1
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Andreani V, South EJ, Dunlop MJ. Generating information-dense promoter sequences with optimal string packing. PLoS Comput Biol 2024; 20:e1012276. [PMID: 39047028 PMCID: PMC11268586 DOI: 10.1371/journal.pcbi.1012276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Dense arrangements of binding sites within nucleotide sequences can collectively influence downstream transcription rates or initiate biomolecular interactions. For example, natural promoter regions can harbor many overlapping transcription factor binding sites that influence the rate of transcription initiation. Despite the prevalence of overlapping binding sites in nature, rapid design of nucleotide sequences with many overlapping sites remains a challenge. Here, we show that this is an NP-hard problem, coined here as the nucleotide String Packing Problem (SPP). We then introduce a computational technique that efficiently assembles sets of DNA-protein binding sites into dense, contiguous stretches of double-stranded DNA. For the efficient design of nucleotide sequences spanning hundreds of base pairs, we reduce the SPP to an Orienteering Problem with integer distances, and then leverage modern integer linear programming solvers. Our method optimally packs sets of 20-100 binding sites into dense nucleotide arrays of 50-300 base pairs in 0.05-10 seconds. Unlike approximation algorithms or meta-heuristics, our approach finds provably optimal solutions. We demonstrate how our method can generate large sets of diverse sequences suitable for library generation, where the frequency of binding site usage across the returned sequences can be controlled by modulating the objective function. As an example, we then show how adding additional constraints, like the inclusion of sequence elements with fixed positions, allows for the design of bacterial promoters. The nucleotide string packing approach we present can accelerate the design of sequences with complex DNA-protein interactions. When used in combination with synthesis and high-throughput screening, this design strategy could help interrogate how complex binding site arrangements impact either gene expression or biomolecular mechanisms in varied cellular contexts.
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Affiliation(s)
- Virgile Andreani
- Biomedical Engineering Department, Boston University, Boston, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
| | - Eric J. South
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, Massachusetts, United States of America
| | - Mary J. Dunlop
- Biomedical Engineering Department, Boston University, Boston, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, Massachusetts, United States of America
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2
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Deal C, De Wannemaeker L, De Mey M. Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes. FEMS Microbiol Rev 2024; 48:fuae004. [PMID: 38383636 PMCID: PMC10911233 DOI: 10.1093/femsre/fuae004] [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: 08/31/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024] Open
Abstract
Promoter sequences are important genetic control elements. Through their interaction with RNA polymerase they determine transcription strength and specificity, thereby regulating the first step in gene expression. Consequently, they can be targeted as elements to control predictability and tuneability of a genetic circuit, which is essential in applications such as the development of robust microbial cell factories. This review considers the promoter elements implicated in the three stages of transcription initiation, detailing the complex interplay of sequence-specific interactions that are involved, and highlighting that DNA sequence features beyond the core promoter elements work in a combinatorial manner to determine transcriptional strength. In particular, we emphasize that, aside from promoter recognition, transcription initiation is also defined by the kinetics of open complex formation and promoter escape, which are also known to be highly sequence specific. Significantly, we focus on how insights into these interactions can be manipulated to lay the foundation for a more rational approach to promoter engineering.
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Affiliation(s)
- Cara Deal
- Centre for Synthetic Biology, Ghent University. Coupure Links 653, BE-9000 Ghent, Belgium
| | - Lien De Wannemaeker
- Centre for Synthetic Biology, Ghent University. Coupure Links 653, BE-9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University. Coupure Links 653, BE-9000 Ghent, Belgium
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3
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Meier D, Rauch C, Wagner M, Klemm P, Blumenkamp P, Müller R, Ellenberger E, Karia KM, Vecchione S, Serrania J, Lechner M, Fritz G, Goesmann A, Becker A. A MoClo-Compatible Toolbox of ECF Sigma Factor-Based Regulatory Switches for Proteobacterial Chassis. BIODESIGN RESEARCH 2024; 6:0025. [PMID: 38384496 PMCID: PMC10880074 DOI: 10.34133/bdr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024] Open
Abstract
The construction of complex synthetic gene circuits with predetermined and reliable output depends on orthogonal regulatory parts that do not inadvertently interfere with the host machinery or with other circuit components. Previously, extracytoplasmic function sigma factors (ECFs), a diverse group of alternative sigma factors with distinct promoter specificities, were shown to have great potential as context-independent regulators, but so far, they have only been used in a few model species. Here, we show that the alphaproteobacterium Sinorhizobium meliloti, which has been proposed as a plant-associated bacterial chassis for synthetic biology, has a similar phylogenetic ECF acceptance range as the gammaproteobacterium Escherichia coli. A common set of orthogonal ECF-based regulators that can be used in both bacterial hosts was identified and used to create 2-step delay circuits. The genetic circuits were implemented in single copy in E. coli by chromosomal integration using an established method that utilizes bacteriophage integrases. In S. meliloti, we demonstrated the usability of single-copy pABC plasmids as equivalent carriers of the synthetic circuits. The circuits were either implemented on a single pABC or modularly distributed on 3 such plasmids. In addition, we provide a toolbox containing pABC plasmids compatible with the Golden Gate (MoClo) cloning standard and a library of basic parts that enable the construction of ECF-based circuits in S. meliloti and in E. coli. This work contributes to building a context-independent and species-overarching ECF-based toolbox for synthetic biology applications.
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Affiliation(s)
- Doreen Meier
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Christian Rauch
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcel Wagner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Paul Klemm
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Raphael Müller
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Eric Ellenberger
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Kinnari M. Karia
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Stefano Vecchione
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
| | - Georg Fritz
- The University of Western Australia, School of Molecular Sciences, Perth, Australia
| | - Alexander Goesmann
- Bioinformatics and Systems Biology,
Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Biology,
Philipps-Universität Marburg, Marburg, Germany
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4
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Ma Y, Ye JW, Lin Y, Yi X, Wang X, Wang H, Huang R, Wu F, Wu Q, Liu X, Chen GQ. Flux optimization using multiple promoters in Halomonas bluephagenesis as a model chassis of the next generation industrial biotechnology. Metab Eng 2024; 81:249-261. [PMID: 38159902 DOI: 10.1016/j.ymben.2023.12.011] [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: 10/15/2023] [Revised: 12/16/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
Predictability and robustness are challenges for bioproduction because of the unstable intracellular synthetic activities. With the deeper understanding of the gene expression process, fine-tuning has become a meaningful tool for biosynthesis optimization. This study characterized several gene expression elements and constructed a multiple inducible system that responds to ten different small chemical inducers in halophile bacterium Halomonas bluephagenesis. Genome insertion of regulators was conducted for the purpose of gene cluster stabilization and regulatory plasmid simplification. Additionally, dynamic ranges of the multiple inducible systems were tuned by promoter sequence mutations to achieve diverse scopes for high-resolution gene expression control. The multiple inducible system was successfully employed to precisely control chromoprotein expression, lycopene and poly-3-hydroxybutyrate (PHB) biosynthesis, resulting in colorful bacterial pictures, optimized cell growth, lycopene and PHB accumulation. This study demonstrates a desirable approach for fine-tuning of rational and efficient gene expressions, displaying the significance for metabolic pathway optimization.
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Affiliation(s)
- Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ruiyan Huang
- Garrison Forest School, Owings Mills, MD, 21117, USA
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Beijing, 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; MOE Key Laboratory for Industrial Biocatalysts, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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5
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Wang X, Xu K, Tan Y, Yu S, Zhao X, Zhou J. Deep Learning-Assisted Design of Novel Promoters in Escherichia coli. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2300184. [PMID: 38099247 PMCID: PMC10716054 DOI: 10.1002/ggn2.202300184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/09/2023] [Indexed: 12/17/2023]
Abstract
Deep learning (DL) approaches have the ability to accurately recognize promoter regions and predict their strength. Here, the potential for controllably designing active Escherichia coli promoter is explored by combining multiple deep learning models. First, "DRSAdesign," which relies on a diffusion model to generate different types of novel promoters is created, followed by predicting whether they are real or fake and strength. Experimental validation showed that 45 out of 50 generated promoters are active with high diversity, but most promoters have relatively low activity. Next, "Ndesign," which relies on generating random sequences carrying functional -35 and -10 motifs of the sigma70 promoter is introduced, and their strength is predicted using the designed DL model. The DL model is trained and validated using 200 and 50 generated promoters, and displays Pearson correlation coefficients of 0.49 and 0.43, respectively. Taking advantage of the DL models developed in this work, possible 6-mers are predicted as key functional motifs of the sigma70 promoter, suggesting that promoter recognition and strength prediction mainly rely on the accommodation of functional motifs. This work provides DL tools to design promoters and assess their functions, paving the way for DL-assisted metabolic engineering.
