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Barger N, Litovco P, Li X, Habib M, Daniel R. Synthetic metabolic computation in a bioluminescence-sensing system. Nucleic Acids Res 2019; 47:10464-10474. [PMID: 31544939 PMCID: PMC6821183 DOI: 10.1093/nar/gkz807] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 02/07/2023] Open
Abstract
Bioluminescence is visible light produced and emitted by living cells using various biological systems (e.g. luxCDABE cassette). Today, this phenomenon is widely exploited in biological research, biotechnology and medical applications as a quantitative technique for the detection of biological signals. However, this technique has mostly been used to detect a single input only. In this work, we re-engineered the complex genetic structure of luxCDABE cassette to build a biological unit that can detect multi-inputs, process the cellular information and report the computation results. We first split the luxCDABE operon into several parts to create a genetic circuit that can compute a soft minimum in living cells. Then, we used the new design to implement an AND logic function with better performance as compared to AND logic functions based on protein-protein interactions. Furthermore, by controlling the reverse reaction of the luxCDABE cassette independently from the forward reaction, we built a comparator with a programmable detection threshold. Finally, we applied the redesigned cassette to build an incoherent feedforward loop that reduced the unwanted crosstalk between stress-responsive promoters (recA, katG). This work demonstrates the construction of genetic circuits that combine regulations of gene expression with metabolic pathways, for sensing and computing in living cells.
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Affiliation(s)
- Natalia Barger
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Phyana Litovco
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Ximing Li
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Mouna Habib
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Ramez Daniel
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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52
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Reis AC, Halper SM, Vezeau GE, Cetnar DP, Hossain A, Clauer PR, Salis HM. Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays. Nat Biotechnol 2019; 37:1294-1301. [PMID: 31591552 DOI: 10.1038/s41587-019-0286-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 09/10/2019] [Indexed: 12/26/2022]
Abstract
Engineering cellular phenotypes often requires the regulation of many genes. When using CRISPR interference, coexpressing many single-guide RNAs (sgRNAs) triggers genetic instability and phenotype loss, due to the presence of repetitive DNA sequences. We stably coexpressed 22 sgRNAs within nonrepetitive extra-long sgRNA arrays (ELSAs) to simultaneously repress up to 13 genes by up to 3,500-fold. We applied biophysical modeling, biochemical characterization and machine learning to develop toolboxes of nonrepetitive genetic parts, including 28 sgRNA handles that bind Cas9. We designed ELSAs by combining nonrepetitive genetic parts according to algorithmic rules quantifying DNA synthesis complexity, sgRNA expression, sgRNA targeting and genetic stability. Using ELSAs, we created three highly selective phenotypes in Escherichia coli, including redirecting metabolism to increase succinic acid production by 150-fold, knocking down amino acid biosynthesis to create a multi-auxotrophic strain and repressing stress responses to reduce persister cell formation by 21-fold. ELSAs enable simultaneous and stable regulation of many genes for metabolic engineering and synthetic biology applications.
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Affiliation(s)
- Alexander C Reis
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Sean M Halper
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Grace E Vezeau
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
| | - Daniel P Cetnar
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Ayaan Hossain
- Bioinformatics and Genomics, Pennsylvania State University, University Park, PA, USA
| | - Phillip R Clauer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Howard M Salis
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA.
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA.
- Bioinformatics and Genomics, Pennsylvania State University, University Park, PA, USA.
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53
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Hudson AJ, Wieden HJ. Rapid generation of sequence-diverse terminator libraries and their parameterization using quantitative Term-Seq. Synth Biol (Oxf) 2019; 4:ysz026. [PMID: 32995547 PMCID: PMC7445774 DOI: 10.1093/synbio/ysz026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/03/2019] [Indexed: 01/09/2023] Open
Abstract
Synthetic biology and the rational design and construction of biological devices require vast numbers of characterized biological parts, as well as reliable design tools to build increasingly complex, multigene architectures. Design principles for intrinsic terminators have been established; however, additional sequence-structure studies are needed to refine parameters for termination-based genetic devices. We report a rapid single-pot method to generate libraries of thousands of randomized bidirectional intrinsic terminators and a modified quantitative Term-Seq (qTerm-Seq) method to simultaneously identify terminator sequences and measure their termination efficiencies (TEs). Using qTerm-Seq, we characterize hundreds of additional strong terminators (TE > 90%) with some terminators reducing transcription read-through by up to 1000-fold in Escherichia coli. Our terminator library and qTerm-Seq pipeline constitute a flexible platform enabling identification of terminator parts that can achieve transcription termination not only over a desired range but also to investigate their sequence-structure features, including for specific genetic and application contexts beyond the common in vivo systems such as E. coli.
