1
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Cheng YY, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM, Venturelli OS. Efficient plasmid transfer via natural competence in a microbial co-culture. Mol Syst Biol 2023; 19:e11406. [PMID: 36714980 PMCID: PMC9996237 DOI: 10.15252/msb.202211406] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - James M Papadopoulos
- Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Jason D Zuke
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin, Madison, WI, USA.,Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
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2
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Restrepo-Pineda S, Pérez NO, Valdez-Cruz NA, Trujillo-Roldán MA. Thermoinducible expression system for producing recombinant proteins in Escherichia coli: advances and insights. FEMS Microbiol Rev 2021; 45:6223457. [PMID: 33844837 DOI: 10.1093/femsre/fuab023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Recombinant protein (RP) production from Escherichia coli has been extensively studied to find strategies for increasing product yields. The thermoinducible expression system is commonly employed at the industrial level to produce various RPs which avoids the addition of chemical inducers, thus minimizing contamination risks. Multiple aspects of the molecular origin and biotechnological uses of its regulatory elements (pL/pR promoters and cI857 thermolabile repressor) derived from bacteriophage λ provide knowledge to improve the bioprocesses using this system. Here, we discuss the main aspects of the potential use of the λpL/pR-cI857 thermoinducible system for RP production in E. coli, focusing on the approaches of investigations that have contributed to the advancement of this expression system. Metabolic and physiological changes that occur in the host cells caused by heat stress and by RP overproduction are also described. Therefore, the current scenario and the future applications of systems that use heat to induce RP production is discussed to understand the relationship between the activation of the bacterial heat shock response, RP accumulation, and its possible aggregation to form inclusion bodies.
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Affiliation(s)
- Sara Restrepo-Pineda
- Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Néstor O Pérez
- Probiomed S.A. de C.V. Planta Tenancingo, Cruce de Carreteras Acatzingo-Zumpahuacan SN, 52400 Tenancingo, Estado de México, México
| | - Norma A Valdez-Cruz
- Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Mauricio A Trujillo-Roldán
- Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
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3
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Tan J, Sastry AV, Fremming KS, Bjørn SP, Hoffmeyer A, Seo S, Voldborg BG, Palsson BO. Independent component analysis of E. coli's transcriptome reveals the cellular processes that respond to heterologous gene expression. Metab Eng 2020; 61:360-368. [PMID: 32710928 DOI: 10.1016/j.ymben.2020.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 10/23/2022]
Abstract
Achieving the predictable expression of heterologous genes in a production host has proven difficult. Each heterologous gene expressed in the same host seems to elicit a different host response governed by unknown mechanisms. Historically, most studies have approached this challenge by manipulating the properties of the heterologous gene through methods like codon optimization. Here we approach this challenge from the host side. We express a set of 45 heterologous genes in the same Escherichia coli strain, using the same expression system and culture conditions. We collect a comprehensive RNAseq set to characterize the host's transcriptional response. Independent Component Analysis of the RNAseq data set reveals independently modulated gene sets (iModulons) that characterize the host response to heterologous gene expression. We relate 55% of variation of the host response to: Fear vs Greed (16.5%), Metal Homeostasis (19.0%), Respiration (6.0%), Protein folding (4.5%), and Amino acid and nucleotide biosynthesis (9.0%). If these responses can be controlled, then the success rate with predicting heterologous gene expression should increase.
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Affiliation(s)
- Justin Tan
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Karoline S Fremming
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Alexandra Hoffmeyer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Sangwoo Seo
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Bjørn G Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.