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Affiliation(s)
- Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Shangyang Yu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Xinyi Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of BiotechnologyJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Science Center for Future FoodsJiangnan University1800 Lihu RoadWuxiJiangsu214122China
- Jiangsu Province Engineering Research Center of Food Synthetic BiotechnologyJiangnan UniversityWuxi214122China
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6
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Van Hove B, De Wannemaeker L, Missiaen I, Maertens J, De Mey M. Taming CRISPRi: Dynamic range tuning through guide RNA diversion. N Biotechnol 2023; 77:50-57. [PMID: 37422184 DOI: 10.1016/j.nbt.2023.07.001] [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: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023]
Abstract
CRISPRi is a powerful technique to repress gene expression in a targeted and highly efficient manner. However, this potency is a double-edged sword in inducible systems, as even leaky expression of guide RNA results in a repression phenotype, complicating applications such as dynamic metabolic engineering. We evaluated three methods to enhance the controllability of CRISPRi by modulating the level of free and DNA-bound guide RNA complexes. Overall repression can be attenuated through rationally designed mismatches in the reversibility determining region of the guide RNA sequence; decoy target sites can selectively modulate repression at low levels of induction; and the implementation of feedback control not only enhances the linearity of induction, but broadens the dynamic range of the output as well. Furthermore, feedback control significantly enhances the recovery rate after induction is removed. Used in combination, these techniques enable the fine-tuning of CRISPRi to meet restrictions imposed by the target and match the input signal required for induction.
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Affiliation(s)
- Bob Van Hove
- Centre for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lien De Wannemaeker
- Centre for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Isolde Missiaen
- Centre for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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7
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Mathony J, Aschenbrenner S, Becker P, Niopek D. Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303496. [PMID: 37562980 PMCID: PMC10558690 DOI: 10.1002/advs.202303496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Domain insertion engineering is a promising approach to recombine the functions of evolutionarily unrelated proteins. Insertion of light-switchable receptor domains into a selected effector protein, for instance, can yield allosteric effectors with light-dependent activity. However, the parameters that determine domain insertion tolerance and allostery are poorly understood. Here, an unbiased screen is used to systematically assess the domain insertion permissibility of several evolutionary unrelated proteins. Training machine learning models on the resulting data allow to dissect features informative for domain insertion tolerance and revealed sequence conservation statistics as the strongest indicators of suitable insertion sites. Finally, extending the experimental pipeline toward the identification of switchable hybrids results in opto-chemogenetic derivatives of the transcription factor AraC that function as single-protein Boolean logic gates. The study reveals determinants of domain insertion tolerance and yielded multimodally switchable proteins with unique functional properties.
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Affiliation(s)
- Jan Mathony
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Sabine Aschenbrenner
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
| | - Philipp Becker
- Center for Synthetic BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of BiologyTechnical University of Darmstadt64287DarmstadtGermany
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Dominik Niopek
- Institute of Pharmacy and Molecular Biotechnology (IPMB)Faculty of Engineering SciencesHeidelberg University69120HeidelbergGermany
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8
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Alexis E, Schulte CCM, Cardelli L, Papachristodoulou A. Regulation strategies for two-output biomolecular networks. J R Soc Interface 2023; 20:20230174. [PMID: 37528680 PMCID: PMC10394417 DOI: 10.1098/rsif.2023.0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023] Open
Abstract
Feedback control theory facilitates the development of self-regulating systems with desired performance which are predictable and insensitive to disturbances. Feedback regulatory topologies are found in many natural systems and have been of key importance in the design of reliable synthetic bio-devices operating in complex biological environments. Here, we study control schemes for biomolecular processes with two outputs of interest, expanding previously described concepts based on single-output systems. Regulation of such processes may unlock new design possibilities but can be challenging due to coupling interactions; also potential disturbances applied on one of the outputs may affect both. We therefore propose architectures for robustly manipulating the ratio/product and linear combinations of the outputs as well as each of the outputs independently. To demonstrate their characteristics, we apply these architectures to a simple process of two mutually activated biomolecular species. We also highlight the potential for experimental implementation by exploring synthetic realizations both in vivo and in vitro. This work presents an important step forward in building bio-devices capable of sophisticated functions.
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Affiliation(s)
- Emmanouil Alexis
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Carolin C. M. Schulte
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Luca Cardelli
- Department of Computer Science, University of Oxford, Oxford OX1 3QD, UK
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9
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Loman TE, Locke JCW. The σB alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics. PLoS Comput Biol 2023; 19:e1011265. [PMID: 37540712 PMCID: PMC10431680 DOI: 10.1371/journal.pcbi.1011265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 08/16/2023] [Accepted: 06/12/2023] [Indexed: 08/06/2023] Open
Abstract
Single-cell approaches are revealing a high degree of heterogeneity, or noise, in gene expression in isogenic bacteria. How gene circuits modulate this noise in gene expression to generate robust output dynamics is unclear. Here we use the Bacillus subtilis alternative sigma factor σB as a model system for understanding the role of noise in generating circuit output dynamics. σB controls the general stress response in B. subtilis and is activated by a range of energy and environmental stresses. Recent single-cell studies have revealed that the circuit can generate two distinct outputs, stochastic pulsing and a single pulse response, but the conditions under which each response is generated are under debate. We implement a stochastic mathematical model of the σB circuit to investigate this and find that the system's core circuit can generate both response types. This is despite one response (stochastic pulsing) being stochastic in nature, and the other (single response pulse) being deterministic. We demonstrate that the main determinant for whichever response is generated is the degree with which the input pathway activates the core circuit, although the noise properties of the input pathway also biases the system towards one or the other type of output. Thus, our work shows how stochastic modelling can reveal the mechanisms behind non-intuitive gene circuit output dynamics.
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Affiliation(s)
- Torkel E. Loman
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - James C. W. Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom
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10
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Adaikpoh BI, Romanowski SB, Eustáquio AS. Understanding Autologous Spliceostatin Transcriptional Regulation to Derive Parts for Heterologous Expression in a Burkholderia Bacterial Host. ACS Synth Biol 2023; 12:1952-1960. [PMID: 37338297 PMCID: PMC10527236 DOI: 10.1021/acssynbio.3c00228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Burkholderia β-Proteobacteria are emerging sources of natural products. We are interested in developing Burkholderia sp. FERM BP-3421 into a synthetic biology chassis to facilitate natural product discovery. FERM BP-3421 produces autologous spliceostatins on gram per liter scale. We reasoned that transcription factors and promoters that regulate spliceostatin biosynthesis would provide valuable parts for heterologous expression. Herein we demonstrate that fr9A encodes a pathway-specific transcriptional activator of spliceostatin biosynthesis. In-frame deletion of fr9A abolished spliceostatin production, which was restored by genetic complementation. Using transcriptomics and green fluorescent protein (GFP) reporter assays, we identified four fr9 promoters, three of which are activated by LuxR-type regulator Fr9A. We then constructed an Fr9A-regulated promoter system that was compared to benchmarks and effectively applied for GFP and capistruin lasso peptide expression in an optimized host background. Our findings enrich the genetic toolbox for optimizing heterologous expression and promoting the discovery and development of natural products from Burkholderia bacteria.
