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Cetnar DP, Salis HM. Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons. ACS Synth Biol 2021; 10:318-332. [PMID: 33464822 DOI: 10.1021/acssynbio.0c00471] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
mRNA degradation is a central process that affects all gene expression levels, and yet, the determinants that control mRNA decay rates remain poorly characterized. Here, we applied a synthetic biology, learn-by-design approach to elucidate the sequence and structural determinants that control mRNA stability in bacterial operons. We designed, constructed, and characterized 82 operons in Escherichia coli, systematically varying RNase binding site characteristics, translation initiation rates, and transcriptional terminator efficiencies in the 5' untranslated region (UTR), intergenic, and 3' UTR regions, followed by measuring their mRNA levels using reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays during exponential growth. We show that introducing long single-stranded RNA into 5' UTRs reduced mRNA levels by up to 9.4-fold and that lowering translation rates reduced mRNA levels by up to 11.8-fold. We also found that RNase binding sites in intergenic regions had much lower effects on mRNA levels. Surprisingly, changing the transcriptional termination efficiency or introducing long single-stranded RNA into 3' UTRs had no effect on upstream mRNA levels. From these measurements, we developed and validated biophysical models of ribosome protection and RNase activity with excellent quantitative agreement. We also formulated design rules to rationally control a mRNA's stability, facilitating the automated design of engineered genetic systems with desired functionalities.
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Rosana ARR, Whitford DS, Migur A, Steglich C, Kujat-Choy SL, Hess WR, Owttrim GW. RNA helicase-regulated processing of the Synechocystis rimO-crhR operon results in differential cistron expression and accumulation of two sRNAs. J Biol Chem 2020; 295:6372-6386. [PMID: 32209657 DOI: 10.1074/jbc.ra120.013148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/19/2020] [Indexed: 12/21/2022] Open
Abstract
The arrangement of functionally-related genes in operons is a fundamental element of how genetic information is organized in prokaryotes. This organization ensures coordinated gene expression by co-transcription. Often, however, alternative genetic responses to specific stress conditions demand the discoordination of operon expression. During cold temperature stress, accumulation of the gene encoding the sole Asp-Glu-Ala-Asp (DEAD)-box RNA helicase in Synechocystis sp. PCC 6803, crhR (slr0083), increases 15-fold. Here, we show that crhR is expressed from a dicistronic operon with the methylthiotransferase rimO/miaB (slr0082) gene, followed by rapid processing of the operon transcript into two monocistronic mRNAs. This cleavage event is required for and results in destabilization of the rimO transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the rimO-crhR transcript in vitro suggested that CrhR plays a role in enhancing the rate of the processing in an auto-regulatory manner. Moreover, two putative small RNAs are generated from additional processing, degradation, or both of the rimO transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in Synechocystis and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.
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Affiliation(s)
- Albert Remus R Rosana
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Denise S Whitford
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Anzhela Migur
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Sonya L Kujat-Choy
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Wolfgang R Hess
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstrasse 19, D-79104 Freiburg, Germany
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Stevens JT, Carothers JM. Programming Gene Expression by Engineering Transcript Stability Control and Processing in Bacteria. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jason T. Stevens
- University of Washington; Center for Synthetic Biology, Molecular Engineering and Sciences Institute, Departments of Chemical Engineering and Bioengineering; 4000 15th Ave NE, Seattle WA 98195-1654 USA
| | - James M. Carothers
- University of Washington; Center for Synthetic Biology, Molecular Engineering and Sciences Institute, Departments of Chemical Engineering and Bioengineering; 4000 15th Ave NE, Seattle WA 98195-1654 USA
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Gordon GC, Cameron JC, Pfleger BF. Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002. Nucleic Acids Res 2018; 46:1984-1997. [PMID: 29373746 PMCID: PMC5829567 DOI: 10.1093/nar/gky041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 12/19/2022] Open
Abstract
RNase III is a ribonuclease that recognizes and cleaves double-stranded RNA. Across bacteria, RNase III is involved in rRNA maturation, CRISPR RNA maturation, controlling gene expression, and turnover of messenger RNAs. Many organisms have only one RNase III while others have both a full-length RNase III and another version that lacks a double-stranded RNA binding domain (mini-III). The genome of the cyanobacterium Synechococcus sp. strain PCC 7002 (PCC 7002) encodes three homologs of RNase III, two full-length and one mini-III, that are not essential even when deleted in combination. To discern if each enzyme had distinct responsibilities, we collected and sequenced global RNA samples from the wild type strain, the single, double, and triple RNase III mutants. Approximately 20% of genes were differentially expressed in various mutants with some operons and regulons showing complex changes in expression levels between mutants. Two RNase III's had a role in 23S rRNA maturation and the third was involved in copy number regulation one of six native plasmids. In vitro, purified RNase III enzymes were capable of cleaving some of the known Escherichia coli RNase III target sequences, highlighting the remarkably conserved substrate specificity between organisms yet complex regulation of gene expression.
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Affiliation(s)
- Gina C Gordon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jeffrey C Cameron
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
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Gamboa-Melendez H, Larroude M, Park YK, Trebul P, Nicaud JM, Ledesma-Amaro R. Synthetic Biology to Improve the Production of Lipases and Esterases (Review). Methods Mol Biol 2018; 1835:229-242. [PMID: 30109656 DOI: 10.1007/978-1-4939-8672-9_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic biology is an emergent field of research whose aim is to make biology an engineering discipline, thus permitting to design, control, and standardize biological processes. Synthetic biology is therefore expected to boost the development of biotechnological processes such as protein production and enzyme engineering, which can be significantly relevant for lipases and esterases.
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Affiliation(s)
- Heber Gamboa-Melendez
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Macarena Larroude
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Young Kyoung Park
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Pauline Trebul
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Sythetic Biology, Imperial College London, London, UK.
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Wurmthaler LA, Klauser B, Hartig JS. Highly motif- and organism-dependent effects of naturally occurring hammerhead ribozyme sequences on gene expression. RNA Biol 2017; 15:231-241. [PMID: 29106331 DOI: 10.1080/15476286.2017.1397870] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent bioinformatics studies have demonstrated a wide-spread occurrence of the hammerhead ribozyme (HHR) and similar small endonucleolytic RNA motifs in all domains of life. It is becoming increasingly evident that such ribozyme motifs participate in important genetic processes in diverse organisms. Although the HHR motif has been studied for more than three decades, only little is known about the consequences of ribozyme activity on gene expression. In the present study we analysed eight different naturally occurring HHR sequences in diverse genetic and organismal contexts. We investigated the influence of active ribozymes incorporated into mRNAs in mammalian, yeast and bacterial expression systems. The experiments show an unexpectedly high degree of organism-specific variability of ribozyme-mediated effects on gene expression. The presented findings demonstrate that ribozyme cleavage profoundly affect gene expression. However, the extent of this effect varies and depends strongly on the respective genetic context. The fast-cleaving type 3 HHRs [CChMVd(-) and sLTSV(-)] generally tended to cause the strongest effects on intracellular gene expression. The presented results are important in order to address potential functions of naturally occurring ribozymes in RNA processing and post-transcriptional regulation of gene expression. Additionally, our results are of interest for biotechnology and synthetic biology approaches that aim at the utilisation of self-cleaving ribozymes as widely applicable tools for controlling genetic processes.
