1
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Eren AM, Banfield JF. Modern microbiology: Embracing complexity through integration across scales. Cell 2024; 187:5151-5170. [PMID: 39303684 DOI: 10.1016/j.cell.2024.08.028] [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: 06/22/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024]
Abstract
Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.
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Affiliation(s)
- A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany; Marine Biological Laboratory, Woods Hole, MA, USA; Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Environmental Science Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
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2
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Kamm C, Beisel CL. Phages to the rescue: in situ editing of the gut microbiota. Trends Microbiol 2024:S0966-842X(24)00227-0. [PMID: 39277459 DOI: 10.1016/j.tim.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Accepted: 09/03/2024] [Indexed: 09/17/2024]
Abstract
The gut microbiome contains numerous bacteria tied to our health. However, genetically modifying this community remains a major challenge. Brödel et al. take a critical step by engineering bacteriophages to efficiently deliver gene editors without propagation of the genetic cargo, efficiently introducing edits to bacteria residing in the mouse gut.
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Affiliation(s)
- Charlotte Kamm
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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3
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Daskalakis V, Papapetros S. Engineering salt-tolerant Cas12f1 variants for gene-editing applications. J Biomol Struct Dyn 2024; 42:7421-7431. [PMID: 37526217 DOI: 10.1080/07391102.2023.2240418] [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: 04/04/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
CRISPR has revolutionized the field of genome editing in life sciences by serving as a versatile and state-of-the-art tool. Cas12f1 is a small nuclease of the bacterial immunity CRISPR system with an ideal size for cellular delivery, in contrast to CRISPR-associated (Cas) proteins like Cas9 or Cas12. However, Cas12f1 works best at low salt concentrations. In this study, we find that the plasticity of certain Cas12f1 regions (K196-Y202 and I452-L515) is negatively affected by increased salt concentrations. On this line, key protein domains (REC1, WED, Nuc, lid) that are involved in the DNA-target recognition and the activation of the catalytic RuvC domain are in turn also affected. We suggest that salt concentration should be taken in to consideration for activity assessments of Cas engineered variants, especially if the mutations are on the protospacer adjacent motif interacting domain. The results can be exploited for the engineering of Cas variants and the assessment of their activity at varying salt concentrations. We propose that the K198Q mutation can restore at great degree the compromised plasticity and could potentially lead to salt-tolerant Cas12f1 variants. The methodology can be also employed for the study of biomolecules in terms of their salinity tolerance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
| | - Spyridon Papapetros
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
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4
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Brödel AK, Charpenay LH, Galtier M, Fuche FJ, Terrasse R, Poquet C, Havránek J, Pignotti S, Krawczyk A, Arraou M, Prevot G, Spadoni D, Yarnall MTN, Hessel EM, Fernandez-Rodriguez J, Duportet X, Bikard D. In situ targeted base editing of bacteria in the mouse gut. Nature 2024; 632:877-884. [PMID: 38987595 PMCID: PMC11338833 DOI: 10.1038/s41586-024-07681-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2024] [Indexed: 07/12/2024]
Abstract
Microbiome research is now demonstrating a growing number of bacterial strains and genes that affect our health1. Although CRISPR-derived tools have shown great success in editing disease-driving genes in human cells2, we currently lack the tools to achieve comparable success for bacterial targets in situ. Here we engineer a phage-derived particle to deliver a base editor and modify Escherichia coli colonizing the mouse gut. Editing of a β-lactamase gene in a model E. coli strain resulted in a median editing efficiency of 93% of the target bacterial population with a single dose. Edited bacteria were stably maintained in the mouse gut for at least 42 days following treatment. This was achieved using a non-replicative DNA vector, preventing maintenance and dissemination of the payload. We then leveraged this approach to edit several genes of therapeutic relevance in E. coli and Klebsiella pneumoniae strains in vitro and demonstrate in situ editing of a gene involved in the production of curli in a pathogenic E. coli strain. Our work demonstrates the feasibility of modifying bacteria directly in the gut, offering a new avenue to investigate the function of bacterial genes and opening the door to the design of new microbiome-targeted therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - David Bikard
- Eligo Bioscience, Paris, France.
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France.
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5
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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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6
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Levrier A, Karpathakis I, Nash B, Bowden SD, Lindner AB, Noireaux V. PHEIGES: all-cell-free phage synthesis and selection from engineered genomes. Nat Commun 2024; 15:2223. [PMID: 38472230 PMCID: PMC10933291 DOI: 10.1038/s41467-024-46585-1] [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: 07/15/2023] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Bacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.
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Affiliation(s)
- Antoine Levrier
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
- Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006, Paris, France
| | - Ioannis Karpathakis
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
- Facultatea de Biotehnologii, USAMV Bucuresti, Sector 1, Cod 011464, Bucureşti, Romania
| | - Bruce Nash
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Steven D Bowden
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Ariel B Lindner
- Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006, Paris, France.