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Affiliation(s)
- Barbara I. Adaikpoh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sean B. Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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11
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Rao Y, Wang J, Yang X, Xie X, Zhan Y, Ma X, Cai D, Chen S. A novel toolbox for precise regulation of gene expression and metabolic engineering in Bacillus licheniformis. Metab Eng 2023; 78:159-170. [PMID: 37307865 DOI: 10.1016/j.ymben.2023.06.004] [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: 02/01/2023] [Revised: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
Despite industrial bio-manufacturing progress using Bacillus licheniformis, the absence of a well-characterized toolbox allowing precise regulation of multiple genes limits its expansion for basic research and application. Here, a novel gene expression toolbox (GET) was developed for precise regulation of gene expression and high-level production of 2-phenylethanol. Firstly, we established a novel promoter core region mosaic combination model to combine, characterize and analyze different core regions. Characterization and orthogonal design of promoter ribbons allowed convenient construction of an adaptable and robust GET, gene gfp expression intensity was 0.64%-16755.77%, with a dynamic range of 2.61 × 104 times, which is the largest regulatory range of GET in Bacillus based on modification of promoter P43. Then we verified the protein and species universality of GET using different proteins expressed in B. licheniformis and Bacillus subtilis. Finally, the GET for 2-phenylethanol metabolic breeding, resulting in a plasmid-free strain producing 6.95 g/L 2-phenylethanol with a yield and productivity of 0.15 g/g glucose and 0.14 g/L/h, respectively, the highest de novo synthesis yield of 2-phenylethanol reported. Taken together, this is the first report elucidating the impact of mosaic combination and tandem of multiple core regions to initiate transcription and improve the output of proteins and metabolites, which provides strong support for gene regulation and diversified product production in Bacillus.
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Affiliation(s)
- Yi Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jiaqi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Xinyuan Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Xinxin Xie
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China.
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12
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Using CIVT-SELEX to Select Aptamers as Genetic Parts to Regulate Gene Circuits in a Cell-Free System. Int J Mol Sci 2023; 24:ijms24032833. [PMID: 36769156 PMCID: PMC9917220 DOI: 10.3390/ijms24032833] [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: 11/01/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
The complexity of genetic circuits has not seen a significant increase over the last decades, even with the rapid development of synthetic biology tools. One of the bottlenecks is the limited number of orthogonal transcription factor-operator pairs. Researchers have tried to use aptamer-ligand pairs as genetic parts to regulate transcription. However, most aptamers selected using traditional methods cannot be directly applied in gene circuits for transcriptional regulation. To that end, we report a new method called CIVT-SELEX to select DNA aptamers that can not only bind to macromolecule ligands but also undergo significant conformational changes, thus affecting transcription. The single-stranded DNA library with affinity to our example ligand human thrombin protein is first selected and enriched. Then, these ssDNAs are inserted into a genetic circuit and tested in the in vitro transcription screening to obtain the ones with significant inhibitory effects on downstream gene transcription when thrombins are present. These aptamer-thrombin pairs can inhibit the transcription of downstream genes, demonstrating the feasibility and robustness of their use as genetic parts in both linear DNAs and plasmids. We believe that this method can be applied to select aptamers of any target ligands and vastly expand the genetic part library for transcriptional regulation.
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Duan Y, Tan Y, Wei X, Pei X, Li M. Versatile Strategy for the Construction of a Transcription Factor-Based Orthogonal Gene Expression Toolbox in Monascus spp. ACS Synth Biol 2023; 12:213-223. [PMID: 36625512 DOI: 10.1021/acssynbio.2c00500] [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: 01/11/2023]
Abstract
Gene expression is needed to be conducted in an orthogonal manner and controllable independently from the host's native regulatory system. However, there is a shortage of gene expression regulatory toolboxes that function orthogonally from each other and toward the host. Herein, we developed a strategy based on the mutant library to generate orthogonal gene expression toolboxes. A transcription factor, MaR, located in the Monascus azaphilone biosynthetic gene cluster, was taken as a typical example. Nine DNA-binding residues of MaR were identified by molecular simulation and site-directed mutagenesis. We created five MaR multi-site saturation mutagenesis libraries consisting of 10743 MaR variants on the basis of five cognate promoters. A functional analysis revealed that all five tested promoters were orthogonally regulated by five different MaR variants, respectively. Furthermore, fine gene expression tunability and high signal sensitivity of this toolbox are demonstrated by introducing chemically inducible expression modules, designing synthetic promoter elements, and creating protein-protein interaction between MaRs. This study paves the way for a bottom-up approach to build orthogonal gene expression toolboxes.
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Affiliation(s)
- Yali Duan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province430070, China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
| | - Yingao Tan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province430070, China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
| | - Xuetuan Wei
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou310012, China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province430070, China.,College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province430070, China
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Guidi C, De Wannemaeker L, De Baets J, Demeester W, Maertens J, De Paepe B, De Mey M. Dynamic feedback regulation for efficient membrane protein production using a small RNA-based genetic circuit in Escherichia coli. Microb Cell Fact 2022; 21:260. [PMID: 36522655 PMCID: PMC9753035 DOI: 10.1186/s12934-022-01983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Membrane proteins (MPs) are an important class of molecules with a wide array of cellular functions and are part of many metabolic pathways. Despite their great potential-as therapeutic drug targets or in microbial cell factory optimization-many challenges remain for efficient and functional expression in a host such as Escherichia coli. RESULTS A dynamically regulated small RNA-based circuit was developed to counter membrane stress caused by overexpression of different MPs. The best performing small RNAs were able to enhance the maximum specific growth rate with 123%. On culture level, the total MP production was increased two-to three-fold compared to a system without dynamic control. This strategy not only improved cell growth and production of the studied MPs, it also suggested the potential use for countering metabolic burden in general. CONCLUSIONS A dynamically regulated feedback circuit was developed that can sense metabolic stress caused by, in casu, the overexpression of an MP and responds to it by balancing the metabolic state of the cell and more specifically by downregulating the expression of the MP of interest. This negative feedback mechanism was established by implementing and optimizing simple-to-use genetic control elements based on post-transcriptional regulation: small non-coding RNAs. In addition to membrane-related stress when the MP accumulated in the cytoplasm as aggregates, the sRNA-based feedback control system was still effective for improving cell growth but resulted in a decreased total protein production. This result suggests promiscuity of the MP sensor for more than solely membrane stress.
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Affiliation(s)
- Chiara Guidi
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | | | - Jasmine De Baets
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Wouter Demeester
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Brecht De Paepe
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, 9000, Ghent, Belgium.
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Plasmids for Controlled and Tunable High-Level Expression in E. coli. Appl Environ Microbiol 2022; 88:e0093922. [PMID: 36342148 PMCID: PMC9680613 DOI: 10.1128/aem.00939-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genetic systems for protein overexpression are required tools in microbiological and biochemical research. Ideally, these systems include standardized genetic parts with predictable behavior, enabling the construction of stable expression systems in the host organism.
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [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: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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Liu YX, Zhuo XZ, Li SY. The Transcription Activator AtxA from Bacillus Anthracis was Employed for Developing a Tight-Control, High-Level, Modulable, and Stationary-Phase Specific Transcription Activity in Escherichia Coli. Synth Biol (Oxf) 2022; 7:ysac014. [PMID: 36046151 PMCID: PMC9424709 DOI: 10.1093/synbio/ysac014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/16/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
The strong transcriptional activity of the virulent gene pagA in Bacillus anthracis has been proven to be anthrax toxin activator (AtxA)-regulated. However, the obscure pagA transcription mechanism hinders practical applications of this strong promoter. In this study, a 509-bp DNA fragment [termed 509sequence, (−508)-(+1) relative to the P2 transcription start site] was cloned upstream of rbs-GFPuv as pTOL02B to elucidate the AtxA-regulated transcription. The 509sequence was dissected into the −10 sequence, −35 sequence, ATrich tract, SLI/SLII and upstream site. In conjunction with the heterologous co-expression of AtxA (under the control of the T7 promoter), the −10 sequence (TATACT) was sufficient for the AtxA-regulated transcription. Integration of pTOL02F + pTOLAtxA as pTOL03F showed that the AtxA-regulated transcription exhibited a strong specific fluorescence intensity/common analytical chemistry term (OD600) of 40 597 ± 446 and an induction/repression ratio of 122. An improved induction/repression ratio of 276 was achieved by cultivating Escherichia coli/pTOL03F in M9 minimal medium. The newly developed promoter system termed PAtxA consists of AtxA, the −10 sequence and Escherichia RNA polymerase. These three elements synergistically and cooperatively formed a previously undiscovered transcription system, which exhibited a tight-control, high-level, modulable and stationary-phase-specific transcription. The PAtxA was used for phaCAB expression for the stationary-phase polyhydroxybutyrate production, and the results showed that a PHB yield, content and titer of 0.20 ± 0.27 g/g-glucose, 68 ± 11% and 1.5 ± 0.4 g/l can be obtained. The positive inducible PAtxA, in contrast to negative inducible, should be a useful tool to diversify the gene information flow in synthetic biology.
