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Rohlhill J, Sandoval NR, Papoutsakis ET. Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol. ACS Synth Biol 2017; 6:1584-1595. [PMID: 28463494 PMCID: PMC5569641 DOI: 10.1021/acssynbio.7b00114] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Tight and tunable control of gene
expression is a highly desirable
goal in synthetic biology for constructing predictable gene circuits
and achieving preferred phenotypes. Elucidating the sequence–function
relationship of promoters is crucial for manipulating gene expression
at the transcriptional level, particularly for inducible systems dependent
on transcriptional regulators. Sort-seq methods employing fluorescence-activated
cell sorting (FACS) and high-throughput sequencing allow for the quantitative
analysis of sequence–function relationships in a robust and
rapid way. Here we utilized a massively parallel sort-seq approach
to analyze the formaldehyde-inducible Escherichia coli promoter (Pfrm) with single-nucleotide
resolution. A library of mutated formaldehyde-inducible promoters
was cloned upstream of gfp on a plasmid. The library
was partitioned into bins via FACS on the basis of green fluorescent
protein (GFP) expression level, and mutated promoters falling into
each expression bin were identified with high-throughput sequencing.
The resulting analysis identified two 19 base pair repressor binding
sites, one upstream of the −35 RNA polymerase (RNAP) binding
site and one overlapping with the −10 site, and assessed the
relative importance of each position and base therein. Key mutations
were identified for tuning expression levels and were used to engineer
formaldehyde-inducible promoters with predictable activities. Engineered
variants demonstrated up to 14-fold lower basal expression, 13-fold
higher induced expression, and a 3.6-fold stronger response as indicated
by relative dynamic range. Finally, an engineered formaldehyde-inducible
promoter was employed to drive the expression of heterologous methanol
assimilation genes and achieved increased biomass levels on methanol,
a non-native substrate of E. coli.
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Affiliation(s)
- Julia Rohlhill
- Department of Chemical & Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
| | - Nicholas R. Sandoval
- Department of Chemical & Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Eleftherios T. Papoutsakis
- Department of Chemical & Biomolecular Engineering and the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
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Portela RM, Vogl T, Kniely C, Fischer JE, Oliveira R, Glieder A. Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species. ACS Synth Biol 2017; 6:471-484. [PMID: 27973777 PMCID: PMC5359585 DOI: 10.1021/acssynbio.6b00178] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Indexed: 01/24/2023]
Abstract
Synthetic biology and metabolic engineering experiments frequently require the fine-tuning of gene expression to balance and optimize protein levels of regulators or metabolic enzymes. A key concept of synthetic biology is the development of modular parts that can be used in different contexts. Here, we have applied a computational multifactor design approach to generate de novo synthetic core promoters and 5' untranslated regions (UTRs) for yeast cells. In contrast to upstream cis-regulatory modules (CRMs), core promoters are typically not subject to specific regulation, making them ideal engineering targets for gene expression fine-tuning. 112 synthetic core promoter sequences were designed on the basis of the sequence/function relationship of natural core promoters, nucleosome occupancy and the presence of short motifs. The synthetic core promoters were fused to the Pichia pastoris AOX1 CRM, and the resulting activity spanned more than a 200-fold range (0.3% to 70.6% of the wild type AOX1 level). The top-ten synthetic core promoters with highest activity were fused to six additional CRMs (three in P. pastoris and three in Saccharomyces cerevisiae). Inducible CRM constructs showed significantly higher activity than constitutive CRMs, reaching up to 176% of natural core promoters. Comparing the activity of the same synthetic core promoters fused to different CRMs revealed high correlations only for CRMs within the same organism. These data suggest that modularity is maintained to some extent but only within the same organism. Due to the conserved role of eukaryotic core promoters, this rational design concept may be transferred to other organisms as a generic engineering tool.
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Affiliation(s)
- Rui M.
C. Portela
- REQUIMTE/LAQV,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Thomas Vogl
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Claudia Kniely
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Jasmin E. Fischer
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
| | - Rui Oliveira
- REQUIMTE/LAQV,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Anton Glieder
- Institute
for Molecular Biotechnology, NAWI Graz University
of Technology, Petersgasse 14/2, 8010 Graz, Austria
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Vogl T, Sturmberger L, Kickenweiz T, Wasmayer R, Schmid C, Hatzl AM, Gerstmann MA, Pitzer J, Wagner M, Thallinger GG, Geier M, Glieder A. A Toolbox of Diverse Promoters Related to Methanol Utilization: Functionally Verified Parts for Heterologous Pathway Expression in Pichia pastoris. ACS Synth Biol 2016; 5:172-86. [PMID: 26592304 DOI: 10.1021/acssynbio.5b00199] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The heterologous expression of biosynthetic pathways for pharmaceutical or fine chemical production requires suitable expression hosts and vectors. In eukaryotes, the pathway flux is typically balanced by stoichiometric fine-tuning of reaction steps by varying the transcript levels of the genes involved. Regulated (inducible) promoters are desirable to allow a separation of pathway expression from cell growth. Ideally, the promoter sequences used should not be identical to avoid loss by recombination. The methylotrophic yeast Pichia pastoris is a commonly used protein production host, and single genes have been expressed at high levels using the methanol-inducible, strong, and tightly regulated promoter of the alcohol oxidase 1 gene (PAOX1). Here, we have studied the regulation of the P. pastoris methanol utilization (MUT) pathway to identify a useful set of promoters that (i) allow high coexpression and (ii) differ in DNA sequence to increase genetic stability. We noticed a pronounced involvement of the pentose phosphate pathway (PPP) and genes involved in the defense of reactive oxygen species (ROS), providing strong promoters that, in part, even outperform PAOX1 and offer novel regulatory profiles. We have applied these tightly regulated promoters together with novel terminators as useful tools for the expression of a heterologous biosynthetic pathway. With the synthetic biology toolbox presented here, P. pastoris is now equipped with one of the largest sets of strong and co-regulated promoters of any microbe, moving it from a protein production host to a general industrial biotechnology host.
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Affiliation(s)
- Thomas Vogl
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Lukas Sturmberger
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Thomas Kickenweiz
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Richard Wasmayer
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Christian Schmid
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Anna-Maria Hatzl
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Michaela A. Gerstmann
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Julia Pitzer
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Marlies Wagner
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, Graz 8010, Austria
| | - Gerhard G. Thallinger
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Omics Center Graz, Stiftingtalstrasse
24, 8036 Graz, Austria
| | - Martina Geier
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, Graz 8010, Austria
| | - Anton Glieder
- Institute
of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, Graz 8010, Austria
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