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Patel RR, Vidyasagar, Singh SK, Singh M. Recent advances in inhibitor development and metabolic targeting in tuberculosis therapy. Microb Pathog 2025; 203:107515. [PMID: 40154850 DOI: 10.1016/j.micpath.2025.107515] [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: 12/27/2024] [Revised: 03/12/2025] [Accepted: 03/25/2025] [Indexed: 04/01/2025]
Abstract
Despite being a preventable and treatable disease, tuberculosis (TB) remained the second leading infectious cause of death globally in 2022, surpassed only by COVID-19. The death rate from TB is influenced by numerous factors that include antibiotic drug resistance, noncompliance with chemotherapy by patients, concurrent infection with the human immunodeficiency virus, delayed diagnosis, varying effectiveness of the Bacille-Calmette-Guerin vaccine, and other factors. Even with the recent advances in our knowledge of Mycobacterium tuberculosis and the accessibility of advanced genomic tools such as proteomics and microarrays, alongside modern methodologies, the pursuit of next-generation inhibitors targeting distinct or multiple molecular pathways remains essential to combat the increasing antimicrobial resistance. Hence, there is an urgent need to identify and develop new drug targets against TB that have unique mechanisms. Novel therapeutic targets might encompass gene products associated with various aspects of mycobacterial biology, such as transcription, metabolism, cell wall formation, persistence, and pathogenesis. This review focuses on the present state of our knowledge and comprehension regarding various inhibitors targeting key metabolic pathways of M. tuberculosis. The discussion encompasses small molecule, synthetic, peptide, natural product and microbial inhibitors and navigates through promising candidates in different phases of clinical development. Additionally, we explore the crucial enzymes and targets involved in metabolic pathways, highlighting their inhibitors. The metabolic pathways explored include nucleotide synthesis, mycolic acid synthesis, peptidoglycan biosynthesis, and energy metabolism. Furthermore, advancements in genetic approaches like CRISPRi and conditional expression systems are discussed, focusing on their role in elucidating gene essentiality and vulnerability in Mycobacteria.
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Affiliation(s)
- Ritu Raj Patel
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Vidyasagar
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sudhir Kumar Singh
- Virus Research and Diagnostic Laboratory, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Meenakshi Singh
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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2
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Sodani M, Misra CS, Kulkarni S, Rath D. CRISPR/Cas12a-mediated gene silencing across diverse functional genes demonstrates single gene-specific spacer efficacy in Mycobacterium smegmatis. J Biol Eng 2025; 19:21. [PMID: 40022115 PMCID: PMC11871654 DOI: 10.1186/s13036-025-00490-3] [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: 08/09/2024] [Accepted: 02/14/2025] [Indexed: 03/03/2025] Open
Abstract
BACKGROUND Tuberculosis, a persistent global health threat, necessitates a comprehensive understanding of the genes and pathways crucial for the survival and virulence of the causative pathogen, Mycobacterium tuberculosis. Working with M. tuberculosis (M.tb) presents significant challenges; therefore, the use of M. smegmatis as a surrogate system for conducting genetic studies of M.tb has proven to be highly valuable. Development of novel genetic tools to probe cellular processes accelerates the progress in the field of drug development and also helps in understanding the basic physiology of the bacterium. RESULTS This study reports the successful implementation and evaluation of the CRISPR-Cas12a system for gene repression in Mycobacterium smegmatis, a surrogate for M. tuberculosis. We engineered a Cas12a-based CRISPR interference (CRISPRi) system and assessed its functionality. Targeting 45 genes with a single sgRNA per gene, we achieved efficient gene repression, leading to marked phenotypic changes. Each knockdown strain was evaluated individually for growth phenotypes, and a comparison of the results with the reported essential gene library probed with dCas9 demonstrated congruous results across diverse gene categories. The study shows that CRISPR/Cas12a system can be effectively utilised with a single gene specific target for efficient silencing of the gene and highlights the importance of subsequent growth assays required to evaluate the vulnerability of targeted gene silencing. CONCLUSION Our findings reveal the robustness and versatility of the dCas12a-CRISPRi system in M. smegmatis, providing a valuable tool for functional genomics research. This work showcases the potential of the dCas12a-CRISPRi system in investigating essential genes, enabling a deeper understanding of the biology and potential therapeutic targets in mycobacterium species.
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Affiliation(s)
- Megha Sodani
- Radiation Medicine Centre, Medical Group, Bhabha Atomic Research Centre, Mumbai- 400085, Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai- 400094, Maharashtra, India
| | - Chitra S Misra
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai- 400085, Mumbai, Maharashtra, India
| | - Savita Kulkarni
- Radiation Medicine Centre, Medical Group, Bhabha Atomic Research Centre, Mumbai- 400085, Mumbai, Maharashtra, India.
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai- 400094, Maharashtra, India.
| | - Devashish Rath
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai- 400085, Mumbai, Maharashtra, India.
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai- 400094, Maharashtra, India.
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Laudouze J, Point V, Achache W, Crauste C, Canaan S, Santucci P. Fluorescence-based CRISPR interference system for controlled genetic repression and live single-cell imaging in mycobacteria. FEBS Lett 2025; 599:488-501. [PMID: 39618159 PMCID: PMC11848015 DOI: 10.1002/1873-3468.15071] [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: 10/06/2024] [Revised: 11/05/2024] [Accepted: 11/10/2024] [Indexed: 02/25/2025]
Abstract
In this research letter, we report the development and validation of a new subset of fluorescence-based CRISPR interference (CRISPRi) tools for our scientific community. The pJL series is directly derived from the original pIRL CRISPRi vectors and conserves all the elements to perform inducible targeted gene repression. These vectors carry two distinct fluorescent markers under the constitutive promoter psmyc to simplify the selection of recombinant clones. We demonstrate the functionality of these vectors by targeting the expression of the glycopeptidolipid translocase mmpL4b and the essential genes rpoB and mmpL3. Finally, we describe an efficient single-step procedure to co-transform mycobacterial species with this integrative genetic tool alongside episomal vectors. Such tools and approaches should be useful to foster discovery in mycobacterial research.
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Affiliation(s)
| | - Vanessa Point
- Aix Marseille Univ, CNRS, LISM, IMM FR3479, IM2BFrance
| | - Wafaa Achache
- Aix Marseille Univ, CNRS, LISM, IMM FR3479, IM2BFrance
- IHU Méditerranée Infection, Aix‐Marseille Univ.France
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Brezovská B, Narasimhan S, Šiková M, Šanderová H, Kovaľ T, Borah N, Shoman M, Pospíšilová D, Vaňková Hausnerová V, Tužinčin D, Černý M, Komárek J, Janoušková M, Kambová M, Halada P, Křenková A, Hubálek M, Trundová M, Dohnálek J, Hnilicová J, Žídek L, Krásný L. MoaB2, a newly identified transcription factor, binds to σ A in Mycobacterium smegmatis. J Bacteriol 2024; 206:e0006624. [PMID: 39499088 PMCID: PMC11656743 DOI: 10.1128/jb.00066-24] [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: 02/22/2024] [Accepted: 09/18/2024] [Indexed: 11/07/2024] Open
Abstract
In mycobacteria, σA is the primary sigma factor. This essential protein binds to RNA polymerase (RNAP) and mediates transcription initiation of housekeeping genes. Our knowledge about this factor in mycobacteria is limited. Here, we performed an unbiased search for interacting partners of Mycobacterium smegmatis σA. The search revealed a number of proteins; prominent among them was MoaB2. The σA-MoaB2 interaction was validated and characterized by several approaches, revealing that it likely does not require RNAP and is specific, as alternative σ factors (e.g., closely related σB) do not interact with MoaB2. The structure of MoaB2 was solved by X-ray crystallography. By immunoprecipitation and nuclear magnetic resonance, the unique, unstructured N-terminal domain of σA was identified to play a role in the σA-MoaB2 interaction. Functional experiments then showed that MoaB2 inhibits σA-dependent (but not σB-dependent) transcription and may increase the stability of σA in the cell. We propose that MoaB2, by sequestering σA, has a potential to modulate gene expression. In summary, this study has uncovered a new binding partner of mycobacterial σA, paving the way for future investigation of this phenomenon.IMPORTANCEMycobacteria cause serious human diseases such as tuberculosis and leprosy. The mycobacterial transcription machinery is unique, containing transcription factors such as RbpA, CarD, and the RNA polymerase (RNAP) core-interacting small RNA Ms1. Here, we extend our knowledge of the mycobacterial transcription apparatus by identifying MoaB2 as an interacting partner of σA, the primary sigma factor, and characterize its effects on transcription and σA stability. This information expands our knowledge of interacting partners of subunits of mycobacterial RNAP, providing opportunities for future development of antimycobacterial compounds.