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4
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Efficient genetic approaches for improvement of plasmid based expression of recombinant protein in Escherichia coli : A review. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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5
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Schofield DM, Templar A, Newton J, Nesbeth DN. Promoter engineering to optimize recombinant periplasmic Fab' fragment production in Escherichia coli. Biotechnol Prog 2016; 32:840-7. [PMID: 27071365 DOI: 10.1002/btpr.2273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/14/2016] [Indexed: 11/11/2022]
Abstract
Fab' fragments have become an established class of biotherapeutic over the last two decades. Likewise, developments in synthetic biology are providing ever more powerful techniques for designing bacterial genes, gene networks and entire genomes that can be used to improve industrial performance of cells used for production of biotherapeutics. We have previously observed significant leakage of an exogenous therapeutic Fab' fragment into the growth medium during high cell density cultivation of an Escherichia coli production strain. In this study we sought to apply a promoter engineering strategy to address the issue of Fab' fragment leakage and its consequent bioprocess challenges. We used site directed mutagenesis to convert the Ptac promoter, present in the plasmid, pTTOD-A33 Fab', to a Ptic promoter which has been shown by others to direct expression at a 35% reduced rate compared to Ptac . We characterized the resultant production trains in which either Ptic or Ptac promoters direct Fab' fragment expression. The Ptic promoter strain showed a 25-30% reduction in Fab' expression relative to the original Ptac strain. Reduced Fab' leakage and increased viability over the course of a fed-batch fermentation were also observed for the Ptic promoter strain. We conclude that cell design steps such as the Ptac to Ptic promoter conversion reported here, can yield significant process benefit and understanding with respect to periplasmic Fab' fragment production. It remains an open question as to whether the influence of transgene expression on periplasmic retention is mediated by global metabolic burden effects or periplasm overcapacity. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:840-847, 2016.
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Affiliation(s)
- Desmond M Schofield
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT
| | - Alex Templar
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT
| | - Joseph Newton
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT
| | - Darren N Nesbeth
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT
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6
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Yu HQ, Wang YG, Yong TM, She YH, Fu FL, Li WC. Heterologous expression of betaine aldehyde dehydrogenase gene from Ammopiptanthus nanus confers high salt and heat tolerance to Escherichia coli. Gene 2014; 549:77-84. [PMID: 25046139 DOI: 10.1016/j.gene.2014.07.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 06/17/2014] [Accepted: 07/17/2014] [Indexed: 11/25/2022]
Abstract
Betaine aldehyde dehydrogenase (BADH) catalyzes the synthesis of glycine betaine, a regulator of osmosis, and therefore BADH is considered to play a significant role in response of plants to abiotic stresses. Here, based on the conserved residues of the deduced amino acid sequences of the homologous BADH genes, we cloned the AnBADH gene from the xerophytic leguminous plant Ammopiptanthus nanus by using reverse transcription PCR and rapid amplification of cDNA ends. The full-length cDNA is 1,868 bp long without intron, and contains an open reading frame of 1512 bp, and 3'- and 5'-untranslated regions of 294 and 62 bp. It encodes a 54.71 kDa protein of 503 amino acids. The deduced amino acid sequence shares high homology, conserved amino acid residues and sequence motifs crucial for the function with the BADHs in other leguminous species. The sequence of the open reading frame was used to construct a prokaryotic expression vector pET32a-AnBADH, and transform Escherichia coli. The transformants expressed the heterologous AnBADH gene under the induction of isopropyl β-D-thiogalactopyranoside, and demonstrated significant enhancement of salt and heat tolerance under the stress conditions of 700 mmol L(-1) NaCl and 55°C high temperature. This result suggests that the AnBADH gene might play a crucial role in adaption of A. nanus to the abiotic stresses, and have the potential to be applied to transgenic operations of commercially important crops for improvement of abiotic tolerance.
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Affiliation(s)
- Hao-Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Ying-Ge Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Tai-Ming Yong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yue-Hui She
- Agronomy Faculty, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Feng-Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
| | - Wan-Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
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7
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Deng LQ, Yu HQ, Liu YP, Jiao PP, Zhou SF, Zhang SZ, Li WC, Fu FL. Heterologous expression of antifreeze protein gene AnAFP from Ammopiptanthus nanus enhances cold tolerance in Escherichia coli and tobacco. Gene 2014; 539:132-40. [PMID: 24502990 DOI: 10.1016/j.gene.2014.01.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 01/02/2014] [Accepted: 01/03/2014] [Indexed: 11/23/2022]
Abstract
Antifreeze proteins are a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival under the subzero environments. Ammopiptanthus nanus is the unique evergreen broadleaf bush endemic to the Mid-Asia deserts. It survives at the west edge of the Tarim Basin from the disappearance of the ancient Mediterranean in the Tertiary Period. Its distribution region is characterized by the arid climate and extreme temperatures, where the extreme temperatures range from -30 °C to 40 °C. In the present study, the antifreeze protein gene AnAFP of A. nanus was used to transform Escherichia coli and tobacco, after bioinformatics analysis for its possible function. The transformed E. coli strain expressed the heterologous AnAFP gene under the induction of isopropyl β-D-thiogalactopyranoside, and demonstrated significant enhancement of cold tolerance. The transformed tobacco lines expressed the heterologous AnAFP gene in response to cold stress, and showed a less change of relative electrical conductivity under cold stress, and a less wilting phenotype after 16 h of -3 °C cold stress and thawing for 1h than the untransformed wild-type plants. All these results imply the potential value of the AnAFP gene to be used in genetic modification of commercially important crops for improvement of cold tolerance.
