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Oliver C. Chicken metabolism, immobilization, and post-industrial production. SOCIAL STUDIES OF SCIENCE 2024:3063127241247022. [PMID: 38825893 DOI: 10.1177/03063127241247022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Chickens have become emblematic of the Anthropocene: They embody the age of acceleration, (post-) industrial value, and intensification in scientific and technological knowledge and practice. Contemporary chickens are the bearers of significant genetic and nutritional knowledge, experimented upon and 'tweaked' so much so that some have denied that contemporary commercial chickens are chickens at all. This article reconsiders chickens through a metabolic lens, and the notion of metabolism through chickens, arguing that attending to chickens opens up new conceptualizations of life and labour in the metabosphere. The article tells a metabolic history of chickens from ornament to enclosed monocrop, by way of the laboratory and nutritional experiments. Then, it looks at chicken metabolism in three conceptual modes: first, as a conduit for value, metabolizing and enhancing human life for the past century; second, through technological innovations extending the gut outside chickens' immobilized bodies; and third, through the planetary impacts of metabolic porosity in geological manifestations, toxic atmospheres, and viral overflow. Ultimately, this article shows how techno-scientific production of chickens has taken place in and created the metabosphere as a site of experimentation and exploitation.
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2
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Collas F, Dronsella BB, Kubis A, Schann K, Binder S, Arto N, Claassens NJ, Kensy F, Orsi E. Engineering the biological conversion of formate into crotonate in Cupriavidus necator. Metab Eng 2023; 79:49-65. [PMID: 37414134 DOI: 10.1016/j.ymben.2023.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
To advance the sustainability of the biobased economy, our society needs to develop novel bioprocesses based on truly renewable resources. The C1-molecule formate is increasingly proposed as carbon and energy source for microbial fermentations, as it can be efficiently generated electrochemically from CO2 and renewable energy. Yet, its biotechnological conversion into value-added compounds has been limited to a handful of examples. In this work, we engineered the natural formatotrophic bacterium C. necator as cell factory to enable biological conversion of formate into crotonate, a platform short-chain unsaturated carboxylic acid of biotechnological relevance. First, we developed a small-scale (150-mL working volume) cultivation setup for growing C. necator in minimal medium using formate as only carbon and energy source. By using a fed-batch strategy with automatic feeding of formic acid, we could increase final biomass concentrations 15-fold compared to batch cultivations in flasks. Then, we engineered a heterologous crotonate pathway in the bacterium via a modular approach, where each pathway section was assessed using multiple candidates. The best performing modules included a malonyl-CoA bypass for increasing the thermodynamic drive towards the intermediate acetoacetyl-CoA and subsequent conversion to crotonyl-CoA through partial reverse β-oxidation. This pathway architecture was then tested for formate-based biosynthesis in our fed-batch setup, resulting in a two-fold higher titer, three-fold higher productivity, and five-fold higher yield compared to the strain not harboring the bypass. Eventually, we reached a maximum product titer of 148.0 ± 6.8 mg/L. Altogether, this work consists in a proof-of-principle integrating bioprocess and metabolic engineering approaches for the biological upgrading of formate into a value-added platform chemical.
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Affiliation(s)
| | - Beau B Dronsella
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Karin Schann
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | | | - Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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3
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Le XH, Millar AH. The diversity of substrates for plant respiration and how to optimize their use. PLANT PHYSIOLOGY 2023; 191:2133-2149. [PMID: 36573332 PMCID: PMC10069909 DOI: 10.1093/plphys/kiac599] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Plant respiration is a foundational biological process with the potential to be optimized to improve crop yield. To understand and manipulate the outputs of respiration, the inputs of respiration-respiratory substrates-need to be probed in detail. Mitochondria house substrate catabolic pathways and respiratory machinery, so transport into and out of these organelles plays an important role in committing substrates to respiration. The large number of mitochondrial carriers and catabolic pathways that remain unidentified hinder this process and lead to confusion about the identity of direct and indirect respiratory substrates in plants. The sources and usage of respiratory substrates vary and are increasing found to be highly regulated based on cellular processes and environmental factors. This review covers the use of direct respiratory substrates following transport through mitochondrial carriers and catabolism under normal and stressed conditions. We suggest the introduction of enzymes not currently found in plant mitochondria to enable serine and acetate to be direct respiratory substrates in plants. We also compare respiratory substrates by assessing energetic yields, availability in cells, and their full or partial oxidation during cell catabolism. This information can assist in decisions to use synthetic biology approaches to alter the range of respiratory substrates in plants. As a result, respiration could be optimized by introducing, improving, or controlling specific mitochondrial transporters and mitochondrial catabolic pathways.
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Affiliation(s)
- Xuyen H Le
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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4
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Asin-Garcia E, Robaey Z, Kampers LFC, Martins Dos Santos VAP. Exploring the Impact of Tensions in Stakeholder Norms on Designing for Value Change: The Case of Biosafety in Industrial Biotechnology. SCIENCE AND ENGINEERING ETHICS 2023; 29:9. [PMID: 36882674 PMCID: PMC9992083 DOI: 10.1007/s11948-023-00432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Synthetic biologists design and engineer organisms for a better and more sustainable future. While the manifold prospects are encouraging, concerns about the uncertain risks of genome editing affect public opinion as well as local regulations. As a consequence, biosafety and associated concepts, such as the Safe-by-design framework and genetic safeguard technologies, have gained notoriety and occupy a central position in the conversation about genetically modified organisms. Yet, as regulatory interest and academic research in genetic safeguard technologies advance, the implementation in industrial biotechnology, a sector that is already employing engineered microorganisms, lags behind. The main goal of this work is to explore the utilization of genetic safeguard technologies for designing biosafety in industrial biotechnology. Based on our results, we posit that biosafety is a case of a changing value, by means of further specification of how to realize biosafety. Our investigation is inspired by the Value Sensitive Design framework, to investigate scientific and technological choices in their appropriate social context. Our findings discuss stakeholder norms for biosafety, reasonings about genetic safeguards, and how these impact the practice of designing for biosafety. We show that tensions between stakeholders occur at the level of norms, and that prior stakeholder alignment is crucial for value specification to happen in practice. Finally, we elaborate in different reasonings about genetic safeguards for biosafety and conclude that, in absence of a common multi-stakeholder effort, the differences in informal biosafety norms and the disparity in biosafety thinking could end up leading to design requirements for compliance instead of for safety.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands.
