1
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Day LA, Carlson HK, Fonseca DR, Arkin AP, Price MN, Deutschbauer AM, Costa KC. High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen. mBio 2024; 15:e0078124. [PMID: 39120137 PMCID: PMC11389366 DOI: 10.1128/mbio.00781-24] [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: 03/14/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that M. maripaludis can utilize additional nitrogen sources including ʟ-glutamine, ᴅ-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize that it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP; group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale data set that can be used as a resource to further understand gene function and metabolism in the archaeal domain.IMPORTANCEArchaea are widespread in the environment, yet basic aspects of their biology remain underexplored. To address this, we apply randomly barcoded transposon libraries (RB-TnSeq) to the model archaeon Methanococcus maripaludis. RB-TnSeq coupled with high-throughput growth assays across over 100 unique conditions identified roles for previously uncharacterized genes, including several encoding proteins with domains of unknown function (DUFs). We also expand on our understanding of carbon and nitrogen metabolism and characterize a group IIId dissimilatory sulfite reductase-like protein as a functional sulfite reductase. This data set encompasses a wide range of additional conditions including stress, nitrogen fixation, amino acid supplementation, and autotrophy, thus providing an extensive data set for the archaeal community to mine for characterizing additional genes of unknown function.
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Affiliation(s)
- Leslie A Day
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dallas R Fonseca
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Plant and Microbial Biology Department, University of California, Berkeley, California, USA
| | - Kyle C Costa
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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2
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Lin X, He K, Gu Z, Zhao X. Emerging chemophysiological diversity of gut microbiota metabolites. Trends Pharmacol Sci 2024; 45:824-838. [PMID: 39129061 DOI: 10.1016/j.tips.2024.07.006] [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: 05/24/2024] [Revised: 07/19/2024] [Accepted: 07/19/2024] [Indexed: 08/13/2024]
Abstract
Human physiology is profoundly influenced by the gut microbiota, which generates a wide array of metabolites. These microbiota-derived compounds serve as signaling molecules, interacting with various cellular targets in the gastrointestinal tract and distant organs, thereby impacting our immune, metabolic, and neurobehavioral systems. Recent advancements have unveiled unique physiological functions of diverse metabolites derived from tryptophan (Trp) and bile acids (BAs). This review highlights the emerging chemophysiological diversity of these metabolites and discusses the role of chemical and biological tools in analyzing and therapeutically manipulating microbial metabolism and host targets, with the aim of bridging the chemical diversity with physiological complexity in host-microbe molecular interactions.
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Affiliation(s)
- Xiaorong Lin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Kaixin He
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China; Jinhua Institute of Zhejiang University, Jinhua 321299, Zhejiang, China; State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhen Gu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China; Jinhua Institute of Zhejiang University, Jinhua 321299, Zhejiang, China; State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, Zhejiang, China; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China; Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, China
| | - Xiaohui Zhao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China; Jinhua Institute of Zhejiang University, Jinhua 321299, Zhejiang, China; State Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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3
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Glockow T, Kaster AK, Rabe KS, Niemeyer CM. Sustainable agriculture: leveraging microorganisms for a circular economy. Appl Microbiol Biotechnol 2024; 108:452. [PMID: 39212740 PMCID: PMC11364797 DOI: 10.1007/s00253-024-13294-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. KEY POINTS: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production.
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Affiliation(s)
- Till Glockow
- Acheron GmbH, Auf Der Muggenburg 30, 28217, Bremen, Germany
| | - Anne-Kristin Kaster
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 5 (IBG-5), Biotechnology and Microbial Genetics, Hermann-Von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Hermann-Von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Hermann-Von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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4
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Wang S, Zhan Y, Jiang X, Lai Y. Engineering Microbial Consortia as Living Materials: Advances and Prospectives. ACS Synth Biol 2024. [PMID: 39174016 DOI: 10.1021/acssynbio.4c00313] [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: 08/24/2024]
Abstract
The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.
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Affiliation(s)
- Shuchen Wang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yuewei Zhan
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xue Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR, China
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yong Lai
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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5
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Saha M, Dittami SM, Chan CX, Raina JB, Stock W, Ghaderiardakani F, Valathuparambil Baby John AM, Corr S, Schleyer G, Todd J, Cardini U, Bengtsson MM, Prado S, Skillings D, Sonnenschein EC, Engelen AH, Wang G, Wichard T, Brodie J, Leblanc C, Egan S. Progress and future directions for seaweed holobiont research. THE NEW PHYTOLOGIST 2024. [PMID: 39137959 DOI: 10.1111/nph.20018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/03/2024] [Indexed: 08/15/2024]
Abstract
In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed-microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.
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Affiliation(s)
- Mahasweta Saha
- Plymouth Marine Laboratory, Marine Ecology and Biodiversity, Prospect Place, Plymouth, PL1 3DH, UK
| | - Simon M Dittami
- CNRS, Integrative Biology of Marine Models Laboratory (LBI2M, UMR 8227), Station Biologique de Roscoff, Place Georges Teissier, Sorbonne Université, Roscoff, 29680, France
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Willem Stock
- Phycology Research Group, Ghent University, Krijgslaan 281 Sterre S8, Ghent, 9000, Belgium
| | - Fatemeh Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, Jena, 07743, Germany
| | | | - Shauna Corr
- Plymouth Marine Laboratory, Marine Ecology and Biodiversity, Prospect Place, Plymouth, PL1 3DH, UK
| | - Guy Schleyer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, Jena, 07745, Germany
| | - Jonathan Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Ulisse Cardini
- Department of Integrative Marine Ecology (EMI), Genoa Marine Centre, Stazione Zoologica Anton Dohrn - National Institute of Marine Biology, Ecology and Biotechnology, Genoa, 16126, Italy
| | - Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, Greifswald, 17489, Germany
| | - Soizic Prado
- National Museum of Natural History, Unit Molecules of Communication and Adaptation of Microorganisms (UMR 7245), Paris, France
| | - Derek Skillings
- Department of Philosophy, University of North Carolina Greensboro, Greensboro, NC, 27402, USA
| | - Eva C Sonnenschein
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | | | - Gaoge Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- MoE Key Laboratory of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, Jena, 07743, Germany
| | - Juliet Brodie
- Natural History Museum, Research, Cromwell Road, London, SW7 5BD, UK
| | - Catherine Leblanc
- CNRS, Integrative Biology of Marine Models Laboratory (LBI2M, UMR 8227), Station Biologique de Roscoff, Place Georges Teissier, Sorbonne Université, Roscoff, 29680, France
| | - Suhelen Egan
- Centre for Marine Science and Innovation (CMSI), School of Biological, Earth and Environmental Sciences (BEES), UNSW Sydney, Sydney, NSW, 2052, Australia
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6
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Hu K, Chou CW, Wilke CO, Finkelstein IJ. Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons. Nat Commun 2024; 15:6653. [PMID: 39103341 DOI: 10.1038/s41467-024-50816-w] [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: 07/11/2023] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we report that CASTs can co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that CASTs co-occur with defense-associated CRISPR systems, with the highest prevalence for type I-B and type V CAST sub-types. Using an E. coli quantitative transposition assay and in vitro reconstitution, we show that CASTs can use CRISPR RNAs from these defense systems. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B CRISPR RNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via an unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA or a single guide RNA reduces, but does not abrogate, off-target integration for type V CASTs. Our findings suggest that some CASTs may exploit defense-associated CRISPR arrays and that this fact must be considered when porting CASTs to heterologous bacterial hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.