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Affiliation(s)
- Andrew J Hudson
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, Alberta, Canada.,Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, Alberta, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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54
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Bordoy AE, O’Connor NJ, Chatterjee A. Construction of Two-Input Logic Gates Using Transcriptional Interference. ACS Synth Biol 2019; 8:2428-2441. [PMID: 31532632 DOI: 10.1021/acssynbio.9b00321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Transcriptional interference (TI) has been shown to regulate gene expression at the DNA level via different molecular mechanisms. The obstacles present on the DNA that a transcribing RNA polymerase might encounter, for example, a DNA-bound protein or another RNA polymerase, can result in TI causing termination of transcription, thus reducing gene expression. However, the potential of TI as a new strategy to engineer complex gene expression modules has not been fully explored yet. Here we created a series of two-input genetic devices that use the presence of a roadblocking protein to control gene expression and analyzed their behaviors using both experimental and mathematical modeling approaches. We explored how multiple characteristics affect the response of genetic devices engineered to act like either AND, OR, or single input logic gates. We show that the dissociation constant of the roadblocking protein, inducer activation of promoter and operator sites, and distance between tandem promoters tune gate behavior. This work highlights the potential of rationally creating different types of genetic responses using the same transcription factors in subtly different genetic architectures.
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55
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Olmedo-Verd E, Brenes-Álvarez M, Vioque A, Muro-Pastor AM. A Heterocyst-Specific Antisense RNA Contributes to Metabolic Reprogramming in Nostoc sp. PCC 7120. PLANT & CELL PHYSIOLOGY 2019; 60:1646-1655. [PMID: 31093664 DOI: 10.1093/pcp/pcz087] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/28/2019] [Indexed: 06/09/2023]
Abstract
Upon nitrogen deficiency, some filamentous cyanobacteria differentiate specialized cells, called heterocysts, devoted to N2 fixation. Heterocysts appear regularly spaced along the filaments and exhibit structural and metabolic adaptations, such as loss of photosynthetic CO2 fixation or increased respiration, to provide a proper microaerobic environment for its specialized function. Heterocyst development is under transcriptional control of the global nitrogen regulator NtcA and the specific regulator HetR. Transcription of a large number of genes is induced or repressed upon nitrogen deficiency specifically in cells undergoing differentiation. In recent years, the HetR regulon has been described to include heterocyst-specific trans-acting small RNAs and antisense RNAs (asRNAs), suggesting that there is an additional layer of post-transcriptional regulation involved in heterocyst development. Here, we characterize in the cyanobacterium Nostoc (Anabaena) sp. PCC 7120 an asRNA, that we call as_glpX, transcribed within the glpX gene encoding the Calvin cycle bifunctional enzyme sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (SBPase). Transcription of as_glpX is restricted to heterocysts and is induced very early during the process of differentiation. Expression of as_glpX RNA promotes the cleavage of the glpX mRNA by RNase III, resulting in a reduced amount of SBPase. Therefore, the early expression of this asRNA could contribute to the quick shut-down of CO2 fixation in those cells in the filament that are undergoing differentiation into heterocysts. In summary, as_glpX is the first naturally occurring asRNA shown to rapidly and dynamically regulate metabolic transformation in Nostoc heterocysts. The use of antisense transcripts to manipulate gene expression specifically in heterocysts could became a useful tool for metabolic engineering in cyanobacteria.
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Affiliation(s)
- Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
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56
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Hao N, Crooks MT, Palmer AC, Dodd IB, Shearwin KE. RNA polymerase pausing at a protein roadblock can enhance transcriptional interference by promoter occlusion. FEBS Lett 2019; 593:903-917. [PMID: 30892685 PMCID: PMC6593788 DOI: 10.1002/1873-3468.13365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 03/16/2019] [Indexed: 12/18/2022]
Abstract
Convergent promoters exert transcriptional interference (TI) by several mechanisms including promoter occlusion, where elongating RNA polymerases (RNAPs) block access to a promoter. Here, we tested whether pausing of RNAPs by obstructive DNA‐bound proteins can enhance TI by promoter occlusion. Using the Lac repressor as a ‘roadblock’ to induce pausing over a target promoter, we found only a small increase in TI, with mathematical modelling suggesting that rapid termination of the stalled RNAP was limiting the occlusion effect. As predicted, the roadblock‐enhanced occlusion was significantly increased in the absence of the Mfd terminator protein. Thus, protein roadblocking of RNAP may cause pause‐enhanced occlusion throughout genomes, and the removal of stalled RNAP may be needed to minimize unwanted TI.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, Australia
| | - Michael T Crooks
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Adam C Palmer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian B Dodd
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Keith E Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
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57
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Hoffmann SA, Hao N, Shearwin KE, Arndt KM. Characterizing Transcriptional Interference between Converging Genes in Bacteria. ACS Synth Biol 2019; 8:466-473. [PMID: 30717589 DOI: 10.1021/acssynbio.8b00477] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antisense transcription is common in naturally occurring genomes and is increasingly being used in synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the expression of convergent genes can be mediated by antisense RNA effects and by transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between convergent genes with untranslated intergenic spacers of increasing length. After controlling for antisense RNA-mediated effects, which contributed about half of the observed total expression inhibition, the TI effect was modeled. To achieve model convergence, RNA polymerase processivity and collision resistance were assumed to be modulated by ribosome trailing. The spontaneous transcription termination rate in regions of untranslated DNA was experimentally determined. Our modeling suggests that an elongating RNA polymerase with a trailing ribosome is about 13 times more likely to resume transcription than an opposing RNA polymerase without a trailing ribosome, upon head-on collision of the two.
