1
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Du Q, Wei Y, Zhang L, Ren D, Gao J, Dong X, Bai L, Li J. An improved CRISPR and CRISPR interference (CRISPRi) toolkit for engineering the model methanogenic archaeon Methanococcus maripaludis. Microb Cell Fact 2024; 23:239. [PMID: 39227830 PMCID: PMC11373211 DOI: 10.1186/s12934-024-02492-0] [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: 05/14/2024] [Accepted: 07/27/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND The type II based CRISPR-Cas system remains restrictedly utilized in archaea, a featured domain of life that ranks parallelly with Bacteria and Eukaryotes. Methanococcus maripaludis, known for rapid growth and genetic tractability, serves as an exemplary model for studying archaeal biology and exploring CO2-based biotechnological applications. However, tools for controlled gene regulation remain deficient and CRISPR-Cas tools still need improved in this archaeon, limiting its application as an archaeal model cellular factory. RESULTS This study not only improved the CRISPR-Cas9 system for optimizing multiplex genome editing and CRISPR plasmid construction efficiencies but also pioneered an effective CRISPR interference (CRISPRi) system for controlled gene regulation in M. maripaludis. We developed two novel strategies for balanced expression of multiple sgRNAs, facilitating efficient multiplex genome editing. We also engineered a strain expressing Cas9 genomically, which simplified the CRISPR plasmid construction and facilitated more efficient genome modifications, including markerless and scarless gene knock-in. Importantly, we established a CRISPRi system using catalytic inactive dCas9, achieving up to 100-fold repression on target gene. Here, sgRNAs targeting near and downstream regions of the transcription start site and the 5'end ORF achieved the highest repression efficacy. Furthermore, we developed an inducible CRISPRi-dCas9 system based on TetR/tetO platform. This facilitated the inducible gene repression, especially for essential genes. CONCLUSIONS Therefore, these advancements not only expand the toolkit for genetic manipulation but also bridge methodological gaps for controlled gene regulation, especially for essential genes, in M. maripaludis. The robust toolkit developed here paves the way for applying M. maripaludis as a vital model archaeal cell factory, facilitating fundamental biological studies and applied biotechnology development of archaea.
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Affiliation(s)
- Qing Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China
| | - Yufei Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Liuyang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
| | - Derong Ren
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Jian Gao
- School of Basic Medical Sciences, School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China.
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China.
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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2
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Zhu P, Molina Resendiz M, von Ossowski I, Scheller S. A promoter-RBS library for fine-tuning gene expression in Methanosarcina acetivorans. Appl Environ Microbiol 2024:e0109224. [PMID: 39132998 DOI: 10.1128/aem.01092-24] [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: 06/04/2024] [Accepted: 07/15/2024] [Indexed: 08/13/2024] Open
Abstract
Methanogens are the main biological producers of methane on Earth. Methanosarcina acetivorans is one of the best characterized methanogens that has powerful genetic tools for genome editing. To study the physiology of this methanogen in further detail as well as to effectively balance the flux of their engineered metabolic pathways in expansive project undertakings, there is the need for controlled gene expression, which then requires the availability of well-characterized promoters and ribosome-binding sites (RBS). In this study, we constructed a library of 33 promoter-RBS combinations that includes 13 wild-type and 14 hybrid combinations, as well as six combination variants in which the 5'-untranslated region (5'UTR) was rationally engineered. The expression strength for each combination was calculated by inducing the expression of the β-glucuronidase reporter gene in M. acetivorans cells in the presence of the two most used growth substrates, either methanol (MeOH) or trimethyl amine (TMA). In this study, the constructed library covers a relatively wide range (140-fold) between the weakest and strongest promoter-RBS combination as well as shows a steady increase and allows different levels of gene expression. Effects on the gene expression strength were also assessed by making measurements at three distinct growth phases for all 33 promoter-RBS combinations. Our promoter-RBS library is effective in enabling the fine-tuning of gene expression in M. acetivorans for physiological studies and the design of metabolic engineering projects that, e.g., aim for the biotechnological valorization of one-carbon compounds. IMPORTANCE Methanogenic archaea are potent producers of the greenhouse gas methane and thus contribute substantially to global warming. Under controlled conditions, these microbes can catalyze the production of biogas, which is a renewable fuel, and might help counter global warming and its effects. Engineering the primary metabolism of Methanosarcina acetivorans to render it better and more useful requires controllable gene expression, yet only a few well-characterized promoters and RBSs are presently available. Our study rectifies this situation by providing a library of 33 different promoter-RBS combinations with a 140-fold dynamic range in expression strength. Future metabolic engineering projects can take advantage of this library by using these promoter-RBS combinations as an efficient and tunable gene expression system for M. acetivorans. Furthermore, the methodologies we developed in this study could also be utilized to construct promoter libraries for other types of methanogens.