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Affiliation(s)
- Lena A Wurmthaler
- a Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , Konstanz , Germany
| | - Benedikt Klauser
- a Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , Konstanz , Germany
| | - Jörg S Hartig
- a Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , Konstanz , Germany
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Felletti M, Bieber A, Hartig JS. The 3'-untranslated region of mRNAs as a site for ribozyme cleavage-dependent processing and control in bacteria. RNA Biol 2017; 14:1522-1533. [PMID: 27690736 DOI: 10.1080/15476286.2016.1240141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Besides its primary informational role, the sequence of the mRNA (mRNA) including its 5'- and 3'- untranslated regions (UTRs), contains important features that are relevant for post-transcriptional and translational regulation of gene expression. In this work a number of bacterial twister motifs are characterized both in vitro and in vivo. The analysis of their genetic contexts shows that these motifs have the potential of being transcribed as part of polycistronic mRNAs, thus we suggest the involvement of bacterial twister motifs in the processing of mRNA. Our data show that the ribozyme-mediated cleavage of the bacterial 3'-UTR has major effects on gene expression. While the observed effects correlate weakly with the kinetic parameters of the ribozymes, they show dependence on motif-specific structural features and on mRNA stabilization properties of the secondary structures that remain on the 3'-UTR after ribozyme cleavage. Using these principles, novel artificial twister-based riboswitches are developed that exert their activity via ligand-dependent cleavage of the 3'-UTR and the removal of the protective intrinsic terminator. Our results provide insights into possible biological functions of these recently discovered and widespread catalytic RNA motifs and offer new tools for applications in biotechnology, synthetic biology and metabolic engineering.
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Affiliation(s)
- Michele Felletti
- a Department of Chemistry , University of Konstanz , Konstanz , Germany.,b Konstanz Research School Chemical Biology (Kors-CB), University of Konstanz Konstanz , Germany
| | - Anna Bieber
- a Department of Chemistry , University of Konstanz , Konstanz , Germany
| | - Jörg S Hartig
- a Department of Chemistry , University of Konstanz , Konstanz , Germany.,b Konstanz Research School Chemical Biology (Kors-CB), University of Konstanz Konstanz , Germany
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8
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Combinatorial pathway optimization for streamlined metabolic engineering. Curr Opin Biotechnol 2017; 47:142-151. [DOI: 10.1016/j.copbio.2017.06.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022]
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9
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Morrison ES, Badyaev AV. The Landscape of Evolution: Reconciling Structural and Dynamic Properties of Metabolic Networks in Adaptive Diversifications. Integr Comp Biol 2016; 56:235-46. [PMID: 27252203 DOI: 10.1093/icb/icw026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The network of the interactions among genes, proteins, and metabolites delineates a range of potential phenotypic diversifications in a lineage, and realized phenotypic changes are the result of differences in the dynamics of the expression of the elements and interactions in this deterministic network. Regulatory mechanisms, such as hormones, mediate the relationship between the structural and dynamic properties of networks by determining how and when the elements are expressed and form a functional unit or state. Changes in regulatory mechanisms lead to variable expression of functional states of a network within and among generations. Functional properties of network elements, and the magnitude and direction of evolutionary change they determine, depend on their location within a network. Here, we examine the relationship between network structure and the dynamic mechanisms that regulate flux through a metabolic network. We review the mechanisms that control metabolic flux in enzymatic reactions and examine structural properties of the network locations that are targets of flux control. We aim to establish a predictive framework to test the contributions of structural and dynamic properties of deterministic networks to evolutionary diversifications.
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Affiliation(s)
- Erin S Morrison
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0001, USA
| | - Alexander V Badyaev
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0001, USA
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10
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11
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Impact of Environmental Factors on Bacteriocin Promoter Activity in Gut-Derived Lactobacillus salivarius. Appl Environ Microbiol 2015; 81:7851-9. [PMID: 26341205 DOI: 10.1128/aem.02339-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/30/2015] [Indexed: 12/27/2022] Open
Abstract
Bacteriocin production is regarded as a desirable probiotic trait that aids in colonization and persistence in the gastrointestinal tract (GIT). Strains of Lactobacillus salivarius, a species associated with the GIT, are regarded as promising probiotic candidates and have a number of associated bacteriocins documented to date. These include multiple class IIb bacteriocins (salivaricin T, salivaricin P, and ABP-118) and the class IId bacteriocin bactofencin A, which show activity against medically important pathogens. However, the production of a bacteriocin in laboratory media does not ensure production under stressful environmental conditions, such as those encountered within the GIT. To allow this issue to be addressed, the promoter regions located upstream of the structural genes encoding the L. salivarius bacteriocins mentioned above were fused to a number of reporter proteins (green fluorescent protein [GFP], red fluorescent protein [RFP], and luciferase [Lux]). Of these, only transcriptional fusions to GFP generated signals of sufficient strength to enable the study of promoter activity in L. salivarius. While analysis of the class IIb bacteriocin promoter regions indicated relatively weak GFP expression, assessment of the promoter of the antistaphylococcal bacteriocin bactofencin A revealed a strong promoter that is most active in the absence of the antimicrobial peptide and is positively induced in the presence of mild environmental stresses, including simulated gastric fluid. Taken together, these data provide information on factors that influence bacteriocin production, which will assist in the development of strategies to optimize in vivo and in vitro production of these antimicrobials.
