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Vialetto E, Yu Y, Collins SP, Wandera KG, Barquist L, Beisel CL. A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13. Cell Host Microbe 2022; 30:1151-1162.e6. [PMID: 35690065 PMCID: PMC9590104 DOI: 10.1016/j.chom.2022.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022]
Abstract
CRISPR-Cas systems must enact robust immunity against foreign genetic material without inducing cytotoxic autoimmunity. For type VI systems that use Cas13 nucleases and recognize RNA targets, immune activation requires extensive CRISPR RNA (crRNA) guide-target complementarity and a target-flanking motif. Here, we report a third requirement shaping the immune response: the expression of the target transcript exceeding a threshold. We found that endogenous non-essential transcripts targeted by crRNAs rarely elicited autoimmunity. Instead, autoimmune induction required over-expressing the targeted transcripts above a threshold. A genome-wide screen confirmed target expression levels as a global determinant of cytotoxic autoimmunity and revealed that this threshold shifts with each guide-target pair. This threshold further ensured defense against a lytic bacteriophage yet allowed the tolerance of a targeted beneficial gene expressed from an invading plasmid. These findings establish target expression levels as an additional criterion for immune defense by RNA-targeting CRISPR-Cas systems, preventing autoimmunity and distinguishing pathogenic and benign invaders.
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Affiliation(s)
- Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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2
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Colarusso A, Lauro C, Calvanese M, Parrilli E, Tutino ML. Improvement of Pseudoalteromonas haloplanktis TAC125 as a Cell Factory: IPTG-Inducible Plasmid Construction and Strain Engineering. Microorganisms 2020; 8:microorganisms8101466. [PMID: 32987756 PMCID: PMC7598627 DOI: 10.3390/microorganisms8101466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023] Open
Abstract
Our group has used the marine bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) as a platform for the successful recombinant production of “difficult” proteins, including eukaryotic proteins, at low temperatures. However, there is still room for improvement both in the refinement of PhTAC125 expression plasmids and in the bacterium’s intrinsic ability to accumulate and handle heterologous products. Here, we present an integrated approach of plasmid design and strain engineering finalized to increment the recombinant expression and optimize the inducer uptake in PhTAC125. To this aim, we developed the IPTG-inducible plasmid pP79 and an engineered PhTAC125 strain called KrPL LacY+. This mutant was designed to express the E. coli lactose permease and to produce only a truncated version of the endogenous Lon protease through an integration-deletion strategy. In the wild-type strain, pP79 assured a significantly better production of two reporters in comparison to the most recent expression vector employed in PhTAC125. Nevertheless, the use of KrPL LacY+ was crucial to achieving satisfying production levels using reasonable IPTG concentrations, even at 0 °C. Both the wild-type and the mutant recombinant strains are characterized by an average graded response upon IPTG induction and they will find different future applications depending on the desired levels of expression.
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3
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Collias D, Leenay RT, Slotkowski RA, Zuo Z, Collins SP, McGirr BA, Liu J, Beisel CL. A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9. SCIENCE ADVANCES 2020; 6:eabb4054. [PMID: 32832642 PMCID: PMC7439565 DOI: 10.1126/sciadv.abb4054] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/28/2020] [Indexed: 05/16/2023]
Abstract
CRISPR technologies have overwhelmingly relied on the Streptococcus pyogenes Cas9 (SpyCas9), with its consensus NGG and less preferred NAG and NGA protospacer-adjacent motifs (PAMs). Here, we report that SpyCas9 also recognizes sequences within an N(A/C/T)GG motif. These sequences were identified on the basis of preferential enrichment in a growth-based screen in Escherichia coli. DNA binding, cleavage, and editing assays in bacteria and human cells validated recognition, with activities paralleling those for NAG(A/C/T) PAMs and dependent on the first two PAM positions. Molecular-dynamics simulations and plasmid-clearance assays with mismatch-intolerant variants supported induced-fit recognition of an extended PAM by SpyCas9 rather than recognition of NGG with a bulged R-loop. Last, the editing location for SpyCas9-derived base editors could be shifted by one nucleotide by selecting between (C/T)GG and adjacent N(C/T)GG PAMs. SpyCas9 and its enhanced variants thus recognize a larger repertoire of PAMs, with implications for precise editing, off-target predictions, and CRISPR-based immunity.
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Affiliation(s)
- D. Collias
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - R. T. Leenay
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - R. A. Slotkowski
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Z. Zuo
- College of Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76129, USA
| | - S. P. Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - B. A. McGirr
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - J. Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76129, USA
| | - C. L. Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
- Helmholtz Institute of RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97078 Würzburg, Germany
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4
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Moser F, Espah Borujeni A, Ghodasara AN, Cameron E, Park Y, Voigt CA. Dynamic control of endogenous metabolism with combinatorial logic circuits. Mol Syst Biol 2018; 14:e8605. [PMID: 30482789 PMCID: PMC6263354 DOI: 10.15252/msb.20188605] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 11/09/2022] Open
Abstract
Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post-translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed (pta or poxB) and respond by turning off the corresponding gene. This work demonstrates how simple circuits can be implemented to enable customizable dynamic gene regulation.
