1
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Hao W, Cui W, Liu Z, Suo F, Wu Y, Han L, Zhou Z. A New-Generation Base Editor with an Expanded Editing Window for Microbial Cell Evolution In Vivo Based on CRISPR‒Cas12b Engineering. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309767. [PMID: 38602436 PMCID: PMC11165516 DOI: 10.1002/advs.202309767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/07/2024] [Indexed: 04/12/2024]
Abstract
Base editors (BEs) are widely used as revolutionary genome manipulation tools for cell evolution. To screen the targeted individuals, it is often necessary to expand the editing window to ensure highly diverse variant library. However, current BEs suffer from a limited editing window of 5-6 bases, corresponding to only 2-3 amino acids. Here, by engineering the CRISPR‒Cas12b, the study develops dCas12b-based CRISPRi system, which can efficiently repress gene expression by blocking the initiation and elongation of gene transcription. Further, based on dCas12b, a new-generation of BEs with an expanded editing window is established, covering the entire protospacer or more. The expanded editing window results from the smaller steric hindrance compared with other Cas proteins. The universality of the new BE is successfully validated in Bacillus subtilis and Escherichia coli. As a proof of concept, a spectinomycin-resistant E. coli strain (BL21) and a 6.49-fold increased protein secretion efficiency in E. coli JM109 are successfully obtained by using the new BE. The study, by tremendously expanding the editing window of BEs, increased the capacity of the variant library exponentially, greatly increasing the screening efficiency for microbial cell evolution.
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Affiliation(s)
- Wenliang Hao
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of BiotechnologyJiangnan University1800 Lihu AvenueWuxi214122China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of BiotechnologyJiangnan University1800 Lihu AvenueWuxi214122China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of BiotechnologyJiangnan University1800 Lihu AvenueWuxi214122China
| | - Feiya Suo
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of BiotechnologyJiangnan University1800 Lihu AvenueWuxi214122China
| | - Yaokang Wu
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of BiotechnologyJiangnan University1800 Lihu AvenueWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Laichuang Han
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of BiotechnologyJiangnan University1800 Lihu AvenueWuxi214122China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology (Ministry of Education), School of BiotechnologyJiangnan University1800 Lihu AvenueWuxi214122China
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2
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Zhao W, Guo Y. Increasing the efficiency of gene editing with CRISPR-Cas9 via concurrent expression of the Beta protein. Int J Biol Macromol 2024; 270:132431. [PMID: 38759853 DOI: 10.1016/j.ijbiomac.2024.132431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/03/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Escherichia coli has emerged as an important host for the production of biopharmaceuticals or other industrially relevant molecules. An efficient gene editing tool is indispensable for ensuring high production levels and optimal release of target products. However, in Escherichia coli, the CRISPR-Cas9 system has been shown to achieve gene modifications with relatively low frequency. Large-scale PCR screening is required, hindering the identification of positive clones. The beta protein, which weakly binds to single-stranded DNA but tightly associates with complementary strand annealing products, offers a promising solution to this issue. In the present study, we describe a targeted and continuous gene editing strategy for the Escherichia coli genome. This strategy involves the coexpression of the beta protein alongside the CRISPR-Cas9 system, enabling a variety of genome modifications such as gene deletion and insertion with an efficiency exceeding 80 %. The integrity of beta proteins is essential for the CRISPR-Cas9/Beta-based gene editing system. In this work, the deletion of either the N- or C-terminal domain significantly impaired system efficiency. Overall, our findings established the CRISPR-Cas9/Beta system as a suitable gene editing tool for various applications in Escherichia coli.
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Affiliation(s)
- Weiyu Zhao
- School of Life Sciences, Shanghai University, No. 99 Shangda Road, Shanghai 200444, China; School of Economics and Management, Tongji University, No. 1239 Siping Road, Shanghai 200092, China; Institute of Logistics Science and Engineering, Shanghai Maritime University, 1550 Haigang Avenue, Shanghai 201306, China
| | - Yanan Guo
- School of Life Sciences, Shanghai University, No. 99 Shangda Road, Shanghai 200444, China; Department of Biology, Georgia State University, Atlanta, GA 30303, United States of America.
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3
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Ham DT, Browne TS, Banglorewala PN, Wilson TL, Michael RK, Gloor GB, Edgell DR. A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets. Nat Commun 2023; 14:5514. [PMID: 37679324 PMCID: PMC10485023 DOI: 10.1038/s41467-023-41143-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
The CRISPR/Cas9 nuclease from Streptococcus pyogenes (SpCas9) can be used with single guide RNAs (sgRNAs) as a sequence-specific antimicrobial agent and as a genome-engineering tool. However, current bacterial sgRNA activity models struggle with accurate predictions and do not generalize well, possibly because the underlying datasets used to train the models do not accurately measure SpCas9/sgRNA activity and cannot distinguish on-target cleavage from toxicity. Here, we solve this problem by using a two-plasmid positive selection system to generate high-quality data that more accurately reports on SpCas9/sgRNA cleavage and that separates activity from toxicity. We develop a machine learning architecture (crisprHAL) that can be trained on existing datasets, that shows marked improvements in sgRNA activity prediction accuracy when transfer learning is used with small amounts of high-quality data, and that can generalize predictions to different bacteria. The crisprHAL model recapitulates known SpCas9/sgRNA-target DNA interactions and provides a pathway to a generalizable sgRNA bacterial activity prediction tool that will enable accurate antimicrobial and genome engineering applications.
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Affiliation(s)
- Dalton T Ham
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada
| | - Tyler S Browne
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada
| | - Pooja N Banglorewala
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada
| | | | | | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada.
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada.
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4
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Li C, Li M, Hu M, Zhang T. Metabolic Engineering of De Novo Pathway for the Production of 2'-Fucosyllactose in Escherichia coli. Mol Biotechnol 2023; 65:1485-1497. [PMID: 36652181 DOI: 10.1007/s12033-023-00657-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
2'-Fucosyllactose (2'-FL), one of the most abundant oligosaccharides in human milk, has gained increased attention owing to its nutraceutical and pharmaceutical potential. However, limited availability and high-cost of preparation have limited its widespread application and in-depth investigation of its potential functions. Here, a modular pathway engineering was implemented to construct an Escherichia coli strain to improve the biosynthesis titer of 2'-FL. Before overexpression of manB, manC, gmd, wcaG, and heterologous expression of futC, genes wcaJ and lacZ encoding UDP-glucose lipid carrier transferase and β-galactosidase, respectively, were inactivated from E. coli BL21 (DE3) with the CRISPR-Cas9 system, which inhibited the production of 2'-FL. The results showed that final shake flask culture yielded a 3.8-fold increase in 2'-FL (0.98 g/L) from the engineered strain ELC07. Fed-batch fermentation conditions were optimized in a 3-L bioreactor. The highest titer of 2'-FL (18.22 g/L) was obtained, corresponding to a yield of 0.25 g/g glycerol and a substrate conversion of 0.88 g/g lactose.
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Affiliation(s)
- Chenchen Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Miaomiao Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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5
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Lim SR, Lee HJ, Kim HJ, Lee SJ. Multiplex Single-Nucleotide Microbial Genome Editing Achieved by CRISPR-Cas9 Using 5'-End-Truncated sgRNAs. ACS Synth Biol 2023; 12:2203-2207. [PMID: 37368988 PMCID: PMC10368013 DOI: 10.1021/acssynbio.3c00323] [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: 05/24/2023] [Indexed: 06/29/2023]
Abstract
Multiplex genome editing with CRISPR-Cas9 offers a cost-effective solution for time and labor savings. However, achieving high accuracy remains a challenge. In an Escherichia coli model system, we achieved highly efficient single-nucleotide level simultaneous editing of the galK and xylB genes using the 5'-end-truncated single-molecular guide RNA (sgRNA) method. Furthermore, we successfully demonstrated the simultaneous editing of three genes (galK, xylB, and srlD) at single-nucleotide resolution. To showcase practical application, we targeted the cI857 and ilvG genes in the genome of E. coli. While untruncated sgRNAs failed to produce any edited cells, the use of truncated sgRNAs allowed us to achieve simultaneous and accurate editing of these two genes with an efficiency of 30%. This enabled the edited cells to retain their lysogenic state at 42 °C and effectively alleviated l-valine toxicity. These results suggest that our truncated sgRNA method holds significant potential for widespread and practical use in synthetic biology.
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Affiliation(s)
| | | | - Hyun Ju Kim
- Department of Systems Biotechnology
and Institute of Microbiomics, Chung-Ang
University, Anseong 17546, Republic
of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology
and Institute of Microbiomics, Chung-Ang
University, Anseong 17546, Republic
of Korea
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6
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Gopalakrishna KP, Hillebrand GH, Bhavana VH, Elder JL, D'Mello A, Tettelin H, Hooven TA. Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects. Commun Biol 2023; 6:620. [PMID: 37296208 PMCID: PMC10256743 DOI: 10.1038/s42003-023-04994-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Group B Streptococcus (GBS; S. agalactiae) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial cell. Several recent publications have shown that GBS Cas9 influences genome-wide transcription through a mechanism uncoupled from its function as a specific, RNA-programmable endonuclease. We examine GBS Cas9 effects on genome-wide transcription through generation of several isogenic variants with specific functional defects. We compare whole-genome RNA-seq from Δcas9 GBS with a full-length Cas9 gene deletion; dcas9 defective in its ability to cleave DNA but still able to bind to frequently occurring protospacer adjacent motifs; and scas9 that retains its catalytic domains but is unable to bind protospacer adjacent motifs. Comparing scas9 GBS to the other variants, we identify nonspecific protospacer adjacent motif binding as a driver of genome-wide, Cas9 transcriptional effects in GBS. We also show that Cas9 transcriptional effects from nonspecific scanning tend to influence genes involved in bacterial defense and nucleotide or carbohydrate transport and metabolism. While genome-wide transcription effects are detectable by analysis of next-generation sequencing, they do not result in virulence changes in a mouse model of sepsis. We also demonstrate that catalytically inactive dCas9 expressed from the GBS chromosome can be used with a straightforward, plasmid-based, single guide RNA expression system to suppress transcription of specific GBS genes without potentially confounding off-target effects. We anticipate that this system will be useful for study of nonessential and essential gene roles in GBS physiology and pathogenesis.