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13
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Bayer T, Milker S, Wiesinger T, Rudroff F, Mihovilovic MD. Designer Microorganisms for Optimized Redox Cascade Reactions - Challenges and Future Perspectives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Jajesniak P, Seng Wong T. From genetic circuits to industrial-scale biomanufacturing: bacterial promoters as a cornerstone of biotechnology. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Eriksen DT, Lian J, Zhao H. Protein design for pathway engineering. J Struct Biol 2013; 185:234-42. [PMID: 23558037 DOI: 10.1016/j.jsb.2013.03.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/23/2013] [Accepted: 03/21/2013] [Indexed: 02/02/2023]
Abstract
Design and construction of biochemical pathways has increased the complexity of biosynthetically-produced compounds when compared to single enzyme biocatalysis. However, the coordination of multiple enzymes can introduce a complicated set of obstacles to overcome in order to achieve a high titer and yield of the desired compound. Metabolic engineering has made great strides in developing tools to optimize the flux through a target pathway, but the inherent characteristics of a particular enzyme within the pathway can still limit the productivity. Thus, judicious protein design is critical for metabolic and pathway engineering. This review will describe various strategies and examples of applying protein design to pathway engineering to optimize the flux through the pathway. The proteins can be engineered for altered substrate specificity/selectivity, increased catalytic activity, reduced mass transfer limitations through specific protein localization, and reduced substrate/product inhibition. Protein engineering can also be expanded to design biosensors to enable high through-put screening and to customize cell signaling networks. These strategies have successfully engineered pathways for significantly increased productivity of the desired product or in the production of novel compounds.
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Affiliation(s)
- Dawn T Eriksen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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16
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Overview of regulatory strategies and molecular elements in metabolic engineering of bacteria. Mol Biotechnol 2013; 52:300-8. [PMID: 22359157 DOI: 10.1007/s12033-012-9514-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
From a viewpoint of biotechnology, metabolic engineering mainly aims to change the natural status of a pathway in a microorganism towards the overproduction of certain bioproducts. The biochemical nature of a pathway implies us that changed pathway is often the collective results of altered behavior of the metabolic enzymes encoded by corresponding genes. By finely modulating the expression of these genes or the properties of the enzyme, we can gain efficient control on the pathway. In this article, we reviewed the typical methods that have been applied to regulate the expression of genes in metabolic engineering. These methods are grouped according to the operation targets in a typical gene. The transcription of a gene is controlled by an indispensable promoter. By utilizing promoters with different strengths, expected levels of expression can be easily achieved, and screening a promoter library may find suitable mutant promoters that can provide tunable expression of a gene. Auto-responsive promoter (quorum sensing (QS)-based or oxygen-inducible) simplifies the induction process by driving the expression of a gene in an automated manner. Light responsive promoter enables reversible and noninvasive control on gene activity, providing a promising method in controlling gene expression with time and space resolution in metabolic engineering involving complicated genetic circuits. Through directed evolution and/or rational design, the encoding sequences of a gene can be altered, leading to the possibly most profound changes in properties of a metabolic enzyme. Introducing an engineered riboswitch in mRNA can make it a regulatory molecule at the same time; ribosomal binding site is commonly engineered to be more attractive for a ribosome through design. Terminator of a gene will affect the stability of an mRNA, and intergenic region will influence the expression of many related genes. Improving the performance of these elements are generally the main activities in metabolic engineering.
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Blank LM, Ebert BE. From measurement to implementation of metabolic fluxes. Curr Opin Biotechnol 2012; 24:13-21. [PMID: 23219184 DOI: 10.1016/j.copbio.2012.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 10/26/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
The intracellular reaction rates (fluxes) are the ultimate outcome of the activities of the complete inventory (from DNA to metabolite) and in their sum determine the cellular phenotype. The genotype-phenotype relationship is fundamental in such different fields as cancer research and biotechnology. Here, we summarize the developments in determining metabolic fluxes, inferring major pathways from the DNA-sequence, estimating optimal flux distributions, and how these flux distributions can be achieved in vivo. The technical advances to intervene with the many levels of the cellular architecture allow the implementation of new strategies in for example Metabolic Engineering.
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Affiliation(s)
- Lars M Blank
- iAMB - Institute of Applied Microbiology, AABt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany.
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Vikram A, Jesudhasan PR, Pillai SD, Patil BS. Isolimonic acid interferes with Escherichia coli O157:H7 biofilm and TTSS in QseBC and QseA dependent fashion. BMC Microbiol 2012; 12:261. [PMID: 23153211 PMCID: PMC3562146 DOI: 10.1186/1471-2180-12-261] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 10/01/2012] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND E. coli O157:H7 (EHEC) is an important human pathogen. The antibiotic treatment of EHEC reportedly results in release of Shiga toxin and is therefore discouraged. Consequently, alternative preventive or therapeutic strategies for EHEC are required. The objective of the current study was to investigate the effect of citrus limonoids on cell-cell signaling, biofilm formation and type III secretion system in EHEC. RESULTS Isolimonic acid and ichangin were the most potent inhibitors of EHEC biofilm (IC25=19.7 and 28.3 μM, respectively) and adhesion to Caco-2 cells. The qPCR analysis revealed that isolimonic acid and ichangin repressed LEE encoded genes by ≈3 to 12 fold. In addition, flhDC was repressed by the two limonoids (≈3 to 7 fold). Further studies suggested that isolimonic acid interferes with AI-3/epinephrine activated cell-cell signaling pathway. Loss of biofilm inhibitory activity of isolimonic acid in ΔqseBC mutant, which could be restored upon complementation, suggested a dependence on functional QseBC. Additionally, overexpression of qseBC in wild type EHEC abated the inhibitory effect of isolimonic acid. Furthermore, the isolimonic acid failed to differentially regulate ler in ΔqseA mutant, while plasmid borne expression of qseA in ΔqseA background restored the repressive effect of isolimonic acid. CONCLUSIONS Altogether, results of study seem to suggest that isolimonic acid and ichangin are potent inhibitors of EHEC biofilm and TTSS. Furthermore, isolimonic acid appears to interfere with AI-3/epinephrine pathway in QseBC and QseA dependent fashion.
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Affiliation(s)
- Amit Vikram
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A &M University, Texas, 77843-2119, USA
| | - Palmy R Jesudhasan
- Food Safety & Environmental Microbiology Program, Texas A&M University, College Station, College Station, Texas, 77843-2472, USA
| | - Suresh D Pillai
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A &M University, Texas, 77843-2119, USA
- Food Safety & Environmental Microbiology Program, Texas A&M University, College Station, College Station, Texas, 77843-2472, USA
| | - Bhimanagouda S Patil
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A &M University, Texas, 77843-2119, USA
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Jarboe LR, Liu P, Kautharapu KB, Ingram LO. Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals. Comput Struct Biotechnol J 2012; 3:e201210005. [PMID: 24688665 PMCID: PMC3962213 DOI: 10.5936/csbj.201210005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 10/21/2012] [Accepted: 10/24/2012] [Indexed: 12/23/2022] Open
Abstract
Microbial biocatalysts such as Escherichia coli and Saccharomyces cerevisiae have been extensively subjected to Metabolic Engineering for the fermentative production of biorenewable fuels and chemicals. This often entails the introduction of new enzymes, deletion of unwanted enzymes and efforts to fine-tune enzyme abundance in order to attain the desired strain performance. Enzyme performance can be quantitatively described in terms of the Michaelis-Menten type parameters Km, turnover number kcat and Ki, which roughly describe the affinity of an enzyme for its substrate, the speed of a reaction and the enzyme sensitivity to inhibition by regulatory molecules. Here we describe examples of where knowledge of these parameters have been used to select, evolve or engineer enzymes for the desired performance and enabled increased production of biorenewable fuels and chemicals. Examples include production of ethanol, isobutanol, 1-butanol and tyrosine and furfural tolerance. The Michaelis-Menten parameters can also be used to judge the cofactor dependence of enzymes and quantify their preference for NADH or NADPH. Similarly, enzymes can be selected, evolved or engineered for the preferred cofactor preference. Examples of exporter engineering and selection are also discussed in the context of production of malate, valine and limonene.
