1
|
Gomez-Hinostroza ES, Gurdo N, Alvan Vargas MVG, Nikel PI, Guazzaroni ME, Guaman LP, Castillo Cornejo DJ, Platero R, Barba-Ostria C. Current landscape and future directions of synthetic biology in South America. Front Bioeng Biotechnol 2023; 11:1069628. [PMID: 36845183 PMCID: PMC9950111 DOI: 10.3389/fbioe.2023.1069628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Synthetic biology (SynBio) is a rapidly advancing multidisciplinary field in which South American countries such as Chile, Argentina, and Brazil have made notable contributions and have established leadership positions in the region. In recent years, efforts have strengthened SynBio in the rest of the countries, and although progress is significant, growth has not matched that of the aforementioned countries. Initiatives such as iGEM and TECNOx have introduced students and researchers from various countries to the foundations of SynBio. Several factors have hindered progress in the field, including scarce funding from both public and private sources for synthetic biology projects, an underdeveloped biotech industry, and a lack of policies to promote bio-innovation. However, open science initiatives such as the DIY movement and OSHW have helped to alleviate some of these challenges. Similarly, the abundance of natural resources and biodiversity make South America an attractive location to invest in and develop SynBio projects.
Collapse
Affiliation(s)
- E. Sebastian Gomez-Hinostroza
- Laboratorio de Investigación en Citogenética y Biomoléculas de Anfibios (LICBA), Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Linda P. Guaman
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | | | - Raúl Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito, Ecuador,Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador,*Correspondence: Carlos Barba-Ostria,
| |
Collapse
|
2
|
Editorial for "Special Issue on the 2019 and 2020 iGEM Proceedings". Synth Syst Biotechnol 2022; 7:878-879. [PMID: 35601825 PMCID: PMC9096464 DOI: 10.1016/j.synbio.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
3
|
|
4
|
Dusek J, Plchova H, Cerovska N, Poborilova Z, Navratil O, Kratochvilova K, Gunter C, Jacobs R, Hitzeroth II, Rybicki EP, Moravec T. Extended Set of GoldenBraid Compatible Vectors for Fast Assembly of Multigenic Constructs and Their Use to Create Geminiviral Expression Vectors. FRONTIERS IN PLANT SCIENCE 2020; 11:522059. [PMID: 33193468 PMCID: PMC7641900 DOI: 10.3389/fpls.2020.522059] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Methods for simple and fast assembly of exchangeable standard DNA parts using Type II S restriction enzymes are becoming more and more popular in plant synthetic and molecular biology. These methods enable routine construction of large and complex multigene DNA structures. Two available frameworks emphasize either high cloning capacity (Modular Cloning, MoClo) or simplicity (GoldenBraid, GB). Here we present a set of novel α-level plasmids compatible with the GB convention that extend the ability of GB to rapidly assemble more complex genetic constructs, while maintaining compatibility with all existing GB parts as well as most MoClo parts and GB modules. With the use of our new plasmids, standard GB parts can be assembled into complex assemblies containing 1, 5, 10 and up to theoretically 50 units in each successive level of infinite loop assembly. Assembled DNA constructs can be also combined with conventional binary GB-assemblies (1, 2, 4, 8… units). We demonstrate the usefulness of our framework on single tube assembly of replicating plant expression constructs based on the geminivirus Bean yellow dwarf virus (BeYDV).
Collapse
Affiliation(s)
- Jakub Dusek
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Helena Plchova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Noemi Cerovska
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Zuzana Poborilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Oldrich Navratil
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Kratochvilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Cornelius Gunter
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Raygaana Jacobs
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Inga I. Hitzeroth
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Edward P. Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Tomas Moravec
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| |
Collapse
|
5
|
Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S. Recent advancements in high-level synthesis of the promising clinical drug, prodigiosin. Appl Microbiol Biotechnol 2019; 103:1667-1680. [PMID: 30637495 DOI: 10.1007/s00253-018-09611-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022]
Abstract
Prodigiosin, a red linear tripyrrole pigment and a member of the prodiginine family, is normally secreted by the human pathogen Serratia marcescens as a secondary metabolite. Studies on prodigiosin have received renewed attention as a result of reported immunosuppressive, antimicrobial and anticancer properties. High-level synthesis of prodigiosin and the bioengineering of strains to synthesise useful prodiginine derivatives have also been a subject of investigation. To exploit the potential use of prodigiosin as a clinical drug targeting bacteria or as a dye for textiles, high-level synthesis of prodigiosin is a prerequisite. This review presents an overview on the biosynthesis of prodigiosin from its natural host Serratia marcescens and through recombinant approaches as well as highlighting the beneficial properties of prodigiosin. We also discuss the prospect of adopting a synthetic biology approach for safe and cost-effective production of prodigiosin in a more industrially compliant surrogate host.