Graphical Abstract
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Affiliation(s)
- Ying-Xing Liu
- Department of Chemical Engineering, National Chung Hsing University , Taichung 402, Taiwan
| | - Xiao-Zhen Zhuo
- Department of Chemical Engineering, National Chung Hsing University , Taichung 402, Taiwan
| | - Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University , Taichung 402, Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University , Taichung 402, Taiwan
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Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria. Cell Chem Biol 2022; 29:1434-1445.e7. [PMID: 35820417 DOI: 10.1016/j.chembiol.2022.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/11/2022] [Accepted: 06/16/2022] [Indexed: 12/26/2022]
Abstract
Bacteriophages are potent therapeutics against biohazardous bacteria, which rapidly develop multidrug resistance. However, routine administration of phage therapy is hampered by a lack of rapid production, safe bioengineering, and detailed characterization of phages. Thus, we demonstrate a comprehensive cell-free platform for personalized production, transient engineering, and proteomic characterization of a broad spectrum of phages. Using mass spectrometry, we validated hypothetical and non-structural proteins and could also monitor the protein expression during phage assembly. Notably, a few microliters of a one-pot reaction produced effective doses of phages against enteroaggregative Escherichia coli (EAEC), Yersinia pestis, and Klebsiella pneumoniae. By co-expressing suitable host factors, we could extend the range of cell-free production to phages targeting gram-positive bacteria. We further introduce a non-genomic phage engineering method, which adds functionalities for only one replication cycle. In summary, we expect this cell-free methodology to foster reverse and forward phage engineering and customized production of clinical-grade bacteriophages.
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PromoterLCNN: A Light CNN-Based Promoter Prediction and Classification Model. Genes (Basel) 2022; 13:genes13071126. [PMID: 35885909 PMCID: PMC9325283 DOI: 10.3390/genes13071126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 01/01/2023] Open
Abstract
Promoter identification is a fundamental step in understanding bacterial gene regulation mechanisms. However, accurate and fast classification of bacterial promoters continues to be challenging. New methods based on deep convolutional networks have been applied to identify and classify bacterial promoters recognized by sigma (σ) factors and RNA polymerase subunits which increase affinity to specific DNA sequences to modulate transcription and respond to nutritional or environmental changes. This work presents a new multiclass promoter prediction model by using convolutional neural networks (CNNs), denoted as PromoterLCNN, which classifies Escherichia coli promoters into subclasses σ70, σ24, σ32, σ38, σ28, and σ54. We present a light, fast, and simple two-stage multiclass CNN architecture for promoter identification and classification. Training and testing were performed on a benchmark dataset, part of RegulonDB. Comparative performance of PromoterLCNN against other CNN-based classifiers using four parameters (Acc, Sn, Sp, MCC) resulted in similar or better performance than those that commonly use cascade architecture, reducing time by approximately 30–90% for training, prediction, and hyperparameter optimization without compromising classification quality.
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20
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Wei M, Li G, Xie H, Yang W, Xu H, Han S, Wang J, Meng Y, Xu Q, Li Y, Chen N, Zhang C. Sustainable production of 4-hydroxyisoleucine with minimised carbon loss by simultaneously utilising glucose and xylose in engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2022; 354:127196. [PMID: 35460845 DOI: 10.1016/j.biortech.2022.127196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
4-Hydroxyisoleucine is a promising drug for diabetes therapy; however, microbial production of 4-hydroxyisoleucine is not economically efficient because of the carbon loss in the form of CO2. This study aims to achieve de novo synthesis of 4-hydroxyisoleucine with minimised carbon loss in engineered Escherichia coli. Initially, an L-isoleucine-producing strain, ILE-5, was established, and the 4-hydroxyisoleucine synthesis pathway was introduced. The flux toward α-ketoglutarate was enhanced by reinforcing the anaplerotic pathway and disrupting competitive pathways. Subsequently, the metabolic flux for 4-hydroxyisoleucine synthesis was redistributed by dynamically modulating the α-ketoglutarate dehydrogenase complex activity, achieving a 4-hydroxyisoleucine production of 16.53 g/L. Finally, carbon loss was minimised by employing the Weimberg pathway, resulting in a 24.5% decrease in sugar consumption and a 31.6% yield increase. The 4-hydroxyisoleucine production by strain IEOH-11 reached 29.16 g/L in a 5-L fermenter. The 4-hydroxyisoleucine yield (0.29 mol/mol sugar) and productivity (0.91 g/(L⋅h)) were higher than those previously reported.
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Affiliation(s)
- Minhua Wei
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guirong Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Haixiao Xie
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenjun Yang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Haoran Xu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shibao Han
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Junzhe Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yan Meng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qingyang Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanjun Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chenglin Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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21
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Han L, Liu X, Cheng Z, Cui W, Guo J, Yin J, Zhou Z. Construction and Application of a High-Throughput In Vivo Screening Platform for the Evolution of Nitrile Metabolism-Related Enzymes Based on a Desensitized Repressive Biosensor. ACS Synth Biol 2022; 11:1577-1587. [PMID: 35266713 DOI: 10.1021/acssynbio.1c00642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcription factor (TF)-based biosensors are expected to serve as powerful tools for the high-throughput screening of biocatalytic systems; however, most of them respond to ligands in a narrow concentration range, which limits their application. In this study, we constructed a heterogenous niacin biosensor using the repressive TF BsNadR and its target promoters from Bacillus subtilis. The fine-tunable output of the niacin biosensor was expanded to a wide range of niacin concentrations (0-50 mM) through desensitization engineering, which was suitable for the accurate identification of differences in enzyme activity. Structural mechanism analysis indicated that weakening the affinity of BsNadR with the ligand niacin and with DNA alters its regulatory properties. Based on the desensitized niacin biosensor, a high-throughput in vivo screening platform was developed for evolving nitrile metabolism-related enzymes. The evolved nitrilase, amidase, and nitrile hydratase with 6.6-, 2.1-, and 21.3-fold improvements in activity were achieved, respectively. In addition, these mutants also exhibited elevated activity toward other cognate substrates, indicating the broad applicability of the screening platform. This study not only provided a universal high-throughput screening platform for different nitrile metabolism-related enzymes but also demonstrated the advantages of repressive biosensors and the vital role of desensitization engineering of the TF in the development of high-throughput screening platforms for enzymes.
