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Ye S, Yang B, Yang L, Wei W, Fu M, Yan Y, Wang B, Li X, Liang C, Zhao W. Stemness subtypes in lower-grade glioma with prognostic biomarkers, tumor microenvironment, and treatment response. Sci Rep 2024; 14:14758. [PMID: 38926605 PMCID: PMC11208487 DOI: 10.1038/s41598-024-65717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Our research endeavors are directed towards unraveling the stem cell characteristics of lower-grade glioma patients, with the ultimate goal of formulating personalized treatment strategies. We computed enrichment stemness scores and performed consensus clustering to categorize phenotypes. Subsequently, we constructed a prognostic risk model using weighted gene correlation network analysis (WGCNA), random survival forest regression analysis as well as full subset regression analysis. To validate the expression differences of key genes, we employed experimental methods such as quantitative Polymerase Chain Reaction (qPCR) and assessed cell line proliferation, migration, and invasion. Three subtypes were assigned to patients diagnosed with LGG. Notably, Cluster 2 (C2), exhibiting the poorest survival outcomes, manifested characteristics indicative of the subtype characterized by immunosuppression. This was marked by elevated levels of M1 macrophages, activated mast cells, along with higher immune and stromal scores. Four hub genes-CDCA8, ORC1, DLGAP5, and SMC4-were identified and validated through cell experiments and qPCR. Subsequently, these validated genes were utilized to construct a stemness risk signature. Which revealed that Lower-Grade Glioma (LGG) patients with lower scores were more inclined to demonstrate favorable responses to immune therapy. Our study illuminates the stemness characteristics of gliomas, which lays the foundation for developing therapeutic approaches targeting CSCs and enhancing the efficacy of current immunotherapies. By identifying the stemness subtype and its correlation with prognosis and TME patterns in glioma patients, we aim to advance the development of personalized treatments, enhancing the ability to predict and improve overall patient prognosis.
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Affiliation(s)
- Shengda Ye
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bin Yang
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liu Yang
- Department of Neurosurgery, Central Theater General Hospital of the Chinese People's Liberation Army, Wuhan, China
| | - Wei Wei
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mingyue Fu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Yan
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bo Wang
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiang Li
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan, China.
- Medical Research Institute, Wuhan University, Wuhan, China.
- Sino-Italian Ascula Brain Science Joint Laboratory, Wuhan, China.
| | - Chen Liang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Cancer Hospital of Zhongnan Hospital of Wuhan University, Wuhan, China.
- Cancer Clinical Study Center of Hubei Province, Wuhan, China.
- Hubei Key Laboratory of Tumor Biological Behavior, Wuhan, China.
| | - Wenyuan Zhao
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
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Helenek C, Krzysztoń R, Petreczky J, Wan Y, Cabral M, Coraci D, Balázsi G. Synthetic gene circuit evolution: Insights and opportunities at the mid-scale. Cell Chem Biol 2024:S2451-9456(24)00219-8. [PMID: 38925113 DOI: 10.1016/j.chembiol.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Directed evolution focuses on optimizing single genetic components for predefined engineering goals by artificial mutagenesis and selection. In contrast, experimental evolution studies the adaptation of entire genomes in serially propagated cell populations, to provide an experimental basis for evolutionary theory. There is a relatively unexplored gap at the middle ground between these two techniques, to evolve in vivo entire synthetic gene circuits with nontrivial dynamic function instead of single parts or whole genomes. We discuss the requirements for such mid-scale evolution, with hypothetical examples for evolving synthetic gene circuits by appropriate selection and targeted shuffling of a seed set of genetic components in vivo. Implementing similar methods should aid the rapid generation, functionalization, and optimization of synthetic gene circuits in various organisms and environments, accelerating both the development of biomedical and technological applications and the understanding of principles guiding regulatory network evolution.
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Affiliation(s)
- Christopher Helenek
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rafał Krzysztoń
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julia Petreczky
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yiming Wan
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariana Cabral
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Damiano Coraci
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA.
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Chaulagain D, Shamabadi NS, Leslie SA, Karig DK. From Natural Microbe Screening to Sustained Chitinase Activity in Exogenous Hosts. ACS Synth Biol 2024; 13:1165-1176. [PMID: 38587290 DOI: 10.1021/acssynbio.3c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Genetic parts and hosts can be sourced from nature to realize new functions for synthetic biology or to improve performance in a particular application environment. Here, we proceed from the discovery and characterization of new parts to stable expression in new hosts with a particular focus on achieving sustained chitinase activity. Chitinase is a key enzyme for various industrial applications that require the breakdown of chitin, the second most abundant biopolymer on the earth. Diverse microbes exhibit chitinase activity, but for applications, the environmental conditions for optimal enzyme activity and microbe fitness must align with the application context. Achieving sustained chitinase activity under broad conditions in heterologous hosts has also proven difficult due to toxic side effects. Toward addressing these challenges, we first screen ocean water samples to identify microbes with chitinase activity. Next, we perform whole genome sequencing and analysis and select a chitinase gene for heterologous expression. Then, we optimize transformation methods for target hosts and introduce chitinase. Finally, to achieve robust function, we optimize ribosome binding sites and discover a beneficial promoter that upregulates chitinase expression in the presence of colloidal chitin in a sense-and-respond fashion. We demonstrate chitinase activity for >21 days in standard (Escherichia coli) and nonstandard (Roseobacter denitrificans) hosts. Besides enhancing chitinase applications, our pipeline is extendable to other functions, identifies natural microbes that can be used directly in non-GMO contexts, generates new parts for synthetic biology, and achieves weeks of stable activity in heterologous hosts.
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Affiliation(s)
- Diptee Chaulagain
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Narges S Shamabadi
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Skylar A Leslie
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - David K Karig
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
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Glass DS, Bren A, Vaisbourd E, Mayo A, Alon U. A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover. Cell 2024; 187:931-944.e12. [PMID: 38320549 PMCID: PMC10882425 DOI: 10.1016/j.cell.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/27/2023] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Differentiation is crucial for multicellularity. However, it is inherently susceptible to mutant cells that fail to differentiate. These mutants outcompete normal cells by excessive self-renewal. It remains unclear what mechanisms can resist such mutant expansion. Here, we demonstrate a solution by engineering a synthetic differentiation circuit in Escherichia coli that selects against these mutants via a biphasic fitness strategy. The circuit provides tunable production of synthetic analogs of stem, progenitor, and differentiated cells. It resists mutations by coupling differentiation to the production of an essential enzyme, thereby disadvantaging non-differentiating mutants. The circuit selected for and maintained a positive differentiation rate in long-term evolution. Surprisingly, this rate remained constant across vast changes in growth conditions. We found that transit-amplifying cells (fast-growing progenitors) underlie this environmental robustness. Our results provide insight into the stability of differentiation and demonstrate a powerful method for engineering evolutionarily stable multicellular consortia.
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Affiliation(s)
- David S Glass
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elizabeth Vaisbourd
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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Arjmand S. Promoters in Pichia pastoris: A Toolbox for Fine-Tuned Gene Expression. Methods Mol Biol 2024; 2844:159-178. [PMID: 39068339 DOI: 10.1007/978-1-0716-4063-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
This chapter reviews the different promoters used to control gene expression in the yeast Pichia pastoris, mainly for recombinant protein production. It covers natural inducible, derepressed, and constitutive promoters, as well as engineered synthetic/hybrid promoters, orthologous promoters from related yeasts, and emerging bidirectional promoters. Key examples, characteristics, and regulatory mechanisms are discussed for each promoter class. Recent efforts in promoter engineering through rational design, mutagenesis, and computational approaches are also highlighted. Looking ahead, we anticipate further developments that will enhance promoter design for Pichia pastoris. Overall, this comprehensive overview underscores the importance of promoter choice and engineering for fully harnessing Pichia pastoris biotechnological potential.
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Affiliation(s)
- Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran.