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Affiliation(s)
- Barbora Brezovská
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Subhash Narasimhan
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Michaela Šiková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Tomáš Kovaľ
- Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Nabajyoti Borah
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Mahmoud Shoman
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Debora Pospíšilová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague, Czechia
| | - Dávid Tužinčin
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Martin Černý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Jan Komárek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Martina Janoušková
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Milada Kambová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Alena Křenková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Mária Trundová
- Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Jan Dohnálek
- Institute of Biotechnology of the Czech Academy of Sciences, Centre BIOCEV, Vestec, Czechia
| | - Jarmila Hnilicová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
- Laboratory of Regulatory RNAs, Faculty of Science, Charles University, Prague, Czechia
| | - Lukáš Žídek
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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Ellis NA, Machner MP. Genetic Approaches for Identifying and Characterizing Effectors in Bacterial Pathogens. Annu Rev Genet 2024; 58:233-247. [PMID: 39585907 DOI: 10.1146/annurev-genet-111523-102030] [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: 11/27/2024]
Abstract
Microbial pathogens have coevolved with their hosts, often for millions of years, and in the process have developed a variety of virulence mechanisms to ensure their survival, typically at the host's expense. At the center of this host-pathogen warfare are proteins called effectors that are delivered by bacteria into their host where they alter the intracellular environment to promote bacterial proliferation. Many effectors are believed to have been acquired by the bacteria from their host during evolution, explaining why researchers are keen to understand their function, as this information may provide insight into both microbial virulence strategies and biological processes that happen within our own cells. Help for accomplishing this goal has come from the recent development of increasingly powerful genetic approaches, which are the focus of this review.
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Affiliation(s)
- Nicole A Ellis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Matthias P Machner
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA; ,
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Shetty A, Kwas H, Rajhi H, Rangareddy H, Fryer J. Revolutionizing Tuberculosis Management With Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas Technology: A Comprehensive Literature Review. Cureus 2024; 16:e71697. [PMID: 39552996 PMCID: PMC11568648 DOI: 10.7759/cureus.71697] [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] [Accepted: 10/16/2024] [Indexed: 11/19/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have gained attention for their revolutionary potential in tuberculosis (TB) management, providing a novel approach to both diagnostics and treatment. This technology, renowned for its ability to accurately target and modify genetic material, offers a promising solution to the limitations of current TB diagnostic methods, which often rely on time-consuming culture techniques or polymerase chain reaction (PCR)-based assays. One of the key advantages of CRISPR-Cas systems is their high specificity and sensitivity, making them well-suited for detecting Mycobacterium tuberculosis, even in low-bacterial-load samples. Techniques such as CRISPR-Cas12 and Cas13 have been employed for rapid detection, utilizing their trans-cleavage activity to produce a fluorescent signal upon recognition of the TB genome. Furthermore, these methods often use isothermal amplification techniques like recombinase polymerase amplification (RPA) or loop-mediated isothermal amplification (LAMP), which require less equipment compared to traditional PCR. Beyond diagnostics, CRISPR-Cas technologies show promise in studying TB resistance mechanisms and potentially treating drug-resistant strains. Genome-editing capabilities enable researchers to manipulate the M. tuberculosis genome, investigating genes linked to virulence or antibiotic resistance. Although challenges such as the development of multiplexed CRISPR assays for detecting multiple mutations simultaneously remain, advancements continue to improve the technology's practicality for clinical use. Incorporating CRISPR into TB management could enhance early detection, inform personalized treatment, and potentially contribute to developing more effective therapies, especially in regions where TB remains a significant public health threat.
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Affiliation(s)
- Achal Shetty
- Community Medicine, Father Muller Medical College, Mangalore, IND
| | - Hamida Kwas
- Pulmonology, University of Sfax, Faculty of Medicine of Sfax, Gabès University Hospital, Gabès, TUN
| | - Hayfa Rajhi
- Analysis Laboratory Research, University Hospital of Gabès, Gabès, TUN
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7
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Du Q, Wei Y, Zhang L, Ren D, Gao J, Dong X, Bai L, Li J. An improved CRISPR and CRISPR interference (CRISPRi) toolkit for engineering the model methanogenic archaeon Methanococcus maripaludis. Microb Cell Fact 2024; 23:239. [PMID: 39227830 PMCID: PMC11373211 DOI: 10.1186/s12934-024-02492-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/27/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND The type II based CRISPR-Cas system remains restrictedly utilized in archaea, a featured domain of life that ranks parallelly with Bacteria and Eukaryotes. Methanococcus maripaludis, known for rapid growth and genetic tractability, serves as an exemplary model for studying archaeal biology and exploring CO2-based biotechnological applications. However, tools for controlled gene regulation remain deficient and CRISPR-Cas tools still need improved in this archaeon, limiting its application as an archaeal model cellular factory. RESULTS This study not only improved the CRISPR-Cas9 system for optimizing multiplex genome editing and CRISPR plasmid construction efficiencies but also pioneered an effective CRISPR interference (CRISPRi) system for controlled gene regulation in M. maripaludis. We developed two novel strategies for balanced expression of multiple sgRNAs, facilitating efficient multiplex genome editing. We also engineered a strain expressing Cas9 genomically, which simplified the CRISPR plasmid construction and facilitated more efficient genome modifications, including markerless and scarless gene knock-in. Importantly, we established a CRISPRi system using catalytic inactive dCas9, achieving up to 100-fold repression on target gene. Here, sgRNAs targeting near and downstream regions of the transcription start site and the 5'end ORF achieved the highest repression efficacy. Furthermore, we developed an inducible CRISPRi-dCas9 system based on TetR/tetO platform. This facilitated the inducible gene repression, especially for essential genes. CONCLUSIONS Therefore, these advancements not only expand the toolkit for genetic manipulation but also bridge methodological gaps for controlled gene regulation, especially for essential genes, in M. maripaludis. The robust toolkit developed here paves the way for applying M. maripaludis as a vital model archaeal cell factory, facilitating fundamental biological studies and applied biotechnology development of archaea.
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Affiliation(s)
- Qing Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China
| | - Yufei Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Liuyang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
| | - Derong Ren
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Jian Gao
- School of Basic Medical Sciences, School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, China.
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing, 100101, China.
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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Agarwal M, Bhaskar A, Singha B, Mukhopadhyay S, Pahuja I, Singh A, Chaturvedi S, Agarwal N, Dwivedi VP, Nandicoori VK. Depletion of essential mycobacterial gene glmM reduces pathogen survival and induces host-protective immune responses against tuberculosis. Commun Biol 2024; 7:949. [PMID: 39107377 PMCID: PMC11303689 DOI: 10.1038/s42003-024-06620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The limitations of TB treatment are the long duration and immune-dampening effects of anti-tuberculosis therapy. The Cell wall plays a crucial role in survival and virulence; hence, enzymes involved in its biosynthesis are good therapeutic targets. Here, we identify Mycobacterium tuberculosis (Mtb) GlmM, (GlmMMtb) engaged in the UDP-GlcNAc synthesis pathway as an essential enzyme. We generated a conditional knockdown strain, Rv-glmMkD using the CRISPR interference-mediated gene silencing approach. Depletion of GlmMMtb affects the morphology and thickness of the cell wall. The Rv-glmMkD strain attenuated Mtb survival in vitro, in the host macrophages (ex vivo), and in a murine mice infection model (in vivo). Results suggest that the depletion of GlmMMtb induces M1 macrophage polarization, prompting a pro-inflammatory cytokine response, apparent from the upregulation of activation markers, including IFNɣ and IL-17 that resists the growth of Mtb. These observations provide a rationale for exploring GlmMMtb as a potential therapeutic target.
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Affiliation(s)
- Meetu Agarwal
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India.
- Department of Molecular Medicine, Jamia Hamdard University, New Delhi, India.
| | - Ashima Bhaskar
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Biplab Singha
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India
| | - Suparba Mukhopadhyay
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Isha Pahuja
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Archna Singh
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
| | - Shivam Chaturvedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Ved Prakash Dwivedi
- Immunobiology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vinay Kumar Nandicoori
- Signal Transduction Laboratory, National Institute of Immunology, New Delhi, India.
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Hyderabad, Telangana, India.
