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Burdette LA, Leach SA, Kennedy N, Ikwuagwu BC, Summers JS, Tullman-Ercek D. Characterization and Engineering of the Type 3 Secretion System Needle Monomer from Salmonella Through the Construction and Screening of a Comprehensive Mutagenesis Library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592225. [PMID: 38746360 PMCID: PMC11092573 DOI: 10.1101/2024.05.02.592225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Protein production strategies in bacteria are often limited due to the need for cell lysis and complicated purification schemes. To avoid these challenges, researchers have developed bacterial strains capable of secreting heterologous protein products outside the cell, but secretion titers often remain too low for commercial applicability. Improved understanding of the link between secretion system structure and its secretory abilities can help overcome the barrier to engineering higher secretion titers. Here we investigated this link with the PrgI protein, the monomer of the secretory channel of the Type 3 Secretion System (T3SS) of Salmonella enterica . Despite detailed knowledge of the PrgI needle's assembly and structure, little is known about how its structure influences its secretory capabilities. To study this, we recently constructed a comprehensive codon mutagenesis library of the PrgI protein utilizing a novel one pot recombineering approach. We then screened this library for functional T3SS assembly and secretion titer by measuring the secretion of alkaline phosphatase using a high-throughput activity assay. This allowed us to construct a first-of-its-kind secretion fitness landscape (SFL) to characterize the PrgI needle's mutability at each position as well as the mutations which lead to enhanced T3SS secretion. We discovered new design rules for building a functional T3SS as well as identified hypersecreting mutants. This work can be used to increase understanding of the T3SS's assembly and identify further targets for engineering. This work also provides a blueprint for future efforts to engineer other complex protein assemblies through the construction of fitness landscapes. Importance Protein secretion offers a simplified alternative method for protein purification from bacterial hosts. However, the current state-of-the-art methods for protein secretion in bacteria are still hindered by low yields relative to traditional protein purification strategies. Engineers are now seeking strategies to enhance protein secretion titers from bacterial hosts, often through genetic manipulations. In this study, we demonstrate that protein engineering strategies focused on altering the secretion apparatus can be a fruitful avenue toward this goal. Specifically, this study focuses on how changes to the PrgI needle protein from the type 3 secretion system from Salmonella enterica can impact secretion titer. We demonstrate that this complex is amenable to comprehensive mutagenesis studies and that this can yield both PrgI variants with increased secretory capabilities and insight into the normal functioning of the type 3 secretion system.
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Construction of a constitutively active type III secretion system for heterologous protein secretion. Appl Microbiol Biotechnol 2023; 107:1785-1800. [PMID: 36786917 DOI: 10.1007/s00253-023-12411-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/15/2023]
Abstract
Proteins comprise a multibillion-dollar industry in enzymes and therapeutics, but bacterial protein production can be costly and inefficient. Proteins of interest (POIs) must be extracted from lysed cells and inclusion bodies, purified, and resolubilized, which adds significant time and cost to the protein-manufacturing process. The Salmonella pathogenicity island 1 (SPI-1) type III secretion system (T3SS) has been engineered to address these problems by secreting soluble, active proteins directly into the culture media, reducing the number of purification steps. However, the current best practices method of T3SS pathway activation is not ideal for industrial scaleup. Previously, the T3SS was activated by plasmid-based overexpression of the T3SS transcriptional regulator, hilA, which requires the addition of a small molecule inducer (IPTG) to the culture media. IPTG adds significant cost to production and plasmid-based expression is subject to instability in large-scale fermentation. Here, we modulate the upstream transcriptional regulator, hilD, to activate the T3SS via three distinct methods. In doing so, we develop a toolbox of T3SS activation methods and construct constitutively active T3SS strains capable of secreting a range of heterologous proteins at titers comparable to plasmid-based hilA overexpression. We also explore how each activation method in our toolbox impacts the SPI-1 regulatory cascade and discover an epistatic relationship between T3SS regulators, hilE and the hilD 3' untranslated region (hilD 3'UTR). Together, these findings further our goal of making an industrially competitive protein production strain that reduces the challenges associated with plasmid induction and maintenance. KEY POINTS: • Characterized 3 new type III secretion system (T3SS) activation methods for heterologous protein secretion, including 2 constitutive activation methods. • Eliminated the need for a second plasmid and a small molecule inducer to activate the system, making it more suitable for industrial production. • Discovered new regulatory insights into the SPI-1 T3SS, including an epistatic relationship between regulators hilE and the hilD 3' untranslated region.