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Affiliation(s)
- Laura R Jarboe
- Chemical and Biological Engineering, Iowa State University, Ames, Iowa, USA ; Microbiology, Iowa State University, Ames, Iowa, USA
| | - Ping Liu
- Microbiology, Iowa State University, Ames, Iowa, USA
| | | | - Lonnie O Ingram
- Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
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21
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Horsman SR, Moore RA, Lewenza S. Calcium chelation by alginate activates the type III secretion system in mucoid Pseudomonas aeruginosa biofilms. PLoS One 2012; 7:e46826. [PMID: 23056471 PMCID: PMC3466208 DOI: 10.1371/journal.pone.0046826] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/05/2012] [Indexed: 11/17/2022] Open
Abstract
The extracellular biofilm matrix includes primarily DNA and exopolysaccharides (EPS), which function to maintain aggregate structures and to protect biofilms from antibiotics and the immune response. Both polymers are anionic and have cation binding activity, however the impact of this activity on biofilms is not fully understood. Host cell contact is considered the primary signal for activation of most type III secretion systems (T3SS), although calcium limitation is frequently used as a trigger of contact-independent T3SS expression. We hypothesized that alginate, which is a known calcium binding exopolysaccharide produced in mucoid Pseudomonas aeruginosa isolates, can activate the T3SS in biofilms. The addition of exogenous purified alginate to planktonic, non-mucoid PAO1 cultures induced expression of exoS, exoT and exoY-lux reporters of the T3SS in a concentration-dependent manner. Induction by alginate was comparable to induction by the calcium chelator NTA. We extended our analysis of the T3SS in flow chamber-cultivated biofilms, and showed that hyperproduction of alginate in mucA22 mucoid isolates resulted in induction of the exoS-gfp transcriptional reporter compared to non-mucoid paired isolates. We confirmed the transcriptional effects of alginate on the T3SS expression using a FlAsH fluorescence method and showed high levels of the ExoT-Cys(4) protein in mucoid biofilms. Induction of the T3SS could be prevented in planktonic cultures and mucoid biofilms treated with excess calcium, indicating that Ca(2+) chelation by the EPS matrix caused contact-independent induction. However, mucoid isolates generally had reduced exoS-lux expression in comparison to paired, non-mucoid isolates when grown as planktonic cultures and agar colonies. In summary, we have shown a mucoid biofilm-specific induction of the type III secretion system and highlight a difference between planktonic and biofilm cultures in the production of virulence factors.
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Affiliation(s)
- Shawn R Horsman
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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22
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Abstract
Advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure. However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism. Such engineering is not based on just one specific feedstock or host organism. Data-driven and synthetic-biology approaches can be used to optimize both the host and pathways to maximize fuel production. Despite some success, challenges still need to be met to move advanced biofuels towards commercialization, and to compete with more conventional fuels.
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23
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Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight SC, Maranas CD, Sauro HM. Computational tools for metabolic engineering. Metab Eng 2012; 14:270-80. [PMID: 22629572 PMCID: PMC3361690 DOI: 10.1016/j.ymben.2012.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A great variety of software applications are now employed in the metabolic engineering field. These applications have been created to support a wide range of experimental and analysis techniques. Computational tools are utilized throughout the metabolic engineering workflow to extract and interpret relevant information from large data sets, to present complex models in a more manageable form, and to propose efficient network design strategies. In this review, we present a number of tools that can assist in modifying and understanding cellular metabolic networks. The review covers seven areas of relevance to metabolic engineers. These include metabolic reconstruction efforts, network visualization, nucleic acid and protein engineering, metabolic flux analysis, pathway prospecting, post-structural network analysis and culture optimization. The list of available tools is extensive and we can only highlight a small, representative portion of the tools from each area.
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Affiliation(s)
- Wilbert B Copeland
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5061, USA.
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24
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Synthetic biology and the development of tools for metabolic engineering. Metab Eng 2012; 14:189-95. [DOI: 10.1016/j.ymben.2012.01.004] [Citation(s) in RCA: 321] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 01/24/2012] [Indexed: 12/21/2022]
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25
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Engineering biological systems with synthetic RNA molecules. Mol Cell 2011; 43:915-26. [PMID: 21925380 DOI: 10.1016/j.molcel.2011.08.023] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/16/2011] [Accepted: 08/21/2011] [Indexed: 01/08/2023]
Abstract
RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory, information processing, and scaffolding activities, has highlighted the advantages of RNA as a programmable design substrate. Recent advances in implementing these engineered RNA molecules as key control elements in synthetic genetic networks are highlighting the functional relevance of this class of synthetic elements in programming cellular behaviors.
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26
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Boyle PM, Silver PA. Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab Eng 2011; 14:223-32. [PMID: 22037345 DOI: 10.1016/j.ymben.2011.10.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 10/05/2011] [Accepted: 10/16/2011] [Indexed: 11/24/2022]
Abstract
Synthetic biologists combine modular biological "parts" to create higher-order devices. Metabolic engineers construct biological "pipes" by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design.
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Affiliation(s)
- Patrick M Boyle
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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27
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Rapid optimization of gene dosage in E. coli using DIAL strains. J Biol Eng 2011; 5:10. [PMID: 21787416 PMCID: PMC3163176 DOI: 10.1186/1754-1611-5-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 07/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Engineers frequently vary design parameters to optimize the behaviour of a system. However, synthetic biologists lack the tools to rapidly explore a critical design parameter, gene expression level, and have no means of systematically varying the dosage of an entire genetic circuit. As a step toward overcoming this shortfall, we have developed a technology that enables the same plasmid to be maintained at different copy numbers in a set of closely related cells. This provides a rapid method for exploring gene or cassette dosage effects. RESULTS We engineered two sets of strains to constitutively provide a trans-acting replication factor, either Pi of the R6K plasmid or RepA of the ColE2 plasmid, at different doses. Each DIAL (different allele) strain supports the replication of a corresponding plasmid at a constant level between 1 and 250 copies per cell. The plasmids exhibit cell-to-cell variability comparable to other popular replicons, but with improved stability. Since the origins are orthogonal, both replication factors can be incorporated into the same cell. We demonstrate the utility of these strains by rapidly assessing the optimal expression level of a model biosynthetic pathway for violecein. CONCLUSIONS The DIAL strains can rapidly optimize single gene expression levels, help balance expression of functionally coupled genetic elements, improve investigation of gene and circuit dosage effects, and enable faster development of metabolic pathways.