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Affiliation(s)
- Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinyue Liu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhongyi Cheng
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenjing Cui
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Junling Guo
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Yin
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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22
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Van Brempt M, Peeters AI, Duchi D, De Wannemaeker L, Maertens J, De Paepe B, De Mey M. Biosensor-driven, model-based optimization of the orthogonally expressed naringenin biosynthesis pathway. Microb Cell Fact 2022; 21:49. [PMID: 35346204 PMCID: PMC8962593 DOI: 10.1186/s12934-022-01775-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/15/2022] [Indexed: 12/30/2022] Open
Abstract
Background The rapidly expanding synthetic biology toolbox allows engineers to develop smarter strategies to tackle the optimization of complex biosynthetic pathways. In such a strategy, multi-gene pathways are subdivided in several modules which are each dynamically controlled to fine-tune their expression in response to a changing cellular environment. To fine-tune separate modules without interference between modules or from the host regulatory machinery, a sigma factor (σ) toolbox was developed in previous work for tunable orthogonal gene expression. Here, this toolbox is implemented in E. coli to orthogonally express and fine-tune a pathway for the heterologous biosynthesis of the industrially relevant plant metabolite, naringenin. To optimize the production of this pathway, a practical workflow is still imperative to balance all steps of the pathway. This is tackled here by the biosensor-driven screening, subsequent genotyping of combinatorially engineered libraries and finally the training of three different computer models to predict the optimal pathway configuration. Results The efficiency and knowledge gained through this workflow is demonstrated here by improving the naringenin production titer by 32% with respect to a random pathway library screen. Our best strain was cultured in a batch bioreactor experiment and was able to produce 286 mg/L naringenin from glycerol in approximately 26 h. This is the highest reported naringenin production titer in E. coli without the supplementation of pathway precursors to the medium or any precursor pathway engineering. In addition, valuable pathway configuration preferences were identified in the statistical learning process, such as specific enzyme variant preferences and significant correlations between promoter strength at specific steps in the pathway and titer. Conclusions An efficient strategy, powered by orthogonal expression, was applied to successfully optimize a biosynthetic pathway for microbial production of flavonoids in E. coli up to high, competitive levels. Within this strategy, statistical learning techniques were combined with combinatorial pathway optimization techniques and an in vivo high-throughput screening method to efficiently determine the optimal operon configuration of the pathway. This “pathway architecture designer” workflow can be applied for the fast and efficient development of new microbial cell factories for different types of molecules of interest while also providing additional insights into the underlying pathway characteristics. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01775-8.
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Affiliation(s)
- Maarten Van Brempt
- Centre For Synthetic Biology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Andries Ivo Peeters
- Centre For Synthetic Biology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Dries Duchi
- Centre For Synthetic Biology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Lien De Wannemaeker
- Centre For Synthetic Biology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Jo Maertens
- Centre For Synthetic Biology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Brecht De Paepe
- Centre For Synthetic Biology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Marjan De Mey
- Centre For Synthetic Biology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
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Forrest D, Warman EA, Erkelens AM, Dame RT, Grainger DC. Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity. Nat Commun 2022; 13:1149. [PMID: 35241653 PMCID: PMC8894471 DOI: 10.1038/s41467-022-28747-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms: Escherichia coli and Bacillus subtilis. In E. coli, silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the B. subtilis Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in E. coli and B. subtilis, largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of B. subtilis, transcriptional promiscuity must be overcome to silence horizontally acquired DNA in E. coli. Bacteria use specific silencing proteins to prevent spurious transcription of horizontally acquired DNA. Here, Forrest et al. describe differences in silencing strategies between E. coli and Bacillus subtilis, driven by the respective specificities of the silencing protein and the RNA polymerase in each organism.
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Affiliation(s)
- David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Emily A Warman
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK.
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Development of highly characterized genetic bioparts for efficient gene expression in CO2-fixing Eubacterium limosum. Metab Eng 2022; 72:215-226. [DOI: 10.1016/j.ymben.2022.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/20/2022] [Accepted: 03/26/2022] [Indexed: 12/22/2022]
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25
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Sybers D, Joka Bernauw A, El Masri D, Ramadan Maklad H, Charlier D, De Mey M, Bervoets I, Peeters E. Engineering transcriptional regulation in Escherichia coli using an archaeal TetR-family transcription factor. Gene 2022; 809:146010. [PMID: 34688814 DOI: 10.1016/j.gene.2021.146010] [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: 05/31/2021] [Revised: 07/28/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022]
Abstract
Synthetic biology requires well-characterized biological parts that can be combined into functional modules. One type of biological parts are transcriptional regulators and their cognate operator elements, which enable to either generate an input-specific response or are used as actuator modules. A range of regulators has already been characterized and used for orthogonal gene expression engineering, however, previous efforts have mostly focused on bacterial regulators. This work aims to design and explore the use of an archaeal TetR family regulator, FadRSa from Sulfolobus acidocaldarius, in a bacterial system, namely Escherichia coli. This is a challenging objective given the fundamental difference between the bacterial and archaeal transcription machinery and the lack of a native TetR-like FadR regulatory system in E. coli. The synthetic σ70-dependent bacterial promoter proD was used as a starting point to design hybrid bacterial/archaeal promoter/operator regions, in combination with the mKate2 fluorescent reporter enabling a readout. Four variations of proD containing FadRSa binding sites were constructed and characterized. While expressional activity of the modified promoter proD was found to be severely diminished for two of the constructs, constructs in which the binding site was introduced adjacent to the -35 promoter element still displayed sufficient basal transcriptional activity and showed up to 7-fold repression upon expression of FadRSa. Addition of acyl-CoA has been shown to disrupt FadRSa binding to the DNA in vitro. However, extracellular concentrations of up to 2 mM dodecanoate, subsequently converted to acyl-CoA by the cell, did not have a significant effect on repression in the bacterial system. This work demonstrates that archaeal transcription regulators can be used to generate actuator elements for use in E. coli, although the lack of ligand response underscores the challenge of maintaining biological function when transferring parts to a phylogenetically divergent host.
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Affiliation(s)
- David Sybers
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Amber Joka Bernauw
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Diala El Masri
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Hassan Ramadan Maklad
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Indra Bervoets
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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Disentangling direct from indirect relationships in association networks. Proc Natl Acad Sci U S A 2022; 119:2109995119. [PMID: 34992138 PMCID: PMC8764688 DOI: 10.1073/pnas.2109995119] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 11/18/2022] Open
Abstract
Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal (P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.
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Mey F, Clauwaert J, Van Brempt M, Stock M, Maertens J, Waegeman W, De Mey M. ProD: A Tool for Predictive Design of Tailored Promoters in Escherichia coli. Methods Mol Biol 2022; 2516:51-59. [PMID: 35922621 DOI: 10.1007/978-1-0716-2413-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A major goal in synthetic biology is the engineering of synthetic gene circuits with a predictable, controlled and designed outcome. This creates a need for building blocks that can modulate gene expression without interference with the native cell system. A tool allowing forward engineering of promoters with predictable transcription initiation frequency is still lacking. Promoter libraries specific for σ70 to ensure the orthogonality of gene expression were built in Escherichia coli and labeled using fluorescence-activated cell sorting to obtain high-throughput DNA sequencing data to train a convolutional neural network. We were able to confirm in vivo that the model is able to predict the promoter transcription initiation frequency (TIF) of new promoter sequences. Here, we provide an online tool for promoter design (ProD) in E. coli, which can be used to tailor output sequences of desired promoter TIF or predict the TIF of a custom sequence.
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Affiliation(s)
- Friederike Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Jim Clauwaert
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Maarten Van Brempt
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Ghent, Belgium.
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28
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Biomolecular mechanisms for signal differentiation. iScience 2021; 24:103462. [PMID: 34927021 PMCID: PMC8649740 DOI: 10.1016/j.isci.2021.103462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 01/05/2023] Open
Abstract
Cells can sense temporal changes of molecular signals, allowing them to predict environmental variations and modulate their behavior. This paper elucidates biomolecular mechanisms of time derivative computation, facilitating the design of reliable synthetic differentiator devices for a variety of applications, ultimately expanding our understanding of cell behavior. In particular, we describe and analyze three alternative biomolecular topologies that are able to work as signal differentiators to input signals around their nominal operation. We propose strategies to preserve their performance even in the presence of high-frequency input signal components which are detrimental to the performance of most differentiators. We find that the core of the proposed topologies appears in natural regulatory networks and we further discuss their biological relevance. The simple structure of our designs makes them promising tools for realizing derivative control action in synthetic biology.
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Ma X, Ma L, Huo YX. Reconstructing the transcription regulatory network to optimize resource allocation for robust biosynthesis. Trends Biotechnol 2021; 40:735-751. [PMID: 34895933 DOI: 10.1016/j.tibtech.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
An ideal microbial cell factory (MCF) should deliver maximal resources to production, which conflicts with the microbe's native growth-oriented resource allocation strategy and can therefore lead to early termination of the high-yield period. Reallocating resources from growth to production has become a critical factor in constructing robust MCFs. Instead of strengthening specific biosynthetic pathways, emerging endeavors are focused on rearranging the gene regulatory network to fundamentally reprogram the resource allocation pattern. Combining this idea with transcriptional regulation within the hierarchical regulatory network, this review discusses recent engineering strategies targeting the transcription machinery, module networks, regulatory edges, and bottom network layer. This global view will help to construct a production-oriented phenotype that fully harnesses the potential of MCFs.