Collapse
Affiliation(s)
- Chee-Hoo Yip
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Orr Yarkoni
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - James Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| |
Collapse
|
6
|
You C, Huang R, Wei X, Zhu Z, Zhang YHP. Protein engineering of oxidoreductases utilizing nicotinamide-based coenzymes, with applications in synthetic biology. Synth Syst Biotechnol 2017; 2:208-218. [PMID: 29318201 PMCID: PMC5655348 DOI: 10.1016/j.synbio.2017.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/08/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
Two natural nicotinamide-based coenzymes (NAD and NADP) are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism, respectively. Most NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic roles. This coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology pathways. Changing the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering, which is closely related to product-oriented synthetic biology projects. This review focuses on the methodology of nicotinamide-based coenzyme engineering, with its application in improving product yields and decreasing production costs. Biomimetic nicotinamide-containing coenzymes have been proposed to replace natural coenzymes because they are more stable and less costly than natural coenzymes. Recent advances in the switching of coenzyme preference from natural to biomimetic coenzymes are also covered in this review. Engineering coenzyme preferences from natural to biomimetic coenzymes has become an important direction for coenzyme engineering, especially for in vitro synthetic pathways and in vivo bioorthogonal redox pathways.
Collapse
Affiliation(s)
- Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yi-Heng Percival Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
| |
Collapse
|
7
|
Wang Z, Wu X, Peng J, Hu Y, Fang B, Huang S. Artificially constructed quorum-sensing circuits are used for subtle control of bacterial population density. PLoS One 2014; 9:e104578. [PMID: 25119347 PMCID: PMC4132116 DOI: 10.1371/journal.pone.0104578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 07/15/2014] [Indexed: 01/31/2023] Open
Abstract
Vibrio fischeri is a typical quorum-sensing bacterium for which lux box, luxR, and luxI have been identified as the key elements involved in quorum sensing. To decode the quorum-sensing mechanism, an artificially constructed cell–cell communication system has been built. In brief, the system expresses several programmed cell-death BioBricks and quorum-sensing genes driven by the promoters lux pR and PlacO-1 in Escherichia coli cells. Their transformation and expression was confirmed by gel electrophoresis and sequencing. To evaluate its performance, viable cell numbers at various time periods were investigated. Our results showed that bacteria expressing killer proteins corresponding to ribosome binding site efficiency of 0.07, 0.3, 0.6, or 1.0 successfully sensed each other in a population-dependent manner and communicated with each other to subtly control their population density. This was also validated using a proposed simple mathematical model.
Collapse
Affiliation(s)
- Zhaoshou Wang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Xin Wu
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Jianghai Peng
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yidan Hu
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Baishan Fang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Chemical Biology of Fujian Province, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
- * E-mail:
| | - Shiyang Huang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| |
Collapse
|
8
|
Binder A, Lambert J, Morbitzer R, Popp C, Ott T, Lahaye T, Parniske M. A modular plasmid assembly kit for multigene expression, gene silencing and silencing rescue in plants. PLoS One 2014; 9:e88218. [PMID: 24551083 PMCID: PMC3923767 DOI: 10.1371/journal.pone.0088218] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/05/2014] [Indexed: 12/16/2022] Open
Abstract
The Golden Gate (GG) modular assembly approach offers a standardized, inexpensive and reliable way to ligate multiple DNA fragments in a pre-defined order in a single-tube reaction. We developed a GG based toolkit for the flexible construction of binary plasmids for transgene expression in plants. Starting from a common set of modules, such as promoters, protein tags and transcribed regions of interest, synthetic genes are assembled, which can be further combined to multigene constructs. As an example, we created T-DNA constructs encoding multiple fluorescent proteins targeted to distinct cellular compartments (nucleus, cytosol, plastids) and demonstrated simultaneous expression of all genes in Nicotiana benthamiana, Lotus japonicus and Arabidopsis thaliana. We assembled an RNA interference (RNAi) module for the construction of intron-spliced hairpin RNA constructs and demonstrated silencing of GFP in N. benthamiana. By combination of the silencing construct together with a codon adapted rescue construct into one vector, our system facilitates genetic complementation and thus confirmation of the causative gene responsible for a given RNAi phenotype. As proof of principle, we silenced a destabilized GFP gene (dGFP) and restored GFP fluorescence by expression of a recoded version of dGFP, which was not targeted by the silencing construct.