- Bioprocess Engineering Group, Wageningen University & Research, 6700, AA, Wageningen, The Netherlands.
| | - Zoë Robaey
- Department of Social Sciences, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
| | - Linde F C Kampers
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
- Bioprocess Engineering Group, Wageningen University & Research, 6700, AA, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
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5
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King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nat Commun 2022; 13:7282. [PMID: 36435948 PMCID: PMC9701214 DOI: 10.1038/s41467-022-35021-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme's global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme's access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Sarah Maxel
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
| | - Yulai Zhang
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
| | - Karissa C Kenney
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Youtian Cui
- Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Emma Luu
- Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Justin B Siegel
- Genome Center, University of California Davis, Davis, CA, 95616, USA
- Department of Chemistry, Molecular Medicine University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine University of California, Davis, Davis, CA, USA
| | - Gregory A Weiss
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
- Department Materials Science and Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Han Li
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA.
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6
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Orsi E, Claassens NJ, Nikel PI, Lindner SN. Optimizing microbial networks through metabolic bypasses. Biotechnol Adv 2022; 60:108035. [PMID: 36096403 DOI: 10.1016/j.biotechadv.2022.108035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
Metabolism has long been considered as a relatively stiff set of biochemical reactions. This somewhat outdated and dogmatic view has been challenged over the last years, as multiple studies exposed unprecedented plasticity of metabolism by exploring rational and evolutionary modifications within the metabolic network of cell factories. Of particular importance is the emergence of metabolic bypasses, which consist of enzymatic reaction(s) that support unnatural connections between metabolic nodes. Such novel topologies can be generated through the introduction of heterologous enzymes or by upregulating native enzymes (sometimes relying on promiscuous activities thereof). Altogether, the adoption of bypasses resulted in an expansion in the capacity of the host's metabolic network, which can be harnessed for bioproduction. In this review, we discuss modifications to the canonical architecture of central carbon metabolism derived from such bypasses towards six optimization purposes: stoichiometric gain, overcoming kinetic limitations, solving thermodynamic barriers, circumventing toxic intermediates, uncoupling product synthesis from biomass formation, and altering redox cofactor specificity. The metabolic costs associated with bypass-implementation are likewise discussed, including tailoring their design towards improving bioproduction.
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Affiliation(s)
- Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany.
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7
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Abstract
Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterized by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of “minor” paralogs and complicates modular and combinatorial metabolic engineering strategies. While isoenzymes might be important in specific environments, they could be dispensable in controlled laboratory or industrial contexts. The present study explores the extent to which the genetic complexity of the central carbon metabolism (CCM) in S. cerevisiae, here defined as the combination of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and a limited number of related pathways and reactions, can be reduced by elimination of (iso)enzymes without major negative impacts on strain physiology. Cas9-mediated, groupwise deletion of 35 of the 111 genes yielded a “minimal CCM” strain which, despite the elimination of 32% of CCM-related proteins, showed only a minimal change in phenotype on glucose-containing synthetic medium in controlled bioreactor cultures relative to a congenic reference strain. Analysis under a wide range of other growth and stress conditions revealed remarkably few phenotypic changes from the reduction of genetic complexity. Still, a well-documented context-dependent role of GPD1 in osmotolerance was confirmed. The minimal CCM strain provides a model system for further research into genetic redundancy of yeast genes and a platform for strategies aimed at large-scale, combinatorial remodeling of yeast CCM.
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Yau MCM, Hayes M, Kalathil S. Biocatalytic conversion of sunlight and carbon dioxide to solar fuels and chemicals. RSC Adv 2022; 12:16396-16411. [PMID: 35754911 PMCID: PMC9169074 DOI: 10.1039/d2ra00673a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
This review discusses the progress in the assembly of photosynthetic biohybrid systems using enzymes and microbes as the biocatalysts which are capable of utilising light to reduce carbon dioxide to solar fuels. We begin by outlining natural photosynthesis, an inspired biomachinery to develop artificial photosystems, and the rationale and motivation to advance and introduce biological substrates to create more novel, and efficient, photosystems. The case studies of various approaches to the development of CO2-reducing microbial semi-artificial photosystems are also summarised, showcasing a variety of methods for hybrid microbial photosystems and their potential. Finally, approaches to investigate the relatively ambiguous electron transfer mechanisms in such photosystems are discussed through the presentation of spectroscopic techniques, eventually leading to what this will mean for the future of microbial hybrid photosystems.
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Affiliation(s)
- Mandy Ching Man Yau
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University Newcastle NE1 8ST UK
| | - Martin Hayes
- Johnson Matthey Technology Centre Cambridge Science Park, Milton Road Cambridge CB4 0FP UK
| | - Shafeer Kalathil
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University Newcastle NE1 8ST UK
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9
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Perkins ML, Gandara L, Crocker J. A synthetic synthesis to explore animal evolution and development. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200517. [PMID: 35634925 PMCID: PMC9149795 DOI: 10.1098/rstb.2020.0517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identifying the general principles by which genotypes are converted into phenotypes remains a challenge in the post-genomic era. We still lack a predictive understanding of how genes shape interactions among cells and tissues in response to signalling and environmental cues, and hence how regulatory networks generate the phenotypic variation required for adaptive evolution. Here, we discuss how techniques borrowed from synthetic biology may facilitate a systematic exploration of evolvability across biological scales. Synthetic approaches permit controlled manipulation of both endogenous and fully engineered systems, providing a flexible platform for investigating causal mechanisms in vivo. Combining synthetic approaches with multi-level phenotyping (phenomics) will supply a detailed, quantitative characterization of how internal and external stimuli shape the morphology and behaviour of living organisms. We advocate integrating high-throughput experimental data with mathematical and computational techniques from a variety of disciplines in order to pursue a comprehensive theory of evolution. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Mindy Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lautaro Gandara
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin Crocker
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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10
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Iacometti C, Marx K, Hönick M, Biletskaia V, Schulz-Mirbach H, Dronsella B, Satanowski A, Delmas VA, Berger A, Dubois I, Bouzon M, Döring V, Noor E, Bar-Even A, Lindner SN. Activating Silent Glycolysis Bypasses in Escherichia coli. BIODESIGN RESEARCH 2022; 2022:9859643. [PMID: 37850128 PMCID: PMC10521649 DOI: 10.34133/2022/9859643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/08/2022] [Indexed: 10/19/2023] Open
Abstract
All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal and the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal seemed to immediately operate in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary to restore growth of the strain. Furthermore, we engineered the "serine shunt" which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection, we performed an adaptive laboratory evolution study using an enolase deletion strain. Our experiments suggest that the evolved mutants use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.