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Affiliation(s)
- Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China; Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, People's Republic of China.
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30
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Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
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Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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31
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Sun X, Li S, Zhang F, Sun T, Chen L, Zhang W. Development of a N-Acetylneuraminic Acid-Based Sensing and Responding Switch for Orthogonal Gene Regulation in Cyanobacterial Synechococcus Strains. ACS Synth Biol 2021; 10:1920-1930. [PMID: 34370452 DOI: 10.1021/acssynbio.1c00139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in synthetic biology have allowed photosynthetic cyanobacteria as promising "green cell factories" for sustainable production of biofuels and biochemicals. However, a limited of genetic switches developed in cyanobacteria restrict the complex and orthogonal metabolic regulation. In addition, suitable and controllable switches sensing and responding to specific inducers would allow for the separation of cellular growth and expression of exogenous genes or pathways that cause metabolic burden or toxicity. Here in this study, we developed a genetic switch repressed by NanR and induced by N-acetylneuraminic acid (Neu5Ac) in a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 along with its highly homologous strain S. elongatus PCC 7942. First, nanR from Escherichia coli and a previously optimized cognate promoter PJ23119H10 were introduced into Syn2973 to control the expression of the reporter gene lacZ encoding β-galactosidase, achieving induction with negligible leakage. Second, the switch was systemically optimized to reach ∼738-fold induction by fine-tuning the expression level of NanR and introducing additional transporter of Neu5Ac. Finally, the orthogonality between the NanR/Neu5Ac switch and theophylline-responsive riboregulator was investigated, achieving a coordinated regulation or binary regulation toward the target gene. Our work here provided a new switch for transcriptional control and orthogonal regulation strategies in cyanobacteria, which would promote the metabolic regulation for the cyanobacterial chassis in the future.
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Affiliation(s)
- Xuyang Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Fenfang Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, People’s Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, People’s Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People’s Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, People’s Republic of China
- Law School of Tianjin University, Tianjin 300072, People’s Republic of China
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33
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Schwall CP, Loman TE, Martins BMC, Cortijo S, Villava C, Kusmartsev V, Livesey T, Saez T, Locke JCW. Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit. Mol Syst Biol 2021; 17:e9832. [PMID: 34286912 PMCID: PMC8287880 DOI: 10.15252/msb.20209832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.
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Affiliation(s)
| | | | - Bruno M C Martins
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | | | | | - Toby Livesey
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Teresa Saez
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
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34
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Cui W, Lin Q, Hu R, Han L, Cheng Z, Zhang L, Zhou Z. Data-Driven and in Silico-Assisted Design of Broad Host-Range Minimal Intrinsic Terminators Adapted for Bacteria. ACS Synth Biol 2021; 10:1438-1450. [PMID: 34015924 DOI: 10.1021/acssynbio.1c00050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Efficient transcription termination relying on intrinsic terminators is critical to maintain cell fitness by avoiding unwanted read-through in bacteria. Natural intrinsic terminator (NIT) typically appears in mRNA as a hairpin followed by approximately eight conserved uridines (U-tract) at the 3' terminus. Owing to their simple structure, small size, and protein independence, assorted NITs have been redesigned as robust tools to construct gene circuits. However, most NITs exert functions to adapt to their physiological requirements rather than the demand for building synthetic gene circuits, rendering uncertain working performance when they are constructed intact in synthetic gene circuits. Here, rather than modifying NITs, we established a data-driven and in silico-assisted (DISA) design framework to forward engineer minimal intrinsic terminators (MITs). By comprehensively analyzing 75 natural intrinsic terminators from Bacillus subtilis, we revealed that two pivotal features, the length of the U-tract and the thermodynamics of the terminator hairpin, were involved in the sequence-activity relationship (SAR) of termination efficiency (TE). As per the SAR, we leveraged DISA to fabricate an array of MITs composed of in silico-assisted designed minimal hairpins and fixed U-tracts. Most of these MITs exhibited high TE in diverse Gram-positive and Gram-negative bacteria. In contrast, the TEs of the NITs were highly varied in different hosts. Moreover, TEs of MITs were flexibly tuned over a wide range by modulating the length of the U-tract. Overall, these results demonstrate an efficient framework to forward design functional and broad host-range terminators independent of tedious and iterative screening of mutagenesis libraries of natural terminators.
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Affiliation(s)
- Wenjing Cui
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qiao Lin
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ruichun Hu
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Linpei Zhang
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, Jiangsu 226500, China
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Pieters PA, Nathalia BL, van der Linden AJ, Yin P, Kim J, Huck WTS, de Greef TFA. Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits. ACS Synth Biol 2021; 10:1406-1416. [PMID: 34061505 PMCID: PMC8218305 DOI: 10.1021/acssynbio.1c00024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Regulatory pathways
inside living cells employ feed-forward architectures
to fulfill essential signal processing functions that aid in the interpretation
of various types of inputs through noise-filtering, fold-change detection
and adaptation. Although it has been demonstrated computationally
that a coherent feed-forward loop (CFFL) can function as noise filter,
a property essential to decoding complex temporal signals, this motif
has not been extensively characterized experimentally or integrated
into larger networks. Here we use post-transcriptional regulation
to implement and characterize a synthetic CFFL in an Escherichia
coli cell-free transcription-translation system and build
larger composite feed-forward architectures. We employ microfluidic
flow reactors to probe the response of the CFFL circuit using both
persistent and short, noise-like inputs and analyze the influence
of different circuit components on the steady-state and dynamics of
the output. We demonstrate that our synthetic CFFL implementation
can reliably repress background activity compared to a reference circuit,
but displays low potential as a temporal filter, and validate these
findings using a computational model. Our results offer practical
insight into the putative noise-filtering behavior of CFFLs and show
that this motif can be used to mitigate leakage and increase the fold-change
of the output of synthetic genetic circuits.
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Affiliation(s)
- Pascal A. Pieters
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bryan L. Nathalia
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ardjan J. van der Linden
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Jongmin Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Eindhoven, The Netherlands
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Wilson EH, Groom JD, Sarfatis MC, Ford SM, Lidstrom ME, Beck DAC. A Computational Framework for Identifying Promoter Sequences in Nonmodel Organisms Using RNA-seq Data Sets. ACS Synth Biol 2021; 10:1394-1405. [PMID: 33988977 DOI: 10.1021/acssynbio.1c00017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Engineering microorganisms into biological factories that convert renewable feedstocks into valuable materials is a major goal of synthetic biology; however, for many nonmodel organisms, we do not yet have the genetic tools, such as suites of strong promoters, necessary to effectively engineer them. In this work, we developed a computational framework that can leverage standard RNA-seq data sets to identify sets of constitutive, strongly expressed genes and predict strong promoter signals within their upstream regions. The framework was applied to a diverse collection of RNA-seq data measured for the methanotroph Methylotuvimicrobium buryatense 5GB1 and identified 25 genes that were constitutively, strongly expressed across 12 experimental conditions. For each gene, the framework predicted short (27-30 nucleotide) sequences as candidate promoters and derived -35 and -10 consensus promoter motifs (TTGACA and TATAAT, respectively) for strong expression in M. buryatense. This consensus closely matches the canonical E. coli sigma-70 motif and was found to be enriched in promoter regions of the genome. A subset of promoter predictions was experimentally validated in a XylE reporter assay, including the consensus promoter, which showed high expression. The pmoC, pqqA, and ssrA promoter predictions were additionally screened in an experiment that scrambled the -35 and -10 signal sequences, confirming that transcription initiation was disrupted when these specific regions of the predicted sequence were altered. These results indicate that the computational framework can make biologically meaningful promoter predictions and identify key pieces of regulatory systems that can serve as foundational tools for engineering diverse microorganisms for biomolecule production.