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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] [Download PDF] [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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10
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Hajizadeh Y, Badmasti F, Oloomi M. Inhibition of the bla OXA-48 gene expression in Klebsiella pneumoniae by a plasmid carrying CRISPRi-Cas9 system. Gene 2024; 910:148332. [PMID: 38431235 DOI: 10.1016/j.gene.2024.148332] [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: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Antibiotic resistance is an increasing concern that threatens the effectiveness of treating bacterial infections. The spread of carbapenem resistant Klebsiella pneumoniae poses a significant threat to global public health. To combat this issue, the clustered regularly interspaced short palindromic repeats interference (CRISPRi) system is being developed. This system includes a single guide RNA (sgRNA) and a nuclease dead Cas9 (dCas9), which work together to downregulate gene expression. Our project involved the use of the CRISPRi system to reduce gene expression of the beta-lactamase oxacillin-48 (blaOXA-48) gene in K. pneumoniae. We designed a sgRNA and cloned it into pJMP1363 plasmid harboring the CRISPRi system. The pJMP1363-sgRNA construct was transformed in K. pneumoniae harboring the blaOXA-48 gene. The MIC test was used to evaluate the antimicrobial resistance, and quantitative real-time RT-PCR was used to confirm the inhibition of the OXA-48 producing K. pneumoniae harboring the pJMP1363-sgRNA construct expression. The Galleria mellonella larvae model was also utilized for in vivo assay. Following the transformation, the MIC test indicated a 4-fold reduction in meropenem resistance, and qRT-PCR analysis revealed a 60-fold decrease in the mRNA OXA-48 harboring the pJMP1363-sgRNA construct expression. Additionally, G. mellonella larvae infected with OXA-48 producing K. pneumoniae harboring the pJMP1363-sgRNA showed higher survival rates. Based on the findings, it can be concluded that the CRISPR interference technique has successfully reduced antibiotic resistance and virulence in the K. pneumoniae harboring the blaOXA-48 gene.
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Affiliation(s)
- Yeganeh Hajizadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Mana Oloomi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran.
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Rani N, Surolia A. Targeted suppression of MEP pathway genes DXS, IspD and IspF to explore the mycobacterial metabolism and survival. Int J Biol Macromol 2024; 272:132727. [PMID: 38823743 DOI: 10.1016/j.ijbiomac.2024.132727] [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: 12/13/2023] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/03/2024]
Abstract
Due to the uniqueness and essentiality of MEP pathway for the synthesis of crucial metabolites- isoprenoids, hopanoids, menaquinone etc. in mycobacterium, enzymes of this pathway are considered promising anti-tubercular drug targets. In the present study we seek to understand the consequences of downregulation of three of the essential genes- DXS, IspD, and IspF of MEP pathway using CRISPRi approach combined with transcriptomics in Mycobacterium smegmatis. Conditional knock down of either DXS or IspD or IspF gene showed strong bactericidal effect and a profound change in colony morphology. Impaired MEP pathway due to downregulation of these genes increased the susceptibility to frontline anti-tubercular drugs. Further, reduced EtBr accumulation in all the knock down strains in the presence and absence of efflux inhibitor indicated altered cell wall topology. Subsequently, transcriptional analysis validated by qRT-PCR of +154DXS, +128IspD, +104IspF strains showed that modifying the expression of these MEP pathway enzymes affects the regulation of mycobacterial core components. Among the DEGs, expression of small and large ribosomal binding proteins (rpsL, rpsJ, rplN, rplX, rplM, rplS, etc), essential protein translocases (secE, secY and infA, infC), transcriptional regulator (CarD and SigB) and metabolic enzymes (acpP, hydA, ald and fabD) were significantly depleted causing the bactericidal effect. However, mycobacteria survived under these damaging conditions by upregulating mostly the genes needed for the repair of DNA damage (DNA polymerase IV, dinB), synthesis of essential metabolites (serB, LeuA, atpD) and those strengthening the cell wall integrity (otsA, murA, D-alanyl-D-alanine dipeptidase etc.).
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Affiliation(s)
- Nidhi Rani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; Dr.Reddy's Institute of Life Science, Hyderabad 500046, India.
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12
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Singh M, Dhanwal A, Verma A, Augustin L, Kumari N, Chakraborti S, Agarwal N, Sriram D, Dey RJ. Discovery of potent antimycobacterial agents targeting lumazine synthase (RibH) of Mycobacterium tuberculosis. Sci Rep 2024; 14:12170. [PMID: 38806590 PMCID: PMC11133327 DOI: 10.1038/s41598-024-63051-6] [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: 07/28/2023] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
Tuberculosis (TB) continues to be a global health crisis, necessitating urgent interventions to address drug resistance and improve treatment efficacy. In this study, we validate lumazine synthase (RibH), a vital enzyme in the riboflavin biosynthetic pathway, as a potential drug target against Mycobacterium tuberculosis (M. tb) using a CRISPRi-based conditional gene knockdown strategy. We employ a high-throughput molecular docking approach to screen ~ 600,000 compounds targeting RibH. Through in vitro screening of 55 shortlisted compounds, we discover 3 compounds that exhibit potent antimycobacterial activity. These compounds also reduce intracellular burden of M. tb during macrophage infection and prevent the resuscitation of the nutrient-starved persister bacteria. Moreover, these three compounds enhance the bactericidal effect of first-line anti-TB drugs, isoniazid and rifampicin. Corroborating with the in silico predicted high docking scores along with favourable ADME and toxicity profiles, all three compounds demonstrate binding affinity towards purified lumazine synthase enzyme in vitro, in addition these compounds exhibit riboflavin displacement in an in vitro assay with purified lumazine synthase indicative of specificity of these compounds to the active site. Further, treatment of M. tb with these compounds indicate reduced production of flavin adenine dinucleotide (FAD), the ultimate end product of the riboflavin biosynthetic pathway suggesting the action of these drugs on riboflavin biosynthesis. These compounds also show acceptable safety profile in mammalian cells, with a high selective index. Hence, our study validates RibH as an important drug target against M. tb and identifies potent antimycobacterial agents.
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Affiliation(s)
- Monica Singh
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Anannya Dhanwal
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Arpita Verma
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Linus Augustin
- Translational Health Science and Technology Institute, Faridabad, Haryana, 121001, India
| | - Niti Kumari
- National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, 500032, India
| | - Soumyananda Chakraborti
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
- National Institute of Malaria Research, Indian Council of Medical Research (ICMR), New Delhi, 110077, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, Faridabad, Haryana, 121001, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India
| | - Ruchi Jain Dey
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, 500078, India.
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13
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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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14
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Shi L, Gu R, Long J, Duan G, Yang H. Application of CRISPR-cas-based technology for the identification of tuberculosis, drug discovery and vaccine development. Mol Biol Rep 2024; 51:466. [PMID: 38551745 DOI: 10.1007/s11033-024-09424-6] [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: 10/08/2023] [Accepted: 03/06/2024] [Indexed: 04/02/2024]
Abstract
Tuberculosis (TB), which caused by Mycobacterium tuberculosis, is the leading cause of death from a single infectious agent and continues to be a major public health burden for the global community. Despite being the only globally licenced prophylactic vaccine, Bacillus Calmette-Guérin (BCG) has multiple deficiencies, and effective diagnostic and therapeutic options are limited. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is an adaptive immune system that is found in bacteria and has great potential for the development of novel antituberculosis drugs and vaccines. In addition, CRISPR-Cas is currently recognized as a prospective tool for the development of therapies for TB infection with potential diagnostic and therapeutic value, and CRISPR-Cas may become a viable tool for eliminating TB in the future. Herein, we systematically summarize the current applications of CRISPR-Cas-based technology for TB detection and its potential roles in drug discovery and vaccine development.
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Affiliation(s)
- Liqin Shi
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Ruiqi Gu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001, China.
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15
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Zhou P, G. C. B, Stolte F, Wu C. Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum. Appl Environ Microbiol 2024; 90:e0166523. [PMID: 38185820 PMCID: PMC10880640 DOI: 10.1128/aem.01665-23] [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: 09/19/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Gene inactivation by creating in-frame deletion mutations in Fusobacterium nucleatum is time consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPR interference (CRISPRi) system. This system employs the nuclease-inactive Streptococcus pyogenes Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single-guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes, ftsX and radD, which are pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline, ftsX suppression caused filamentous cell formation akin to chromosomal ftsX deletion, while targeting radD significantly reduced RadD protein levels, abolishing RadD-mediated coaggregation. The system was then extended to probe essential genes bamA and ftsZ, which are vital for outer membrane biogenesis and cell division. Impressively, bamA suppression disrupted membrane integrity and bacterial separation, stalling growth, while ftsZ targeting yielded elongated cells in broth with compromised agar growth. Further studies on F. nucleatum clinical strain CTI-2 and Fusobacterium periodonticum revealed reduced indole synthesis when targeting tnaA. Moreover, silencing clpB in F. periodonticum decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains.IMPORTANCEHow can we effectively investigate the gene functions in Fusobacterium nucleatum, given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPR interference (CRISPRi) system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and single-guide RNA expression is driven by the robust, constitutive rpsJ promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered genetically intractable strains like CTI-2 and Fusobacterium periodonticum. With CRISPRi's potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
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Affiliation(s)
- Peng Zhou
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Bibek G. C.