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Affiliation(s)
- Camillo Iacometti
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Katharina Marx
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maria Hönick
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Viktoria Biletskaia
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Helena Schulz-Mirbach
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beau Dronsella
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Valérie A. Delmas
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Anne Berger
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Ivan Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Volker Döring
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Steffen N. Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany
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Theodosiou E, Tüllinghoff A, Toepel J, Bühler B. Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis. Front Bioeng Biotechnol 2022; 10:855715. [PMID: 35497353 PMCID: PMC9043136 DOI: 10.3389/fbioe.2022.855715] [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: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.
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Affiliation(s)
- Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Adrian Tüllinghoff
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- *Correspondence: Bruno Bühler,
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Khan AL, Numan M, Bilal S, Asaf S, Crafword K, Imran M, Al-Harrasi A, Al-Sabahi JN, Rehman NU, A-Rawahi A, Lee IJ. Mangrove's rhizospheric engineering with bacterial inoculation improve degradation of diesel contamination. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127046. [PMID: 34481398 DOI: 10.1016/j.jhazmat.2021.127046] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Mangroves (Avicennia marina) growing in intertidal areas are often exposed to diesel spills, adversely damaging the ecosystem. Herein, we showed for the first time that mangrove seedlings' associations with bacteria could reprogram host-growth, physiology, and ability to degrade diesel. We found four bacterial strains [Sphingomonas sp.-LK11, Rhodococcus corynebacterioides-NZ1, Bacillus subtilis-EP1 Bacillus safensis-SH10] exhibiting significant growth during diesel degradation (2% and 5%, v/v) and higher expression of alkane monooxygenase compared to control. This is in synergy with reduced long-chain n-alkanes (C24-C30) during microbe-diesel interactions in the bioreactor. Among individual strains, SH10 exhibited significantly higher potential to improve mangrove seedling's morphology, anatomy and growth during diesel treatment in rhizosphere compared to control. This was also evidenced by reduced activities and gene expression of antioxidant enzymes (catalases, peroxidases, ascorbic peroxidases, superoxide dismutases and polyphenol peroxidases) and lipid peroxidation during microbe-diesel interactions. Interestingly, we noticed significantly higher soil-enzyme activities (phosphatases and glucosidases) and essential metabolites in seedling's rhizosphere after bacteria and diesel treatments. Degradation of longer n-alkane chains in the rhizosphere also revealed a potential pathway that benefits mangroves by bacterial strains during diesel contaminations. Current results support microbes' application to rhizoengineer plant growth, responses, and phytoextraction abilities in environments contaminated with diesel spills. AVAILABILITY OF DATA AND MATERIALS: The datasets generated during the current study are available in the NCBI GenBank ((https://www.ncbi.nlm.nih.gov).
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Affiliation(s)
- Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, 616, Oman; Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA.
| | - Muhammad Numan
- Department of Biology, University of North Carolina at Greensboro, NC 27412, USA
| | - Saqib Bilal
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - Sajjad Asaf
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - Kerri Crafword
- Department of Biology and Biochemistry, College of Natural Science and Mathematics, University of Houston, TX, USA
| | - Muhammad Imran
- School of Applied Biosciences, Kyungpook National University, Daegu Korea, South Korea
| | - Ahmed Al-Harrasi
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA.
| | - Jamal Nasser Al-Sabahi
- Central Instrument Laboratory, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Najeeb Ur Rehman
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - Ahmed A-Rawahi
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu Korea, South Korea.
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13
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Boecker S, Slaviero G, Schramm T, Szymanski W, Steuer R, Link H, Klamt S. Deciphering the physiological response of Escherichia coli under high ATP demand. Mol Syst Biol 2021; 17:e10504. [PMID: 34928538 PMCID: PMC8686765 DOI: 10.15252/msb.202110504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 11/20/2022] Open
Abstract
One long-standing question in microbiology is how microbes buffer perturbations in energy metabolism. In this study, we systematically analyzed the impact of different levels of ATP demand in Escherichia coli under various conditions (aerobic and anaerobic, with and without cell growth). One key finding is that, under all conditions tested, the glucose uptake increases with rising ATP demand, but only to a critical level beyond which it drops markedly, even below wild-type levels. Focusing on anaerobic growth and using metabolomics and proteomics data in combination with a kinetic model, we show that this biphasic behavior is induced by the dual dependency of the phosphofructokinase on ATP (substrate) and ADP (allosteric activator). This mechanism buffers increased ATP demands by a higher glycolytic flux but, as shown herein, it collapses under very low ATP concentrations. Model analysis also revealed two major rate-controlling steps in the glycolysis under high ATP demand, which could be confirmed experimentally. Our results provide new insights on fundamental mechanisms of bacterial energy metabolism and guide the rational engineering of highly productive cell factories.
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Affiliation(s)
- Simon Boecker
- Analysis and Redesign of Biological NetworksMax Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Giulia Slaviero
- Analysis and Redesign of Biological NetworksMax Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Thorben Schramm
- Dynamic Control of Metabolic NetworksMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Witold Szymanski
- Core Facility for Mass Spectrometry and ProteomicsMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Ralf Steuer
- Institute for BiologyHumboldt‐University of BerlinBerlinGermany
| | - Hannes Link
- Dynamic Control of Metabolic NetworksMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Steffen Klamt
- Analysis and Redesign of Biological NetworksMax Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
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14
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Hayat IF, Plan M, Ebert BE, Dumsday G, Vickers CE, Peng B. Auxin-mediated induction of GAL promoters by conditional degradation of Mig1p improves sesquiterpene production in Saccharomyces cerevisiae with engineered acetyl-CoA synthesis. Microb Biotechnol 2021; 14:2627-2642. [PMID: 34499421 PMCID: PMC8601163 DOI: 10.1111/1751-7915.13880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae uses the pyruvate dehydrogenase-bypass for acetyl-CoA biosynthesis. This relatively inefficient pathway limits production potential for acetyl-CoA-derived biochemical due to carbon loss and the cost of two high-energy phosphate bonds per molecule of acetyl-CoA. Here, we attempted to improve acetyl-CoA production efficiency by introducing heterologous acetylating aldehyde dehydrogenase and phosphoketolase pathways for acetyl-CoA synthesis to enhance production of the sesquiterpene trans-nerolidol. In addition, we introduced auxin-mediated degradation of the glucose-dependent repressor Mig1p to allow induced expression of GAL promoters on glucose so that production potential on glucose could be examined. The novel genes that we used to reconstruct the heterologous acetyl-CoA pathways did not sufficiently complement the loss of endogenous acetyl-CoA pathways, indicating that superior heterologous enzymes are necessary to establish fully functional synthetic acetyl-CoA pathways and properly explore their potential for nerolidol synthesis. Notwithstanding this, nerolidol production was improved twofold to a titre of ˜ 900 mg l-1 in flask cultivation using a combination of heterologous acetyl-CoA pathways and Mig1p degradation. Conditional Mig1p depletion is presented as a valuable strategy to improve the productivities in the strains engineered with GAL promoters-controlled pathways when growing on glucose.