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Affiliation(s)
| | - Gideon H Hillebrand
- University of Pittsburgh School of Medicine, Program in Microbiology and Immunology, Pittsburgh, PA, USA
| | - Venkata H Bhavana
- University of Pittsburgh School of Medicine, Department of Pediatrics, Pittsburgh, PA, USA
| | - Jordan L Elder
- The Cleveland Clinic, Clinical Laboratory Services, Cleveland, OH, USA
| | - Adonis D'Mello
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Thomas A Hooven
- University of Pittsburgh School of Medicine, Department of Pediatrics, Pittsburgh, PA, USA.
- Richard King Mellon Institute for Pediatric Research, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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7
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Li Q, Sun M, Lv L, Zuo Y, Zhang S, Zhang Y, Yang S. Improving the Editing Efficiency of CRISPR-Cas9 by Reducing the Generation of Escapers Based on the Surviving Mechanism. ACS Synth Biol 2023; 12:672-680. [PMID: 36867054 DOI: 10.1021/acssynbio.2c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Due to the high specificity in targeting DNA and highly convenient programmability, CRISPR-Cas-based antimicrobials applied for eliminating specific strains such as antibiotic-resistant bacteria in the microbiome were gradually developed. However, the generation of escapers makes the elimination efficiency far lower than the acceptable rate (10-8) recommended by the National Institutes of Health. Here, a systematic study was carried out providing insight into the escaping mechanisms in Escherichia coli, and strategies for reducing the escapers were devised accordingly. We first showed an escape rate of 10-5-10-3 in E. coli MG1655 under the editing of pEcCas/pEcgRNA established previously. Detailed analysis of the escapers obtained at ligA site in E. coli MG1655 uncovered that the disruption of cas9 was the main cause of the generation of survivors, notably the frequent insertion of IS5. Hence, the sgRNA was next designed to target the "perpetrator" IS5, and subsequently the killing efficiency was improved 4-fold. Additionally, the escape rate in IS-free E. coli MDS42 was also tested at the ligA site, ∼10-fold decrease compared with MG1655, but the disruption of cas9 was still observed in all survivors manifested in the form of frameshifts or point mutations. Thus, we optimized the tool itself by increasing the copy number of cas9 to retain some cas9 that still has the correct DNA sequence. Fortunately, the escape rates dropped below 10-8 at 9 of the 16 tested genes. Furthermore, the λ-Red recombination system was added to generate the pEcCas-2.0, and a 100% gene deletion efficiency was achieved at genes cadA, maeB, and gntT in MG1655, whereas those genes were edited with low efficiency previously. Last, the application of pEcCas-2.0 was then expanded to the E. coli B strain BL21(DE3) and W strain ATCC9637. This study reveals the mechanism of E. coli surviving Cas9-mediated death, and a highly efficient editing tool is established based on the mechanism, which will accelerate the further application of CRISPR-Cas.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Mingjun Sun
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Lu Lv
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Yong Zuo
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
| | - Suyi Zhang
- Luzhou Laojiao Co., Ltd, Luzhou 646000, Sichuan China
| | - Ying Zhang
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Huzhou 313000, China
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8
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Hao M, Tang J, Ge S, Li T, Xia N. Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research. Microorganisms 2023; 11:microorganisms11030589. [PMID: 36985163 PMCID: PMC10056367 DOI: 10.3390/microorganisms11030589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Herpesviruses are major pathogens that infect humans and animals. Manipulating the large genome is critical for exploring the function of specific genes and studying the pathogenesis of herpesviruses and developing novel anti-viral vaccines and therapeutics. Bacterial artificial chromosome (BAC) technology significantly advanced the capacity of herpesviruses researchers to manipulate the virus genomes. In the past years, advancements in BAC-based genome manipulating and screening strategies of recombinant BACs have been achieved, which has promoted the study of the herpes virus. This review summarizes the advances in BAC-based gene editing technology and selection strategies. The merits and drawbacks of BAC-based herpesvirus genome editing methods and the application of BAC-based genome manipulation in viral research are also discussed. This review provides references relevant for researchers in selecting gene editing methods in herpes virus research. Despite the achievements in the genome manipulation of the herpes viruses, the efficiency of BAC-based genome manipulation is still not satisfactory. This review also highlights the need for developing more efficient genome-manipulating methods for herpes viruses.
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Affiliation(s)
- Mengling Hao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jiabao Tang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
- Correspondence:
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
- The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen 361102, China
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9
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Wei H, Li X. Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes. Front Genet 2023; 14:1087267. [PMID: 36713072 PMCID: PMC9878224 DOI: 10.3389/fgene.2023.1087267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Unveiling how genetic variations lead to phenotypic variations is one of the key questions in evolutionary biology, genetics, and biomedical research. Deep mutational scanning (DMS) technology has allowed the mapping of tens of thousands of genetic variations to phenotypic variations efficiently and economically. Since its first systematic introduction about a decade ago, we have witnessed the use of deep mutational scanning in many research areas leading to scientific breakthroughs. Also, the methods in each step of deep mutational scanning have become much more versatile thanks to the oligo-synthesizing technology, high-throughput phenotyping methods and deep sequencing technology. However, each specific possible step of deep mutational scanning has its pros and cons, and some limitations still await further technological development. Here, we discuss recent scientific accomplishments achieved through the deep mutational scanning and describe widely used methods in each step of deep mutational scanning. We also compare these different methods and analyze their advantages and disadvantages, providing insight into how to design a deep mutational scanning study that best suits the aims of the readers' projects.
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Affiliation(s)
- Huijin Wei
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China
| | - Xianghua Li
- Zhejiang University—University of Edinburgh Institute, Zhejiang University, Haining, Zhejiang, China,Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom,The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China,Biomedical and Health Translational Centre of Zhejiang Province, Haining, Zhejiang, China,*Correspondence: Xianghua Li,
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10
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Li M, Li C, Luo Y, Hu M, Liu Z, Zhang T. Multi-level metabolic engineering of Escherichia coli for high-titer biosynthesis of 2'-fucosyllactose and 3-fucosyllactose. Microb Biotechnol 2022; 15:2970-2981. [PMID: 36134689 PMCID: PMC9733645 DOI: 10.1111/1751-7915.14152] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022] Open
Abstract
Fucosyllactoses (FL), including 2'-fucosyllactose (2'-FL) and 3-fucosyllactose (3-FL), have garnered considerable interest for their value in newborn formula and pharmaceuticals. In this study, an engineered Escherichia coli was developed for high-titer FL biosynthesis by introducing multi-level metabolic engineering strategies, including (1) individual construction of the 2'/3-FL-producing strains through gene combination optimization of the GDP-L-fucose module; (2) screening of rate-limiting enzymes (α-1,2-fucosyltransferase and α-1,3-fucosyltransferase); (3) analysis of critical intermediates and inactivation of competing pathways to redirect carbon fluxes to FL biosynthesis; (4) enhancement of the catalytic performance of rate-limiting enzymes by the RBS screening, fusion peptides and multi-copy gene cloning. The final strains EC49 and EM47 produced 9.36 g/L for 2'-FL and 6.28 g/L for 3-FL in shake flasks with a modified-M9CA medium. Fed-batch cultivations of the two strains generated 64.62 g/L of 2'-FL and 40.68 g/L of 3-FL in the 3-L bioreactors, with yields of 0.65 mol 2'-FL/mol lactose and 0.67 mol 3-FL/mol lactose, respectively. This research provides a viable platform for other high-value-added compounds production in microbial cell factories.
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Affiliation(s)
- Mengli Li
- State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxiJiangsuChina
| | - Chenchen Li
- State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxiJiangsuChina
| | - Yejiao Luo
- State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxiJiangsuChina
| | - Miaomiao Hu
- State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxiJiangsuChina
| | - Zhu Liu
- Zhejiang Institute for Food and Drug ControlHangzhouChina
| | - Tao Zhang
- State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxiJiangsuChina
- International Joint Laboratory on Food Science and SafetyJiangnan UniversityWuxiJiangsuChina
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11
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Bubnov DM, Yuzbashev TV, Khozov AA, Melkina OE, Vybornaya TV, Stan GB, Sineoky SP. Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs. Nucleic Acids Res 2022; 50:8947-8960. [PMID: 35920321 PMCID: PMC9410887 DOI: 10.1093/nar/gkac649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Despite advances in bacterial genome engineering, delivery of large synthetic constructs remains challenging in practice. In this study, we propose a straightforward and robust approach for the markerless integration of DNA fragments encoding whole metabolic pathways into the genome. This approach relies on the replacement of a counterselection marker with cargo DNA cassettes via λRed recombineering. We employed a counterselection strategy involving a genetic circuit based on the CI repressor of λ phage. Our design ensures elimination of most spontaneous mutants, and thus provides a counterselection stringency close to the maximum possible. We improved the efficiency of integrating long PCR-generated cassettes by exploiting the Ocr antirestriction function of T7 phage, which completely prevents degradation of unmethylated DNA by restriction endonucleases in wild-type bacteria. The employment of highly restrictive counterselection and ocr-assisted λRed recombineering allowed markerless integration of operon-sized cassettes into arbitrary genomic loci of four enterobacterial species with an efficiency of 50–100%. In the case of Escherichia coli, our strategy ensures simple combination of markerless mutations in a single strain via P1 transduction. Overall, the proposed approach can serve as a general tool for synthetic biology and metabolic engineering in a range of bacterial hosts.
