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Köbbing S, Lechtenberg T, Wynands B, Blank LM, Wierckx N. Reliable Genomic Integration Sites in Pseudomonas putida Identified by Two-Dimensional Transcriptome Analysis. ACS Synth Biol 2024; 13:2060-2072. [PMID: 38968167 PMCID: PMC11264328 DOI: 10.1021/acssynbio.3c00747] [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: 12/13/2023] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 07/07/2024]
Abstract
Genomic integration is commonly used to engineer stable production hosts. However, so far, for many microbial workhorses, only a few integration sites have been characterized, thereby restraining advanced strain engineering that requires multiple insertions. Here, we report on the identification of novel genomic integration sites, so-called landing pads, for Pseudomonas putida KT2440. We identified genomic regions with constant expression patterns under diverse experimental conditions by using RNA-Seq data. Homologous recombination constructs were designed to insert heterologous genes into intergenic sites in these regions, allowing condition-independent gene expression. Ten potential landing pads were characterized using four different msfGFP expression cassettes. An insulated probe sensor was used to study locus-dependent effects on recombinant gene expression, excluding genomic read-through of flanking promoters under changing cultivation conditions. While the reproducibility of expression in the landing pads was very high, the msfGFP signals varied strongly between the different landing pads, confirming a strong influence of the genomic context. To showcase that the identified landing pads are also suitable candidates for heterologous gene expression in other Pseudomonads, four equivalent landing pads were identified and characterized in Pseudomonas taiwanensis VLB120. This study shows that genomic "hot" and "cold" spots exist, causing strong promoter-independent variations in gene expression. This highlights that the genomic context is an additional parameter to consider when designing integrable genomic cassettes for tailored heterologous expression. The set of characterized genomic landing pads presented here further increases the genetic toolbox for deep metabolic engineering in Pseudomonads.
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Affiliation(s)
- Sebastian Köbbing
- Aachen
Biology and Biotechnology-ABBt, Institute of Applied Microbiology-iAMB, RWTH Aachen University, 52074 Aachen, Germany
| | - Thorsten Lechtenberg
- Institute
of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Benedikt Wynands
- Institute
of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Lars M. Blank
- Aachen
Biology and Biotechnology-ABBt, Institute of Applied Microbiology-iAMB, RWTH Aachen University, 52074 Aachen, Germany
| | - Nick Wierckx
- Aachen
Biology and Biotechnology-ABBt, Institute of Applied Microbiology-iAMB, RWTH Aachen University, 52074 Aachen, Germany
- Institute
of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52428 Jülich, Germany
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2
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Meng H, Köbbing S, Blank LM. Establishing a straightforward I-SceI-mediated recombination one-plasmid system for efficient genome editing in P. putida KT2440. Microb Biotechnol 2024; 17:e14531. [PMID: 39031514 PMCID: PMC11258999 DOI: 10.1111/1751-7915.14531] [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: 01/24/2024] [Accepted: 07/04/2024] [Indexed: 07/22/2024] Open
Abstract
Pseudomonas putida has become an increasingly important chassis for producing valuable bioproducts. This development is not least due to the ever-improving genetic toolbox, including gene and genome editing techniques. Here, we present a novel, one-plasmid design of a critical genetic tool, the pEMG/pSW system, guaranteeing one engineering cycle to be finalized in 3 days. The pEMG/pSW system proved in the last decade to be valuable for targeted genome engineering in Pseudomonas, as it enables the deletion of large regions of the genome, the integration of heterologous gene clusters or the targeted generation of point mutations. Here, to expedite genetic engineering, two alternative plasmids were constructed: (1) The sacB gene from Bacillus subtilis was integrated into the I-SceI expressing plasmid pSW-2 as a counterselection marker to accelerated plasmid curing; (2) double-strand break introducing gene I-sceI and sacB counterselection marker were integrated into the backbone of the original pEMG vector, named pEMG-RIS. The single plasmid of pEMG-RIS allows rapid genome editing despite the low transcriptional activity of a single copy of the I-SceI encoding gene. Here, the usability of the pEMG-RIS is shown in P. putida KT2440 by integrating an expression cassette including an msfGFP gene in 3 days. In addition, a large fragment of 12.1 kb was also integrated. In summary, we present an updated pEMG/pSW genome editing system that allows efficient and rapid genome editing in P. putida. All plasmids designed in this study will be available via the Addgene platform.
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Affiliation(s)
- Hao Meng
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Sebastian Köbbing
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Lars M. Blank
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
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3
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Bao Z, Gao Y, Song Y, Ding N, Li W, Wu Q, Zhang X, Zheng Y, Li J, Hu X. Construction of an Escherichia coli chassis for efficient biosynthesis of human-like N-linked glycoproteins. Front Bioeng Biotechnol 2024; 12:1370685. [PMID: 38572355 PMCID: PMC10987854 DOI: 10.3389/fbioe.2024.1370685] [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: 01/15/2024] [Accepted: 03/08/2024] [Indexed: 04/05/2024] Open
Abstract
The production of N-linked glycoproteins in genetically engineered Escherichia coli holds significant potential for reducing costs, streamlining bioprocesses, and enhancing customization. However, the construction of a stable and low-cost microbial cell factory for the efficient production of humanized N-glycosylated recombinant proteins remains a formidable challenge. In this study, we developed a glyco-engineered E. coli chassis to produce N-glycosylated proteins with the human-like glycan Gal-β-1,4-GlcNAc-β-1,3-Gal-β-1,3-GlcNAc-, containing the human glycoform Gal-β-1,4-GlcNAc-β-1,3-. Our initial efforts were to replace various loci in the genome of the E. coli XL1-Blue strain with oligosaccharyltransferase PglB and the glycosyltransferases LsgCDEF to construct the E. coli chassis. In addition, we systematically optimized the promoter regions in the genome to regulate transcription levels. Subsequently, utilizing a plasmid carrying the target protein, we have successfully obtained N-glycosylated proteins with 100% tetrasaccharide modification at a yield of approximately 320 mg/L. Furthermore, we constructed the metabolic pathway for sialylation using a plasmid containing a dual-expression cassette of the target protein and CMP-sialic acid synthesis in the tetrasaccharide chassis cell, resulting in a 40% efficiency of terminal α-2,3- sialylation and a production of 65 mg/L of homogeneously sialylated glycoproteins in flasks. Our findings pave the way for further exploration of producing different linkages (α-2,3/α-2,6/α-2,8) of sialylated human-like N-glycoproteins in the periplasm of the plug-and-play E. coli chassis, laying a strong foundation for industrial-scale production.
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Affiliation(s)
- Zixin Bao
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Yuting Gao
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Yitong Song
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Ning Ding
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
- Dalian Key Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
| | - Wei Li
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Qiong Wu
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Xiaomei Zhang
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Yang Zheng
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
| | - Junming Li
- Department of Clinical Laboratory, Yantai Yuhuangding Hospital, Yantai, China
| | - Xuejun Hu
- Academic Centre for Medical Research, Medical College, Dalian University, Dalian, China
- Dalian Key Laboratory of Oligosaccharide Recombination and Recombinant Protein Modification, Dalian, China
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4
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Liao Y, Lao C, Wu J, Yuan L, Xu Y, Jin W, Sun J, Zhang Q, Chen X, Yao J. High-Yield Synthesis of Lacto- N-Neotetraose from Glycerol and Glucose in Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5325-5338. [PMID: 38275134 DOI: 10.1021/acs.jafc.3c08239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Lacto-N-neotetraose (LNnT) is a neutral human milk oligosaccharide with important biological functions. However, the low LNnT productivity and the incomplete conversion of the intermediate lacto-N-tetraose II (LNT II) currently limited the sustainable biosynthesis of LNnT. First, the LNnT biosynthetic module was integrated in Escherichia coli. Next, the LNnT export system was optimized to alleviate the inhibition of intracellular LNnT synthesis. Furthermore, by utilizing rate-limiting enzyme diagnosis, the expressions of LNnT synthesis pathway genes were finely regulated to further enhance the production yield of LNnT. Subsequently, a strategy of cofermentation using a glucose/glycerol (4:6, g/g) mixed feed was employed to regulate carbon flux distribution. Finally, by overexpressing key transferases, LNnT and LNT II titers reached 112.47 and 7.42 g/L, respectively, in a 5 L fermenter, and 107.4 and 2.08 g/L, respectively, in a 1000 L fermenter. These are the highest reported titers of LNnT to date, indicating its significant potential for industrial production.