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Flynn Stolte
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Chenggang Wu
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
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16
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Jiang T, Li Y, Hong W, Lin M. A robust CRISPR interference gene repression system in Vibrio parahaemolyticus. Arch Microbiol 2023; 206:41. [PMID: 38147133 PMCID: PMC10751265 DOI: 10.1007/s00203-023-03770-y] [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: 10/02/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 12/27/2023]
Abstract
Vibrio parahaemolyticus is a significant cause of seafood-associated gastroenteritis and pestilence in aquaculture worldwide. Despite extensive research, strategies for protein depletion in this pathogen remain limited. Herein, we constructed a new CRISPR interference (CRISPRi) system for gene repression based on the combination of a shuttle vector pVv3 and the nuclease-null Cas9 variant (dead Cas9, or dCas9) from Streptococcus pyrogens. This CRISPRi is induced by adding both IPTG and arabinose. We showed that gene repression is scalable via the use of multiple sgRNAs. We also demonstrated that this gene repression can be precisely tuned by adjusting the amount of two different inducers and can be reversed by removing the inducers. This system provides a simple approach for selective gene repression on a genome-wide scale in V. parahaemolyticus. Application of this system will dramatically accelerate investigations of this bacterium, including studies of physiology, pathogenesis, and drug target discovery.
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Affiliation(s)
- Taoyuan Jiang
- Department of Respiratory Medicine, Nan'an Hospital, 330, Ximei Residential District, Xinhua Street, Quanzhou, Fujian Province, China.
| | - Yuhuan Li
- The Second People's Hospital of Three Gorges University, 18, Tiyuchang Road, Yichang, Hubei Province, China
| | - Wencong Hong
- Department of Respiratory Medicine, Nan'an Hospital, 330, Ximei Residential District, Xinhua Street, Quanzhou, Fujian Province, China
| | - Mingyu Lin
- Department of Respiratory Medicine, Nan'an Hospital, 330, Ximei Residential District, Xinhua Street, Quanzhou, Fujian Province, China
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17
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Dergham Y, Le Coq D, Bridier A, Sanchez-Vizuete P, Jbara H, Deschamps J, Hamze K, Yoshida KI, Noirot-Gros MF, Briandet R. Bacillus subtilis NDmed, a model strain for biofilm genetic studies. Biofilm 2023; 6:100152. [PMID: 37694162 PMCID: PMC10485040 DOI: 10.1016/j.bioflm.2023.100152] [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: 03/27/2023] [Revised: 06/20/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023] Open
Abstract
The Bacillus subtilis strain NDmed was isolated from an endoscope washer-disinfector in a medical environment. NDmed can form complex macrocolonies with highly wrinkled architectural structures on solid medium. In static liquid culture, it produces thick pellicles at the interface with air as well as remarkable highly protruding ''beanstalk-like'' submerged biofilm structures at the solid surface. Since these mucoid submerged structures are hyper-resistant to biocides, NDmed has the ability to protect pathogens embedded in mixed-species biofilms by sheltering them from the action of these agents. Additionally, this non-domesticated and highly biofilm forming strain has the propensity of being genetically manipulated. Due to all these properties, the NDmed strain becomes a valuable model for the study of B. subtilis biofilms. This review focuses on several studies performed with NDmed that have highlighted the sophisticated genetic dynamics at play during B. subtilis biofilm formation. Further studies in project using modern molecular tools of advanced technologies with this strain, will allow to deepen our knowledge on the emerging properties of multicellular bacterial life.
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Affiliation(s)
- Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, Anses, 35300, Fougères, France
| | - Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hadi Jbara
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kassem Hamze
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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18
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Yang ZX, Fu YW, Zhao JJ, Zhang F, Li SA, Zhao M, Wen W, Zhang L, Cheng T, Zhang JP, Zhang XB. Superior Fidelity and Distinct Editing Outcomes of SaCas9 Compared with SpCas9 in Genome Editing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1206-1220. [PMID: 36549468 PMCID: PMC11082263 DOI: 10.1016/j.gpb.2022.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 11/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
A series of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9) systems have been engineered for genome editing. The most widely used Cas9 is SpCas9 from Streptococcus pyogenes and SaCas9 from Staphylococcus aureus. However, a comparison of their detailed gene editing outcomes is still lacking. By characterizing the editing outcomes of 11 sites in human induced pluripotent stem cells (iPSCs) and K562 cells, we found that SaCas9 could edit the genome with greater efficiencies than SpCas9. We also compared the effects of spacer lengths of single-guide RNAs (sgRNAs; 18-21 nt for SpCas9 and 19-23 nt for SaCas9) and found that the optimal spacer lengths were 20 nt and 21 nt for SpCas9 and SaCas9, respectively. However, the optimal spacer length for a particular sgRNA was 18-21 nt for SpCas9 and 21-22 nt for SaCas9. Furthermore, SpCas9 exhibited a more substantial bias than SaCas9 for nonhomologous end-joining (NHEJ) +1 insertion at the fourth nucleotide upstream of the protospacer adjacent motif (PAM), indicating a characteristic of a staggered cut. Accordingly, editing with SaCas9 led to higher efficiencies of NHEJ-mediated double-stranded oligodeoxynucleotide (dsODN) insertion or homology-directed repair (HDR)-mediated adeno-associated virus serotype 6 (AAV6) donor knock-in. Finally, GUIDE-seq analysis revealed that SaCas9 exhibited significantly reduced off-target effects compared with SpCas9. Our work indicates the superior performance of SaCas9 to SpCas9 in transgene integration-based therapeutic gene editing and the necessity to identify the optimal spacer length to achieve desired editing results.
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Affiliation(s)
- Zhi-Xue Yang
- 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
| | - Ya-Wen Fu
- 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
| | - Juan-Juan Zhao
- 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
| | - Feng Zhang
- 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
| | - Si-Ang Li
- 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
| | - Mei Zhao
- 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
| | - Wei Wen
- 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
| | - Lei Zhang
- 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
| | - Tao Cheng
- 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; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Jian-Ping Zhang
- 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.
| | - Xiao-Bing Zhang
- 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.
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19
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Liu F, Qiao K, Meng W, Liu J, Gao Y, Zhu J. Construction of a CRISPR Interference System for Gene Knockdown in Stenotrophomonas maltophilia AGS-1 from Aerobic Granular Sludge. ACS Synth Biol 2023; 12:3497-3504. [PMID: 37906167 DOI: 10.1021/acssynbio.3c00480] [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: 11/02/2023]
Abstract
To identify the function of attachment genes involved in biofilm formation in Stenotrophomonas maltophilia AGS-1 isolated from aerobic granular sludge, an effective gene molecular tool is needed. We developed a two-plasmid CRISPRi system in Stenotrophomonas maltophilia AGS-1. One plasmid expressed dCas9 protein with the l-arabinose inducible promoter, and the other plasmid contained the sgRNA cassette complementary to the target gene. Under control of the araC-inducible promoter, this system exhibited little leaky basal expression and highly induced expression that silenced endogenous and exogenous genes with reversible knockdown. This system achieved up to 211-fold suppression for mCherry expression on the nontemplate strand compared to the template strand (91-fold). The utility of the developed CRISPRi platform was also characterized by suppressing the xanA and rpfF genes. The expression of these two genes was rapidly depleted and the adhesion ability decreased, which demonstrated that the modulation of either gene was an important factor for biofilm formation of the AGS-1 strain. The system also tested the ability to simultaneously silence transcriptional suppression of multiple targeted genes, an entire operon, or part of it. Lastly, the use of CRISPRi allowed us to dissect the gene intricacies involved in flagellar biosynthesis. Collectively, these results demonstrated that the CRISPRi system was a simple, feasible, and controllable manipulation system of gene expression in the AGS-1 strain.
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Affiliation(s)
- Fan Liu
- School of Environment, Beijing Normal University, Beijing 100875, China
- R & D Centre of Aerobic Granule Technology, Beijing 100875, China
| | - Kai Qiao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Meng
- School of Environment, Beijing Normal University, Beijing 100875, China
- State Key Laboratory of Water Simulation, Beijing 100875, China
| | - Jia Liu
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yiyun Gao
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jianrong Zhu
- School of Environment, Beijing Normal University, Beijing 100875, China
- R & D Centre of Aerobic Granule Technology, Beijing 100875, China
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20
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Zhou P, G C B, Stolte F, Wu C. Use of CRISPR interference for efficient and rapid gene inactivation in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558491. [PMID: 37781593 PMCID: PMC10541141 DOI: 10.1101/2023.09.19.558491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Gene inactivation via creating in-frame deletion mutations in Fusobacterium nucleatum is time-consuming, and most fusobacterial strains are genetically intractable. Addressing these problems, we introduced a riboswitch-based inducible CRISPRi system. This system employs the nuclease-inactive Streptococcus pyogenes Cas9 protein (dCas9), specifically guided to the gene of interest by a constantly expressed single guide RNA (sgRNA). Mechanistically, this dCas9-sgRNA complex serves as an insurmountable roadblock for RNA polymerase, thus repressing the target gene transcription. Leveraging this system, we first examined two non-essential genes, ftsX, and radD , pivotal for fusobacterial cytokinesis and coaggregation. Upon adding the inducer, theophylline, ftsX suppression caused filamentous cell formation akin to chromosomal ftsX deletion, while targeting radD significantly reduced RadD protein levels, abolishing coaggregation. The system was then extended to probe essential genes bamA and ftsZ , vital for outer membrane biogenesis and cell division. Impressively, bamA suppression disrupted membrane integrity and bacterial separation, stalling growth, while ftsZ- targeting yielded elongated cells in broth with compromised agar growth. Further studies on F. nucleatum clinical strain CTI-2 and Fusobacterium periodonticum revealed reduced indole synthesis when targeting tnaA . Moreover, silencing clpB in F. periodonticum decreased ClpB, increasing thermal sensitivity. In summary, our CRISPRi system streamlines gene inactivation across various fusobacterial strains. IMPORTANCE How can we effectively investigate the gene functions in Fusobacterium nucleatum , given the dual challenges of gene inactivation and the inherent genetic resistance of many strains? Traditional methods have been cumbersome and often inadequate. Addressing this, our work introduces a novel inducible CRISPRi system in which dCas9 expression is controlled at the translation level by a theophylline-responsive riboswitch unit, and sgRNA expression is driven by the robust, constitutive rpsJ promoter. This approach simplifies gene inactivation in the model organism (ATCC 23726) and extends its application to previously considered resistant strains like CTI-2 and Fusobacterium periodontium . With CRISPRi's potential, it is a pivotal tool for in-depth genetic studies into fusobacterial pathogenesis, potentially unlocking targeted therapeutic strategies.
