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Schmidt M, Pei L, Budisa N. Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:301-315. [PMID: 28567486 DOI: 10.1007/10_2016_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.
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Affiliation(s)
- Markus Schmidt
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria.
| | - Lei Pei
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria
| | - Nediljko Budisa
- AK Biokatalyse, Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
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Quin MB, Schmidt-Dannert C. Designer microbes for biosynthesis. Curr Opin Biotechnol 2014; 29:55-61. [PMID: 24646570 DOI: 10.1016/j.copbio.2014.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/19/2014] [Accepted: 02/20/2014] [Indexed: 01/01/2023]
Abstract
Microbes have long been adapted for the biosynthetic production of useful compounds. There is increasing demand for the rapid and cheap microbial production of diverse molecules in an industrial setting. Microbes can now be designed and engineered for a particular biosynthetic purpose, thanks to recent developments in genome sequencing, metabolic engineering, and synthetic biology. Advanced tools exist for the genetic manipulation of microbes to create novel metabolic circuits, making new products accessible. Metabolic processes can be optimized to increase yield and balance pathway flux. Progress is being made towards the design and creation of fully synthetic microbes for biosynthetic purposes. Together, these emerging technologies will facilitate the production of designer microbes for biosynthesis.
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Affiliation(s)
- Maureen B Quin
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 2012; 8:536-46. [PMID: 22596205 DOI: 10.1038/nchembio.970] [Citation(s) in RCA: 507] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, Petzold CJ. Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics 2012; 12:1289-99. [PMID: 22577029 DOI: 10.1002/pmic.201100482] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/13/2011] [Indexed: 11/09/2022]
Abstract
As synthetic biology matures to compete with chemical transformation of commodity and high-value compounds, a wide variety of well-characterized biological parts are needed to facilitate system design. Protein quantification based on selected-reaction monitoring (SRM) mass spectrometry compliments metabolite and transcript analysis for system characterization and optimizing flux through engineered pathways. By using SRM quantification, we assayed red fluorescent protein (RFP) expressed from plasmids containing several inducible and constitutive promoters and subsequently assessed protein production from the same promoters driving expression of eight mevalonate pathway proteins in Escherichia coli. For each of the promoter systems, the protein level for the first gene in the operon followed that of RFP, however, the levels of proteins produced from genes farther from the promoter were much less consistent. Second, we used targeted proteomics to characterize tyrosine biosynthesis pathway proteins after removal of native regulation. The changes were not expected to cause significant impact on protein levels, yet significant variation in protein abundance was observed and tyrosine production for these strains spanned a range from less than 1 mg/L to greater than 250 mg/L. Overall, our results underscore the importance of targeted proteomics for determining accurate protein levels in engineered systems and fine-tuning metabolic pathways.
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Affiliation(s)
- Pragya Singh
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
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Pinto F, van Elburg KA, Pacheco CC, Lopo M, Noirel J, Montagud A, Urchueguía JF, Wright PC, Tamagnini P. Construction of a chassis for hydrogen production: physiological and molecular characterization of a Synechocystis sp. PCC 6803 mutant lacking a functional bidirectional hydrogenase. MICROBIOLOGY-SGM 2011; 158:448-464. [PMID: 22096147 DOI: 10.1099/mic.0.052282-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are promising 'low-cost' microbial cell factories due to their simple nutritional requirements and metabolic plasticity, and the availability of tools for their genetic manipulation. The unicellular non-nitrogen-fixing Synechocystis sp. PCC 6803 is the best studied cyanobacterial strain and its genome was the first to be sequenced. The vast amount of physiological and molecular data available, together with a relatively small genome, makes Synechocystis suitable for computational metabolic modelling and to be used as a photoautotrophic chassis in synthetic biology applications. To prepare it for the introduction of a synthetic hydrogen producing device, a Synechocystis sp. PCC 6803 deletion mutant lacking an active bidirectional hydrogenase (ΔhoxYH) was produced and characterized at different levels: physiological, proteomic and transcriptional. The results showed that, under conditions favouring hydrogenase activity, 17 of the 210 identified proteins had significant differential fold changes in comparisons of the mutant with the wild-type. Most of these proteins are related to the redox and energy state of the cell. Transcriptional studies revealed that only six genes encoding those proteins exhibited significant differences in transcript levels. Moreover, the mutant exhibits similar growth behaviour compared with the wild-type, reflecting Synechocystis plasticity and metabolic adaptability. Overall, this study reveals that the Synechocystis ΔhoxYH mutant is robust and can be used as a photoautotrophic chassis for the integration of synthetic constructs, i.e. molecular constructs assembled from well characterized biological and/or synthetic parts (e.g. promoters, regulators, coding regions, terminators) designed for a specific purpose.
