1
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Núñez D, Oyarzún P, González S, Martínez I. Toward biomanufacturing of next-generation bacterial nanocellulose (BNC)-based materials with tailored properties: A review on genetic engineering approaches. Biotechnol Adv 2024; 74:108390. [PMID: 38823654 DOI: 10.1016/j.biotechadv.2024.108390] [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: 01/08/2024] [Revised: 05/01/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Bacterial nanocellulose (BNC) is a biopolymer that is drawing significant attention for a wide range of applications thanks to its unique structure and excellent properties, such as high purity, mechanical strength, high water holding capacity and biocompatibility. Nevertheless, the biomanufacturing of BNC is hindered due to its low yield, the instability of microbial strains and cost limitations that prevent it from being mass-produced on a large scale. Various approaches have been developed to address these problems by genetically modifying strains and to produce BNC-based biomaterials with added value. These works are summarized and discussed in the present article, which include the overexpression and knockout of genes related and not related with the nanocellulose biosynthetic operon, the application of synthetic biology approaches and CRISPR/Cas techniques to modulate BNC biosynthesis. Further discussion is provided on functionalized BNC-based biomaterials with tailored properties that are incorporated in-vivo during its biosynthesis using genetically modified strains either in single or co-culture systems (in-vivo manufacturing). This novel strategy holds potential to open the road toward cost-effective production processes and to find novel applications in a variety of technology and industrial fields.
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Affiliation(s)
- Dariela Núñez
- Departamento de Química Ambiental, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile; Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile.
| | - Patricio Oyarzún
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| | - Sebastián González
- Laboratorio de Biotecnología y Materiales Avanzados, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Alonso de Ribera 2850, Concepción, Chile
| | - Irene Martínez
- Centre for Biotechnology and Bioengineering (CeBiB), University of Chile, Beauchef 851, Santiago, Chile; Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago, Chile.
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2
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Cardiff RAL, Carothers JM, Zalatan JG, Sauro HM. Systems-Level Modeling for CRISPR-Based Metabolic Engineering. ACS Synth Biol 2024. [PMID: 39119666 DOI: 10.1021/acssynbio.4c00053] [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: 08/10/2024]
Abstract
The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. The advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.
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Affiliation(s)
- Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James M Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jesse G Zalatan
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Herbert M Sauro
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
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3
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Mol M, de Maayer P. Elucidating the biotechnological potential of the genera Parageobacillus and Saccharococcus through comparative genomic and pan-genome analysis. BMC Genomics 2024; 25:723. [PMID: 39054411 PMCID: PMC11270796 DOI: 10.1186/s12864-024-10635-1] [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: 02/20/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The genus Geobacillus and its associated taxa have been the focal point of numerous thermophilic biotechnological investigations, both at the whole cell and enzyme level. By contrast, comparatively little research has been done on its recently delineated sister genus, Parageobacillus. Here we performed pan-genomic analyses on a subset of publicly available Parageobacillus and Saccharococcus genomes to elucidate their biotechnological potential. RESULTS Phylogenomic analysis delineated the compared taxa into two distinct genera, Parageobacillus and Saccharococcus, with P. caldoxylosilyticus isolates clustering with S. thermophilus in the latter genus. Both genera present open pan-genomes, with the species P. toebii being characterized with the highest novel gene accrual. Diversification of the two genera is driven through the variable presence of plasmids, bacteriophages and transposable elements. Both genera present a range of potentially biotechnologically relevant features, including a source of novel antimicrobials, thermostable enzymes including DNA-active enzymes, carbohydrate active enzymes, proteases, lipases and carboxylesterases. Furthermore, they present a number of metabolic pathways pertinent to degradation of complex hydrocarbons and xenobiotics and for green energy production. CONCLUSIONS Comparative genomic analyses of Parageobacillus and Saccharococcus suggest that taxa in both of these genera can serve as a rich source of biotechnologically and industrially relevant secondary metabolites, thermostable enzymes and metabolic pathways that warrant further investigation.
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Affiliation(s)
- Michael Mol
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Pieter de Maayer
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, 2000, South Africa.
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4
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Karpov DS. CRISPR-Cas Systems and Genome Editing: Beginning the Era of CRISPR/Cas Therapies for Humans. Int J Mol Sci 2024; 25:5292. [PMID: 38791336 PMCID: PMC11121477 DOI: 10.3390/ijms25105292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Harnessing of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated genes) systems for detection, chemical modification, and sequence editing of nucleic acids dramatically changed many fields of fundamental science, biotechnology, and biomedicine [...].
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Affiliation(s)
- Dmitry S Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia
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5
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Barbier I, Kusumawardhani H, Chauhan L, Harlapur PV, Jolly MK, Schaerli Y. Synthetic Gene Circuits Combining CRISPR Interference and CRISPR Activation in E. coli: Importance of Equal Guide RNA Binding Affinities to Avoid Context-Dependent Effects. ACS Synth Biol 2023; 12:3064-3071. [PMID: 37813387 PMCID: PMC10594877 DOI: 10.1021/acssynbio.3c00375] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Indexed: 10/11/2023]
Abstract
Gene expression control based on clustered regularly interspaced short palindromic repeats (CRISPR) has emerged as a powerful approach for constructing synthetic gene circuits. While the use of CRISPR interference (CRISPRi) is already well-established in prokaryotic circuits, CRISPR activation (CRISPRa) is less mature, and a combination of the two in the same circuits is only just emerging. Here, we report that combining CRISPRi with SoxS-based CRISPRa in Escherichia coli can lead to context-dependent effects due to different affinities in the formation of CRISPRa and CRISPRi complexes, resulting in loss of predictable behavior. We show that this effect can be avoided by using the same scaffold guide RNA structure for both complexes.