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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7
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Chanchal DK, Chaudhary JS, Kumar P, Agnihotri N, Porwal P. CRISPR-Based Therapies: Revolutionizing Drug Development and Precision Medicine. Curr Gene Ther 2024; 24:193-207. [PMID: 38310456 DOI: 10.2174/0115665232275754231204072320] [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: 09/15/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 02/05/2024]
Abstract
With the discovery of CRISPR-Cas9, drug development and precision medicine have undergone a major change. This review article looks at the new ways that CRISPR-based therapies are being used and how they are changing the way medicine is done. CRISPR technology's ability to precisely and flexibly edit genes has opened up new ways to find, validate, and develop drug targets. Also, it has made way for personalized gene therapies, precise gene editing, and advanced screening techniques, all of which hold great promise for treating a wide range of diseases. In this article, we look at the latest research and clinical trials that show how CRISPR could be used to treat genetic diseases, cancer, infectious diseases, and other hard-to-treat conditions. However, ethical issues and problems with regulations are also discussed in relation to CRISPR-based therapies, which shows how important it is to use them safely and responsibly. As CRISPR continues to change how drugs are made and used, this review shines a light on the amazing things that have been done and what the future might hold in this rapidly changing field.
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Affiliation(s)
- Dilip Kumar Chanchal
- Department of Pharmacy, Smt. Vidyawati College of Pharmacy, Jhansi, Uttar Pradesh, India
- Glocal School of Pharmacy, Glocal University Mirzapur Pole, Saharanpur - 247121, Uttar Pradesh, India
| | | | - Pushpendra Kumar
- Faculty of Pharmacy, Uttar Pradesh University of Medical Sciences, Saifai, Etawah 206130, Uttar Pradesh, India
| | - Neha Agnihotri
- Department of Pharmacy, Maharana Pratap College of Pharmacy, Kothi, Mandhana, Kanpur-209217, Uttar Pradesh, India
| | - Prateek Porwal
- Glocal School of Pharmacy, Glocal University Mirzapur Pole, Saharanpur - 247121, Uttar Pradesh, India
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8
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Hassim A, Lekota KE. Isolation of Bacteriophages from Soil Samples in a Poorly Equipped Field Laboratory in Kruger National Park. Methods Mol Biol 2024; 2738:91-103. [PMID: 37966593 DOI: 10.1007/978-1-0716-3549-0_5] [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: 11/16/2023]
Abstract
Bacteriophages are viruses that infect bacteria. Bacteriophages are ubiquitous and are the most abundant organisms on the planet. Despite this, very little is known about the influence and effect of bacteriophages within terrestrial environments. Additionally, the natural soil microbiome profiles remain largely unexplored. Here we describe protocols that can be used, in field or rural laboratories containing only basic equipment, to make bacteriophage isolation more accessible and to facilitate such research.
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Affiliation(s)
- Ayesha Hassim
- Department of Veterinary Tropical Disease, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Kgaugelo Edward Lekota
- Unit for Environmental Sciences and Management, Microbiology, North West University, Potchefstroom, South Africa
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9
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Piya D, Nolan N, Moore ML, Ramirez Hernandez LA, Cress BF, Young R, Arkin AP, Mutalik VK. Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages. PLoS Biol 2023; 21:e3002416. [PMID: 38048319 PMCID: PMC10695390 DOI: 10.1371/journal.pbio.3002416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/02/2023] [Indexed: 12/06/2023] Open
Abstract
Phages are one of the key ecological drivers of microbial community dynamics, function, and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor intensive and are generally phage specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage-host combinations that facilitate the identification of nonessential genes. As a proof of concept, we use an arrayed genome-wide CRISPR interference (CRISPRi) assay to map gene essentiality landscape in the canonical coliphages λ and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification, and tracking of phages in diverse applications.
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Affiliation(s)
- Denish Piya
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
| | - Nicholas Nolan
- Department of Bioengineering, University of California-Berkeley, Berkeley, California, United States of America
| | - Madeline L. Moore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luis A. Ramirez Hernandez
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Brady F. Cress
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California, United States of America
| | - Ry Young
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, Texas, United States of America
| | - Adam P. Arkin
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
- Department of Bioengineering, University of California-Berkeley, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Vivek K. Mutalik
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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10
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Singh P, Vaishnav A, Liu H, Xiong C, Singh HB, Singh BK. Seed biopriming for sustainable agriculture and ecosystem restoration. Microb Biotechnol 2023; 16:2212-2222. [PMID: 37490280 PMCID: PMC10686123 DOI: 10.1111/1751-7915.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
The utilization of microbial inoculants in the realm of sustainable agricultural and ecosystem restoration has witnessed a surge in recent decades. This rise is largely attributed to advancements in our understanding of plant-microbe interactions, the urgency to reduce the dependence on agrochemicals and the growing societal demand for sustainable strategies in ecosystem management. However, despite the rapid growth of bio-inoculants sector, certain limitations persist concerning their efficacy and performance under the field condition. Here, we propose that seed biopriming, an effective microbial inoculant technique integrating both biological agents (the priming of beneficial microbes on seeds) and physiological aspects (hydration of seeds for improved metabolically activity), has a significant potential to mitigate these limitations. This method increases the protection of seeds against soil-borne pathogens and soil pollutants, such as salts and heavy metals, while promoting germination rate and uniformity, leading to overall improved primary productivity and soil health. Furthermore, we argue that a microbial coating on seeds can facilitate transgenerational associations of beneficial microbes, refine plant and soil microbiomes, and maintain soil legacies of beneficial microflora. This review article aims to improve our understanding of the seed biopriming approach as a potent and valuable tool in achieving sustainable agriculture and successful ecosystem restoration.