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28
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Weeks AM, Chang MCY. Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. Biochemistry 2011; 50:5404-18. [PMID: 21591680 DOI: 10.1021/bi200416g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Living organisms have evolved a vast array of catalytic functions that make them ideally suited for the production of medicinally and industrially relevant small-molecule targets. Indeed, native metabolic pathways in microbial hosts have long been exploited and optimized for the scalable production of both fine and commodity chemicals. Our increasing capacity for DNA sequencing and synthesis has revealed the molecular basis for the biosynthesis of a variety of complex and useful metabolites and allows the de novo construction of novel metabolic pathways for the production of new and exotic molecular targets in genetically tractable microbes. However, the development of commercially viable processes for these engineered pathways is currently limited by our ability to quickly identify or engineer enzymes with the correct reaction and substrate selectivity as well as the speed by which metabolic bottlenecks can be determined and corrected. Efforts to understand the relationship among sequence, structure, and function in the basic biochemical sciences can advance these goals for synthetic biology applications while also serving as an experimental platform for elucidating the in vivo specificity and function of enzymes and reconstituting complex biochemical traits for study in a living model organism. Furthermore, the continuing discovery of natural mechanisms for the regulation of metabolic pathways has revealed new principles for the design of high-flux pathways with minimized metabolic burden and has inspired the development of new tools and approaches to engineering synthetic pathways in microbial hosts for chemical production.
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Affiliation(s)
- Amy M Weeks
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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29
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Hajimorad M, Gray PR, Keasling JD. A framework and model system to investigate linear system behavior in Escherichia coli. J Biol Eng 2011; 5:3. [PMID: 21510907 PMCID: PMC3110104 DOI: 10.1186/1754-1611-5-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 04/22/2011] [Indexed: 11/21/2022] Open
Abstract
Background The ability to compose biological systems from smaller elements that act independently of the other upon assembly may help make the forward engineering of biological systems practical. Engineering biology in this manner is made difficult by the inherent nonlinear response of organisms to genetic devices. Devices are inevitably coupled to one another in the cell because they share the same transcriptional machinery for expression. Thus, new properties can emerge when devices that had been characterized in isolation are expressed concurrently. We show in this report that, similar to physical systems, the Escherichia coli (E. coli) transcriptional system can exhibit linear behavior under "small" perturbation conditions. This, in turn, allows devices to be treated as independent modules. Results We developed a framework and model system consisting of three devices to investigate linear system behavior in E. coli. Our framework employed the transfer curve concept to determine the amount of nonlinearity elicited by the E. coli transcriptional system in response to the devices. To this effect, the model system was quantitatively characterized using real-time quantitative PCR to produce device transfer curves (DTCs). Two of the devices encoded the bacterial neomycin phosphotransferase II (nptII) and chloramphenicol acetyl transferase (cat), while the third encoded the jellyfish-originating green fluorescent protein (gfp). The gfp device was the most nonlinear in our system, with nptII and cat devices eliciting linear responses. Superposition experiments verified these findings, with independence among the three devices having been lost when gfp was present at copy numbers above the lowest one used. Conclusions We show that linear system behavior is possible in E. coli. Elucidation of the mechanism underlying the nonlinearity observed in gfp may lead to design rules that ensure linear system behavior, enabling the accurate prediction of the quantitative behavior of a system assembled from individually characterized devices. Our work suggests that biological systems follow principles similar to physical ones, and that concepts borrowed from the latter (such as DTCs) may be of use in the characterization and design of biological systems.
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Affiliation(s)
- Meghdad Hajimorad
- Synthetic Biology Engineering Research Center, University of California, Berkeley, CA 94720, USA.
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30
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Abstract
To avoid costly biomass recovery in photosynthetic microbial biofuel production, we genetically modified cyanobacteria to produce and secrete fatty acids. Starting with introducing an acyl-acyl carrier protein thioesterase gene, we made six successive generations of genetic modifications of cyanobacterium Synechocystis sp. PCC6803 wild type (SD100). The fatty acid secretion yield was increased to 197 ± 14 mg/L of culture in one improved strain at a cell density of 1.0 × 10(9) cells/mL by adding codon-optimized thioesterase genes and weakening polar cell wall layers. Although these strains exhibited damaged cell membranes at low cell densities, they grew more rapidly at high cell densities in late exponential and stationary phase and exhibited less cell damage than cells in wild-type cultures. Our results suggest that fatty acid secreting cyanobacteria are a promising technology for renewable biofuel production.
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31
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Continuous control of the flow in biochemical pathways through 5' untranslated region sequence modifications in mRNA expressed from the broad-host-range promoter Pm. Appl Environ Microbiol 2011; 77:2648-55. [PMID: 21335387 DOI: 10.1128/aem.02091-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The inducible Pm promoter integrated into broad-host-range plasmid RK2 replicons can be fine-tuned continuously between the uninduced and maximally induced levels by varying the inducer concentrations. To lower the uninduced background level while still maintaining the inducibility for applications in, for example, metabolic engineering and synthetic (systems) biology, we report here the use of mutations in the Pm DNA region corresponding to the 5' untranslated region of mRNA (UTR). Five UTR variants obtained by doped oligonucleotide mutagenesis and selection, apparently reducing the efficiency of translation, were all found to display strongly reduced uninduced expression of three different reporter genes (encoding β-lactamase, luciferase, and phosphoglucomutase) in Escherichia coli. The ratio between induced and uninduced expression remained the same or higher compared to cells containing a corresponding plasmid with the wild-type UTR. Interestingly, the UTR variants also displayed similar effects on expression when substituted for the native UTR in another and constitutive promoter, P1 (P(antitet)), indicating a broad application potential of these UTR variants. Two of the selected variants were used to control the production of the C(50) carotenoid sarcinaxanthin in an engineered strain of E. coli that produces the precursor lycopene. Sarcinaxanthin is produced in this particular strain by expressing three Micrococcus luteus derived genes from the promoter Pm. The results indicated that UTR variants can be used to eliminate sarcinaxanthin production under uninduced conditions, whereas cells containing the corresponding plasmid with a wild-type UTR produced ca. 25% of the level observed under induced conditions.