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Affiliation(s)
- Felix Moser
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amin Espah Borujeni
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amar N Ghodasara
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ewen Cameron
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongjin Park
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
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Zong DM, Cinar S, Shis DL, Josić K, Ott W, Bennett MR. Predicting Transcriptional Output of Synthetic Multi-input Promoters. ACS Synth Biol 2018; 7:1834-1843. [PMID: 30040895 DOI: 10.1021/acssynbio.8b00165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Recent advances in synthetic biology have led to a wealth of well-characterized genetic parts. As parts libraries grow, so too does the potential to create novel multi-input promoters that integrate disparate signals to determine transcriptional output. Our ability to construct such promoters will outpace our ability to characterize promoter performance, due to the vast number of input combinations. In this study, we examine the input-output relations of recently developed synthetic multi-input promoters and describe two methods for predicting their behavior. The first method uses 1-dimensional induction data obtained from experiments on single-input systems to predict the n-dimensional induction responses of systems with n inputs. We demonstrate that this approach accurately predicts Boolean (on/off) responses of multi-input systems consisting of novel chimeric transcription factors and hybrid promoters in Escherichia coli. The second method uses only a small amount of multi-input response data to accurately predict analog system response over the entire landscape of input combinations. Taken together, these methods facilitate the design of synthetic circuits that utilize multi-input promoters.
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Affiliation(s)
| | - Selahittin Cinar
- Department of Mathematics, ⊥Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | | | - Krešimir Josić
- Department of Mathematics, ⊥Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
| | - William Ott
- Department of Mathematics, ⊥Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004, United States
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Marschall L, Sagmeister P, Herwig C. Tunable recombinant protein expression in E. coli: promoter systems and genetic constraints. Appl Microbiol Biotechnol 2017; 101:501-512. [PMID: 27999902 PMCID: PMC5566544 DOI: 10.1007/s00253-016-8045-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/26/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022]
Abstract
Tuning of transcription is a promising strategy to overcome challenges associated with a non-suitable expression rate like outgrowth of segregants, inclusion body formation, metabolic burden and inefficient translocation. By adjusting the expression rate-even on line-to purposeful levels higher product titres and more cost-efficient production processes can be achieved by enabling culture long-term stability and constant product quality. Some tunable systems are registered for patents or already commercially available. Within this contribution, we discuss the induction mechanisms of various Escherichia coli inherent promoter systems with respect to their tunability and review studies using these systems for expression tuning. According to the current level of knowledge, some promoter systems were successfully used for expression tuning, and in some cases, analytical evidence on single-cell level is still pending. However, only a few studies using tunable strains apply a suitable process control strategy. So far, expression tuning has only gathered little attention, but we anticipate that expression tuning harbours great potential for enabling and optimizing the production of a broad spectrum of products in E. coli.
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Affiliation(s)
- Lukas Marschall
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria
| | | | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria.
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna University of Technology, Gumpendorferstrasse 1a/166-4, A-1060, Vienna, Austria.
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Spot 42 sRNA regulates arabinose-inducible araBAD promoter activity by repressing synthesis of the high-affinity low-capacity arabinose transporter. J Bacteriol 2016; 199:e00691-16. [PMID: 27849174 DOI: 10.1128/jb.00691-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The L-arabinose-inducible araBAD promoter (PBAD) allows tightly controlled and tunable expression of genes of interest in a broad range of bacterial species. It has been successfully used to study bacterial sRNA regulation, where PBAD drives expression of target mRNA translational fusions. Here we report that in Escherichia coli, Spot 42 sRNA can regulate PBAD promoter activity by affecting arabinose uptake. We demonstrate that Spot 42 sRNA represses araF, a gene encoding the AraF subunit of the high-affinity low-capacity arabinose transporter AraFGH, through direct base pairing interactions. We further show that endogenous Spot 42 sRNA is sufficient to repress araF expression under various growth conditions. Finally, we demonstrate this posttranscriptional repression has a biological consequence, decreasing the induction of PBAD at low levels of arabinose. This problem can be circumvented using strategies reported previously for avoiding all-or-none induction behavior, that is through constitutive expression of the low-affinity high-capacity arabinose transporter AraE or induction with higher concentration of inducers. This work adds araF to the set of Spot 42-regulated genes, in agreement with previous studies suggesting that Spot 42, itself negatively regulated by cAMP-CRP complex, reinforces the catabolite repression network. IMPORTANCE The bacterial arabinose inducible system is widely used for titratable control of gene expression. We demonstrate here that a post-transcriptional mechanism mediated by the Spot 42 sRNA contributes to the functionality of the PBAD system at subsaturating inducer concentrations by affecting inducer uptake. Our finding extends the inputs into the known transcriptional control for the PBAD system, and has implications for improving its usage for tunable gene expression.