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Affiliation(s)
- Dmitrii M Bubnov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
| | - Tigran V Yuzbashev
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Andrey A Khozov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills 1-12, Moscow 119234, Russia
| | - Olga E Melkina
- Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Laboratory of Bacterial Genetics, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Tatiana V Vybornaya
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Genomic Center, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
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12
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Graffeuil A, Guerrero-Castro J, Assefa A, Uhlin BE, Cisneros DA. Polar mutagenesis of polycistronic bacterial transcriptional units using Cas12a. Microb Cell Fact 2022; 21:139. [PMID: 35831865 PMCID: PMC9277811 DOI: 10.1186/s12934-022-01844-y] [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: 02/11/2022] [Accepted: 06/02/2022] [Indexed: 11/30/2022] Open
Abstract
Background Functionally related genes in bacteria are often organized and transcribed as polycistronic transcriptional units. Examples are the fim operon, which codes for biogenesis of type 1 fimbriae in Escherichia coli, and the atp operon, which codes for the FoF1 ATP synthase. We tested the hypothesis that markerless polar mutations could be efficiently engineered using CRISPR/Cas12a in these loci. Results Cas12a-mediated engineering of a terminator sequence inside the fimA gene occurred with efficiencies between 10 and 80% and depended on the terminator’s sequence, whilst other types of mutations, such as a 97 bp deletion, occurred with 100% efficiency. Polar mutations using a terminator sequence were also engineered in the atp locus, which induced its transcriptional shutdown and produced identical phenotypes as a deletion of the whole atp locus (ΔatpIBEFHAGDC). Measuring the expression levels in the fim and atp loci showed that many supposedly non-polar mutants induced a significant polar effect on downstream genes. Finally, we also showed that transcriptional shutdown or deletion of the atp locus induces elevated levels of intracellular ATP during the exponential growth phase. Conclusions We conclude that Cas12a-mediated mutagenesis is an efficient simple system to generate polar mutants in E. coli. Different mutations were induced with varying degrees of efficiency, and we confirmed that all these mutations abolished the functions encoded in the fim and atp loci. We also conclude that it is difficult to predict which mutagenesis strategy will induce a polar effect in genes downstream of the mutation site. Furthermore the strategies described here can be used to manipulate the metabolism of E. coli as showcased by the increase in intracellular ATP in the markerless ΔatpIBEFHAGDC mutant. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01844-y.
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Affiliation(s)
- Antoine Graffeuil
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Julio Guerrero-Castro
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Aster Assefa
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - David A Cisneros
- Department of Molecular Biology, Umeå University, Umeå, Sweden. .,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
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13
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Tomasi M, Caproni E, Benedet M, Zanella I, Giorgetta S, Dalsass M, König E, Gagliardi A, Fantappiè L, Berti A, Tamburini S, Croia L, Di Lascio G, Bellini E, Valensin S, Licata G, Sebastiani G, Dotta F, Armanini F, Cumbo F, Asnicar F, Blanco-Míguez A, Ruggiero E, Segata N, Grandi G, Grandi A. Outer Membrane Vesicles From The Gut Microbiome Contribute to Tumor Immunity by Eliciting Cross-Reactive T Cells. Front Oncol 2022; 12:912639. [PMID: 35847919 PMCID: PMC9281500 DOI: 10.3389/fonc.2022.912639] [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: 04/04/2022] [Accepted: 05/20/2022] [Indexed: 12/03/2022] Open
Abstract
A growing body of evidence supports the notion that the gut microbiome plays an important role in cancer immunity. However, the underpinning mechanisms remain to be fully elucidated. One attractive hypothesis envisages that among the T cells elicited by the plethora of microbiome proteins a few exist that incidentally recognize neo-epitopes arising from cancer mutations (“molecular mimicry (MM)” hypothesis). To support MM, the human probiotic Escherichia coli Nissle was engineered with the SIINFEKL epitope (OVA-E.coli Nissle) and orally administered to C57BL/6 mice. The treatment with OVA-E.coli Nissle, but not with wild type E. coli Nissle, induced OVA-specific CD8+ T cells and inhibited the growth of tumors in mice challenged with B16F10 melanoma cells expressing OVA. The microbiome shotgun sequencing and the sequencing of TCRs from T cells recovered from both lamina propria and tumors provide evidence that the main mechanism of tumor inhibition is mediated by the elicitation at the intestinal site of cross-reacting T cells, which subsequently reach the tumor environment. Importantly, the administration of Outer Membrane Vesicles (OMVs) from engineered E. coli Nissle, as well as from E. coli BL21(DE3)ΔompA, carrying cancer-specific T cell epitopes also elicited epitope-specific T cells in the intestine and inhibited tumor growth. Overall, our data strengthen the important role of MM in tumor immunity and assign a novel function of OMVs in host-pathogen interaction. Moreover, our results pave the way to the exploitation of probiotics and OMVs engineered with tumor specific-antigens as personalized mucosal cancer vaccines.
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Affiliation(s)
- Michele Tomasi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Elena Caproni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Benedet
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Toscana Life Sciences Foundation, Siena, Italy
| | - Ilaria Zanella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sebastiano Giorgetta
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Dalsass
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Enrico König
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Toscana Life Sciences Foundation, Siena, Italy
| | | | | | - Alvise Berti
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Silvia Tamburini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Lorenzo Croia
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Di Lascio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | | | - Giada Licata
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences Foundation, Siena, Italy
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences Foundation, Siena, Italy
| | - Francesco Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences Foundation, Siena, Italy
- Tuscany Centre for Precision Medicine (CReMeP), Siena, Italy
| | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Aitor Blanco-Míguez
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Eliana Ruggiero
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCSS) Ospedale San Raffaele, Milan, Italy
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- *Correspondence: Guido Grandi, ; Alberto Grandi,
| | - Alberto Grandi
- Toscana Life Sciences Foundation, Siena, Italy
- BiOMViS Srl, Siena, Italy
- *Correspondence: Guido Grandi, ; Alberto Grandi,
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14
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Li M, Li C, Hu M, Zhang T. Metabolic engineering strategies of de novo pathway for enhancing 2'-fucosyllactose synthesis in Escherichia coli. Microb Biotechnol 2021; 15:1561-1573. [PMID: 34843640 PMCID: PMC9049618 DOI: 10.1111/1751-7915.13977] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Accepted: 11/14/2021] [Indexed: 11/28/2022] Open
Abstract
2′‐Fucosyllactose (2′‐FL), one of the most abundant human milk oligosaccharides (HMOs), is used as a promising infant formula ingredient owing to its multiple health benefits for newborns. However, limited availability and high‐cost preparation have restricted its extensive use and intensive research on its potential functions. In this work, a powerful Escherichia coli cell factory was developed to ulteriorly increase 2′‐FL production. Initially, a modular pathway engineering was strengthened to balance the synthesis pathway through different plasmid combinations with a resulting maximum 2′‐FL titre of 1.45 g l−1. To further facilitate the metabolic flux from GDP‐l‐fucose towards 2′‐FL, the CRISPR‐Cas9 system was utilized to inactivate the genes including lacZ and wcaJ, increasing the titre by 6.59‐fold. Notably, the co‐introduction of NADPH and GTP regeneration pathways was confirmed to be more conducive to 2′‐FL formation, achieving a 2′‐FL titre of 2.24 g l−1. Moreover, comparisons of various exogenous α1,2‐fucosyltransferase candidates revealed that futC from Helicobacter pylori generated the highest titre of 2′‐FL. Finally, the viability of scaled‐up production of 2′‐FL was evidenced in a 3 l bioreactor with a maximum titre of 22.3 g l−1 2′‐FL and a yield of 0.53 mole 2′‐FL mole−1 lactose.
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Affiliation(s)
- Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chenchen Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Miaomiao Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.,International Joint Laboratory on Food Science and Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China
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15
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Chawley P, Rana A, Jagadevan S. Envisioning role of ammonia oxidizing bacteria in bioenergy production and its challenges: a review. Crit Rev Biotechnol 2021; 42:931-952. [PMID: 34641754 DOI: 10.1080/07388551.2021.1976099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB - Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented.
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Affiliation(s)
- Parmita Chawley
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Anu Rana
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
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16
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Zhang B, Wang H, Zhao W, Shan C, Liu C, Gao L, Zhao R, Ao P, Xiao P, Lv L, Gao H. New insights into the construction of wild-type Saba pig-derived Escherichia coli irp2 gene deletion strains. 3 Biotech 2021; 11:408. [PMID: 34466347 PMCID: PMC8363713 DOI: 10.1007/s13205-021-02951-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/27/2021] [Indexed: 01/24/2023] Open
Abstract
To construct wild-type E. coli irp2 gene deletion strains, CRISPR/Cas9 gene editing technology was used, and the difficulty and key points of gene editing of wild-type strains were analyzed. Based on the resistance of the CRISPR/Cas9 system expression vector, 4 strains of 41 E. coli strains isolated from Saba pigs were selected as the target strains for the deletion of the irp2 gene, which were sensitive to both ampicillin and kanamycin. Then, CRISPR/Cas9 technology was combined with homologous recombination technology to construct recombinant vectors containing Cas9, sgRNA and donor sequences to knock out the irp2 gene. Finally, the absence of the irp2 gene in E. coli was further verified by iron uptake assays, iron carrier production assays and growth curve measurements. The results showed that three of the selected strains showed single base mutations and deletions (Δirp2-1, Δirp2-2 and Δirp2-3). The deletion of the irp2 gene reduced the ability of E. coli to take up iron ions and produce iron carriers, but not affect the growth characteristics of E. coli. It is shown that the CRISPR/Cas9 knock-out system constructed in this study can successfully knock out the irp2 gene of the wild-type E. coli. Our results providing new insights into genome editing in wild-type strains, which enable further functional studies of the irp2 gene in wild-type E. coli.
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Affiliation(s)
- Bo Zhang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Hongdan Wang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Weiwei Zhao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Chunlan Shan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Chaoying Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Libo Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Ru Zhao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Pingxing Ao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Peng Xiao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Longbao Lv
- Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Hong Gao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201 Yunnan China
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17
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Okano K, Sato Y, Hizume T, Honda K. Genome editing by miniature CRISPR/Cas12f1 enzyme in Escherichia coli. J Biosci Bioeng 2021; 132:120-124. [PMID: 34023220 DOI: 10.1016/j.jbiosc.2021.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/01/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system is a valuable genome editing tool for microorganisms. However, the commonly used Cas9 nuclease derived from Streptococcus pyogenes (SpCas9) is not applicable to many industrially relevant bacteria, due to its cytotoxicity and large size (1368 amino acids [aa]). We developed an alternative genome editing system using a miniature Cas12f1 nuclease (529 aa) derived from an uncultured archaeon, Un1Cas12f1. When editing four dispensable genes in Escherichia coli MG1655 and BW25113, the CRISPR/Un1Cas12f1 system showed higher efficiency (63%-100%) than the CRISPR/SpCas9 system (50%-79%). The CRISPR/Un1Cas12f1 genome editing system is expected to be applied to the genome editing of a wide variety of bacteria.