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Affiliation(s)
- Irfan Farabi Hayat
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- School of Chemistry and Molecular Biosciences (SCMB)the University of QueenslandBrisbaneQld4072Australia
| | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | | | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
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15
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Apura P, Gonçalves LG, Viegas SC, Arraiano CM. The world of ribonucleases from pseudomonads: a short trip through the main features and singularities. Microb Biotechnol 2021; 14:2316-2333. [PMID: 34427985 PMCID: PMC8601179 DOI: 10.1111/1751-7915.13890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/30/2021] [Indexed: 11/27/2022] Open
Abstract
The development of synthetic biology has brought an unprecedented increase in the number molecular tools applicable into a microbial chassis. The exploration of such tools into different bacteria revealed not only the challenges of context dependency of biological functions but also the complexity and diversity of regulatory layers in bacterial cells. Most of the standardized genetic tools and principles/functions have been mostly based on model microorganisms, namely Escherichia coli. In contrast, the non-model pseudomonads lack a deeper understanding of their regulatory layers and have limited molecular tools. They are resistant pathogens and promising alternative bacterial chassis, making them attractive targets for further studies. Ribonucleases (RNases) are key players in the post-transcriptional control of gene expression by degrading or processing the RNA molecules in the cell. These enzymes act according to the cellular requirements and can also be seen as the recyclers of ribonucleotides, allowing a continuous input of these cellular resources. This makes these post-transcriptional regulators perfect candidates to regulate microbial physiology. This review summarizes the current knowledge and unique properties of ribonucleases in the world of pseudomonads, taking into account genomic context analysis, biological function and strategies to use ribonucleases to improve biotechnological processes.
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Affiliation(s)
- Patrícia Apura
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Luis G. Gonçalves
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Sandra C. Viegas
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da República, EANOeiras2780‐157Portugal
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16
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Zhu L, Zhang J, Yang J, Jiang Y, Yang S. Strategies for optimizing acetyl-CoA formation from glucose in bacteria. Trends Biotechnol 2021; 40:149-165. [PMID: 33965247 DOI: 10.1016/j.tibtech.2021.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022]
Abstract
Acetyl CoA is an important precursor for various chemicals. We provide a metabolic engineering guideline for the production of acetyl-CoA and other end products from a bacterial chassis. Among 13 pathways that produce acetyl-CoA from glucose, 11 lose carbon in the process, and two do not. The first 11 use the Embden-Meyerhof-Parnas (EMP) pathway to produce redox cofactors and gain or lose ATP. The other two pathways function via phosphoketolase with net consumption of ATP, so they must therefore be combined with one of the 11 glycolytic pathways or auxiliary pathways. Optimization of these pathways can maximize the theoretical acetyl-CoA yield, thereby minimizing the overall cost of subsequent acetyl-CoA-derived molecules. Other strategies for generating hyper-producer strains are also addressed.
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Affiliation(s)
- Li Zhu
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai 200240, China
| | - Jieze Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Jiawei Yang
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China; Shanghai Taoyusheng Biotechnology Company Ltd, Shanghai 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China.
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17
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Li S, Ye Z, Moreb EA, Hennigan JN, Castellanos DB, Yang T, Lynch MD. Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli. Metab Eng 2021; 64:26-40. [PMID: 33460820 DOI: 10.1016/j.ymben.2021.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/23/2020] [Accepted: 01/10/2021] [Indexed: 12/24/2022]
Abstract
We report improved NADPH flux and xylitol biosynthesis in engineered E. coli. Xylitol is produced from xylose via an NADPH dependent reductase. We utilize 2-stage dynamic metabolic control to compare two approaches to optimize xylitol biosynthesis, a stoichiometric approach, wherein competitive fluxes are decreased, and a regulatory approach wherein the levels of key regulatory metabolites are reduced. The stoichiometric and regulatory approaches lead to a 20-fold and 90-fold improvement in xylitol production, respectively. Strains with reduced levels of enoyl-ACP reductase and glucose-6-phosphate dehydrogenase, led to altered metabolite pools resulting in the activation of the membrane bound transhydrogenase and an NADPH generation pathway, consisting of pyruvate ferredoxin oxidoreductase coupled with NADPH dependent ferredoxin reductase, leading to increased NADPH fluxes, despite a reduction in NADPH pools. These strains produced titers of 200 g/L of xylitol from xylose at 86% of theoretical yield in instrumented bioreactors. We expect dynamic control over the regulation of the membrane bound transhydrogenase as well as NADPH production through pyruvate ferredoxin oxidoreductase to broadly enable improved NADPH dependent bioconversions or production via NADPH dependent metabolic pathways.
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Affiliation(s)
- Shuai Li
- Department of Chemistry, Duke University, USA
| | - Zhixia Ye
- Department of Biomedical Engineering, Duke University, USA
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, USA
| | | | | | - Tian Yang
- Department of Biomedical Engineering, Duke University, USA
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18
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Satanowski A, Dronsella B, Noor E, Vögeli B, He H, Wichmann P, Erb TJ, Lindner SN, Bar-Even A. Awakening a latent carbon fixation cycle in Escherichia coli. Nat Commun 2020; 11:5812. [PMID: 33199707 PMCID: PMC7669889 DOI: 10.1038/s41467-020-19564-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Carbon fixation is one of the most important biochemical processes. Most natural carbon fixation pathways are thought to have emerged from enzymes that originally performed other metabolic tasks. Can we recreate the emergence of a carbon fixation pathway in a heterotrophic host by recruiting only endogenous enzymes? In this study, we address this question by systematically analyzing possible carbon fixation pathways composed only of Escherichia coli native enzymes. We identify the GED (Gnd-Entner-Doudoroff) cycle as the simplest pathway that can operate with high thermodynamic driving force. This autocatalytic route is based on reductive carboxylation of ribulose 5-phosphate (Ru5P) by 6-phosphogluconate dehydrogenase (Gnd), followed by reactions of the Entner-Doudoroff pathway, gluconeogenesis, and the pentose phosphate pathway. We demonstrate the in vivo feasibility of this new-to-nature pathway by constructing E. coli gene deletion strains whose growth on pentose sugars depends on the GED shunt, a linear variant of the GED cycle which does not require the regeneration of Ru5P. Several metabolic adaptations, most importantly the increased production of NADPH, assist in establishing sufficiently high flux to sustain this growth. Our study exemplifies a trajectory for the emergence of carbon fixation in a heterotrophic organism and demonstrates a synthetic pathway of biotechnological interest.