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6
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Arbel-Groissman M, Menuhin-Gruman I, Naki D, Bergman S, Tuller T. Fighting the battle against evolution: designing genetically modified organisms for evolutionary stability. Trends Biotechnol 2023; 41:1518-1531. [PMID: 37442714 DOI: 10.1016/j.tibtech.2023.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has made significant progress in many areas, but a major challenge that has received limited attention is the evolutionary stability of synthetic constructs made of heterologous genes. The expression of these constructs in microorganisms, that is, production of proteins that are not necessary for the organism, is a metabolic burden, leading to a decrease in relative fitness and make the synthetic constructs unstable over time. This is a significant concern for the synthetic biology community, particularly when it comes to bringing this technology out of the laboratory. In this review, we discuss the issue of evolutionary stability in synthetic biology and review the available tools to address this challenge.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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Chlebek JL, Leonard SP, Kang-Yun C, Yung MC, Ricci DP, Jiao Y, Park DM. Prolonging genetic circuit stability through adaptive evolution of overlapping genes. Nucleic Acids Res 2023; 51:7094-7108. [PMID: 37260076 PMCID: PMC10359631 DOI: 10.1093/nar/gkad484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023] Open
Abstract
The development of synthetic biological circuits that maintain functionality over application-relevant time scales remains a significant challenge. Here, we employed synthetic overlapping sequences in which one gene is encoded or 'entangled' entirely within an alternative reading frame of another gene. In this design, the toxin-encoding relE was entangled within ilvA, which encodes threonine deaminase, an enzyme essential for isoleucine biosynthesis. A functional entanglement construct was obtained upon modification of the ribosome-binding site of the internal relE gene. Using this optimized design, we found that the selection pressure to maintain functional IlvA stabilized the production of burdensome RelE for >130 generations, which compares favorably with the most stable kill-switch circuits developed to date. This stabilizing effect was achieved through a complete alteration of the allowable landscape of mutations such that mutations inactivating the entangled genes were disfavored. Instead, the majority of lineages accumulated mutations within the regulatory region of ilvA. By reducing baseline relE expression, these more 'benign' mutations lowered circuit burden, which suppressed the accumulation of relE-inactivating mutations, thereby prolonging kill-switch function. Overall, this work demonstrates the utility of sequence entanglement paired with an adaptive laboratory evolution campaign to increase the evolutionary stability of burdensome synthetic circuits.
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Affiliation(s)
- Jennifer L Chlebek
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean P Leonard
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Christina Kang-Yun
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Mimi C Yung
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dante P Ricci
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Yongqin Jiao
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Dan M Park
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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8
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Chen H, Liu Y, Yin Z, Chen H, Wang Y, Qian Y. Homologous repair deficiency-associated genes in invasive breast cancer revealed by WGCNA co-expression network analysis and genetic perturbation similarity analysis. Cell Cycle 2023; 22:1077-1100. [PMID: 36757135 PMCID: PMC10081085 DOI: 10.1080/15384101.2023.2174339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Homologous repair deficiency (HRD) causes double-strand break repair to be impeded, which is a common driver of carcinogenesis. However, the therapeutic and prognostic potential of HRD in invasive breast cancer (BRCA) has not been fully explored using comprehensive bioinformatics analysis. MATERIALS AND METHODS HRD score was defined as the unweighted sum of LOH, TAI, and LST scores and obtained from the previous study according to Theo A et al. To characterize BRCA tumor microenvironment (TME) subtypes, "ConsensusClusterPlus" R package was used to conduct unsupervised clustering. The xCell algorithm was utilized for tumor composition analysis to estimate the TME in TCGA-BRCA. A WGCNA analysis was conducted to uncover the gene coexpression modules and hub genes in the HRD-related gene module of BRCA. The functional enrichment study was carried out using Metascape. A novel analysis pipeline, Genetic Perturbation Similarity Analysis (GPSA), was used to explore the single-gene perturbation closely related to HRD based on 3048 stable knockdown/knockout cell lines. The prognostic variables were evaluated using univariate COX analysis. Kaplan-Meier (KM) survival analysis was performed to assess the prognostic potential of HRD score. Receiver operator characteristic (ROC) curve was utilized to judge the diagnostic utility. Drug sensitivity was estimated through the R package "oncoPredict" and Genomics of Drug Sensitivity in Cancer (GDSC) database. XSum algorithm was performed to screen the candidate small molecule drugs based on the connectivity map (CMAP) database. RESULTS Low HRD score suggested a better prognosis in BRCA patients. The tumor with low HRD score had considerably greater degree of infiltration of stromal cells and infiltration of immunocytes was significantly enhanced in the high HRD score group. Using WGCNA, ten co-expression modules were obtained. The turquoise module and 25 hub genes were identified as the most correlated with HRD in BRCA. Functional enrichment analysis revealed that the turquoise gene module was mainly concentrated in the "cell cycle" pathways. Candidate HRD-related gene signatures (MELK) were screened out through WGCNA and GPSA analysis pipeline and then validated on independent validation sets. A small molecule drug (Clofibrate) that has the potential to reverse the increase of high HRD score was screened out to improve oncological outcomes in BRCA. Molecular docking suggested MELK to be one of possible molecular targets in the Clofibrate treatment of BRCA. CONCLUSION Based on bioinformatic analysis, we fully explored the therapeutic and prognostic potential of HRD in BRCA. A novel HRD-related gene signature (MELK) were identified through the combination of WGCNA and GPSA analysis. In addition, we detailed the TME landscape in BRCA and identified four unique TME subtypes in group with high or low HRD score group. Moreover, Clofibrate were screened out to improve oncological outcomes in BRCA by reversing the increase of high HRD score. Thus, our study contributes to the development of personalized clinical management and treatment regimens of BRCA.
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Affiliation(s)
- Haohao Chen
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yanyan Liu
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhenglang Yin
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hao Chen
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yao Wang
- Department of Digestive Endoscopy, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Yeben Qian
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Jodlbauer J, Rieder L, Glieder A, Wiltschi B. Bidirectional Promoter Libraries Enable the Balanced Co-expression of Two Target Genes in E. coli. Methods Mol Biol 2023; 2617:75-86. [PMID: 36656517 DOI: 10.1007/978-1-0716-2930-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this chapter, we present a bidirectional promoter library toolbox to evaluate fast and efficiently the optimal conditions for the balanced co-expression of two target genes. As a proof-of-concept, we demonstrate the co-expression of CYP505x and the GroEL/ES complex, which resulted in noticeably elevated enzyme activity with one of the de-novo-designed promoters of the library. The new toolbox offers a straightforward one-pot cloning approach and is highly modular. As such, the method presented here should be of great interest to any gene co-expression study.
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Affiliation(s)
- Julia Jodlbauer
- acib - Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Lukas Rieder
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Birgit Wiltschi
- acib - Austrian Centre of Industrial Biotechnology, Graz, Austria. .,Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria. .,Institute of Bioprocess Science and Engineering Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
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10
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Bidirectional hybrid erythritol-inducible promoter for synthetic biology in Yarrowia lipolytica. Microb Cell Fact 2023; 22:7. [PMID: 36635727 PMCID: PMC9835291 DOI: 10.1186/s12934-023-02020-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The oleaginous yeast Yarrowia lipolytica is increasingly used as a chassis strain for generating bioproducts. Several hybrid promoters with different strengths have been developed by combining multiple copies of an upstream activating sequence (UAS) associated with a TATA box and a core promoter. These promoters display either constitutive, phase-dependent, or inducible strong expression. However, there remains a lack of bidirectional inducible promoters for co-expressing genes in Y. lipolytica. RESULTS This study built on our previous work isolating and characterizing the UAS of the erythritol-induced genes EYK1 and EYD1 (UAS-eyk1). We found an erythritol-inducible bidirectional promoter (BDP) located in the EYK1-EYL1 intergenic region. We used the BDP to co-produce YFP and RedStarII fluorescent proteins and demonstrated that the promoter's strength was 2.7 to 3.5-fold stronger in the EYL1 orientation compared to the EYK1 orientation. We developed a hybrid erythritol-inducible bidirectional promoter (HBDP) containing five copies of UAS-eyk1 in both orientations. It led to expression levels 8.6 to 19.2-fold higher than the native bidirectional promoter. While the BDP had a twofold-lower expression level than the strong constitutive TEF promoter, the HBDP had a 5.0-fold higher expression level when oriented toward EYL1 and a 2.4-fold higher expression level when oriented toward EYK1. We identified the optimal media for BDP usage by exploring yeast growth under microbioreactor conditions. Additionally, we constructed novel Golden Gate biobricks and a destination vector for general use. CONCLUSIONS In this research, we developed novel bidirectional and hybrid bidirectional promoters of which expression can be fine-tuned, responding to the need for versatile promoters in the yeast Y. lipolytica. This study provides effective tools that can be employed to smoothly adjust the erythritol-inducible co-expression of two target genes in biotechnology applications. BDPs developed in this study have potential applications in the fields of heterologous protein production, metabolic engineering, and synthetic biology.
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11
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Halvorsen TM, Ricci DP, Park DM, Jiao Y, Yung MC. Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape. ACS Synth Biol 2022; 11:3785-3796. [PMID: 36346907 DOI: 10.1021/acssynbio.2c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression of a toxin gene. A major challenge in kill switch engineering is balancing evolutionary stability with robust cell killing activity in application relevant host strains. Understanding host-specific containment dynamics and modes of failure helps to develop potent yet stable kill switches. To guide the design of robust kill switches in the agriculturally relevant strain Pseudomonas fluorescens SBW25, we present a comparison of lethality, stability, and genetic escape of eight different toxic effectors in the presence of their cognate inactivators (i.e., toxin-antitoxin modules, polymorphic exotoxin-immunity systems, restriction endonuclease-methyltransferase pair). We find that cell killing capacity and evolutionary stability are inversely correlated and dependent on the level of protection provided by the inactivator gene. Decreasing the proteolytic stability of the inactivator protein can increase cell killing capacity, but at the cost of long-term circuit stability. By comparing toxins within the same genetic context, we determine that modes of genetic escape increase with circuit complexity and are driven by toxin activity, the protective capacity of the inactivator, and the presence of mutation-prone sequences within the circuit. Collectively, the results of our study reveal that circuit complexity, toxin choice, inactivator stability, and DNA sequence design are powerful drivers of kill switch stability and valuable targets for optimization of biocontainment systems.
