1
|
Zhou S, Alper HS, Zhou J, Deng Y. Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level. Crit Rev Biotechnol 2022; 43:646-663. [PMID: 35450502 DOI: 10.1080/07388551.2022.2040415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of intracellular, biosensor-based dynamic regulation strategies to regulate and improve the production of useful compounds have progressed significantly over previous decades. By employing such an approach, it is possible to simultaneously realize high productivity and optimum growth states. However, industrial fermentation conditions contain a mixture of high- and low-performance non-genetic variants, as well as young and aged cells at all growth phases. Such significant individual variations would hinder the precise controlling of metabolic flux at the single-cell level to achieve high productivity at the macroscopic population level. Intracellular biosensors, as the regulatory centers of metabolic networks, can real-time sense intra- and extracellular conditions and, thus, could be synthetically adapted to balance the biomass formation and overproduction of compounds by individual cells. Herein, we highlight advances in the designing and engineering approaches to intracellular biosensors. Then, the spatiotemporal properties of biosensors associated with the distribution of inducers are compared. Also discussed is the use of such biosensors to dynamically control the cellular metabolic flux. Such biosensors could achieve single-cell regulation or collective regulation goals, depending on whether or not the inducer distribution is only intracellular.
Collapse
Affiliation(s)
- Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| |
Collapse
|
2
|
Hwang HJ, Kim JW, Ju SY, Park JH, Lee PC. Application of an oxygen-inducible nar promoter system in metabolic engineering for production of biochemicals in Escherichia coli. Biotechnol Bioeng 2016; 114:468-473. [PMID: 27543929 DOI: 10.1002/bit.26082] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 12/28/2022]
Abstract
The nar promoter, a dissolved oxygen (DO)-dependent promoter in Escherichia coli, is simply induced and functional in any cell growth phase, which are advantageous for producing biochemicals/fuels on an industrial scale. To demonstrate the feasibility of using the nar promoter in the metabolic engineering of biochemicals/biofuels in E. coli, three target pathways were examined: the d-lactate, 2,3-butandiol (2,3-BDO), and 1,3-propanediol (1,3-PDO) pathways consisting of one, three, and six genes, respectively. Each pathway gene was expressed under the control of the nar promoter. When the ldhD gene was expressed in fed-batch culture, the titer, yield, and productivity of d-lactate were 113.12 ± 2.37 g/L, 0.91 ± 0.07 g/g-glucose, and 4.19 ± 0.09 g/L/h, respectively. When three 2,3-BDO pathway genes (ilvBN, aldB, bdh1) were expressed in fed-batch culture, the titer, yield, and productivity of (R,R)-2,3-BDO were 48.0 ± 8.48 g/L, 0.43 ± 0.07 g/g glucose, and 0.76 ± 0.13 g/L/h, respectively. When six 1,3-PDO pathway genes (dhaB1B2B3, yqhD, gdrA, and gdrB) were expressed in fed-batch culture, the titer, yield, and productivity of 1,3-PDO were 15.8 ± 0.62 g/L, 0.35 ± 0.01 g/g-glycerol, and 0.25 ± 0.01 g/L/h, respectively. Based on the reasonable performance comparable to that observed in previous studies using different promoters in metabolic engineering, the nar promoter can serve as a controlled expression tool for developing a microbial system to efficiently produce biochemicals and biofuels. Biotechnol. Bioeng. 2017;114: 468-473. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hee J Hwang
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749, South Korea
| | - Jin W Kim
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749, South Korea
| | - Si Y Ju
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749, South Korea
| | - Jin H Park
- BioMaterials Lab, Samsung Advanced Institute of Technology, Suwon, 443-803, South Korea
| | - Pyung C Lee
- Department of Molecular Science and Technology, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, 443-749, South Korea
| |
Collapse
|
3
|
Construction of non-invasively constitutive expression vectors using a metagenome-derived promoter for soluble expression of proteins. Bioprocess Biosyst Eng 2013; 36:667-76. [DOI: 10.1007/s00449-013-0890-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 01/10/2013] [Indexed: 11/24/2022]
|
4
|
Chang HN, Kim MI, Fei Q, Choi JDR, Shang L, Kim NJ, Kim JA, Park HG. Economic evaluation of off-gas recycle pressure swing adsorption (PSA) in industrial scale poly(3-hydroxybutyrate) fermentation. BIOTECHNOL BIOPROC E 2011. [DOI: 10.1007/s12257-010-0114-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
5
|
Kim NJ, Choi JH, Kim YC, Lee J, Lee SY, Chang HN, Lee PC. Development of anaerobically inducible nar promoter expression vectors for the expression of recombinant proteins in Escherichia coli. J Biotechnol 2011; 151:102-7. [DOI: 10.1016/j.jbiotec.2010.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 10/24/2010] [Accepted: 11/15/2010] [Indexed: 11/15/2022]
|
6