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Guzmán-Herrador DL, Fernández-Gómez A, Llosa M. Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation. Front Cell Infect Microbiol 2023; 13:1146000. [PMID: 36949816 PMCID: PMC10025392 DOI: 10.3389/fcimb.2023.1146000] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.
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Jin Q, Pan F, Hu CF, Lee SY, Xia XX, Qian ZG. Secretory production of spider silk proteins in metabolically engineered Corynebacterium glutamicum for spinning into tough fibers. Metab Eng 2022; 70:102-114. [DOI: 10.1016/j.ymben.2022.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/06/2022] [Accepted: 01/17/2022] [Indexed: 12/19/2022]
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Burdette LA, Wong HT, Tullman-Ercek D. An optimized growth medium for increased recombinant protein secretion titer via the type III secretion system. Microb Cell Fact 2021; 20:44. [PMID: 33588857 PMCID: PMC7885374 DOI: 10.1186/s12934-021-01536-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/02/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Protein secretion in bacteria is an attractive strategy for heterologous protein production because it retains the high titers and tractability of bacterial hosts while simplifying downstream processing. Traditional intracellular production strategies require cell lysis and separation of the protein product from the chemically similar cellular contents, often a multi-step process that can include an expensive refolding step. The type III secretion system of Salmonella enterica Typhimurium transports proteins from the cytoplasm to the extracellular environment in a single step and is thus a promising solution for protein secretion in bacteria. Product titer is sensitive to extracellular environmental conditions, however, and T3SS regulation is integrated with essential cellular functions. Instead of attempting to untangle a complex web of regulatory input, we took an "outside-in" approach to elucidate the effect of growth medium components on secretion titer. RESULTS We dissected the individual and combined effects of carbon sources, buffers, and salts in a rich nutrient base on secretion titer. Carbon sources alone decreased secretion titer, secretion titer increased with salt concentration, and the combination of a carbon source, buffer, and high salt concentration had a synergistic effect on secretion titer. Transcriptional activity measured by flow cytometry showed that medium composition affected secretion system activity, and prolonged secretion system activation correlated strongly with increased secretion titer. We found that an optimal combination of glycerol, phosphate, and sodium chloride provided at least a fourfold increase in secretion titer for a variety of proteins. Further, the increase in secretion titer provided by the optimized medium was additive with strain enhancements. CONCLUSIONS We leveraged the sensitivity of the type III secretion system to the extracellular environment to increase heterologous protein secretion titer. Our results suggest that maximizing secretion titer via the type III secretion system is not as simple as maximizing secreted protein expression-one must also optimize secretion system activity. This work advances the type III secretion system as a platform for heterologous protein secretion in bacteria and will form a basis for future engineering efforts.