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Affiliation(s)
- Long-Qun Deng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Hao-Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yan-Ping Liu
- Faculty of Plant Science, Tarim University, Alar, Xinjiang 843300, PR China
| | - Pei-Pei Jiao
- Faculty of Plant Science, Tarim University, Alar, Xinjiang 843300, PR China
| | - Shu-Feng Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Su-Zhi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Wan-Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
| | - Feng-Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
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8
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Rodríguez-Carmona E, Cano-Garrido O, Dragosits M, Maurer M, Mader A, Kunert R, Mattanovich D, Villaverde A, Vázquez F. Recombinant Fab expression and secretion in Escherichia coli continuous culture at medium cell densities: Influence of temperature. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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9
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Chi L, Fan DD, Ma XX, Mi Y, Luo YE, Zhu CH, Zhu XL, Xue WJ. A genetic algorithm for the optimization of the thermoinduction protocol for high-level production of recombinant human-like collagen from Escherichia coli. Biotechnol Appl Biochem 2011; 58:175-84. [PMID: 21679241 DOI: 10.1002/bab.25] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 03/14/2011] [Indexed: 11/12/2022]
Abstract
Production of recombinant human-like collagen (RHLC) by thermoinduction of recombinant Escherichia coli BL 21 during high cell density cultivation was investigated in a 30 L bioreactor. The effects of induction temperature (T), pH, and carbon-to-nitrogen molar ratio of the nutrient medium (C/N) were examined. The optimal thermoinduction protocol for RHLC production was determined by using a model coupling genetic algorithm and artificial neural networks. The optimal operating conditions were as follows: maintenance of induction temperature at 42°C for 3 H and then at 39.4°C until the end, induction pH at 7.03, and C/N at 4.8 (mol/mol). The theoretical maximum concentration of RHLC was 12.5 g/L, whereas the experimental value was 12.1 g/L under the optimal induction conditions.
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Affiliation(s)
- Lei Chi
- Shaanxi R&D Center of Biomaterial and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, People's Republic of China
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10
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Abstract
In the past decade, the tendency to move from a global, one-size-fits-all treatment philosophy to personalized medicine is based, in part, on the nuanced differences and sub-classifications of disease states. Our knowledge of these varied states stems from not only the ability to diagnose, classify, and perform experiments on cell populations as a whole, but also from new technologies that allow interrogation of cell populations at the individual cell level. Such departures from conventional thinking are driven by the recognition that clonal cell populations have numerous activities that manifest as significant levels of non-genetic heterogeneity. Clonal populations by definition originate from a single genetic origin so are regarded as having a high level of homogeneity as compared to genetically distinct cell populations. However, analysis at the single cell level has revealed a different phenomenon; cells and organisms require an inherent level of non-genetic heterogeneity to function properly, and in some cases, to survive. The growing understanding of this occurrence has lead to the development of methods to monitor, analyze, and better characterize the heterogeneity in cell populations. Following the trend of DNA- and protein microarrays, platforms capable of simultaneously monitoring each cell in a population have been developed. These cellular microarray platforms and other related formats allow for continuous monitoring of single live cells and simultaneously generate individual cell and average population data that are more descriptive and information-rich than traditional bulk methods. These technological advances have helped develop a better understanding of the intricacies associated with biological processes and afforded greater insight into complex biological systems. The associated instruments, techniques, and reagents now allow for highly multiplexed analyses, which enable multiple cellular activities, processes, or pathways to be monitored simultaneously. This critical review will discuss the paradigm shift associated with cellular heterogeneity, speak to the key developments that have lead to our better understanding of systems biology, and detail the future directions of the discipline (281 references).