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Affiliation(s)
- Stefan A Hoffmann
- Molecular Biotechnology, Institute for Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Straße 24-25 , 14476 Potsdam-Golm , Germany
| | - Nan Hao
- Discipline of Biochemistry, Department of Molecular and Biomedical Science, School of Biological Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
- CSIRO Synthetic Biology Future Science Platform , GPO Box 1700, Canberra , Australian Capital Territory 2601 , Australia
| | - Keith E Shearwin
- Discipline of Biochemistry, Department of Molecular and Biomedical Science, School of Biological Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
| | - Katja M Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology , University of Potsdam , Karl-Liebknecht-Straße 24-25 , 14476 Potsdam-Golm , Germany
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58
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Extracytoplasmic Function σ Factors Can Be Implemented as Robust Heterologous Genetic Switches in Bacillus subtilis. iScience 2019; 13:380-390. [PMID: 30897511 PMCID: PMC6426705 DOI: 10.1016/j.isci.2019.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/14/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023] Open
Abstract
In bacteria, the promoter specificity of RNA polymerase is determined by interchangeable σ subunits. Extracytoplasmic function σ factors (ECFs) form the largest and most diverse family of alternative σ factors, and their suitability for constructing genetic switches and circuits was already demonstrated. However, a systematic study on how genetically determined perturbations affect the behavior of these switches is still lacking, which impairs our ability to predict their behavior in complex circuitry. Here, we implemented four ECF switches in Bacillus subtilis and comprehensively characterized their robustness toward genetic perturbations, including changes in copy number, protein stability, or antisense transcription. All switches show characteristic dose-response behavior that varies depending on the individual ECF-promoter pair. Most perturbations had performance costs. Although some general design rules could be derived, a detailed characterization of each ECF switch before implementation is recommended to understand and thereby accommodate its individual behavior. Four heterologous ECF-based genetic switches were implemented in Bacillus subtilis Each ECF switch was excessively modified and comprehensively evaluated The robustness to genetic perturbations differed significantly between switches B. subtilis has a narrow phylogenetic acceptance range for heterologous ECFs
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59
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Koopal B, Kruis AJ, Claassens NJ, Nobrega FL, van der Oost J. Incorporation of a Synthetic Amino Acid into dCas9 Improves Control of Gene Silencing. ACS Synth Biol 2019; 8:216-222. [PMID: 30668910 DOI: 10.1021/acssynbio.8b00347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The CRISPR-Cas9 nuclease has been repurposed as a tool for gene repression (CRISPRi). This catalytically dead Cas9 (dCas9) variant inhibits transcription by blocking either initiation or elongation by the RNA polymerase complex. Conditional control of dCas9-mediated repression has been achieved with inducible promoters that regulate the expression of the dcas9 gene. However, as dCas9-mediated gene silencing is very efficient, even slightly leaky dcas9 expression leads to significant background levels of repression of the target gene. In this study, we report on the development of optimized control of dCas9-mediated silencing through additional regulation at the translation level. We have introduced the TAG stop codon in the dcas9 gene in order to insert a synthetic amino acid, l-biphenylalanine (BipA), at a permissive site in the dCas9 protein. In the absence of BipA, a nonfunctional, truncated dCas9 is produced, but when BipA is present, the TAG codon is translated resulting in a functional, full-length dCas9 protein. This synthetic, BipA-containing dCas9 variant (dCas9-BipA) could still fully repress gene transcription. Comparison of silencing mediated by dCas9 to dCas9-BipA revealed a 14-fold reduction in background repression by the latter system. The here developed proof-of-principle system thus reduces unwanted background levels of gene silencing, allowing for tight and timed control of target gene expression.
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Affiliation(s)
- Balwina Koopal
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Aleksander J. Kruis
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nico J. Claassens
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Franklin L. Nobrega
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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60
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Abate D, De Miccolis Angelini RM, Rotolo C, Pollastro S, Faretra F. Mating System in the Brown Rot Pathogens Monilinia fructicola, M. laxa, and M. fructigena. PHYTOPATHOLOGY 2018; 108:1315-1325. [PMID: 29767553 DOI: 10.1094/phyto-03-18-0074-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Monilinia fructicola, M. laxa, and M. fructigena are the most important pathogens responsible for brown rot disease of stone and pome fruits. Information on their mating system and sexual behavior is scant. A mating-type-specific PCR-based assay was developed and applied to 155 Monilinia isolates from 10 countries and 10 different host plants. We showed that single isolates carry only one of two opposite idiomorphs at the MAT1 locus consistent with a heterothallic mating system for all three species. MAT1-1 and MAT1-2 mating types were detected in similar proportions in samples of isolates of each species and hence there do not appear to be genetic obstacles to the occurrence of sexual reproduction in their populations. Inter simple sequence repeat markers suggested that asexual reproduction is prevalent, but that sexual recombination occurs in M. fructicola populations in Italy. The genetic architectures of the MAT1 loci of the three pathogens were analyzed. MAT1-1 and MAT1-2 idiomorphs are flanked upstream and downstream by the APN2 and SLA2 genes and resemble those of Botrytis cinerea and other heterothallic fungi in the family Sclerotiniaceae. Each idiomorph contains a specific couple of genes, MAT1-1-1 (with alpha-box domain) and MAT1-1-5 in MAT1-1, and MAT1-2-1 (with HMG-box domain) and MAT1-2-10 in MAT1-2. Small gene fragments (dMAT1-1-1 and dMAT1-2-1) from the opposite idiomorph were detected close to their flanking regions. Constitutive expression of the four MAT1 genes during vegetative growth was ascertained by transcriptomic analysis (RNA-Seq). Antisense transcription of the MAT1-1-1 and MAT1-2-1 genes and intergenic transcribed regions of the MAT1 locus were detected. These results represent new insights into the mating systems of these three economically-important pathogens which could contribute to improve the knowledge on their population biology.