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Affiliation(s)
- Ping Zhu
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Mariana Molina Resendiz
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Ingemar von Ossowski
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
| | - Silvan Scheller
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, Finland
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3
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Myers T, Dykstra CM. Teaching old dogs new tricks: genetic engineering methanogens. Appl Environ Microbiol 2024; 90:e0224723. [PMID: 38856201 PMCID: PMC11267900 DOI: 10.1128/aem.02247-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
Methanogenic archaea, which are integral to global carbon and nitrogen cycling, currently face challenges in genetic manipulation due to unique physiology and limited genetic tools. This review provides a survey of current and past developments in the genetic engineering of methanogens, including selection and counterselection markers, reporter systems, shuttle vectors, mutagenesis methods, markerless genetic exchange, and gene expression control. This review discusses genetic tools and emphasizes challenges tied to tool scarcity for specific methanogenic species. Mutagenesis techniques for methanogens, including physicochemical, transposon-mediated, liposome-mediated mutagenesis, and natural transformation, are outlined, along with achievements and challenges. Markerless genetic exchange strategies, such as homologous recombination and CRISPR/Cas-mediated genome editing, are also detailed. Finally, the review concludes by examining the control of gene expression in methanogens. The information presented underscores the urgent need for refined genetic tools in archaeal research. Despite historical challenges, recent advancements, notably CRISPR-based systems, hold promise for overcoming obstacles, with implications for global health, agriculture, climate change, and environmental engineering. This comprehensive review aims to bridge existing gaps in the literature, guiding future research in the expanding field of archaeal genetic engineering.
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Affiliation(s)
- Tyler Myers
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Christy M. Dykstra
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, California, USA
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4
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Xu Q, Du Q, Gao J, Chen L, Dong X, Li J. A robust genetic toolbox for fine-tuning gene expression in the CO 2-Fixing methanogenic archaeon Methanococcus maripaludis. Metab Eng 2023; 79:130-145. [PMID: 37495072 DOI: 10.1016/j.ymben.2023.07.007] [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: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Libraries of well-characterized genetic elements for fine-tuning gene expression are essential for biological and biotechnological research and applications. The fast-growing and genetically tractable methanogen, Methanococcus maripaludis, is a promising host organism for biotechnological conversion of carbon dioxide and renewable hydrogen into fuels and value-added products, as well as fundamental biological studies of archaea. However, the lack of molecular tools for gene expression has hindered its application as a workhorse to fine-tune gene and metabolic pathway expressions. In this study, we developed a genetic toolbox, including libraries of promoters, ribosome binding sites (RBS), and neutral sites for chromosomal integration, to facilitate precise gene expression in M. maripaludis. We generated a promoter library consisting of 81 constitutive promoters with expression strengths spanning a ∼104-fold dynamic range. Importantly, we identified a base composition rule for strong archaeal promoters and successfully remodeled weak promoters, enhancing their activities by up to 120-fold. We also established an RBS library containing 42 diverse RBS sequences with translation strengths covering a ∼100-fold dynamic range. Additionally, we identified eight neutral sites and developed a one-step, Cas9-based marker-less knock-in approach for chromosomal integration. We successfully applied the characterized promoter and RBS elements to significantly improve recombinant protein expression by 41-fold and modulate essential gene expression to generate corresponding physiological changes in M. maripaludis. Therefore, this work establishes a solid foundation for utilizing this autotrophic methanogen as an ideal workhorse for archaeal biology and biotechnological studies and applications.