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Affiliation(s)
- Maureen A Walling
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA
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11
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Zoonens M, Miroux B. Expression of membrane proteins at the Escherichia coli membrane for structural studies. Methods Mol Biol 2010; 601:49-66. [PMID: 20099139 DOI: 10.1007/978-1-60761-344-2_4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Structural biology of membrane proteins is often limited by the first steps in obtaining sufficient yields of proteins because native sources are seldom. Heterologous systems like bacteria are then commonly employed for membrane protein over-expression. Escherichia coli is the main bacterial host used. However, overproduction of a foreign membrane protein at a non-physiological level is usually toxic for cells or leads to inclusion body formation. Those effects can be reduced by optimizing the cell growth conditions, choosing the suitable bacterial strain and expression vector, and finally co-expressing the target protein and the b-subunit of E. coli adenosine triphosphate (ATP)-synthase, which triggers the proliferation of intracytoplasmic membranes. This chapter is devoted to help the experimenter in choosing the appropriate plasmid/bacterial host combination for optimizing the amount of the target membrane protein produced in its correct folded state.
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Affiliation(s)
- Manuela Zoonens
- Université Paris, Institut de Biologie Physico-Chimique, France
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12
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Gasser B, Saloheimo M, Rinas U, Dragosits M, Rodríguez-Carmona E, Baumann K, Giuliani M, Parrilli E, Branduardi P, Lang C, Porro D, Ferrer P, Tutino ML, Mattanovich D, Villaverde A. Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microb Cell Fact 2008; 7:11. [PMID: 18394160 PMCID: PMC2322954 DOI: 10.1186/1475-2859-7-11] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 04/04/2008] [Indexed: 11/17/2022] Open
Abstract
Different species of microorganisms including yeasts, filamentous fungi and bacteria have been used in the past 25 years for the controlled production of foreign proteins of scientific, pharmacological or industrial interest. A major obstacle for protein production processes and a limit to overall success has been the abundance of misfolded polypeptides, which fail to reach their native conformation. The presence of misfolded or folding-reluctant protein species causes considerable stress in host cells. The characterization of such adverse conditions and the elicited cell responses have permitted to better understand the physiology and molecular biology of conformational stress. Therefore, microbial cell factories for recombinant protein production are depicted here as a source of knowledge that has considerably helped to picture the extremely rich landscape of in vivo protein folding, and the main cellular players of this complex process are described for the most important cell factories used for biotechnological purposes.
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Affiliation(s)
- Brigitte Gasser
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | | | - Ursula Rinas
- Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Martin Dragosits
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | - Escarlata Rodríguez-Carmona
- Autonomous University of Barcelona, Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology, and CIBER-BBN Network in Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Kristin Baumann
- Autonomous University of Barcelona, Department of Chemical Engineering, Barcelona, Spain
| | - Maria Giuliani
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Ermenegilda Parrilli
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Paola Branduardi
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, Milan, Italy
| | - Christine Lang
- Technical University Berlin, Faculty III, Institute for Microbiology and Genetics, Berlin, Germany
| | - Danilo Porro
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, Milan, Italy
| | - Pau Ferrer
- Autonomous University of Barcelona, Department of Chemical Engineering, Barcelona, Spain
| | - Maria Luisa Tutino
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Diethard Mattanovich
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | - Antonio Villaverde
- Autonomous University of Barcelona, Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology, and CIBER-BBN Network in Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
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13
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Fernández G, Vera A, Villaverde A, Martínez MA. Analysis of recombinant protein toxicity in E. coli through a phage λ-based genetic screening system. Biotechnol Lett 2007; 29:1381-6. [PMID: 17479218 DOI: 10.1007/s10529-007-9390-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 04/02/2007] [Accepted: 04/03/2007] [Indexed: 11/30/2022]
Abstract
The aspartic protease from the human immunodeficiency virus type 1 (HIV-1) is highly toxic to E. coli, thus impairing its yield in production processes. Proteolytic cleavage of essential cellular proteins is probably a major contributor to the bacteriocidal effect but this has not been proven. Through an adapted high-throughput lambda-based screening system, we have analyzed a set of HIV-1 protease mutants with distinguishable catalytic properties and we show that inactive enzymes are as toxic to E. coli cells as the wild-type enzyme. Together with additional data from directed molecular evolution approaches, these results indicate that the toxicity of the viral protease is not linked to its proteolytic activity. Our study also reveals that the lambda-based screening system is a robust new tool for the genetic analysis of highly toxic recombinant products in E. coli.