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Affiliation(s)
- Kuang Hu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Claus O Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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7
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Beattie GA, Bayliss KL, Jacobson DA, Broglie R, Burkett-Cadena M, Sessitsch A, Kankanala P, Stein J, Eversole K, Lichens-Park A. From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture. PHYTOPATHOLOGY 2024; 114:1742-1752. [PMID: 38776137 DOI: 10.1094/phyto-02-24-0054-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.
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Affiliation(s)
- Gwyn A Beattie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50014, U.S.A
| | - Kirsty L Bayliss
- Food Futures Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Daniel A Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37830, U.S.A
| | - Richard Broglie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
| | | | - Angela Sessitsch
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Bioresources Unit, AIT Austrian Institute of Technology, 3430 Tulln, Austria
| | | | - Joshua Stein
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Ann Lichens-Park
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
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8
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Rahman SU, Khan MO, Ullah R, Ahmad F, Raza G. Agrobacterium-Mediated Transformation for the Development of Transgenic Crops; Present and Future Prospects. Mol Biotechnol 2024; 66:1836-1852. [PMID: 37573566 DOI: 10.1007/s12033-023-00826-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 07/14/2023] [Indexed: 08/15/2023]
Abstract
Plant transformation based on Agrobacterium-mediated transformation is a technique that mimics the natural agrobacterium system for gene(s) introduction into crops. Through this technique, various crop species have been improved/modified for different trait/s, showing a successful genetic transformation so far. This technique has many advantages over other transformation methods such as stable integration of transgene, cost effective. However, there are many limitations of this technology such as mostly the crops are recalcitrant to agrobacterium, low transformation efficiency, transgene integration as well as off targets. So, it's very important to explore the major limitations and possible solutions for Agrobacterium-mediated transformation in order to increase its genetic transformation efficiency. Therefore, the present review article gives a comprehensive study how the transgenic crops are developed using Agrobacterium-mediated transformation, crops that have already been modified through this method, and risks associated with transgenic plants based on Agrobacterium-mediated transformation. Moreover, the challenges and problems associated with Agrobacterium-mediated transformation and how those problems can be solved in future for a successful genetic transformation of crops using modern biotechnology techniques such as CRISPR/Cas9 systems. The present review article will be really helpful for the audience those working on Genome editing of crops using Agrobacterium-mediated transformation and will opens many ways for future plant genetic transformation.
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Affiliation(s)
- Saleem Ur Rahman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad, Pakistan
| | - Muhammad Omar Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad, Pakistan
| | - Rahim Ullah
- Department of Biotechnology, Shahid Benazir Bhatoo University Sheringal, Upper Dir, Khyber Pakhtunkhwa, Pakistan
| | - Fayaz Ahmad
- Agriculture Research Institute (ARI), Swat, Mingora, Khyber Pakhtunkhwa, Pakistan
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, Faisalabad, Pakistan.
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9
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Song Y, Prather KLJ. Strategies in engineering sustainable biochemical synthesis through microbial systems. Curr Opin Chem Biol 2024; 81:102493. [PMID: 38971129 DOI: 10.1016/j.cbpa.2024.102493] [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: 04/16/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 07/08/2024]
Abstract
Growing environmental concerns and the urgency to address climate change have increased demand for the development of sustainable alternatives to fossil-derived fuels and chemicals. Microbial systems, possessing inherent biosynthetic capabilities, present a promising approach for achieving this goal. This review discusses the coupling of systems and synthetic biology to enable the elucidation and manipulation of microbial phenotypes for the production of chemicals that can substitute for petroleum-derived counterparts and contribute to advancing green biotechnology. The integration of artificial intelligence with metabolic engineering to facilitate precise and data-driven design of biosynthetic pathways is also discussed, along with the identification of current limitations and proposition of strategies for optimizing biosystems, thereby propelling the field of chemical biology towards sustainable chemical production.
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Affiliation(s)
- Yoseb Song
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Chang CW, Truong VA, Pham NN, Hu YC. RNA-guided genome engineering: paradigm shift towards transposons. Trends Biotechnol 2024; 42:970-985. [PMID: 38443218 DOI: 10.1016/j.tibtech.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
CRISPR-Cas systems revolutionized the genome engineering field but need to induce double-strand breaks (DSBs) and may be difficult to deliver due to their large protein size. Tn7-like transposons such as CRISPR-associated transposons (CASTs) can be repurposed for RNA-guided DSB-free integration, and obligate mobile element guided activity (OMEGA) proteins of the IS200/IS605 transposon family have been developed as hypercompact RNA-guided genome editing tools. CASTs and OMEGA are exciting, innovative genome engineering tools that can improve the precision and efficiency of editing. This review explores the recent developments and uses of CASTs and OMEGA in genome editing across prokaryotic and eukaryotic cells. The pros and cons of these transposon-based systems are deliberated in comparison to other CRISPR systems.
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Affiliation(s)
- Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Vy Anh Truong
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300, Taiwan.
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11
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Enright AL, Heelan WJ, Ward RD, Peters JM. CRISPRi functional genomics in bacteria and its application to medical and industrial research. Microbiol Mol Biol Rev 2024; 88:e0017022. [PMID: 38809084 PMCID: PMC11332340 DOI: 10.1128/mmbr.00170-22] [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] [Indexed: 05/30/2024] Open
Abstract
SUMMARYFunctional genomics is the use of systematic gene perturbation approaches to determine the contributions of genes under conditions of interest. Although functional genomic strategies have been used in bacteria for decades, recent studies have taken advantage of CRISPR (clustered regularly interspaced short palindromic repeats) technologies, such as CRISPRi (CRISPR interference), that are capable of precisely modulating expression of all genes in the genome. Here, we discuss and review the use of CRISPRi and related technologies for bacterial functional genomics. We discuss the strengths and weaknesses of CRISPRi as well as design considerations for CRISPRi genetic screens. We also review examples of how CRISPRi screens have defined relevant genetic targets for medical and industrial applications. Finally, we outline a few of the many possible directions that could be pursued using CRISPR-based functional genomics in bacteria. Our view is that the most exciting screens and discoveries are yet to come.