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Affiliation(s)
- Qing Xu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing Du
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China
| | - Jian Gao
- School of Basic Medical Sciences and School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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5
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Application of the Fluorescence-Activating and Absorption-Shifting Tag (FAST) for Flow Cytometry in Methanogenic Archaea. Appl Environ Microbiol 2023; 89:e0178622. [PMID: 36920214 PMCID: PMC10132111 DOI: 10.1128/aem.01786-22] [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: 03/16/2023] Open
Abstract
Methane-producing archaea play a crucial role in the global carbon cycle and are used for biotechnological fuel production. Methanogenic model organisms such as Methanococcus maripaludis and Methanosarcina acetivorans have been biochemically characterized and can be genetically engineered by using a variety of existing molecular tools. The anaerobic lifestyle and autofluorescence of methanogens, however, restrict the use of common fluorescent reporter proteins (e.g., GFP and derivatives), which require oxygen for chromophore maturation. Recently, the use of a novel oxygen-independent fluorescent activation and absorption-shifting tag (FAST) was demonstrated with M. maripaludis. Similarly, we now describe the use of the tandem activation and absorption-shifting tag protein 2 (tdFAST2), which fluoresces when the cell-permeable fluorescent ligand (fluorogen) 4-hydroxy-3,5-dimethoxybenzylidene rhodanine (HBR-3,5DOM) is present. Expression of tdFAST2 in M. acetivorans and M. maripaludis is noncytotoxic and tdFAST2:HBR-3,5DOM fluorescence is clearly distinguishable from the autofluorescence. In flow cytometry experiments, mixed methanogen cultures can be distinguished, thereby allowing for the possibility of high-throughput investigations of the characteristic dynamics within single and mixed cultures. IMPORTANCE Methane-producing archaea play an essential role in the global carbon cycle and demonstrate great potential for various biotechnological applications, e.g., biofuel production, carbon dioxide capture, and electrochemical systems. Oxygen sensitivity and high autofluorescence hinder the use of common fluorescent proteins for studying methanogens. By using tdFAST2:HBR-3,5DOM fluorescence, which functions under anaerobic conditions and is distinguishable from the autofluorescence, real-time reporter studies and high-throughput investigation of the mixed culture dynamics of methanogens via flow cytometry were made possible. This will further help accelerate the sustainable exploitation of methanogens.
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6
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Lyu Z, Rotaru AE, Pimentel M, Zhang CJ, Rittmann SKMR. Editorial: The methane moment - Cross-boundary significance of methanogens: Preface. Front Microbiol 2022; 13:1055494. [PMID: 36504803 PMCID: PMC9731359 DOI: 10.3389/fmicb.2022.1055494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Zhe Lyu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Zhe Lyu
| | - Amelia-Elena Rotaru
- Nordic Center for Earth Evolution (NORDCEE), University of Southern Denmark, Odense, Denmark,Amelia-Elena Rotaru
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States,Mark Pimentel
| | - Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China,Cui-Jing Zhang
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,Simon K.-M. R. Rittmann
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7
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Li J, Akinyemi TS, Shao N, Chen C, Dong X, Liu Y, Whitman WB. Genetic and Metabolic Engineering of Methanococcus spp. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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8
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Shao N, Fan Y, Chou CW, Yavari S, Williams RV, Amster IJ, Brown SM, Drake IJ, Duin EC, Whitman WB, Liu Y. Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea. Commun Biol 2022; 5:1113. [PMID: 36266535 PMCID: PMC9584954 DOI: 10.1038/s42003-022-04057-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/30/2022] [Indexed: 11/08/2022] Open
Abstract
Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.