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Affiliation(s)
- Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Beau Dronsella
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Bastian Vögeli
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Hai He
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Philipp Wichmann
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), 35043, Marburg, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany.
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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19
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Oliver JC, Laghi L, Parolin C, Foschi C, Marangoni A, Liberatore A, Dias ALT, Cricca M, Vitali B. Metabolic profiling of Candida clinical isolates of different species and infection sources. Sci Rep 2020; 10:16716. [PMID: 33028931 PMCID: PMC7541501 DOI: 10.1038/s41598-020-73889-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/22/2020] [Indexed: 12/27/2022] Open
Abstract
Candida species are the most common cause of opportunistic fungal infections. Rapid identification and novel approaches for the characterization of these fungi are of great interest to improve the diagnosis and the knowledge about their pathogenic properties. This study aimed to characterize clinical isolates of Candida spp. by proteomics (MALDI-TOF MS) and metabolomics (1H-NMR), and to correlate their metabolic profiles with Candida species, source of infection and different virulence associated parameters. In particular, 49 Candida strains from different sources (blood, n = 15; vagina, n = 18; respiratory tract, n = 16), belonging mainly to C. albicans complex (61%), C. glabrata (20%) and C. parapsilosis (12%) species were used. Several extracellular and intracellular metabolites showed significantly different concentrations among isolates recovered from different sources of infection, as well as among different Candida species. These metabolites were mainly related to the glycolysis or gluconeogenesis, tricarboxylic acid cycle, nucleic acid synthesis and amino acid and lipid metabolism. Moreover, we found specific metabolic fingerprints associated with the ability to form biofilm, the antifungal resistance (i.e. caspofungin and fluconazole) and the production of secreted aspartyl proteinase. In conclusion, 1H-NMR-based metabolomics can be useful to deepen Candida spp. virulence and pathogenicity properties.
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Affiliation(s)
- Josidel Conceição Oliver
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Microbiology and Immunology, Federal University of Alfenas, Minas Gerais, Brazil
| | - Luca Laghi
- Centre of Foodomics, Department of Agro-Food Science and Technology, Alma Mater Studiorum, University of Bologna, Cesena, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Claudio Foschi
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Antonella Marangoni
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Andrea Liberatore
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | | | - Monica Cricca
- Microbiology, DIMES, Alma Mater Studiorum, University of Bologna, Bologna, Italy.
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, Bologna, Italy
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20
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Multiplex Design of the Metabolic Network for Production of l-Homoserine in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.01477-20. [PMID: 32801175 PMCID: PMC7531971 DOI: 10.1128/aem.01477-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/01/2020] [Indexed: 12/02/2022] Open
Abstract
In this study, the bottlenecks that sequentially limit l-homoserine biosynthesis were identified and resolved, based on rational and efficient metabolic-engineering strategies, coupled with CRISPR interference (CRISPRi)-based systematic analysis. The metabolomics data largely expanded our understanding of metabolic effects and revealed relevant targets for further modification to achieve better performance. The systematic analysis strategy, as well as metabolomics analysis, can be used to rationally design cell factories for the production of highly valuable chemicals. l-Homoserine, which is one of the few amino acids that is not produced on a large scale by microbial fermentation, plays a significant role in the synthesis of a series of valuable chemicals. In this study, systematic metabolic engineering was applied to target Escherichia coli W3110 for the production of l-homoserine. Initially, a basic l-homoserine producer was engineered through the strategies of overexpressing thrA (encoding homoserine dehydrogenase), removing the degradative and competitive pathways by knocking out metA (encoding homoserine O-succinyltransferase) and thrB (encoding homoserine kinase), reinforcing the transport system, and redirecting the carbon flux by deleting iclR (encoding the isocitrate lyase regulator). The resulting strain constructed by these strategies yielded 3.21 g/liter of l-homoserine in batch cultures. Moreover, based on CRISPR-Cas9/dCas9 (nuclease-dead Cas9)-mediated gene repression for 50 genes, the iterative genetic modifications of biosynthesis pathways improved the l-homoserine yield in a stepwise manner. The rational integration of glucose uptake and recovery of l-glutamate increased l-homoserine production to 7.25 g/liter in shake flask cultivation. Furthermore, the intracellular metabolic analysis further provided targets for strain modification by introducing the anaplerotic route afforded by pyruvate carboxylase to oxaloacetate formation, which resulted in accumulating 8.54 g/liter l-homoserine (0.33 g/g glucose, 62.4% of the maximum theoretical yield) in shake flask cultivation. Finally, a rationally designed strain gave 37.57 g/liter l-homoserine under fed-batch fermentation, with a yield of 0.31 g/g glucose. IMPORTANCE In this study, the bottlenecks that sequentially limit l-homoserine biosynthesis were identified and resolved, based on rational and efficient metabolic-engineering strategies, coupled with CRISPR interference (CRISPRi)-based systematic analysis. The metabolomics data largely expanded our understanding of metabolic effects and revealed relevant targets for further modification to achieve better performance. The systematic analysis strategy, as well as metabolomics analysis, can be used to rationally design cell factories for the production of highly valuable chemicals.
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21
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Calzadiaz-Ramirez L, Calvó-Tusell C, Stoffel GMM, Lindner SN, Osuna S, Erb TJ, Garcia-Borràs M, Bar-Even A, Acevedo-Rocha CG. In Vivo Selection for Formate Dehydrogenases with High Efficiency and Specificity toward NADP . ACS Catal 2020; 10:7512-7525. [PMID: 32733773 PMCID: PMC7384739 DOI: 10.1021/acscatal.0c01487] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/06/2020] [Indexed: 02/06/2023]
Abstract
The efficient regeneration of cofactors is vital for the establishment of biocatalytic processes. Formate is an ideal electron donor for cofactor regeneration due to its general availability, low reduction potential, and benign byproduct (CO2). However, formate dehydrogenases (FDHs) are usually specific to NAD+, such that NADPH regeneration with formate is challenging. Previous studies reported naturally occurring FDHs or engineered FDHs that accept NADP+, but these enzymes show low kinetic efficiencies and specificities. Here, we harness the power of natural selection to engineer FDH variants to simultaneously optimize three properties: kinetic efficiency with NADP+, specificity toward NADP+, and affinity toward formate. By simultaneously mutating multiple residues of FDH from Pseudomonas sp. 101, which exhibits practically no activity toward NADP+, we generate a library of >106 variants. We introduce this library into an E. coli strain that cannot produce NADPH. By selecting for growth with formate as the sole NADPH source, we isolate several enzyme variants that support efficient NADPH regeneration. We find that the kinetically superior enzyme variant, harboring five mutations, has 5-fold higher efficiency and 14-fold higher specificity in comparison to the best enzyme previously engineered, while retaining high affinity toward formate. By using molecular dynamics simulations, we reveal the contribution of each mutation to the superior kinetics of this variant. We further determine how nonadditive epistatic effects improve multiple parameters simultaneously. Our work demonstrates the capacity of in vivo selection to identify highly proficient enzyme variants carrying multiple mutations which would be almost impossible to find using conventional screening methods.