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Affiliation(s)
- Tiffany M Halvorsen
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dante P Ricci
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Dan M Park
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Yongqin Jiao
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California 94550, United States
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Baek J, Kim C, Eun Song Y, Kong DS, Mutyala S, Seol EH, Kim JR. Bioelectrochemical metabolic regulation of a heterologously expressed glycerol reductive pathway in E. coli BL21(DE3). Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Jaishankar J, Keshav A, Jayaram B, Chavan S, Srivastava P. Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194843. [PMID: 35840055 DOI: 10.1016/j.bbagrm.2022.194843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Divergent promoters are often responsible for controlling gene expression of related genes of the same pathway or for coordinating regulation at different time points. There are relatively few reports on characterization of divergent promoters in bacteria. In the present study, microarray profiling was carried out to analyze gene expression during growth of Gordonia sp. IITR100, which led to the identification of 35 % of adjacent gene candidates that are divergently transcribed. We focus here on the in-depth characterization of one such pair of genes. Two divergent promoters, PmaiA and Phyd, drive the expression of genes encoding maleate cis-trans isomerase (maiA) and hydantoinase (hyd), respectively. Our findings reveal asymmetric promoter activity with higher activity in the reverse orientation (Phyd) as compared to the forward orientation (PmaiA). Minimal promoter region for each orientation was identified by deletion mapping. Deletion of a 5'-untranslated region of each gene resulted in an increase in promoter activity. A putative binding site for CRP (Catabolite Repressor Protein) transcription regulator was also identified in the 80 bp common regulatory region between the -35 hexamers of the two promoters. The results of this study suggest that CRP-mediated repression of PmaiA occurs only in the cells grown in glucose. Phyd, on the other hand, is not repressed by CRP. However, deletion of the CRP binding site located between -95 to -110 upstream to the transcription start site of the maiA gene resulted in increased activity of PmaiA and decreased activity of Phyd. A single CRP binding site, therefore, affects the two promoters differently.
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Affiliation(s)
- Jananee Jaishankar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Aditi Keshav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Bijjiga Jayaram
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Sourabh Chavan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India.
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14
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Sun ML, Shi TQ, Lin L, Ledesma-Amaro R, Ji XJ. Advancing Yarrowia lipolytica as a superior biomanufacturing platform by tuning gene expression using promoter engineering. BIORESOURCE TECHNOLOGY 2022; 347:126717. [PMID: 35031438 DOI: 10.1016/j.biortech.2022.126717] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Yarrowia lipolytica is recognized as an excellent non-conventional yeast in the field of biomanufacturing, where it is used as a host to produce oleochemicals, terpenes, organic acids, polyols and recombinant proteins. Consequently, metabolic engineering of this yeast is becoming increasingly popular to advance it as a superior biomanufacturing platform, of which promoters are the most basic elements for tuning gene expression. Endogenous promoters of Yarrowia lipolytica were reviewed, which are the basis for promoter engineering. The engineering strategies, such as hybrid promoter engineering, intron enhancement promoter engineering, and transcription factor-based inducible promoter engineering are described. Additionally, the applications of Yarrowia lipolytica promoter engineering to rationally reconstruct biosynthetic gene clusters and improve the genome-editing efficiency of the CRISPR-Cas systems were reviewed. Finally, research needs and future directions for promoter engineering are also discussed in this review.
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Affiliation(s)
- Mei-Li Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210046, People's Republic of China
| | - Lu Lin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
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15
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Abdelaal AS, Yazdani SS. A genetic toolkit for co-expression of multiple proteins of diverse physiological implication. BIOTECHNOLOGY REPORTS 2021; 32:e00692. [PMID: 34917492 PMCID: PMC8666340 DOI: 10.1016/j.btre.2021.e00692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022]
Abstract
A novel 3 vector system designed to co-express 3 target genes/operons in E. coli. Co-expression of GFPuv, EYFP and TurboRFP studied in 6 different combinations. Each combination exhibited diverse impact on growth, plasmid stability, expression. GFP and RFP the most and the least favorable protein for the cells, respectively. Favorability is because of their impact on production of other co-expressed proteins.
Construction of plasmids is crucial for expression of functional proteins of diverse physiological impact in E. coli. Here, we first designed and constructed a novel pair of bacterial expression vectors, i.e., pAS01 and pAS02, to be co-transformed with pQE30 for the co-expression of three target genes. The three plasmids contain ColE1, p15A and pSC101 origin of replication for high, medium and low copy plasmids, respectively, and same promoter (T5) and RBS. We then cloned genes encoding three reporter proteins (GFPuv, TurboRFP, and EYFP) in each of these plasmids and co-expressed in E. coli in six different combinations. Each of these reporter proteins exhibited diverse impact on growth, plasmid copy number and stability, and expression of other reporter proteins. Our results indicate that GFP and RFP were the most and the least favorable proteins for the cells, respectively, in terms of these parameters, especially on impacting expression of other co-expressed proteins.
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16
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Decrulle AL, Frénoy A, Meiller-Legrand TA, Bernheim A, Lotton C, Gutierrez A, Lindner AB. Engineering gene overlaps to sustain genetic constructs in vivo. PLoS Comput Biol 2021; 17:e1009475. [PMID: 34624014 PMCID: PMC8528312 DOI: 10.1371/journal.pcbi.1009475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 10/20/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time. Genomes are translated by triplets of nucleotides on two different strands, allowing for six different reading frames. This permits the existence of gene overlaps, often observed in microbial genomes, where two different proteins are encoded on the same piece of DNA, but in different reading frames. Gene overlaps are classically considered an obstacle for both evolution and genetic engineering, as mutations in overlapping regions likely have pleitrotropic effects on several genes. In 2013, we identified specific evolutionary scenarios where the decrease in evolutionary potential caused by gene overlaps could instead be advantageous and selected for. In this work, we demonstrate the use of gene overlaps in another context where reducing evolutionary potential can be useful: preventing evolution from inactivating synthetic circuits. We show that gene overlaps can be engineered to increase the evolutionary stability of genes that are costly to their hosts, by entangling these costly genes with essential genes.
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Affiliation(s)
| | - Antoine Frénoy
- Université de Paris, INSERM U1001, Paris, France
- Université Grenoble Alpes, CNRS UMR5525, Grenoble, France
- * E-mail: (AF); (ABL)
| | | | | | | | | | - Ariel B. Lindner
- Université de Paris, INSERM U1001, Paris, France
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
- * E-mail: (AF); (ABL)
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17
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Ahmad SS, Samia NSN, Khan AS, Turjya RR, Khan MAAK. Bidirectional promoters: an enigmatic genome architecture and their roles in cancers. Mol Biol Rep 2021; 48:6637-6644. [PMID: 34378109 DOI: 10.1007/s11033-021-06612-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Bidirectional promoters are the transcription regulatory regions of genes positioned head-to-head on opposite strands. Specific sequence signals, chromatin modifications and three-dimensional structures of the transcription site facilitate the unconventional yet tightly regulated transcription proceeding in both directions from these promoters. Mutations or aberrant epigenetic changes can lead to abnormal enhanced or reduced expression from either of the bidirectionally transcribed genes resulting in tumorigenesis. Moreover, bidirectionally transcribed genes might also contribute towards the immune regulation in tumor microenvironment. In this review, we aimed to expound the characteristic features of bidirectional promoters alongside their transcriptional regulations, and ultimately, the association of these enigmatic genomic elements in different cancers.
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Affiliation(s)
- Sheikh Shafin Ahmad
- Department of Mathematics and Natural Sciences, Brac University, Dhaka, Bangladesh
| | | | - Auroni Semonti Khan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Rafeed Rahman Turjya
- Department of Mathematics and Natural Sciences, Brac University, Dhaka, Bangladesh
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18
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Son HI, Weiss A, You L. Design patterns for engineering genetic stability. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 19. [PMID: 34308010 DOI: 10.1016/j.cobme.2021.100297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The past 20 years have witnessed enormous progress in synthetic biology in the development of engineered cells for diverse applications, including biomanufacturing, materials fabrication, and potential therapeutics and diagnostics. However, it still remains a major challenge to maintain long-term performance of synthetic gene circuits, due to the emergence of mutants that lose circuit function. Here, we highlight major vulnerabilities of synthetic gene circuits resulting in circuit failure and mutant escape. We also discuss engineering strategies to enhance long-term circuit stability and performance. These approaches can be divided into two strategies: the suppression of the emergence of mutants and the suppression of their relative fitness if mutants do emerge. We anticipate that mechanistic understanding of the modes of circuit failure will facilitate future efforts to design evolutionarily robust synthetic biology-inspired applications.