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8
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Marschall L, Sagmeister P, Herwig C. Tunable recombinant protein expression in E. coli: enabler for continuous processing? Appl Microbiol Biotechnol 2016; 100:5719-28. [PMID: 27170324 PMCID: PMC4957632 DOI: 10.1007/s00253-016-7550-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 02/06/2023]
Abstract
Tuning of transcription is a powerful process technological tool for efficient recombinant protein production in Escherichia coli. Many challenges such as product toxicity, formation of inclusion bodies, cell death, and metabolic burden are associated with non-suitable (too high or too low) levels of recombinant protein expression. Tunable expression systems allow adjusting the recombinant protein expression using process technological means. This enables to exploit the cell's metabolic capacities to a maximum. Within this article, we review genetic and process technological aspects of tunable expression systems in E. coli, providing a roadmap for the industrial exploitation of the reviewed technologies. We attempt to differentiate the term "expression tuning" from its inflationary use by providing a concise definition and highlight interesting fields of application for this versatile new technology. Dependent on the type of inducer (metabolizable or non-metabolizable), different process strategies are required in order to achieve tuning. To fully profit from the benefits of tunable systems, an independent control of growth rate and expression rate is indispensable. Being able to tackle problems such as long-term culture stability and constant product quality expression tuning is a promising enabler for continuous processing in biopharmaceutical production.
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Affiliation(s)
- Lukas Marschall
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Vienna, Austria
| | | | - Christoph Herwig
- Exputec GmbH, Vienna, Austria. .,Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna University of Technology, Gumpendorferstraße 1a/166-4, 1060, Vienna, Austria.
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9
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Programmable genetic circuits for pathway engineering. Curr Opin Biotechnol 2015; 36:115-21. [DOI: 10.1016/j.copbio.2015.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 08/04/2015] [Accepted: 08/09/2015] [Indexed: 02/06/2023]
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10
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Abstract
Bacteria are known to consume some sugars over others, although recent work reported by Koirala and colleagues in this issue of the Journal of Bacteriology (S. Koirala, X. Wang, and C. V. Rao, J Bacteriol 198:386-393, 2016, http://dx.doi.org/10.1128/JB.00709-15) revealed that individual cells do not necessarily follow this hierarchy. By studying the preferential consumption of l-arabinose over d-xylose in Escherichia coli, those authors found that subpopulations consume one, the other, or both sugars through cross-repression between utilization pathways. Their findings challenge classic assertions about established hierarchies and can guide efforts to engineer the simultaneous utilization of multiple sugars.
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11
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Afroz T, Luo ML, Beisel CL. Impact of Residual Inducer on Titratable Expression Systems. PLoS One 2015; 10:e0137421. [PMID: 26348036 PMCID: PMC4562711 DOI: 10.1371/journal.pone.0137421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
Inducible expression systems are widely employed for the titratable control of gene expression, yet molecules inadvertently present in the growth medium or synthesized by the host cells can alter the response profile of some of these systems. Here, we explored the quantitative impact of these residual inducers on the apparent response properties of inducible systems. Using a simple mathematical model, we found that the presence of residual inducer shrinks the apparent dynamic range and causes the apparent Hill coefficient to converge to one. We also found that activating systems were more sensitive than repressing systems to the presence of residual inducer and the response parameters were most heavily dependent on the original Hill coefficient. Experimental interrogation of common titratable systems based on an L-arabinose inducible promoter or a thiamine pyrophosphate-repressing riboswitch in Escherichia coli confirmed the predicted trends. We finally found that residual inducer had a distinct effect on "all-or-none" systems, which exhibited increased sensitivity to the added inducer until becoming fully induced. Our findings indicate that residual inducer or repressor alters the quantitative response properties of titratable systems, impacting their utility for scientific discovery and pathway engineering.
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Affiliation(s)
- Taliman Afroz
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Michelle L Luo
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
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Afroz T, Biliouris K, Kaznessis Y, Beisel CL. Bacterial sugar utilization gives rise to distinct single-cell behaviours. Mol Microbiol 2014; 93:1093-1103. [PMID: 24976172 DOI: 10.1111/mmi.12695] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2014] [Indexed: 12/15/2022]
Abstract
Inducible utilization pathways reflect widespread microbial strategies to uptake and consume sugars from the environment. Despite their broad importance and extensive characterization, little is known how these pathways naturally respond to their inducing sugar in individual cells. Here, we performed single-cell analyses to probe the behaviour of representative pathways in the model bacterium Escherichia coli. We observed diverse single-cell behaviours, including uniform responses (d-lactose, d-galactose, N-acetylglucosamine, N-acetylneuraminic acid), 'all-or-none' responses (d-xylose, l-rhamnose) and complex combinations thereof (l-arabinose, d-gluconate). Mathematical modelling and probing of genetically modified pathways revealed that the simple framework underlying these pathways - inducible transport and inducible catabolism - could give rise to most of these behaviours. Sugar catabolism was also an important feature, as disruption of catabolism eliminated tunable induction as well as enhanced memory of previous conditions. For instance, disruption of catabolism in pathways that respond to endogenously synthesized sugars led to full pathway induction even in the absence of exogenous sugar. Our findings demonstrate the remarkable flexibility of this simple biological framework, with direct implications for environmental adaptation and the engineering of synthetic utilization pathways as titratable expression systems and for metabolic engineering.
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Affiliation(s)
- Taliman Afroz
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Konstantinos Biliouris
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yiannis Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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