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Affiliation(s)
- Yingxue Liao
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science & Technology of China, Hefei 230026, China
| | - Caiwen Lao
- Hefei CAS Health Bio-Industrial Technology Institute Co., Ltd., Hefei 230031, China
| | - Jinyong Wu
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Lixia Yuan
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yanyi Xu
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science & Technology of China, Hefei 230026, China
| | - Weijian Jin
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science & Technology of China, Hefei 230026, China
| | - Jian Sun
- Hefei CAS Health Bio-Industrial Technology Institute Co., Ltd., Hefei 230031, China
| | - Qiang Zhang
- Hefei CAS Health Bio-Industrial Technology Institute Co., Ltd., Hefei 230031, China
| | - Xiangsong Chen
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Jianming Yao
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science & Technology of China, Hefei 230026, China
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5
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Kruse L, Loeschcke A, de Witt J, Wierckx N, Jaeger K, Thies S. Halopseudomonas species: Cultivation and molecular genetic tools. Microb Biotechnol 2024; 17:e14369. [PMID: 37991430 PMCID: PMC10832565 DOI: 10.1111/1751-7915.14369] [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: 08/14/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
The Halopseudomonas species, formerly classified as Pseudomonas pertucinogena lineage, form a unique phylogenetic branch within the Pseudomonads. Most strains have recently been isolated from challenging habitats including oil- or metal-polluted sites, deep sea, and intertidal zones, suggesting innate resilience to physical and chemical stresses. Despite their comparably small genomes, these bacteria synthesise several biomolecules with biotechnological potential and a role in the degradation of anthropogenic pollutants has been suggested for some Halopseudomonads. Until now, these bacteria are not readily amenable to existing cultivation and cloning methods. We addressed these limitations by selecting four Halopseudomonas strains of particular interest, namely H. aestusnigri, H. bauzanensis, H. litoralis, and H. oceani to establish microbiological and molecular genetic methods. We found that C4 -C10 dicarboxylic acids serve as viable carbon sources in both complex and mineral salt cultivation media. We also developed plasmid DNA transfer protocols and assessed vectors with different origins of replication and promoters inducible with isopropyl-β-d-thiogalactopyranoside, l-arabinose, and salicylate. Furthermore, we have demonstrated the simultaneous genomic integration of expression cassettes into one and two attTn7 integration sites. Our results provide a valuable toolbox for constructing robust chassis strains and highlight the biotechnological potential of Halopseudomonas strains.
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Affiliation(s)
- Luzie Kruse
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
| | - Anita Loeschcke
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
| | - Jan de Witt
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyJülichGermany
| | - Nick Wierckx
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyJülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyJülichGermany
| | - Stephan Thies
- Institute of Molecular Enzyme TechnologyHeinrich Heine UniversityDüsseldorfGermany
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6
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Li J, Li P, Liu Q, Li J, Qi H. Translation initiation consistency between in vivo and in vitro bacterial protein expression systems. Front Bioeng Biotechnol 2023; 11:1201580. [PMID: 37304134 PMCID: PMC10248181 DOI: 10.3389/fbioe.2023.1201580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/17/2023] [Indexed: 06/13/2023] Open
Abstract
Strict on-demand control of protein synthesis is a crucial aspect of synthetic biology. The 5'-terminal untranslated region (5'-UTR) is an essential bacterial genetic element that can be designed for the regulation of translation initiation. However, there is insufficient systematical data on the consistency of 5'-UTR function among various bacterial cells and in vitro protein synthesis systems, which is crucial for the standardization and modularization of genetic elements in synthetic biology. Here, more than 400 expression cassettes comprising the GFP gene under the regulation of various 5'-UTRs were systematically characterized to evaluate the protein translation consistency in the two popular Escherichia coli strains of JM109 and BL21, as well as an in vitro protein expression system based on cell lysate. In contrast to the very strong correlation between the two cellular systems, the consistency between in vivo and in vitro protein translation was lost, whereby both in vivo and in vitro translation evidently deviated from the estimation of the standard statistical thermodynamic model. Finally, we found that the absence of nucleotide C and complex secondary structure in the 5'-UTR significantly improve the efficiency of protein translation, both in vitro and in vivo.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Peixian Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Qian Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jinjin Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing, China
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7
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Elston KM, Phillips LE, Leonard SP, Young E, Holley JAC, Ahsanullah T, McReynolds B, Moran NA, Barrick JE. The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae. ISME COMMUNICATIONS 2023; 3:49. [PMID: 37225918 PMCID: PMC10209150 DOI: 10.1038/s43705-023-00255-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 04/18/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]
Abstract
Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli, a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying microbial ecology and host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.
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Affiliation(s)
- Katherine M Elston
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Laila E Phillips
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Eleanor Young
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jo-Anne C Holley
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Tasneem Ahsanullah
- Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Braydin McReynolds
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Nancy A Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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8
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Luelf UJ, Böhmer LM, Li S, Urlacher VB. Effect of chromosomal integration on catalytic performance of a multi-component P450 system in Escherichia coli. Biotechnol Bioeng 2023. [PMID: 37186287 DOI: 10.1002/bit.28404] [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: 02/07/2023] [Revised: 04/04/2023] [Accepted: 04/09/2023] [Indexed: 05/17/2023]
Abstract
Cytochromes P450 are useful biocatalysts in synthetic chemistry and important bio-bricks in synthetic biology. Almost all bacterial P450s require separate redox partners for their activity, which are often expressed in recombinant Escherichia coli using multiple plasmids. However, the application of CRISPR/Cas recombineering facilitated chromosomal integration of heterologous genes which enables more stable and tunable expression of multi-component P450 systems for whole-cell biotransformations. Herein, we compared three E. coli strains W3110, JM109, and BL21(DE3) harboring three heterologous genes encoding a P450 and two redox partners either on plasmids or after chromosomal integration in two genomic loci. Both loci proved to be reliable and comparable for the model regio- and stereoselective two-step oxidation of (S)-ketamine. Furthermore, the CRISPR/Cas-assisted integration of the T7 RNA polymerase gene enabled an easy extension of T7 expression strains. Higher titers of soluble active P450 were achieved in E. coli harboring a single chromosomal copy of the P450 gene compared to E. coli carrying a medium copy pET plasmid. In addition, improved expression of both redox partners after chromosomal integration resulted in up to 80% higher (S)-ketamine conversion and more than fourfold increase in total turnover numbers.
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Affiliation(s)
- U Joost Luelf
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisa M Böhmer
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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9
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Pasotti L, De Marchi D, Casanova M, Frusteri Chiacchiera A, Cusella De Angelis MG, Calvio C, Magni P. Design of a stable ethanologenic bacterial strain without heterologous plasmids and antibiotic resistance genes for efficient ethanol production from concentrated dairy waste. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:57. [PMID: 37005680 PMCID: PMC10067303 DOI: 10.1186/s13068-023-02298-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/03/2023] [Indexed: 04/04/2023]
Abstract
Engineering sustainable bioprocesses that convert abundant waste into fuels is pivotal for efficient production of renewable energy. We previously engineered an Escherichia coli strain for optimized bioethanol production from lactose-rich wastewater like concentrated whey permeate (CWP), a dairy effluent obtained from whey valorization processes. Although attractive fermentation performances were reached, significant improvements are required to eliminate recombinant plasmids, antibiotic resistances and inducible promoters, and increase ethanol tolerance. Here, we report a new strain with chromosomally integrated ethanologenic pathway under the control of a constitutive promoter, without recombinant plasmids and resistance genes. The strain showed extreme stability in 1-month subculturing, with CWP fermentation performances similar to the ethanologenic plasmid-bearing strain. We then investigated conditions enabling efficient ethanol production and sugar consumption by changing inoculum size and CWP concentration, revealing toxicity- and nutritional-related bottlenecks. The joint increase of ethanol tolerance, via adaptive evolution, and supplementation of small ammonium sulphate amounts (0.05% w/v) enabled a fermentation boost with 6.6% v/v ethanol titer, 1.2 g/L/h rate, 82.5% yield, and cell viability increased by three orders of magnitude. Our strain has attractive features for industrial settings and represents a relevant improvement in the existing ethanol production biotechnologies.
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Affiliation(s)
- Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.
- Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.
| | - Davide De Marchi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
- Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Michela Casanova
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
- Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Angelica Frusteri Chiacchiera
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
- Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Maria Gabriella Cusella De Angelis
- Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Via Forlanini 8, 27100, Pavia, Italy
| | - Cinzia Calvio
- Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
- Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
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10
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Chen Y, Zhu Y, Wang H, Chen R, Liu Y, Zhang W, Mu W. De novo biosynthesis of 2'-fucosyllactose in a metabolically engineered Escherichia coli using a novel ɑ1,2-fucosyltransferase from Azospirillum lipoferum. BIORESOURCE TECHNOLOGY 2023; 374:128818. [PMID: 36868425 DOI: 10.1016/j.biortech.2023.128818] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Human milk oligosaccharides are complex, indigestible oligosaccharides that provide ideal nutrition for infant development. Here, 2'-fucosyllactose was efficiently produced in Escherichia coli by using a biosynthetic pathway. For this, both lacZ and wcaJ (encoding β-galactosidase and UDP-glucose lipid carrier transferase, respectively) were deleted to enhance the 2'-fucosyllactose biosynthesis. To further enhance 2'-fucosyllactose production, SAMT from Azospirillum lipoferum was inserted into the chromosome of the engineered strain, and the native promoter was replaced with a strong constitutive promoter (PJ23119). The titer of 2'-fucosyllactose was increased to 8.03 g/L by introducing the regulators rcsA and rcsB into the recombinant strains. Compared to wbgL-based strains, only 2'-fucosyllactose was produced in SAMT-based strains without other by-products. Finally, the highest titer of 2'-fucosyllactose reached 112.56 g/L in a 5 L bioreactor by fed-batch cultivation, with a productivity of 1.10 g/L/h and a yield of 0.98 mol/mol lactose, indicating a strong potential in industrial production.