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Affiliation(s)
- Lisa Ann Burdette
- Department of Chemical and Biomolecular Engineering, University of California-Berkeley, Berkeley, USA
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Han Teng Wong
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, USA
- Present Address: Institute of Molecular and Cell Biology, 61 Biopolis Way, Singapore, 138673 Singapore
| | - Danielle Tullman-Ercek
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
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Delivery of Heterologous Proteins, Enzymes, and Antigens via the Bacterial Type III Secretion System. Microorganisms 2020; 8:microorganisms8050777. [PMID: 32455678 PMCID: PMC7285344 DOI: 10.3390/microorganisms8050777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 12/27/2022] Open
Abstract
The Type III Secretion System (T3SS) is a multimeric protein complex composed of over 20 different proteins, utilized by Gram-negative bacteria to infect eukaryotic host cells. The T3SS has been implicated as a virulence factor by which pathogens cause infection and has recently been characterized as a communication tool between bacteria and plant cells in the rhizosphere. The T3SS has been repurposed to be used as a tool for the delivery of non-native or heterologous proteins to eukaryotic cells or the extracellular space for a variety of purposes, including drug discovery and drug delivery. This review covers the methodology of heterologous protein secretion as well as multiple cases of utilizing the T3SS to deliver heterologous proteins or artificial materials. The research covered in this review will serve to outline the scope and limitations of utilizing the T3SS as a tool for protein delivery.
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Burdette LA, Leach SA, Wong HT, Tullman-Ercek D. Developing Gram-negative bacteria for the secretion of heterologous proteins. Microb Cell Fact 2018; 17:196. [PMID: 30572895 PMCID: PMC6302416 DOI: 10.1186/s12934-018-1041-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/08/2018] [Indexed: 11/10/2022] Open
Abstract
Gram-negative bacteria are attractive hosts for recombinant protein production because they are fast growing, easy to manipulate, and genetically stable in large cultures. However, the utility of these microbes would expand if they also could secrete the product at commercial scales. Secretion of biotechnologically relevant proteins into the extracellular medium increases product purity from cell culture, decreases downstream processing requirements, and reduces overall cost. Thus, researchers are devoting significant attention to engineering Gram-negative bacteria to secrete recombinant proteins to the extracellular medium. Secretion from these bacteria operates through highly specialized systems, which are able to translocate proteins from the cytosol to the extracellular medium in either one or two steps. Building on past successes, researchers continue to increase the secretion efficiency and titer through these systems in an effort to make them viable for industrial production. Efforts include modifying the secretion tags required for recombinant protein secretion, developing methods to screen or select rapidly for clones with higher titer or efficiency, and improving reliability and robustness of high titer secretion through genetic manipulations. An additional focus is the expression of secretion machineries from pathogenic bacteria in the "workhorse" of biotechnology, Escherichia coli, to reduce handling of pathogenic strains. This review will cover recent advances toward the development of high-expressing, high-secreting Gram-negative production strains.
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Affiliation(s)
- Lisa Ann Burdette
- Department of Chemical and Biomolecular Engineering, University of California-Berkeley, Berkeley, USA
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Samuel Alexander Leach
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
| | - Han Teng Wong
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, USA
- Present Address: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, USA
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Metcalf KJ, Slininger Lee MF, Jakobson CM, Tullman-Ercek D. An estimate is worth about a thousand experiments: using order-of-magnitude estimates to identify cellular engineering targets. Microb Cell Fact 2018; 17:135. [PMID: 30165868 PMCID: PMC6117934 DOI: 10.1186/s12934-018-0979-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/10/2022] Open
Abstract
Biotechnological processes use microbes to convert abundant molecules, such as glucose, into high-value products, such as pharmaceuticals, commodity and fine chemicals, and energy. However, from the outset of the development of a new bioprocess, it is difficult to determine the feasibility, expected yields, and targets for engineering. In this review, we describe a methodology that uses rough estimates to assess the feasibility of a process, approximate the expected product titer of a biological system, and identify variables to manipulate in order to achieve the desired performance. This methodology uses estimates from literature and biological intuition, and can be applied in the early stages of a project to help plan future engineering. We highlight recent literature examples, as well as two case studies from our own work, to demonstrate the use and power of rough estimates. Describing and predicting biological function using estimates guides the research and development phase of new bioprocesses and is a useful first step to understand and build a new microbial factory.