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21
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Sun L, Zheng P, Sun J, Wendisch VF, Wang Y. Genome-scale CRISPRi screening: A powerful tool in engineering microbiology. ENGINEERING MICROBIOLOGY 2023; 3:100089. [PMID: 39628933 PMCID: PMC11611010 DOI: 10.1016/j.engmic.2023.100089] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 12/06/2024]
Abstract
Deciphering gene function is fundamental to engineering of microbiology. The clustered regularly interspaced short palindromic repeats (CRISPR) system has been adapted for gene repression across a range of hosts, creating a versatile tool called CRISPR interference (CRISPRi) that enables genome-scale analysis of gene function. This approach has yielded significant advances in the design of genome-scale CRISPRi libraries, as well as in applications of CRISPRi screening in medical and industrial microbiology. This review provides an overview of the recent progress made in pooled and arrayed CRISPRi screening in microorganisms and highlights representative studies that have employed this method. Additionally, the challenges associated with CRISPRi screening are discussed, and potential solutions for optimizing this strategy are proposed.
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Affiliation(s)
- Letian Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Yu Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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22
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Shaban AK, Gebretsadik G, Hakamata M, Takihara H, Inouchi E, Nishiyama A, Ozeki Y, Tateishi Y, Nishiuchi Y, Yamaguchi T, Ohara N, Okuda S, Matsumoto S. Mycobacterial DNA-binding protein 1 is critical for BCG survival in stressful environments and simultaneously regulates gene expression. Sci Rep 2023; 13:14157. [PMID: 37644087 PMCID: PMC10465568 DOI: 10.1038/s41598-023-40941-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
Survival of the live attenuated Bacillus Calmette-Guérin (BCG) vaccine amidst harsh host environments is key for BCG effectiveness as it allows continuous immune response induction and protection against tuberculosis. Mycobacterial DNA binding protein 1 (MDP1), a nucleoid associated protein, is essential in BCG. However, there is limited knowledge on the extent of MDP1 gene regulation and how this influences BCG survival. Here, we demonstrate that MDP1 conditional knockdown (cKD) BCG grows slower than vector control in vitro, and dies faster upon exposure to antibiotics (bedaquiline) and oxidative stress (H2O2 and menadione). MDP1-cKD BCG also exhibited low infectivity and survival in THP-1 macrophages and mice indicating possible susceptibility to host mediated stress. Consequently, low in vivo survival resulted in reduced cytokine (IFN-gamma and TNF-alpha) production by splenocytes. Temporal transcriptome profiling showed more upregulated (81-240) than downregulated (5-175) genes in response to MDP1 suppression. Pathway analysis showed suppression of biosynthetic pathways that coincide with low in vitro growth. Notable was the deferential expression of genes involved in stress response (sigI), maintenance of DNA integrity (mutT1), REDOX balance (WhiB3), and host interactions (PE/PE_PGRS). Thus, this study shows MDP1's importance in BCG survival and highlights MDP1-dependent gene regulation suggesting its role in growth and stress adaptation.
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Affiliation(s)
- Amina K Shaban
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.
| | - Gebremichal Gebretsadik
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Department of Biology, Assosa University, Assosa, Ethiopia
| | - Mariko Hakamata
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Department of Respiratory Medicine and Infectious Disease, School of Medicine, Niigata University, Niigata, Japan
| | - Hayato Takihara
- Bioinformatics Department, School of Medicine, Niigata University, Niigata, Japan
| | - Erina Inouchi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
| | - Yukiko Nishiuchi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Toneyama Tuberculosis Research Institute, Osaka Metropolitan University, Osaka, Japan
- Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, Hiroshima, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan
- Department of Pharmacology, Osaka Metropolitan University, Osaka, Japan
| | - Naoya Ohara
- Department of Oral Microbiology, Okayama University, Okayama, Japan
| | - Shujiro Okuda
- Bioinformatics Department, School of Medicine, Niigata University, Niigata, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, School of Medicine, Niigata University, Niigata, Japan.
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Surabaya, East Java, Indonesia.
- Division of Research Aids, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan.
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23
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Zhang Y, Peng Q, Zhang R, Li C, Xu Q, Xia L, Wang Y, Liu P, Pan H. Advances in CRISPR/Cas-Based Strategies on Zoonosis. Transbound Emerg Dis 2023; 2023:9098445. [PMID: 40303816 PMCID: PMC12017210 DOI: 10.1155/2023/9098445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/04/2023] [Accepted: 07/05/2023] [Indexed: 05/02/2025]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) has emerged as the predominant technique for gene editing technique due to its high efficiency and low cost. In the area of zoonosis, CRISPR/Cas is also widely used in different research areas. This paper reviewed the principles of CRISPR/Cas technique and its applications in zoonosis. Moreover, we analyze the shortcomings and weaknesses that currently limit its use, highlight its direction for improvement, and foresee its application prospects in the prevention and treatment of zoonosis. For the purpose of preventing and controlling zoonosis, we need to develop diagnostic method with high sensitivity and specificity, highly protective vaccines, and also better understanding of the pathogenesis. Our review aimed to promote the application and improvement of CRISPR/Cas technique in the above-mentioned areas, and provide brief and comprehensive references for CRISPR/Cas-based research. Through reviewing the advances in CRISPR/Cas-based strategies on zoonosis, we believe that CRISPR/Cas technique will provide more powerful assistance for the prevention and control of zoonosis.
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Affiliation(s)
- Yi Zhang
- Institute of Zoonosis, College of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Maternal and Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi, China
| | - Qifeng Peng
- Institute of Zoonosis, College of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Maternal and Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi, China
| | - Renjun Zhang
- Center for Animal Disease Control and Prevention of Guizhou Province, Guiyang, China
| | - Chao Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Quangang Xu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Luming Xia
- Center for Animal Disease Control and Prevention of Shanghai City, Shanghai, China
| | - Youming Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Ping Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Hong Pan
- Institute of Zoonosis, College of Public Health, Zunyi Medical University, Zunyi, China
- Key Laboratory of Maternal and Child Health and Exposure Science of Guizhou Higher Education Institutes, Zunyi, China
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24
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Pal P, Khan MY, Sharma S, Kumar Y, Mangla N, Kaushal PS, Agarwal N. ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis. Commun Biol 2023; 6:708. [PMID: 37433855 DOI: 10.1038/s42003-023-05059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/21/2023] [Indexed: 07/13/2023] Open
Abstract
Survival response of the human tuberculosis pathogen, Mycobacterium tuberculosis (Mtb) to a diverse environmental cues is governed through its versatile transcription regulatory mechanisms with the help of a large pool of transcription regulators (TRs). Rv1830 is one such conserved TR, which remains uncharacterized in Mtb. It was named as McdR based on an effect on cell division upon its overexpression in Mycobacterium smegmatis. Recently, it has been implicated in antibiotic resilience in Mtb and reannotated as ResR. While Rv1830 affects cell division by modulating the expression of M. smegmatis whiB2, the underlying cause of its essentiality and regulation of drug resilience in Mtb is yet to be deciphered. Here we show that ResR/McdR, encoded by ERDMAN_2020 in virulent Mtb Erdman, is pivotal for bacterial proliferation and crucial metabolic activities. Importantly, ResR/McdR directly regulates ribosomal gene expression and protein synthesis, requiring distinct disordered N-terminal sequence. Compared to control, bacteria depleted with resR/mcdR exhibit delayed recovery post-antibiotic treatment. A similar effect upon knockdown of rplN operon genes further implicates ResR/McdR-regulated protein translation machinery in attributing drug resilience in Mtb. Overall, findings from this study suggest that chemical inhibitors of ResR/McdR may be proven effective as adjunctive therapy for shortening the duration of TB treatment.