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Affiliation(s)
- Hye-In Son
- Department of Biomedical Engineering, Duke University
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University
| | - Lingchong You
- Department of Biomedical Engineering, Duke University.,Center for Genomic and Computational Biology, Duke University.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine
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19
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Guo L, Zhao M, Tang Y, Han J, Gui Y, Ge J, Jiang S, Dai Q, Zhang W, Lin M, Zhou Z, Wang J. Modular Assembly of Ordered Hydrophilic Proteins Improve Salinity Tolerance in Escherichia coli. Int J Mol Sci 2021; 22:ijms22094482. [PMID: 33923104 PMCID: PMC8123400 DOI: 10.3390/ijms22094482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 11/24/2022] Open
Abstract
Most late embryogenesis abundant group 3 (G3LEA) proteins are highly hydrophilic and disordered, which can be transformed into ordered α-helices to play an important role in responding to diverse stresses in numerous organisms. Unlike most G3LEA proteins, DosH derived from Dinococcus radiodurans is a naturally ordered G3LEA protein, and previous studies have found that the N-terminal domain (position 1–103) of DosH protein is the key region for its folding into an ordered secondary structure. Synthetic biology provides the possibility for artificial assembling ordered G3LEA proteins or their analogues. In this report, we used the N-terminal domain of DosH protein as module A (named DS) and the hydrophilic domains (DrHD, BnHD, CeHD, and YlHD) of G3LEA protein from different sources as module B, and artificially assembled four non-natural hydrophilic proteins, named DS + DrHD, DS + BnHD, DS + CeHD, and DS + YlHD, respectively. Circular dichroism showed that the four hydrophile proteins were highly ordered proteins, in which the α-helix contents were DS + DrHD (56.1%), DS + BnHD (53.7%), DS + CeHD (49.1%), and DS + YLHD (64.6%), respectively. Phenotypic analysis showed that the survival rate of recombinant Escherichia coli containing ordered hydrophilic protein was more than 10% after 4 h treatment with 1.5 M NaCl, which was much higher than that of the control group. Meanwhile, in vivo enzyme activity results showed that they had higher activities of superoxide dismutase, catalase, lactate dehydrogenase and less malondialdehyde production. Based on these results, the N-terminal domain of DosH protein can be applied in synthetic biology due to the fact that it can change the order of hydrophilic domains, thus increasing stress resistance.
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Affiliation(s)
- Leizhou Guo
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
| | - Mingming Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Yin Tang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Yuan Gui
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Jiaming Ge
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Shijie Jiang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
| | - Qilin Dai
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
- Correspondence: (Z.Z.); (J.W.)
| | - Jin Wang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
- Correspondence: (Z.Z.); (J.W.)
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20
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Bi G, Liang J, Zheng Y, Li R, Zhao M, Huang Y, Zhan C, Xu S, Fan H. Multi-omics characterization and validation of invasiveness-related molecular features across multiple cancer types. J Transl Med 2021; 19:124. [PMID: 33766047 PMCID: PMC7995758 DOI: 10.1186/s12967-021-02773-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Tumor invasiveness reflects many biological changes associated with tumorigenesis, progression, metastasis, and drug resistance. Therefore, we performed a systematic assessment of invasiveness-related molecular features across multiple human cancers. Materials and methods Multi-omics data, including gene expression, miRNA, DNA methylation, and somatic mutation, in approximately 10,000 patients across 30 cancer types from The Cancer Genome Atlas, Gene Expression Omnibus, PRECOG, and our institution were enrolled in this study. Results Based on a robust gene signature, we established an invasiveness score and found that the score was significantly associated with worse prognosis in almost all cancers. Then, we identified common invasiveness-associated dysregulated molecular features between high- and low-invasiveness score group across multiple cancers, as well as investigated their mutual interfering relationships thus determining whether the dysregulation of invasiveness-related genes was caused by abnormal promoter methylation or miRNA expression. We also analyzed the correlations between the drug sensitivity data from cancer cell lines and the expression level of 685 invasiveness-related genes differentially expressed in at least ten cancer types. An integrated analysis of the correlations among invasiveness-related genetic features and drug response were conducted in esophageal carcinoma patients to outline the complicated regulatory mechanism of tumor invasiveness status in multiple dimensions. Moreover, functional enrichment suggests the invasiveness score might serve as a predictive biomarker for cancer patients receiving immunotherapy. Conclusion Our pan-cancer study provides a comprehensive atlas of tumor invasiveness and may guide more precise therapeutic strategies for tumor patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02773-x
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Affiliation(s)
- Guoshu Bi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Jiaqi Liang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yuansheng Zheng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Runmei Li
- Department of Biostatistics, Public Health, Fudan University, Shanghai, 200000, China
| | - Mengnan Zhao
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Yiwei Huang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
| | - Songtao Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China
| | - Hong Fan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No. 180 Fenglin Rd, Xuhui District, Shanghai, 200032, China.
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21
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Wang T, Tague N, Whelan SA, Dunlop MJ. Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites. Nucleic Acids Res 2021; 49:1163-1172. [PMID: 33367820 PMCID: PMC7826281 DOI: 10.1093/nar/gkaa1234] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/12/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.
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Affiliation(s)
- Tiebin Wang
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Nathan Tague
- Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Mary J Dunlop
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
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22
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Xiong X, Chen S. Expanding Toolbox for Genes Expression of Yarrowia lipolytica to Include Novel Inducible, Repressible, and Hybrid Promoters. ACS Synth Biol 2020; 9:2208-2213. [PMID: 32584553 DOI: 10.1021/acssynbio.0c00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Promoters are critical tools to precisely control gene expression for both synthetic biology and metabolic engineering. Although Yarrowia lipolytica has demonstrated many industrially relevant advantages, promoter discovery efforts on this non-conventional yeast are limited due to the challenge in finding suitable inducible and repressible promoters. Six copper-inducible promoters and five repressible promoters were isolated in this work. Especially, Cu2+-repressible promoters showed relatively high activity under non-repressing conditions compared with a constitutive promoter, but the strength could be almost fully repressed by a supplement of a low content of Cu2+. The six Cu2+-inducible promoters were engineered to improve their dynamic regulation range with a tandem upstream activation sequence. An engineered promoter was successfully used to construct a more productive pathway for production of a novel bioproduct, wax ester, than that used for both Cu2+-inducible promoter and constitutive promoter. This study provides effective tools applicable to fine-tune the gene expression in this microbial host.
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Affiliation(s)
- Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
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23
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Tagliaferri TL, Guimarães NR, Pereira MDPM, Vilela LFF, Horz HP, Dos Santos SG, Mendes TADO. Exploring the Potential of CRISPR-Cas9 Under Challenging Conditions: Facing High-Copy Plasmids and Counteracting Beta-Lactam Resistance in Clinical Strains of Enterobacteriaceae. Front Microbiol 2020; 11:578. [PMID: 32425894 PMCID: PMC7203346 DOI: 10.3389/fmicb.2020.00578] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/16/2020] [Indexed: 01/21/2023] Open
Abstract
The antimicrobial resistance (AMR) crisis urgently requires countermeasures for reducing the dissemination of plasmid-borne resistance genes. Of particular concern are opportunistic pathogens of Enterobacteriaceae. One innovative approach is the CRISPR-Cas9 system which has recently been used for plasmid curing in defined strains of Escherichia coli. Here we exploited this system further under challenging conditions: by targeting the blaTEM–1 AMR gene located on a high-copy plasmid (i.e., 100–300 copies/cell) and by directly tackling blaTEM–1-positive clinical isolates. Upon CRISPR-Cas9 insertion into a model strain of E. coli harboring blaTEM–1 on the plasmid pSB1A2, the plasmid number and, accordingly, the blaTEM–1 gene expression decreased but did not become extinct in a subpopulation of CRISPR-Cas9 treated bacteria. Sequence alterations in blaTEM–1 were observed, likely resulting in a dysfunction of the gene product. As a consequence, a full reversal to an antibiotic sensitive phenotype was achieved, despite plasmid maintenance. In a clinical isolate of E. coli, plasmid clearance and simultaneous re-sensitization to five beta-lactams was possible. Reusability of antibiotics could be confirmed by rescuing larvae of Galleria mellonella infected with CRISPR-Cas9-treated E. coli, as opposed to infection with the unmodified clinical isolate. The drug sensitivity levels could also be increased in a clinical isolate of Enterobacter hormaechei and to a lesser extent in Klebsiella variicola, both of which harbored additional resistance genes affecting beta-lactams. The data show that targeting drug resistance genes is encouraging even when facing high-copy plasmids. In clinical isolates, the simultaneous interference with multiple genes mediating overlapping drug resistance might be the clue for successful phenotype reversal.