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Affiliation(s)
- Amy L. Enright
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - William J. Heelan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan D. Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- DOE Great Lakes Bioenergy Research Center University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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12
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Hassard F, Curtis TP, Dotro GC, Golyshin P, Gutierrez T, Heaven S, Horsfall L, Jefferson B, Jones DL, Krasnogor N, Kumar V, Lea-Smith DJ, Le Corre Pidou K, Liu Y, Lyu T, McCarthy RR, McKew B, Smith C, Yakunin A, Yang Z, Zhang Y, Coulon F. Scaling-up Engineering Biology for Enhanced Environmental Solutions. ACS Synth Biol 2024; 13:1586-1588. [PMID: 38903005 PMCID: PMC11197081 DOI: 10.1021/acssynbio.4c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Indexed: 06/22/2024]
Affiliation(s)
| | | | | | | | | | - Sonia Heaven
- University of Southampton, Southampton SO16 7QF, U.K.
| | | | | | | | | | - Vinod Kumar
- Cranfield University, Bedford MK43 0AL, U.K.
| | | | | | - Yongqiang Liu
- University of Southampton, Southampton SO16 7QF, U.K.
| | - Tao Lyu
- Cranfield University, Bedford MK43 0AL, U.K.
| | | | - Boyd McKew
- University of Essex, Colchester, Essex CO4 3SQ, U.K.
| | - Cindy Smith
- University of Glasgow, Glasgow G12 8LT, U.K.
| | | | - Zhugen Yang
- Cranfield University, Bedford MK43 0AL, U.K.
| | - Yue Zhang
- University of Southampton, Southampton SO16 7QF, U.K.
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13
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Hackmann TJ. The vast landscape of carbohydrate fermentation in prokaryotes. FEMS Microbiol Rev 2024; 48:fuae016. [PMID: 38821505 PMCID: PMC11187502 DOI: 10.1093/femsre/fuae016] [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: 04/05/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.
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Affiliation(s)
- Timothy J Hackmann
- Department of Animal Science, University of California, Davis, CA 95616, United States
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14
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Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
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15
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Gupta SS, Hamza Kh M, Sones CL, Zhang X, Sivaraman GK. The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems. Funct Integr Genomics 2024; 24:110. [PMID: 38806846 DOI: 10.1007/s10142-024-01362-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/30/2024]
Abstract
With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.
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Affiliation(s)
- Sobin Sonu Gupta
- Founder & CEO at Times of Biotech, Navelim Bicholim, Goa-403505, India
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Muneeb Hamza Kh
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Collin L Sones
- Founder and CTO of Highfield Diagnostics, Zepler Institute of Photonics and Nanoelectronics, University of Southampton, SO17 1BJ, Southampton, UK
| | - Xunli Zhang
- School of Engineering & Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India.
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16
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Moon TS. Earth: Extinguishing anthropogenic risks through harmonization. N Biotechnol 2024; 80:69-71. [PMID: 38367910 PMCID: PMC10939714 DOI: 10.1016/j.nbt.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
Human diseases can kill one person at a time, but the COVID-19 pandemic showed massacres could be possible. The climate crisis could be even worse, potentially leading to a bigger number of deaths of the human species and all living systems on Earth. I urge us to change our human-focused mindset to solve many problems, including the climate crisis, which humans caused to the entire ecosystems due to our arrogance: humans own this world. In this perspective article, I propose four recommendations to address climate issues through paradigm change and safe and sustainable technologies.
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Affiliation(s)
- Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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17
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Vazquez-Uribe R, Hedin KA, Licht TR, Nieuwdorp M, Sommer MOA. Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases. Trends Endocrinol Metab 2024:S1043-2760(24)00115-2. [PMID: 38782649 DOI: 10.1016/j.tem.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The rising prevalence of metabolic diseases calls for innovative treatments. Peptide-based drugs have transformed the management of conditions such as obesity and type 2 diabetes. Yet, challenges persist in oral delivery of these peptides. This review explores the potential of 'advanced microbiome therapeutics' (AMTs), which involve engineered microbes for delivery of peptides in situ, thereby enhancing their bioavailability. Preclinical work on AMTs has shown promise in treating animal models of metabolic diseases, including obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease. Outstanding challenges toward realizing the potential of AMTs involve improving peptide expression, ensuring predictable colonization control, enhancing stability, and managing safety and biocontainment concerns. Still, AMTs have potential for revolutionizing the treatment of metabolic diseases, potentially offering dynamic and personalized novel therapeutic approaches.
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Affiliation(s)
- Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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18
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Zheng L, Shen J, Chen R, Hu Y, Zhao W, Leung ELH, Dai L. Genome engineering of the human gut microbiome. J Genet Genomics 2024; 51:479-491. [PMID: 38218395 DOI: 10.1016/j.jgg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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Affiliation(s)
- Linggang Zheng
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruiyue Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucan Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Science, University of Macau, Macau 999078, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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19
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Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: Recent advances and applications. Biotechnol Adv 2024; 72:108343. [PMID: 38521283 DOI: 10.1016/j.biotechadv.2024.108343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering. MGEs, including DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons, offer various advantages, such as a broad host range, genome-wide mutagenesis, efficient large-size DNA integration, multiplexing capabilities, and in situ single-stranded DNA generation. We focused on the components, mechanisms, and features of each MGE-based tool to highlight their cellular applications. Finally, we discussed the current challenges of MGE-based genome engineering and provided insights into the evolving landscape of this transformative technology. In conclusion, the combination of genome engineering with MGE demonstrates remarkable potential for addressing various challenges and advancing the field of genetic manipulation, and promises to revolutionize our ability to engineer and understand the genomes of diverse organisms.
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Affiliation(s)
- Jaeseong Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea.
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20
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Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
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Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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21
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Arévalo S, Pérez Rico D, Abarca D, Dijkhuizen LW, Sarasa-Buisan C, Lindblad P, Flores E, Nierzwicki-Bauer S, Schluepmann H. Genome Engineering by RNA-Guided Transposition for Anabaena sp. PCC 7120. ACS Synth Biol 2024; 13:901-912. [PMID: 38445989 PMCID: PMC10949235 DOI: 10.1021/acssynbio.3c00583] [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: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In genome engineering, the integration of incoming DNA has been dependent on enzymes produced by dividing cells, which has been a bottleneck toward increasing DNA insertion frequencies and accuracy. Recently, RNA-guided transposition with CRISPR-associated transposase (CAST) was reported as highly effective and specific in Escherichia coli. Here, we developed Golden Gate vectors to test CAST in filamentous cyanobacteria and to show that it is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide (sg) RNA encoding the leading but not the reverse complement strand of the target were effective with the protospacer-associated motif (PAM) sequence included in the sgRNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic, which could be used to cure the plasmid. In all six cases analyzed, only the transposon cargo defined by the sequence ranging from left and right elements was inserted at the target loci; therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.
