11/25/2022] Open
Abstract
(−)-Carvone is a monoterpenoid with a spearmint flavor. A sustainable biotechnological production process for (−)-carvone is desirable. Although all enzymes in (−)-carvone biosynthesis have been functionally expressed in Escherichia coli independently, the yield was low in previous studies. When cytochrome P450 limonene-6-hydroxylase (P450)/cytochrome P450 reductase (CPR) and carveol dehydrogenase (CDH) were expressed in a single strain, by-product formation (dihydrocarveol and dihydrocarvone) was detected. We hypothesized that P450 and CDH expression levels differ in E. coli. Thus, two strains independently expressing P450/CPR and CDH were mixed with different ratios, confirming increased carvone production and decreased by-product formation when CDH input was reduced. The optimum ratio of enzyme expression to maximize (−)-carvone production was determined using the proteome analysis quantification concatamer (QconCAT) method. Thereafter, a single strain expressing both P450/CPR and CDH was constructed to imitate the optimum expression ratio. The upgraded strain showed a 15-fold improvement compared to the initial strain, showing a 44 ± 6.3 mg/L (−)-carvone production from 100 mg/L (−)-limonene. Our study showed the usefulness of the QconCAT proteome analysis method for strain development in the industrial biotechnology field.
Collapse
|
4
|
Kappelmann J, Klein B, Papenfuß M, Lange J, Blombach B, Takors R, Wiechert W, Polen T, Noack S. Comprehensive Analysis of C. glutamicum Anaplerotic Deletion Mutants Under Defined d-Glucose Conditions. Front Bioeng Biotechnol 2021; 8:602936. [PMID: 33553115 PMCID: PMC7855459 DOI: 10.3389/fbioe.2020.602936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/17/2020] [Indexed: 01/07/2023] Open
Abstract
Wild-type C. glutamicum ATCC 13032 is known to possess two enzymes with anaplerotic (C4-directed) carboxylation activity, namely phosphoenolpyruvate carboxylase (PEPCx) and pyruvate carboxylase (PCx). On the other hand, C3-directed decarboxylation can be catalyzed by the three enzymes phosphoenolpyruvate carboxykinase (PEPCk), oxaloacetate decarboxylase (ODx), and malic enzyme (ME). The resulting high metabolic flexibility at the anaplerotic node compromises the unambigous determination of its carbon and energy flux in C. glutamicum wild type. To circumvent this problem we performed a comprehensive analysis of selected single or double deletion mutants in the anaplerosis of wild-type C. glutamicum under defined d-glucose conditions. By applying well-controlled lab-scale bioreactor experiments in combination with untargeted proteomics, quantitative metabolomics and whole-genome sequencing hitherto unknown, and sometimes counter-intuitive, genotype-phenotype relationships in these mutants could be unraveled. In comparison to the wild type the four mutants C. glutamiucm Δpyc, C. glutamiucm Δpyc Δodx, C. glutamiucm Δppc Δpyc, and C. glutamiucm Δpck showed lowered specific growth rates and d-glucose uptake rates, underlining the importance of PCx and PEPCk activity for a balanced carbon and energy flux at the anaplerotic node. Most interestingly, the strain C. glutamiucm Δppc Δpyc could be evolved to grow on d-glucose as the only source of carbon and energy, whereas this combination was previously considered lethal. The prevented anaplerotic carboxylation activity of PEPCx and PCx was found in the evolved strain to be compensated by an up-regulation of the glyoxylate shunt, potentially in combination with the 2-methylcitrate cycle.