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Affiliation(s)
- Içvara Barbier
- Department
of Fundamental Microbiology, University
of Lausanne, 1015 Lausanne, Switzerland
| | | | - Lakshya Chauhan
- Department
of Fundamental Microbiology, University
of Lausanne, 1015 Lausanne, Switzerland
- Department
of Bioengineering, Indian Institute of Science, 560012 Bengaluru, India
| | | | - Mohit Kumar Jolly
- Department
of Bioengineering, Indian Institute of Science, 560012 Bengaluru, India
| | - Yolanda Schaerli
- Department
of Fundamental Microbiology, University
of Lausanne, 1015 Lausanne, Switzerland
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6
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Zárate-Chaves CA, Audran C, Medina Culma CA, Escalon A, Javegny S, Gagnevin L, Thomas E, Pimparé LL, López CE, Jacobs JM, Noël LD, Koebnik R, Bernal AJ, Szurek B. CRISPRi in Xanthomonas demonstrates functional convergence of transcription activator-like effectors in two divergent pathogens. THE NEW PHYTOLOGIST 2023; 238:1593-1604. [PMID: 36764921 DOI: 10.1111/nph.18808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Functional analysis of large gene families in plant pathogens can be cumbersome using classical insertional mutagenesis. Additionally, Cas9 toxicity has limited the application of CRISPR-Cas9 for directed mutagenesis in bacteria. Here, we successfully applied a CRISPR interference strategy to investigate the cryptic role of the transcription activator-like effector (tale) multigene family in several plant-pathogenic Xanthomonas bacterial species, owing to their contribution to pathogen virulence. Single guide RNAs (sgRNAs) designed against Xanthomonas phaseoli pv manihotis tale conserved gene sequences efficiently silenced expression of all tales, with concomitant decrease in virulence and TALE-induced host gene expression. The system is readily translatable to other Xanthomonas species infecting rice, citrus, Brassica, and cassava, silencing up to 16 tales in a given strain using a single sgRNA. Complementation with plasmid-borne designer tales lacking the sgRNA-targeted sequence restored molecular and virulence phenotypes in all pathosystems. Our results evidenced that X. campestris pv campestris CN08 tales are relevant for symptom development in cauliflower. They also show that the MeSWEET10a sugar transporter is surprisingly targeted by the nonvascular cassava pathogen X. cassavae, highlighting a new example of TALE functional convergence between phylogenetically distant Xanthomonas. Overall, this novel technology provides a platform for discovery and rapid functional understanding of highly conserved gene families.
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Affiliation(s)
| | - Corinne Audran
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, 31326, France
| | - César Augusto Medina Culma
- Laboratorio de interacciones moleculares de microorganismos agrícolas (LIMMA), Universidad de los Andes, Bogotá, 111711, Colombia
| | - Aline Escalon
- CIRAD, UMR PVBMT, Saint-Pierre, 97410, La Réunion, France
| | | | - Lionel Gagnevin
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Emilie Thomas
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Léa-Lou Pimparé
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Camilo E López
- Manihot Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Jonathan M Jacobs
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, 43210-1358, USA
| | - Laurent D Noël
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, 31326, France
| | - Ralf Koebnik
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
| | - Adriana Jimena Bernal
- Laboratorio de interacciones moleculares de microorganismos agrícolas (LIMMA), Universidad de los Andes, Bogotá, 111711, Colombia
| | - Boris Szurek
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, 34394, France
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7
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Kolasinliler G, Aagre MM, Akkale C, Kaya HB. The use of CRISPR-Cas-based systems in bacterial cell factories. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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8
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Hu M, Chen S, Ni Y, Wei W, Mao W, Ge M, Qian X. CRISPR/Cas9-mediated genome editing in vancomycin-producing strain Amycolatopsis keratiniphila. Front Bioeng Biotechnol 2023; 11:1141176. [PMID: 36937767 PMCID: PMC10020181 DOI: 10.3389/fbioe.2023.1141176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Amycolatopsis is an important source of diverse valuable bioactive natural products. The CRISPR/Cas-mediated gene editing tool has been established in some Amycolatopsis species and has accomplished the deletion of single gene or two genes. The goal of this study was to develop a high-efficient CRISPR/Cas9-mediated genome editing system in vancomycin-producing strain A. keratiniphila HCCB10007 and enhance the production of vancomycin by deleting the large fragments of ECO-0501 BGC. By adopting the promoters of gapdhp and ermE*p which drove the expressions of scocas9 and sgRNA, respectively, the all-in-one editing plasmid by homology-directed repair (HDR) precisely deleted the single gene gtfD and inserted the gene eGFP with the efficiency of 100%. Furthermore, The CRISPR/Cas9-mediated editing system successfully deleted the large fragments of cds13-17 (7.7 kb), cds23 (12.7 kb) and cds22-23 (21.2 kb) in ECO-0501 biosynthetic gene cluster (BGC) with high efficiencies of 81%-97% by selecting the sgRNAs with a suitable PAM sequence. Finally, a larger fragment of cds4-27 (87.5 kb) in ECO-0501 BGC was deleted by a dual-sgRNA strategy. The deletion of the ECO-0501 BGCs revealed a noticeable improvement of vancomycin production, and the mutants, which were deleted the ECO-0501 BGCs of cds13-17, cds22-23 and cds4-27, all achieved a 30%-40% increase in vancomycin yield. Therefore, the successful construction of the CRISPR/Cas9-mediated genome editing system and its application in large fragment deletion in A. keratiniphila HCCB10007 might provide a powerful tool for other Amycolatopsis species.