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Affiliation(s)
- Nana Shao
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Yu Fan
- EMTEC IT, ExxonMobil Technical Computing Company, Annandale, NJ, USA
| | - Chau-Wen Chou
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Shadi Yavari
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA
| | | | | | - Stuart M Brown
- Energy Sciences, ExxonMobil Technology & Engineering Company, Annandale, NJ, USA
| | - Ian J Drake
- Biomedical Sciences, ExxonMobil Technology & Engineering Company, Annandale, NJ, USA
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA
| | | | - Yuchen Liu
- Energy Sciences, ExxonMobil Technology & Engineering Company, Annandale, NJ, USA.
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9
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Gu W, Müller AL, Deutzmann JS, Williamson JR, Spormann AM. Growth rate-dependent coordination of catabolism and anabolism in the archaeon Methanococcus maripaludis under phosphate limitation. THE ISME JOURNAL 2022; 16:2313-2319. [PMID: 35780255 PMCID: PMC9478154 DOI: 10.1038/s41396-022-01278-9] [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: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Catabolic and anabolic processes are finely coordinated in microorganisms to provide optimized fitness under varying environmental conditions. Understanding this coordination and the resulting physiological traits reveals fundamental strategies of microbial acclimation. Here, we characterized the system-level physiology of Methanococcus maripaludis, a niche-specialized methanogenic archaeon, at different dilution rates ranging from 0.09 to 0.003 h-1 in chemostat experiments under phosphate (i.e., anabolic) limitation. Phosphate was supplied as the limiting nutrient, while formate was supplied in excess as the catabolic substrate and carbon source. We observed a decoupling of catabolism and anabolism resulting in lower biomass yield relative to catabolically limited cells at the same dilution rates. In addition, the mass abundance of several coarse-grained proteome sectors (i.e., combined abundance of proteins grouped based on their function) exhibited a linear relationship with growth rate, mostly ribosomes and their biogenesis. Accordingly, cellular RNA content also correlated with growth rate. Although the methanogenesis proteome sector was invariant, the metabolic capacity for methanogenesis, measured as methane production rates immediately after transfer to batch culture, correlated with growth rate suggesting translationally independent regulation that allows cells to only increase catabolic activity under growth-permissible conditions. These observations are in stark contrast to the physiology of M. maripaludis under formate (i.e., catabolic) limitation, where cells keep an invariant proteome including ribosomal content and a high methanogenesis capacity across a wide range of growth rates. Our findings reveal that M. maripaludis employs fundamentally different strategies to coordinate global physiology during anabolic phosphate and catabolic formate limitation.
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Affiliation(s)
- Wenyu Gu
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Albert L Müller
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Jörg S Deutzmann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
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Li J, Zhang L, Xu Q, Zhang W, Li Z, Chen L, Dong X. CRISPR-Cas9 Toolkit for Genome Editing in an Autotrophic CO 2-Fixing Methanogenic Archaeon. Microbiol Spectr 2022; 10:e0116522. [PMID: 35766512 PMCID: PMC9430280 DOI: 10.1128/spectrum.01165-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/04/2022] [Indexed: 11/23/2022] Open
Abstract
The CRISPR-Cas9 system is a robust genome editing tool that is widely applied in eukaryotes and bacteria. However, use of this technique has only been developed for one species of Archaea, a domain of life ranking in parallel with Eukarya and Bacteria. In this study, we applied the CRISPR-Cas9 genome editing technique to Methanococcus maripaludis, an autotrophic and hydrogenotrophic methanogenic archaeon with a remarkably polyploid genome comprising up to ~55 chromosomal copies per cell. An editing plasmid was designed that encodes small guide RNA (sgRNA), Cas9 protein and an ~1-kb repair template (donor). Highly efficient (75% to 100%) and precise genome editing was achieved following one-step transformation. Significantly, the Cas9-based system efficiently deleted one or two genes and a large DNA fragment (~9 kb) and even synchronously deleted 13 genes located at three loci in all chromosomal copies of M. maripaludis. Moreover, precise in situ genome modifications, such as gene tagging and multiple- and even single-nucleotide