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Affiliation(s)
- Kenji Okano
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Yu Sato
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tatsuya Hizume
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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18
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Li Q, Sun B, Chen J, Zhang Y, Jiang Y, Yang S. A modified pCas/pTargetF system for CRISPR-Cas9-assisted genome editing in Escherichia coli. Acta Biochim Biophys Sin (Shanghai) 2021; 53:620-627. [PMID: 33764372 DOI: 10.1093/abbs/gmab036] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (Cas9)-based genome editing tool pCas/pTargetF system that we established previously has been widely used in Escherichia coli MG1655. However, this system failed to manipulate the genome of E. coli BL21(DE3), owing to the potential higher leaky transcription of the gRNA-pMB1 specific to pTargetF in this strain. In this study, we modified the pCas/pTargetF system by replacing the promoter of gRNA-pMB1 with a tightly regulated promoter PrhaB, changing the replicon of pCas to a nontemperature-sensitive replicon, adding the sacB gene into pCas, and replacing the original N20-specific sequence of pTargetF with ccdB gene. We call this updated system as pEcCas/pEcgRNA. We found that gRNA-pMB1 indeed showed a slightly higher leaky expression in the pCas/pTargetF system compared with pEcCas/pEcgRNA. We also confirmed that genome editing can successfully be performed in BL21(DE3) by pEcCas/pEcgRNA with high efficiency. The application of pEcCas/pEcgRNA was then expanded to the E. coli B strain BL21 StarTM (DE3), K-12 strains MG1655, DH5α, CGMCC3705, Nissle1917, W strain ATCC9637, and also another species of Enterobacteriaceae, Tatumella citrea DSM13699, without any specific modifications. Finally, the plasmid curing process was optimized to shorten the time from $\sim$60 h to $\sim$32 h. The entire protocol (including plasmid construction, editing, electroporation and mutant verification, and plasmid elimination) took only $\sim$5.5 days per round in the pEcCas/pEcgRNA system, whereas it took $\sim$7.5 days in the pCas/pTargetF system. This study established a faster-acting genome editing tool that can be used in a wider range of E. coli strains and will also be useful for other Enterobacteriaceae species.
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Affiliation(s)
- Qi Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Bingbing Sun
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiwen Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou 313000, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou 313000, China
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19
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Liang Y, Li B, Zhang Q, Zhang S, He X, Jiang L, Jin Y. Interaction analyses based on growth parameters of GWAS between Escherichia coli and Staphylococcus aureus. AMB Express 2021; 11:34. [PMID: 33646434 PMCID: PMC7921238 DOI: 10.1186/s13568-021-01192-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/09/2021] [Indexed: 01/02/2023] Open
Abstract
To accurately explore the interaction mechanism between Escherichia coli and Staphylococcus aureus, we designed an ecological experiment to monoculture and co-culture E. coli and S. aureus. We co-cultured 45 strains of E. coli and S. aureus, as well as each species individually to measure growth over 36 h. We implemented a genome wide association study (GWAS) based on growth parameters (λ, R, A and s) to identify significant single nucleotide polymorphisms (SNPs) of the bacteria. Three commonly used growth regression equations, Logistic, Gompertz, and Richards, were used to fit the bacteria growth data of each strain. Then each equation's Akaike's information criterion (AIC) value was calculated as a commonly used information criterion. We used the optimal growth equation to estimate the four parameters above for strains in co-culture. By plotting the estimates for each parameter across two strains, we can visualize how growth parameters respond ecologically to environment stimuli. We verified that different genotypes of bacteria had different growth trajectories, although they were the same species. We reported 85 and 52 significant SNPs that were associated with interaction in E. coli and S. aureus, respectively. Many significant genes might play key roles in interaction, such as yjjW, dnaK, aceE, tatD, ftsA, rclR, ftsK, fepA in E. coli, and scdA, trpD, sdrD, SAOUHSC_01219 in S. aureus. Our study illustrated that there were multiple genes working together to affect bacterial interaction, and laid a solid foundation for the later study of more complex inter-bacterial interaction mechanisms.
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20
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Zanella I, König E, Tomasi M, Gagliardi A, Frattini L, Fantappiè L, Irene C, Zerbini F, Caproni E, Isaac SJ, Grigolato M, Corbellari R, Valensin S, Ferlenghi I, Giusti F, Bini L, Ashhab Y, Grandi A, Grandi G. Proteome-minimized outer membrane vesicles from Escherichia coli as a generalized vaccine platform. J Extracell Vesicles 2021; 10:e12066. [PMID: 33643549 PMCID: PMC7886703 DOI: 10.1002/jev2.12066] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/26/2020] [Accepted: 01/13/2021] [Indexed: 02/01/2023] Open
Abstract
Because of their potent adjuvanticity, ease of manipulation and simplicity of production Gram‐negative Outer Membrane Vesicles OMVs have the potential to become a highly effective vaccine platform. However, some optimization is required, including the reduction of the number of endogenous proteins, the increase of the loading capacity with respect to heterologous antigens, the enhancement of productivity in terms of number of vesicles per culture volume. In this work we describe the use of Synthetic Biology to create Escherichia coli BL21(DE3)Δ60, a strain releasing OMVs (OMVsΔ60) deprived of 59 endogenous proteins. The strain produces large quantities of vesicles (> 40 mg/L under laboratory conditions), which can accommodate recombinant proteins to a level ranging from 5% to 30% of total OMV proteins. Moreover, also thanks to the absence of immune responses toward the inactivated endogenous proteins, OMVsΔ60 decorated with heterologous antigens/epitopes elicit elevated antigens/epitopes‐specific antibody titers and high frequencies of epitope‐specific IFN‐γ‐producing CD8+ T cells. Altogether, we believe that E. coli BL21(DE3)Δ60 have the potential to become a workhorse factory for novel OMV‐based vaccines.
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Affiliation(s)
- Ilaria Zanella
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Enrico König
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Michele Tomasi
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Assunta Gagliardi
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Luca Frattini
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | | | - Carmela Irene
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Francesca Zerbini
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Elena Caproni
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Samine J Isaac
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Martina Grigolato
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | - Riccardo Corbellari
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
| | | | | | | | - Luca Bini
- Department of Life Sciences Functional Proteomics Laboratories University of Siena Siena Italy
| | - Yaqoub Ashhab
- Palestine-Korea Biotechnology Center Palestine Polytechnic University Hebron Palestine
| | - Alberto Grandi
- Toscana Life Sciences Foundation Siena Italy.,BiOMViS Srl Siena Italy
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO) Laboratory of Synthetic and Structural Vaccinology University of Trento Trento Italy
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21
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Wang J, Sui X, Ding Y, Fu Y, Feng X, Liu M, Zhang Y, Xian M, Zhao G. A fast and robust iterative genome-editing method based on a Rock-Paper-Scissors strategy. Nucleic Acids Res 2021; 49:e12. [PMID: 33270888 PMCID: PMC7826264 DOI: 10.1093/nar/gkaa1141] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 11/07/2020] [Indexed: 01/22/2023] Open
Abstract
The production of optimized strains of a specific phenotype requires the construction and testing of a large number of genome modifications and combinations thereof. Most bacterial iterative genome-editing methods include essential steps to eliminate selection markers, or to cure plasmids. Additionally, the presence of escapers leads to time-consuming separate single clone picking and subsequent cultivation steps. Herein, we report a genome-editing method based on a Rock-Paper-Scissors (RPS) strategy. Each of three constructed sgRNA plasmids can cure, or be cured by, the other two plasmids in the system; plasmids from a previous round of editing can be cured while the current round of editing takes place. Due to the enhanced curing efficiency and embedded double check mechanism, separate steps for plasmid curing or confirmation are not necessary, and only two times of cultivation are needed per genome-editing round. This method was successfully demonstrated in Escherichia coli and Klebsiella pneumoniae with both gene deletions and replacements. To the best of our knowledge, this is the fastest and most robust iterative genome-editing method, with the least times of cultivation decreasing the possibilities of spontaneous genome mutations.
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Affiliation(s)
- Jichao Wang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinyue Sui
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yamei Ding
- Institute of Oceanology, Chinese Academy of Sciences, 266071 Qingdao, China
| | - Yingxin Fu
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Min Liu
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Guang Zhao
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
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22
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Fenster JA, Eckert CA. High-Throughput Functional Genomics for Energy Production. Curr Opin Biotechnol 2020; 67:7-14. [PMID: 33152605 DOI: 10.1016/j.copbio.2020.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Additionally, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.
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Affiliation(s)
- Jacob A Fenster
- Chemical and Biological Engineering, University of Colorado, Boulder CO, United States; Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States
| | - Carrie A Eckert
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States; National Renewable Energy Laboratory, Golden CO, United States.
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23
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Kim HJ, Oh SY, Lee SJ. Single-Base Genome Editing in Corynebacterium glutamicum with the Help of Negative Selection by Target-Mismatched CRISPR/Cpf1. J Microbiol Biotechnol 2020; 30:1583-1591. [PMID: 32807756 PMCID: PMC9728170 DOI: 10.4014/jmb.2006.06036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
CRISPR/Cpf1 has emerged as a new CRISPR-based genome editing tool because, in comparison with CRIPSR/Cas9, it has a different T-rich PAM sequence to expand the target DNA sequence. Single-base editing in the microbial genome can be facilitated by oligonucleotide-directed mutagenesis (ODM) followed by negative selection with the CRISPR/Cpf1 system. However, single point mutations aided by Cpf1 negative selection have been rarely reported in Corynebacterium glutamicum. This study aimed to introduce an amber stop codon in crtEb encoding lycopene hydratase, through ODM and Cpf1-mediated negative selection; deficiency of this enzyme causes pink coloration due to lycopene accumulation in C. glutamicum. Consequently, on using double-, triple-, and quadruple-basemutagenic oligonucleotides, 91.5-95.3% pink cells were obtained among the total live C. glutamicum cells. However, among the negatively selected live cells, 0.6% pink cells were obtained using single-base-mutagenic oligonucleotides, indicating that very few single-base mutations were introduced, possibly owing to mismatch tolerance. This led to the consideration of various targetmismatched crRNAs to prevent the death of single-base-edited cells. Consequently, we obtained 99.7% pink colonies after CRISPR/Cpf1-mediated negative selection using an appropriate singlemismatched crRNA. Furthermore, Sanger sequencing revealed that single-base mutations were successfully edited in the 99.7% of pink cells, while only two of nine among 0.6% of pink cells were correctly edited. The results indicate that the target-mismatched Cpf1 negative selection can assist in efficient and accurate single-base genome editing methods in C. glutamicum.