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Affiliation(s)
- Pramila Pal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, Delhi, India
| | - Mohd Younus Khan
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, Delhi, India
| | - Shivani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Nikita Mangla
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, Delhi, India
| | - Prem S Kaushal
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India.
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25
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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26
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Mangla N, Singh R, Agarwal N. HtpG Is a Metal-Dependent Chaperone Which Assists the DnaK/DnaJ/GrpE Chaperone System of Mycobacterium tuberculosis via Direct Association with DnaJ2. Microbiol Spectr 2023; 11:e0031223. [PMID: 37022172 PMCID: PMC10269695 DOI: 10.1128/spectrum.00312-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Protein folding is a crucial process in maintaining protein homeostasis, also known as proteostasis, in the cell. The requirement for the assistance of molecular chaperones in the appropriate folding of several proteins has already called into question the previously held view of spontaneous protein folding. These chaperones are highly ubiquitous cellular proteins, which not only help in mediating the proper folding of other nascent polypeptides but are also involved in refolding of the misfolded or the aggregated proteins. Hsp90 family proteins such as high-temperature protein G (HtpG) are abundant and ubiquitously expressed in both eukaryotic and prokaryotic cells. Although HtpG is known as an ATP-dependent chaperone protein in most organisms, function of this protein remains obscured in mycobacterial pathogens. Here, we aim to investigate significance of HtpG as a chaperone in the physiology of Mycobacterium tuberculosis. We report that M. tuberculosis HtpG (mHtpG) is a metal-dependent ATPase which exhibits chaperonin activity towards denatured proteins in coordination with the DnaK/DnaJ/GrpE chaperone system via direct association with DnaJ2. Increased expression of DnaJ1, DnaJ2, ClpX, and ClpC1 in a ΔhtpG mutant strain further suggests cooperativity of mHtpG with various chaperones and proteostasis machinery in M. tuberculosis. IMPORTANCE M. tuberculosis is exposed to variety of extracellular stressful conditions and has evolved mechanisms to endure and adapt to the adverse conditions for survival. mHtpG, despite being dispensable for M. tuberculosis growth under in vitro conditions, exhibits a strong and direct association with DnaJ2 cochaperone and assists the mycobacterial DnaK/DnaJ/GrpE (KJE) chaperone system. These findings suggest the potential role of mHtpG in stress management of the pathogen. Mycobacterial chaperones are responsible for folding of nascent protein as well as reactivation of protein aggregates. M. tuberculosis shows differential adaptive response subject to the availability of mHtpG. While its presence facilitates improved protein refolding via stimulation of the KJE chaperone activity, in the absence of mHtpG, M. tuberculosis enhances expression of DnaJ1/J2 cochaperones as well as Clp protease machinery for maintenance of proteostasis. Overall, this study provides a framework for future investigation to better decipher the mycobacterial proteostasis network in the light of stress adaptability and/or survival.
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Affiliation(s)
- Nikita Mangla
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
- Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
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27
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Zein-Eddine R, Refrégier G, Cervantes J, Yokobori NK. The future of CRISPR in Mycobacterium tuberculosis infection. J Biomed Sci 2023; 30:34. [PMID: 37245014 DOI: 10.1186/s12929-023-00932-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic repeats (CRISPR)-Cas systems rapidly raised from a bacterial genetic curiosity to the most popular tool for genetic modifications which revolutionized the study of microbial physiology. Due to the highly conserved nature of the CRISPR locus in Mycobacterium tuberculosis, the etiological agent of one of the deadliest infectious diseases globally, initially, little attention was paid to its CRISPR locus, other than as a phylogenetic marker. Recent research shows that M. tuberculosis has a partially functional Type III CRISPR, which provides a defense mechanism against foreign genetic elements mediated by the ancillary RNAse Csm6. With the advent of CRISPR-Cas based gene edition technologies, our possibilities to explore the biology of M. tuberculosis and its interaction with the host immune system are boosted. CRISPR-based diagnostic methods can lower the detection threshold to femtomolar levels, which could contribute to the diagnosis of the still elusive paucibacillary and extrapulmonary tuberculosis cases. In addition, one-pot and point-of-care tests are under development, and future challenges are discussed. We present in this literature review the potential and actual impact of CRISPR-Cas research on human tuberculosis understanding and management. Altogether, the CRISPR-revolution will revitalize the fight against tuberculosis with more research and technological developments.
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Affiliation(s)
- Rima Zein-Eddine
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, Route de Saclay 91120, Palaiseau, France
| | - Guislaine Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-Sur-Yvette, France
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Noemí Kaoru Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS and CONICET, C1282AFF, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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28
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Harnessing CRISRP-Cas9 as an anti-mycobacterial system. Microbiol Res 2023; 270:127319. [PMID: 36780784 DOI: 10.1016/j.micres.2023.127319] [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: 08/11/2022] [Revised: 12/31/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Rapid emergence of drug resistance has posed new challenges to the treatment of mycobacterial infections. As the pace of development of new drugs is slow, alternate treatment approaches are required. Recently, CRISPR-Cas systems have emerged as potential antimicrobials. These sequence-specific nucleases introduce double strand cuts in the target DNA, which if left unrepaired, prove fatal to the host. For most bacteria, homologous recombination repair (HRR) is the only pathway for repair and survival. Mycobacteria is one of the few bacteria which possesses the non-homologous end joining (NHEJ) system in addition to HRR for double strand break repair. To assess the antimicrobial potential of CRISPR-system, Cas9-induced breaks were introduced in the genome of Mycobacterium smegmatis and the survival was studied. While the single strand breaks were efficiently repaired, the organism was unable to repair the double strand breaks efficiently. In a mixed population of antibiotic-resistant and sensitive mycobacterial cells, selectively targeting a factor that confers hygromycin resistance, turned the entire population sensitive to the drug. Further, we demonstrate that the sequence-specific targeting could also be used for curing plasmids from mycobacterium cells. Considering the growing interest in nucleic acid-based therapy to curtail infections and combat antimicrobial resistance, our data shows that CRISPR-systems hold promise for future use as an antimicrobial against drug-resistant mycobacterial infections.
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29
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Villao L, Chávez T, Pacheco R, Sánchez E, Bonilla J, Santos E. Genetic improvement in Musa through modern biotechnological methods. BIONATURA 2023. [DOI: 10.21931/rb/2023.08.01.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Bananas, one of the most valued fruits worldwide, are produced in more than 135 countries in the tropics and subtropics for local consumption and export due to their tremendous nutritional value and ease of access.
The genetic improvement of commercial crops is a crucial strategy for managing pests or other diseases and abiotic stress factors. Although conventional breeding has developed new hybrids with highly productive or agronomic performance characteristics, in some banana cultivars, due to the high level of sterility, the traditional breeding strategy is hampered. Therefore, modern biotechniques have been developed in a banana for genetic improvement. In vitro, culture techniques have been a basis for crop micropropagation for elite banana varieties and the generation of methods for genetic modification. This review includes topics of great interest for improving bananas and their products worldwide, from their origins to the different improvement alternatives.
Keywords. Banana, genetic improvement, pest management, diseases, abiotic stress factors.