mutagenesis, were also introduced with high efficiency. Further, as a proof of concept, precise mutagenesis at the nucleotide level allowed the engineering of both transcriptional and translational activities. Mutations were introduced into an archaeal promoter BRE (transcription factor B [TFB] recognition element), a terminator U-tract region, and a gene coding region. Stop codon introduction into a gene through single-nucleotide substitution shut down its expression, providing an alternative strategy for gene inactivation. In conclusion, the robust CRISPR-Cas9 genetic toolkit developed in this investigation greatly facilitates the application of M. maripaludis as a model system in the study of archaeal biology and biotechnology development, particularly CO2-based biotechnologies. IMPORTANCE Archaea are prokaryotes with intriguing biological characteristics. They possess bacterial cell structures but eukaryotic homologous information processing machinery and eukaryotic featured proteins. Archaea also display excellent adaptability to extreme environments and play pivotal roles in ecological processes, thus exhibiting valuable biotechnological potential. However, the in-depth understanding and practical application of archaea are much lagging, because only a minority of pure cultures are available, and even worse, very few can be genetically manipulated. This work developed CRISPR-Cas9-based genome editing technology in Methanococcus maripaludis, a CO2-fixing methanogenic archaeon. The CRISPR-Cas9 approach developed in this study provides an elegant and efficient genome editing toolkit that can be applied in the knockout of single or multiple genes, in situ gene tagging, multiple- or single-nucleotide mutagenesis, and inactivation of gene expression by introduction of stop codons. The successful development of the CRISPR-Cas9 toolkit will facilitate the application of M. maripaludis in archaeal biology research and biotechnology development, particularly CO2-derived biotechnologies.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liuyang Zhang
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Qing Xu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihua Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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11
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Bao J, de Dios Mateos E, Scheller S. Efficient CRISPR/Cas12a-Based Genome-Editing Toolbox for Metabolic Engineering in Methanococcus maripaludis. ACS Synth Biol 2022; 11:2496-2503. [PMID: 35730587 PMCID: PMC9295151 DOI: 10.1021/acssynbio.2c00137] [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] [Indexed: 01/05/2023]
Abstract
![]()
The rapid-growing
and genetically tractable methanogen Methanococcus
maripaludis is a promising host organism
for the biotechnological conversion of carbon dioxide and renewable
hydrogen to fuels and value-added products. Expansion of its product
scope through metabolic engineering necessitates reliable and efficient
genetic tools, particularly for genome edits that affect the primary
metabolism and cell growth. Here, we have designed a genome-editing
toolbox by utilizing Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) in combination with the homology-directed repair
machinery endogenously present in M. maripaludis. This toolbox can delete target genes with a success rate of up
to 95%, despite the hyperpolyploidy of M. maripaludis. For the purpose of demonstrating a large deletion, the M. maripaludis flagellum operon (∼8.9 kbp)
was replaced by the Escherichia coli β-glucuronidase gene. To facilitate metabolic engineering
and flux balancing in M. maripaludis, the relative strength of 15 different promoters was quantified
in the presence of two common growth substrates, either formate or
carbon dioxide and hydrogen. This CRISPR/LbCas12a toolbox can be regarded
as a reliable and quick method for genome editing in a methanogen.
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Affiliation(s)
- Jichen Bao
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Enrique de Dios Mateos
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
| | - Silvan Scheller
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, FI-02150 Espoo, Finland
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12
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Gendron A, Allen KD. Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression. Front Microbiol 2022; 13:867342. [PMID: 35547147 PMCID: PMC9081873 DOI: 10.3389/fmicb.2022.867342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/01/2022] [Indexed: 12/02/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.
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Affiliation(s)
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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