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Affiliation(s)
- Hyun Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Se Young Oh
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea,Corresponding author Phone: +82-31-670-3356 E-mail:
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24
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Kerry RG, Das G, Golla U, Del Pilar Rodriguez-Torres M, Shin H, Patra JK. Engineered probiotic and prebiotic nutraceutical supplementations in combating non-communicable disorders: A review. Curr Pharm Biotechnol 2020; 23:72-97. [PMID: 33050862 DOI: 10.2174/1389201021666201013153142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 11/22/2022]
Abstract
Nutritional supplementations are a form of nutrition sources that may help in improving health complexities throughout the life span of a person. Under the umbrella of food supplementations, nutraceuticals are products extracted from edible sources that provide medical benefits along with primary nutritional value, these can be considered as functional foods. These nutraceutical supplementations are also evidenced in altering the commensal gut microbiota and help to prevent or fight against chronic non-communicable degenerative diseases in adults including neurological disorders (Autism Spectrum Disorder [ASD], Parkinson's disease [PD] and Multiple sclerosis [MS]) and metabolic disorder (Type-II Diabetes, Obesity and non-alcoholic fatty liver disease). Even the complexities of preterm babies like extra-uterine growth restriction, necrotizing enterocolitis, infant eczema and allergy (during pregnancy) and bronchopulmonary dysplasia, etc. could also be lessened up by providing proper nutrition. Molecular perceptive of inflammatory and apoptotic modulators regulating the pathogenesis of these health risks, their control and management by probiotics and prebiotics could further emphasize the scientific overview of their utility. The pivotal role of nutraceutical supplementations in regulating or modulating molecular pathways coupled with the above mentioned non-communicable diseases are briefly described. Lastly, an overall introduction to the sophisticated genome-editing techniques and advanced delivery systems in therapeutic activities applicable under these health risks are also emphasized in this paper.
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Affiliation(s)
| | - Gitishree Das
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Upendarrao Golla
- Division of Hematology and Oncology, Penn State College of Medicine, Hershey, PA 17033. United States
| | - Maria Del Pilar Rodriguez-Torres
- Laboratorio de Ondas de Choque (LOCH), Centro de Física Aplicada y Tecnología Avanzada (CFATA), Universidad Nacional Autónoma de México, Campus UNAM Juriquilla Boulevard Juriquilla no. 3001, Santiago de Querétaro, Qro., C.P. 76230. Mexico
| | - HanSeung Shin
- Department of Food Science and Biotechnology, Dongguk University-Seoul, Goyangsi 10326. Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Goyangsi 10326. Korea
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25
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Hao W, Suo F, Lin Q, Chen Q, Zhou L, Liu Z, Cui W, Zhou Z. Design and Construction of Portable CRISPR-Cpf1-Mediated Genome Editing in Bacillus subtilis 168 Oriented Toward Multiple Utilities. Front Bioeng Biotechnol 2020; 8:524676. [PMID: 32984297 PMCID: PMC7492563 DOI: 10.3389/fbioe.2020.524676] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
Bacillus subtilis is an important Gram-positive bacterium for industrial biotechnology, which has been widely used to produce diverse high-value added chemicals and industrially and pharmaceutically relevant proteins. Robust and versatile toolkits for genome editing in B. subtilis are highly demanding to design higher version chassis. Although the Streptococcus pyogenes (Sp) CRISPR-Cas9 has been extensively adapted for genome engineering of multiple bacteria, it has many defects, such as higher molecular weight which leads to higher carrier load, low deletion efficiency and complexity of sgRNA construction for multiplex genome editing. Here, we designed a CRISPR-Cpf1-based toolkit employing a type V Cas protein, Cpf1 from Francisella novicida. Using this platform, we precisely deleted single gene and gene cluster in B. subtilis with high editing efficiency, such as sacA, ganA, ligD & ligV, and bac operon. Especially, an extremely large gene cluster of 38 kb in B. subtilis genome was accurately deleted from the genome without introducing any unexpected mutations. Meanwhile, the synthetic platform was further upgraded to a version for multiplex genome editing, upon which two genes sacA and aprE were precisely and efficiently deleted using only one plasmid harboring two targeting sequences. In addition, we successfully inserted foreign genes into the genome of the chassis using the CRISPR-Cpf1 platform. Our work highlighted the availability of CRISPR-Cpf1 to gene manipulation in B. subtilis, including the flexible deletion of a single gene and multiple genes or a gene cluster, and gene knock-in. The designed genome-editing platform was easily and broadly applicable to other microorganisms. The novel platforms we constructed in this study provide a promising tool for efficient genome editing in diverse bacteria.
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Affiliation(s)
- Wenliang Hao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Feiya Suo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiao Lin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiaoqing Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Jiangnan University (Rugao) Food Biotechnology Research Institute, Jiangsu, China
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26
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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27
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Ding W, Zhang Y, Shi S. Development and Application of CRISPR/Cas in Microbial Biotechnology. Front Bioeng Biotechnol 2020; 8:711. [PMID: 32695770 PMCID: PMC7338305 DOI: 10.3389/fbioe.2020.00711] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has been rapidly developed as versatile genomic engineering tools with high efficiency, accuracy and flexibility, and has revolutionized traditional methods for applications in microbial biotechnology. Here, key points of building reliable CRISPR/Cas system for genome engineering are discussed, including the Cas protein, the guide RNA and the donor DNA. Following an overview of various CRISPR/Cas tools for genome engineering, including gene activation, gene interference, orthogonal CRISPR systems and precise single base editing, we highlighted the application of CRISPR/Cas toolbox for multiplexed engineering and high throughput screening. We then summarize recent applications of CRISPR/Cas systems in metabolic engineering toward production of chemicals and natural compounds, and end with perspectives of future advancements.
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Affiliation(s)
- Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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28
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Parveen S, Akhtar N, Ghauri MA, Akhtar K. Conventional genetic manipulation of desulfurizing bacteria and prospects of using CRISPR-Cas systems for enhanced desulfurization activity. Crit Rev Microbiol 2020; 46:300-320. [PMID: 32530374 DOI: 10.1080/1040841x.2020.1772195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Highly active and stable biocatalysts are the prerequisite for industrial scale application of the biodesulfurization process. Scientists are making efforts for increasing the desulfurizing activity of native strains by employing various genetic engineering approaches. Nevertheless, the achieved desulfurization rate is lower than the industrial requirements. Thus, there is a dire need to use efficient genetic tools for precise genome editing of desulfurizing bacteria for enhanced efficiency. In comparison to the previously used genetic engineering tools the newly developed CRISPR-Cas is a more efficient and simple genetic tool that has been successfully applied for targeted genome modification of eukaryotes as well as prokaryotes. In this paper, we have reviewed the approaches, previously used to enhance the biodesulfurization rates of the sulfur metabolizing microorganisms and have discussed the potential of CRISPR-Cas systems in engineering desulfurizing biocatalysts. We have also proposed a model to construct competent desulfurizing recombinants involving use of CRISPR-Cas technology. The model can be used to over-express the dsz genes under a constitutive promoter in a suitable heterologous host, to get a steady expression of desulfurization pathway. This may serve as an inducement to develop better performing desulfurizing recombinant strains using CRISPR-Cas systems, which can be helpful in increasing the rate of biodesulfurization in future.
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Affiliation(s)
- Sana Parveen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad A Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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29
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Choudhury A, Fankhauser RG, Freed EF, Oh EJ, Morgenthaler AB, Bassalo MC, Copley SD, Kaar JL, Gill RT. Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli. ACS Synth Biol 2020; 9:1083-1099. [PMID: 32298586 DOI: 10.1021/acssynbio.9b00440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In E. coli, editing efficiency with Cas9-mediated recombineering varies across targets due to differences in the level of Cas9:gRNA-mediated DNA double-strand break (DSB)-induced cell death. We found that editing efficiency with the same gRNA and repair template can also change with target position, cas9 promoter strength, and growth conditions. Incomplete editing, off-target activity, nontargeted mutations, and failure to cleave target DNA even if Cas9 is bound also compromise editing efficiency. These effects on editing efficiency were gRNA-specific. We propose that differences in the efficiency of Cas9:gRNA-mediated DNA DSBs, as well as possible differences in binding of Cas9:gRNA complexes to their target sites, account for the observed variations in editing efficiency between gRNAs. We show that editing behavior using the same gRNA can be modified by mutating the gRNA spacer, which changes the DNA DSB activity. Finally, we discuss how variable editing with different gRNAs could limit high-throughput applications and provide strategies to overcome these limitations.
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Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- IAME, UMR 1137, INSERM, Universités Paris Diderot et Paris Nord, Paris, 75018, France
| | - Reilly G Fankhauser
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Emily F Freed
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Eun Joong Oh
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Andrew B Morgenthaler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Marcelo C Bassalo
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, Colorado 80303, United States
- Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Copenhagen 2800, Denmark
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30
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Pines G, Fankhauser RG, Eckert CA. Predicting Drug Resistance Using Deep Mutational Scanning. Molecules 2020; 25:E2265. [PMID: 32403408 PMCID: PMC7248951 DOI: 10.3390/molecules25092265] [Citation(s) in RCA: 5] [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: 04/12/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a major healthcare challenge, resulting in a continuous need to develop new inhibitors. The development of these inhibitors requires an understanding of the mechanisms of resistance for a critical mass of occurrences. Recent genome editing technologies based on high-throughput DNA synthesis and sequencing may help to predict mutations resulting in resistance by testing large mutagenesis libraries. Here we describe the rationale of this approach, with examples and relevance to drug development and resistance in malaria.