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Affiliation(s)
- Yihan Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hao Wang
- Bloomage Biotechnology Corp., Ltd., Jinan, Shandong 250010, People's Republic of China
| | - Roulin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yuanlin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
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11
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Song Z, Lin W, Duan X, Song L, Wang C, Yang H, Lu X, Ji X, Tian Y, Liu H. Increased Cordycepin Production in Yarrowia lipolytica Using Combinatorial Metabolic Engineering Strategies. ACS Synth Biol 2023; 12:780-787. [PMID: 36791366 DOI: 10.1021/acssynbio.2c00570] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
As the first nucleoside antibiotic discovered in fungi, cordycepin, with its various biological activities, has wide applications. At present, cordycepin is mainly obtained from the natural fruiting bodies of Cordyceps militaris. However, due to long production periods, low yields, and low extraction efficiency, harvesting cordycepin from natural C. militaris is not ideal, making it difficult to meet market demands. In this study, an engineered Yarrowia lipolytica YlCor-18 strain, constructed by combining metabolic engineering strategies, achieved efficient de novo cordycepin production from glucose. First, the cordycepin biosynthetic pathway derived from C. militaris was introduced into Y. lipolytica. Furthermore, metabolic engineering strategies including promoter, protein, adenosine triphosphate, and precursor engineering were combined to enhance the synthetic ability of engineered strains of cordycepin. Fermentation conditions were also optimized, after which, the production titer and yields of cordycepin in the engineered strain YlCor-18 under fed-batch fermentation were improved to 4362.54 mg/L and 213.85 mg/g, respectively, after 168 h. This study demonstrates the potential of Y. lipolytica as a cell factory for cordycepin synthesis, which will serve as the model for the green biomanufacturing of other nucleoside antibiotics using artificial cell factories.
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Affiliation(s)
- Zeqi Song
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Wenbo Lin
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Xiyu Duan
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Liping Song
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Hui Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Xiangyang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Xiaojun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Huhu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
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12
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Systematic metabolic engineering of Escherichia coli for the enhanced production of cinnamaldehyde. Metab Eng 2023; 76:63-74. [PMID: 36639020 DOI: 10.1016/j.ymben.2023.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Cinnamaldehyde (CAD) derived from cinnamon bark has received much attention for its potential as a nematicide and food additive. Previously, we have succeeded in developing an Escherichia coli strain (YHP05) capable of synthesizing cinnamaldehyde; however, the production titer (75 mg/L) was not sufficient for commercialization. Herein, to develop an economical and sustainable production bioprocess, we further engineered the YHP05 strain for non-auxotrophic, antibiotic-free, inducer-free hyperproduction of CAD using systematic metabolic engineering. First, the conversion of trans-cinnamic acid (t-CA) to CAD was improved by the co-expression of carboxylic acid reductase and phosphopantetheinyl transferase (PPTase) genes. Second, to prevent the spontaneous conversion of CAD to cinnamyl alcohol, 10 endogenous reductase and dehydrogenase genes were deleted. Third, all expression cassettes were integrated into the chromosomal DNA using an auto-inducible system for antibiotic- and inducer-free production. Subsequently, to facilitate CAD production, available pools of cofactors (NADPH, CoA, and ATP) were increased, and acetate pathways were deleted. With the final antibiotic-, plasmid-, and inducer-free strain (H-11MPmR), fed-batch cultivations combined with in situ product recovery (ISPR) were performed, and the production titer of CAD as high as 3.8 g/L could be achieved with 49.1 mg/L/h productivity, which is the highest CAD titer ever reported.
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13
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Singh B, Kumar A, Saini AK, Saini RV, Thakur R, Mohammed SA, Tuli HS, Gupta VK, Areeshi MY, Faidah H, Jalal NA, Haque S. Strengthening microbial cell factories for efficient production of bioactive molecules. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36809927 DOI: 10.1080/02648725.2023.2177039] [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: 08/11/2022] [Accepted: 01/21/2023] [Indexed: 02/24/2023]
Abstract
High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.
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Affiliation(s)
- Bharat Singh
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Ankit Kumar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gurugram, India
| | - Adesh Kumar Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Reena Vohra Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Rahul Thakur
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Shakeel A Mohammed
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Hardeep Singh Tuli
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Mohammed Y Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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14
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Elston KM, Phillips LE, Leonard SP, Young E, Holley JAC, Ahsanullah T, McReynolds B, Moran NA, Barrick JE. The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila -colonizing Orbaceae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528778. [PMID: 36824770 PMCID: PMC9949093 DOI: 10.1101/2023.02.15.528778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli , a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying new host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species. IMPORTANCE To fully understand how microbes have evolved to interact with their environments, one must be able to modify their genomes. However, it can be difficult and laborious to discover which genetic tools and approaches work for a new isolate. Bacteria from the recently described Orbaceae family are common in the microbiomes of insects. We developed the Pathfinder plasmid toolkit for testing the compatibility of different genetic parts with newly cultured bacteria. We demonstrate its utility by engineering Orbaceae strains isolated from flies to express fluorescent proteins and characterizing how they colonize the Drosophila melanogaster gut. Orbaceae are widespread in Drosophila in the wild but have not been included in laboratory studies examining how the gut microbiome affects fly nutrition, health, and longevity. Our work establishes a path for genetic studies aimed at understanding and altering interactions between these and other newly isolated bacteria and their hosts.
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Affiliation(s)
- Katherine M. Elston
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Laila E. Phillips
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sean P. Leonard
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Eleanor Young
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jo-anne C. Holley
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tasneem Ahsanullah
- Freshman Research Initiative, The University of Texas at Austin, Austin, TX 78712, USA
| | - Braydin McReynolds
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nancy A. Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E. Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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15
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Ting WW, Ng IS. Effective 5-aminolevulinic acid production via T7 RNA polymerase and RuBisCO equipped Escherichia coli W3110. Biotechnol Bioeng 2023; 120:583-592. [PMID: 36302745 DOI: 10.1002/bit.28273] [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: 09/09/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 01/13/2023]
Abstract
Chromosome-based engineering is a superior approach for gene integration generating a stable and robust chassis. Therefore, an effective amplifier, T7 RNA polymerase (T7RNAP) from bacteriophage, has been incorporated into Escherichia coli W3110 by site-specific integration. Herein, we performed the 5-aminolevulinic acid (5-ALA) production in four T7RNAP-equipped W3110 strains using recombinant 5-aminolevulinic synthase and further explored the metabolic difference in best strain. The fastest glucose consumption resulted in the highest biomass and the 5-ALA production reached to 5.5 g/L; thus, the least by-product of acetate was shown in RH strain in which T7RNAP was inserted at HK022 phage attack site. Overexpression of phosphoenolpyruvate (PEP) carboxylase would pull PEP to oxaloacetic acid in tricarboxylic acid cycle, leading to energy conservation and even no acetate production, thus, 6.53 g/L of 5-ALA was achieved. Amino acid utilization in RH deciphered the major metabolic flux in α-ketoglutaric acid dominating 5-ALA production. Finally, the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and phosphoribulokinase were expressed for carbon dioxide recycling; a robust and efficient chassis toward low-carbon assimilation and high-level of 5-ALA production up to 11.2 g/L in fed-batch fermentation was established.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
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16
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Xiao J, Guo S, Shi X. Metabolic engineering of Escherichia coli for the production of (R)-α-lipoic acid. Biotechnol Lett 2023; 45:273-286. [PMID: 36586051 DOI: 10.1007/s10529-022-03341-z] [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: 09/01/2022] [Revised: 11/08/2022] [Accepted: 12/16/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To increase the production of (R)-α-lipoic acid directly from octanoic acid using engineered Escherichia coli with the regeneration of S-adenosylmethionine. RESULTS The biosynthesis of (R)-α-lipoic acid (LA) in E. coli BL21(DE3) is improved by co-expression of lipoate-protein ligase A (LplA) from E. coli MG1655 and lipoate synthase (LipA) from Vibrio vulnificus. The engineered strain produces 20.99 µg l-1 of LA in shake flask cultures. The titers of LA are increased to 169.28 µg l-1 after the optimization of the medium components and fermentation conditions. We find that the [4Fe-4S] cluster is important for the activity of LipA and co-expression of iscSUA promotes the regeneration of the [4Fe-4S] cluster and leads to the highest LA titer of 589.30 µg l-1. CONCLUSION The method described here can be widely applied for the biosynthesis of (R)-α-lipoic acid and other metabolites.
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Affiliation(s)
- Jianbin Xiao
- College of Biological Science and Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China
| | - Shaobin Guo
- College of Biological Science and Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China.
| | - Xian'ai Shi
- College of Biological Science and Engineering, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China.,Fujian Key Lab of Medical Instrument and Biopharmaceutical Technology, Fuzhou University, No. 2 Xueyuan Road, Fuzhou, 350108, China
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17
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Schiffer CJ, Grätz C, Pfaffl MW, Vogel RF, Ehrmann MA. Characterization of the Staphylococcus xylosus methylome reveals a new variant of type I restriction modification system in staphylococci. Front Microbiol 2023; 14:946189. [PMID: 36970683 PMCID: PMC10030836 DOI: 10.3389/fmicb.2023.946189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restriction modification (RM) systems are known to provide a strong barrier to the exchange of DNA between and within bacterial species. Likewise, DNA methylation is known to have an important function in bacterial epigenetics regulating essential pathways such as DNA replication and the phase variable expression of prokaryotic phenotypes. To date, research on staphylococcal DNA methylation focused mainly on the two species Staphylococcus aureus and S. epidermidis. Less is known about other members of the genus such as S. xylosus, a coagulase-negative commensal of mammalian skin. The species is commonly used as starter organism in food fermentations but is also increasingly considered to have an as yet elusive function in bovine mastitis infections. We analyzed the methylomes of 14 S. xylosus strains using single-molecular, real-time (SMRT) sequencing. Subsequent in silico sequence analysis allowed identification of the RM systems and assignment of the respective enzymes to the discovered modification patterns. Hereby the presence of type I, II, III and IV RM systems in varying numbers and combinations among the different strains was revealed, clearly distinguishing the species from what is known for other members of the genus so far. In addition, the study characterizes a newly discovered type I RM system, encoded by S. xylosus but also by a variety of other staphylococcal species, with a hitherto unknown gene arrangement that involves two specificity units instead of one (hsdRSMS). Expression of different versions of the operon in E. coli showed proper base modification only when genes encoding both hsdS subunits were present. This study provides new insights into the general understanding of the versatility and function of RM systems as well as the distribution and variations in the genus Staphylococcus.