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Affiliation(s)
- Sergio Arévalo
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Daniel Pérez Rico
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dolores Abarca
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Laura W. Dijkhuizen
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cristina Sarasa-Buisan
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Peter Lindblad
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
| | - Enrique Flores
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Sandra Nierzwicki-Bauer
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Henriette Schluepmann
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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22
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Nogué F, Causse M, Debaeke P, Déjardin A, Lemarié S, Richard G, Rogowsky P, Caranta C. Can genome editing help transitioning to agroecology? iScience 2024; 27:109159. [PMID: 38405612 PMCID: PMC10884958 DOI: 10.1016/j.isci.2024.109159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Meeting the challenges of agroecological transition in a context of climate change requires the use of various strategies such as biological regulations, adapted animal and plant genotypes, diversified production systems, and digital technologies. Seeds and plants, through plant breeding, play a crucial role in driving these changes. The emergence of genome editing presents a new opportunity in plant breeding practices. However, like any technological revolution involving living organisms, it is essential to assess its potential contributions, limits, risks, socio-economic implications, and the associated controversies. This article aims to provide a comprehensive review of scientific knowledge on genome editing for agroecological transition, drawing on multidisciplinary approaches encompassing biological, agronomic, economic, and social sciences.
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Affiliation(s)
- Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Mathilde Causse
- INRAE, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143 Montfavet Avignon, France
| | - Philippe Debaeke
- University Toulouse, INRAE, UMR AGIR, 31320 Castanet-Tolosan, France
| | - Annabelle Déjardin
- INRAE, ONF, BioForA, 2163 Avenue de la pomme de pin, 45075 Orléans, France
| | - Stéphane Lemarié
- Université Grenoble Alpes, CNRS, INRAE, Grenoble INP, 38400 Saint-Martin-d'Hères, France
| | - Guy Richard
- INRAE Direction de l’expertise scientifique collective, de la prospective et des études (DEPE), 147 rue de l’Université 75338 PARIS Cedex 07, France
| | - Peter Rogowsky
- Laboratoire Reproduction et Développement des Plantes, University Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69342 Lyon, France
| | - Carole Caranta
- INRAE, 147 rue de l'Université, 75338 Paris cedex 07, France
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23
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Chen X, Du J, Yun S, Xue C, Yao Y, Rao S. Recent advances in CRISPR-Cas9-based genome insertion technologies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102138. [PMID: 38379727 PMCID: PMC10878794 DOI: 10.1016/j.omtn.2024.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Programmable genome insertion (or knock-in) is vital for both fundamental and translational research. The continuously expanding number of CRISPR-based genome insertion strategies demonstrates the ongoing development in this field. Common methods for site-specific genome insertion rely on cellular double-strand breaks repair pathways, such as homology-directed repair, non-homologous end-joining, and microhomology-mediated end joining. Recent advancements have further expanded the toolbox of programmable genome insertion techniques, including prime editing, integrase coupled with programmable nuclease, and CRISPR-associated transposon. These tools possess their own capabilities and limitations, promoting tremendous efforts to enhance editing efficiency, broaden targeting scope and improve editing specificity. In this review, we first summarize recent advances in programmable genome insertion techniques. We then elaborate on the cons and pros of each technique to assist researchers in making informed choices when using these tools. Finally, we identify opportunities for future improvements and applications in basic research and therapeutics.
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Affiliation(s)
- Xinwen Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingjing Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shaowei Yun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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24
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Chia SPS, Pang JKS, Soh BS. Current RNA strategies in treating cardiovascular diseases. Mol Ther 2024; 32:580-608. [PMID: 38291757 PMCID: PMC10928165 DOI: 10.1016/j.ymthe.2024.01.028] [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: 09/14/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
Cardiovascular disease (CVD) continues to impose a significant global health burden, necessitating the exploration of innovative treatment strategies. Ribonucleic acid (RNA)-based therapeutics have emerged as a promising avenue to address the complex molecular mechanisms underlying CVD pathogenesis. We present a comprehensive review of the current state of RNA therapeutics in the context of CVD, focusing on the diverse modalities that bring about transient or permanent modifications by targeting the different stages of the molecular biology central dogma. Considering the immense potential of RNA therapeutics, we have identified common gene targets that could serve as potential interventions for prevalent Mendelian CVD caused by single gene mutations, as well as acquired CVDs developed over time due to various factors. These gene targets offer opportunities to develop RNA-based treatments tailored to specific genetic and molecular pathways, presenting a novel and precise approach to address the complex pathogenesis of both types of cardiovascular conditions. Additionally, we discuss the challenges and opportunities associated with delivery strategies to achieve targeted delivery of RNA therapeutics to the cardiovascular system. This review highlights the immense potential of RNA-based interventions as a novel and precise approach to combat CVD, paving the way for future advancements in cardiovascular therapeutics.
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Affiliation(s)
- Shirley Pei Shan Chia
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Jeremy Kah Sheng Pang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Boon-Seng Soh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore; Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
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25
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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [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: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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26
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Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [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: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
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Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
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27
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Gelsinger DR, Vo PLH, Klompe SE, Ronda C, Wang HH, Sternberg SH. Bacterial genome engineering using CRISPR-associated transposases. Nat Protoc 2024; 19:752-790. [PMID: 38216671 DOI: 10.1038/s41596-023-00927-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/02/2023] [Indexed: 01/14/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated transposases have the potential to transform the technology landscape for kilobase-scale genome engineering, by virtue of their ability to integrate large genetic payloads with high accuracy, easy programmability and no requirement for homologous recombination machinery. These transposons encode efficient, CRISPR RNA-guided transposases that execute genomic insertions in Escherichia coli at efficiencies approaching ~100%. Moreover, they generate multiplexed edits when programmed with multiple guides, and function robustly in diverse Gram-negative bacterial species. Here we present a detailed protocol for engineering bacterial genomes using CRISPR-associated transposase (CAST) systems, including guidelines on the available vectors, customization of guide RNAs and DNA payloads, selection of common delivery methods, and genotypic analysis of integration events. We further describe a computational CRISPR RNA design algorithm to avoid potential off-targets, and a CRISPR array cloning pipeline for performing multiplexed DNA insertions. The method presented here allows the isolation of clonal strains containing a novel genomic integration event of interest within 1-2 weeks using available plasmid constructs and standard molecular biology techniques.