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Affiliation(s)
- Prachi Singh
- Rabindranath Tagore Agriculture College, DeogharBirsa Agriculture UniversityRanchiJharkhandIndia
| | - Anukool Vaishnav
- Department of BiotechnologyGLA UniversityMathuraUttar PradeshIndia
| | - Hongwei Liu
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Chao Xiong
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | | | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- Global Centre for Land‐Based InnovationWestern Sydney UniversityPenrithNew South WalesAustralia
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11
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Jo SJ, Kwon J, Kim SG, Lee SJ. The Biotechnological Application of Bacteriophages: What to Do and Where to Go in the Middle of the Post-Antibiotic Era. Microorganisms 2023; 11:2311. [PMID: 37764155 PMCID: PMC10534921 DOI: 10.3390/microorganisms11092311] [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: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Amid the escalating challenges of antibiotic resistance, bacterial infections have emerged as a global threat. Bacteriophages (phages), viral entities capable of selectively infecting bacteria, are gaining momentum as promising alternatives to traditional antibiotics. Their distinctive attributes, including host specificity, inherent self-amplification, and potential synergy with antibiotics, render them compelling candidates. Phage engineering, a burgeoning discipline, involves the strategic modification of bacteriophages to enhance their therapeutic potential and broaden their applications. The integration of CRISPR-Cas systems facilitates precise genetic modifications, enabling phages to serve as carriers of functional genes/proteins, thereby enhancing diagnostics, drug delivery, and therapy. Phage engineering holds promise in transforming precision medicine, addressing antibiotic resistance, and advancing diverse applications. Emphasizing the profound therapeutic potential of phages, this review underscores their pivotal role in combatting bacterial diseases and highlights their significance in the post-antibiotic era.
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Affiliation(s)
- Su Jin Jo
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jun Kwon
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan City 54596, Republic of Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Seung-Jun Lee
- Department of Pharmaceutical Science and Engineering, Seowon University, 377-3 Musimseoro, Seowon-gu, Cheong-ju City 28674, Republic of Korea
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12
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Chen X, McAndrew MJ, Lapinaite A. Unlocking the secrets of ABEs: the molecular mechanism behind their specificity. Biochem Soc Trans 2023; 51:1635-1646. [PMID: 37526140 PMCID: PMC10586758 DOI: 10.1042/bst20221508] [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: 04/13/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
CRISPR-Cas, the bacterial immune systems, have transformed the field of genome editing by providing efficient, easily programmable, and accessible tools for targeted genome editing. DNA base editors (BE) are state-of-the-art CRISPR-based technology, allowing for targeted modifications of individual nucleobases within the genome. Among the BEs, adenine base editors (ABEs) have shown great potential due to their ability to convert A-to-G with high efficiency. However, current ABEs have limitations in terms of their specificity and targeting range. In this review, we provide an overview of the molecular mechanism of ABEs, with a focus on the mechanism of deoxyadenosine deamination by evolved tRNA-specific adenosine deaminase (TadA). We discuss how mutations and adjustments introduced via both directed evolution as well as rational design have improved ABE efficiency and specificity. This review offers insights into the molecular mechanism of ABEs, providing a roadmap for future developments in the precision genome editing field.
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Affiliation(s)
- Xiaoyu Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, U.S.A
| | | | - Audrone Lapinaite
- School of Molecular Sciences, Arizona State University, Tempe, AZ, U.S.A
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, U.S.A
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, U.S.A
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13
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Ijaz M, Khan F, Zaki HEM, Khan MM, Radwan KSA, Jiang Y, Qian J, Ahmed T, Shahid MS, Luo J, Li B. Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091911. [PMID: 37176969 PMCID: PMC10180734 DOI: 10.3390/plants12091911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The "clustered regularly interspaced short palindromic repeats (CRISPR)" and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant-pathogen interactions have been discussed.
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Affiliation(s)
- Munazza Ijaz
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fahad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS 7250, Australia
| | - Haitham E M Zaki
- Horticulture Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
- Applied Biotechnology Department, University of Technology and Applied Sciences-Sur, Sur 411, Oman
| | - Muhammad Munem Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khlode S A Radwan
- Plant Pathology Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
| | - Yugen Jiang
- Agricultural Technology Extension Center of Fuyang District, Hangzhou 311400, China
| | - Jiahui Qian
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod 123, Oman
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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