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Affiliation(s)
- Guerau Fernández
- Fundació irsiCaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, 08916, Badalona, Spain
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14
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González-Montalbán N, Carrió MM, Cuatrecasas S, Arís A, Villaverde A. Bacterial inclusion bodies are cytotoxic in vivo in absence of functional chaperones DnaK or GroEL. J Biotechnol 2005; 118:406-12. [PMID: 16024126 DOI: 10.1016/j.jbiotec.2005.05.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 05/06/2005] [Accepted: 05/12/2005] [Indexed: 11/22/2022]
Abstract
Cytotoxicity of cytoplasmic bacterial inclusion bodies has been explored in vivo in cells producing a model, misfolding-prone beta-galactosidase fusion protein. The formation of such aggregates does not result in detectable toxicity on Escherichia coli producing cells. However, a deficiency in the main chaperones DnaK or GroEL but not in other components of the heat shock system such as the chaperone ClpA or the protease Lon, promotes a dramatic inhibition of cell growth. The role of DnaK and GroEL in minimizing toxicity of in vivo protein aggregation is discussed in the context of the conformational stress and the protein quality control system.
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Affiliation(s)
- Nuria González-Montalbán
- Institut de Biotecnologia i de Biomedicina, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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15
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Kuang Y, Walt DR. Monitoring “promiscuous” drug effects on single cells of multiple cell types. Anal Biochem 2005; 345:320-5. [PMID: 16099418 DOI: 10.1016/j.ab.2005.06.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 06/08/2005] [Accepted: 06/14/2005] [Indexed: 11/22/2022]
Abstract
Recent advances in genomics and molecular pathogenesis studies have determined that many diseases are caused by a multiplicity of factors. New drug regimens may consist of multiple biologically active agents designed to act synergistically on multiple biochemical targets. Live cell assays are becoming a standard for identifying new drug candidates with an emphasis on "homogeneous" living cell assays in which multiple cell lines are mixed and monitored simultaneously. In this study, we used a high-density single living cell array, based on an optical imaging fiber bundle microwell array, to simultaneously monitor "promiscuous" drug effects on single cells of multiple cell types. Such a capability allows for a more comprehensive understanding of how cells dynamically respond to combinatorial drug libraries or how different cellular pathways and regulation circuits respond cooperatively to drugs in individual cells.
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Affiliation(s)
- Yina Kuang
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
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16
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LeThanh H, Neubauer P, Hoffmann F. The small heat-shock proteins IbpA and IbpB reduce the stress load of recombinant Escherichia coli and delay degradation of inclusion bodies. Microb Cell Fact 2005; 4:6. [PMID: 15707488 PMCID: PMC552319 DOI: 10.1186/1475-2859-4-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 02/11/2005] [Indexed: 11/23/2022] Open
Abstract
Background The permanently impaired protein folding during recombinant protein production resembles the stress encountered at extreme temperatures, under which condition the putative holding chaperones, IbpA/IbpB, play an important role. We evaluated the impact of ibpAB deletion or overexpression on stress responses and the inclusion body metabolism during production of yeast α-glucosidase in Escherichia coli. Results Deletion of ibpAB, which is innocuous under physiological conditions, impaired culture growth during α-glucosidase production. At higher temperatures, accumulation of stress proteins including disaggregation chaperones (DnaK and ClpB) and components of the RNA degradosome, enolase and PNP, was intensified. Overexpression of ibpAB, conversely, suppressed the heat-shock response under these conditions. Inclusion bodies of α-glucosidase started to disaggregate after arrest of protein synthesis in a ClpB and DnaK dependent manner, followed by degradation or reactivation. IbpA/IbpB decelerated disaggregation and degradation at higher temperatures, but did hardly influence the disaggregation kinetics at 15°C. Overexpression of ibpAB concomitant to production at 42°C increased the yield of α-glucosidase activity during reactivation. Conclusions IbpA/IbpB attenuate the accumulation of stress proteins, and – at high temperatures – save disaggregated proteins from degradation, at the cost, however, of delayed removal of aggregates. Without ibpAB, inclusion body removal is faster, but cells encounter more intense stress and growth impairment. IbpA/IbpB thus exert a major function in cell protection during stressful situations.