Collapse
Affiliation(s)
- Andreas Binder
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Jayne Lambert
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Robert Morbitzer
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Claudia Popp
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Thomas Ott
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Thomas Lahaye
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Martin Parniske
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| |
Collapse
|
9
|
Sarrion-Perdigones A, Palaci J, Granell A, Orzaez D. Design and construction of multigenic constructs for plant biotechnology using the GoldenBraid cloning strategy. Methods Mol Biol 2014; 1116:133-51. [PMID: 24395362 DOI: 10.1007/978-1-62703-764-8_10] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
GoldenBraid (GB) is an iterative and standardized DNA assembling system specially designed for Multigene Engineering in Plant Synthetic Biology. GB is based on restriction-ligation reactions using type IIS restriction enzymes. GB comprises a collection of standard DNA pieces named "GB parts" and a set of destination plasmids (pDGBs) that incorporate the multipartite assembly of standardized DNA parts. GB reactions are extremely efficient: two transcriptional units (TUs) can be assembled from several basic GBparts in one T-DNA less than 24 h. Moreover, larger assemblies comprising 4-5 TUs are routinely built in less than 2 working weeks. Here we provide a detailed view of the GB methodology. As a practical example, a Bimolecular Fluorescence Complementation construct comprising four TUs in a 12 kb DNA fragment is presented.
Collapse
Affiliation(s)
- Alejandro Sarrion-Perdigones
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia, Valencia, Spain
| | | | | | | |
Collapse
|
10
|
Sarrion-Perdigones A, Vazquez-Vilar M, Palací J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A, Orzaez D. GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology. PLANT PHYSIOLOGY 2013; 162:1618-31. [PMID: 23669743 PMCID: PMC3707536 DOI: 10.1104/pp.113.217661] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/10/2013] [Indexed: 05/18/2023]
Abstract
Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene structures at the DNA level while enabling the exchange of genetic building blocks among plant bioengineers. Here, we describe GoldenBraid 2.0 (GB2.0), a comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GB2.0 relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GB2.0 toolkit offers an evergrowing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc. Use of the GB2.0 framework is facilitated by a number of Web resources that include a publicly available database, tutorials, and a software package that provides in silico simulations and laboratory protocols for GB2.0 part domestication and multigene engineering. In short, GB2.0 provides a framework to exchange both information and physical DNA elements among bioengineers to help implement plant synthetic biology projects.
Collapse
Affiliation(s)
| | | | - Jorge Palací
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (A.S.-P., M.V.-V., J.P., B.C., J.F., A.G., D.O.), and Centro de Conservación y Mejora de la Agrodiversidad Valenciana (P.Z., J.B.), Universitat Politècnica de València, 46022 Valencia, Spain
| | - Bas Castelijns
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (A.S.-P., M.V.-V., J.P., B.C., J.F., A.G., D.O.), and Centro de Conservación y Mejora de la Agrodiversidad Valenciana (P.Z., J.B.), Universitat Politècnica de València, 46022 Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (A.S.-P., M.V.-V., J.P., B.C., J.F., A.G., D.O.), and Centro de Conservación y Mejora de la Agrodiversidad Valenciana (P.Z., J.B.), Universitat Politècnica de València, 46022 Valencia, Spain
| | - Peio Ziarsolo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (A.S.-P., M.V.-V., J.P., B.C., J.F., A.G., D.O.), and Centro de Conservación y Mejora de la Agrodiversidad Valenciana (P.Z., J.B.), Universitat Politècnica de València, 46022 Valencia, Spain
| | - José Blanca
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (A.S.-P., M.V.-V., J.P., B.C., J.F., A.G., D.O.), and Centro de Conservación y Mejora de la Agrodiversidad Valenciana (P.Z., J.B.), Universitat Politècnica de València, 46022 Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (A.S.-P., M.V.-V., J.P., B.C., J.F., A.G., D.O.), and Centro de Conservación y Mejora de la Agrodiversidad Valenciana (P.Z., J.B.), Universitat Politècnica de València, 46022 Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas (A.S.-P., M.V.-V., J.P., B.C., J.F., A.G., D.O.), and Centro de Conservación y Mejora de la Agrodiversidad Valenciana (P.Z., J.B.), Universitat Politècnica de València, 46022 Valencia, Spain
| |
Collapse
|
11
|
Osella M, Lagomarsino MC. Growth-rate-dependent dynamics of a bacterial genetic oscillator. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:012726. [PMID: 23410378 DOI: 10.1103/physreve.87.012726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/22/2012] [Indexed: 05/26/2023]
Abstract
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular "chassis" in which the circuits are embedded. For example, the intracellular macromolecular composition of fast-growing bacteria changes with growth rate. As a consequence, important parameters of gene expression, such as ribosome concentration or cell volume, are growth-rate dependent, ultimately coupling the dynamics of genetic circuits with cell physiology. This work addresses the effects of growth rate on the dynamics of a paradigmatic example of genetic oscillator, the repressilator. Making use of empirical growth-rate dependencies of parameters in bacteria, we show that the repressilator dynamics can switch between oscillations and convergence to a fixed point depending on the cellular state of growth, and thus on the nutrients it is fed. The physical support of the circuit (type of plasmid or gene positions on the chromosome) also plays an important role in determining the oscillation stability and the growth-rate dependence of period and amplitude. This analysis has potential application in the field of synthetic biology, and suggests that the coupling between endogenous genetic oscillators and cell physiology can have substantial consequences for their functionality.