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Affiliation(s)
| | - Carla Calvó-Tusell
- Institut de Quı́mica Computacional i Catàlisi and Departament de Quı́mica, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
| | - Gabriele M. M. Stoffel
- Max Planck Institute of Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
| | - Steffen N. Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sílvia Osuna
- Institut de Quı́mica Computacional i Catàlisi and Departament de Quı́mica, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Tobias J. Erb
- Max Planck Institute of Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 16, D-35043 Marburg, Germany
| | - Marc Garcia-Borràs
- Institut de Quı́mica Computacional i Catàlisi and Departament de Quı́mica, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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22
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Abstract
Metabolic engineering is crucial in the development of production strains for platform chemicals, pharmaceuticals and biomaterials from renewable resources. The central carbon metabolism (CCM) of heterotrophs plays an essential role in the conversion of biomass to the cellular building blocks required for growth. Yet, engineering the CCM ultimately aims toward a maximization of flux toward products of interest. The most abundant dissimilative carbohydrate pathways amongst prokaryotes (and eukaryotes) are the Embden-Meyerhof-Parnas (EMP) and the Entner-Doudoroff (ED) pathways, which build the basics for heterotrophic metabolic chassis strains. Although the EMP is regarded as the textbook example of a carbohydrate pathway owing to its central role in production strains like Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis, it is either modified, complemented or even replaced by alternative carbohydrate pathways in different organisms. The ED pathway also plays key roles in biotechnological relevant bacteria, like Zymomonas mobilis and Pseudomonas putida, and its importance was recently discovered in photoautotrophs and marine microorganisms. In contrast to the EMP, the ED pathway and its variations are not evolutionary optimized for high ATP production and it differs in key principles such as protein cost, energetics and thermodynamics, which can be exploited in the construction of unique metabolic designs. Single ED pathway enzymes and complete ED pathway modules have been used to rewire carbon metabolisms in production strains and for the construction of cell-free enzymatic pathways. This review focuses on the differences of the ED and EMP pathways including their variations and discusses the use of alternative pathway strategies for in vivo and cell-free metabolic engineering.
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Affiliation(s)
- Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
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23
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Matsuoka Y, Kurata H. Computer-Aided Rational Design of Efficient NADPH Production System by Escherichia coli pgi Mutant Using a Mixture of Glucose and Xylose. Front Bioeng Biotechnol 2020; 8:277. [PMID: 32318559 PMCID: PMC7154054 DOI: 10.3389/fbioe.2020.00277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/16/2020] [Indexed: 12/02/2022] Open
Abstract
Lignocellulosic biomass can be hydrolyzed into two major sugars of glucose and xylose, and thus the strategy for the efficient consumption of both sugars is highly desirable. NADPH is the essential molecule for the production of industrially important value-added chemicals, and thus its availability is quite important. Escherichia coli mutant lacking the pgi gene encoding phosphoglucose isomerase (Pgi) has been preferentially used to overproduce the NADPH. However, there exists a disadvantage that the cell growth rate becomes low for the mutant grown on glucose. This limits the efficient NADPH production, and therefore, it is quite important to investigate how addition of different carbon source such as xylose (other than glucose) effectively improves the NADPH production. In this study, we have developed a kinetic model to propose an efficient NADPH production system using E. coli pgi-knockout mutant with a mixture of glucose and xylose. The proposed system adds xylose to glucose medium to recover the suppressed growth of the pgi mutant, and determines the xylose content to maximize the NADPH productivity. Finally, we have designed a mevalonate (MVA) production system by implementing ArcA overexpression into the pgi-knockout mutant using a mixture of glucose and xylose. In addition to NADPH overproduction, the accumulation of acetyl-CoA (AcCoA) is necessary for the efficient MVA production. In the present study, therefore, we considered to overexpress ArcA, where ArcA overexpression suppresses the TCA cycle, causing the overflow of AcCoA, a precursor of MVA. We predicted the xylose content that maximizes the MVA production. This approach demonstrates the possibility of a great progress in the computer-aided rational design of the microbial cell factories for useful metabolite production.
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Affiliation(s)
- Yu Matsuoka
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan.,Biomedical Informatics R&D Center, Kyushu Institute of Technology, Iizuka, Japan
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Guo X, Liu Y, Wang Q, Wang X, Li Q, Liu W, Zhao ZK. Non‐natural Cofactor and Formate‐Driven Reductive Carboxylation of Pyruvate. Angew Chem Int Ed Engl 2020; 59:3143-3146. [DOI: 10.1002/anie.201915303] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Xiaojia Guo
- Division of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yuxue Liu
- Division of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Qian Wang
- Division of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
- Dalian Key Laboratory of Energy BiotechnologyDalian Institute of Chemical Physics, CAS Dalian 116023 China
| | - Xueying Wang
- Division of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
- Dalian Key Laboratory of Energy BiotechnologyDalian Institute of Chemical Physics, CAS Dalian 116023 China
| | - Qing Li
- Division of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Wujun Liu
- Division of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
| | - Zongbao K. Zhao
- Division of BiotechnologyDalian Institute of Chemical PhysicsChinese Academy of Sciences Dalian 116023 China
- State Key Laboratory of CatalysisDalian Institute of Chemical Physics, CAS Dalian 116023 China
- Dalian Key Laboratory of Energy BiotechnologyDalian Institute of Chemical Physics, CAS Dalian 116023 China
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Guo X, Liu Y, Wang Q, Wang X, Li Q, Liu W, Zhao ZK. Non‐natural Cofactor and Formate‐Driven Reductive Carboxylation of Pyruvate. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Xiaojia Guo
- Division of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yuxue Liu
- Division of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China
| | - Qian Wang
- Division of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China
- Dalian Key Laboratory of Energy Biotechnology Dalian Institute of Chemical Physics, CAS Dalian 116023 China
| | - Xueying Wang
- Division of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China
- Dalian Key Laboratory of Energy Biotechnology Dalian Institute of Chemical Physics, CAS Dalian 116023 China
| | - Qing Li
- Division of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Wujun Liu
- Division of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China
| | - Zongbao K. Zhao
- Division of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China
- State Key Laboratory of Catalysis Dalian Institute of Chemical Physics, CAS Dalian 116023 China
- Dalian Key Laboratory of Energy Biotechnology Dalian Institute of Chemical Physics, CAS Dalian 116023 China
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Peabody GL, Elmore JR, Martinez-Baird J, Guss AM. Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:295. [PMID: 31890023 PMCID: PMC6927180 DOI: 10.1186/s13068-019-1627-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/04/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Efficient conversion of plant biomass to commodity chemicals is an important challenge that needs to be solved to enable a sustainable bioeconomy. Deconstruction of biomass to sugars and lignin yields a wide variety of low molecular weight carbon substrates that need to be funneled to product. Pseudomonas putida KT2440 has emerged as a potential platform for bioconversion of lignin and the other components of plant biomass. However, P. putida is unable to natively utilize several of the common sugars in hydrolysate streams, including galactose. RESULTS In this work, we integrated a De Ley-Doudoroff catabolic pathway for galactose catabolism into the chromosome of P. putida KT2440, using genes from several different organisms. We found that the galactonate catabolic pathway alone (DgoKAD) supported slow growth of P. putida on galactose. Further integration of genes to convert galactose to galactonate and to optimize the transporter expression level resulted in a growth rate of 0.371 h-1. Additionally, the best-performing strain was demonstrated to co-utilize galactose with glucose. CONCLUSIONS We have engineered P. putida to catabolize galactose, which will allow future engineered strains to convert more plant biomass carbon to products of interest. Further, by demonstrating co-utilization of glucose and galactose, continuous bioconversion processes for mixed sugar streams are now possible.