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Affiliation(s)
- Filipe Pinto
- Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Karin A van Elburg
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mapping Street, Sheffield S1 3JD, UK
| | - Catarina C Pacheco
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Miguel Lopo
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Josselin Noirel
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mapping Street, Sheffield S1 3JD, UK
| | - Arnau Montagud
- Instituto Universitario de Matemática Pura y Aplicada, Universidad Politécnica de Valencia, Camí de Vera, E-46071 Valencia, Spain
| | - Javier F Urchueguía
- Instituto Universitario de Matemática Pura y Aplicada, Universidad Politécnica de Valencia, Camí de Vera, E-46071 Valencia, Spain
| | - Phillip C Wright
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mapping Street, Sheffield S1 3JD, UK
| | - Paula Tamagnini
- Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
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Repurposing lipoic acid changes electron flow in two important metabolic pathways of Escherichia coli. Proc Natl Acad Sci U S A 2011; 108:7991-6. [PMID: 21521794 DOI: 10.1073/pnas.1105429108] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, cysteines of cytoplasmic proteins, including the essential enzyme ribonucleotide reductase (RNR), are maintained in the reduced state by the thioredoxin and glutathione/glutaredoxin pathways. An Escherichia coli mutant lacking both glutathione reductase and thioredoxin reductase cannot grow because RNR is disulfide bonded and nonfunctional. Here we report that suppressor mutations in the lpdA gene, which encodes the oxidative enzyme lipoamide dehydrogenase required for tricarboxylic acid (TCA) cycle functioning, restore growth to this redox-defective mutant. The suppressor mutations reduce LpdA activity, causing the accumulation of dihydrolipoamide, the reduced protein-bound form of lipoic acid. Dihydrolipoamide can then provide electrons for the reactivation of RNR through reduction of glutaredoxins. Dihydrolipoamide is oxidized in the process, restoring function to the TCA cycle. Thus, two electron transfer pathways are rewired to meet both oxidative and reductive needs of the cell: dihydrolipoamide functionally replaces glutathione, and the glutaredoxins replace LpdA. Both lipoic acid and glutaredoxins act in the reverse manner from their normal cellular functions. Bioinformatic analysis suggests that such activities may also function in other bacteria.
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Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms. Appl Microbiol Biotechnol 2011; 90:407-16. [DOI: 10.1007/s00253-011-3172-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
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Pandhal J, Ow SY, Noirel J, Wright PC. Improving N-glycosylation efficiency in Escherichia coli using shotgun proteomics, metabolic network analysis, and selective reaction monitoring. Biotechnol Bioeng 2010; 108:902-12. [PMID: 21404263 DOI: 10.1002/bit.23011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 11/01/2010] [Indexed: 02/05/2023]
Abstract
Recently, the prospect of using Escherichia coli as a host for human glycoprotein production has increased due to detailed characterization of the prokaryotic N-glycosylation process and the ability to transfer the system into this bacterium. Although functionality of the native Campylobacter jejuni N-glycosylation system in E. coli has been demonstrated, the efficiency of the process using the well-characterized C. jejuni glycoprotein AcrA, was found to be low at 13.4±0.9% of total extracted protein. A combined approach using isobaric labeling of peptides and probability-based network analysis of metabolic changes was applied to forward engineer E. coli to improve glycosylation efficiency of AcrA. Enhancing flux through the glyoxylate cycle was identified as a potential metabolic manipulation to improve modification efficiency and was achieved by increasing the expression of isocitrate lyase. While the overall recombinant protein titre did not change significantly, the amount of glycosylated protein increased by approximately 300%.
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Affiliation(s)
- Jagroop Pandhal
- Department of Chemical and Biological Engineering, ChELSI Institute, Biological and Environmental Systems Group, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
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Mathematical modeling: bridging the gap between concept and realization in synthetic biology. J Biomed Biotechnol 2010; 2010:541609. [PMID: 20589069 PMCID: PMC2878679 DOI: 10.1155/2010/541609] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 03/07/2010] [Indexed: 11/17/2022] Open
Abstract
Mathematical modeling plays an important and often indispensable role in synthetic biology because it serves as a crucial link between the concept and realization of a biological circuit. We review mathematical modeling concepts and methodologies as relevant to synthetic biology, including assumptions that underlie a model, types of modeling frameworks (deterministic and stochastic), and the importance of parameter estimation and optimization in modeling. Additionally we expound mathematical techniques used to analyze a model such as sensitivity analysis and bifurcation analysis, which enable the identification of the conditions that cause a synthetic circuit to behave in a desired manner. We also discuss the role of modeling in phenotype analysis such as metabolic and transcription network analysis and point out some available modeling standards and software. Following this, we present three case studies—a metabolic oscillator, a synthetic counter, and a bottom-up gene regulatory network—which have incorporated mathematical modeling as a central component of synthetic circuit design.
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Special focus: Synthetic biology. Biotechnol J 2009. [DOI: 10.1002/biot.200990087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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