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Affiliation(s)
- Kevin James Metcalf
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Marilyn F Slininger Lee
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,U.S. Army Edgewood Chemical Biological Center, Gunpowder, MD, 21010, USA
| | - Christopher Matthew Jakobson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
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Glasgow AA, Tullman-Ercek D. Type III Secretion Filaments as Templates for Metallic Nanostructure Synthesis. Methods Mol Biol 2018; 1798:155-171. [PMID: 29868958 DOI: 10.1007/978-1-4939-7893-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanostructured materials can be interfaced with living cells to enable unique chemical and biological outcomes. However, it is challenging to precisely control the shape and chemical composition of submillimeter sized, cell-associated materials. In this protocol, we describe how to genetically modify and isolate a self-assembling filament protein from Salmonella enterica, PrgI, to bind Au nanoparticles. Au-conjugated filaments can be chemically reduced in vitro to form contiguous wires and networks that are several micrometers in length. We also describe a strategy to assemble PrgI-based filaments on live cells, which can then be sheared or remain tethered to cells for gold conjugation. These methods form the basis of a strategy for interactions between inorganic and organic systems, and could be expanded to introduce interactions with other metal nanoparticles for which peptide binding partners are known.
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Affiliation(s)
- Anum Azam Glasgow
- Department of Bioengineering and Therapeutic Sciences, UC San Francisco, San Francisco, CA, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
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Glasgow AA, Wong HT, Tullman-Ercek D. A Secretion-Amplification Role for Salmonella enterica Translocon Protein SipD. ACS Synth Biol 2017; 6:1006-1015. [PMID: 28301138 DOI: 10.1021/acssynbio.6b00335] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterial type III secretion system (T3SS) is an important target for enabling high-titer production of proteins of biotechnological interest as well as for synthetic biology applications that rely on protein delivery to host cells. The T3SS forms a membrane-embedded needle complex that is capped by the translocon proteins and extends into the extracellular space. The needle tip complex in Salmonella enterica consists of three translocon proteins: SipB, SipC, and SipD. It is known that knocking out sipD disrupts T3SS regulation to cause constitutive secretion of native proteins. However, we discovered that complementation of SipD in trans via exogenous addition to T3SS-expressing cultures further improves heterologous protein secretion titers, suggesting a previously unknown but important role for this protein. Building on this knowledge, we have engineered a hyper-secreting strain of S. enterica for a greater than 100-fold improvement in the production of a variety of biotechnologically valuable heterologous proteins that are challenging to produce, such as toxic antimicrobial peptides and proteolysis-prone biopolymer proteins. We determined that transcription by several T3SS promoters is upregulated with the addition of SipD, that the N-terminal domain of SipD is sufficient to observe the increased secretion phenotype, and that the effect is post-transcriptional and post-translational. These results lend support to the use of bacterial secretion as a powerful protein production strategy, and the hypothesis that translocon proteins contribute to type III secretion regulation.
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Affiliation(s)
- Anum Azam Glasgow
- UC
Berkeley-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Han Teng Wong
- Department
of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, United States
| | - Danielle Tullman-Ercek
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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Metcalf KJ, Bevington JL, Rosales SL, Burdette LA, Valdivia E, Tullman-Ercek D. Proteins adopt functionally active conformations after type III secretion. Microb Cell Fact 2016; 15:213. [PMID: 28010734 PMCID: PMC5180411 DOI: 10.1186/s12934-016-0606-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/25/2016] [Indexed: 11/17/2022] Open
Abstract
Background Bacterial production of natively folded heterologous proteins by secretion to the extracellular space can improve protein production by simplifying purification and enabling continuous processing. In a typical bacterial protein production process, the protein of interest accumulates in the cytoplasm of the cell, requiring cellular lysis and extensive purification to separate the desired protein from other cellular constituents. The type III secretion system of Gram-negative bacteria is used to secrete proteins from the cytosol to the extracellular space in one step, but proteins must unfold during translocation, necessitating the folding of secreted proteins in the extracellular space for an efficient production process. We evaluated type III secretion as a protein production strategy by characterizing and quantifying the extent of correct folding after secretion. Results We probed correct folding by assaying the function after secretion of two enzymes—beta-lactamase and alkaline phosphatase—and one single-chain variable fragment of an antibody. Secreted proteins are correctly folded and functional after unfolding, secretion, and refolding in the extracellular space. Furthermore, structural and chemical features required for protein function, such as multimerization and disulfide bond formation, are evident in the secreted protein samples. Finally, the concentration of NaCl in the culture media affects the folding efficiency of secreted proteins in a protein-specific manner. Conclusions In the extracellular space, secreted proteins are able to fold to active conformations, which entails post-translational modifications including: folding, multimerization, acquisition of metal ion cofactors, and formation of disulfide bonds. Further, different proteins have different propensities to refold in the extracellular space and are sensitive to the chemical environment in the extracellular space. Our results reveal strategies to control the secretion and correct folding of diverse target proteins during bacterial cell culture. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0606-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin James Metcalf
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - James Lea Bevington
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Sandy Lisette Rosales
- Department of Nutritional Science and Toxicology, University of California, Berkeley, CA, 94720, USA
| | - Lisa Ann Burdette
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Elias Valdivia
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA.