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Affiliation(s)
- Gur Pines
- Department of Entomology, Agricultural Research Organization, Volcani Center, P.O.B 15159, Rishon LeZion 7505101, Israel
| | - Reilly G. Fankhauser
- Department of Dermatology, Oregon Health & Science University, Baird Hall 3225 SW Pavilion Loop, Portland, OR 97239, USA;
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, 027 UCB, Boulder, CO 80309, USA
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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31
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Choudhury A, Fenster JA, Fankhauser RG, Kaar JL, Tenaillon O, Gill RT. CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli. Mol Syst Biol 2020; 16:e9265. [PMID: 32175691 PMCID: PMC7073797 DOI: 10.15252/msb.20199265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/14/2023] Open
Abstract
Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single gRNA pre-validated for high efficiency. Tracking mutation frequency through deep sequencing revealed biases in the position and the number of the introduced mutations. We overcame these biases by increasing the homology arm length and blocking mismatch repair to achieve a mutation efficiency of 85% for non-essential genes and 55% for essential genes. These experiments also improved our understanding of poorly characterized recombineering process using dsDNA donors with single nucleotide changes. Finally, we applied our technology to target rpoB, the beta subunit of RNA polymerase, to study resistance against rifampicin. In a single experiment, we validate multiple biochemical and clinical observations made in the previous decades and provide insights into resistance compensation with the study of double mutants.
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Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- IAMEINSERMUniversité de ParisParisFrance
| | - Jacob A Fenster
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Joel L Kaar
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Ryan T Gill
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- Renewable & Sustainable Energy InstituteUniversity of ColoradoBoulderCOUSA
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityCopenhagenDenmark
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32
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Wang L, Zhang J. Prediction of sgRNA on-target activity in bacteria by deep learning. BMC Bioinformatics 2019; 20:517. [PMID: 31651233 PMCID: PMC6814057 DOI: 10.1186/s12859-019-3151-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/04/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND One of the main challenges for the CRISPR-Cas9 system is selecting optimal single-guide RNAs (sgRNAs). Recently, deep learning has enhanced sgRNA prediction in eukaryotes. However, the prokaryotic chromatin structure is different from eukaryotes, so models trained on eukaryotes may not apply to prokaryotes. RESULTS We designed and implemented a convolutional neural network to predict sgRNA activity in Escherichia coli. The network was trained and tested on the recently-released sgRNA activity dataset. Our convolutional neural network achieved excellent performance, yielding average Spearman correlation coefficients of 0.5817, 0.7105, and 0.3602, respectively for Cas9, eSpCas9 and Cas9 with a recA coding region deletion. We confirmed that the sgRNA prediction models trained on prokaryotes do not apply to eukaryotes and vice versa. We adopted perturbation-based approaches to analyze distinct biological patterns between prokaryotic and eukaryotic editing. Then, we improved the predictive performance of the prokaryotic Cas9 system by transfer learning. Finally, we determined that potential off-target scores accumulated on a genome-wide scale affect on-target activity, which could slightly improve on-target predictive performance. CONCLUSIONS We developed convolutional neural networks to predict sgRNA activity for wild type and mutant Cas9 in prokaryotes. Our results show that the prediction accuracy of our method is improved over state-of-the-art models.
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Affiliation(s)
- Lei Wang
- School of Life Science, Beijing Institute of Technology, South Zhongguancun Street, Beijing, 100081 China
| | - Juhua Zhang
- School of Life Science, Beijing Institute of Technology, South Zhongguancun Street, Beijing, 100081 China
- Key Laboratory of Convergence Medical Engineering System and Healthcare Technology, The Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
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33
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Liu D, Huang C, Guo J, Zhang P, Chen T, Wang Z, Zhao X. Development and characterization of a CRISPR/Cas9n-based multiplex genome editing system for Bacillus subtilis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:197. [PMID: 31572493 PMCID: PMC6764132 DOI: 10.1186/s13068-019-1537-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in multiplex genome editing technologies. However, simultaneously modulating multiple genes on the chromosome remains challenging in Bacillus subtilis. Thus, developing an efficient and convenient method for B. subtilis multiplex genome editing is imperative. RESULTS Here, we developed a CRISPR/Cas9n-based multiplex genome editing system for iterative genome editing in B. subtilis. This system enabled us to introduce various types of genomic modifications with more satisfying efficiency than using CRISPR/Cas9, especially in multiplex gene editing. Our system achieved at least 80% efficiency for 1-8 kb gene deletions, at least 90% efficiency for 1-2 kb gene insertions, near 100% efficiency for site-directed mutagenesis, 23.6% efficiency for large DNA fragment deletion and near 50% efficiency for three simultaneous point mutations. The efficiency for multiplex gene editing was further improved by regulating the nick repair mechanism mediated by ligD gene, which finally led to roughly 65% efficiency for introducing three point mutations on the chromosome. To demonstrate its potential, we applied our system to simultaneously fine-tune three genes in the riboflavin operon and significantly improved the production of riboflavin in a single cycle. CONCLUSIONS We present not only the iterative CRISPR/Cas9n system for B. subtilis but also the highest efficiency for simultaneous modulation of multiple genes on the chromosome in B. subtilis reported to date. We anticipate this CRISPR/Cas9n mediated system to greatly enhance the optimization of diverse biological systems via metabolic engineering and synthetic biology.
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Affiliation(s)
- Dingyu Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Can Huang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Jiaxin Guo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Peiji Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Xueming Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
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Liu Q, Shi X, Song L, Liu H, Zhou X, Wang Q, Zhang Y, Cai M. CRISPR-Cas9-mediated genomic multiloci integration in Pichia pastoris. Microb Cell Fact 2019; 18:144. [PMID: 31434578 PMCID: PMC6704636 DOI: 10.1186/s12934-019-1194-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pichia pastoris (syn. Komagataella phaffii) is a widely used generally recognized as safe host for heterologous expression of proteins in both industry and academia. Recently, it has been shown to be a potentially good chassis host for the production of high-value pharmaceuticals and chemicals. Nevertheless, limited availability of selective markers and low efficiency of homologous recombination make this process difficult and time-consuming, particularly in the case of multistep biosynthetic pathways. Therefore, it is crucial to develop an efficient and marker-free multiloci gene knock-in method in P. pastoris. RESULTS A non-homologous-end-joining defective strain (Δku70) was first constructed using the CRISPR-Cas9 based gene deficiency approach. It was then used as a parent strain for multiloci gene integration. Ten guide RNA (gRNA) targets were designed within 100 bp upstream of the promoters or downstream of terminator, and then tested using an eGFP reporter and confirmed as suitable single-locus integration sites. Three high-efficiency gRNA targets (PAOX1UP-g2, PTEF1UP-g1, and PFLD1UP-g1) were selected for double- and triple-locus co-integration. The integration efficiency ranged from 57.7 to 70% and 12.5 to 32.1% for double-locus and triple-locus integration, respectively. In addition, biosynthetic pathways of 6-methylsalicylic acid and 3-methylcatechol were successfully assembled using the developed method by one-step integration of functional genes. The desired products were obtained, which further established the effectiveness and applicability of the developed CRISPR-Cas9-mediated gene co-integration method in P. pastoris. CONCLUSIONS A CRISPR-Cas9-mediated multiloci gene integration method was developed with efficient gRNA targets in P. pastoris. Using this method, multiple gene cassettes can be simultaneously integrated into the genome without employing selective markers. The multiloci integration strategy is beneficial for pathway assembly of complicated pharmaceuticals and chemicals expressed in P. pastoris.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Xiaona Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Haifeng Liu
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai, 200237 China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
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Guo J, Wang T, Guan C, Liu B, Luo C, Xie Z, Zhang C, Xing XH. Improved sgRNA design in bacteria via genome-wide activity profiling. Nucleic Acids Res 2019; 46:7052-7069. [PMID: 29982721 PMCID: PMC6101607 DOI: 10.1093/nar/gky572] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/14/2018] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas9 is a promising tool in prokaryotic genome engineering, but its success is limited by the widely varying on-target activity of single guide RNAs (sgRNAs). Based on the association of CRISPR/Cas9-induced DNA cleavage with cellular lethality, we systematically profiled sgRNA activity by co-expressing a genome-scale library (∼70 000 sgRNAs) with Cas9 or its specificity-improved mutant in Escherichia coli. Based on this large-scale dataset, we constructed a comprehensive and high-density sgRNA activity map, which enables selecting highly active sgRNAs for any locus across the genome in this model organism. We also identified ‘resistant’ genomic loci with respect to CRISPR/Cas9 activity, notwithstanding the highly accessible DNA in bacterial cells. Moreover, we found that previous sgRNA activity prediction models that were trained on mammalian cell datasets were inadequate when coping with our results, highlighting the key limitations and biases of previous models. We hence developed an integrated algorithm to accurately predict highly effective sgRNAs, aiming to facilitate CRISPR/Cas9-based genome engineering, screenings and antimicrobials design in bacteria. We also isolated the important sgRNA features that contribute to DNA cleavage and characterized their key differences among wild type Cas9 and its mutant, shedding light on the biophysical mechanisms of the CRISPR/Cas9 system.
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Affiliation(s)
- Jiahui Guo
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Tianmin Wang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Changge Guan
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Bing Liu
- Beijing Syngentech Co., Ltd., Beijing 102206, China
| | - Cheng Luo
- Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Tsinghua National Lab for Information Science and Technology, Tsinghua University, Beijing 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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36
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Landon S, Rees-Garbutt J, Marucci L, Grierson C. Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering. Essays Biochem 2019; 63:267-284. [PMID: 31243142 PMCID: PMC6610458 DOI: 10.1042/ebc20180045] [Citation(s) in RCA: 10] [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: 02/28/2019] [Revised: 05/19/2019] [Accepted: 05/23/2019] [Indexed: 01/04/2023]
Abstract
Producing 'designer cells' with specific functions is potentially feasible in the near future. Recent developments, including whole-cell models, genome design algorithms and gene editing tools, have advanced the possibility of combining biological research and mathematical modelling to further understand and better design cellular processes. In this review, we will explore computational and experimental approaches used for metabolic and genome design. We will highlight the relevance of modelling in this process, and challenges associated with the generation of quantitative predictions about cell behaviour as a whole: although many cellular processes are well understood at the subsystem level, it has proved a hugely complex task to integrate separate components together to model and study an entire cell. We explore these developments, highlighting where computational design algorithms compensate for missing cellular information and underlining where computational models can complement and reduce lab experimentation. We will examine issues and illuminate the next steps for genome engineering.
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Affiliation(s)
- Sophie Landon
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
| | - Joshua Rees-Garbutt
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, U.K
| | - Lucia Marucci
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K.