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Affiliation(s)
- Ha LeThanh
- Institute for Biotechnology, Department of Biochemistry/Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle, Germany
| | - Peter Neubauer
- Bioprocess Engineering Laboratory, P.O. Box 4300, Department of Process and Environmental Engineering, Biocenter Oulu, University of Oulu, FIN-90014 Oulu, Finland
| | - Frank Hoffmann
- Institute for Biotechnology, Department of Biochemistry/Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120 Halle, Germany
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Lin H, Hoffmann F, Rozkov A, Enfors SO, Rinas U, Neubauer P. Change of extracellular cAMP concentration is a sensitive reporter for bacterial fitness in high-cell-density cultures of Escherichia coli. Biotechnol Bioeng 2005; 87:602-13. [PMID: 15352058 DOI: 10.1002/bit.20152] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Guanosine-3',5'-tetraphosphate (ppGpp) and sigmaS, two regulators of the starvation response of Escherichia coli, have received increasing attention for monitoring cell physiological changes in production processes, although both are difficult to quantify. The kinetics of cAMP formation and degradation were not yet investigated in such processes, although the complex regulation of cAMP by synthesis, release, and degradation in connection with straightforward methods for analysis renders it a highly informative target. Therefore, we followed the cAMP concentration in various nonrecombinant and in four different recombinant glucose-limited fed-batch processes in different production scales. The intracellular cAMP concentration increases strongly at the end of the batch phase. Most cAMP is released to the cultivation medium. The rates of accumulation and degradation of extracellular cAMP are growth-rate-dependent and show a distinct maximum at a growth rate of about 0.35 h(-1). At very low growth rates, below 0.05 h(-1), extracellular cAMP is not produced but rather degraded, independent of whether this low growth rate is caused by glucose limitation or by the high metabolic load of recombinant protein production. In contrast to intracellular cAMP, which is highly unstable, analysis of extracellular cAMP is simpler and the kinetics of accumulation and degradation reflect well the physiological situation, including unlimited growth, limitation, and severe starvation of a production host.
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Affiliation(s)
- Hongying Lin
- Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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18
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Menart V, Jevsevar S, Vilar M, Trobis A, Pavko A. Constitutive versus thermoinducible expression of heterologous proteins in Escherichia coli based on strong PR,PL promoters from phage lambda. Biotechnol Bioeng 2003; 83:181-90. [PMID: 12768624 DOI: 10.1002/bit.10660] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Constitutive and thermoinducible expression plasmids based on strong P(R),P(L) promoters from phage lambda were compared for production of TNF-alpha and its analogs under various conditions. Much higher accumulation of TNF was obtained in a constitutive system, so the wider applicability of such systems was studied. In constitutive systems, proteolytically susceptible proteins can be produced easily at low cultivation temperatures and the addition of expensive or toxic chemical inducers is not required. On the other hand, toxic proteins cannot be produced and selection pressure must be strictly maintained to ensure segregational stability of plasmids. Accumulation of TNF-alpha and various analogs at levels up to 25% of total soluble protein was repeatedly achieved, which was 2-3-fold higher than in a thermoinducible system. The stable behavior of the constitutive system in laboratory fermentors was also confirmed. We propose the constitutive system described here as a general model for many currently used expression systems containing strong but not completely repressed promoters. Such systems may be considered as constitutive ones with reduced promoter strengths, but still exhibiting all the intrinsic properties of constitutive expression systems. Although all modern expression systems are inducible, wider use of a constitutive system is evidently possible.