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Affiliation(s)
- Thaysa Leite Tagliaferri
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Natália Rocha Guimarães
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Liza Figueiredo Felicori Vilela
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Simone Gonçalves Dos Santos
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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24
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Montagud-Martínez R, Ventura J, Ballesteros-Garrido R, Rosado A, Rodrigo G. Probing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular changes and time. J Biol Eng 2020; 14:12. [PMID: 32226483 PMCID: PMC7098154 DOI: 10.1186/s13036-020-00234-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/10/2020] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology aims at engineering gene regulatory circuits to end with cells (re)programmed on purpose to implement novel functions or discover natural behaviors. However, one overlooked question is whether the resulting circuits perform as intended in variety of environments or with time. Here, we considered a recently engineered genetic system that allows programming the cell to work as a minimal computer (arithmetic logic unit) in order to analyze its operability regime. This system involves transcriptional and post-transcriptional regulations. In particular, we studied the analog behavior of the system, the effect of physicochemical changes in the environment, the impact on cell growth rate of the heterologous expression, and the ability to maintain the arithmetic functioning over time. Conclusively, our results suggest 1) that there are wide input concentration ranges that the system can correctly process, the resulting outputs being predictable with a simple mathematical model, 2) that the engineered circuitry is quite sensitive to temperature effects, 3) that the expression of heterologous small RNAs is costly for the cell, not only of heterologous proteins, and 4) that a proper genetic reorganization of the system to reduce the amount of heterologous DNA in the cell can improve its evolutionary stability.
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Affiliation(s)
- Roser Montagud-Martínez
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
| | - Jordi Ventura
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
| | - Rafael Ballesteros-Garrido
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain.,2Present address: Department of Organic Chemistry, University of Valencia, 46100 Burjassot, Valencia Spain
| | - Arantxa Rosado
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
| | - Guillermo Rodrigo
- 1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain
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25
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Deckers M, Deforce D, Fraiture MA, Roosens NHC. Genetically Modified Micro-Organisms for Industrial Food Enzyme Production: An Overview. Foods 2020; 9:E326. [PMID: 32168815 PMCID: PMC7143438 DOI: 10.3390/foods9030326] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
The use of food enzymes (FE) by the industrial food industry is continuously increasing. These FE are mainly obtained by microbial fermentation, for which both wild-type (WT) and genetically modified (GM) strains are used. The FE production yield can be increased by optimizing the fermentation process, either by using genetically modified micro-organism (GMM) strains or by producing recombinant enzymes. This review provides a general overview of the different methods used to produce FE preparations and how the use of GMM can increase the production yield. Additionally, information regarding the construction of these GMM strains is provided. Thereafter, an overview of the different European regulations concerning the authorization of FE preparations on the European market and the use of GMM strains is given. Potential issues related to the authorization and control of FE preparations sold on the European market are then identified and illustrated by a case study. This process highlighted the importance for control of FE preparations and the consequent need for appropriate detection methods targeting the presence of GMM, which is used in fermentation products.
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Affiliation(s)
- Marie Deckers
- Transversal Activities in Applied Genomics (TAG), Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Marie-Alice Fraiture
- Transversal Activities in Applied Genomics (TAG), Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics (TAG), Sciensano, Rue Juliette Wytsmanstraat 14, 1050 Brussels, Belgium
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26
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Bai J, Wang X, Wu H, Ling F, Zhao Y, Lin Y, Wang R. Comprehensive construction strategy of bidirectional green tissue-specific synthetic promoters. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:668-678. [PMID: 31393049 PMCID: PMC7004895 DOI: 10.1111/pbi.13231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
Bidirectional green tissue-specific promoters have important application prospects in genetic engineering and crop genetic improvement. However, there is no report on the application of them, mainly due to undiscovered natural bidirectional green tissue-specific promoters and the lack of a comprehensive approach for the synthesis of these promoters. In order to compensate for this vacancy, the present study reports a novel strategy for the expression regulatory sequence selection and the bidirectional green tissue-specific synthetic promoter construction. Based on this strategy, seven promoters were synthesized and introduced into rice by agrobacterium-mediated transformation. The functional identification of these synthetic promoters was performed by the expression pattern of GFP and GUS reporter genes in two reverse directions in transgenic rice. The results indicated that all the synthetic promoters possessed bidirectional expression activities in transgenic rice, and four synthetic promoters (BiGSSP2, BiGSSP3, BiGSSP6, BiGSSP7) showed highly bidirectional expression efficiencies specifically in green tissues (leaf, sheath, panicle, stem), which could be widely applied to agricultural biotechnology. Our study provided a feasible strategy for the construction of synthetic promoters, and we successfully created four bidirectional green tissue-specific synthetic promoters. It is the first report on bidirectional green tissue-specific promoters that could be efficiently applied in genetic engineering.
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Affiliation(s)
- Jiuyuan Bai
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Xin Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Hao Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Fei Ling
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Yun Zhao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Rui Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
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27
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Chockalingam K, Peng Z, Vuong CN, Berghman LR, Chen Z. Golden Gate assembly with a bi-directional promoter (GBid): A simple, scalable method for phage display Fab library creation. Sci Rep 2020; 10:2888. [PMID: 32076016 PMCID: PMC7031318 DOI: 10.1038/s41598-020-59745-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022] Open
Abstract
Fabs offer an attractive platform for monoclonal antibody discovery/engineering, but library construction can be cumbersome. We report a simple method – Golden Gate assembly with a bi-directional promoter (GBid) – for constructing phage display Fab libraries. In GBid, the constant domains of the Fabs are located in the backbone of the phagemid vector and the library insert comprises only the variable regions of the antibodies and a central bi-directional promoter. This vector design reduces the process of Fab library construction to “scFv-like” simplicity and the double promoter ensures robust expression of both constituent chains. To maximize the library size, the 3 fragments comprising the insert – two variable chains and one bi-directional promoter – are assembled via a 3-fragment overlap extension PCR and the insert is incorporated into the vector via a high-efficiency one-fragment, one-pot Golden Gate assembly. The reaction setup requires minimal preparatory work and enzyme quantities, making GBid highly scalable. Using GBid, we constructed a chimeric chicken-human Fab phage display library comprising 1010 variants targeting the multi-transmembrane protein human CD20 (hCD20). Selection/counter-selection on transfected whole cells yielded hCD20-specific antibodies in four rounds of panning. The simplicity and scalability of GBid makes it a powerful tool for the discovery/engineering of Fabs and IgGs.
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Affiliation(s)
- Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA
| | - Zeyu Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA.,Biosion, Inc., Nanjing, 210061, China
| | - Christine N Vuong
- Department of Poultry Science, Texas A&M University, College Station, Texas, 77843, USA.,Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, 72703, USA
| | - Luc R Berghman
- Department of Poultry Science, Texas A&M University, College Station, Texas, 77843, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA.
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28
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Matsumura I, Chyong D. Statistical noise from recombinant plasmids can be abated via complementation of a ribosomal protein gene deletion. Protein Eng Des Sel 2019; 32:433-441. [PMID: 32328658 DOI: 10.1093/protein/gzaa007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 11/14/2022] Open
Abstract
The phenotypes conferred by recombinant plasmids upon host cells often exhibit variability between replicate populations. This statistical noise is mostly a consequence of adaptive evolution in response to fitness burdens imposed by the plasmids themselves. We developed a novel strategy, 'ribosome pegging', to exclude common unwanted mutations that benefit host cells at the expense of heterologous gene expression. Plasmids that constitutively co-expressed the fluorescent reporter tagRFP and ribosomal protein L23 (rplW) were used to transform Escherichia coli cells that lacked the essential chromosomal rplW gene. Cells within the population that expressed too little L23, or too much, were evidently inviable. Ribosome pegging obviates the need for antibiotics, thus facilitating the deployment of recombinant bacteria in uncontrolled environments. We show that ribosome-pegged E. coli carrying a plasmid that constitutively expresses L23 and an artificially evolved enzyme protects fruit flies from otherwise toxic doses of the insecticide malathion.