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Affiliation(s)
- Erin H. Wilson
- The Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Joseph D. Groom
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - M. Claire Sarfatis
- Department of Microbiology, University of Washington, Seattle, Washington 98195, United States
| | - Stephanie M. Ford
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Mary E. Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Department of Microbiology, University of Washington, Seattle, Washington 98195, United States
| | - David A. C. Beck
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- eScience Institute, University of Washington, Seattle, Washington 98195, United States
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Lyu Y, He W, Li S, Zou Q, Guo F. iPro2L-PSTKNC: A Two-Layer Predictor for Discovering Various Types of Promoters by Position Specific of Nucleotide Composition. IEEE J Biomed Health Inform 2021; 25:2329-2337. [PMID: 32976109 DOI: 10.1109/jbhi.2020.3026735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Promoters are DNA regulatory elements located proximal to the transcription start site, which are in charge of the initiation of specific gene transcription. In Escherichia coli, promoters can be recognized by σ factors that have multiple families based on distinct function and structure, such as σ24, σ28, σ32, σ38, σ54 and σ70. At present, biological methods are mainly used to identify these promoters. However, because it is time-consuming and material-consuming to do biological experiments, computational biology algorithm has emerged as a more effective way to predict the classification. In this study, we develop a novel two-layer seamless predictor called iPro2L-PSTKNC to identify the promoters of the E. coli genome, which based on the feature extraction model we newly proposed that is named as the position specific tendencies of k-mer nucleotide composition (PSTKNC). On the first layer, it is a binary classification predicting whether a sequence is promoter or not. And the second layer is a multiple classification identifying which type the identified promoter belongs to. The ensemble classification SVM performsbest comparing with other algorithms, which gets a promising accuracy and the Matthews correlation coefficient (MCC) at [Formula: see text] and [Formula: see text]. Our data and code are available at https://github.com/lyuyinuo/iPro2L-PSTKNC.
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A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. Commun Biol 2021; 4:582. [PMID: 33990691 PMCID: PMC8121941 DOI: 10.1038/s42003-021-02107-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
The conjugative plasmid (pBV71) possibly confers a selective advantage to Bacillus velezensis strain GH1-13, although a selective marker gene is yet to be identified. Here we show that few non-mucoid wild-type GH1-13 cells are spontaneously converted to mucoid variants with or without the loss of pBV71. Mucoid phenotypes, which contain or lack the plasmid, become sensitive to bacitracin, gramicidin, selenite, and tellurite. Using the differences in antibiotic resistance and phenotype, we isolated a reverse complement (COM) and a transconjugant of strain FZB42 with the native pBV71. Transformed COM and FZB42p cells were similar to the wild-type strain GH1-13 with high antibiotic resistance and slow growth rates on lactose compared to those of mucoid phenotypes. RT-PCR analysis revealed that the expression of plasmid-encoded orphan aspartate phosphatase (pRapD) was coordinated with a new quorum-sensing (QS) cassette of RapF2-PhrF2 present in the chromosome of strain GH1-13, but not in strain FZB42. Multi-omics analysis on wild-type and plasmid-cured cells of strain GH1-13 suggested that the conjugative plasmid expression has a crucial role in induction of early envelope stress response that promotes cell morphogenesis, biofilm formation, catabolite repression, and biosynthesis of extracellular-matrix components and antibiotics for protection of host cell during exponential phase.
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de Dios R, Santero E, Reyes-Ramírez F. Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses. Int J Mol Sci 2021; 22:ijms22083900. [PMID: 33918849 PMCID: PMC8103513 DOI: 10.3390/ijms22083900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/03/2023] Open
Abstract
The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria.
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40
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Zhang Y, Ding W, Wang Z, Zhao H, Shi S. Development of Host-Orthogonal Genetic Systems for Synthetic Biology. Adv Biol (Weinh) 2021; 5:e2000252. [PMID: 33729696 DOI: 10.1002/adbi.202000252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/18/2020] [Indexed: 12/17/2022]
Abstract
The construction of a host-orthogonal genetic system can not only minimize the impact of host-specific nuances on fine-tuning of gene expression, but also expand cellular functions such as in vivo continuous evolution of genes based on an error-prone DNA polymerase. It represents an emerging powerful approach for making biology easier to engineer. In this review, the recent advances are described on the design of genetic systems that can be stably inherited in the host cells and are responsible for important biological processes including DNA replication, RNA transcription, protein translation, and gene regulation. Their applications in synthetic biology are summarized and the future challenges and opportunities are discussed in developing such systems.
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Affiliation(s)
- Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.,Key Laboratory of Food Nutrition and Safety (Tianjin University of Science and Technology) Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, TEDA, Tianjin, 300457, P. R. China
| | - Zhihui Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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Abstract
Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. The complexity and amount of data necessitate an objective and streamlined data processing workflow that extends beyond commercial instrument software. No full overview of the necessary steps regarding the computational analysis of microbial flow cytometry data currently exists. In this review, we provide an overview of the full data analysis pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial ecology. At every step, we highlight computational methods that are potentially useful, for which we provide a short nontechnical description. We place this overview in the context of a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.
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Affiliation(s)
| | - Ruben Props
- Center for Microbial Ecology & Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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42
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Costello A, Badran AH. Synthetic Biological Circuits within an Orthogonal Central Dogma. Trends Biotechnol 2021; 39:59-71. [PMID: 32586633 PMCID: PMC7746572 DOI: 10.1016/j.tibtech.2020.05.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022]
Abstract
Synthetic biology strives to reliably control cellular behavior, typically in the form of user-designed interactions of biological components to produce a predetermined output. Engineered circuit components are frequently derived from natural sources and are therefore often hampered by inadvertent interactions with host machinery, most notably within the host central dogma. Reliable and predictable gene circuits require the targeted reduction or elimination of these undesirable interactions to mitigate negative consequences on host fitness and develop context-independent bioactivities. Here, we review recent advances in biological orthogonalization, namely the insulation of researcher-dictated bioactivities from host processes, with a focus on systematic developments that may culminate in the creation of an orthogonal central dogma and novel cellular functions.
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Affiliation(s)
- Alan Costello
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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43
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Noh MH, Cha S, Kim M, Jung GY. Recent Advances in Microbial Cell Growth Regulation Strategies for Metabolic Engineering. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0511-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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44
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Zhang C, Li Y, Zhu F, Li Z, Lu N, Li Y, Xu Q, Chen N. Metabolic engineering of an auto-regulated Corynebacterium glutamicum chassis for biosynthesis of 5-aminolevulinic acid. BIORESOURCE TECHNOLOGY 2020; 318:124064. [PMID: 32905949 DOI: 10.1016/j.biortech.2020.124064] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
One challenge in metabolic engineering for industrial applications is the construction of highly efficient microbial cell factories. For this purpose, dynamic regulation of metabolic flux may be indispensable. In this study, an auto-regulated Corynebacterium glutamicum chassis for 5-aminolevulinic acid (5-ALA) biosynthesis was constructed. First, the expression of critical genes involved in 5-ALA synthesis and cofactor regeneration was precisely modulated. Furthermore, odhA expression was controlled using the strategies of static metabolic engineering (SME, with a weak promoter), dynamic metabolic engineering (DME, with a temperature-sensitive plasmid), and auto-inducible metabolic engineering (AME, with a growth-related promoter). The AME strategy showed the best effect and dynamically balanced the tradeoff between cell growth and 5-ALA synthesis. Additionally, the expression of exporter-encoding rhtA was regulated using AME strategy by the two-component system HrrSA in response to extracellular heme. The final strain A30 achieved the highest 5-ALA production (3.16 g/L) ever reported in C. glutamicum through C5 pathway.
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Affiliation(s)
- Chenglin Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanjun Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Fuzhou Zhu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhixiang Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nan Lu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yuhong Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qingyang Xu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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45
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Van Brempt M, Clauwaert J, Mey F, Stock M, Maertens J, Waegeman W, De Mey M. Predictive design of sigma factor-specific promoters. Nat Commun 2020; 11:5822. [PMID: 33199691 PMCID: PMC7670410 DOI: 10.1038/s41467-020-19446-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
To engineer synthetic gene circuits, molecular building blocks are developed which can modulate gene expression without interference, mutually or with the host's cell machinery. As the complexity of gene circuits increases, automated design tools and tailored building blocks to ensure perfect tuning of all components in the network are required. Despite the efforts to develop prediction tools that allow forward engineering of promoter transcription initiation frequency (TIF), such a tool is still lacking. Here, we use promoter libraries of E. coli sigma factor 70 (σ70)- and B. subtilis σB-, σF- and σW-dependent promoters to construct prediction models, capable of both predicting promoter TIF and orthogonality of the σ-specific promoters. This is achieved by training a convolutional neural network with high-throughput DNA sequencing data from fluorescence-activated cell sorted promoter libraries. This model functions as the base of the online promoter design tool (ProD), providing tailored promoters for tailored genetic systems.