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Affiliation(s)
- Domenico Abate
- First, second, third, fourth, an fifth authors: Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy; and second, fourth, and firth authors: SELGE Network of Public Research Laboratories, via Amendola 165/A, 70126 Bari, Italy
| | - Rita M De Miccolis Angelini
- First, second, third, fourth, an fifth authors: Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy; and second, fourth, and firth authors: SELGE Network of Public Research Laboratories, via Amendola 165/A, 70126 Bari, Italy
| | - Caterina Rotolo
- First, second, third, fourth, an fifth authors: Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy; and second, fourth, and firth authors: SELGE Network of Public Research Laboratories, via Amendola 165/A, 70126 Bari, Italy
| | - Stefania Pollastro
- First, second, third, fourth, an fifth authors: Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy; and second, fourth, and firth authors: SELGE Network of Public Research Laboratories, via Amendola 165/A, 70126 Bari, Italy
| | - Francesco Faretra
- First, second, third, fourth, an fifth authors: Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy; and second, fourth, and firth authors: SELGE Network of Public Research Laboratories, via Amendola 165/A, 70126 Bari, Italy
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Lee J, Arun Kumar S, Jhan YY, Bishop CJ. Engineering DNA vaccines against infectious diseases. Acta Biomater 2018; 80:31-47. [PMID: 30172933 PMCID: PMC7105045 DOI: 10.1016/j.actbio.2018.08.033] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 08/14/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022]
Abstract
Engineering vaccine-based therapeutics for infectious diseases is highly challenging, as trial formulations are often found to be nonspecific, ineffective, thermally or hydrolytically unstable, and/or toxic. Vaccines have greatly improved the therapeutic landscape for treating infectious diseases and have significantly reduced the threat by therapeutic and preventative approaches. Furthermore, the advent of recombinant technologies has greatly facilitated growth within the vaccine realm by mitigating risks such as virulence reversion despite making the production processes more cumbersome. In addition, seroconversion can also be enhanced by recombinant technology through kinetic and nonkinetic approaches, which are discussed herein. Recombinant technologies have greatly improved both amino acid-based vaccines and DNA-based vaccines. A plateau of interest has been reached between 2001 and 2010 for the scientific community with regard to DNA vaccine endeavors. The decrease in interest may likely be attributed to difficulties in improving immunogenic properties associated with DNA vaccines, although there has been research demonstrating improvement and optimization to this end. Despite improvement, to the extent of our knowledge, there are currently no regulatory body-approved DNA vaccines for human use (four vaccines approved for animal use). This article discusses engineering DNA vaccines against infectious diseases while discussing advantages and disadvantages of each, with an emphasis on applications of these DNA vaccines. Statement of Significance This review paper summarizes the state of the engineered/recombinant DNA vaccine field, with a scope entailing “Engineering DNA vaccines against infectious diseases”. We endeavor to emphasize recent advances, recapitulating the current state of the field. In addition to discussing DNA therapeutics that have already been clinically translated, this review also examines current research developments, and the challenges thwarting further progression. Our review covers: recombinant DNA-based subunit vaccines; internalization and processing; enhancing immune protection via adjuvants; manufacturing and engineering DNA; the safety, stability and delivery of DNA vaccines or plasmids; controlling gene expression using plasmid engineering and gene circuits; overcoming immunogenic issues; and commercial successes. We hope that this review will inspire further research in DNA vaccine development.
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62
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Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol 2018; 3:135-149. [PMID: 30345399 PMCID: PMC6190536 DOI: 10.1016/j.synbio.2018.09.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.
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Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Xiao Jia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuan Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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63
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Abstract
ABSTRACT
Although bacterial genomes are usually densely protein-coding, genome-wide mapping approaches of transcriptional start sites revealed that a significant fraction of the identified promoters drive the transcription of noncoding RNAs. These can be
trans
-acting RNAs, mainly originating from intergenic regions and, in many studied examples, possessing regulatory functions. However, a significant fraction of these noncoding RNAs consist of natural antisense transcripts (asRNAs), which overlap other transcriptional units. Naturally occurring asRNAs were first observed to play a role in bacterial plasmid replication and in bacteriophage λ more than 30 years ago. Today’s view is that asRNAs abound in all three domains of life. There are several examples of asRNAs in bacteria with clearly defined functions. Nevertheless, many asRNAs appear to result from pervasive initiation of transcription, and some data point toward global functions of such widespread transcriptional activity, explaining why the search for a specific regulatory role is sometimes futile. In this review, we give an overview about the occurrence of antisense transcription in bacteria, highlight particular examples of functionally characterized asRNAs, and discuss recent evidence pointing at global relevance in RNA processing and transcription-coupled DNA repair.