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12
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Use of Transcriptional Control to Increase Secretion of Heterologous Proteins in T3S Systems. Methods Mol Biol 2016. [PMID: 27837482 DOI: 10.1007/978-1-4939-6649-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Heterologous proteins can be produced in a bacterial host and purified from the cellular constituents. Secretion of the protein of interest to the extracellular space simplifies the purification process and is thought to alleviate toxicity problems associated with intracellular accumulation of the protein of interest. In this protocol, we describe a strategy to engineer protein secretion in a bacterial culture using transcriptional control. The transcription factor HilA is inducibly produced to control production of the secretion machine, and in turn signals the production and secretion of a protein of interest. This allows for high titer of secreted protein in optimized culturing conditions and the effect is observed with all proteins tested.
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13
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Boyarskiy S, Davis López S, Kong N, Tullman-Ercek D. Transcriptional feedback regulation of efflux protein expression for increased tolerance to and production of n-butanol. Metab Eng 2015; 33:130-137. [PMID: 26656942 DOI: 10.1016/j.ymben.2015.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/28/2015] [Accepted: 11/23/2015] [Indexed: 01/11/2023]
Abstract
Microorganisms can be engineered to produce a variety of biofuels and commodity chemicals. The accumulation of these products, however, is often toxic to the cells and subsequently lowers production yields. Efflux pumps are a natural mechanism for alleviating toxicity through secretion of the product; unfortunately, pump overexpression also often inhibits growth. Tuning expression levels with inducible promoters is time-consuming and the reliance on small-molecule inducers is cost-prohibitive in industry. We design an expression regulation system utilizing a native Escherichia coli stress promoter, PgntK, to provide negative feedback to regulate transporter expression levels. We test the promoter in the context of the efflux pump AcrB and its butanol-secreting variant, AcrBv2. PgntK-driven AcrBv2 confers increased tolerance to n-butanol and increased titers of n-butanol in production. Furthermore, the system is responsive to stress from toxic overexpression of other membrane-associated proteins. Our results suggest a use for feedback regulation networks in membrane protein expression.
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Affiliation(s)
- Sergey Boyarskiy
- Joint Graduate Group in Bioengineering at UC Berkeley and UCSF, 306 Stanley Hall, Berkeley, CA 94720, United States
| | - Stephanie Davis López
- Department of Chemistry, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States
| | - Niwen Kong
- Department of Molecular and Cell Biology, University of California Berkeley, 142 LSA #3200, Berkeley, CA 94720, United States
| | - Danielle Tullman-Ercek
- Joint Graduate Group in Bioengineering at UC Berkeley and UCSF, 306 Stanley Hall, Berkeley, CA 94720, United States; Department of Chemistry, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States; Department of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, CA 94720, United States.