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Affiliation(s)
- Maarten Van Brempt
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Jim Clauwaert
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Friederike Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium.
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Coussement P, Bauwens D, Peters G, Maertens J, De Mey M. Mapping and refactoring pathway control through metabolic and protein engineering: The hexosamine biosynthesis pathway. Biotechnol Adv 2020; 40:107512. [DOI: 10.1016/j.biotechadv.2020.107512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/07/2019] [Accepted: 09/30/2019] [Indexed: 01/14/2023]
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47
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Han L, Cui W, Lin Q, Chen Q, Suo F, Ma K, Wang Y, Hao W, Cheng Z, Zhou Z. Efficient Overproduction of Active Nitrile Hydratase by Coupling Expression Induction and Enzyme Maturation via Programming a Controllable Cobalt-Responsive Gene Circuit. Front Bioeng Biotechnol 2020; 8:193. [PMID: 32266230 PMCID: PMC7105576 DOI: 10.3389/fbioe.2020.00193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/27/2020] [Indexed: 11/13/2022] Open
Abstract
A robust and portable expression system is of great importance in enzyme production, metabolic engineering, and synthetic biology, which maximizes the performance of the engineered system. In this study, a tailor-made cobalt-induced expression system (CIES) was developed for low-cost and eco-friendly nitrile hydratase (NHase) production. First, the strong promoter Pveg from Bacillus subtilis, the Ni(II)/Co(II) responsive repressor RcnR, and its operator were reorganized to construct a CIES. In this system, the expression of reporter green fluorescent protein (GFP) was specifically triggered by Co(II) over a broad range of concentration. The performance of the cobalt-induced system was evolved to version 2.0 (CIES 2.0) for adaptation to different concentrations of Co(II) through programming a homeostasis system that rebalances cobalt efflux and influx with RcnA and NiCoT, respectively. Harnessing these synthetic platforms, the induced expression of NHase was coupled with enzyme maturation by Co(II) in a synchronizable manner without requiring additional inducers, which is a unique feature relative to other induced systems for production of NHase. The yield of NHase was 111.2 ± 17.9 U/ml using CIES and 114.9 ± 1.4 U/ml using CIES 2.0, which has a producing capability equivalent to that of commonly used isopropyl thiogalactoside (IPTG)-induced systems. In a scale-up system using a 5-L fermenter, the yielded enzymatic activity reached 542.2 ± 42.8 U/ml, suggesting that the designer platform for NHase is readily applied to the industry. The design of CIES in this study not only provided a low-cost and eco-friendly platform to overproduce NHase but also proposed a promising pipeline for development of synthetic platforms for expression of metalloenzymes.
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Affiliation(s)
- Laichuang Han
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Qiao Lin
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Qiaoqing Chen
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Feiya Suo
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Ke Ma
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Yang Wang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Wenliang Hao
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
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48
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Han L, Chen Q, Lin Q, Cheng J, Zhou L, Liu Z, Guo J, Zhang L, Cui W, Zhou Z. Realization of Robust and Precise Regulation of Gene Expression by Multiple Sigma Recognizable Artificial Promoters. Front Bioeng Biotechnol 2020; 8:92. [PMID: 32140461 PMCID: PMC7042180 DOI: 10.3389/fbioe.2020.00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/31/2020] [Indexed: 01/28/2023] Open
Abstract
Precise regulation of gene expression is fundamental for tailor-made gene circuit design in synthetic biology. Current strategies for this type of development are mainly based on directed evolution beginning with a native promoter template. The performances of engineered promoters are usually limited by the growth phase because only one promoter is recognized by one type of sigma factor (σ). Here, we constructed multiple-σ recognizable artificial hybrid promoters (AHPs) composed of tandems of dual and triple natural minimal promoters (NMPs). These NMPs, which use σA, σH and σW, had stable functions in different growth phases. The functions of these NMPs resulted from an effect called transcription compensation, in which AHPs sequentially use one type of σ in the corresponding growth phase. The strength of the AHPs was influenced by the combinatorial order of each NMP and the length of the spacers between the NMPs. More importantly, the output of the precise regulation was achieved by equipping AHPs with synthetic ribosome binding sites and by redesigning them for induced systems. This strategy might offer promising applications to rationally design robust synthetic promoters in diverse chassis to spur the construction of more complex gene circuits, which will further the development of synthetic biology.
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Affiliation(s)
- Laichuang Han
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiaoqing Chen
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiao Lin
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jintao Cheng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Linpei Zhang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
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49
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Kędzierska-Mieszkowska S, Potrykus K, Arent Z, Krajewska J. Identification of σ E-Dependent Promoter Upstream of clpB from the Pathogenic Spirochaete Leptospira interrogans by Applying an E. coli Two-Plasmid System. Int J Mol Sci 2019; 20:ijms20246325. [PMID: 31847479 PMCID: PMC6941012 DOI: 10.3390/ijms20246325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 11/16/2022] Open
Abstract
There is limited information on gene expression in the pathogenic spirochaete Leptospira interrogans and genetic mechanisms controlling its virulence. Transcription is the first step in gene expression that is often determined by environmental effects, including infection-induced stresses. Alterations in the environment result in significant changes in the transcription of many genes, allowing effective adaptation of Leptospira to mammalian hosts. Thus, promoter and transcriptional start site identification are crucial for determining gene expression regulation and for the understanding of genetic regulatory mechanisms existing in Leptospira. Here, we characterized the promoter region of the L. interrogans clpB gene (clpBLi) encoding an AAA+ molecular chaperone ClpB essential for the survival of this spirochaete under thermal and oxidative stresses, and also during infection of the host. Primer extension analysis demonstrated that transcription of clpB in L. interrogans initiates at a cytidine located 41 bp upstream of the ATG initiation codon, and, to a lesser extent, at an adenine located 2 bp downstream of the identified site. Transcription of both transcripts was heat-inducible. Determination of clpBLi transcription start site, combined with promoter transcriptional activity assays using a modified two-plasmid system in E. coli, revealed that clpBLi transcription is controlled by the ECF σE factor. Of the ten L. interrogans ECF σ factors, the factor encoded by LIC_12757 (LA0876) is most likely to be the key regulator of clpB gene expression in Leptospira cells, especially under thermal stress. Furthermore, clpB expression may be mediated by ppGpp in Leptospira.
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Affiliation(s)
- Sabina Kędzierska-Mieszkowska
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, 80-308 Gdańsk, Poland;
- Correspondence: ; Tel./Fax: +48-58-523-6064
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland;
| | - Zbigniew Arent
- University Centre of Veterinary Medicine, University of Agriculture in Krakow, 30-059 Krakow, Poland;
| | - Joanna Krajewska
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, 80-308 Gdańsk, Poland;
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50
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Kent R, Dixon N. Contemporary Tools for Regulating Gene Expression in Bacteria. Trends Biotechnol 2019; 38:316-333. [PMID: 31679824 DOI: 10.1016/j.tibtech.2019.09.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Insights from novel mechanistic paradigms in gene expression control have led to the development of new gene expression systems for bioproduction, control, and sensing applications. Coupled with a greater understanding of synthetic burden and modern creative biodesign approaches, contemporary bacterial gene expression tools and systems are emerging that permit fine-tuning of expression, enabling greater predictability and maximisation of specific productivity, while minimising deleterious effects upon cell viability. These advances have been achieved by using a plethora of regulatory tools, operating at all levels of the so-called 'central dogma' of molecular biology. In this review, we discuss these gene regulation tools in the context of their design, prototyping, integration into expression systems, and biotechnological application.
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Affiliation(s)
- Ross Kent
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, UK.
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