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64
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Yona AH, Alm EJ, Gore J. Random sequences rapidly evolve into de novo promoters. Nat Commun 2018; 9:1530. [PMID: 29670097 PMCID: PMC5906472 DOI: 10.1038/s41467-018-04026-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/28/2018] [Indexed: 11/09/2022] Open
Abstract
How new functions arise de novo is a fundamental question in evolution. We studied de novo evolution of promoters in Escherichia coli by replacing the lac promoter with various random sequences of the same size (~100 bp) and evolving the cells in the presence of lactose. We find that ~60% of random sequences can evolve expression comparable to the wild-type with only one mutation, and that ~10% of random sequences can serve as active promoters even without evolution. Such a short mutational distance between random sequences and active promoters may improve the evolvability, yet may also lead to accidental promoters inside genes that interfere with normal expression. Indeed, our bioinformatic analyses indicate that E. coli was under selection to reduce accidental promoters inside genes by avoiding promoter-like sequences. We suggest that a low threshold for functionality balanced by selection against undesired targets can increase the evolvability by making new beneficial features more accessible. Bacterial promoters initiate gene transcription and have distinct sequence features. Here, the authors show that random sequences that contain no information are just on the verge of functioning as promoters in Escherichia coli.
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Affiliation(s)
- Avihu H Yona
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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65
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Bittihn P, Din MO, Tsimring LS, Hasty J. Rational engineering of synthetic microbial systems: from single cells to consortia. Curr Opin Microbiol 2018; 45:92-99. [PMID: 29574330 DOI: 10.1016/j.mib.2018.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/06/2018] [Accepted: 02/19/2018] [Indexed: 12/11/2022]
Abstract
One promise of synthetic biology is to provide solutions for biomedical and industrial problems by rational design of added functionality in living systems. Microbes are at the forefront of this biological engineering endeavor due to their general ease of handling and their relevance in many potential applications from fermentation to therapeutics. In recent years, the field has witnessed an explosion of novel regulatory tools, from synthetic orthogonal transcription factors to posttranslational mechanisms for increased control over the behavior of synthetic circuits. Tool development has been paralleled by the discovery of principles that enable increased modularity and the management of host-circuit interactions. Engineered cell-to-cell communication bridges the scales from intracellular to population-level coordination. These developments facilitate the translation of more than a decade of circuit design into applications.
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Affiliation(s)
- Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Omar Din
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Molecular Biology Section, Division of Biological Science, University of California, San Diego, La Jolla, CA 92093, USA.
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66
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Vigouroux A, Oldewurtel E, Cui L, Bikard D, van Teeffelen S. Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes. Mol Syst Biol 2018; 14:e7899. [PMID: 29519933 PMCID: PMC5842579 DOI: 10.15252/msb.20177899] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/08/2018] [Accepted: 02/14/2018] [Indexed: 02/06/2023] Open
Abstract
Over the past few years, tools that make use of the Cas9 nuclease have led to many breakthroughs, including in the control of gene expression. The catalytically dead variant of Cas9 known as dCas9 can be guided by small RNAs to block transcription of target genes, in a strategy also known as CRISPRi. Here, we reveal that the level of complementarity between the guide RNA and the target controls the rate at which RNA polymerase "kicks out" dCas9 from the target and completes transcription. We use this mechanism to precisely and robustly reduce gene expression by defined relative amounts. Alternatively, tuning repression by changing dCas9 concentration is noisy and promoter-strength dependent. We demonstrate broad applicability of this method to the study of genetic regulation and cellular physiology. First, we characterize feedback strength of a model auto-repressor. Second, we study the impact of amount variations of cell-wall synthesizing enzymes on cell morphology. Finally, we multiplex the system to obtain any combination of fractional repression of two genes.
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Affiliation(s)
- Antoine Vigouroux
- Synthetic Biology Laboratory, Institut Pasteur, Paris, France
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Enno Oldewurtel
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Lun Cui
- Synthetic Biology Laboratory, Institut Pasteur, Paris, France
| | - David Bikard
- Synthetic Biology Laboratory, Institut Pasteur, Paris, France
| | - Sven van Teeffelen
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
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67
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Wu F, Zhang Q, Wang X. Design of Adjacent Transcriptional Regions to Tune Gene Expression and Facilitate Circuit Construction. Cell Syst 2018; 6:206-215.e6. [PMID: 29428414 PMCID: PMC5832616 DOI: 10.1016/j.cels.2018.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/05/2017] [Accepted: 01/08/2018] [Indexed: 01/23/2023]
Abstract
Polycistronic architecture is common for synthetic gene circuits, however, it remains unknown how expression of one gene is affected by the presence of other genes/noncoding regions in the operon, termed adjacent transcriptional regions (ATR). Here, we constructed synthetic operons with a reporter gene flanked by different ATRs, and we found that ATRs with high GC content, small size, and low folding energy lead to high gene expression. Based on these results, we built a model of gene expression and generated a metric that takes into account ATRs. We used the metric to design and construct logic gates with low basal expression and high sensitivity and nonlinearity. Furthermore, we rationally designed synthetic 5'ATRs with different GC content and sizes to tune protein expression levels over a 300-fold range and used these to build synthetic toggle switches with varying basal expression and degrees of bistability. Our comprehensive model and gene expression metric could facilitate the future engineering of more complex synthetic gene circuits.