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Affiliation(s)
- Diego Rivera Gelsinger
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Vertex Pharmaceuticals, Inc, Boston, MA, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Carlotta Ronda
- Department of Systems Biology, Columbia University, New York, NY, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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28
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Cui Y, Qu X. CRISPR-Cas systems of lactic acid bacteria and applications in food science. Biotechnol Adv 2024; 71:108323. [PMID: 38346597 DOI: 10.1016/j.biotechadv.2024.108323] [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: 08/14/2023] [Revised: 12/29/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) systems are widely distributed in lactic acid bacteria (LAB), contributing to their RNA-mediated adaptive defense immunity. The CRISPR-Cas-based genetic tools have exhibited powerful capability. It has been highly utilized in different organisms, accelerating the development of life science. The review summarized the components, adaptive immunity mechanisms, and classification of CRISPR-Cas systems; analyzed the distribution and characteristics of CRISPR-Cas system in LAB. The review focuses on the development of CRISPR-Cas-based genetic tools in LAB for providing latest development and future trend. The diverse and broad applications of CRISPR-Cas systems in food/probiotic industry are introduced. LAB harbor a plenty of CRISPR-Cas systems, which contribute to generate safer and more robust strains with increased resistance against bacteriophage and prevent the dissemination of plasmids carrying antibiotic-resistance markers. Furthermore, the CRISPR-Cas system from LAB could be used to exploit novel, flexible, programmable genome editing tools of native host and other organisms, resolving the limitation of genetic operation of some LAB species, increasing the important biological functions of probiotics, improving the adaptation of probiotics in complex environments, and inhibiting the growth of foodborne pathogens. The development of the genetic tools based on CRISPR-Cas system in LAB, especially the endogenous CRISPR-Cas system, will open new avenues for precise regulation, rational design, and flexible application of LAB.
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Affiliation(s)
- Yanhua Cui
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
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29
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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [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: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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30
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Nishiyama K, Kato Y, Nishimura A, Mi X, Nagata R, Mori Y, Azuma YT, Nishida M. Pharmacological Activation of TRPC6 Channel Prevents Colitis Progression. Int J Mol Sci 2024; 25:2401. [PMID: 38397074 PMCID: PMC10889536 DOI: 10.3390/ijms25042401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
We recently reported that transient receptor potential canonical (TRPC) 6 channel activity contributes to intracellular Zn2+ homeostasis in the heart. Zn2+ has also been implicated in the regulation of intestinal redox and microbial homeostasis. This study aims to investigate the role of TRPC6-mediated Zn2+ influx in the stress resistance of the intestine. The expression profile of TRPC1-C7 mRNAs in the actively inflamed mucosa from inflammatory bowel disease (IBD) patients was analyzed using the GEO database. Systemic TRPC3 knockout (KO) and TRPC6 KO mice were treated with dextran sulfate sodium (DSS) to induce colitis. The Zn2+ concentration and the mRNA expression levels of oxidative/inflammatory markers in colon tissues were quantitatively analyzed, and gut microbiota profiles were compared. TRPC6 mRNA expression level was increased in IBD patients and DSS-treated mouse colon tissues. DSS-treated TRPC6 KO mice, but not TRPC3 KO mice, showed severe weight loss and increased disease activity index compared with DSS-treated WT mice. The mRNA abundances of antioxidant proteins were basically increased in the TRPC6 KO colon, with changes in gut microbiota profiles. Treatment with TRPC6 activator prevented the DSS-induced colitis progression accompanied by increasing Zn2+ concentration. We suggest that TRPC6-mediated Zn2+ influx activity plays a key role in stress resistance against IBD, providing a new strategy for treating colitis.
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Affiliation(s)
- Kazuhiro Nishiyama
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.N.); (Y.K.); (X.M.)
- Laboratory of Prophylactic Pharmacology, Osaka Metropolitan University Graduate School of Veterinary Science, Osaka 598-8531, Japan;
| | - Yuri Kato
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.N.); (Y.K.); (X.M.)
| | - Akiyuki Nishimura
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan;
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- SOKENDAI (Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies), Okazaki 444-8787, Japan
| | - Xinya Mi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.N.); (Y.K.); (X.M.)
| | - Ryu Nagata
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan;
| | - Yasuo Mori
- Graduate School of Engineering, Kyoto University, Kyoto 615-8530, Japan;
| | - Yasu-Taka Azuma
- Laboratory of Prophylactic Pharmacology, Osaka Metropolitan University Graduate School of Veterinary Science, Osaka 598-8531, Japan;
| | - Motohiro Nishida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.N.); (Y.K.); (X.M.)
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan;
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- SOKENDAI (Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies), Okazaki 444-8787, Japan
- Department of Physiology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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31
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Ragland CJ, Shih KY, Dinneny JR. Choreographing root architecture and rhizosphere interactions through synthetic biology. Nat Commun 2024; 15:1370. [PMID: 38355570 PMCID: PMC10866969 DOI: 10.1038/s41467-024-45272-5] [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: 07/17/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.
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Affiliation(s)
- Carin J Ragland
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Y Shih
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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32
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Tao X, Yang Z, Feng J, Jian S, Yang Y, Bates CT, Wang G, Guo X, Ning D, Kempher ML, Liu XJA, Ouyang Y, Han S, Wu L, Zeng Y, Kuang J, Zhang Y, Zhou X, Shi Z, Qin W, Wang J, Firestone MK, Tiedje JM, Zhou J. Experimental warming accelerates positive soil priming in a temperate grassland ecosystem. Nat Commun 2024; 15:1178. [PMID: 38331994 PMCID: PMC10853207 DOI: 10.1038/s41467-024-45277-0] [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: 05/04/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Unravelling biosphere feedback mechanisms is crucial for predicting the impacts of global warming. Soil priming, an effect of fresh plant-derived carbon (C) on native soil organic carbon (SOC) decomposition, is a key feedback mechanism that could release large amounts of soil C into the atmosphere. However, the impacts of climate warming on soil priming remain elusive. Here, we show that experimental warming accelerates soil priming by 12.7% in a temperate grassland. Warming alters bacterial communities, with 38% of unique active phylotypes detected under warming. The functional genes essential for soil C decomposition are also stimulated, which could be linked to priming effects. We incorporate lab-derived information into an ecosystem model showing that model parameter uncertainty can be reduced by 32-37%. Model simulations from 2010 to 2016 indicate an increase in soil C decomposition under warming, with a 9.1% rise in priming-induced CO2 emissions. If our findings can be generalized to other ecosystems over an extended period of time, soil priming could play an important role in terrestrial C cycle feedbacks and climate change.