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Affiliation(s)
- Ichiro Matsumura
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, U.S.A
| | - Donian Chyong
- Columbia College, Columbia University, New York, New York, U.S.A
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29
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Iriki H, Kawata T, Muramoto T. Generation of deletions and precise point mutations in Dictyostelium discoideum using the CRISPR nickase. PLoS One 2019; 14:e0224128. [PMID: 31622451 PMCID: PMC6797129 DOI: 10.1371/journal.pone.0224128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/07/2019] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system enables targeted genome modifications across a range of eukaryotes. Although we have reported that transient introduction of all-in-one vectors that express both Cas9 and sgRNAs can efficiently induce multiple gene knockouts in Dictyostelium discoideum, concerns remain about off-target effects and false-positive amplification during mutation detection via PCR. To minimise these effects, we modified the system to permit gene deletions of greater than 1 kb via use of paired sgRNAs and Cas9 nickase. An all-in-one vector expressing the Cas9 nickase and sgRNAs was transiently introduced into D. discoideum, and the resulting mutants showed long deletions with a relatively high efficiency of 10-30%. By further improving the vector, a new dual sgRNA expression vector was also constructed to allow simultaneous insertion of two sgRNAs via one-step cloning. By applying this system, precise point mutations and genomic deletions were generated in the target locus via simultaneous introduction of the vector and a single-stranded oligonucleotide template without integrating a drug resistance cassette. These systems enable simple and straightforward genome editing that requires high specificity, and they can serve as an alternative to the conventional homologous recombination-based gene disruption method in D. discoideum.
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Affiliation(s)
- Hoshie Iriki
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Takefumi Kawata
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
| | - Tetsuya Muramoto
- Department of Biology, Faculty of Science, Toho University, Funabashi, Chiba, Japan
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30
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Nyerges Á, Bálint B, Cseklye J, Nagy I, Pál C, Fehér T. CRISPR-interference-based modulation of mobile genetic elements in bacteria. Synth Biol (Oxf) 2019; 4:ysz008. [PMID: 31008359 PMCID: PMC6462304 DOI: 10.1093/synbio/ysz008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 11/12/2022] Open
Abstract
Spontaneous mutagenesis of synthetic genetic constructs by mobile genetic elements frequently results in the rapid loss of engineered functions. Previous efforts to minimize such mutations required the exceedingly time-consuming manipulation of bacterial chromosomes and the complete removal of insertional sequences (ISes). To this aim, we developed a single plasmid-based system (pCRIS) that applies CRISPR-interference to inhibit the transposition of bacterial ISes. pCRIS expresses multiple guide RNAs to direct inactivated Cas9 (dCas9) to simultaneously silence IS1, IS3, IS5 and IS150 at up to 38 chromosomal loci in Escherichia coli, in vivo. As a result, the transposition rate of all four targeted ISes dropped to negligible levels at both chromosomal and episomal targets. Most notably, pCRIS, while requiring only a single plasmid delivery performed within a single day, provided a reduction of IS-mobility comparable to that seen in genome-scale chromosome engineering projects. The fitness cost of multiple IS-knockdown, detectable in flask-and-shaker systems was readily outweighed by the less frequent inactivation of the transgene, as observed in green fluorescent protein (GFP)-overexpression experiments. In addition, global transcriptomics analysis revealed only minute alterations in the expression of untargeted genes. Finally, the transposition-silencing effect of pCRIS was easily transferable across multiple E. coli strains. The plasticity and robustness of our IS-silencing system make it a promising tool to stabilize bacterial genomes for synthetic biology and industrial biotechnology applications.
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Affiliation(s)
- Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,Seqomics Biotechnology Ltd, Mórahalom, Hungary
| | | | - István Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,Seqomics Biotechnology Ltd, Mórahalom, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Tamás Fehér
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
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31
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Ren Q, Zhong Z, Wang Y, You Q, Li Q, Yuan M, He Y, Qi C, Tang X, Zheng X, Zhang T, Qi Y, Zhang Y. Bidirectional Promoter-Based CRISPR-Cas9 Systems for Plant Genome Editing. FRONTIERS IN PLANT SCIENCE 2019; 10:1173. [PMID: 31616455 PMCID: PMC6764340 DOI: 10.3389/fpls.2019.01173] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/27/2019] [Indexed: 05/21/2023]
Abstract
CRISPR-Cas systems can be expressed in multiple ways, with different capabilities regarding tissue-specific expression, efficiency, and expression levels. Thus far, three expression strategies have been demonstrated in plants: mixed dual promoter systems, dual Pol II promoter systems, and single transcript unit (STU) systems. We explored a fourth strategy to express CRISPR-Cas9 in the model and crop plant, rice, where a bidirectional promoter (BiP) is used to express Cas9 and single guide RNA (sgRNA) in opposite directions. We first tested an engineered BiP system based on double-mini 35S promoter and an Arabidopsis enhancer, which resulted in 20.7% and 52.9% genome editing efficiencies at two target sites in T0 stable transgenic rice plants. We further improved the BiP system drastically by using a rice endogenous BiP, OsBiP1. The endogenous BiP expression system had higher expression strength and led to 75.9-93.3% genome editing efficiencies in rice T0 generation, when the sgRNAs were processed by either tRNA or Csy4. We provided a proof-of-concept study of applying BiP systems for expressing two-component CRISPR-Cas9 genome editing reagents in rice. Our work could promote future research and adoption of BiP systems for CRISPR-Cas-based genome engineering in plants.
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Affiliation(s)
- Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qi You
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Qian Li
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Mingzhu Yuan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Caiyan Qi
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Tao Zhang, ; Yiping Qi, ; Yong Zhang,
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
- *Correspondence: Tao Zhang, ; Yiping Qi, ; Yong Zhang,
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- *Correspondence: Tao Zhang, ; Yiping Qi, ; Yong Zhang,
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32
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Vogl T, Kickenweiz T, Pitzer J, Sturmberger L, Weninger A, Biggs BW, Köhler EM, Baumschlager A, Fischer JE, Hyden P, Wagner M, Baumann M, Borth N, Geier M, Ajikumar PK, Glieder A. Engineered bidirectional promoters enable rapid multi-gene co-expression optimization. Nat Commun 2018; 9:3589. [PMID: 30181586 DOI: 10.1038/s41467-018-0591-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/25/2018] [Indexed: 05/22/2023] Open
Abstract
Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature's use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications.
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Affiliation(s)
- Thomas Vogl
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Thomas Kickenweiz
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Julia Pitzer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | - Lukas Sturmberger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | - Astrid Weninger
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Bradley W Biggs
- Manus Biosynthesis, 1030 Massachusetts Avenue, Suite 300, Cambridge, MA, 02138, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Eva-Maria Köhler
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Armin Baumschlager
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Jasmin Elgin Fischer
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Patrick Hyden
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Marlies Wagner
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martina Geier
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | | | - Anton Glieder
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
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33
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Engineered bidirectional promoters enable rapid multi-gene co-expression optimization. Nat Commun 2018; 9:3589. [PMID: 30181586 PMCID: PMC6123417 DOI: 10.1038/s41467-018-05915-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/25/2018] [Indexed: 01/24/2023] Open
Abstract
Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature’s use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications. Classic monodirectional promoters are of limited use for multiple gene co-expression. Here the authors generate a library of 168 bidirectional promoters for the yeast K. phaffii (syn. P. pastoris) with diverse expression profiles to optimize metabolic pathway design.
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34
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Abramson BW, Lensmire J, Lin YT, Jennings E, Ducat DC. Redirecting carbon to bioproduction via a growth arrest switch in a sucrose-secreting cyanobacterium. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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35
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Balikó G, Vernyik V, Karcagi I, Györfy Z, Draskovits G, Fehér T, Pósfai G. Rational Efforts to Streamline the Escherichia coliGenome. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gabriella Balikó
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Viktor Vernyik
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Ildikó Karcagi
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Zsuzsanna Györfy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Gábor Draskovits
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Tamás Fehér
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - György Pósfai
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
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36
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Abstract
Evolution in the form of selective breeding has long been harnessed as a useful tool by humans. However, rapid evolution can also be a danger to our health and a stumbling block for biotechnology. Unwanted evolution can underlie the emergence of drug and pesticide resistance, cancer, and weeds. It makes live vaccines and engineered cells inherently unreliable and unpredictable, and therefore potentially unsafe. Yet, there are strategies that have been and can possibly be used to stop or slow many types of evolution. We review and classify existing population genetics-inspired methods for arresting evolution. Then, we discuss how genome editing techniques enable a radically new set of approaches to limit evolution.
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Umenhoffer K, Draskovits G, Nyerges Á, Karcagi I, Bogos B, Tímár E, Csörgő B, Herczeg R, Nagy I, Fehér T, Pál C, Pósfai G. Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis. ACS Synth Biol 2017; 6:1471-1483. [PMID: 28426191 DOI: 10.1021/acssynbio.6b00378] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, nonessential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization. Here, we sought to establish a rapid methodology to improve the stability of microbial hosts. The novel workflow involves genome shuffling between a mobile genetic element-free strain and the target cell, and subsequent rounds of CRISPR/Cas-assisted MAGE on multiplex targets. The power and speed of the procedure was demonstrated on E. coli BL21(DE3), a host routinely used for plasmid-based heterologous protein expression. All 9 prophages and 50 insertion elements were efficiently deleted or inactivated. Together with additional targeted manipulations (e.g., inactivation of error-prone DNA-polymerases), the changes resulted in an improved bacterial host with a hybrid (harboring segments of K-12 DNA), 9%-downsized and clean genome. The combined capacity of phage-mediated generalized transduction and CRISPR/Cas-selected MAGE offers a way for rapid, large scale editing of bacterial genomes.