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Affiliation(s)
- Fuqing Wu
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Qi Zhang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA.
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68
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Heinsch SC, Das SR, Smanski MJ. Simulation Modeling to Compare High-Throughput, Low-Iteration Optimization Strategies for Metabolic Engineering. Front Microbiol 2018. [PMID: 29535690 PMCID: PMC5835107 DOI: 10.3389/fmicb.2018.00313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increasing the final titer of a multi-gene metabolic pathway can be viewed as a multivariate optimization problem. While numerous multivariate optimization algorithms exist, few are specifically designed to accommodate the constraints posed by genetic engineering workflows. We present a strategy for optimizing expression levels across an arbitrary number of genes that requires few design-build-test iterations. We compare the performance of several optimization algorithms on a series of simulated expression landscapes. We show that optimal experimental design parameters depend on the degree of landscape ruggedness. This work provides a theoretical framework for designing and executing numerical optimization on multi-gene systems.
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Affiliation(s)
- Stephen C. Heinsch
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- Bioinformatics and Computational Biology Program, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
| | - Siba R. Das
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
| | - Michael J. Smanski
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- Bioinformatics and Computational Biology Program, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN, United States
- *Correspondence: Michael J. Smanski,
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69
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Gorochowski TE, Espah Borujeni A, Park Y, Nielsen AA, Zhang J, Der BS, Gordon DB, Voigt CA. Genetic circuit characterization and debugging using RNA-seq. Mol Syst Biol 2017; 13:952. [PMID: 29122925 PMCID: PMC5731345 DOI: 10.15252/msb.20167461] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genetic circuits implement computational operations within a cell. Debugging them is difficult because their function is defined by multiple states (e.g., combinations of inputs) that vary in time. Here, we develop RNA‐seq methods that enable the simultaneous measurement of: (i) the states of internal gates, (ii) part performance (promoters, insulators, terminators), and (iii) impact on host gene expression. This is applied to a three‐input one‐output circuit consisting of three sensors, five NOR/NOT gates, and 46 genetic parts. Transcription profiles are obtained for all eight combinations of inputs, from which biophysical models can extract part activities and the response functions of sensors and gates. Various unexpected failure modes are identified, including cryptic antisense promoters, terminator failure, and a sensor malfunction due to media‐induced changes in host gene expression. This can guide the selection of new parts to fix these problems, which we demonstrate by using a bidirectional terminator to disrupt observed antisense transcription. This work introduces RNA‐seq as a powerful method for circuit characterization and debugging that overcomes the limitations of fluorescent reporters and scales to large systems composed of many parts.
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Affiliation(s)
- Thomas E Gorochowski
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amin Espah Borujeni
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongjin Park
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alec Ak Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jing Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bryan S Der
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - D Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA .,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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70
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Li H, Hao C, Xu D. Development of a novel vector for cloning and expressing extremely toxic genes in Escherichia coli. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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71
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Zhou L, Shen J. Signal Transmission of Biological Reaction-Diffusion System by Using Synchronization. Front Comput Neurosci 2017; 11:92. [PMID: 29066966 PMCID: PMC5641312 DOI: 10.3389/fncom.2017.00092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 09/25/2017] [Indexed: 11/16/2022] Open
Abstract
Molecular signal transmission in cell is very crucial for information exchange. How to understand its transmission mechanism has attracted many researchers. In this paper, we prove that signal transmission problem between neural tumor molecules and drug molecules can be achieved by synchronous control. To achieve our purpose, we derive the Fokker-Plank equation by using the Langevin equation and theory of random walk, this is a model which can express the concentration change of neural tumor molecules. Second, according to the biological character that vesicles in cell can be combined with cell membrane to release the cargo which plays a role of signal transmission, we preliminarily analyzed the mechanism of tumor-drug molecular interaction. Third, we propose the view of synchronous control which means the process of vesicle docking with their target membrane is a synchronization process, and we can achieve the precise treatment of disease by using synchronous control. We believe this synchronous control mechanism is reasonable and two examples are given to illustrate the correctness of our results obtained in this paper.
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Affiliation(s)
- Lingli Zhou
- School of Mathematics and Statistics, Zhengzhou University, Zhengzhou, China.,Institute of Applied Mathematics, Xuchang University, Xuchang, China
| | - Jianwei Shen
- Institute of Applied Mathematics, Xuchang University, Xuchang, China
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72
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Ghodasara A, Voigt CA. Balancing gene expression without library construction via a reusable sRNA pool. Nucleic Acids Res 2017; 45:8116-8127. [PMID: 28609783 PMCID: PMC5737548 DOI: 10.1093/nar/gkx530] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/07/2017] [Indexed: 01/06/2023] Open
Abstract
Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt ‘target’ sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼103-fold range of strengths, yielding ∼107 combinations. This pool can simultaneously optimize up to six genes in a system. This requires building only a single system-specific construct by placing a target sequence upstream of each gene and transforming it with the pre-built sRNA pool. The resulting library is screened and the top clone is sequenced to determine the promoter controlling each sRNA, from which the fold-repression of the genes can be inferred. The system is then rebuilt by rationally selecting parts that implement the optimal expression of each gene. We demonstrate the versatility of this approach by using the same pool to optimize a metabolic pathway (β-carotene) and genetic circuit (XNOR logic gate).