|
Garcia JR, Cha HJ, Rao G, Marten MR, Bentley WE. Microbial nar-GFP cell sensors reveal oxygen limitations in highly agitated and aerated laboratory-scale fermentors. Microb Cell Fact 2009; 8:6. [PMID: 19146688 PMCID: PMC2630296 DOI: 10.1186/1475-2859-8-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 01/15/2009] [Indexed: 11/10/2022] Open
Abstract
Background Small-scale microbial fermentations are often assumed to be homogeneous, and oxygen limitation due to inadequate micromixing is often overlooked as a potential problem. To assess the relative degree of micromixing, and hence propensity for oxygen limitation, a new cellular oxygen sensor has been developed. The oxygen responsive E. coli nitrate reductase (nar) promoter was used to construct an oxygen reporter plasmid (pNar-GFPuv) which allows cell-based reporting of oxygen limitation. Because there are greater than 109 cells in a fermentor, one can outfit a vessel with more than 109 sensors. Our concept was tested in high density, lab-scale (5 L), fed-batch, E. coli fermentations operated with varied mixing efficiency – one verses four impellers. Results In both cases, bioreactors were maintained identically at greater than 80% dissolved oxygen (DO) during batch phase and at approximately 20% DO during fed-batch phase. Trends for glucose consumption, biomass and DO showed nearly identical behavior. However, fermentations with only one impeller showed significantly higher GFPuv expression than those with four, indicating a higher degree of fluid segregation sufficient for cellular oxygen deprivation. As the characteristic time for GFPuv expression (approx 90 min.) is much larger than that for mixing (approx 10 s), increased specific fluorescence represents an averaged effect of oxygen limitation over time and by natural extension, over space. Conclusion Thus, the pNar-GFPuv plasmid enabled bioreactor-wide oxygen sensing in that bacterial cells served as individual recirculating sensors integrating their responses over space and time. We envision cell-based oxygen sensors may find utility in a wide variety of bioprocessing applications.
Collapse
Affiliation(s)
- Jose R Garcia
- Department of Chemical and Biochemical Engineering, University of Maryland Baltimore County, Baltimore, MD 21052, USA.
| | | | | | | | | |
Collapse
|
7
|
Lee KH, Cho MH, Chung T, Chang HN, Lim SH, Lee J. Characterization of an oxygen-dependent inducible promoter, the Escherichia coli nar promoter, in gram-negative host strains. Biotechnol Bioeng 2003; 82:271-7. [PMID: 12599253 DOI: 10.1002/bit.10567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The Escherichia coli nar promoter is maximally induced under anaerobic conditions in the presence of nitrate ion or under anaerobic only conditions, depending on the genotype of the E. coli nar promoter. Previously, we found that the E. coli nar promoter has some desirable characteristics as an inducible promoter in the E. coli host strains. In this study, the E. coli nar promoter with lacZ gene at the downstream was cloned onto a broad-host-range Gram-negative vector, pBBR122. It was then induced in some other Gram-negative host strains, such as Agrobacterium, Pseudomonas, and Rhizobium, to determine whether the E. coli nar promoter could be used as an inducible promoter in these strains. From shake-flask experiments it was found that the wild-type E. coli nar promoter cloned onto pBBR122, pNW61, was suppressed under aerobic conditions in an Agrobacterium host strain, was partially induced under microaerobic only conditions, and was maximally induced under microaerobic conditions in the presence of nitrate ion. Whereas the mutant-type E. coli nar promoter cloned onto pBBR122, pNW618, was suppressed under aerobic conditions and was maximally induced under microaerobic conditions, regardless of the presence of nitrate ion. This kind of induction pattern observed for the E. coli nar promoters in the Agrobacterium host strain was similar to that observed for the E. coli nar promoters in the E. coli host strain. On the other hand, it was found that both of the E. coli nar promoters, pNW61 and pNW618, in a Pseudomonas host strain were partially induced under aerobic conditions and were maximally induced under microaerobic conditions, regardless of the presence of nitrate. Finally, it was found that both of the E. coli nar promoters in a Rhizobium host strain were minimally induced, regardless of the presence of oxygen or nitrate ion. Similar induction patterns for the three strains were also observed from fermentor experiments in which the dissolved oxygen (DO) level was tightly controlled. From an evolutionary point of view, the results from the three Gram-negative host strains indicate that the E. coli nar promoter system, including the promoter and regulatory proteins, was best conserved in the Agrobacterium host strain and the least conserved in the Rhizobium host strain. From an industrial point of view, the results indicate that the E. coli nar promoter system can be used as an oxygen-dependent inducible promoter in both Agrobacterium and Pseudomonas host strains.