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Affiliation(s)
- George L. Peabody
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Joshua R. Elmore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Present Address: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | | | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Shimizu K, Matsuoka Y. Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation. Biotechnol Adv 2019; 37:107441. [PMID: 31472206 DOI: 10.1016/j.biotechadv.2019.107441] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/04/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
Abstract
The micro-aerophilic organisms and aerobes as well as yeast and higher organisms have evolved to gain energy through respiration (via oxidative phosphorylation), thereby enabling them to grow much faster than anaerobes. However, during respiration, reactive oxygen species (ROSs) are inherently (inevitably) generated, and threaten the cell's survival. Therefore, living organisms (or cells) must furnish the potent defense systems to keep such ROSs at harmless level, where the cofactor balance plays crucial roles. Namely, NADH is the source of energy generation (catabolism) in the respiratory chain reactions, through which ROSs are generated, while NADPH plays important roles not only for the cell synthesis (anabolism) but also for detoxifying ROSs. Therefore, the cell must rebalance the redox ratio by modulating the fluxes of the central carbon metabolism (CCM) by regulating the multi-level regulation machinery upon genetic perturbations and the change in the growth conditions. Here, we discuss about how aerobes accomplish such cofactor homeostasis against redox perturbations. In particular, we consider how single-gene mutants (including pgi, pfk, zwf, gnd and pyk mutants) modulate their metabolisms in relation to cofactor rebalance (and also by adaptive laboratory evolution). We also discuss about how the overproduction of NADPH (by the pathway gene mutation) can be utilized for the efficient production of useful value-added chemicals such as medicinal compounds, polyhydroxyalkanoates, and amino acids, all of which require NADPH in their synthetic pathways. We then discuss about the metabolic responses against oxidative stress, where αketoacids play important roles not only for the coordination between catabolism and anabolism, but also for detoxifying ROSs by non-enzymatic reactions, as well as for reducing the production of ROSs by repressing the activities of the TCA cycle and respiration (via carbon catabolite repression). Thus, we discuss about the mechanisms (basic strategies) that modulate the metabolism from respiration to respiro-fermentative metabolism causing overflow, based on the role of Pyk activity, affecting the NADPH production at the oxidative pentose phosphate (PP) pathway, and the roles of αketoacids for the change in the source of energy generation from the oxidative phosphorylation to the substrate level phosphorylation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio university, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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Guo W, Huang Q, Liu H, Hou S, Niu S, Jiang Y, Bao X, Shen Y, Fang X. Rational Engineering of Chorismate-Related Pathways in Saccharomyces cerevisiae for Improving Tyrosol Production. Front Bioeng Biotechnol 2019; 7:152. [PMID: 31334226 PMCID: PMC6616077 DOI: 10.3389/fbioe.2019.00152] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/10/2019] [Indexed: 11/26/2022] Open
Abstract
Tyrosol is extensively used in the pharmaceutical industry as an important natural product from plants. In this study, an exogenous pathway involved in catalyzing tyrosine to tyrosol was introduced into Saccharomyces cerevisiae. Furthermore, The pyruvate decarboxylase gene pdc1 was deleted to redirect the flux distribution at the pyruvate node, and a bifunctional NAD+-dependent fused chorismate mutase/prephenate dehydrogenase from E. coli (EcTyrA) and its' tyrosine inhibition resistant mutant (EcTyrAM53I/A354V) were heterologously expression in S. cerevisiae to tuning up the chorismate metabolism effectively directed the metabolic flux toward tyrosol production. Finally, the tyrosol yield of the engineered strain GFT-4 was improved to 126.74 ± 6.70 mg/g DCW at 48 h, increased 440 times compared with that of the control strain GFT-0 (0.28 ± 0.01 mg/g DCW). The new synergetic engineering strategy developed in this study can be further applied to increase the production of high value-added aromatic compounds derived from aromatic amino acid or shikimate in S. cerevisiae.