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Affiliation(s)
- Xuanyu Tao
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhifeng Yang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jiajie Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Siyang Jian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China.
| | - Colin T Bates
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Gangsheng Wang
- Institute for Water-Carbon Cycles and Carbon Neutrality, and State Key Laboratory of Water Resources Engineering and Management, Wuhan University, 430072, Wuhan, China
| | - Xue Guo
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Megan L Kempher
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiao Jun A Liu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Shun Han
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Linwei Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Jialiang Kuang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Ya Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Xishu Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Zheng Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Wei Qin
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, 210008, Nanjing, China
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- School of Computer Sciences, University of Oklahoma, Norman, OK, 73019, USA.
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Sintsova A, Ruscheweyh HJ, Field CM, Feer L, Nguyen BD, Daniel B, Hardt WD, Vorholt JA, Sunagawa S. mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. Bioinformatics 2024; 40:btae078. [PMID: 38341646 PMCID: PMC10885212 DOI: 10.1093/bioinformatics/btae078] [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: 07/31/2023] [Revised: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills. RESULTS Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery. AVAILABILITY AND IMPLEMENTATION The tool is implemented in Python. The source code is freely available (https://github.com/MicrobiologyETHZ/mbarq) and the web app can be accessed at: https://microbiomics.io/tools/mbarq-app.
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Affiliation(s)
- Anna Sintsova
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Lilith Feer
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Bidong D Nguyen
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Benjamin Daniel
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Wolf-Dietrich Hardt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Julia A Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
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34
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Garza Elizondo AM, Chappell J. Targeted Transcriptional Activation Using a CRISPR-Associated Transposon System. ACS Synth Biol 2024; 13:328-336. [PMID: 38085703 DOI: 10.1021/acssynbio.3c00563] [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: 01/23/2024]
Abstract
Synthetic perturbation of gene expression is central to our ability to reliably uncover genotype-phenotype relationships in microbes. Here, we present a novel transcription activation strategy that uses the Vibrio cholerae CRISPR-Associated Transposon (CAST) system to selectively insert promoter elements upstream of genes of interest. Through this strategy, we show robust activation of both recombinant and endogenous genes across the Escherichia coli chromosome. We then demonstrate the precise tuning of expression levels by exchanging the promoter elements being inserted. Finally, we demonstrate that CAST activation can be used to synthetically induce ampicillin-resistant phenotypes in E. coli.
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Affiliation(s)
| | - James Chappell
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
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35
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Lyu X, Nuhu M, Candry P, Wolfanger J, Betenbaugh M, Saldivar A, Zuniga C, Wang Y, Shrestha S. Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass. J Ind Microbiol Biotechnol 2024; 51:kuae025. [PMID: 39003244 PMCID: PMC11287213 DOI: 10.1093/jimb/kuae025] [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: 04/11/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
Abstract
Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted. ONE-SENTENCE SUMMARY This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.
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Affiliation(s)
- Xuejiao Lyu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mujaheed Nuhu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Pieter Candry
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Jenna Wolfanger
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexis Saldivar
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Cristal Zuniga
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Ying Wang
- Department of Soil and Crop Sciences, Texas A&M University, TX 77843, USA
| | - Shilva Shrestha
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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36
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Schmitz M, Querques I. DNA on the move: mechanisms, functions and applications of transposable elements. FEBS Open Bio 2024; 14:13-22. [PMID: 38041553 PMCID: PMC10761935 DOI: 10.1002/2211-5463.13743] [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: 03/27/2023] [Revised: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023] Open
Abstract
Transposons are mobile genetic elements that have invaded all domains of life by moving between and within their host genomes. Due to their mobility (or transposition), transposons facilitate horizontal gene transfer in bacteria and foster the evolution of new molecular functions in prokaryotes and eukaryotes. As transposition can lead to detrimental genomic rearrangements, organisms have evolved a multitude of molecular strategies to control transposons, including genome defense mechanisms provided by CRISPR-Cas systems. Apart from their biological impacts on genomes, DNA transposons have been leveraged as efficient gene insertion vectors in basic research, transgenesis and gene therapy. However, the close to random insertion profile of transposon-based tools limits their programmability and safety. Despite recent advances brought by the development of CRISPR-associated genome editing nucleases, a strategy for efficient insertion of large, multi-kilobase transgenes at user-defined genomic sites is currently challenging. The discovery and experimental characterization of bacterial CRISPR-associated transposons (CASTs) led to the attractive hypothesis that these systems could be repurposed as programmable, site-specific gene integration technologies. Here, we provide a broad overview of the molecular mechanisms underpinning DNA transposition and of its biological and technological impact. The second focus of the article is to describe recent mechanistic and functional analyses of CAST transposition. Finally, current challenges and desired future advances of CAST-based genome engineering applications are briefly discussed.
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Affiliation(s)
| | - Irma Querques
- Department of BiochemistryUniversity of ZurichSwitzerland
- Max Perutz Labs, Vienna Biocenter Campus (VBC)Austria
- Department of Structural and Computational Biology, Center for Molecular BiologyUniversity of ViennaAustria
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37
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Zhang H, Xie Y, Cao F, Song X. Gut microbiota-derived fatty acid and sterol metabolites: biotransformation and immunomodulatory functions. Gut Microbes 2024; 16:2382336. [PMID: 39046079 PMCID: PMC11271093 DOI: 10.1080/19490976.2024.2382336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/26/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
Commensal microorganisms in the human gut produce numerous metabolites by using small molecules derived from the host or diet as precursors. Host or dietary lipid molecules are involved in energy metabolism and maintaining the structural integrity of cell membranes. Notably, gut microbes can convert these lipids into bioactive signaling molecules through their biotransformation and synthesis pathways. These microbiota-derived lipid metabolites can affect host physiology by influencing the body's immune and metabolic processes. This review aims to summarize recent advances in the microbial transformation and host immunomodulatory functions of these lipid metabolites, with a special focus on fatty acids and steroids produced by our gut microbiota.
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Affiliation(s)
- Haohao Zhang
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yadong Xie
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Fei Cao
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xinyang Song
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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38
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Chen JJ. Interfacial Electron Transfer in Chemical and Biological Transformation of Pollutants in Environmental Catalysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21540-21549. [PMID: 38086095 DOI: 10.1021/acs.est.3c05608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Interfacial electron transfer (IET) is essential for chemical and biological transformation of pollutants, operative across diverse lengths and time scales. This Perspective presents an array of multiscale molecular simulation methodologies, supplemented by in situ monitoring and imaging techniques, serving as robust tools to decode IET enhancement mechanisms such as interface molecular modification, catalyst coordination mode, and atomic composition regulation. In addition, three IET-based pollutant transformation systems, an electrocatalytic oxidation system, a bioelectrochemical spatial coupling system, and an enzyme-inspired electrocatalytic system, were developed, demonstrating a high effect in transforming and degrading pollutants. To improve the effectiveness and scalability of IET-based strategies, the refinement of these systems is necessitated through rigorous research and theoretical exploration, particularly in the context of practical wastewater treatment scenarios. Future endeavors aim to elucidate the synergy between biological and chemical modules, edit the environmental functional microorganisms, and harness machine learning for designing advanced environmental catalysts to boost efficiency. This Perspective highlights the powerful potential of IET-focused environmental remediation strategies, emphasizing the critical role of interdisciplinary research in addressing the urgent global challenge of water pollution.