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Login FH, Wolf-Watz H. YscU/FlhB of Yersinia pseudotuberculosis Harbors a C-terminal Type III Secretion Signal. J Biol Chem 2015; 290:26282-91. [PMID: 26338709 DOI: 10.1074/jbc.m114.633677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 12/20/2022] Open
Abstract
All type III secretion systems (T3SS) harbor a member of the YscU/FlhB family of proteins that is characterized by an auto-proteolytic process that occurs at a conserved cytoplasmic NPTH motif. We have previously demonstrated that YscUCC, the C-terminal peptide generated by auto-proteolysis of Yersinia pseudotuberculosis YscU, is secreted by the T3SS when bacteria are grown in Ca(2+)-depleted medium at 37 °C. Here, we investigated the secretion of this early T3S-substrate and showed that YscUCC encompasses a specific C-terminal T3S signal within the 15 last residues (U15). U15 promoted C-terminal secretion of reporter proteins like GST and YopE lacking its native secretion signal. Similar to the "classical" N-terminal secretion signal, U15 interacted with the ATPase YscN. Although U15 is critical for YscUCC secretion, deletion of the C-terminal secretion signal of YscUCC did neither affect Yop secretion nor Yop translocation. However, these deletions resulted in increased secretion of YscF, the needle subunit. Thus, these results suggest that YscU via its C-terminal secretion signal is involved in regulation of the YscF secretion.
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Affiliation(s)
- Frédéric H Login
- From the Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-901 87 Umeå, Sweden
| | - Hans Wolf-Watz
- From the Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-901 87 Umeå, Sweden
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15
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Cangelosi C, Hannagan S, Santiago CP, Wilson JW. Transfer of the cloned Salmonella SPI-1 type III secretion system and characterization of its expression mechanisms in Gram negative bacteria in comparison with cloned SPI-2. Microbiol Res 2015; 180:57-64. [PMID: 26505312 DOI: 10.1016/j.micres.2015.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/16/2015] [Accepted: 07/18/2015] [Indexed: 12/23/2022]
Abstract
Cloned type III secretion systems have much potential to be used for bacterial engineering purposes involving protein secretion and substrate translocation directly into eukaryotic cells. We have previously cloned the SPI-1 and SPI-2 type III systems from the Salmonella enterica serovar Typhimurium genome using plasmid R995 which can conveniently capture large genomic segments for transfer between bacterial strains. However, though expressed and functional in Salmonella strains, cloned SPI-1 was previously observed to have a serious expression defect in other Gram negative bacteria including Escherichia coli. Here we show that cloned SPI-1 expression and secretion can be detected in the secretion preps from E. coli and Citrobacter indicating the first observation of non-Salmonella SPI-1 expression. We describe a compatible plasmid system to introduce engineered SPI-1 substrates into cloned SPI-1 strains. However, a SPI-1 translocation defect is still observed in E. coli, and we show that this is likely due to a defect in SipB expression/secretion in this species. In addition, we also examined the requirement for the hilA and ssrAB regulators in the expression of cloned SPI-1 and SPI-2, respectively. We found a strict requirement for hilA for full cloned SPI-1 expression and secretion. However, though we found that ssrAB is required for full cloned SPI-2 expression in a range of media across different bacteria, it is not required for cloned SPI-2 expression in MgM8 inducing media in S. Typhimurium. This suggests that under SPI-2 inducing conditions in S. Typhimurium, other factors can substitute for loss of ssrAB in cloned SPI-2 expression. The results provide key foundational information for the future use of these cloned systems in bacteria.
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Affiliation(s)
- Chris Cangelosi
- Department of Biology, Villanova University, Villanova, PA, United States
| | - Susan Hannagan
- Department of Biology, Villanova University, Villanova, PA, United States
| | - Clayton P Santiago
- Department of Biology, Villanova University, Villanova, PA, United States
| | - James W Wilson
- Department of Biology, Villanova University, Villanova, PA, United States.