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Affiliation(s)
- Carolin J. Schiffer
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- *Correspondence: Carolin J. Schiffer,
| | - Christian Grätz
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael W. Pfaffl
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rudi F. Vogel
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthias A. Ehrmann
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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18
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Lee JA, Kim HU, Na JG, Ko YS, Cho JS, Lee SY. Factors affecting the competitiveness of bacterial fermentation. Trends Biotechnol 2022; 41:798-816. [PMID: 36357213 DOI: 10.1016/j.tibtech.2022.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
Abstract
Sustainable production of chemicals and materials from renewable non-food biomass using biorefineries has become increasingly important in an effort toward the vision of 'net zero carbon' that has recently been pledged by countries around the world. Systems metabolic engineering has allowed the efficient development of microbial strains overproducing an increasing number of chemicals and materials, some of which have been translated to industrial-scale production. Fermentation is one of the key processes determining the overall economics of bioprocesses, but has recently been attracting less research attention. In this Review, we revisit and discuss factors affecting the competitiveness of bacterial fermentation in connection to strain development by systems metabolic engineering. Future perspectives for developing efficient fermentation processes are also discussed.
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Affiliation(s)
- Jong An Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea; Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Republic of Korea
| | - Yoo-Sung Ko
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Jae Sung Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea.
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19
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Gupta M, Wong M, Jawed K, Gedeon K, Barrett H, Bassalo M, Morrison C, Eqbal D, Yazdani SS, Gill RT, Huang J, Douaisi M, Dordick J, Belfort G, Koffas MA. Isobutanol production by combined in vivo and in vitro metabolic engineering. Metab Eng Commun 2022; 15:e00210. [PMID: 36325486 PMCID: PMC9619177 DOI: 10.1016/j.mec.2022.e00210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/03/2022] [Accepted: 10/16/2022] [Indexed: 12/12/2022] Open
Abstract
The production of the biofuel, isobutanol, in E. coli faces limitations due to alcohol toxicity, product inhibition, product recovery, and long-term industrial feasibility. Here we demonstrate an approach of combining both in vivo with in vitro metabolic engineering to produce isobutanol. The in vivo production of α-ketoisovalerate (KIV) was conducted through CRISPR mediated integration of the KIV pathway in bicistronic design (BCD) in E. coli and inhibition of competitive valine pathway using CRISPRi technology. The subsequent in vitro conversion to isobutanol was carried out with engineered enzymes for 2-ketoacid decarboxylase (KIVD) and alcohol dehydrogenase (ADH). For the in vivo production of KIV and subsequent in vitro production of isobutanol, this two-step serial approach resulted in yields of 56% and 93%, productivities of 0.62 and 0.074 g L-1 h-1, and titers of 5.6 and 1.78 g L-1, respectively. Thus, this combined biosynthetic system can be used as a modular approach for producing important metabolites, like isobutanol, without the limitations associated with in vivo production using a consolidated bioprocess.
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Affiliation(s)
- Mamta Gupta
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Department of Botany and Environmental Studies, DAV University, Jalandhar, 144 001, Punjab, India
| | - Matthew Wong
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Kamran Jawed
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,DBT-ICGEB Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kamil Gedeon
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Hannah Barrett
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Marcelo Bassalo
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Clifford Morrison
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Danish Eqbal
- DBT-ICGEB Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Syed Shams Yazdani
- DBT-ICGEB Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ryan T. Gill
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Jiaqi Huang
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Marc Douaisi
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Jonathan Dordick
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Mattheos A.G. Koffas
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Corresponding author. Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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20
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Effendi SSW, Ng IS. Reprogramming T7RNA Polymerase in Escherichia coli Nissle 1917 under Specific Lac Operon for Efficient p-Coumaric Acid Production. ACS Synth Biol 2022; 11:3471-3481. [PMID: 36087056 DOI: 10.1021/acssynbio.2c00363] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Lac operon is the standard regulator used to control the orthogonality of T7RNA polymerase (T7RNAP) and T7 promoter inEscherichia coli BL21(DE3) strain for protein expression. However,E. coliNissle 1917 (EcN), the unique probiotic strain, has seldom been precisely adapted to the T7 system. Herein, we applied bioinformatics analysis on Lac operon from different strains, and it was observed that a weak promoter for LacI repressor existed in EcN. Furthermore, X-gal assay revealed a strong expression of lacZ in EcN. We demonstrated that Lac operon significantly affected the protein expression in the two T7-derived EcN, in which T7RNAP was integrated at lambda (ET7L) and HK022 (ET7H), respectively. Different combinations of replication origin, chaperonin GroELS, inducer, and medium were explored to fine-tune the best strain with tyrosine ammonia-lyase (TAL) for p-coumaric acid (pCA) production, which is one of the essential bioactive compounds for human health. Finally, the highest pCA conversion of 78.8% was achieved using RRtL (plasmid form) under the optimum condition, and a 51.5% conversion was obtained with L::Rt strain which has integrated T7-RtTAL at HK022 of ET7L in the simulated gut environment. The appropriate reprogramming of T7RNAP expedites EcN as an effective and promising cell factory for live bacterial therapeutics in the future.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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21
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Bayer C, Sepulchro AGV, Rennig M, Nørholm MH. Efficient Bacterial Genome Engineering throughout the Central Dogma Using the Dual-Selection Marker tetAOPT. ACS Synth Biol 2022; 11:3440-3450. [PMID: 36206506 PMCID: PMC9594774 DOI: 10.1021/acssynbio.2c00345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Indexed: 01/24/2023]
Abstract
Engineering of bacterial genomes is a fundamental craft in contemporary biotechnology. The ability to precisely edit chromosomes allows for the development of cells with specific phenotypes for metabolic engineering and for the creation of minimized genomes. Genetic tools are needed to select for cells that underwent editing, and dual-selection markers that enable both positive and negative selection are highly useful. Here, we present an optimized and easy-to-use version of the tetA dual-selection marker and demonstrate how this tetAOPT can be used efficiently to engineer at different stages of the central dogma of molecular biology. On the DNA level, tetAOPT can be used to create scarless knockouts across the Escherichia coli genome with efficiency above 90%, whereas recombinant gene integrations can be achieved with approximately 50% efficiency. On the RNA and protein level, we show that tetAOPT enables advanced genome engineering of both gene translation and transcription by introducing sequence variation in the translation initiation region or by exchanging promoters. Finally, we demonstrate the use of tetAOPT for genome engineering in the industrially relevant probiotic strain E. coli Nissle.
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Affiliation(s)
- Carolyn
N. Bayer
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ana G. V. Sepulchro
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maja Rennig
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Morten H.H. Nørholm
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
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Scholz SA, Lindeboom CD, Freddolino PL. Genetic context effects can override canonical cis regulatory elements in Escherichia coli. Nucleic Acids Res 2022; 50:10360-10375. [PMID: 36134716 PMCID: PMC9561378 DOI: 10.1093/nar/gkac787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 09/02/2022] [Indexed: 11/12/2022] Open
Abstract
Recent experiments have shown that in addition to control by cis regulatory elements, the local chromosomal context of a gene also has a profound impact on its transcription. Although this chromosome-position dependent expression variation has been empirically mapped at high-resolution, the underlying causes of the variation have not been elucidated. Here, we demonstrate that 1 kb of flanking, non-coding synthetic sequences with a low frequency of guanosine and cytosine (GC) can dramatically reduce reporter expression compared to neutral and high GC-content flanks in Escherichia coli. Natural and artificial genetic context can have a similarly strong effect on reporter expression, regardless of cell growth phase or medium. Despite the strong reduction in the maximal expression level from the fully-induced reporter, low GC synthetic flanks do not affect the time required to reach the maximal expression level after induction. Overall, we demonstrate key determinants of transcriptional propensity that appear to act as tunable modulators of transcription, independent of regulatory sequences such as the promoter. These findings provide insight into the regulation of naturally occurring genes and an independent control for optimizing expression of synthetic biology constructs.
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Affiliation(s)
- Scott A Scholz
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chase D Lindeboom
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
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Moschner C, Wedd C, Bakshi S. The context matrix: Navigating biological complexity for advanced biodesign. Front Bioeng Biotechnol 2022; 10:954707. [PMID: 36082163 PMCID: PMC9445834 DOI: 10.3389/fbioe.2022.954707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/29/2022] [Indexed: 12/05/2022] Open
Abstract
Synthetic biology offers many solutions in healthcare, production, sensing and agriculture. However, the ability to rationally engineer synthetic biosystems with predictable and robust functionality remains a challenge. A major reason is the complex interplay between the synthetic genetic construct, its host, and the environment. Each of these contexts contains a number of input factors which together can create unpredictable behaviours in the engineered biosystem. It has become apparent that for the accurate assessment of these contextual effects a more holistic approach to design and characterisation is required. In this perspective article, we present the context matrix, a conceptual framework to categorise and explore these contexts and their net effect on the designed synthetic biosystem. We propose the use and community-development of the context matrix as an aid for experimental design that simplifies navigation through the complex design space in synthetic biology.