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Affiliation(s)
- Kinga Umenhoffer
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Gábor Draskovits
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Ákos Nyerges
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Ildikó Karcagi
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Balázs Bogos
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Edit Tímár
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Bálint Csörgő
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | | | - István Nagy
- SeqOmics Biotechnology Ltd, 6782 Mórahalom, Hungary
- Institute
of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Tamás Fehér
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - Csaba Pál
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | - György Pósfai
- Synthetic
and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
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Bartley BA, Kim K, Medley JK, Sauro HM. Synthetic Biology: Engineering Living Systems from Biophysical Principles. Biophys J 2017; 112:1050-1058. [PMID: 28355534 DOI: 10.1016/j.bpj.2017.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/06/2017] [Accepted: 02/16/2017] [Indexed: 01/02/2023] Open
Abstract
Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties.
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Affiliation(s)
- Bryan A Bartley
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Kyung Kim
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - J Kyle Medley
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, Washington.
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Wang R, Yan Y, Zhu M, Yang M, Zhou F, Chen H, Lin Y. Isolation and Functional Characterization of Bidirectional Promoters in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:766. [PMID: 27303432 PMCID: PMC4885881 DOI: 10.3389/fpls.2016.00766] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/17/2016] [Indexed: 05/19/2023]
Abstract
Bidirectional promoters, which show great application potential in genetic improvement of plants, have aroused great research interest recently. However, most bidirectional promoters were cloned individually in the studies of single genes. Here, we initiatively combined RNA-seq data and cDNA microarray data to discover the potential bidirectional promoters in rice genome. Based on the expression level and correlation of each adjacent and oppositely transcribed gene pair, we selected four candidate gene pairs. Then, the intergenic region between each pair was isolated and cloned into a dual reporter vector pDX2181 for functional identification. GUS and GFP assays of the transgenic plants indicated that all the intergenic regions showed bidirectional expression activity in various tissues. Through 5' and 3' deletion analysis on one of the above bidirectional promoters, we identified the enhancing region which sharply increased its bidirectional expression efficiency and the essential regions respectively responsible for its 5' and 3' basic expression activity. The bidirectional arrangement of the four gene pairs in six gramineous plants was also analyzed, showing the conserved characteristics of the four bidirectional promoters identified in our study. In addition, two novel cis-sequences conserved in the four bidirectional promoters were discovered by bioinformatic identification. Our study proposes a feasible method for selecting, cloning, and functionally identifying bidirectional promoters as well as for discovering their bidirectional regulatory regions and conserved sequences in rice.
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Affiliation(s)
- Rui Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Yan Yan
- Chinese Academy of Tropical Agricultural SciencesHainan, China
| | - Menglin Zhu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Mei Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural UniversityWuhan, China
- *Correspondence: Yongjun Lin
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Choi JW, Yim SS, Kim MJ, Jeong KJ. Enhanced production of recombinant proteins with Corynebacterium glutamicum by deletion of insertion sequences (IS elements). Microb Cell Fact 2015; 14:207. [PMID: 26715464 PMCID: PMC4696348 DOI: 10.1186/s12934-015-0401-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In most bacteria, various jumping genetic elements including insertion sequences elements (IS elements) cause a variety of genetic rearrangements resulting in harmful effects such as genome and recombinant plasmid instability. The genetic stability of a plasmid in a host is critical for high-level production of recombinant proteins, and in this regard, the development of an IS element-free strain could be a useful strategy for the enhanced production of recombinant proteins. Corynebacterium glutamicum, which is a workhorse in the industrial-scale production of various biomolecules including recombinant proteins, also has several IS elements, and it is necessary to identify the critical IS elements and to develop IS element deleted strain. RESULTS From the cultivation of C. glutamicum harboring a plasmid for green fluorescent protein (GFP) gene expression, non-fluorescent clones were isolated by FACS (fluorescent activated cell sorting). All the isolated clones had insertions of IS elements in the GFP coding region, and two major IS elements (ISCg1 and ISCg2 families) were identified. By co-cultivating cells harboring either the isolated IS element-inserted plasmid or intact plasmid, it was clearly confirmed that cells harboring the IS element-inserted plasmids became dominant during the cultivation due to their growth advantage over cells containing intact plasmids, which can cause a significant reduction in recombinant protein production during cultivation. To minimize the harmful effects of IS elements on the expression of heterologous genes in C. glutamicum, two IS element free C. glutamicum strains were developed in which each major IS element was deleted, and enhanced productivity in the engineered C. glutamicum strain was successfully demonstrated with three models: GFP, poly(3-hydroxybutyrate) [P(3HB)] and γ-aminobutyrate (GABA). CONCLUSIONS Our findings clearly indicate that the hopping of IS elements could be detrimental to the production of recombinant proteins in C. glutamicum, emphasizing the importance of developing IS element free host strains.
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Affiliation(s)
- Jae Woong Choi
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Sung Sun Yim
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Min Jeong Kim
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,Institute for the BioCentury, KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Versatile plasmid-based expression systems for Gram-negative bacteria—General essentials exemplified with the bacterium Ralstonia eutropha H16. N Biotechnol 2015; 32:552-8. [DOI: 10.1016/j.nbt.2015.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 12/13/2022]
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Behura SK, Severson DW. Bidirectional promoters of insects: genome-wide comparison, evolutionary implication and influence on gene expression. J Mol Biol 2014; 427:521-36. [PMID: 25463441 DOI: 10.1016/j.jmb.2014.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/31/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
Bidirectional promoters are widespread in insect genomes. By analyzing 23 insect genomes we show that the frequency of bidirectional gene pairs varies according to genome compactness and density of genes among the species. The density of bidirectional genes expected based on number of genes per megabase of genome explains the observed density suggesting that bidirectional pairing of genes may be due to random event. We identified specific transcription factor binding motifs that are enriched in bidirectional promoters across insect species. Furthermore, we observed that bidirectional promoters may act as transcriptional hotspots in insect genomes where protein coding genes tend to aggregate in significantly biased (p < 0.001) manner compared to unidirectional promoters. Natural selection seems to have an association with the extent of bidirectionality of genes among the species. The rate of non-synonymous-to-synonymous changes (dN/dS) shows a second-order polynomial distribution with bidirectionality between species indicating that bidirectionality is dependent upon evolutionary pressure acting on the genomes. Analysis of genome-wide microarray expression data of multiple insect species suggested that bidirectionality has a similar association with transcriptome variation across species. Furthermore, bidirectional promoters show significant association with correlated expression of the divergent gene pairs depending upon their motif composition. Analysis of gene ontology showed that bidirectional genes tend to have a common association with functions related to "binding" (including ion binding, nucleotide binding and protein binding) across genomes. Such functional constraint of bidirectional genes may explain their widespread persistence in genome of diverse insect species.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - David W Severson
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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43
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Gonçalves GAL, Oliveira PH, Gomes AG, Prather KLJ, Lewis LA, Prazeres DMF, Monteiro GA. Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters. Appl Microbiol Biotechnol 2014; 98:6609-19. [PMID: 24769900 DOI: 10.1007/s00253-014-5695-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 01/29/2023]
Abstract
Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3' region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability.
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Affiliation(s)
- Geisa A L Gonçalves
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Lisbon, Portugal
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44
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Renda BA, Hammerling MJ, Barrick JE. Engineering reduced evolutionary potential for synthetic biology. MOLECULAR BIOSYSTEMS 2014; 10:1668-78. [PMID: 24556867 DOI: 10.1039/c3mb70606k] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of synthetic biology seeks to engineer reliable and predictable behaviors in organisms from collections of standardized genetic parts. However, unlike other types of machines, genetically encoded biological systems are prone to changes in their designed sequences due to mutations in their DNA sequences after these devices are constructed and deployed. Thus, biological engineering efforts can be confounded by undesired evolution that rapidly breaks the functions of parts and systems, particularly when they are costly to the host cell to maintain. Here, we explain the fundamental properties that determine the evolvability of biological systems. Then, we use this framework to review current efforts to engineer the DNA sequences that encode synthetic biology devices and the genomes of their microbial hosts to reduce their ability to evolve and therefore increase their genetic reliability so that they maintain their intended functions over longer timescales.