Collapse
Affiliation(s)
- Kil Ho Lee
- School of Chemical Engineering and Technology, Yeungnam University, Kyungbuk, Korea
| | | | | | | | | | | |
Collapse
|
8
|
Chang HN, Han SJ, Yim SC, Han MR, Lee J. Fed-batch cultures of Escherichia coli cells with oxygen-dependent nar promoter systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2002; 74:171-81. [PMID: 11991178 DOI: 10.1007/3-540-45736-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The recombinant proteins produced from Escherichia coli as a host cell need to be made at as low a cost as possible because of the end of the monopoly following expiry of the patent on early pharmaceutical proteins, and thus expanding applications to non-pharmaceutical large-scale products. We review in this article how the various promoters used in recombinant E. coli could affect its protein products, especially with emphasis on relatively new oxygen-dependent nar promoters for beta-galactosidase production. Several studies carried out in the authors' laboratory show that the nar promoter does not require any chemicals except 1% nitrate and oxygen for protein production. And according to recent work with the modified strains it is possible to produce the enzyme (beta-galactosidase) even without the nitrate ions at 45% of its total protein content when its cell density reached OD = 176.
Collapse
Affiliation(s)
- Ho Nam Chang
- Department of Chemical Engineering, KAIST, Taejon, Korea.
| | | | | | | | | |
Collapse
|
9
|
Abstract
The demands for recombinant proteins, in addition to plasmid DNA, for therapeutic use are steadily increasing. Bacterial fermentation processes have long been and still are the major tool for production of these molecules. The key objective of process optimization is to attain a high yield of the required quality, which is determined, to a large extent, by plasmid replication rates, metabolic capacity and the properties of the specific gene construct. When high copy number plasmids are used, the metabolic capacity of the host cell is often overstrained and efficient protein production is impaired. The plasmid copy number is the key parameter in the exploitation of the host cell, and can be maximized by optimal control of the flux ratios between biosynthesis of host cell proteins and recombinant proteins.
Collapse
Affiliation(s)
- Reingard Grabherr
- University of Agricultural Sciences, Institute of Applied Microbiology, Muthgasse 18, A-1190, Vienna, Austria.
| | | |
Collapse
|
10
|
Balbás P. Understanding the art of producing protein and nonprotein molecules in Escherichia coli. Mol Biotechnol 2001; 19:251-67. [PMID: 11721622 DOI: 10.1385/mb:19:3:251] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The high-level production of functional proteins in E. coli is a very extense field of research in biotechnology. A number of important aspects to be considered in the initial design of an expression system and their interplay, were clear years ago. However, in recent times, strategies that go beyond transcription, translation, stability, vector, and strain choice, have been developed; so now expression of active peptides can be viewed as a more integrated process. Coexpression of protein subunits, foldases and chaperones, protein folding, location and purification schemes, metabolic engineering of the cell's central metabolism, and in vitro refolding strategies, are some of the novelties that are now available to aid in the success of an efficient expression system for active heterologous proteins. This review presents a compilation of the basic issues that influence the success in the production of protein and nonprotein products in Escherichia coli, as well as some general strategies designed to facilitate downstream process operations and improve biosynthesis yields.
Collapse
Affiliation(s)
- P Balbás
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos CP 62210, México.
| |
Collapse
|
11
|
Han SJ, Chang HN, Lee J. Characterization of an oxygen-dependent inducible promoter, thenar promoter ofEscherichia coli, to utilize in metabolic engineering. Biotechnol Bioeng 2001. [DOI: 10.1002/1097-0290(20010305)72:5<573::aid-bit1022>3.0.co;2-i] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|