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24
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Liu Y, Zhu Y, Wan L, Chen R, Zhang W, Mu W. High-Level De Novo Biosynthesis of 2'-Fucosyllactose by Metabolically Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9017-9025. [PMID: 35834320 DOI: 10.1021/acs.jafc.2c02484] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
2'-Fucosyllactose (2'-FL) is the most abundant oligosaccharide in human milk. In this study, a highly efficient biosynthetic route for 2'-FL production was designed via the de novo pathway of GDP-l-fucose using engineered Escherichia coli BL21(DE3). Specifically, plasmid-based strains with previously deleted lacZ and wcaJ were further reconstructed by introducing de novo pathway genes and α1,2-fucosyltransferase-encoding wbgL to realize 2'-FL synthesis. The 2'-FL titer was enhanced to 3.92 g/L by further introducing rcsA and rcsB. Subsequently, the additional wbgL expression cassette was chromosomally integrated into recA locus to strengthen fucosylation reaction and a strong constitutive promoter (PJ23119) was used to replace the original promoters of manC-manB and gmd-wcaG to improve 2'-FL synthesis. The maximal 2'-FL titer reached 9.06 and 79.23 g/L in shake-flask and fed-batch cultivation, respectively. The 2'-FL productivity reached 1.45 g/L/h, showing remarkable production potential in large-scale industrial application.
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Affiliation(s)
- Yuanlin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Roulin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
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25
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Zhang J, Zhu Y, Zhang W, Mu W. Efficient Production of a Functional Human Milk Oligosaccharide 3'-Sialyllactose in Genetically Engineered Escherichia coli. ACS Synth Biol 2022; 11:2837-2845. [PMID: 35802806 DOI: 10.1021/acssynbio.2c00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
3'-Sialyllactose (3'-SL) is one of the most important and simplest sialylated human milk oligosaccharides. In this study, a plasmid-based pathway optimization along with chromosomal integration strategies was applied for 3'-SL production. Specifically, the precursor CMP-Neu5Ac synthesis pathway genes and α2,3-sialyltransferase-encoding gene were introduced into Escherichia coli BL21(DE3)ΔlacZ to realize 3'-SL synthesis. Genes nanA and nanK involved in Neu5Ac catabolism were further deleted to reduce the metabolic flux of competitive pathway. Several α2,3-sialyltransferases from different species were selected to evaluate the sialylation effect. The precursor pools were balanced and improved by optimizing key enzyme expression involved in the UDP-GlcNAc and CMP-Neu5Ac synthesis pathway. Finally, an additional α2,3-sialyltransferase expression cassette was integrated into chromosome to maximize 3'-SL synthesis, and 4.5 g/L extracellular 3'-SL was produced at a shake-flask level. The extracellular 3'-SL concentration was raised to 23.1 g/L in a 5 L bioreactor fermentation, which represents the highest extracellular value ever reported.
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Affiliation(s)
- Jiameng Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, People's Republic of China
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26
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Lauer I, Philipps G, Jennewein S. Metabolic engineering of Clostridium ljungdahlii for the production of hexanol and butanol from CO 2 and H 2. Microb Cell Fact 2022; 21:85. [PMID: 35568911 PMCID: PMC9107641 DOI: 10.1186/s12934-022-01802-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The replacement of fossil fuels and petrochemicals with sustainable alternatives is necessary to mitigate the effects of climate change and also to counteract diminishing fossil resources. Acetogenic microorganisms such as Clostridium spp. are promising sources of fuels and basic chemical precursors because they efficiently utilize CO and CO2 as carbon source. However the conversion into high titers of butanol and hexanol is challenging. RESULTS Using a metabolic engineering approach we transferred a 17.9-kb gene cluster via conjugation, containing 13 genes from C. kluyveri and C. acetobutylicum for butanol and hexanol biosynthesis, into C. ljungdahlii. Plasmid-based expression resulted in 1075 mg L-1 butanol and 133 mg L-1 hexanol from fructose in complex medium, and 174 mg L-1 butanol and 15 mg L-1 hexanol from gaseous substrate (20% CO2 and 80% H2) in minimal medium. Product formation was increased by the genomic integration of the heterologous gene cluster. We confirmed the expression of all 13 enzymes by targeted proteomics and identified potential rate-limiting steps. Then, we removed the first-round selection marker using CRISPR/Cas9 and integrated an additional 7.8 kb gene cluster comprising 6 genes from C. carboxidivorans. This led to a significant increase in the hexanol titer (251 mg L-1) at the expense of butanol (158 mg L-1), when grown on CO2 and H2 in serum bottles. Fermentation of this strain at 2-L scale produced 109 mg L-1 butanol and 393 mg L-1 hexanol. CONCLUSIONS We thus confirmed the function of the butanol/hexanol biosynthesis genes and achieved hexanol biosynthesis in the syngas-fermenting species C. ljungdahlii for the first time, reaching the levels produced naturally by C. carboxidivorans. The genomic integration strain produced hexanol without selection and is therefore suitable for continuous fermentation processes.
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Affiliation(s)
- Ira Lauer
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany
| | - Gabriele Philipps
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany
| | - Stefan Jennewein
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, 52074, Aachen, Germany.
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27
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Kay EJ, Mauri M, Willcocks SJ, Scott TA, Cuccui J, Wren BW. Engineering a suite of E. coli strains for enhanced expression of bacterial polysaccharides and glycoconjugate vaccines. Microb Cell Fact 2022; 21:66. [PMID: 35449016 PMCID: PMC9026721 DOI: 10.1186/s12934-022-01792-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycoengineering, in the biotechnology workhorse bacterium, Escherichia coli, is a rapidly evolving field, particularly for the production of glycoconjugate vaccine candidates (bioconjugation). Efficient production of glycoconjugates requires the coordinated expression within the bacterial cell of three components: a carrier protein, a glycan antigen and a coupling enzyme, in a timely fashion. Thus, the choice of a suitable E. coli host cell is of paramount importance. Microbial chassis engineering has long been used to improve yields of chemicals and biopolymers, but its application to vaccine production is sparse. RESULTS In this study we have engineered a family of 11 E. coli strains by the removal and/or addition of components rationally selected for enhanced expression of Streptococcus pneumoniae capsular polysaccharides with the scope of increasing yield of pneumococcal conjugate vaccines. Importantly, all strains express a detoxified version of endotoxin, a concerning contaminant of therapeutics produced in bacterial cells. The genomic background of each strain was altered using CRISPR in an iterative fashion to generate strains without antibiotic markers or scar sequences. CONCLUSIONS Amongst the 11 modified strains generated in this study, E. coli Falcon, Peregrine and Sparrowhawk all showed increased production of S. pneumoniae serotype 4 capsule. Eagle (a strain without enterobacterial common antigen, containing a GalNAc epimerase and PglB expressed from the chromosome) and Sparrowhawk (a strain without enterobacterial common antigen, O-antigen ligase and chain length determinant, containing a GalNAc epimerase and chain length regulators from Streptococcus pneumoniae) respectively produced an AcrA-SP4 conjugate with 4 × and 14 × more glycan than that produced in the base strain, W3110. Beyond their application to the production of pneumococcal vaccine candidates, the bank of 11 new strains will be an invaluable resource for the glycoengineering community.
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Affiliation(s)
- Emily J Kay
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Marta Mauri
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Sam J Willcocks
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Timothy A Scott
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jon Cuccui
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
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28
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Zhu HZ, Jiang S, Wu JJ, Zhou XR, Liu PY, Huang FH, Wan X. Production of High Levels of 3 S,3' S-Astaxanthin in Yarrowia lipolytica via Iterative Metabolic Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2673-2683. [PMID: 35191700 DOI: 10.1021/acs.jafc.1c08072] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Astaxanthin is a highly value-added keto-carotenoid compound. The astaxanthin 3S,3'S-isomer is more desirable for food additives, cosmetics, and pharmaceuticals due to health concerns about chemically synthesized counterparts with a mixture of three isomers. Biosynthesis of 3S,3'S-astaxanthin suffers from limited content and productivity. We engineered Yarrowia lipolytica to produce high levels of 3S,3'S-astaxanthin. We first assessed various β-carotene ketolases (CrtW) and β-carotene hydroxylases (CrtZ) from two algae and a plant. HpCrtW and HpCrtZ from Haematococcus pluvialis exhibited the strongest activity in converting β-carotene into astaxanthin in Y. lipolytica. We then fine-tuned the HpCrtW and HpCrtZ transcriptional expression by increasing the rounds of gene integration into the genome and applied a modular enzyme assembly of HpCrtW and HpCrtZ simultaneously. Next, we rescued leucine biosynthesis in the engineered Y. lipolytica, leading to a five-fold increase in biomass. The astaxanthin production achieved from these strategies was 3.3 g/L or 41.3 mg/g dry cell weight under fed-batch conditions, which is the highest level reported in microbial chassis to date. This study provides the potential for industrial production of 3S,3'S-astaxanthin, and this strategy empowers us to build a sustainable biorefinery platform for generating other value-added carotenoids in the future.