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Affiliation(s)
- Mengyi Hu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yao Ni
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Wenwei Mao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Xiuping Qian
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
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9
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Malcı K, Jonguitud-Borrego N, van der Straten Waillet H, Puodžiu̅naitė U, Johnston EJ, Rosser SJ, Rios-Solis L. ACtivE: Assembly and CRISPR-Targeted in Vivo Editing for Yeast Genome Engineering Using Minimum Reagents and Time. ACS Synth Biol 2022; 11:3629-3643. [PMID: 36252276 PMCID: PMC9680028 DOI: 10.1021/acssynbio.2c00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Thanks to its sophistication, the CRISPR/Cas system has been a widely used yeast genome editing method. However, CRISPR methods generally rely on preassembled DNAs and extra cloning steps to deliver gRNA, Cas protein, and donor DNA. These laborious steps might hinder its usefulness. Here, we propose an alternative method, Assembly and CRISPR-targeted in vivo Editing (ACtivE), that only relies on in vivo assembly of linear DNA fragments for plasmid and donor DNA construction. Thus, depending on the user's need, these parts can be easily selected and combined from a repository, serving as a toolkit for rapid genome editing without any expensive reagent. The toolkit contains verified linear DNA fragments, which are easy to store, share, and transport at room temperature, drastically reducing expensive shipping costs and assembly time. After optimizing this technique, eight loci proximal to autonomously replicating sequences (ARS) in the yeast genome were also characterized in terms of integration and gene expression efficiencies and the impacts of the disruptions of these regions on cell fitness. The flexibility and multiplexing capacity of the ACtivE were shown by constructing a β-carotene pathway. In only a few days, >80% integration efficiency for single gene integration and >50% integration efficiency for triplex integration were achieved on Saccharomyces cerevisiae BY4741 from scratch without using in vitro DNA assembly methods, restriction enzymes, or extra cloning steps. This study presents a standardizable method to be readily employed to accelerate yeast genome engineering and provides well-defined genomic location alternatives for yeast synthetic biology and metabolic engineering purposes.
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Affiliation(s)
- Koray Malcı
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.
| | - Nestor Jonguitud-Borrego
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.
| | | | - Urtė Puodžiu̅naitė
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Emily J. Johnston
- Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Susan J. Rosser
- Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Leonardo Rios-Solis
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Natural and Environmental Sciences, Newcastle
University, Newcastle upon TyneNE1 7RU, U.K.,
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10
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Ma Z, Meliana C, Munawaroh HSH, Karaman C, Karimi-Maleh H, Low SS, Show PL. Recent advances in the analytical strategies of microbial biosensor for detection of pollutants. CHEMOSPHERE 2022; 306:135515. [PMID: 35772520 DOI: 10.1016/j.chemosphere.2022.135515] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/10/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Microbial biosensor which integrates different types of microorganisms, such as bacteria, microalgae, fungi, and virus have become suitable technologies to address limitations of conventional analytical methods. The main applications of biosensors include the detection of environmental pollutants, pathogenic bacteria and compounds related to illness, and food quality. Each type of microorganisms possesses advantages and disadvantages with different mechanisms to detect the analytes of interest. Furthermore, there is an increasing trend in genetic modifications for the development of microbial biosensors due to potential for high-throughput analysis and portability. Many review articles have discussed the applications of microbial biosensor, but many of them focusing only about bacterial-based biosensor although other microbes also possess many advantages. Additionally, reviews on the applications of all microbes as biosensor especially viral and microbial fuel cell biosensors are also still limited. Therefore, this review summarizes all the current applications of bacterial-, microalgal-, fungal-, viral-based biosensor in regard to environmental, food, and medical-related applications. The underlying mechanism of each microbes to detect the analytes are also discussed. Additionally, microbial fuel cell biosensors which have great potential in the future are also discussed. Although many advantageous microbial-based biosensors have been discovered, other areas such as forensic detection, early detection of bacteria or virus species that can lead to pandemics, and others still need further investigation. With that said, microbial-based biosensors have promising potential for vast applications where the biosensing performance of various microorganisms are presented in this review along with future perspectives to resolve problems related on microbial biosensors.
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Affiliation(s)
- Zengling Ma
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
| | - Catarina Meliana
- Department of Food Science and Nutrition, Faculty of Life Science, Indonesia International Institute of Life Sciences, Jakarta, 13210, Indonesia
| | - Heli Siti Halimatul Munawaroh
- Study Program of Chemistry, Department of Chemistry Education, Universitas Pendidikan Indonesia, Jalan Dr. Setiabudhi 229, Bandung, 40154, Indonesia
| | - Ceren Karaman
- Akdeniz University, Department of Electricity and Energy, Antalya, 07070, Turkey
| | - Hassan Karimi-Maleh
- School of Resources and Environment, University of Electronic Science and Technology of China, P.O. Box 611731, Xiyuan Ave, Chengdu, PR China; Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 9477177870, Iran
| | - Sze Shin Low
- Research Centre of Life Science and Healthcare, China Beacons Institute, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo, 315100, Zhejiang, China.