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Affiliation(s)
- Wei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiulan Huang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hao Liu
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Shaoli Hou
- Shandong Henglu Biological Technology Co. Ltd, Jinan, China
| | - Suhao Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Jinan, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Erwinia amylovora Auxotrophic Mutant Exometabolomics and Virulence on Apples. Appl Environ Microbiol 2019; 85:AEM.00935-19. [PMID: 31152019 DOI: 10.1128/aem.00935-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/30/2019] [Indexed: 02/06/2023] Open
Abstract
The Gram-negative bacterium Erwinia amylovora causes fire blight disease of apples and pears. While the virulence systems of E. amylovora have been studied extensively, relatively little is known about its parasitic behavior. The aim of this study was to identify primary metabolites that must be synthesized by this pathogen for full virulence. A series of auxotrophic E. amylovora mutants, representing 21 metabolic pathways, were isolated and characterized for metabolic defects and virulence in apple immature fruits and shoots. On detached apple fruitlets, mutants defective in arginine, guanine, hexosamine, isoleucine/valine, leucine, lysine, proline, purine, pyrimidine, sorbitol, threonine, tryptophan, and glucose metabolism had reduced virulence compared to the wild type, while mutants defective in asparagine, cysteine, glutamic acid, histidine, and serine biosynthesis were as virulent as the wild type. Auxotrophic mutant growth in apple fruitlet medium had a modest positive correlation with virulence in apple fruitlet tissues. Apple tree shoot inoculations with a representative subset of auxotrophs confirmed the apple fruitlet results. Compared to the wild type, auxotrophs defective in virulence caused an attenuated hypersensitive immune response in tobacco, with the exception of an arginine auxotroph. Metabolomic footprint analyses revealed that auxotrophic mutants which grew poorly in fruitlet medium nevertheless depleted environmental resources. Pretreatment of apple flowers with an arginine auxotroph inhibited the growth of the wild-type E. amylovora, while heat-killed auxotroph cells did not exhibit this effect, suggesting nutritional competition with the virulent strain on flowers. The results of our study suggest that certain nonpathogenic E. amylovora auxotrophs could have utility as fire blight biocontrol agents.IMPORTANCE This study has revealed the availability of a range of host metabolites to E. amylovora cells growing in apple tissues and has examined whether these metabolites are available in sufficient quantities to render bacterial de novo synthesis of these metabolites partially or even completely dispensable for disease development. The metabolomics analysis revealed that auxotrophic E. amylovora mutants have substantial impact on their environment in culture, including those that fail to grow appreciably. The reduced growth of virulent E. amylovora on flowers treated with an arginine auxotroph is consistent with the mutant competing for limiting resources in the flower environment. This information could be useful for novel fire blight management tool development, including the application of nonpathogenic E. amylovora auxotrophs to host flowers as an environmentally friendly biocontrol method. Fire blight management options are currently limited mainly to antibiotic sprays onto open blossoms and pruning of infected branches, so novel management options would be attractive to growers.
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Sheldon RA, Brady D. Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis. CHEMSUSCHEM 2019; 12:2859-2881. [PMID: 30938093 DOI: 10.1002/cssc.201900351] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/05/2019] [Accepted: 03/04/2019] [Indexed: 05/21/2023]
Abstract
This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new-to-nature biocatalytic reactions.
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Affiliation(s)
- Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
- Department of Biotechnology, Delft University of Technology, Section BOC, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, 2050, South Africa
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31
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A critical comparison of cellular and cell-free bioproduction systems. Curr Opin Biotechnol 2019; 60:221-229. [PMID: 31207555 DOI: 10.1016/j.copbio.2019.05.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/07/2019] [Indexed: 12/22/2022]
Abstract
Conversion of biological feedstocks into value-added chemicals is mostly performed via microbial fermentation. An emerging alternative approach is the use of cell-free systems, consisting of purified enzymes and cofactors. Unfortunately, the in vivo and in vitro research communities rarely interact, which leads to oversimplifications and exaggerations that do not permit fair comparison of the two strategies and impede synergistic interactions. Here, we provide a comprehensive account for the advantages and drawbacks associated with each strategy, and further discuss recent research efforts that aim to breach the limits of cellular and cell-free production. We also explore emerging hybrid solutions that integrate the benefits of both worlds and could expand the boundaries of biosynthesis.
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Fernández‐Cabezón L, Cros A, Nikel PI. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnol J 2019; 14:e1800439. [DOI: 10.1002/biot.201800439] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Lorena Fernández‐Cabezón
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
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33
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Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98-124. [PMID: 29926529 PMCID: PMC6302729 DOI: 10.1111/1751-7915.13292] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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34
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Huang WE, Nikel PI. The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back. Microb Biotechnol 2019; 12:5-7. [PMID: 30461208 PMCID: PMC6302714 DOI: 10.1111/1751-7915.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
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35
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Lindner SN, Ramirez LC, Krüsemann JL, Yishai O, Belkhelfa S, He H, Bouzon M, Döring V, Bar-Even A. NADPH-Auxotrophic E. coli: A Sensor Strain for Testing in Vivo Regeneration of NADPH. ACS Synth Biol 2018; 7:2742-2749. [PMID: 30475588 DOI: 10.1021/acssynbio.8b00313] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Insufficient rate of NADPH regeneration often limits the activity of biosynthetic pathways. Expression of NADPH-regenerating enzymes is commonly used to address this problem and increase cofactor availability. Here, we construct an Escherichia coli NADPH-auxotroph strain, which is deleted in all reactions that produce NADPH with the exception of 6-phosphogluconate dehydrogenase. This strain grows on a minimal medium only if gluconate is added as NADPH source. When gluconate is omitted, the strain serves as a "biosensor" for the capability of enzymes to regenerate NADPH in vivo. We show that the NADPH-auxotroph strain can be used to quantitatively assess different NADPH-regenerating enzymes and provide essential information on expression levels and concentrations of reduced substrates required to support optimal NADPH production rate. The NADPH-auxotroph strain thus serves as an effective metabolic platform for evaluating NADPH regeneration within the cellular context.
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Affiliation(s)
- Steffen N. Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | | | - Jan L. Krüsemann
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Oren Yishai
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Sophia Belkhelfa
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Hai He
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Volker Döring
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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36
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De Mol ML, Snoeck N, De Maeseneire SL, Soetaert WK. Hidden antibiotics: Where to uncover? Biotechnol Adv 2018; 36:2201-2218. [DOI: 10.1016/j.biotechadv.2018.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 01/21/2023]
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Zhang Y, Fernie AR. On the role of the tricarboxylic acid cycle in plant productivity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1199-1216. [PMID: 29917310 DOI: 10.1111/jipb.12690] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/18/2018] [Indexed: 05/10/2023]
Abstract
The tricarboxylic acid (TCA) cycle is one of the canonical energy pathways of living systems, as well as being an example of a pathway in which dynamic enzyme assemblies, or metabolons, are well characterized. The role of the enzymes have been the subject of saturated transgenesis approaches, whereby the expression of the constituent enzymes were reduced or knocked out in order to ascertain their in vivo function. Some of the resultant plants exhibited improved photosynthesis and plant growth, under controlled greenhouse conditions. In addition, overexpression of the endogenous genes, or heterologous forms of a number of the enzymes, has been carried out in tomato fruit and the roots of a range of species, and in some instances improvement in fruit yield and postharvest properties and plant performance, under nutrient limitation, have been reported, respectively. Given a number of variants, in nature, we discuss possible synthetic approaches involving introducing these variants, or at least a subset of them, into plants. We additionally discuss the likely consequences of introducing synthetic metabolons, wherein certain pairs of reactions are artificially permanently assembled into plants, and speculate as to future strategies to further improve plant productivity by manipulation of the core metabolic pathway.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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38
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Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142-155. [DOI: 10.1016/j.ymben.2018.05.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
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