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32
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Agnew DE, Pfleger BF. Optimization of synthetic operons using libraries of post-transcriptional regulatory elements. Methods Mol Biol 2011; 765:99-111. [PMID: 21815089 PMCID: PMC9146903 DOI: 10.1007/978-1-61779-197-0_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Constructing polycistronic operons is an advantageous strategy for coordinating the expression of -multiple genes in a prokaryotic host. Unfortunately, a basic construct consisting of an inducible promoter and genes cloned in series does not generally lead to optimal results. Here, a combinatorial approach for tuning relative gene expression in operons is presented. The method constructs libraries of post--transcriptional regulatory elements that can be cloned into the noncoding sequence between genes. Libraries can be screened to identify sequences that optimize expression of metabolic pathways, multisubunit proteins, or other situations where precise stoichiometric ratios of proteins are desired.
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Affiliation(s)
- Daniel E. Agnew
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, United States
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, United States
- Corresponding author. 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States. Phone: +1 608 890 1940. Fax: +1 608 262-5434.
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33
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Abstract
Metabolic engineering has the potential to produce from simple, readily available, inexpensive starting materials a large number of chemicals that are currently derived from nonrenewable resources or limited natural resources. Microbial production of natural products has been achieved by transferring product-specific enzymes or entire metabolic pathways from rare or genetically intractable organisms to those that can be readily engineered, and production of unnatural specialty chemicals, bulk chemicals, and fuels has been enabled by combining enzymes or pathways from different hosts into a single microorganism and by engineering enzymes to have new function. Whereas existing production routes use well-known, safe, industrial microorganisms, future production schemes may include designer cells that are tailor-made for the desired chemical and production process. In any future, metabolic engineering will soon rival and potentially eclipse synthetic organic chemistry.
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Affiliation(s)
- Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.
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34
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Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010; 2010:130781. [PMID: 20150964 PMCID: PMC2817555 DOI: 10.1155/2010/130781] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/28/2009] [Indexed: 11/17/2022] Open
Abstract
The general central
dogma frames the emergent properties of life,
which make biology both necessary and difficult
to engineer. In a process engineering paradigm,
each biological process stream and process unit
is heavily influenced by regulatory interactions
and interactions with the surrounding
environment. Synthetic biology is developing the
tools and methods that will increase control
over these interactions, eventually resulting in
an integrative synthetic biology that will allow
ground-up cellular optimization. In this review,
we attempt to contextualize the areas of
synthetic biology into three tiers: (1) the
process units and associated streams of the
central dogma, (2) the intrinsic regulatory
mechanisms, and (3) the extrinsic physical and
chemical environment. Efforts at each of these
three tiers attempt to control cellular systems
and take advantage of emerging tools and
approaches. Ultimately, it will be possible to
integrate these approaches and realize the
vision of integrative synthetic biology when
cells are completely rewired for
biotechnological goals. This review will
highlight progress towards this goal as well as
areas requiring further research.
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35
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Toward engineering synthetic microbial metabolism. J Biomed Biotechnol 2009; 2010:459760. [PMID: 20037734 PMCID: PMC2796345 DOI: 10.1155/2010/459760] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Accepted: 10/09/2009] [Indexed: 11/18/2022] Open
Abstract
The generation of well-characterized parts and the formulation of biological design principles in synthetic biology are laying the foundation for more complex and advanced microbial metabolic engineering. Improvements in de novo DNA synthesis and codon-optimization alone are already contributing to the manufacturing of pathway enzymes with improved or novel function. Further development of analytical and computer-aided design tools should accelerate the forward engineering of precisely regulated synthetic pathways by providing a standard framework for the predictable design of biological systems from well-characterized parts. In this review we discuss the current state of synthetic biology within a four-stage framework (design, modeling, synthesis, analysis) and highlight areas requiring further advancement to facilitate true engineering of synthetic microbial metabolism.
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36
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Win MN, Liang JC, Smolke CD. Frameworks for programming biological function through RNA parts and devices. ACTA ACUST UNITED AC 2009; 16:298-310. [PMID: 19318211 DOI: 10.1016/j.chembiol.2009.02.011] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/09/2009] [Accepted: 02/24/2009] [Indexed: 12/30/2022]
Abstract
One of the long-term goals of synthetic biology is to reliably engineer biological systems that perform human-defined functions. Currently, researchers face several scientific and technical challenges in designing and building biological systems, one of which is associated with our limited ability to access, transmit, and control molecular information through the design of functional biomolecules exhibiting novel properties. The fields of RNA biology and nucleic acid engineering, along with the tremendous interdisciplinary growth of synthetic biology, are fueling advances in the emerging field of RNA programming in living systems. Researchers are designing functional RNA molecules that exhibit increasingly complex functions and integrating these molecules into cellular circuits to program higher-level biological functions. The continued integration and growth of RNA design and synthetic biology presents exciting potential to transform how we interact with and program biology.
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Affiliation(s)
- Maung Nyan Win
- Division of Chemistry and Chemical Engineering, 1200 E. California Boulevard, MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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37
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Timing and dynamics of single cell gene expression in the arabinose utilization system. Biophys J 2008; 95:2103-15. [PMID: 18469087 DOI: 10.1529/biophysj.107.127191] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The arabinose utilization system of Escherichia coli displays a stochastic all-or-nothing response at intermediate levels of arabinose, where the population divides into a fraction catabolizing the sugar at a high rate (on-state) and a fraction not utilizing arabinose (off-state). Here we study this decision process in individual cells, focusing on the dynamics of the transition from the off- to the on-state. Using quantitative time-lapse microscopy, we determine the time delay between inducer addition and fluorescence onset of a GFP reporter. Through independent characterization of the GFP maturation process, we can separate the lag time caused by the reporter from the intrinsic activation time of the arabinose system. The resulting distribution of intrinsic time delays scales inversely with the external arabinose concentration, and is compatible with a simple stochastic model for arabinose uptake. Our findings support the idea that the heterogeneous timing of gene induction is causally related to a broad distribution of uptake proteins at the time of sugar addition.