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Affiliation(s)
- Brian A Renda
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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45
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Arkin AP. A wise consistency: engineering biology for conformity, reliability, predictability. Curr Opin Chem Biol 2013; 17:893-901. [PMID: 24268562 DOI: 10.1016/j.cbpa.2013.09.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
The next generation of synthetic biology applications will increasingly involve engineered organisms that exist in intimate contact with humans, animals and the rest of the environment. Examples include cellular and viral approaches for maintaining and improving health in humans and animals. The need for reliable and specific function in these environments may require more complex system designs than previously. In these cases the uncertainties in the behavior of biological building blocks, their hosts and their environments present a challenge for design of predictable and safe systems. Here, we review systematic methods for the effective characterization of these uncertainties that are lowering the barriers to predictive design of reliable complex biological systems.
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Affiliation(s)
- Adam Paul Arkin
- Department of Bioengineering, University of California, 2151 Berkeley Way, Berkeley, CA 94704-5230, United States; Physical Biosciences Division, E. O. Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mailstop 955-512L, Berkeley, CA 94720, United States.
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An intergenic region shared by At4g35985 and At4g35987 in Arabidopsis thaliana is a tissue specific and stress inducible bidirectional promoter analyzed in transgenic arabidopsis and tobacco plants. PLoS One 2013; 8:e79622. [PMID: 24260266 PMCID: PMC3834115 DOI: 10.1371/journal.pone.0079622] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/03/2013] [Indexed: 11/23/2022] Open
Abstract
On chromosome 4 in the Arabidopsis genome, two neighboring genes (calmodulin methyl transferase At4g35987 and senescence associated gene At4g35985) are located in a head-to-head divergent orientation sharing a putative bidirectional promoter. This 1258 bp intergenic region contains a number of environmental stress responsive and tissue specific cis-regulatory elements. Transcript analysis of At4g35985 and At4g35987 genes by quantitative real time PCR showed tissue specific and stress inducible expression profiles. We tested the bidirectional promoter-function of the intergenic region shared by the divergent genes At4g35985 and At4g35987 using two reporter genes (GFP and GUS) in both orientations in transient tobacco protoplast and Agro-infiltration assays, as well as in stably transformed transgenic Arabidopsis and tobacco plants. In transient assays with GFP and GUS reporter genes the At4g35985 promoter (P85) showed stronger expression (about 3.5 fold) compared to the At4g35987 promoter (P87). The tissue specific as well as stress responsive functional nature of the bidirectional promoter was evaluated in independent transgenic Arabidopsis and tobacco lines. Expression of P85 activity was detected in the midrib of leaves, leaf trichomes, apical meristemic regions, throughout the root, lateral roots and flowers. The expression of P87 was observed in leaf-tip, hydathodes, apical meristem, root tips, emerging lateral root tips, root stele region and in floral tissues. The bidirectional promoter in both orientations shows differential up-regulation (2.5 to 3 fold) under salt stress. Use of such regulatory elements of bidirectional promoters showing spatial and stress inducible promoter-functions in heterologous system might be an important tool for plant biotechnology and gene stacking applications.
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Sleight SC, Sauro HM. Randomized BioBrick assembly: a novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways. ACS Synth Biol 2013; 2:506-18. [PMID: 23841916 DOI: 10.1021/sb4000542] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The optimization of genetic circuits and metabolic pathways often involves constructing various iterations of the same construct or using directed evolution to achieve the desired function. Alternatively, a method that randomizes individual parts in the same assembly reaction could be used for optimization by allowing for the ability to screen large numbers of individual clones expressing randomized circuits or pathways for optimal function. Here we describe a new assembly method to randomize genetic circuits and metabolic pathways from modular DNA fragments derived from PCR-amplified BioBricks. As a proof-of-principle for this method, we successfully assembled CMY (Cyan-Magenta-Yellow) three-gene circuits using Gibson Assembly that express CFP, RFP, and YFP with independently randomized promoters, ribosome binding sites, transcriptional terminators, and all parts randomized simultaneously. Sequencing results from 24 CMY circuits with various parts randomized show that 20/24 circuits are distinct and expression varies over a 200-fold range above background levels. We then adapted this method to randomize the same parts with enzyme coding sequences from the lycopene biosynthesis pathway instead of fluorescent proteins, designed to independently express each enzyme in the pathway from a different promoter. Lycopene production is improved using this randomization method by about 30% relative to the highest polycistronic-expressing pathway. These results demonstrate the potential of generating nearly 20,000 unique circuit or pathway combinations when three parts are permutated at each position in a three-gene circuit or pathway, and the methodology can likely be adapted to other circuits and pathways to maximize products of interest.
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Affiliation(s)
- Sean C. Sleight
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
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48
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Sleight SC, Sauro HM. Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits. ACS Synth Biol 2013; 2:519-28. [PMID: 24004180 DOI: 10.1021/sb400055h] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Strain engineering for synthetic biology and metabolic engineering applications often requires the expression of foreign proteins that can reduce cellular fitness. In order to quantify and visualize the evolutionary stability dynamics in engineered populations of Escherichia coli , we constructed randomized CMY (cyan-magenta-yellow) genetic circuits with independently randomized promoters, ribosome binding sites, and transcriptional terminators that express cyan fluorescent protein (CFP), red fluorescent protein (RFP), and yellow fluorescent protein (YFP). Using a CMY color system allows for a spectrum of different colors to be produced under UV light since the relative ratio of fluorescent proteins vary between circuits, and this system can be used for the visualization of evolutionary stability dynamics. Evolutionary stability results from 192 evolved populations (24 CMY circuits with 8 replicates each) indicate that both the number of repeated sequences and overall expression levels contribute to circuit stability. The most evolutionarily robust circuit has no repeated parts, lower expression levels, and is about 3-fold more stable relative to a rationally designed circuit. Visualization results show that evolutionary dynamics are highly stochastic between replicate evolved populations and color changes over evolutionary time are consistent with quantitative data. We also measured the competitive fitness of different mutants in an evolved population and find that fitness is highest in mutants that express a lower number of genes (0 and 1 > 2 > 3). In addition, we find that individual circuits with expression levels below 10% of the maximum have significantly higher evolutionary stability, suggesting there may be a hypothetical "fitness threshold" that can be used for robust circuit design.
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Affiliation(s)
- Sean C Sleight
- University of Washington , Dept. of Bioengineering, Seattle, Washington 98195, United States
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49
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Abstract
Live, attenuated viruses provide many of the most effective vaccines. For the better part of a century, the standard method of attenuation has been viral growth in novel environments, whereby the virus adapts to the new environment but incurs a reduced ability to grow in the original host. The downsides of this approach were that it produced haphazard results, and even when it achieved sufficient attenuation for vaccine production, the attenuated virus was prone to evolve back to high virulence. Using bacteriophage T7, we apply a synthetic biology approach for creating attenuated genomes and specifically study their evolutionary stability. Three different genome rearrangements are used, and although some initial fitness recovery occurs, all exhibit greatly impaired abilities to recover wild-type fitness over a hundred or more generations. Different degrees of stable attenuation appear to be attainable by different rearrangements. Efforts to predict fitness recovery using the extensive background of T7 genetics and biochemistry were only sometimes successful. The use of genome rearrangement thus offers a practical mechanism of evolutionary stable viral attenuation, with some progress toward prediction.
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50
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Zucca S, Pasotti L, Politi N, Cusella De Angelis MG, Magni P. A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli. J Biol Eng 2013; 7:12. [PMID: 23663425 PMCID: PMC3662617 DOI: 10.1186/1754-1611-7-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/18/2013] [Indexed: 11/10/2022] Open
Abstract
Background The chromosomal integration of biological parts in the host genome enables the engineering of plasmid-free stable strains with single-copy insertions of the desired gene networks. Although different integrative vectors were proposed, no standard pre-assembled genetic tool is available to carry out this task. Synthetic biology concepts can contribute to the development of standardized and user friendly solutions to easily produce engineered strains and to rapidly characterize the desired genetic parts in single-copy context. Results In this work we report the design of a novel integrative vector that allows the genomic integration of biological parts compatible with the RFC10, RFC23 and RFC12 BioBrick™ standards in Escherichia coli. It can also be specialized by using BioBrick™ parts to target the desired integration site in the host genome. The usefulness of this vector has been demonstrated by integrating a set of BioBrick™ devices in two different loci of the E. coli chromosome and by characterizing their activity in single-copy. Construct stability has also been evaluated and compared with plasmid-borne solutions. Conclusions Physical modularity of biological parts has been successfully applied to construct a ready-to-engineer BioBrick™ vector, suitable for a stable chromosomal insertion of standard parts via the desired recombination method, i.e. the bacteriophage integration mechanism or homologous recombination. In contrast with previously proposed solutions, it is a pre-assembled vector containing properly-placed restriction sites for the direct transfer of various formats of BioBrick™ parts. This vector can facilitate the characterization of parts avoiding copy number artefacts and the construction of antibiotic resistance-free engineered microbes, suitable for industrial use.
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Affiliation(s)
- Susanna Zucca
- Dipartimento di Ingegneria Industriale e dell'Informazione, Università degli Studi di Pavia, via Ferrata 3, Pavia, Italy.
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