| | - Pau Loke Show
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
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11
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Ortiz-Cartagena C, Fernández-García L, Blasco L, Pacios O, Bleriot I, López M, Cantón R, Tomás M. Reverse Transcription-Loop-Mediated Isothermal Amplification-CRISPR-Cas13a Technology as a Promising Diagnostic Tool for SARS-CoV-2. Microbiol Spectr 2022; 10:e0239822. [PMID: 36169448 PMCID: PMC9604158 DOI: 10.1128/spectrum.02398-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/07/2022] [Indexed: 01/04/2023] Open
Abstract
At the end of 2019, a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a pandemic that persists to date and has resulted in more than 6.2 million deaths. In the last couple of years, researchers have made great efforts to develop a diagnostic technique that maintains high levels of sensitivity and specificity, since an accurate and early diagnosis is required to minimize the prevalence of SARS-CoV-2 infection. In this context, CRISPR-Cas systems are proposed as promising tools for development as diagnostic techniques due to their high specificity, highlighting that Cas13 endonuclease discriminates single nucleotide changes and displays collateral activity against single-stranded RNA molecules. With the aim of improving the sensitivity of diagnosis, this technology is usually combined with isothermal preamplification reactions (SHERLOCK, DETECTR). Based on this, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP)-CRISPR-Cas13a method for SARS-CoV-2 virus detection in nasopharyngeal samples without using RNA extraction that exhibits 100% specificity and 83% sensitivity, as well as a positive predictive value (PPV) of 100% and negative predictive values (NPVs) of 100%, 81%, 79.1%, and 66.7% for cycle threshold (CT) values of <20, 20 to 30, >30 and overall, respectively. IMPORTANCE The coronavirus disease 2019 (COVID-19) crisis has driven the development of innovative molecular diagnosis methods, including CRISPR-Cas technology. In this work, we performed a protocol, working with RNA extraction kit-free samples and using RT-LAMP-CRISPR-Cas13a technology; our results place this method at the forefront of rapid and specific diagnostic methods for COVID-19 due to the high specificity (100%), sensitivity (83%), PPVs (100%), and NPVs (81% for high viral loads) obtained with clinical samples.
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Affiliation(s)
- Concha Ortiz-Cartagena
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Laura Fernández-García
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Lucia Blasco
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Olga Pacios
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Inés Bleriot
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María López
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - María Tomás
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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12
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Mu Y, Zhang C, Li T, Jin FJ, Sung YJ, Oh HM, Lee HG, Jin L. Development and Applications of CRISPR/Cas9-Based Genome Editing in Lactobacillus. Int J Mol Sci 2022; 23:12852. [PMID: 36361647 PMCID: PMC9656040 DOI: 10.3390/ijms232112852] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 09/25/2023] Open
Abstract
Lactobacillus, a genus of lactic acid bacteria, plays a crucial function in food production preservation, and probiotics. It is particularly important to develop new Lactobacillus strains with superior performance by gene editing. Currently, the identification of its functional genes and the mining of excellent functional genes mainly rely on the traditional gene homologous recombination technology. CRISPR/Cas9-based genome editing is a rapidly developing technology in recent years. It has been widely applied in mammalian cells, plants, yeast, and other eukaryotes, but less in prokaryotes, especially Lactobacillus. Compared with the traditional strain improvement methods, CRISPR/Cas9-based genome editing can greatly improve the accuracy of Lactobacillus target sites and achieve traceless genome modification. The strains obtained by this technology may even be more efficient than the traditional random mutation methods. This review examines the application and current issues of CRISPR/Cas9-based genome editing in Lactobacillus, as well as the development trend of CRISPR/Cas9-based genome editing in Lactobacillus. In addition, the fundamental mechanisms of CRISPR/Cas9-based genome editing are also presented and summarized.
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Affiliation(s)
- Yulin Mu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Chengxiao Zhang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Taihua Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yun-Ju Sung
- BioNanotechnology Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Long Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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13
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Schusterbauer V, Fischer JE, Gangl S, Schenzle L, Rinnofner C, Geier M, Sailer C, Glieder A, Thallinger GG. Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 in Komagataella phaffii: A Budding Yeast in Distress. J Fungi (Basel) 2022; 8:jof8100992. [PMID: 36294556 PMCID: PMC9605565 DOI: 10.3390/jof8100992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The industrially important non-conventional yeast Komagataella phaffii suffers from low rates of homologous recombination, making site specific genetic engineering tedious. Therefore, genome editing using CRISPR/Cas represents a simple and efficient alternative. To characterize on- and off-target mutations caused by CRISPR/Cas9 followed by non-homologous end joining repair, we chose a diverse set of CRISPR/Cas targets and conducted whole genome sequencing on 146 CRISPR/Cas9 engineered single colonies. We compared the outcomes of single target CRISPR transformations to double target experiments. Furthermore, we examined the extent of possible large deletions by targeting a large genomic region, which is likely to be non-essential. The analysis of on-target mutations showed an unexpectedly high number of large deletions and chromosomal rearrangements at the CRISPR target loci. We also observed an increase of on-target structural variants in double target experiments as compared to single target experiments. Targeting of two loci within a putatively non-essential region led to a truncation of chromosome 3 at the target locus in multiple cases, causing the deletion of 20 genes and several ribosomal DNA repeats. The identified de novo off-target mutations were rare and randomly distributed, with no apparent connection to unspecific CRISPR/Cas9 off-target binding sites.