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Azam A, Li C, Metcalf KJ, Tullman-Ercek D. Type III secretion as a generalizable strategy for the production of full-length biopolymer-forming proteins. Biotechnol Bioeng 2015; 113:2313-20. [PMID: 25993982 DOI: 10.1002/bit.25656] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/29/2015] [Accepted: 05/11/2015] [Indexed: 12/29/2022]
Abstract
Biopolymer-forming proteins are integral in the development of customizable biomaterials, but recombinant expression of these proteins is challenging. In particular, biopolymer-forming proteins have repetitive, glycine-rich domains and, like many heterologously expressed proteins, are prone to incomplete translation, aggregation, and proteolytic degradation in the production host. This necessitates tailored purification processes to isolate each full-length protein of interest from the truncated forms as well as other contaminating proteins; owing to the repetitive nature of these proteins, the truncated polypeptides can have very similar chemistry to the full-length form and are difficult to separate from the full-length protein. We hypothesized that bacterial expression and secretion would be a promising alternative option for biomaterials-forming proteins, simplifying isolation of the full-length target protein. By using a selective secretion system, truncated forms of the protein are not secreted and thus are not found in the culture harvest. We show that a synthetically upregulated type III secretion system leads to a general increase in secretion titer for each protein that we tested. Moreover, we observe a substantial enhancement in the homogeneity of full-length forms of pro-resilin, tropo-elastin crosslinking domains, and silk proteins produced in this manner, as compared with proteins purified from the cytosol. Secretion via the type III apparatus limits co-purification of truncated forms of the target protein and increases protein purity without extensive purification steps. Demonstrating the utility of such a system, we introduce several modifications to resilin-based peptides and use an un-optimized, single-column process to purify these proteins. The resulting materials are of sufficiently high quantity and yield for the production of antimicrobial hydrogels with highly reproducible rheological properties. The ease of this process and its applicability to an array of engineered biomaterial-forming peptides lend support for the application of bacterial expression and secretion for other proteins that are traditionally difficult to express and isolate from the bacterial cytoplasm. Biotechnol. Bioeng. 2016;113: 2313-2320. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Anum Azam
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California
| | - Cheng Li
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California
| | - Kevin J Metcalf
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, 94720
| | - Danielle Tullman-Ercek
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California. .,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California, 94720.
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Kim EY, Jakobson CM, Tullman-Ercek D. Engineering transcriptional regulation to control Pdu microcompartment formation. PLoS One 2014; 9:e113814. [PMID: 25427074 PMCID: PMC4245221 DOI: 10.1371/journal.pone.0113814] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/30/2014] [Indexed: 12/18/2022] Open
Abstract
Bacterial microcompartments (MCPs) show great promise for the organization of engineered metabolic pathways within the bacterial cytoplasm. This subcellular organelle is composed of a protein shell of 100-200 nm diameter that natively encapsulates multi-enzyme pathways. The high energy cost of synthesizing the thousands of protein subunits required for each MCP demands precise regulation of MCP formation for both native and engineered systems. Here, we study the regulation of the propanediol utilization (Pdu) MCP, for which growth on 1,2-propanediol induces expression of the Pdu operon for the catabolism of 1,2-propanediol. We construct a fluorescence-based transcriptional reporter to investigate the activation of the Ppdu promoter, which drives the transcription of 21 pdu genes. Guided by this reporter, we find that MCPs can be expressed in strains grown in rich media, provided that glucose is not present. We also characterize the response of the Ppdu promoter to a transcriptional activator of the pdu operon, PocR, and find PocR to be a necessary component of Pdu MCP formation. Furthermore, we find that MCPs form normally upon the heterologous expression of PocR even in the absence of the natural inducer 1,2-propanediol and in the presence of glucose, and that Pdu MCPs formed in response to heterologous PocR expression can metabolize 1,2-propanediol in vivo. We anticipate that this technique of overexpressing a key transcription factor may be used to study and engineer the formation, size, and/or number of MCPs for the Pdu and related MCP systems.
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Affiliation(s)
- Edward Y. Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
| | - Christopher M. Jakobson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
| | - Danielle Tullman-Ercek
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
- * E-mail:
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