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38
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Abstract
The richness and versatility of biological systems make them ideally suited to solve some of the world's most significant challenges, such as converting cheap, renewable resources into energy-rich molecules; producing high-quality, inexpensive drugs to fight disease; and remediating polluted sites. Over the years, significant strides have been made in engineering microorganisms to produce fuels, bulk chemicals, and valuable drugs from inexpensive starting materials; to detect and degrade nerve agents as well as less toxic organic pollutants; and to accumulate metals and reduce radionuclides. The components needed to engineer the chemistry inside a microbial cell are significantly different from those commonly used to overproduce pharmaceutical proteins. Synthetic biology has had and will continue to have a significant impact on the development of these components to engineer cellular metabolism and microbial chassis to host the chemistry. The ready availability of more well-characterized gene expression components and hosts for chemical synthesis, standards for the connection of these components to make larger functioning devices, computer-aided design software, and debugging tools for biological designs will decrease both the time and the support needed to construct these designs. Some of the most important tools for engineering bacterial metabolism and their use for production of the antimalarial drug artemisinin are reviewed.
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Affiliation(s)
- Jay D. Keasling
- Departments of Chemical Engineering and Bioengineering, University of California, Berkeley, Berkeley, California 94720, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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39
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Kime L, Jourdan SS, McDowall KJ. Identifying and characterizing substrates of the RNase E/G family of enzymes. Methods Enzymol 2008; 447:215-41. [PMID: 19161846 DOI: 10.1016/s0076-6879(08)02212-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of RNA decay and processing in Escherichia coli has revealed a central role for RNase E, an endonuclease that is essential for cell viability. This enzyme is required for the normal rapid decay of many transcripts and is involved in the processing of precursors of 16S and 5S ribosomal RNA, transfer RNA, the transfer-messenger RNA, and the RNA component of RNase P. Although there is reasonable knowledge of the repertoire of transcripts cleaved by RNase E in E. coli, a detailed understanding of the molecular recognition events that control the cleavage of RNA by this key enzyme is only starting to emerge. Here we describe methods for identifying sites of endonucleolytic cleavage and determining whether they depend on functional RNase E. This is illustrated with the pyrG eno bicistronic transcript, which is cleaved in the intergenic region primarily by an RNase E-dependent activity and not as previously thought by RNase III. We also describe the use of oligoribonucleotide and in vitro-transcribed substrates to investigate cis-acting factors such as 5'-monophosphorylation, which can significantly enhance the rate of cleavage but is insufficient to ensure processivity. Most of the approaches that we describe can be applied to the study of homologs of E. coli RNase E, which have been found in approximately half of the eubacteria that have been sequenced.
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Affiliation(s)
- Louise Kime
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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40
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Bursey EH, Kim CY, Yu M, Terwilliger TC, Hung LW. An automated high-throughput screening method for the identification of high-yield, soluble protein variants using cell-free expression and systematic truncation. ACTA ACUST UNITED AC 2007; 7:139-47. [PMID: 17541730 DOI: 10.1007/s10969-007-9017-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Accepted: 03/26/2007] [Indexed: 10/23/2022]
Abstract
A highly automated method for rapidly identifying soluble protein variants with good expression yields has been developed. This method is based on a commercially available in vitro protein expression system. It consists of two polymerase chain reactions (PCR) followed by in vitro protein expression and protein quantification by dot blot. The PCR protocols have been improved and optimized to allow automation using commercial fluid handling devices. A PCR primer design program has also been implemented to streamline protein variant design. This automated protocol is highly reliable and has tremendously improved the throughput of expression screening as compared to conventional cell-based methods and manual in vitro methods. We have applied this method to 32 problematic targets from the TB Structural Genomics Consortium. Experimental results of these studies are reported.
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Affiliation(s)
- Evan H Bursey
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
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41
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Pfleger BF, Pitera DJ, Smolke CD, Keasling JD. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 2006; 24:1027-32. [PMID: 16845378 DOI: 10.1038/nbt1226] [Citation(s) in RCA: 397] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 05/21/2006] [Indexed: 11/08/2022]
Abstract
Many applications of synthetic biology require the balanced expression of multiple genes. Although operons facilitate coordinated expression of multiple genes in prokaryotes and eukaryotes, coordinating the many post-transcriptional processes that determine the relative levels of gene expression in operons by a priori design remains a challenge. We describe a method for tuning the expression of multiple genes within operons by generating libraries of tunable intergenic regions (TIGRs), recombining various post-transcriptional control elements and screening for the desired relative expression levels. TIGRs can vary the relative expression of two reporter genes over a 100-fold range and balance expression of three genes in an operon that encodes a heterologous mevalonate biosynthetic pathway, resulting in a sevenfold increase in mevalonate production. This technology should be useful for optimizing the expression of multiple genes in synthetic operons, both in prokaryotes and eukaryotes.
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Affiliation(s)
- Brian F Pfleger
- Department of Chemical Engineering, University of California-Berkeley, Berkeley, CA 94720-1462, USA
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42
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Abstract
Circadian rhythms possess the ability to robustly entrain to the environmental cycles. This ability relies on the phase synchronization of circadian rhythm gene regulation to different environmental cues, of which light is the most obvious and important. The elucidation of the mechanism of circadian entrainment requires an understanding of circadian phase behavior. This article presents two phase analyses of oscillatory systems for infinitesimal and finite perturbations based on isochrons as a phase metric of a limit cycle. The phase response curve of circadian rhythm can be computed from the results of the analyses. The application to a mechanistic Drosophila circadian rhythm model gives experimentally testable hypotheses for the control mechanisms of circadian phase responses and evidence for the role of phase and period modulations in circadian photic entrainment.
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Affiliation(s)
- Rudiyanto Gunawan
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, CA, USA
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43
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Lee SK, Keasling JD. Propionate-regulated high-yield protein production inEscherichia coli. Biotechnol Bioeng 2006; 93:912-8. [PMID: 16333863 DOI: 10.1002/bit.20784] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A new expression system containing the Salmonella enterica prpBCDE promoter (P(prpB)) responsible for expression of the propionate catabolic genes (prp BCDE) and prpR encoding the positive regulator of this promoter has been developed and tested. The main features of the expression system compared to those based on the bacteriophage T7 promoter are low background expression and high induced expression in Escherichia coli strains BL21, BL21(DE3), MG1655, and W3110. In addition, propionate is an inexpensive, simple-to-use, nontoxic inducer that is attractive for large-scale protein production. Hence, this new system is highly complementary to the widely used T7 promoter-driven expression systems.
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Affiliation(s)
- Sung Kuk Lee
- Department of Chemical Engineering and Bioengineering, University of California, Synthetic Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Abstract
A series of new expression vectors (pPro) have been constructed for the regulated expression of genes in Escherichia coli. The pPro vectors contain the prpBCDE promoter (P(prpB)) responsible for expression of the propionate catabolic genes (prpBCDE) and prpR encoding the positive regulator of this promoter. The efficiency and regulatory properties of the prpR-P(prpB) system were measured by placing the gene encoding the green fluorescent protein (gfp) under the control of the inducible P(prpB) of E. coli. This system provides homogenous expression in individual cells, highly regulatable expression over a wide range of propionate concentrations, and strong expression (maximal 1,500-fold induction) at high propionate concentrations. Since the prpBCDE promoter has CAP-dependent activation, the prpR-P(prpB) system exhibited negligible basal expression by addition of glucose to the medium.