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Affiliation(s)
- L, Villao
- Escuela Superior Politécnica del Litoral, ESPOL, Biotechnological Research Center of Ecuador, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador
| | - T, Chávez
- Escuela Superior Politécnica del Litoral, ESPOL, Biotechnological Research Center of Ecuador, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador
| | - R, Pacheco
- Escuela Superior Politécnica del Litoral, ESPOL, Biotechnological Research Center of Ecuador, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador
| | - E. Sánchez
- Escuela Superior Politécnica del Litoral, ESPOL, Biotechnological Research Center of Ecuador, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador; Escuela Superior Politécnica del Litoral, ESPOL, Faculty of Life Sciences, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador
| | - J. Bonilla
- Escuela Superior Politécnica del Litoral, ESPOL, Biotechnological Research Center of Ecuador, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador ; Escuela Superior Politécnica del Litoral, ESPOL, Faculty of Life Sciences, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador
| | - E. Santos
- Escuela Superior Politécnica del Litoral, ESPOL, Biotechnological Research Center of Ecuador, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador ; Escuela Superior Politécnica del Litoral, ESPOL, Faculty of Life Sciences, Gustavo Galindo Campus Km. 30.5 Vía Perimetral, PO Box 09-01-5863, Guayaquil, Ecuador
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30
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Silveiro C, Marques M, Olivença F, Pires D, Mortinho D, Nunes A, Pimentel M, Anes E, Catalão MJ. CRISPRi-mediated characterization of novel anti-tuberculosis targets: Mycobacterial peptidoglycan modifications promote beta-lactam resistance and intracellular survival. Front Cell Infect Microbiol 2023; 13:1089911. [PMID: 37009497 PMCID: PMC10050696 DOI: 10.3389/fcimb.2023.1089911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
The lack of effective therapeutics against emerging multi-drug resistant strains of Mycobacterium tuberculosis (Mtb) prompts the identification of novel anti-tuberculosis targets. The essential nature of the peptidoglycan (PG) layer of the mycobacterial cell wall, which features several distinctive modifications, such as the N-glycolylation of muramic acid and the amidation of D-iso-glutamate, makes it a target of particular interest. To understand their role in susceptibility to beta-lactams and in the modulation of host-pathogen interactions, the genes encoding the enzymes responsible for these PG modifications (namH and murT/gatD, respectively) were silenced in the model organism Mycobacterium smegmatis using CRISPR interference (CRISPRi). Although beta-lactams are not included in TB-therapy, their combination with beta-lactamase inhibitors is a prospective strategy to treat MDR-TB. To uncover synergistic effects between the action of beta-lactams and the depletion of these PG modifications, knockdown mutants were also constructed in strains lacking the major beta-lactamase of M. smegmatis BlaS, PM965 (M. smegmatis ΔblaS1) and PM979 (M. smegmatis ΔblaS1 ΔnamH). The phenotyping assays affirmed the essentiality of the amidation of D-iso-glutamate to the survival of mycobacteria, as opposed to the N-glycolylation of muramic acid. The qRT-PCR assays confirmed the successful repression of the target genes, along with few polar effects and differential knockdown level depending on PAM strength and target site. Both PG modifications were found to contribute to beta-lactam resistance. While the amidation of D-iso-glutamate impacted cefotaxime and isoniazid resistance, the N-glycolylation of muramic acid substantially promoted resistance to the tested beta-lactams. Their simultaneous depletion provoked synergistic reductions in beta-lactam MICs. Moreover, the depletion of these PG modifications promoted a significantly faster bacilli killing by J774 macrophages. Whole-genome sequencing revealed that these PG modifications are highly conserved in a set of 172 clinical strains of Mtb, demonstrating their potential as therapeutic targets against TB. Our results support the development of new therapeutic agents targeting these distinctive mycobacterial PG modifications.
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Affiliation(s)
- Cátia Silveiro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Mariana Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Olivença
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - David Pires
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Centre for Interdisciplinary Research in Health, Lisbon, Portugal
| | - Diana Mortinho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Alexandra Nunes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
- Faculty of Veterinary Medicine, Universidade Lusófona, Lisbon, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Elsa Anes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- *Correspondence: Maria João Catalão,
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31
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Du X, McManus DP, French JD, Collinson N, Sivakumaran H, MacGregor SR, Fogarty CE, Jones MK, You H. CRISPR interference for sequence-specific regulation of fibroblast growth factor receptor A in Schistosoma mansoni. Front Immunol 2023; 13:1105719. [PMID: 36713455 PMCID: PMC9880433 DOI: 10.3389/fimmu.2022.1105719] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Employing the flatworm parasite Schistosoma mansoni as a model, we report the first application of CRISPR interference (CRISPRi) in parasitic helminths for loss-of-function studies targeting the SmfgfrA gene which encodes the stem cell marker, fibroblast growth factor receptor A (FGFRA). SmFGFRA is essential for maintaining schistosome stem cells and critical in the schistosome-host interplay. The SmfgfrA gene was targeted in S. mansoni adult worms, eggs and schistosomula using a catalytically dead Cas9 (dCas9) fused to a transcriptional repressor KRAB. We showed that SmfgfrA repression resulted in considerable phenotypic differences in the modulated parasites compared with controls, including reduced levels of SmfgfrA transcription and decreased protein expression of SmFGFRA, a decline in EdU (thymidine analog 5-ethynyl-2'-deoxyuridine, which specifically stains schistosome stem cells) signal, and an increase in cell apoptosis. Notably, reduced SmfgfrA transcription was evident in miracidia hatched from SmfgfrA-repressed eggs, and resulted in a significant change in miracidial behavior, indicative of a durable repression effect caused by CRISPRi. Intravenous injection of mice with SmfgfrA-repressed eggs resulted in granulomas that were markedly reduced in size and a decline in the level of serum IgE, emphasizing the importance of SmFGFRA in regulating the host immune response induced during schistosome infection. Our findings show the feasibility of applying CRISPRi for effective, targeted transcriptional repression in schistosomes, and provide the basis for employing CRISPRi to selectively perturb gene expression in parasitic helminths on a genome-wide scale.
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Affiliation(s)
- Xiaofeng Du
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Donald P. McManus
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Juliet D. French
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Natasha Collinson
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Haran Sivakumaran
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Skye R. MacGregor
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Conor E. Fogarty
- Genecology Research Centre, University of the Sunshine Coast, Sunshine Coast, QLD, Australia
| | - Malcolm K. Jones
- School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Hong You
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia,*Correspondence: Hong You,
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32
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Hurtado-Páez U, Álvarez Zuluaga N, Arango Isaza RE, Contreras-Moreira B, Rouzaud F, Robledo J. Pan-genome association study of Mycobacterium tuberculosis lineage-4 revealed specific genes related to the high and low prevalence of the disease in patients from the North-Eastern area of Medellín, Colombia. Front Microbiol 2023; 13:1076797. [PMID: 36687645 PMCID: PMC9846648 DOI: 10.3389/fmicb.2022.1076797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) lineage 4 is responsible for the highest burden of tuberculosis (TB) worldwide. This lineage has been the most prevalent lineage in Colombia, especially in the North-Eastern (NE) area of Medellin, where it has been shown to have a high prevalence of LAM9 SIT42 and Haarlem1 SIT62 sublineages. There is evidence that regardless of environmental factors and host genetics, differences among sublineages of Mtb strains play an important role in the course of infection and disease. Nevertheless, the genetic basis of the success of a sublineage in a specific geographic area remains uncertain. We used a pan-genome-wide association study (pan-GWAS) of 47 Mtb strains isolated from NE Medellin between 2005 and 2008 to identify the genes responsible for the phenotypic differences among high and low prevalence sublineages. Our results allowed the identification of 12 variants in 11 genes, of which 4 genes showed the strongest association to low prevalence (mmpL12, PPE29, Rv1419, and Rv1762c). The first three have been described as necessary for invasion and intracellular survival. Polymorphisms identified in low prevalence isolates may suggest related to a fitness cost of Mtb, which might reflect a decrease in their capacity to be transmitted or to cause an active infection. These results contribute to understanding the success of some sublineages of lineage-4 in a specific geographical area.
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Affiliation(s)
- Uriel Hurtado-Páez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,*Correspondence: Uriel Hurtado-Páez,
| | | | - Rafael Eduardo Arango Isaza
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,Facultad de Ciencias, Universidad Nacional de Colombia (UNAL), Medellín, Colombia
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei–Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain,Fundación ARAID, Zaragoza, Spain
| | | | - Jaime Robledo
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia,Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana (UPB), Medellín, Colombia
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33
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Gupta R, Rohde KH. Implementation of a mycobacterial CRISPRi platform in Mycobacterium abscessus and demonstration of the essentiality of ftsZ Mab. Tuberculosis (Edinb) 2023; 138:102292. [PMID: 36495774 PMCID: PMC11552333 DOI: 10.1016/j.tube.2022.102292] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/04/2022]
Abstract
Mycobacterium abscessus (Mab) is a highly drug-resistant non-tuberculous mycobacterial species that causes debilitating TB-like pulmonary infections. The lack of genetic tools has hampered characterization of its extensive repertoire of virulence factors, antimicrobial resistance mechanisms, and drug targets. In this study, we evaluated the performance of a mycobacterial single plasmid CRISPRi-dCas9 system optimized for M. tuberculosis and M. smegmatis for inducible gene silencing in Mab. The efficacy of CRISPRi-mediated repression of two antibiotic resistance genes (blaMab, whiB7Mab) and two putative essential genes (ftsZMab,topAMab) was determined by measuring mRNA transcript levels and phenotypic outcomes. While our results support the utility of this mycobacterial CRISPRi dCas9Sth1 single-plasmid platform for inducible silencing of specific target genes in Mab, they also highlighted several caveats and nuances that may warrant species-specific optimization for Mab. We observed overall lower levels of gene repression in Mab including variable silencing of different target genes despite use of PAMs of similar predicted strength. In addition, leaky gene repression in the absence of inducer was noted for some genes but not others. Nonetheless, using CRISPRi we demonstrated the silencing of multiple target genes and validated ftsZMab as an essential gene and promising drug target for the first time.
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Affiliation(s)
- Rashmi Gupta
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd, FL, 32827, USA.
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd, FL, 32827, USA.