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Affiliation(s)
- Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
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39
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Tenjo-Castaño F, Montoya G, Carabias A. Transposons and CRISPR: Rewiring Gene Editing. Biochemistry 2023; 62:3521-3532. [PMID: 36130724 PMCID: PMC10734217 DOI: 10.1021/acs.biochem.2c00379] [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: 06/27/2022] [Revised: 08/11/2022] [Indexed: 11/30/2022]
Abstract
CRISPR-Cas is driving a gene editing revolution because of its simple reprogramming. However, off-target effects and dependence on the double-strand break repair pathways impose important limitations. Because homology-directed repair acts primarily in actively dividing cells, many of the current gene correction/replacement approaches are restricted to a minority of cell types. Furthermore, current approaches display low efficiency upon insertion of large DNA cargos (e.g., sequences containing multiple gene circuits with tunable functionalities). Recent research has revealed new links between CRISPR-Cas systems and transposons providing new scaffolds that might overcome some of these limitations. Here, we comment on two new transposon-associated RNA-guided mechanisms considering their potential as new gene editing solutions. Initially, we focus on a group of small RNA-guided endonucleases of the IS200/IS605 family of transposons, which likely evolved into class 2 CRISPR effector nucleases (Cas9s and Cas12s). We explore the diversity of these nucleases (named OMEGA, obligate mobile element-guided activity) and analyze their similarities with class 2 gene editors. OMEGA nucleases can perform gene editing in human cells and constitute promising candidates for the design of new compact RNA-guided platforms. Then, we address the co-option of the RNA-guided activity of different CRISPR effector nucleases by a specialized group of Tn7-like transposons to target transposon integration. We describe the various mechanisms used by these RNA-guided transposons for target site selection and integration. Finally, we assess the potential of these new systems to circumvent some of the current gene editing challenges.
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Affiliation(s)
- Francisco Tenjo-Castaño
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Arturo Carabias
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
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40
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Xu Z, Chen S, Wu W, Wen Y, Cao H. Type I CRISPR-Cas-mediated microbial gene editing and regulation. AIMS Microbiol 2023; 9:780-800. [PMID: 38173969 PMCID: PMC10758571 DOI: 10.3934/microbiol.2023040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
There are six major types of CRISPR-Cas systems that provide adaptive immunity in bacteria and archaea against invasive genetic elements. The discovery of CRISPR-Cas systems has revolutionized the field of genetics in many organisms. In the past few years, exploitations of the most abundant class 1 type I CRISPR-Cas systems have revealed their great potential and distinct advantages to achieve gene editing and regulation in diverse microorganisms in spite of their complicated structures. The widespread and diversified type I CRISPR-Cas systems are becoming increasingly attractive for the development of new biotechnological tools, especially in genetically recalcitrant microbial strains. In this review article, we comprehensively summarize recent advancements in microbial gene editing and regulation by utilizing type I CRISPR-Cas systems. Importantly, to expand the microbial host range of type I CRISPR-Cas-based applications, these structurally complicated systems have been improved as transferable gene-editing tools with efficient delivery methods for stable expression of CRISPR-Cas elements, as well as convenient gene-regulation tools with the prevention of DNA cleavage by obviating deletion or mutation of the Cas3 nuclease. We envision that type I CRISPR-Cas systems will largely expand the biotechnological toolbox for microbes with medical, environmental and industrial importance.
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Affiliation(s)
- Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Weiyan Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yongqi Wen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Huiluo Cao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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41
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Chen D, Yin Y, Hu Y, Cao L, Zhao C, Li B. Transposon-aided capture (TRACA) of plasmids from the human gut. Lett Appl Microbiol 2023; 76:ovad132. [PMID: 38031336 DOI: 10.1093/lambio/ovad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
The gut microbiota consists of a vast and diverse assemblage of microorganisms that play a pivotal role in maintaining host health. Nevertheless, a significant portion of the human gut microbiota remains uncultivated. Plasmids, a type of MGE, assume a critical function in the biological evolution and adaptation of bacteria to varying environments. To investigate the plasmids present within the gut microbiota community, we used the transposon-aided capture method (TRACA) to explore plasmids derived from the gut microbiota. In this study, fecal samples were collected from two healthy human volunteers and subsequently subjected to the TRACA method for plasmid isolation. Then, the complete sequence of the plasmids was obtained using the genome walking method, and sequence identity was also analyzed. A total of 15 plasmids were isolated. At last, 13 plasmids were successfully sequenced, of which 12 plasmids were highly identical to the plasmids in the National Center for Biotechnology Information (NCBI) database and were all small plasmids. Furthermore, a putative novel plasmid, named pMRPHD, was isolated, which had mobilized elements (oriT and oriV) and a potential type II restriction-modification (R-M) system encoded by DNA cytosine methyltransferase and type II restriction enzyme (Ban I), whose specific functions and applications warrant further exploration.
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Affiliation(s)
- Dan Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Yeshi Yin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Yunfei Hu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Linyan Cao
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Changhui Zhao
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
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42
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Jansson JK, McClure R, Egbert RG. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 2023; 41:1716-1728. [PMID: 37903921 DOI: 10.1038/s41587-023-01932-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/01/2023] [Indexed: 11/01/2023]
Abstract
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
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Affiliation(s)
- Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G Egbert
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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43
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Mahmoudi N, Wilhelm RC. Can we manage microbial systems to enhance carbon storage? Environ Microbiol 2023; 25:3011-3018. [PMID: 37431673 DOI: 10.1111/1462-2920.16462] [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: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Climate change is an urgent environmental issue with wide-ranging impacts on ecosystems and society. Microbes are instrumental in maintaining the balance between carbon (C) accumulation and loss in the biosphere, actively regulating greenhouse gas fluxes from vast reservoirs of organic C stored in soils, sediments and oceans. Heterotrophic microbes exhibit varying capacities to access, degrade and metabolise organic C-leading to variations in remineralisation and turnover rates. The present challenge lies in effectively translating this accumulated knowledge into strategies that effectively steer the fate of organic C towards prolonged sequestration. In this article, we discuss three ecological scenarios that offer potential avenues for shaping C turnover rates in the environment. Specifically, we explore the promotion of slow-cycling microbial byproducts, the facilitation of higher carbon use efficiency, and the influence of biotic interactions. The ability to harness and control these processes relies on the integration of ecological principles and management practices, combined with advances in economically viable technologies to effectively manage microbial systems in the environment.