Collapse
Affiliation(s)
- Matteo Osella
- Genomic Physics Group, UMR7238 CNRS Microorganism Genomics, 15, rue de l'École de Médecine, Paris, France.
| | | |
Collapse
|
12
|
Dewall MT, Cheng DW. The minimal genome: a metabolic and environmental comparison. Brief Funct Genomics 2012; 10:312-5. [PMID: 21987714 DOI: 10.1093/bfgp/elr030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The field of Synthetic Biology seeks to apply engineering principles to biology in order to produce novel biological systems. One approach to accomplish this goal is the genome-driven cell engineering approach, which searches for functioning minimal genomes in naturally occurring microorganisms, which can then be used as a template for future systems. Currently a prototypical minimal genome has not been discovered. This review analyzes the organisms Mycoplasma pneumoniae, Pelagibacter ubique, Vesicomyosocius okutanii and Prochlorococcus marinus as models of heterotrophic symbiont, heterotrophic free-living, autotrophic symbiont and autotrophic free-living organisms respectively and compares them to the current minimal cell model in order to determine which most closely resembles a true minimal genome. M. pneumoniae possesses a genome of 816 394 base pairs (bp) with 688 open reading frames (ORF) and a severely limited metabolism. Pelagibacter ubique possesses a 1 308 000 bp genome with 1354 ORF and has a fully functional metabolism but requires a reduced form of sulphur. Vesicomyosocius okutanii possesses a 1 020 000 bp genome with 975 ORF and is deficient in the production of threonine, isoleucine and ubiquinone. Prochlorococcus marinus possesses a 1 751 080 bp genome with 1884 ORF and has a complete metabolism with no deficiencies. The current minimal cell model requires a genome to be of limited size, culturalble and having minimal media requirements as such it is the conclusion of this review that P. marinus best fits this model. Further, future research should concentrate on genome reduction experiments using P. marinus and the search for additional minimal genomes should concentrate on autotrophic free-living organisms.
Collapse
Affiliation(s)
- Michael Thomas Dewall
- Department of Biology, Research Infrastructure for Minority Institutions, California State University, Fresno, CA 93740, USA
| | | |
Collapse
|
13
|
Danchin A. Scaling up synthetic biology: Do not forget the chassis. FEBS Lett 2012; 586:2129-37. [DOI: 10.1016/j.febslet.2011.12.024] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 12/16/2011] [Accepted: 12/19/2011] [Indexed: 11/28/2022]
|
14
|
Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, Orzaez D. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One 2011; 6:e21622. [PMID: 21750718 PMCID: PMC3131274 DOI: 10.1371/journal.pone.0021622] [Citation(s) in RCA: 213] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 06/03/2011] [Indexed: 12/12/2022] Open
Abstract
Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop ("braid") topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described.
Collapse
Affiliation(s)
- Alejandro Sarrion-Perdigones
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Erica Elvira Falconi
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Sara I. Zandalinas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Paloma Juárez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Asun Fernández-del-Carmen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| |
Collapse
|
15
|
Vinuselvi P, Park S, Kim M, Park JM, Kim T, Lee SK. Microfluidic technologies for synthetic biology. Int J Mol Sci 2011; 12:3576-93. [PMID: 21747695 PMCID: PMC3131579 DOI: 10.3390/ijms12063576] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/20/2011] [Accepted: 05/26/2011] [Indexed: 12/24/2022] Open
Abstract
Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.