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Affiliation(s)
- Veronika Schusterbauer
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
- Institute of Biomedical Imaging, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
| | | | - Sarah Gangl
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Lisa Schenzle
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | | | - Martina Geier
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Christian Sailer
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
| | - Anton Glieder
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Gerhard G. Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, 8010 Graz, Austria
- Correspondence: ; Tel.: +43-316-873-5343
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14
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Spangler JR, Leski TA, Schultzhaus Z, Wang Z, Stenger DA. Large scale screening of CRISPR guide RNAs using an optimized high throughput robotics system. Sci Rep 2022; 12:13953. [PMID: 35977955 PMCID: PMC9385653 DOI: 10.1038/s41598-022-17474-8] [Citation(s) in RCA: 4] [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: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
All CRISPR/CAS systems utilize CRISPR guide RNAs (crRNAs), the design of which depend on the type of CAS protein, genetic target and the environment/matrix. While machine learning approaches have recently been developed to optimize some crRNA designs, candidate crRNAs must still be screened for efficacy under relevant conditions. Here, we demonstrate a high-throughput method to screen hundreds of candidate crRNAs for activation of Cas13a collateral RNA cleavage. Entire regions of a model gene transcript (Y. pestis lcrV gene) were tiled to produce overlapping crRNA sets. We tested for possible effects that included crRNA/target sequence, size and secondary structures, and the commercial source of DNA oligomers used to generate crRNAs. Detection of a 981 nt target RNA was initially successful with 271 out of 296 tested guide RNAs, and that was improved to 287 out of 296 (97%) after protocol optimizations. For this specific example, we determined that crRNA efficacy did not strongly depend on the target region or crRNA physical properties, but was dependent on the source of DNA oligomers used for RNA preparation. Our high-throughput methods for screening crRNAs has general applicability to the optimization of Cas12 and Cas13 guide RNA designs.
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Affiliation(s)
- J R Spangler
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA.
| | - T A Leski
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - Z Schultzhaus
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Z Wang
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - D A Stenger
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
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15
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Antony JS, Hinz JM, Wyrick JJ. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:924914. [PMID: 35706506 PMCID: PMC9190257 DOI: 10.3389/fbioe.2022.924914] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The versatility of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) genome editing makes it a popular tool for many research and biotechnology applications. Recent advancements in genome editing in eukaryotic organisms, like fungi, allow for precise manipulation of genetic information and fine-tuned control of gene expression. Here, we provide an overview of CRISPR genome editing technologies in yeast, with a particular focus on Saccharomyces cerevisiae. We describe the tools and methods that have been previously developed for genome editing in Saccharomyces cerevisiae and discuss tips and experimental tricks for promoting efficient, marker-free genome editing in this model organism. These include sgRNA design and expression, multiplexing genome editing, optimizing Cas9 expression, allele-specific editing in diploid cells, and understanding the impact of chromatin on genome editing. Finally, we summarize recent studies describing the potential pitfalls of using CRISPR genome targeting in yeast, including the induction of background mutations.
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Affiliation(s)
- Jacob S. Antony
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John M. Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
- *Correspondence: John J. Wyrick,
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16
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Akram F, Sahreen S, Aamir F, Haq IU, Malik K, Imtiaz M, Naseem W, Nasir N, Waheed HM. An Insight into Modern Targeted Genome-Editing Technologies with a Special Focus on CRISPR/Cas9 and its Applications. Mol Biotechnol 2022; 65:227-242. [PMID: 35474409 PMCID: PMC9041284 DOI: 10.1007/s12033-022-00501-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/13/2022] [Indexed: 01/18/2023]
Abstract
Genome-editing technology has enabled scientists to make changes in model organisms' DNA at the genomic level to get biotechnologically important products from them. Most commonly employed technologies for this purpose are transcription activator like effector nucleases (TALENs), homing-endonucleases or meganucleases, zinc finger nucleases (ZFNs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9). Among these tools, CRISPR/Cas9 is most preferred because it's easy to use, has a small mutation rate, has great effectiveness, low cost of development, and decreased rate of advancement. CRISPR/Cas9 has a lot of applications in plants, animals, humans, and microbes. It also has applications in many fields such as horticulture, cancer, food biotechnology, and targeted human genome treatments. CRISPR technology has shown great potential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic to provide early and easy detection methods, possible treatment, and vaccine development. In the present review, genome-editing tools with their basic assembly and features have been discussed. Exceptional notice has been paid to CRISPR technology on basis of its structure and significant applications in humans, plants, animals, and microbes such as bacteria, viruses, and fungi. The review has also shed a little light on current CRISPR challenges and future perspectives.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Sania Sahreen
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Farheen Aamir
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Ikram ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan ,Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Kausar Malik
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Memoona Imtiaz
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Waqas Naseem
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Narmeen Nasir
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Hafiza Mariam Waheed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
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17