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Affiliation(s)
- Sung Kuk Lee
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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Lee SK, Newman JD, Keasling JD. Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: evidence for involvement of the cyclic AMP receptor protein. J Bacteriol 2005; 187:2793-800. [PMID: 15805526 PMCID: PMC1070369 DOI: 10.1128/jb.187.8.2793-2800.2005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies with Salmonella enterica serovar Typhimurium LT2 demonstrated that transcriptional activation of the prpBCDE operon requires the function of transcription factor PrpR, sigma-54, and IHF. In this study, we found that transcription from the prpBCDE and prpR promoters was down-regulated by the addition of glucose or glycerol, indicating that these genes may be regulated by the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex. Targeted mutagenesis of a putative CRP-binding site in the promoter region between prpR and prpBCDE suggested that these genes are under the control of CRP. Furthermore, cells with defects in cya or crp exhibited reduced transcriptional activation of prpR and prpBCDE in Escherichia coli. These results demonstrate that propionate metabolism is subject to catabolite repression by the global transcriptional regulator CRP and that this regulation is effected through control of both the regulator gene prpR and the prpBCDE operon itself. The unique properties of the regulation of these two divergent promoters may have important implications for mechanisms of CRP-dependent catabolite repression acting in conjunction with a member of the sigma-54 family of transcriptional activators.
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Affiliation(s)
- Sung Kuk Lee
- Department of Chemical Engineering, University of California, Berkeley, CA 94720-1462, USA
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Bayer TS, Smolke CD. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 2005; 23:337-43. [PMID: 15723047 DOI: 10.1038/nbt1069] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Accepted: 01/05/2005] [Indexed: 01/29/2023]
Abstract
Recent studies have demonstrated the importance of noncoding RNA elements in regulating gene expression networks. We describe the design of a class of small trans-acting RNAs that directly regulate gene expression in a ligand-dependent manner. These allosteric riboregulators, which we call antiswitches, are made fully tunable and modular by rational design. They offer flexible control strategies by adopting active or inactive forms in response to ligand binding, depending on their design. They can be tailor-made to regulate the expression of target transcripts in response to different cellular effectors. Coupled with in vitro selection technologies for generating nucleic acid ligand-binding species, antiswitches present a platform for programming cellular behavior and genetic networks with respect to cellular state and environmental stimuli.
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Pfleger BF, Fawzi NJ, Keasling JD. Optimization of DsRed production inEscherichia coli: Effect of ribosome binding site sequestration on translation efficiency. Biotechnol Bioeng 2005; 92:553-8. [PMID: 16247774 DOI: 10.1002/bit.20630] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DsRed-Express, a popular reporter protein, cannot be expressed in Escherichia coli using a consensus ribosome binding site (RBS) potentially due to basepairing in the RBS that inhibits translation initiation. Saturation mutagenesis was used to probe for a gene sequence that minimized basepairing in the RBS while maintaining the same spectral properties and maturation characteristics as DsRed-Express. The new DsRed, designated here as RFP(EC) for E. coli optimized red fluorescent protein, fluoresces 2.5 times greater than DsRed-Express when expressed from the same vector.
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Affiliation(s)
- Brian F Pfleger
- Department of Chemical Engineering, University of California Berkeley, California, USA
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Smolke CD, Keasling JD. Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon. Biotechnol Bioeng 2002; 80:762-76. [PMID: 12402322 DOI: 10.1002/bit.10434] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The effects of endoribonuclease sites, secondary structures in mRNA, and gene placement on protein production and mRNA stability and steady-state levels were tested in a dual-gene operon containing the genes encoding beta-galactosidase (lacZ) from Escherichia coli and green fluorescent protein (gfp) from Aequorea victoria. Two previously identified RNase E sites were placed separately between the coding regions to direct cleavage in this area and produce two secondary transcripts, each containing a single-gene coding region. Novel secondary structures were engineered into the 3' and 5' ends of each of the coding regions to protect the transcript from inactivation by endoribonucleases (5' hairpins) and degradation by exoribonucleases (3' hairpins). In addition, the effects of relative gene placement were examined by switching the locations of the two coding regions. Depending on the particular secondary structures and RNase E sites placed between the genes the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 2.5-fold and 4-fold, respectively. By changing gene location and incorporating secondary structures and RNase E sites the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 100-fold and 750-fold, respectively.
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Affiliation(s)
- Christina D Smolke
- Department of Chemical Engineering, University of California, Berkeley 94720-1462, USA
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Smolke CD, Keasling JD. Effect of copy number and mRNA processing and stabilization on transcript and protein levels from an engineered dual-gene operon. Biotechnol Bioeng 2002; 78:412-24. [PMID: 11948448 DOI: 10.1002/bit.10218] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To study the effect of mRNA stability and DNA copy number on protein production from a dual-gene operon, a synthetic operon containing the reporter genes gfp and lacZ under the control of the araBAD promoter was placed in pMB1-based (approximately 100 copies/cell) and F plasmid-based (approximately 1 copy/cell) vectors. DNA cassettes encoding secondary structures were placed at the 5' and 3' ends of the genes and a putative RNase E site was placed between the two genes. Although the copy number of the pMB1-based vectors was approximately 100-fold greater than the copy number of the F plasmid-based vectors, transcript and protein levels from the pMB1-based vector were not 100-fold greater than from the F plasmid-based vectors. In identical plasmid backbones, different combinations of mRNA control elements were used to alter steady-state levels of transcripts. Control elements that amplified the stability of one coding region relative to another amplified the ratio of protein produced from those transcripts. The effects of mRNA stability control elements were greater at low inducer concentrations, where mRNA levels limit protein production, than at high inducer concentrations. Although we can alter mRNA and protein levels through copy number, induction level, and mRNA stability control elements, some aspect of gene expression remains dependent on inherent characteristics of the coding region.
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Affiliation(s)
- Christina D Smolke
- Department of Chemical Engineering, University of California, 201 Gilman Hall, Berkeley 94720-1462, USA
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Abstract
In recent years, the number of recombinant proteins used for therapeutic applications has increased dramatically. Many of these applications involve complex glycoproteins and antibodies with relatively high production needs. These demands have driven the development of a variety of improvements in protein expression technology, particularly involving mammalian and microbial culture systems.
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Affiliation(s)
- Dana C Andersen
- Cell Culture & Fermentation Research & Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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