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Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montréal, Quebec, Canada
| | - Roland C Wilhelm
- Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana, USA
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44
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Tan Y, Liang J, Lai M, Wan S, Luo X, Li F. Advances in synthetic biology toolboxes paving the way for mechanistic understanding and strain engineering of gut commensal Bacteroides spp. and Clostridium spp. Biotechnol Adv 2023; 69:108272. [PMID: 37844770 DOI: 10.1016/j.biotechadv.2023.108272] [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: 08/13/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.
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Affiliation(s)
- Yang Tan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
| | - Jing Liang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingchi Lai
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Sai Wan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuli Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
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45
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Han T, Nazarbekov A, Zou X, Lee SY. Recent advances in systems metabolic engineering. Curr Opin Biotechnol 2023; 84:103004. [PMID: 37778304 DOI: 10.1016/j.copbio.2023.103004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Systems metabolic engineering, which integrates metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, has revolutionized the sustainable production of fuels and materials through the creation of efficient microbial cell factories. Recent advancements in systems metabolic engineering targeting different biological components of the host cell have enabled the creation of highly productive microbial cell factories. This article provides a review of the recent tools and strategies used for enzyme-, genetic module-, pathway-, flux-, genome-, and cell-level engineering, supported by illustrative examples. Furthermore, we highlight recent trends in systems metabolic engineering, which involve the application of multiple tools discussed in this review. Finally, the paper addresses the challenges and perspectives of transitioning academic-level metabolic engineering studies to commercial-scale production.
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Affiliation(s)
- Taehee Han
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, the Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, the Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 34141 Daejeon, the Republic of Korea
| | - Alisher Nazarbekov
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, the Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, the Republic of Korea
| | - Xuan Zou
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, the Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, the Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 34141 Daejeon, the Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, the Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, the Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 34141 Daejeon, the Republic of Korea; Graduate School of Engineering Biology, KAIST, Daejeon 34141, the Republic of Korea.
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46
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Dhingra Y, Sashital DG. A tool for more specific DNA integration. Science 2023; 382:768-769. [PMID: 37972178 DOI: 10.1126/science.adl0863] [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] [Indexed: 11/19/2023]
Abstract
The efficiency of targeted DNA insertion by CRISPR transposons is improved.
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Affiliation(s)
- Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
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47
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George JT, Acree C, Park JU, Kong M, Wiegand T, Pignot YL, Kellogg EH, Greene EC, Sternberg SH. Mechanism of target site selection by type V-K CRISPR-associated transposases. Science 2023; 382:eadj8543. [PMID: 37972161 PMCID: PMC10771339 DOI: 10.1126/science.adj8543] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/23/2023] [Indexed: 11/19/2023]
Abstract
CRISPR-associated transposases (CASTs) repurpose nuclease-deficient CRISPR effectors to catalyze RNA-guided transposition of large genetic payloads. Type V-K CASTs offer potential technology advantages but lack accuracy, and the molecular basis for this drawback has remained elusive. Here, we reveal that type V-K CASTs maintain an RNA-independent, "untargeted" transposition pathway alongside RNA-dependent integration, driven by the local availability of TnsC filaments. Using cryo-electron microscopy, single-molecule experiments, and high-throughput sequencing, we found that a minimal, CRISPR-less transpososome preferentially directs untargeted integration at AT-rich sites, with additional local specificity imparted by TnsB. By exploiting this knowledge, we suppressed untargeted transposition and increased type V-K CAST specificity up to 98.1% in cells without compromising on-target integration efficiency. These findings will inform further engineering of CAST systems for accurate, kilobase-scale genome engineering applications.
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Affiliation(s)
- Jerrin Thomas George
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Christopher Acree
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jung-Un Park
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Muwen Kong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yanis Luca Pignot
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Elizabeth H. Kellogg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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48
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Lou YC, Rubin BE, Schoelmerich MC, DiMarco KS, Borges AL, Rovinsky R, Song L, Doudna JA, Banfield JF. Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species. Nat Commun 2023; 14:7417. [PMID: 37973815 PMCID: PMC10654741 DOI: 10.1038/s41467-023-43279-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2'-fucosyllactose (2'FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2'FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2'FL breakdown, thus critical for B. breve's growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2'FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual's microbiome.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland
| | - Kaden S DiMarco
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Leo Song
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
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49
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Liu Z, Liu J, Yang Z, Zhu L, Zhu Z, Huang H, Jiang L. Endogenous CRISPR-Cas mediated in situ genome editing: State-of-the-art and the road ahead for engineering prokaryotes. Biotechnol Adv 2023; 68:108241. [PMID: 37633620 DOI: 10.1016/j.biotechadv.2023.108241] [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: 04/18/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
The CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing in various prokaryotes. However, the perturbation of DNA homeostasis and the inherent toxicity of Cas9/12a proteins could easily lead to cell death, which led to the development of endogenous CRISPR-Cas systems. Programming the widespread endogenous CRISPR-Cas systems for in situ genome editing represents a promising tool in prokaryotes, especially in genetically intractable species. Here, this review briefly summarizes the advances of endogenous CRISPR-Cas-mediated genome editing, covering aspects of establishing and optimizing the genetic tools. In particular, this review presents the application of different types of endogenous CRISPR-Cas tools for strain engineering, including genome editing and genetic regulation. Notably, this review also provides a detailed discussion of the transposon-associated CRISPR-Cas systems, and the programmable RNA-guided transposition using endogenous CRISPR-Cas systems to enable editing of microbial communities for understanding and control. Therefore, they will be a powerful tool for targeted genetic manipulation. Overall, this review will not only facilitate the development of standard genetic manipulation tools for non-model prokaryotes but will also enable more non-model prokaryotes to be genetically tractable.
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Affiliation(s)
- Zhenlei Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jiayu Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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50
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Liu Y, Zhu Z, Jiang L. Programming therapeutic probiotics by self-tunable sense-and-respond genetic circuits. Trends Microbiol 2023; 31:1099-1101. [PMID: 37620240 DOI: 10.1016/j.tim.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Probiotics can be programmed to sense and respond to intracellular disease signals to deliver the desired therapeutic effectors. The sense-and-respond genetic circuits, especially self-tunable ones, hold promise in improving the precision, effectiveness, and intelligence of therapeutic activities. Here, we present notable advances in the creation of engineered probiotics that harbour sense-and-respond genetic circuits.
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Affiliation(s)
- Yuxin Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Material-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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