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Affiliation(s)
- Amar Ghodasara
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
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73
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Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks. N Biotechnol 2017; 39:199-205. [DOI: 10.1016/j.nbt.2017.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022]
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74
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Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA. An engineering design approach to systems biology. Integr Biol (Camb) 2017; 9:574-583. [PMID: 28590470 PMCID: PMC6534349 DOI: 10.1039/c7ib00014f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.
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Affiliation(s)
- Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA.
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75
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Yeung E, Dy AJ, Martin KB, Ng AH, Del Vecchio D, Beck JL, Collins JJ, Murray RM. Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks. Cell Syst 2017; 5:11-24.e12. [DOI: 10.1016/j.cels.2017.06.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/08/2017] [Accepted: 06/05/2017] [Indexed: 01/25/2023]
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76
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Kumar A, Bansal M. Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression. DNA Res 2017; 24:25-35. [PMID: 27803028 PMCID: PMC5381344 DOI: 10.1093/dnares/dsw045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/23/2016] [Indexed: 01/28/2023] Open
Abstract
Next-generation sequencing studies have revealed that a variety of transcripts are present in the prokaryotic transcriptome and a significant fraction of them are functional, being involved in various regulatory activities apart from coding for proteins. Identification of promoters associated with different transcripts is necessary for characterization of the transcriptome. Promoter regions have been shown to have unique structural features as compared with their flanking region, in organisms covering all domains of life. Here we report an in silico analysis of DNA sequence dependent structural properties like stability, bendability and curvature in the promoter region of six different prokaryotic transcriptomes. Using these structural features, we predicted promoters associated with different categories of transcripts (mRNA, internal, antisense and non-coding), which constitute the transcriptome. Promoter annotation using structural features is fairly accurate and reliable with about 50% of the primary promoters being characterized by all three structural properties while at least one property identifies 95%. We also studied the relative differences of these structural features in terms of gene expression and found that the features, viz. lower stability, lesser bendability and higher curvature are more prominent in the promoter regions which are associated with high gene expression as compared with low expression genes. Hence, promoters, which are associated with higher gene expression, get annotated well using DNA structural features as compared with those, which are linked to lower gene expression.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012 Karnataka, India
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77
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Hao N, Palmer AC, Dodd IB, Shearwin KE. Directing traffic on DNA-How transcription factors relieve or induce transcriptional interference. Transcription 2017; 8:120-125. [PMID: 28129043 PMCID: PMC5423467 DOI: 10.1080/21541264.2017.1285851] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Transcriptional interference (TI) is increasingly recognized as a widespread mechanism of gene control, particularly given the pervasive nature of transcription, both sense and antisense, across all kingdoms of life. Here, we discuss how transcription factor binding kinetics strongly influence the ability of a transcription factor to relieve or induce TI.
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Affiliation(s)
- Nan Hao
- a Department of Molecular and Cellular Biology , School of Biological Sciences, University of Adelaide , Adelaide , SA , Australia
| | - Adam C Palmer
- b Department of Systems Biology , Harvard Medical School , Boston , MA , USA
| | - Ian B Dodd
- a Department of Molecular and Cellular Biology , School of Biological Sciences, University of Adelaide , Adelaide , SA , Australia
| | - Keith E Shearwin
- a Department of Molecular and Cellular Biology , School of Biological Sciences, University of Adelaide , Adelaide , SA , Australia
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78
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Hughes RA, Ellington AD. Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology. Cold Spring Harb Perspect Biol 2017; 9:9/1/a023812. [PMID: 28049645 DOI: 10.1101/cshperspect.a023812] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The chemical synthesis of DNA oligonucleotides and their assembly into synthons, genes, circuits, and even entire genomes by gene synthesis methods has become an enabling technology for modern molecular biology and enables the design, build, test, learn, and repeat cycle underpinning innovations in synthetic biology. In this perspective, we briefly review the techniques and technologies that enable the synthesis of DNA oligonucleotides and their assembly into larger DNA constructs with a focus on recent advancements that have sought to reduce synthesis cost and increase sequence fidelity. The development of lower-cost methods to produce high-quality synthetic DNA will allow for the exploration of larger biological hypotheses by lowering the cost of use and help to close the DNA read-write cost gap.