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Vuong P, Wise MJ, Whiteley AS, Kaur P. Small investments with big returns: environmental genomic bioprospecting of microbial life. Crit Rev Microbiol 2022; 48:641-655. [PMID: 35100064 DOI: 10.1080/1040841x.2021.2011833] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms and their natural products are major drivers of ecological processes and industrial applications. Microbial bioprospecting has been critical for the advancement in various fields such as pharmaceuticals, sustainable industries, food security and bioremediation. Next generation sequencing has been paramount in the exploration of diverse environmental microbiomes. It presents a culture-independent approach to investigating hitherto uncultured taxa, resulting in the creation of massive sequence databases, which are available in the public domain. Genome mining searches available (meta)genomic data for target biosynthetic genes, and combined with the large-scale public data, this in-silico bioprospecting method presents an efficient and extensive way to uncover microbial bioproducts. Bioinformatic tools have progressed to a stage where we can recover genomes from the environment; these metagenome-assembled genomes present a way to understand the metabolic capacity of microorganisms in a physiological and ecological context. Environmental sampling been extensive across various ecological settings, including microbiomes with unique physicochemical properties that could influence the discovery of novel functions and metabolic pathways. Although in-silico methods cannot completely substitute in-vitro studies, the contextual information it provides is invaluable for understanding the ecological and taxonomic distribution of microbial genotypes and to form effective strategies for future microbial bioprospecting efforts.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
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18
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Ding W, Meng Q, Dong G, Qi N, Zhao H, Shi S. Metabolic engineering of threonine catabolism enables Saccharomyces cerevisiae to produce propionate under aerobic conditions. Biotechnol J 2022; 17:e2100579. [PMID: 35086163 DOI: 10.1002/biot.202100579] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Propionate is widely used as a preservative in the food and animal feed industries. Propionate is currently produced by petrochemical processes, and fermentative production of propionate remains challenging. METHODS AND RESULTS In this study, a synthetic propionate pathway was constructed in the budding yeast Saccharomyces cerevisiae, for propionate production under aerobic conditions. Through expression of tdcB and aldH from Escherichia coli and kivD from Lactococcus lactis, L-threonine was converted to propionate via 2-ketobutyrate and propionaldehyde. The resulting yeast aerobically produced 0.21 g/L propionate from glucose in a shake flask. Subsequent overexpression of pathway genes and elimination of competing pathways increased propionate production to 0.37 g/L. To further increase propionate production, carbon flux was pulled into the propionate pathway by weakened expression of pyruvate kinase (PYK1), together with overexpression of phosphoenolpyruvate carboxylase (ppc). The final propionate production reached 1.05 g/L during fed-batch fermentation in a fermenter. CONCLUSIONS AND IMPLICATIONS In this work, a yeast cell factory was constructed using synthetic biology and metabolic engineering strategies to enable propionate production under aerobic conditions. Our study demonstrates engineered S. cerevisiae as a promising alternative for the production of propionate and its derivatives. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China.,Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No. 9, 13th Avenue, TEDA, Tianjin, 300457, China
| | - Qiongyu Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
| | - Genlai Dong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
| | - Nailing Qi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
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19
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Shelake RM, Pramanik D, Kim JY. In Vivo Rapid Investigation of CRISPR-Based Base Editing Components in Escherichia coli (IRI-CCE): A Platform for Evaluating Base Editing Tools and Their Components. Int J Mol Sci 2022; 23:ijms23031145. [PMID: 35163069 PMCID: PMC8834901 DOI: 10.3390/ijms23031145] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid assessment of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing (GE) tools and their components is a critical aspect for successful GE applications in different organisms. In many bacteria, double-strand breaks (DSBs) generated by CRISPR/Cas tool generally cause cell death due to the lack of an efficient nonhomologous end-joining pathway and restricts its use. CRISPR-based DSB-free base editors (BEs) have been applied for precise nucleotide (nt) editing in bacteria, which does not need to make DSBs. However, optimization of newer BE tools in bacteria is challenging owing to the toxic effects of BE reagents expressed using strong promoters. Improved variants of two main BEs, cytidine base editor (CBE) and adenine base editor (ABE), capable of converting C to T and A to G, respectively, have been recently developed but yet to be tested for editing characteristics in bacteria. Here, we report a platform for in vivo rapid investigation of CRISPR-BE components in Escherichia coli (IRI-CCE) comprising a combination of promoters and terminators enabling the expression of nCas9-based BE and sgRNA to nontoxic levels, eventually leading to successful base editing. We demonstrate the use of IRI-CCE to characterize different variants of CBEs (PmCDA1, evoCDA1, APOBEC3A) and ABEs (ABE8e, ABE9e) for bacteria, exhibiting that each independent BE has its specific editing pattern for a given target site depending on protospacer length. In summary, CRISPR-BE components expressed without lethal effects on cell survival in the IRI-CCE allow an analysis of various BE tools, including cloned biopart modules and sgRNAs.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Correspondence: (R.M.S.); (J.-Y.K.)
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
- Correspondence: (R.M.S.); (J.-Y.K.)
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20
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Abstract
Abstract Clustered regularly interspaced short palindromic repeats (CRISPR) technology, an easy, rapid, cost-effective, and precise gene-editing technique, has revolutionized diagnostics and gene therapy. Fast and accurate diagnosis of diseases is essential for point-of-care-testing
(POCT) and specialized medical institutes. The CRISPR-associated (Cas) proteins system shed light on the new diagnostics methods at point-of-care (POC) owning to its advantages. In addition, CRISPR/Cas-based gene-editing technology has led to various breakthroughs in gene therapy. It has been
employed in clinical trials for a variety of untreatable diseases, including cancer, blood disorders, and other syndromes. Currently, the clinical application of CRISPR/Cas has been mainly focused on ex vivo therapies. Recently, tremendous efforts have been made in the development of
ex vivo gene therapy based on CRISPR-Cas9. Despite these efforts, in vivo CRISPR/Cas gene therapy is only in its initial stage. Here, we review the milestones of CRISPR/Cas technologies that advanced the field of diagnostics and gene therapy. We also highlight the recent advances
of diagnostics and gene therapy based on CRISPR/Cas technology. In the last section, we discuss the strength and significant challenges of the CRISPR/Cas technology for its future clinical usage in diagnosis and gene therapy.