Collapse
Affiliation(s)
- Parisutham Vinuselvi
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (P.V.); (J.M.P.)
| | - Seongyong Park
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (S.P.); (M.K.)
| | - Minseok Kim
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (S.P.); (M.K.)
| | - Jung Min Park
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (P.V.); (J.M.P.)
| | - Taesung Kim
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (S.P.); (M.K.)
| | - Sung Kuk Lee
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (P.V.); (J.M.P.)
| |
Collapse
|
16
|
Abstract
The choice of promoter is a critical step in optimizing the efficiency and stability of recombinant protein production in mammalian cell lines. Artificial promoters that provide stable expression across cell lines and can be designed to the desired strength constitute an alternative to the use of viral promoters. Here, we show how the nucleotide characteristics of highly active human promoters can be modelled via the genome-wide frequency distribution of short motifs: by overlapping motifs that occur infrequently in the genome, we constructed contiguous sequence that is rich in GC and CpGs, both features of known promoters, but lacking homology to real promoters. We show that snippets from this sequence, at 100 base pairs or longer, drive gene expression in vitro in a number of mammalian cells, and are thus candidates for use in protein production. We further show that expression is driven by the general transcription factors TFIIB and TFIID, both being ubiquitously present across cell types, which results in less tissue- and species-specific regulation compared to the viral promoter SV40. We lastly found that the strength of a promoter can be tuned up and down by modulating the counts of GC and CpGs in localized regions. These results constitute a "proof-of-concept" for custom-designing promoters that are suitable for biotechnological and medical applications.
Collapse
|
17
|
Huber SC. Grand challenges in plant physiology: the underpinning of translational research. FRONTIERS IN PLANT SCIENCE 2011; 2:48. [PMID: 22639597 PMCID: PMC3355685 DOI: 10.3389/fpls.2011.00048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 08/22/2011] [Indexed: 05/04/2023]
Affiliation(s)
- Steven C. Huber
- United States Department of Agriculture–Agricultural Research Service, University of IllinoisUrbana-Champaign, IL, USA
- Departments of Plant Biology and Crop Science, University of IllinoisUrbana-Champaign, IL, USA
- *Correspondence:
| |
Collapse
|
18
|
Purcell O, Savery NJ, Grierson CS, di Bernardo M. A comparative analysis of synthetic genetic oscillators. J R Soc Interface 2010; 7:1503-24. [PMID: 20591848 DOI: 10.1098/rsif.2010.0183] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic biology is a rapidly expanding discipline at the interface between engineering and biology. Much research in this area has focused on gene regulatory networks that function as biological switches and oscillators. Here we review the state of the art in the design and construction of oscillators, comparing the features of each of the main networks published to date, the models used for in silico design and validation and, where available, relevant experimental data. Trends are apparent in the ways that network topology constrains oscillator characteristics and dynamics. Also, noise and time delay within the network can both have constructive and destructive roles in generating oscillations, and stochastic coherence is commonplace. This review can be used to inform future work to design and implement new types of synthetic oscillators or to incorporate existing oscillators into new designs.
Collapse
Affiliation(s)
- Oliver Purcell
- Bristol Centre for Complexity Sciences, Department of Engineering Mathematics, University of Bristol, Bristol, UK.
| | | | | | | |
Collapse
|
19
|
Munteanu A, Constante M, Isalan M, Solé RV. Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation. BMC SYSTEMS BIOLOGY 2010; 4:66. [PMID: 20478019 PMCID: PMC2898670 DOI: 10.1186/1752-0509-4-66] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 05/17/2010] [Indexed: 11/24/2022]
Abstract
Background The ultimate goal of synthetic biology is the conception and construction of genetic circuits that are reliable with respect to their designed function (e.g. oscillators, switches). This task remains still to be attained due to the inherent synergy of the biological building blocks and to an insufficient feedback between experiments and mathematical models. Nevertheless, the progress in these directions has been substantial. Results It has been emphasized in the literature that the architecture of a genetic oscillator must include positive (activating) and negative (inhibiting) genetic interactions in order to yield robust oscillations. Our results point out that the oscillatory capacity is not only affected by the interaction polarity but by how it is implemented at promoter level. For a chosen oscillator architecture, we show by means of numerical simulations that the existence or lack of competition between activator and inhibitor at promoter level affects the probability of producing oscillations and also leaves characteristic fingerprints on the associated period/amplitude features. Conclusions In comparison with non-competitive binding at promoters, competition drastically reduces the region of the parameters space characterized by oscillatory solutions. Moreover, while competition leads to pulse-like oscillations with long-tail distribution in period and amplitude for various parameters or noisy conditions, the non-competitive scenario shows a characteristic frequency and confined amplitude values. Our study also situates the competition mechanism in the context of existing genetic oscillators, with emphasis on the Atkinson oscillator.
Collapse
Affiliation(s)
- Andreea Munteanu
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra (PRBB-GRIB), Dr Aiguader 88, 08003 Barcelona, Spain.
| | | | | | | |
Collapse
|