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Affiliation(s)
- Randall A Hughes
- Applied Research Laboratories, The University of Texas at Austin, Austin, Texas 78758
| | - Andrew D Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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79
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Bordoy AE, Varanasi US, Courtney CM, Chatterjee A. Transcriptional Interference in Convergent Promoters as a Means for Tunable Gene Expression. ACS Synth Biol 2016; 5:1331-1341. [PMID: 27346626 DOI: 10.1021/acssynbio.5b00223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An important goal of synthetic biology involves the extension and standardization of novel biological elements for applications in medicine and biotechnology. Transcriptional interference, occurring in sets of convergent promoters, offers a promising mechanism for building elements for the design of tunable gene regulation. Here, we investigate the transcriptional interference mechanisms of antisense roadblock and RNA polymerase traffic in a set of convergent promoters as novel modules for synthetic biology. We show examples of elements, including antisense roadblock, relative promoter strengths, interpromoter distance, and sequence content that can be tuned to give rise to repressive as well as cooperative behaviors, therefore resulting in distinct gene expression patterns. Our approach will be useful toward engineering new biological devices and will bring new insights to naturally occurring cis-antisense systems. Therefore, we are reporting a new biological tool that can be used for synthetic biology.
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Affiliation(s)
- Antoni E. Bordoy
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
| | - Usha S. Varanasi
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
| | - Colleen M. Courtney
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, ‡BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, UCB 596, Boulder, Colorado 80303, United States
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80
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Avcilar-Kucukgoze I, Ignatova Z. Rewiring host activities for synthetic circuit production: a translation view. Biotechnol Lett 2016; 39:25-31. [DOI: 10.1007/s10529-016-2229-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/30/2016] [Indexed: 11/30/2022]
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81
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Bradley RW, Buck M, Wang B. Recognizing and engineering digital-like logic gates and switches in gene regulatory networks. Curr Opin Microbiol 2016; 33:74-82. [DOI: 10.1016/j.mib.2016.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/14/2016] [Accepted: 07/06/2016] [Indexed: 02/08/2023]
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82
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Hao N, Palmer AC, Ahlgren-Berg A, Shearwin KE, Dodd IB. The role of repressor kinetics in relief of transcriptional interference between convergent promoters. Nucleic Acids Res 2016; 44:6625-38. [PMID: 27378773 PMCID: PMC5001618 DOI: 10.1093/nar/gkw600] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 06/22/2016] [Indexed: 01/09/2023] Open
Abstract
Transcriptional interference (TI), where transcription from a promoter is inhibited by the activity of other promoters in its vicinity on the same DNA, enables transcription factors to regulate a target promoter indirectly, inducing or relieving TI by controlling the interfering promoter. For convergent promoters, stochastic simulations indicate that relief of TI can be inhibited if the repressor at the interfering promoter has slow binding kinetics, making it either sensitive to frequent dislodgement by elongating RNA polymerases (RNAPs) from the target promoter, or able to be a strong roadblock to these RNAPs. In vivo measurements of relief of TI by CI or Cro repressors in the bacteriophage λ PR-PRE system show strong relief of TI and a lack of dislodgement and roadblocking effects, indicative of rapid CI and Cro binding kinetics. However, repression of the same λ promoter by a catalytically dead CRISPR Cas9 protein gave either compromised or no relief of TI depending on the orientation at which it binds DNA, consistent with dCas9 being a slow kinetics repressor. This analysis shows how the intrinsic properties of a repressor can be evolutionarily tuned to set the magnitude of relief of TI.
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Affiliation(s)
- Nan Hao
- Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Adam C Palmer
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Alexandra Ahlgren-Berg
- Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Keith E Shearwin
- Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ian B Dodd
- Discipline of Biochemistry, Department of Molecular and Cellular Biology, The University of Adelaide, Adelaide, South Australia 5005, Australia
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83
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Abstract
A surprise that has emerged from transcriptomics is the prevalence of genomic antisense transcription, which occurs counter to gene orientation. While frequent, the roles of antisense transcription in regulation are poorly understood. We built a synthetic system in Escherichia coli to study how antisense transcription can change the expression of a gene and tune the response characteristics of a regulatory circuit. We developed a new genetic part that consists of a unidirectional terminator followed by a constitutive antisense promoter and demonstrate that this part represses gene expression proportionally to the antisense promoter strength. Chip‐based oligo synthesis was applied to build a large library of 5,668 terminator–promoter combinations that was used to control the expression of three repressors (PhlF, SrpR, and TarA) in a simple genetic circuit (NOT gate). Using the library, we demonstrate that antisense promoters can be used to tune the threshold of a regulatory circuit without impacting other properties of its response function. Finally, we determined the relative contributions of antisense RNA and transcriptional interference to repressing gene expression and introduce a biophysical model to capture the impact of RNA polymerase collisions on gene repression. This work quantifies the role of antisense transcription in regulatory networks and introduces a new mode to control gene expression that has been previously overlooked in genetic engineering.
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Affiliation(s)
- Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Li Y, Li S, Ge X, Tian P. Development of a Red recombinase system and antisense RNA technology in Klebsiella pneumoniae for the production of chemicals. RSC Adv 2016. [DOI: 10.1039/c6ra12511e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Red recombinase system and antisense RNA technology were developed inKlebsiella pneumoniae.
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Affiliation(s)
- Ying Li
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- People's Republic of China
| | - Sha Li
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- People's Republic of China
| | - Xizhen Ge
- College of Biochemical Engineering
- Beijing Union University
- Beijing 100023
- People's Republic of China
| | - Pingfang Tian
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- People's Republic of China
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