Collapse
Affiliation(s)
- Jannick Kappelmann
- Institute of Bio- and Geosciences 1, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Bianca Klein
- Institute of Bio- and Geosciences 1, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Mathias Papenfuß
- Institute of Biochemical Engineering, Braunschweig University of Technology, Braunschweig, Germany
| | - Julian Lange
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences 1, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences 1, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences 1, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| |
Collapse
|
5
|
Jansen RP, Müller MF, Schröter SE, Kappelmann J, Klein B, Oldiges M, Noack S. Parallelized disruption of prokaryotic and eukaryotic cells via miniaturized and automated bead mill. Eng Life Sci 2020; 20:350-356. [PMID: 32774207 PMCID: PMC7401235 DOI: 10.1002/elsc.202000002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/17/2020] [Indexed: 11/07/2022] Open
Abstract
The application of integrated microbioreactor systems is rapidly becoming of more interest to accelerate strain characterization and bioprocess development. However, available high-throughput screening capabilities are often limited to target extracellular compounds only. Consequently, there is a great demand for automated technologies allowing for miniaturized and parallel cell disruption providing access to intracellular measurements. In this study, a fully automated bead mill workflow was developed and validated for four different industrial platform organisms: Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Aspergillus niger. The workflow enables up to 48 parallel cell disruptions in microtiter plates and is applicable at-line to running lab-scale cultivations. The resulting cell extracts form the basis for quantitative omics studies where no rapid metabolic quenching is required (e.g., genomics and proteomics).
Collapse
Affiliation(s)
- Roman P. Jansen
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
| | | | | | | | - Bianca Klein
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
| | - Marco Oldiges
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
- Bioeconomy Science Center (BioSC)Forschungszentrum Jülich GmbHJülichGermany
| | - Stephan Noack
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
- Bioeconomy Science Center (BioSC)Forschungszentrum Jülich GmbHJülichGermany
| |
Collapse
|
6
|
Shen J, Chen J, Jensen PR, Solem C. Sweet As Sugar-Efficient Conversion of Lactose into Sweet Sugars Using a Novel Whole-Cell Catalyst. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6257-6262. [PMID: 31117497 DOI: 10.1021/acs.jafc.9b01529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lactose, the sugar contained in milk, has a low sweetness. We have constructed an efficient whole-cell catalyst (WCC) that can be grown on dairy waste and that is able to convert lactose into a mixture of sugars as sweet as sucrose. The WCC is based on Corynebacterium glutamicum ATCC13032, which has been engineered to metabolize lactose, to express xylose and arabinose isomerase, and to eliminate byproduct formation. When introduced in concentrated cheese whey permeate, its content of 98 g/L lactose was completely hydrolyzed and the liberated sugars partially isomerized into 23.5 g/L fructose and 20.4 g/L tagatose, which corresponds to a 49% conversion of the glucose and a 44% conversion of galactose. The latter is similar to what can be obtained using purified enzymes. The new technology enables better resource utilization and allows for dairy waste to be converted into a valuable food sweetener with many potential uses.
Collapse
Affiliation(s)
- Jing Shen
- National Food Institute , Technical University of Denmark , 2800 Kongens Lyngby , Denmark
| | - Jun Chen
- National Food Institute , Technical University of Denmark , 2800 Kongens Lyngby , Denmark
| | - Peter Ruhdal Jensen
- National Food Institute , Technical University of Denmark , 2800 Kongens Lyngby , Denmark
| | - Christian Solem
- National Food Institute , Technical University of Denmark , 2800 Kongens Lyngby , Denmark
| |
Collapse
|
7
|
Noack S, Baumgart M. Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction. Trends Biotechnol 2019; 37:126-139. [DOI: 10.1016/j.tibtech.2018.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022]
|
8
|
Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
Collapse
Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
9
|
Abernathy MH, He L, Tang YJ. Channeling in native microbial pathways: Implications and challenges for metabolic engineering. Biotechnol Adv 2017. [DOI: 10.1016/j.biotechadv.2017.06.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
10
|
The linkage between nutrient supply, intracellular enzyme abundances and bacterial growth: New evidences from the central carbon metabolism of Corynebacterium glutamicum. J Biotechnol 2017. [DOI: 10.1016/j.jbiotec.2017.06.407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
11
|
Heider SAE, Wendisch VF. Engineering microbial cell factories: Metabolic engineering ofCorynebacterium glutamicumwith a focus on non-natural products. Biotechnol J 2015. [DOI: 10.1002/biot.201400590] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|