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Affiliation(s)
- Hang-Zhi Zhu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Shan Jiang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun-Jie Wu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | | | - Peng-Yang Liu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Feng-Hong Huang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
- Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan 430062, China
| | - Xia Wan
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
- Key Laboratory of Oilseeds Processing, Ministry of Agriculture, Wuhan 430062, China
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29
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Upstream Activation Sequence Can Function as an Insulator for Chromosomal Regulation of Heterologous Pathways Against Position Effects in Saccharomyces cerevisiae. Appl Biochem Biotechnol 2022; 194:1841-1849. [DOI: 10.1007/s12010-021-03654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022]
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30
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Terra VS, Mauri M, Sannasiddappa TH, Smith AA, Stevens MP, Grant AJ, Wren BW, Cuccui J. PglB function and glycosylation efficiency is temperature dependent when the pgl locus is integrated in the Escherichia coli chromosome. Microb Cell Fact 2022; 21:6. [PMID: 34986868 PMCID: PMC8728485 DOI: 10.1186/s12934-021-01728-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background Campylobacter is an animal and zoonotic pathogen of global importance, and a pressing need exists for effective vaccines, including those that make use of conserved polysaccharide antigens. To this end, we adapted Protein Glycan Coupling Technology (PGCT) to develop a versatile Escherichia coli strain capable of generating multiple glycoconjugate vaccine candidates against Campylobacter jejuni. Results We generated a glycoengineering E. coli strain containing the conserved C. jejuni heptasaccharide coding region integrated in its chromosome as a model glycan. This methodology confers three advantages: (i) reduction of plasmids and antibiotic markers used for PGCT, (ii) swift generation of many glycan-protein combinations and consequent rapid identification of the most antigenic proteins or peptides, and (iii) increased genetic stability of the polysaccharide coding-region. In this study, by using the model glycan expressing strain, we were able to test proteins from C. jejuni, Pseudomonas aeruginosa (both Gram-negative), and Clostridium perfringens (Gram-positive) as acceptors. Using this pgl integrant E. coli strain, four glycoconjugates were readily generated. Two glycoconjugates, where both protein and glycan are from C. jejuni (double-hit vaccines), and two glycoconjugates, where the glycan antigen is conjugated to a detoxified toxin from a different pathogen (single-hit vaccines). Because the downstream application of Live Attenuated Vaccine Strains (LAVS) against C. jejuni is to be used in poultry, which have a higher body temperature of 42 °C, we investigated the effect of temperature on protein expression and glycosylation in the E. coli pgl integrant strain. Conclusions We determined that glycosylation is temperature dependent and that for the combination of heptasaccharide and carriers used in this study, the level of PglB available for glycosylation is a step limiting factor in the glycosylation reaction. We also demonstrated that temperature affects the ability of PglB to glycosylate its substrates in an in vitro glycosylation assay independent of its transcriptional level. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01728-7.
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Affiliation(s)
- Vanessa S Terra
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK
| | - Marta Mauri
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK
| | - Thippeswamy H Sannasiddappa
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Alexander A Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Mark P Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Brendan W Wren
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK.
| | - Jon Cuccui
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E7HT, UK.
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31
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Methods for the Development of Recombinant Microorganisms for the Production of Natural Products. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2396:1-17. [PMID: 34786671 DOI: 10.1007/978-1-0716-1822-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Metabolic engineering strives to develop microbial strains that are capable of producing a target chemical in a biological organism. There are still many challenges to overcome in order to achieve titers, yields, and productivities necessary for industrial production. The use of recombinant microorganisms to meet these needs is the next step for metabolic engineers. In this chapter, we aim to provide insight on both the applications of metabolic engineering for natural product biosynthesis as well as optimization methods.
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32
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Wang ZK, Gong JS, Qin J, Li H, Lu ZM, Shi JS, Xu ZH. Improving the Intensity of Integrated Expression for Microbial Production. ACS Synth Biol 2021; 10:2796-2807. [PMID: 34738786 DOI: 10.1021/acssynbio.1c00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chromosomal integration of exogenous genes is preferred for industrially related fermentation, as plasmid-mediated fermentation leads to extra metabolic burden and genetic instability. Moreover, with the development and advancement of genome engineering and gene editing technologies, inserting genes into chromosomes has become more convenient; integration expression is extensively utilized in microorganisms for industrial bioproduction and expected to become the trend of recombinant protein expression. However, in actual research and application, it is important to enhance the expression of heterologous genes at the host genome level. Herein, we summarized the basic principles and characteristics of genomic integration; furthermore, we highlighted strategies to improve the expression of chromosomal integration of genes and pathways in host strains from three aspects, including chassis cell optimization, regulation of expression elements in gene expression cassettes, optimization of gene dose level and integration sites on chromosomes. Moreover, we reviewed and summarized the relevant studies on the application of integrated expression in the exploration of gene function and the various types of industrial microorganism production. Consequently, this review would serve as a reference for the better application of integrated expression.
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Affiliation(s)
- Zi-Kai Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Jiufu Qin
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Hui Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Zhen-Ming Lu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, PR China
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33
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Cen YK, Gong H, Xue YP, Zheng YG. Biosynthesis of l-phosphinothricin with enzymes from chromosomal integrated expression in E. coli. 3 Biotech 2021; 11:477. [PMID: 34777934 DOI: 10.1007/s13205-021-03037-7] [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: 05/24/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphinothricin (PPT) is one of the most prevalently using herbicides. The commercial phosphinothricin products are generally in the form of a racemic mixture, of which only the l-phosphinothricin (L-PPT) gives herbicidal function. Synthesis of optically pure L-PPT by deracemization of D/L-PPT is a promising way to cut down the environmental burden and manufacturing cost. To convert D/L-PPT to L-PPT, we expressed the catalytic enzymes by genomic integration in E. coli. The whole production was implemented in two steps in one pot using four catalytic enzymes, namely d-amino acid oxidase, catalase, glutamate dehydrogenase, and glucose dehydrogenase. Finally, after a series of process optimization, the results showed that with our system the overall L-PPT yield reached 86%. Our study demonstrated a new strategy for L-PPT synthesis, based on enzymes from chromosomal integrated expression, which does not depend on antibiotic selection, and shows a high potential for future industrial application.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Huo Gong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
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Bayer CN, Rennig M, Ehrmann AK, Nørholm MHH. A standardized genome architecture for bacterial synthetic biology (SEGA). Nat Commun 2021; 12:5876. [PMID: 34620865 PMCID: PMC8497626 DOI: 10.1038/s41467-021-26155-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/21/2021] [Indexed: 02/08/2023] Open
Abstract
Chromosomal recombinant gene expression offers a number of advantages over plasmid-based synthetic biology. However, the methods applied for bacterial genome engineering are still challenging and far from being standardized. Here, in an attempt to realize the simplest recombinant genome technology imaginable and facilitate the transition from recombinant plasmids to genomes, we create a simplistic methodology and a comprehensive strain collection called the Standardized Genome Architecture (SEGA). In its simplest form, SEGA enables genome engineering by combining only two reagents: a DNA fragment that can be ordered from a commercial vendor and a stock solution of bacterial cells followed by incubation on agar plates. Recombinant genomes are identified by visual inspection using green-white colony screening akin to classical blue-white screening for recombinant plasmids. The modular nature of SEGA allows precise multi-level control of transcriptional, translational, and post-translational regulation. The SEGA architecture simultaneously supports increased standardization of genetic designs and a broad application range by utilizing well-characterized parts optimized for robust performance in the context of the bacterial genome. Ultimately, its adaption and expansion by the scientific community should improve predictability and comparability of experimental outcomes across different laboratories.
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Affiliation(s)
- Carolyn N Bayer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Maja Rennig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Anja K Ehrmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Mauri M, Sannasiddappa TH, Vohra P, Corona-Torres R, Smith AA, Chintoan-Uta C, Bremner A, Terra VS, Abouelhadid S, Stevens MP, Grant AJ, Cuccui J, Wren BW. Multivalent poultry vaccine development using Protein Glycan Coupling Technology. Microb Cell Fact 2021; 20:193. [PMID: 34600535 PMCID: PMC8487346 DOI: 10.1186/s12934-021-01682-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Poultry is the world's most popular animal-based food and global production has tripled in the past 20 years alone. Low-cost vaccines that can be combined to protect poultry against multiple infections are a current global imperative. Glycoconjugate vaccines, which consist of an immunogenic protein covalently coupled to glycan antigens of the targeted pathogen, have a proven track record in human vaccinology, but have yet to be used for livestock due to prohibitively high manufacturing costs. To overcome this, we use Protein Glycan Coupling Technology (PGCT), which enables the production of glycoconjugates in bacterial cells at considerably reduced costs, to generate a candidate glycan-based live vaccine intended to simultaneously protect against Campylobacter jejuni, avian pathogenic Escherichia coli (APEC) and Clostridium perfringens. Campylobacter is the most common cause of food poisoning, whereas colibacillosis and necrotic enteritis are widespread and devastating infectious diseases in poultry. RESULTS We demonstrate the functional transfer of C. jejuni protein glycosylation (pgl) locus into the genome of APEC χ7122 serotype O78:H9. The integration caused mild attenuation of the χ7122 strain following oral inoculation of chickens without impairing its ability to colonise the respiratory tract. We exploit the χ7122 pgl integrant as bacterial vectors delivering a glycoprotein decorated with the C. jejuni heptasaccharide glycan antigen. To this end we engineered χ7122 pgl to express glycosylated NetB toxoid from C. perfringens and tested its ability to reduce caecal colonisation of chickens by C. jejuni and protect against intra-air sac challenge with the homologous APEC strain. CONCLUSIONS We generated a candidate glycan-based multivalent live vaccine with the potential to induce protection against key avian and zoonotic pathogens (C. jejuni, APEC, C. perfringens). The live vaccine failed to significantly reduce Campylobacter colonisation under the conditions tested but was protective against homologous APEC challenge. Nevertheless, we present a strategy towards the production of low-cost "live-attenuated multivalent vaccine factories" with the ability to express glycoconjugates in poultry.
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Affiliation(s)
- Marta Mauri
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Thippeswamy H Sannasiddappa
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Prerna Vohra
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Ricardo Corona-Torres
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Alexander A Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK
| | - Cosmin Chintoan-Uta
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Abi Bremner
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK
| | - Vanessa S Terra
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Sherif Abouelhadid
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Mark P Stevens
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh, EH25 9RG, UK.