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Affiliation(s)
- Viktor Menart
- Lek d.d., Recombinant Biotechnology Department, Recombinant Pharmaceuticals, Laboratory location: Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
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Lee J, Kim HC, Kim SW, Kim SW, Hong SI, Park YH. Interplay of SOS induction, recombinant gene expression, and multimerization of plasmid vectors in Escherichia coli. Biotechnol Bioeng 2002; 80:84-92. [PMID: 12209789 DOI: 10.1002/bit.10354] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using pBR322- and pUC-derived plasmid vectors, a homologous (Escherichia coli native esterase) and three heterologous proteins (human interleukin-2, human interleukin-6, and Zymomonas levansucrase) were synthesized in E. coli IC2015(recA::lacZ) and GY4786 (sfiA::lacZ) strains. Via time-course measurement of beta-galactosidase activity in each recombinant culture, the SOS induction was estimated in detail and the results were systematically compared. In recombinant E. coli, the SOS response did not happen either with the recombinant insert-negative plasmid backbone alone or the expression vectors containing the homologous gene. Irrespective of gene expression level and toxic activity of synthesized foreign proteins, the SOS response was induced only when the heterologous genes were expressed using a particular plasmid vector, indicating strong dependence on the recombinant gene clone and the selection of a plasmid vector system. It is suggested that in recombinant E. coli the SOS response (i.e., activation of recA expression and initial sfiA expression) may be related neither to metabolic burden nor toxic cellular event(s) by synthesized heterologous protein, but may be provoked by foreign gene-specific interaction between a foreign gene and a plasmid vector. Unlike in E. coli XL1-blue(recA(-)) strains used, all expression vectors encoding each of the three heterologous proteins were multimerized in E. coli IC2015 strains in the course of cultivation, whereas the expression vectors containing the homologous gene never formed the plasmid multimers. The extent of multimerization was also dependent on a foreign gene insert in the expression vector. As a dominant effect of the SOS induction, recombinant plasmid vectors used for heterologous protein expression appear to significantly form various multimers in the recA(+) E. coli host.
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Affiliation(s)
- Jeewon Lee
- Department of Chemical and Biological Engineering, Korea University, 1,5 Ka, Anam-Dong, Seongbuk-Ku, Seoul 136-701, South Korea.
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Medina MG, Carbonell X, Villaverde A. Connection between gene dosage and protein stability revealed by a high-yield production of recombinant proteins in an E. coli LexA1(Ind-) background. Biotechnol Bioeng 2002; 78:722-30. [PMID: 12001164 DOI: 10.1002/bit.10253] [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: 11/11/2022]
Abstract
Bacterial production of a plasmid-encoded bacteriophage P22 tailspike protein shows different yield and impact on cell viability in RecA+ LexA+, RecA- LexA+ and RecA+ LexA1(Ind-) backgrounds. In a LexA1(Ind-) context, we have observed lesser toxicity and higher productivity than in the wild-type strain, in which the bacterial growth was inhibited after induction of recombinant gene expression. Also, a negative effect of the incubation temperature on the growth of producing cells was also detected. By exploring the molecular basis of these inhibitory events, we found a connection between the dosage of the recombinant gene and the proteolytic stability of the encoded protein. Under both genetic and environmental conditions favoring higher plasmid copy number and consequently increasing the synthesis rate of the recombinant protein, enhanced protein degradation was observed in parallel with an important growth inhibition. Altogether, the obtained data suggest the existence of a critical concentration of recombinant protein over which cell proteolysis is stimulated at rates not compatible with optimal physiological conditions for bacterial growth.