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
| | - Claire Grierson
- BrisSynBio, University of Bristol, Bristol BS8 1TQ, U.K.
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, U.K
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37
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Barriers to genome editing with CRISPR in bacteria. J Ind Microbiol Biotechnol 2019; 46:1327-1341. [PMID: 31165970 DOI: 10.1007/s10295-019-02195-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
Genome editing is essential for probing genotype-phenotype relationships and for enhancing chemical production and phenotypic robustness in industrial bacteria. Currently, the most popular tools for genome editing couple recombineering with DNA cleavage by the CRISPR nuclease Cas9 from Streptococcus pyogenes. Although successful in some model strains, CRISPR-based genome editing has been slow to extend to the multitude of industrially relevant bacteria. In this review, we analyze existing barriers to implementing CRISPR-based editing across diverse bacterial species. We first compare the efficacy of current CRISPR-based editing strategies. Next, we discuss alternatives when the S. pyogenes Cas9 does not yield colonies. Finally, we describe different ways bacteria can evade editing and how elucidating these failure modes can improve CRISPR-based genome editing across strains. Together, this review highlights existing obstacles to CRISPR-based editing in bacteria and offers guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains.
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Abstract
Our bodies are colonized by a complex ecosystem of bacteria, unicellular eukaryotes and their viruses that together play a major role in our health. Over the past few years tools derived from the prokaryotic immune system known as CRISPR-Cas have empowered researchers to modify and study organisms with unprecedented ease and efficiency. Here we discuss how various types of CRISPR-Cas systems can be used to modify the genome of gut microorganisms and bacteriophages. CRISPR-Cas systems can also be delivered to bacterial population and programmed to specifically eliminate members of the microbiome. Finally, engineered CRISPR-Cas systems can be used to control gene expression and modulate the production of metabolites and proteins. Together these tools provide exciting opportunities to investigate the complex interplay between members of the microbiome and our bodies, and present new avenues for the development of drugs that target the microbiome. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
| | - David Bikard
- Synthetic Biology Group, Department of Microbiology, Institut Pasteur, Paris 75015, France
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39
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Zhang J, Yang F, Yang Y, Jiang Y, Huo YX. Optimizing a CRISPR-Cpf1-based genome engineering system for Corynebacterium glutamicum. Microb Cell Fact 2019; 18:60. [PMID: 30909908 PMCID: PMC6432761 DOI: 10.1186/s12934-019-1109-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/19/2019] [Indexed: 11/10/2022] Open
Abstract
Background Corynebacterium glutamicum is an important industrial strain for the production of a diverse range of chemicals. Cpf1 nucleases are highly specific and programmable, with efficiencies comparable to those of Cas9. Although the Francisella novicida (Fn) CRISPR-Cpf1 system has been adapted for genome editing in C. glutamicum, the editing efficiency is currently less than 15%, due to false positives caused by the poor targeting efficiency of the crRNA. Results To address this limitation, a screening strategy was developed in this study to systematically evaluate crRNA targeting efficiency in C. glutamicum. We quantitatively examined various parameters of the C. glutamicum CRISPR-Cpf1 system, including the protospacer adjacent motif (PAM) sequence, the length of the spacer sequence, and the type of repair template. We found that the most efficient C. glutamicum crRNA contained a 5′-NYTV-3′ PAM and a 21 bp spacer sequence. Moreover, we observed that linear DNA could be used to repair double strand breaks. Conclusions Here, we identified optimized PAM-related parameters for the CRISPR-Cpf1 system in C. glutamicum. Our study sheds light on the function of the FnCpf1 endonuclease and Cpf1-based genome editing. This optimized system, with higher editing efficiency, could be used to increase the production of bulk chemicals, such as isobutyrate, in C. glutamicum. Electronic supplementary material The online version of this article (10.1186/s12934-019-1109-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiao Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Fayu Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Yunpeng Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China.,UCLA Institute of Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yu Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China. .,UCLA Institute of Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China.
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40
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Chemical transformation mediated CRISPR/Cas9 genome editing in Escherichia coli. Biotechnol Lett 2018; 41:293-303. [PMID: 30547274 DOI: 10.1007/s10529-018-02639-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 12/08/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVES To develop a convenient chemical transformation mediated CRISPR/Cas9 (CT-CRISPR/Cas9) system for genome editing in Escherichia coli. RESULTS Here, we have constructed a CT-CRISPR/Cas9 system, which can precisely edit bacterial genome (replacing, deleting, inserting or point mutating a target gene) through chemical transformation. Compared with the traditional electroporation mediated CRISPR/Cas9 (ET-CRISPR/Cas9) system, genome editing with the CT-CRISPR/Cas9 system is much cheaper and simpler. In the CT-CRISPR/Cas9 system, we observed efficient genome editing on LB-agar plates. The CT-CRISPR/Cas9 system has successfully modified the target gene with the editing template flanked by short homologous DNA fragments (~ 50 bp) which were designed in primers. We used the lab-made CaCl2 solution to perform the CT-CRISPR/Cas9 experiment and successfully edited the genome of E. coli. Potential application of the CT-CRISPR/Cas9 system in high-throughput genome editing was evaluated in two E. coli strains by using a multiwell plate. CONCLUSIONS Our work provides a simple and cheap genome-editing method, that is expected to be widely applied as a routine genetic engineering method.
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41
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Snoeck N, De Mol ML, Van Herpe D, Goormans A, Maryns I, Coussement P, Peters G, Beauprez J, De Maeseneire SL, Soetaert W. Serine integrase recombinational engineering (SIRE): A versatile toolbox for genome editing. Biotechnol Bioeng 2018; 116:364-374. [PMID: 30345503 DOI: 10.1002/bit.26854] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/24/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022]
Abstract
Chromosomal integration of biosynthetic pathways for the biotechnological production of high-value chemicals is a necessity to develop industrial strains with a high long-term stability and a low production variability. However, the introduction of multiple transcription units into the microbial genome remains a difficult task. Despite recent advances, current methodologies are either laborious or efficiencies highly fluctuate depending on the length and the type of the construct. Here we present serine integrase recombinational engineering (SIRE), a novel methodology which combines the ease of recombinase-mediated cassette exchange (RMCE) with the selectivity of orthogonal att sites of the PhiC31 integrase. As a proof of concept, this toolbox is developed for Escherichia coli. Using SIRE we were able to introduce a 10.3 kb biosynthetic gene cluster on different locations throughout the genome with an efficiency of 100% for the integrating step and without the need for selection markers on the knock-in cassette. Next to integrating large fragments, the option for multitargeting, for deleting operons, as well as for performing in vivo assemblies further expand and proof the versatility of the SIRE toolbox for E. coli. Finally, the serine integrase PhiC31 was also applied in the yeast Saccharomyces cerevisiae as a marker recovery tool, indicating the potential and portability of this toolbox.
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Affiliation(s)
- Nico Snoeck
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Maarten L De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Dries Van Herpe
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anke Goormans
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Isabelle Maryns
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wim Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biochemical and Microbial Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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42
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Yang ZK, Luo H, Zhang Y, Wang B, Gao F. Pan-genomic analysis provides novel insights into the association of E.coli with human host and its minimal genome. Bioinformatics 2018; 35:1987-1991. [DOI: 10.1093/bioinformatics/bty938] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhi-Kai Yang
- Department of Physics, School of Science
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
- SinoGenoMax Co., Ltd./Chinese National Human Genome Center, Beijing, China
| | - Hao Luo
- Department of Physics, School of Science
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Yanming Zhang
- SinoGenoMax Co., Ltd./Chinese National Human Genome Center, Beijing, China
| | - Baijing Wang
- SinoGenoMax Co., Ltd./Chinese National Human Genome Center, Beijing, China
| | - Feng Gao
- Department of Physics, School of Science
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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43
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Arazoe T, Kondo A, Nishida K. Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering. Biotechnol J 2018; 13:e1700596. [PMID: 29862665 DOI: 10.1002/biot.201700596] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/15/2018] [Indexed: 12/31/2022]
Abstract
Since the emergence of programmable RNA-guided nucleases based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems, genome editing technologies have become a simplified and versatile tool for genome editing in various organisms and cell types. Although genome editing enables efficient genome manipulations, such as gene disruptions, gene knockins, and chromosomal translocations via DNA double-strand break (DSB) repair in eukaryotes, DSBs induced by the CRISPR/Cas system are lethal or severely toxic to many microorganisms. Therefore, in many prokaryotes, including industrially useful microbes, the CRISPR/Cas system is often used as a negative selection component in combination with recombineering or other related strategies. Novel and revolutionary technologies have been recently developed to re-write targeted nucleotides (C:G to T:A and A:T to G:C) without DSBs and donor DNA templates. These technologies rely on the recruitment of deaminases at specific target loci using the nuclease-deficient CRISPR/Cas system. Here, the authors review and compare CRISPR-based genome editing, current base editing platforms and their spectra. The authors discuss how these technologies can be applied in various aspects of microbial metabolic engineering to overcome barriers to cellular regulation in prokaryotes.
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Affiliation(s)
- Takayuki Arazoe
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Keiji Nishida
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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44
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Górski A, Międzybrodzki R, Łobocka M, Głowacka-Rutkowska A, Bednarek A, Borysowski J, Jończyk-Matysiak E, Łusiak-Szelachowska M, Weber-Dąbrowska B, Bagińska N, Letkiewicz S, Dąbrowska K, Scheres J. Phage Therapy: What Have We Learned? Viruses 2018; 10:E288. [PMID: 29843391 PMCID: PMC6024844 DOI: 10.3390/v10060288] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/11/2018] [Accepted: 05/22/2018] [Indexed: 02/07/2023] Open
Abstract
In this article we explain how current events in the field of phage therapy may positively influence its future development. We discuss the shift in position of the authorities, academia, media, non-governmental organizations, regulatory agencies, patients, and doctors which could enable further advances in the research and application of the therapy. In addition, we discuss methods to obtain optimal phage preparations and suggest the potential of novel applications of phage therapy extending beyond its anti-bacterial action.
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Affiliation(s)
- Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Ryszard Międzybrodzki
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Nowoursynowska Street 159, 02-776 Warsaw, Poland.
| | - Aleksandra Głowacka-Rutkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
| | - Agnieszka Bednarek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego Street 5 A, 02-106 Warsaw, Poland.
| | - Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Nowogrodzka Street 59, 02-006 Warsaw, Poland.