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, Cambridgeshire, UK.
| | - Jon Cuccui
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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36
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The spatial position effect: synthetic biology enters the era of 3D genomics. Trends Biotechnol 2021; 40:539-548. [PMID: 34607694 DOI: 10.1016/j.tibtech.2021.09.001] [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: 07/23/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022]
Abstract
Microbial cell factories are critical to achieving green biomanufacturing. A position effect occurs when a synthetic gene circuit is expressed from different positions in the chassis strain genome. Here, we propose the concept of the 'spatial position effect,' which uses technologies in 3D genomics to reveal the spatial structure characteristics of the 3D genome of the chassis. On this basis, we propose to rationally design the integration sites of synthetic gene circuits, use reporter genes for preliminary screening, and integrate synthetic gene circuits into promising sites for further experiments. This approach can produce stable and efficient chassis strains for green biomanufacturing. The proposed spatial position effect brings synthetic biology into the era of 3D genomics.
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Engineering of Escherichia coli for the Economic Production L-phenylalanine in Large-scale Bioreactor. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0313-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Wong M, Badri A, Gasparis C, Belfort G, Koffas M. Modular optimization in metabolic engineering. Crit Rev Biochem Mol Biol 2021; 56:587-602. [PMID: 34180323 DOI: 10.1080/10409238.2021.1937928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
There is an increasing demand for bioproducts produced by metabolically engineered microbes, such as pharmaceuticals, biofuels, biochemicals and other high value compounds. In order to meet this demand, modular optimization, the optimizing of subsections instead of the whole system, has been adopted to engineer cells to overproduce products. Research into modularity has focused on traditional approaches such as DNA, RNA, and protein-level modularity of intercellular machinery, by optimizing metabolic pathways for enhanced production. While research into these traditional approaches continues, limitations such as scale-up and time cost hold them back from wider use, while at the same time there is a shift to more novel methods, such as moving from episomal expression to chromosomal integration. Recently, nontraditional approaches such as co-culture systems and cell-free metabolic engineering (CFME) are being investigated for modular optimization. Co-culture modularity looks to optimally divide the metabolic burden between different hosts. CFME seeks to modularly optimize metabolic pathways in vitro, both speeding up the design of such systems and eliminating the issues associated with live hosts. In this review we will examine both traditional and nontraditional approaches for modular optimization, examining recent developments and discussing issues and emerging solutions for future research in metabolic engineering.
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Affiliation(s)
- Matthew Wong
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Abinaya Badri
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Christopher Gasparis
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Mattheos Koffas
- Howard P. Isermann Department of Chemical and Biological Engineering and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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Han JH, Jung ST, Oh MK. Improved Yield of Recombinant Protein via Flagella Regulator Deletion in Escherichia coli. Front Microbiol 2021; 12:655072. [PMID: 33790884 PMCID: PMC8005581 DOI: 10.3389/fmicb.2021.655072] [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: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Protein production requires a significant amount of intracellular energy. Eliminating the flagella has been proposed to help Escherichia coli improve protein production by reducing energy consumption. In this study, the gene encoding a subunit of FlhC, a master regulator of flagella assembly, was deleted to reduce the expression of flagella-related genes. FlhC knockout in the ptsG-deleted strain triggered significant growth retardation with increased ATP levels and a higher NADPH/NADP+ ratio. Metabolic flux analysis using a 13C-labeled carbon substrate showed increased fluxes toward the pentose phosphate and tricarboxylic acid cycle pathways in the flhC- and ptsG-deleted strains. Introduction of a high copy number plasmid or overexpression of the recombinant protein in this strain restored growth rate without increasing glucose consumption. These results suggest that the metabolic burden caused by flhC deletion was resolved by recombinant protein production. The recombinant enhanced green fluorescent protein yield per glucose consumption increased 1.81-fold in the flhC mutant strain. Thus, our study demonstrates that high-yield production of the recombinant protein was achieved with reduced flagella formation.
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Affiliation(s)
- Jae-Ho Han
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
| | - Sang Taek Jung
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
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40
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Redondo A, Wood D, Amaral S, Ferré J, Goti D, Bertran J. Production of Toxoplasma gondii Recombinant Antigens in Genome-Edited Escherichia coli. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Morrison M, Razo-Mejia M, Phillips R. Reconciling kinetic and thermodynamic models of bacterial transcription. PLoS Comput Biol 2021; 17:e1008572. [PMID: 33465069 PMCID: PMC7845990 DOI: 10.1371/journal.pcbi.1008572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/29/2021] [Accepted: 11/28/2020] [Indexed: 11/18/2022] Open
Abstract
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including fluorescence and sequencing readouts have raised the bar for what it means to quantitatively understand transcriptional regulation. In particular our understanding of the simplest genetic circuit is sufficiently refined both experimentally and theoretically that it has become possible to carefully discriminate between different conceptual pictures of how this regulatory system works. This regulatory motif, originally posited by Jacob and Monod in the 1960s, consists of a single transcriptional repressor binding to a promoter site and inhibiting transcription. In this paper, we show how seven distinct models of this so-called simple-repression motif, based both on thermodynamic and kinetic thinking, can be used to derive the predicted levels of gene expression and shed light on the often surprising past success of the thermodynamic models. These different models are then invoked to confront a variety of different data on mean, variance and full gene expression distributions, illustrating the extent to which such models can and cannot be distinguished, and suggesting a two-state model with a distribution of burst sizes as the most potent of the seven for describing the simple-repression motif.
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Affiliation(s)
- Muir Morrison
- Department of Physics, California Institute of Technology, Pasadena, California, USA
| | - Manuel Razo-Mejia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Rob Phillips
- Department of Physics, California Institute of Technology, Pasadena, California, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- * E-mail:
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42
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Yin H, Hu T, Zhuang Y, Liu T. Metabolic engineering of Saccharomyces cerevisiae for high-level production of gastrodin from glucose. Microb Cell Fact 2020; 19:218. [PMID: 33243241 PMCID: PMC7690157 DOI: 10.1186/s12934-020-01476-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The natural phenolic glycoside gastrodin is the major bioactive ingredient in the well-known Chinese herb Tianma and is widely used as a neuroprotective medicine in the clinic. Microbial production from sustainable resources is a promising method to replace plant extraction and chemical synthesis which were currently used in industrial gastrodin production. Saccharomyces cerevisiae is considered as an attractive host to produce natural plant products used in the food and pharmaceutical fields. In this work, we intended to explore the potential of S. cerevisiae as the host for high-level production of gastrodin from glucose. RESULTS Here, we first identified the plant-derived glucosyltransferase AsUGT to convert 4-hydroxybenzyl alcohol to gastrodin with high catalytic efficiency in yeast. Then, we engineered de novo production of gastrodin by overexpressing codon-optimized AsUGTsyn, the carboxylic acid reductase gene CARsyn from Nocardia species, the phosphopantetheinyl transferase gene PPTcg-1syn from Corynebacterium glutamicum, the chorismate pyruvate-lyase gene UbiCsyn from Escherichia coli, and the mutant ARO4K229L. Finally, we achieved an improved product titer by a chromosomal multiple-copy integration strategy and enhancement of metabolic flux toward the aglycon 4-hydroxybenzyl alcohol. The best optimized strain produced 2.1 g/L gastrodin in mineral medium with glucose as the sole carbon source by flask fermentation, which was 175 times higher than that of the original gastrodin-producing strain. CONCLUSIONS The de novo high-level production of gastrodin was first achieved. Instead of chemical synthesis or plants extraction, our work provides an alternative strategy for the industrial production of gastrodin by microbial fermentation from a sustainable resource.
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Affiliation(s)
- Hua Yin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tiandong Hu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yibin Zhuang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Barajas C, Del Vecchio D. Effects of spatial heterogeneity on bacterial genetic circuits. PLoS Comput Biol 2020; 16:e1008159. [PMID: 32925923 PMCID: PMC7515207 DOI: 10.1371/journal.pcbi.1008159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 09/24/2020] [Accepted: 07/17/2020] [Indexed: 12/17/2022] Open
Abstract
Intracellular spatial heterogeneity is frequently observed in bacteria, where the chromosome occupies part of the cell's volume and a circuit's DNA often localizes within the cell. How this heterogeneity affects core processes and genetic circuits is still poorly understood. In fact, commonly used ordinary differential equation (ODE) models of genetic circuits assume a well-mixed ensemble of molecules and, as such, do not capture spatial aspects. Reaction-diffusion partial differential equation (PDE) models have been only occasionally used since they are difficult to integrate and do not provide mechanistic understanding of the effects of spatial heterogeneity. In this paper, we derive a reduced ODE model that captures spatial effects, yet has the same dimension as commonly used well-mixed models. In particular, the only difference with respect to a well-mixed ODE model is that the association rate constant of binding reactions is multiplied by a coefficient, which we refer to as the binding correction factor (BCF). The BCF depends on the size of interacting molecules and on their location when fixed in space and it is equal to unity in a well-mixed ODE model. The BCF can be used to investigate how spatial heterogeneity affects the behavior of core processes and genetic circuits. Specifically, our reduced model indicates that transcription and its regulation are more effective for genes located at the cell poles than for genes located on the chromosome. The extent of these effects depends on the value of the BCF, which we found to be close to unity. For translation, the value of the BCF is always greater than unity, it increases with mRNA size, and, with biologically relevant parameters, is substantially larger than unity. Our model has broad validity, has the same dimension as a well-mixed model, yet it incorporates spatial heterogeneity. This simple-to-use model can be used to both analyze and design genetic circuits while accounting for spatial intracellular effects.