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Affiliation(s)
- Meiyu Qiu
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Pei Li
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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21
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Zhang X, Gu S, Zheng X, Peng S, Li Y, Lin Y, Liang S. A Novel and Efficient Genome Editing Tool Assisted by CRISPR-Cas12a/Cpf1 for Pichia pastoris. ACS Synth Biol 2021; 10:2927-2937. [PMID: 34644057 DOI: 10.1021/acssynbio.1c00172] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pichia pastoris has been widely exploited for the 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 chemicals and pharmaceuticals. Effective synthetic biology tools for genetic engineering are essential for industrial and biotechnological research in this yeast. Here, we describe a novel and efficient genome editing method mediated by the CRISPR-Cpf1 system, which could facilitate the deletion of large DNA fragments and integration of multiplexed gene fragments. The CRISPR-Cpf1 system exhibited a precise and high editing efficiency for single-gene disruption (99 ± 0.8%), duplex genome editing (65 ± 2.5% to 80 ± 3%), and triplex genome editing (30 ± 2.5%). In addition, the deletion of large DNA fragments of 20kb and one-step integration of multiple genes were first achieved using the developed CRISPR-Cpf1 system. Taken together, this study provides an efficient and simple gene editing tool for P. pastoris. The novel multiloci gene integration method mediated by CRISPR-Cpf1 may accelerate the ability to engineer this methylotrophic yeast for metabolic engineering and genome evolution in both biotechnological and biomedical applications.
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Affiliation(s)
- Xinying Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Songjie Gu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xueyun Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Siqi Peng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yanru Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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22
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CRISPR-Cas Technology: Emerging Applications in Clinical Microbiology and Infectious Diseases. Pharmaceuticals (Basel) 2021; 14:ph14111171. [PMID: 34832953 PMCID: PMC8625472 DOI: 10.3390/ph14111171] [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: 08/26/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
Through the years, many promising tools for gene editing have been developed including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), CRISPR-associated protein 9 (Cas9), and homing endonucleases (HEs). These novel technologies are now leading new scientific advancements and practical applications at an inimitable speed. While most work has been performed in eukaryotes, CRISPR systems also enable tools to understand and engineer bacteria. The increase in the number of multi-drug resistant strains highlights a necessity for more innovative approaches to the diagnosis and treatment of infections. CRISPR has given scientists a glimmer of hope in this area that can provide a novel tool to fight against antimicrobial resistance. This system can provide useful information about the functions of genes and aid us to find potential targets for antimicrobials. This paper discusses the emerging use of CRISPR-Cas systems in the fields of clinical microbiology and infectious diseases with a particular emphasis on future prospects.
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23
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Tran VG, Zhao H. Engineering robust microorganisms for organic acid production. J Ind Microbiol Biotechnol 2021; 49:6373449. [PMID: 34549297 PMCID: PMC9118992 DOI: 10.1093/jimb/kuab067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/11/2021] [Indexed: 11/24/2022]
Abstract
Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.
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Affiliation(s)
- Vinh G Tran
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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24
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Peng H, Zheng Y, Zhao Z, Li J. Multigene editing: current approaches and beyond. Brief Bioinform 2021; 22:bbaa396. [PMID: 33428725 DOI: 10.1093/bib/bbaa396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/15/2020] [Accepted: 12/03/2020] [Indexed: 11/14/2022] Open
Abstract
CRISPR/Cas9 multigene editing is an active and widely studied topic in the fields of biomedicine and biology. It involves a simultaneous participation of multiple single-guide RNAs (sgRNAs) to edit multiple target genes in a way that each gene is edited by one of these sgRNAs. There are possibly numerous sgRNA candidates capable of on-target editing on each of these genes with various efficiencies. Meanwhile, each of these sgRNA candidates may cause unwanted off-target editing at many other genes. Therefore, selection optimization of these multiple sgRNAs is demanded so as to minimize the number of sgRNAs and thus reduce the collective negative effects caused by the off-target editing. This survey reviews wet-laboratory approaches to the implementation of multigene editing and their needs of computational tools for better design. We found that though off-target editing is unavoidable during the gene editing, those disfavored cuttings by some target genes' sgRNAs can potentially become on-target editing sites for some other genes of interests. This off-to-on role conversion is beneficial to optimize the sgRNA selection in multigene editing. We present a preference cutting score to assess those beneficial off-target cutting sites, which have a few mismatches with their host genes' on-target editing sites. These potential sgRNAs can be prioritized for recommendation via ranking their on-target average cutting efficiency, the total off-target site number and their average preference cutting score. We also present case studies on cancer-associated genes to demonstrate tremendous usefulness of the new method.
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Affiliation(s)
- Hui Peng
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
- School of Computing, National University of Singapore, 13 Computing Drive, 117417, Singapore
| | - Yi Zheng
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
| | - Zhixun Zhao
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
| | - Jinyan Li
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
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Microbial production of chemicals driven by CRISPR-Cas systems. Curr Opin Biotechnol 2021; 73:34-42. [PMID: 34303184 DOI: 10.1016/j.copbio.2021.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
Microorganisms have provided an attractive route for biosynthesis of various chemicals from renewable resources. CRISPR-Cas systems have served as powerful mechanisms for generating cell factories with desirable properties by manipulating nucleic acids quickly and efficiently. The CRISPR-Cas system provides a toolbox with excellent opportunities for identifying better biocatalysts, multiplexed fine-tuning of metabolic flux, efficient utilization of low-cost substrates, and improvement of metabolic robustness. The overall goal of this review highlights recent advances in the development of microbial cell factories for chemical production using various CRISPR-Cas systems. The perspectives for further development or applications of CRISPR-Cas systems for strain improvement are also discussed.