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Affiliation(s)
- Manel G Medina
- Institut de Biologia Fonamental and Departament de Genètica and Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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21
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Abstract
Bacterial inclusion bodies (IBs) are refractile aggregates of protease-resistant misfolded protein that often occur in recombinant bacteria upon gratuitous overexpression of cloned genes. In biotechnology, the formation of IBs represents a main obstacle for protein production since even favouring high protein yields, the in vitro recovery of functional protein from insoluble deposits depends on technically diverse and often complex re-folding procedures. On the other hand, IBs represent an exciting model to approach the in vivo analysis of protein folding and to explore aggregation dynamics. Recent findings on the molecular organisation of embodied polypeptides and on the kinetics of inclusion body formation have revealed an unexpected dynamism of these protein aggregates, from which polypeptides are steadily released in living cells to be further refolded or degraded. The close connection between in vivo protein folding, aggregation, solubilisation and proteolytic digestion offers an integrated view of the bacterial protein quality control system of which IBs might be an important component especially in recombinant bacteria.
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Affiliation(s)
- M M Carrió
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
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Wegrzyn G, Wegrzyn A. Stress responses and replication of plasmids in bacterial cells. Microb Cell Fact 2002; 1:2. [PMID: 12076355 PMCID: PMC115368 DOI: 10.1186/1475-2859-1-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2002] [Accepted: 05/13/2002] [Indexed: 11/30/2022] Open
Abstract
Plasmids, DNA (or rarely RNA) molecules which replicate in cells autonomously (independently of chromosomes) as non-essential genetic elements, play important roles for microbes grown under specific environmental conditions as well as in scientific laboratories and in biotechnology. For example, bacterial plasmids are excellent models in studies on regulation of DNA replication, and their derivatives are the most commonly used vectors in genetic engineering. Detailed mechanisms of replication initiation, which is the crucial process for efficient maintenance of plasmids in cells, have been elucidated for several plasmids. However, to understand plasmid biology, it is necessary to understand regulation of plasmid DNA replication in response to different environmental conditions in which host cells exist. Knowledge of such regulatory processes is also very important for those who use plasmids as expression vectors to produce large amounts of recombinant proteins. Variable conditions in large-scale fermentations must influence replication of plasmid DNA in cells, thus affecting the efficiency of recombinant gene expression significantly. Contrary to extensively investigated biochemistry of plasmid replication, molecular mechanisms of regulation of plasmid DNA replication in response to various environmental stress conditions are relatively poorly understood. There are, however, recently published studies that add significant data to our knowledge on relations between cellular stress responses and control of plasmid DNA replication. In this review we focus on plasmids derived from bacteriophage lambda that are among the best investigated replicons. Nevertheless, recent results of studies on other plasmids are also discussed shortly.
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Affiliation(s)
- Grzegorz Wegrzyn
- Department of Molecular Biology, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
- Institute of Oceanology, Polish Academy of Sciences, Sw. Wojciecha 5, 81-347 Gdynia, Poland
| | - Alicja Wegrzyn
- Laboratory of Molecular Biology (affiliated with the University of Gdansk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kladki 24, 80-822 Gdansk, Poland
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DeLisa MP, Valdes JJ, Bentley WE. Quorum signaling via AI-2 communicates the "Metabolic Burden" associated with heterologous protein production in Escherichia coli. Biotechnol Bioeng 2001; 75:439-50. [PMID: 11668443 DOI: 10.1002/bit.10034] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent reports have shown that bacterial cell-cell communication or quorum sensing is quite prevalent in pathogenic Escherichia coli, especially at high cell density; however, the role of quorum sensing in nonpathogenic E. coli is less clear and, in particular, there is no information regarding the role of quorum sensing in overexpression of plasmid-encoded genes. In this work, it was found that the activity of a quorum signaling molecule, autoinducer-2 (AI-2), decreased significantly following induction of several plasmid-encoded genes in both low and high-cell-density cultures of E. coli. Furthermore, we show that AI-2 signaling level was linearly related to the accumulation level of each protein product and that, in general, the highest rates of recombinant protein accumulation resulted in the greatest attenuation of AI-2 signaling. Importantly, our findings demonstrate for the first time that recombinant E. coli communicate the stress or burden of overexpressing heterologous genes through the quorum-based AI-2 signaling pathway.
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Affiliation(s)
- M P DeLisa
- Center for Agricultural Biotechnology, University of Maryland Biotechnological Institute, University of Maryland, College Park, MD, USA
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