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Affiliation(s)
- Carlos Barajas
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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Yang B, Feng X, Li C. Microbial Cell Factory for Efficiently Synthesizing Plant Natural Products via Optimizing the Location and Adaptation of Pathway on Genome Scale. Front Bioeng Biotechnol 2020; 8:969. [PMID: 32923436 PMCID: PMC7457125 DOI: 10.3389/fbioe.2020.00969] [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: 04/17/2020] [Accepted: 07/27/2020] [Indexed: 01/03/2023] Open
Abstract
Plant natural products (PNPs) possess important pharmacological activities and are widely used in cosmetics, health care products, and as food additives. Currently, most PNPs are mainly extracted from cultivated plants, and the yield is limited by the long growth cycle, climate change and complex processing steps, which makes the process unsustainable. However, the complex structure of PNPs significantly reduces the efficiency of chemical synthesis. With the development of metabolic engineering and synthetic biology, heterologous biosynthesis of PNPs in microbial cell factories offers an attractive alternative. Based on the in-depth mining and analysis of genome and transcriptome data, the biosynthetic pathways of a number of natural products have been successfully elucidated, which lays the crucial foundation for heterologous production. However, there are several problems in the microbial synthesis of PNPs, including toxicity of intermediates, low enzyme activity, multiple auxotrophic dependence, and uncontrollable metabolic network. Although various metabolic engineering strategies have been developed to solve these problems, optimizing the location and adaptation of pathways on the whole-genome scale is an important strategy in microorganisms. From this perspective, this review introduces the application of CRISPR/Cas9 in editing PNPs biosynthesis pathways in model microorganisms, the influences of pathway location, and the approaches for optimizing the adaptation between metabolic pathways and chassis hosts for facilitating PNPs biosynthesis.
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Affiliation(s)
- Bo Yang
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xudong Feng
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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45
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Comprehensive study on Escherichia coli genomic expression: Does position really matter? Metab Eng 2020; 62:10-19. [PMID: 32795614 DOI: 10.1016/j.ymben.2020.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
As a biorefinery platform host, Escherichia coli has been used extensively to produce metabolites of commercial interest. Integration of foreign DNA onto the bacterial genome allows for stable expression overcoming the need for plasmid expression and its associated instability. Despite the development of numerous tools and genome editing technologies, the question of where to incorporate a synthetic pathway remains unanswered. To address this issue, we studied the genomic expression in E. coli and linked it not only to 26 rationally selected genomic locations, but also to the gene direction in relation to the DNA replication fork, to the carbon and nitrogen source, to DNA folding and supercoiling, and to metabolic burden. To enable these experiments, we have designed a fluorescent expression cassette to eliminate specific local effects on gene expression. Overall it can be concluded that although the expression range obtained by changing the genomic location of a pathway is small compared to the range typically seen in promoter-RBS libraries, the effect of culture medium, environmental stress and metabolic burden can be substantial. The characterization of multiple effects on genomic expression, and the associated libraries of well-characterized strains, will only stimulate and improve the creation of stable production hosts fit for industrial settings.
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46
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Zhao Y, Yao Z, Ploessl D, Ghosh S, Monti M, Schindler D, Gao M, Cai Y, Qiao M, Yang C, Cao M, Shao Z. Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories. ACS Synth Biol 2020; 9:1736-1752. [PMID: 32396718 DOI: 10.1021/acssynbio.0c00123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We broadened the usage of DNA transposon technology by demonstrating its capacity for the rapid creation of expression libraries for long biochemical pathways, which is beyond the classical application of building genome-scale knockout libraries in yeasts. This strategy efficiently leverages the readily available fine-tuning impact provided by the diverse transcriptional environment surrounding each random integration locus. We benchmark the transposon-mediated integration against the nonhomologous end joining-mediated strategy. The latter strategy was demonstrated for achieving pathway random integration in other yeasts but is associated with a high false-positive rate in the absence of a high-throughput screening method. Our key innovation of a nonreplicable circular DNA platform increased the possibility of identifying top-producing variants to 97%. Compared to the classical DNA transposition protocol, the design of a nonreplicable circular DNA skipped the step of counter-selection for plasmid removal and thus not only reduced the time required for the step of library creation from 10 to 5 d but also efficiently removed the "transposition escapers", which undesirably represented almost 80% of the entire population as false positives. Using one endogenous product (i.e., shikimate) and one heterologous product (i.e., (S)-norcoclaurine) as examples, we presented a streamlined procedure to rapidly identify high-producing variants with titers significantly higher than the reported data in the literature. We selected Scheffersomyces stipitis, a representative nonconventional yeast, as a demo, but the strategy can be generalized to other nonconventional yeasts. This new exploration of transposon technology, therefore, adds a highly versatile tool to accelerate the development of novel species as microbial cell factories for producing value-added chemicals.
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Affiliation(s)
- Yuxin Zhao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zhanyi Yao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Marco Monti
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Daniel Schindler
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Yizhi Cai
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Chao Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa, United States
- Bioeconomy Institute, Iowa State University, Ames, Iowa, United States
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa, United States
- The Ames Laboratory, Ames, Iowa, United States
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Nichols TM, Kennedy NW, Tullman-Ercek D. A genomic integration platform for heterologous cargo encapsulation in 1,2-propanediol utilization bacterial microcompartments. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Liang C, Zhang X, Wu J, Mu S, Wu Z, Jin JM, Tang SY. Dynamic control of toxic natural product biosynthesis by an artificial regulatory circuit. Metab Eng 2020; 57:239-246. [DOI: 10.1016/j.ymben.2019.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/13/2019] [Accepted: 12/11/2019] [Indexed: 01/10/2023]
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Vecchione S, Fritz G. CRIMoClo plasmids for modular assembly and orthogonal chromosomal integration of synthetic circuits in Escherichia coli. J Biol Eng 2019; 13:92. [PMID: 31798686 PMCID: PMC6883643 DOI: 10.1186/s13036-019-0218-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023] Open
Abstract
Background Synthetic biology heavily depends on rapid and simple techniques for DNA engineering, such as Ligase Cycling Reaction (LCR), Gibson assembly and Golden Gate assembly, all of which allow for fast, multi-fragment DNA assembly. A major enhancement of Golden Gate assembly is represented by the Modular Cloning (MoClo) system that allows for simple library propagation and combinatorial construction of genetic circuits from reusable parts. Yet, one limitation of the MoClo system is that all circuits are assembled in low- and medium copy plasmids, while a rapid route to chromosomal integration is lacking. To overcome this bottleneck, here we took advantage of the conditional-replication, integration, and modular (CRIM) plasmids, which can be integrated in single copies into the chromosome of Escherichia coli and related bacteria by site-specific recombination at different phage attachment (att) sites. Results By combining the modularity of the MoClo system with the CRIM plasmids features we created a set of 32 novel CRIMoClo plasmids and benchmarked their suitability for synthetic biology applications. Using CRIMoClo plasmids we assembled and integrated a given genetic circuit into four selected phage attachment sites. Analyzing the behavior of these circuits we found essentially identical expression levels, indicating orthogonality of the loci. Using CRIMoClo plasmids and four different reporter systems, we illustrated a framework that allows for a fast and reliable sequential integration at the four selected att sites. Taking advantage of four resistance cassettes the procedure did not require recombination events between each round of integration. Finally, we assembled and genomically integrated synthetic ECF σ factor/anti-σ switches with high efficiency, showing that the growth defects observed for circuits encoded on medium-copy plasmids were alleviated. Conclusions The CRIMoClo system enables the generation of genetic circuits from reusable, MoClo-compatible parts and their integration into 4 orthogonal att sites into the genome of E. coli. Utilizing four different resistance modules the CRIMoClo system allows for easy, fast, and reliable multiple integrations. Moreover, utilizing CRIMoClo plasmids and MoClo reusable parts, we efficiently integrated and alleviated the toxicity of plasmid-borne circuits. Finally, since CRIMoClo framework allows for high flexibility, it is possible to utilize plasmid-borne and chromosomally integrated circuits simultaneously. This increases our ability to permute multiple genetic modules and allows for an easier design of complex synthetic metabolic pathways in E. coli.
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Affiliation(s)
- Stefano Vecchione
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, 35032 Marburg, Germany
| | - Georg Fritz
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, 35032 Marburg, Germany
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Kopp J, Slouka C, Spadiut O, Herwig C. The Rocky Road From Fed-Batch to Continuous Processing With E. coli. Front Bioeng Biotechnol 2019; 7:328. [PMID: 31824931 PMCID: PMC6880763 DOI: 10.3389/fbioe.2019.00328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli still serves as a beloved workhorse for the production of many biopharmaceuticals as it fulfills essential criteria, such as having fast doubling times, exhibiting a low risk of contamination, and being easy to upscale. Most industrial processes in E. coli are carried out in fed-batch mode. However, recent trends show that the biotech industry is moving toward time-independent processing, trying to improve the space-time yield, and especially targeting constant quality attributes. In the 1950s, the term "chemostat" was introduced for the first time by Novick and Szilard, who followed up on the previous work performed by Monod. Chemostat processing resulted in a major hype 10 years after its official introduction. However, enthusiasm decreased as experiments suffered from genetic instabilities and physiology issues. Major improvements in strain engineering and the usage of tunable promotor systems facilitated chemostat processes. In addition, critical process parameters have been identified, and the effects they have on diverse quality attributes are understood in much more depth, thereby easing process control. By pooling the knowledge gained throughout the recent years, new applications, such as parallelization, cascade processing, and population controls, are applied nowadays. However, to control the highly heterogeneous cultivation broth to achieve stable productivity throughout long-term cultivations is still tricky. Within this review, we discuss the current state of E. coli fed-batch process understanding and its tech transfer potential within continuous processing. Furthermore, the achievements in the continuous upstream applications of E. coli and the continuous downstream processing of intracellular proteins will be discussed.
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Affiliation(s)
- Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
| | - Christoph Slouka
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
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