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Fan YY, Tang Q, Li Y, Li FH, Wu JH, Li WW, Yu HQ. Rapid and highly efficient genomic engineering with a novel iEditing device for programming versatile extracellular electron transfer of electroactive bacteria. Environ Microbiol 2021; 23:1238-1255. [PMID: 33369000 DOI: 10.1111/1462-2920.15374] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/17/2022]
Abstract
The advances in synthetic biology bring exciting new opportunities to reprogram microorganisms with novel functionalities for environmental applications. For real-world applications, a genetic tool that enables genetic engineering in a stably genomic inherited manner is greatly desired. In this work, we design a novel genetic device for rapid and efficient genome engineering based on the intron-encoded homing-endonuclease empowered genome editing (iEditing). The iEditing device enables rapid and efficient genome engineering in Shewanella oneidensis MR-1, the representative strain of the electroactive bacteria group. Moreover, combining with the Red or RecET recombination system, the genome-editing efficiency was greatly improved, up to approximately 100%. Significantly, the iEditing device itself is eliminated simultaneously when genome editing occurs, thereby requiring no follow-up to remove the encoding system. Then, we develop a new extracellular electron transfer (EET) engineering strategy by programming the parallel EET systems to enhance versatile EET. The engineered strains exhibit sufficiently enhanced electron output and pollutant reduction ability. Furthermore, this device has demonstrated its great potential to be extended for genome editing in other important microbes. This work provides a useful and efficient tool for the rapid generation of synthetic microorganisms for various environmental applications.
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Affiliation(s)
- Yang-Yang Fan
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Qiang Tang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang Li
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Feng-He Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Jing-Hang Wu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Wei Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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Meng J, Qiu Y, Shi S. CRISPR/Cas9 Systems for the Development of Saccharomyces cerevisiae Cell Factories. Front Bioeng Biotechnol 2020; 8:594347. [PMID: 33330425 PMCID: PMC7710542 DOI: 10.3389/fbioe.2020.594347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/19/2020] [Indexed: 01/09/2023] Open
Abstract
Synthetic yeast cell factories provide a remarkable solution for the sustainable supply of a range of products, ranging from large-scale industrial chemicals to high-value pharmaceutical compounds. Synthetic biology is a field in which metabolic pathways are intensively studied and engineered. The clustered, regularly interspaced, short, palindromic repeat-associated (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has emerged as the state-of-the-art gene editing technique for synthetic biology. Recently, the use of different CRISPR/Cas9 systems has been extended to the field of yeast engineering for single-nucleotide resolution editing, multiple-gene editing, transcriptional regulation, and genome-scale modifications. Such advancing systems have led to accelerated microbial engineering involving less labor and time and also enhanced the understanding of cellular genetics and physiology. This review provides a brief overview of the latest research progress and the use of CRISPR/Cas9 systems in genetic manipulation, with a focus on the applications of Saccharomyces cerevisiae cell factory engineering.
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Affiliation(s)
- Jie Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yue Qiu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Gu Y, Cao H, Li F, Yu J, Nian R, Feng D, Lin J, Song H, Liu W. Production of functional human nerve growth factor from the submandibular glands of mice using a CRISPR/Cas9 genome editing system. World J Microbiol Biotechnol 2020; 36:176. [PMID: 33103226 DOI: 10.1007/s11274-020-02951-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/14/2020] [Indexed: 11/24/2022]
Abstract
Nerve growth factor (NGF) is an essential trophic factor for the growth and survival of neurons in the central and peripheral nervous systems. For many years, mouse NGF (mNGF) has been used to treat various neuronal and non-neuronal disorders. However, the biological activity of human NGF (hNGF) is significantly higher than that of mNGF in human cells. Using the CRISPR/Cas9 system, we constructed the transgenic mice expressing hNGF specifically in their submandibular glands. As demonstrated by fluorescence immunohistochemical staining, these mice produced hNGF successfully, with 0.8 mg produced per gram of submandibular glands. hNGF with 99% purity was successfully extracted by two-step ion-exchange chromatography and one-step size-exclusion chromatography from the submandibular glands of these transgenic mice. Further, the purified hNGF was verified by LC-MS/MS. We analyzed the NH2-terminus of hNGF using both Edman degradation and LC-MS/MS-based methods. Both results showed that the obtained hNGF lost the NH2-terminal octapeptide (SSSHPIFH). Moreover, the produced hNGF demonstrated a strong promotion in the proliferation of TF1 cells.
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Affiliation(s)
- Yi Gu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing, 100049, China
| | - Hui Cao
- Shenzhen Innova Nanobodi Co., Ltd, No. 7018 Caitian Road, Shenzhen, 518000, China
| | - Fei Li
- Shenzhen Innova Nanobodi Co., Ltd, No. 7018 Caitian Road, Shenzhen, 518000, China
| | - Jianli Yu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing, 100049, China
| | - Rui Nian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
| | - Dongxiao Feng
- Shenzhen Innova Nanobodi Co., Ltd, No. 7018 Caitian Road, Shenzhen, 518000, China
| | - Jingtao Lin
- Dalang Hospital of Dongguan, No. 85 Jinlangzhong Road, Dalang, 523770, Dongguan, China
| | - Haipeng Song
- Shenzhen Innova Nanobodi Co., Ltd, No. 7018 Caitian Road, Shenzhen, 518000, China.
| | - Wenshuai Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China.
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