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Marzanna Łusiak-Szelachowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Natalia Bagińska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
| | - Sławomir Letkiewicz
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Medical Sciences Institute, Katowice School of Economics, Harcerzy Września Street 3, 40-659 Katowice, Poland.
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla Street 12, 53-114 Wroclaw, Poland.
- Research and Development Center, Regional Specialized Hospital, Kamieńskiego 73a, 51-124 Wrocław, Poland.
| | - Jacques Scheres
- National Institute of Public Health NIZP, Chocimska Street 24, 00-971 Warsaw, Poland.
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Gao W, Yin J, Bao L, Wang Q, Hou S, Yue Y, Yao W, Gao X. Engineering Extracellular Expression Systems in Escherichia coli Based on Transcriptome Analysis and Cell Growth State. ACS Synth Biol 2018; 7:1291-1302. [PMID: 29668266 DOI: 10.1021/acssynbio.7b00400] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli extracellular expression systems have a number of advantages over other systems, such as lower pyrogen levels and a simple purification process. Various approaches, such as the generation of leaky mutants via chromosomal engineering, have been explored for this expression system. However, extracellular protein yields in leaky mutants are relatively low compared to that in intracellular expression systems and therefore need to be improved. In this work, we describe the construction, characterization, and mechanism of enhanced extracellular expression in Escherichia coli. On the basis of the localizations, functions, and transcription levels of cell envelope proteins, we systematically elucidated the effects of multiple gene deletions on cell growth and extracellular expression using modified CRISPR/Cas9-based genome editing and a FlAsH labeling assay. High extracellular yields of heterologous proteins of different sizes were obtained by screening multiple gene mutations. The enhancement of extracellular secretion was associated with the derepression of translation and translocation. This work utilized universal methods in the design of extracellular expression systems for genes not directly associated with protein synthesis that were used to generate strains with higher protein expression capability. We anticipate that extracellular expression systems may help to shed light on the poorly understood aspects of these secretion processes as well as to further assist in the construction of engineered prokaryotic cells for efficient extracellular production of heterologous proteins.
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Affiliation(s)
- Wen Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Jun Yin
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Lichen Bao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Qun Wang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Shan Hou
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Yali Yue
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Wenbing Yao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
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Wang J, Zhao P, Li Y, Xu L, Tian P. Engineering CRISPR interference system in Klebsiella pneumoniae for attenuating lactic acid synthesis. Microb Cell Fact 2018; 17:56. [PMID: 29622042 PMCID: PMC5887262 DOI: 10.1186/s12934-018-0903-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/31/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a promising industrial species for bioproduction of bulk chemicals such as 1,3-propanediol, 2,3-butanediol and 3-hydroxypropionic acid (3-HP). However, lactic acid is a troublesome by-product when optimizing for 3-HP production. Therefore, it is highly desirable to minimize lactic acid. RESULTS Here, we show that lactic acid synthesis can be largely blocked by an engineered CRISPR interference (CRISPRi) system in K. pneumoniae. EGFP was recruited as a reporter of this CRISPRi system. Fluorescence assay of this CRISPRi system showed that enhanced green fluorescent protein (EGFP) expression level was repressed by 85-90%. To further test this CRISPRi system, guide RNAs were designed to individually or simultaneously target four lactate-producing enzyme genes. Results showed that all lactate-producing enzyme genes were significantly repressed. Notably, D-lactate dehydrogenase (ldhA) was shown to be the most influential enzyme for lactic acid formation in micro-aerobic conditions, as inhibiting ldhA alone led to lactic acid level similar to simultaneously repressing four genes. In shake flask cultivation, the strain coexpressing puuC (an aldehyde dehydrogenase catalyzing 3-hydroxypropionaldehyde to 3-HP) and dCas9-sgRNA inhibiting ldhA produced 1.37-fold 3-HP relative to the reference strain. Furthermore, in bioreactor cultivation, this CRISPRi strain inhibiting ldhA produced 36.7 g/L 3-HP, but only generated 1 g/L lactic acid. Clearly, this engineered CRISPRi system largely simplified downstream separation of 3-HP from its isomer lactic acid, an extreme challenge for 3-HP bioprocess. CONCLUSIONS This study offers a deep understanding of lactic acid metabolism in diverse species, and we believe that this CRISPRi system will facilitate biomanufacturing and functional genome studies of K. pneumoniae or beyond.
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Affiliation(s)
- Jingxuan Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People’s Republic of China
| | - Peng Zhao
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People’s Republic of China
| | - Ying Li
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023 People’s Republic of China
| | - Lida Xu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People’s Republic of China
| | - Pingfang Tian
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People’s Republic of China
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König E, Zerbini F, Zanella I, Fraccascia D, Grandi G. Multiple Stepwise Gene Knockout Using CRISPR/Cas9 in Escherichia coli. Bio Protoc 2018; 8:e2688. [PMID: 34179238 PMCID: PMC8203979 DOI: 10.21769/bioprotoc.2688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/24/2017] [Accepted: 12/25/2017] [Indexed: 11/02/2022] Open
Abstract
With the recent implementation of the CRISPR/Cas9 technology as a standard tool for genome editing, laboratories all over the world are undergoing one of the biggest advancements in molecular biology since PCR. The key advantage of this method is its simplicity and universal applicability for species of any phylum. Of particular interest is the extensively studied Gram-negative bacterium Escherichia coli, as it is considered as the workhorse for both research and industrial purposes. Here, we present a simple, robust and effective protocol using the CRISPR/Cas9 system in combination with the λ Red machinery for gene knockout in E. coli. Crucial in our procedure is the use of a double-stranded donor DNA and a curing strategy for removal of the guide RNA encoding plasmid that allows starting a new mutation after only two working days. Our protocol allows multiple, stepwise gene knockout strains with high mutagenesis efficiencies applicable for high-throughput approaches.
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Affiliation(s)
- Enrico König
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Francesca Zerbini
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Ilaria Zanella
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Davide Fraccascia
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
| | - Guido Grandi
- Synthetic and Structural Vaccinology Unit, CIBIO, University of Trento, Via Sommarive, 9, Trento, Italy
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Moreb EA, Hoover B, Yaseen A, Valyasevi N, Roecker Z, Menacho-Melgar R, Lynch MD. Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity. ACS Synth Biol 2017; 6:2209-2218. [PMID: 28915012 DOI: 10.1021/acssynbio.7b00174] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.
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Affiliation(s)
- Eirik Adim Moreb
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Benjamin Hoover
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Adam Yaseen
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Nisakorn Valyasevi
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Zoe Roecker
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Lynch
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
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Peng F, Wang X, Sun Y, Dong G, Yang Y, Liu X, Bai Z. Efficient gene editing in Corynebacterium glutamicum using the CRISPR/Cas9 system. Microb Cell Fact 2017; 16:201. [PMID: 29137643 PMCID: PMC5686833 DOI: 10.1186/s12934-017-0814-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/08/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Corynebacterium glutamicum (C. glutamicum) has traditionally been used as a microbial cell factory for the industrial production of many amino acids and other industrially important commodities. C. glutamicum has recently been established as a host for recombinant protein expression; however, some intrinsic disadvantages could be improved by genetic modification. Gene editing techniques, such as deletion, insertion, or replacement, are important tools for modifying chromosomes. RESULTS In this research, we report a CRISPR/Cas9 system in C. glutamicum for rapid and efficient genome editing, including gene deletion and insertion. The system consists of two plasmids: one containing a target-specific guide RNA and a homologous sequence to a target gene, the other expressing Cas9 protein. With high efficiency (up to 100%), this system was used to disrupt the porB, mepA, clpX and Ncgl0911 genes, which affect the ability to express proteins. The porB- and mepA-deletion strains had enhanced expression of green fluorescent protein, compared with the wild-type stain. This system can also be used to engineer point mutations and gene insertions. CONCLUSIONS In this study, we adapted the CRISPR/Cas9 system from S. pyogens to gene deletion, point mutations and insertion in C. glutamicum. Compared with published genome modification methods, methods based on the CRISPR/Cas9 system can rapidly and efficiently achieve genome editing. Our research provides a powerful tool for facilitating the study of gene function, metabolic pathways, and enhanced productivity in C. glutamicum.
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Affiliation(s)
- Feng Peng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xinyue Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Yang Sun
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Guibin Dong
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
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Eriksson S, Jonas E, Rydhmer L, Röcklinsberg H. Invited review: Breeding and ethical perspectives on genetically modified and genome edited cattle. J Dairy Sci 2017; 101:1-17. [PMID: 29102147 DOI: 10.3168/jds.2017-12962] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022]
Abstract
The hot topic of genetic modification and genome editing is sometimes presented as a rapid solution to various problems in the field of animal breeding and genetics. These technologies hold potential for future use in agriculture but we need to be aware of difficulties in large-scale application and integration in breeding schemes. In this review, we discuss applications of both classical genetic modifications (GM) using vectors and genome editing in dairy cattle breeding. We use an interdisciplinary approach considering both ethical and animal breeding perspectives. Decisions on how to make use of these techniques need to be made based not only on what is possible, but on what is reasonable to do. Principles of animal integrity, naturalness, risk perception, and animal welfare issues are examples of ethically relevant factors to consider. These factors also influence public perception and decisions about regulations by authorities. We need to acknowledge that we lack complete understanding of the genetic background of complex traits. It may be difficult, therefore, to predict the full effect of certain modifications in large-scale breeding programs. We present 2 potential applications: genome editing to dispense with dehorning, and insertion of human genes in bovine genomes to improve udder health as an example of classical GM. Both of these cases could be seen as beneficial for animal welfare but they differ in other aspects. In the former case, a genetic variant already present within the species is introduced, whereas in the latter case, transgenic animals are generated-this difference may influence how society regards the applications. We underline that the use of GM, as well as genome editing, of farm animals such as cattle is not independent of the context, and should be considered as part of an entire process, including, for example, the assisted reproduction technology that needs to be used. We propose that breeding organizations and breeding companies should take an active role in ethical discussions about the use of these techniques and thereby signal to society that these questions are being responsibly addressed.
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Affiliation(s)
- S Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.
| | - E Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - L Rydhmer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - H Röcklinsberg
- Department of Animal Environment and Health, 75007 Uppsala, Sweden
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