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34
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Nadolinskaia NI, Goncharenko AV. CRISPR Interference in Regulation of Bacterial Gene Expression. Mol Biol 2022. [DOI: 10.1134/s0026893322060139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Barman A, Shaw R, Bhawsinghka N, Das Gupta SK. A CRISPRi-based investigation reveals that multiple promoter elements drive gene expression from the genome of mycobacteriophage D29. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748635 DOI: 10.1099/mic.0.001276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A unique feature found in the genomes of mycobacteriophages such as L5 belonging to the A cluster is the presence of multiple dispersed repeated elements known as stoperators. The phage repressor binds these repeat elements, shutting off transcription globally and thereby promoting lysogeny. Interestingly, the sequence of these stoperators closely matches that of the consensus -35 region of prokaryotic promoters, leading us to propose that they may have a role to play in the initiation of transcription by serving as RNA polymerase binding sites. Mycobacteriophage D29 is closely related to phage L5, and their genome organizations are very similar. As in L5, there are multiple stoperators in the genome of D29. The positions occupied by the stoperators in the two genomes are almost identical. The significant difference between the two phages is that D29 lacks the gene encoding the equivalent of the L5 repressor. Since phage D29 does not produce a repressor, we considered it to be a suitable model for testing our hypothesis that the stoperators function as promoters in the absence of the repressor. To prove our point, we targeted CRISPR guide RNAs against six stoperators. In the case of five out of the six, we found a significant reduction in downstream gene expression and phage growth. Based on this observation and primer extension assays, we conclude that promoting gene expression is likely to be the primary function of stoperators.
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Affiliation(s)
- Anik Barman
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India
| | - Rahul Shaw
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India
| | - Niketa Bhawsinghka
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India.,Present address: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Sujoy K Das Gupta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata-700054, India
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36
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Enhanced immunogenicity of Mycobacterium bovis BCG through CRISPRi mediated depletion of AftC. Cell Surf 2022; 8:100088. [PMID: 36405350 PMCID: PMC9651938 DOI: 10.1016/j.tcsw.2022.100088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium tuberculosis causes the disease tuberculosis and affects a third of the world’s population. The recent COVID-19 pandemic exacerbated the situation with a projected 27% increase in tuberculosis related deaths. M. tuberculosis has an elaborate cell wall consisting of peptidoglycan, arabinogalactan and mycolic acids which shield the bacilli from the toxic bactericidal milieu within phagocytes. Amongst, the numerous glycosyltransferase enzymes involved in mycobacterial cell wall biosynthesis, arabinofuranosyltransferase C (aftC) is responsible for the branching of the arabinan domain in both arabinogalactan and lipoarabinomannan. Using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) we have generated aftC knockdowns in Mycobacterium bovis BCG and demonstrated the generation of a truncated, immunogenic lipoarabinomannan within its cell envelope. The aftC depleted BCG mutants were unable to form characteristic mycobacterial pellicular biofilms and elicit a potent immunostimulatory phenotype compared to wild type M. bovis BCG in a THP1 cell line. This study paves the way to further explore novel BCG mutants as promising vaccine boosters in preventing pulmonary tuberculosis.
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37
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Poulton NC, Rock JM. Unraveling the mechanisms of intrinsic drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:997283. [PMID: 36325467 PMCID: PMC9618640 DOI: 10.3389/fcimb.2022.997283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/30/2022] [Indexed: 02/03/2023] Open
Abstract
Tuberculosis (TB) is among the most difficult infections to treat, requiring several months of multidrug therapy to produce a durable cure. The reasons necessitating long treatment times are complex and multifactorial. However, one major difficulty of treating TB is the resistance of the infecting bacterium, Mycobacterium tuberculosis (Mtb), to many distinct classes of antimicrobials. This review will focus on the major gaps in our understanding of intrinsic drug resistance in Mtb and how functional and chemical-genetics can help close those gaps. A better understanding of intrinsic drug resistance will help lay the foundation for strategies to disarm and circumvent these mechanisms to develop more potent antitubercular therapies.
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38
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Costigan R, Stoakes E, Floto RA, Parkhill J, Grant AJ. Development and validation of a CRISPR interference system for gene regulation in Campylobacter jejuni. BMC Microbiol 2022; 22:238. [PMID: 36199015 PMCID: PMC9533551 DOI: 10.1186/s12866-022-02645-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Campylobacter spp. are the leading cause of bacterial food-borne illness in humans worldwide, with Campylobacter jejuni responsible for 80% of these infections. There is an urgent need to understand fundamental C. jejuni biology for the development of new strategies to prevent and treat infections. The range of molecular tools available to regulate gene expression in C. jejuni is limited, which in turn constrains our ability to interrogate the function of essential and conditionally essential genes. We have addressed this by developing and utilising a CRISPR-based interference system known as CRISPRi in C. jejuni to control gene expression. To achieve this, a catalytically inactive ("dead") cas9 and sgRNA backbone from the Streptococcus pyogenes CRISPRi system was combined with C. jejuni-derived promoters of predetermined expression activities to develop a CRISPRi-based repression tool in C. jejuni strains M1Cam and 81-176. RESULTS The CRISPRi tool was validated through successful repression of the arylsulphatase-encoding gene astA using a range of sgRNA target sequences spanning the astA gene. The tool was also applied to target astA in an M1Cam CRISPR-Cas9 deletion strain, which showed that the presence of an endogenous CRISPR-Cas9 system did not affect the activity of the CRISPRi-based repression tool. The tool was further validated against the hippicurase-encoding gene hipO. Following this, the flagella genes flgR, flaA, flaB and both flaA and flaB were targeted for CRISPRi-based repression, which resulted in varying levels of motility reduction and flagella phenotypes as determined by phenotypical assays and transmission electron microscopy (TEM). CONCLUSIONS This is the first report of a CRISPRi-based tool in C. jejuni, which will provide a valuable resource to the Campylobacter community.
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Affiliation(s)
- Ruby Costigan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Emily Stoakes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Department of Medicine, MRC-Laboratory of Molecular Biology, Molecular Immunity Unit, University of Cambridge, Cambridge, UK
- University of Cambridge, Centre for AI in Medicine, Cambridge, UK
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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39
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Lysocin E Targeting Menaquinone in the Membrane of Mycobacterium tuberculosis Is a Promising Lead Compound for Antituberculosis Drugs. Antimicrob Agents Chemother 2022; 66:e0017122. [PMID: 35969044 PMCID: PMC9487456 DOI: 10.1128/aac.00171-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis remains a public health crisis and a health security threat. There is an urgent need to develop new antituberculosis drugs with novel modes of action to cure drug-resistant tuberculosis and shorten the chemotherapy period by sterilizing tissues infected with dormant bacteria. Lysocin E is an antibiotic that showed antibacterial activity against Staphylococcus aureus by binding to its menaquinone (commonly known as vitamin K2). Unlike S. aureus, menaquinone is essential in both growing and dormant Mycobacterium tuberculosis. This study aims to evaluate the antituberculosis activities of lysocin E and decipher its mode of action. We show that lysocin E has high in vitro activity against both drug-susceptible and drug-resistant Mycobacterium tuberculosis var. tuberculosis and dormant mycobacteria. Lysocin E is likely bound to menaquinone, causing M. tuberculosis membrane disruption, inhibition of oxygen consumption, and ATP synthesis. Thus, we have concluded that the high antituberculosis activity of lysocin E is attributable to its synergistic effects of membrane disruption and respiratory inhibition. The efficacy of lysocin E against intracellular M. tuberculosis in macrophages was lower than its potent activity against M. tuberculosis in culture medium, probably due to its low ability to penetrate cells, but its efficacy in mice was still superior to that of streptomycin. Our findings indicate that lysocin E is a promising lead compound for the development of a new tuberculosis drug that cures drug-resistant and latent tuberculosis in a shorter period.
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40
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Boeck L, Burbaud S, Skwark M, Pearson WH, Sangen J, Wuest AW, Marshall EKP, Weimann A, Everall I, Bryant JM, Malhotra S, Bannerman BP, Kierdorf K, Blundell TL, Dionne MS, Parkhill J, Andres Floto R. Mycobacterium abscessus pathogenesis identified by phenogenomic analyses. Nat Microbiol 2022; 7:1431-1441. [PMID: 36008617 PMCID: PMC9418003 DOI: 10.1038/s41564-022-01204-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/19/2022] [Indexed: 12/12/2022]
Abstract
The medical and scientific response to emerging and established pathogens is often severely hampered by ignorance of the genetic determinants of virulence, drug resistance and clinical outcomes that could be used to identify therapeutic drug targets and forecast patient trajectories. Taking the newly emergent multidrug-resistant bacteria Mycobacterium abscessus as an example, we show that combining high-dimensional phenotyping with whole-genome sequencing in a phenogenomic analysis can rapidly reveal actionable systems-level insights into bacterial pathobiology. Through phenotyping of 331 clinical isolates, we discovered three distinct clusters of isolates, each with different virulence traits and associated with a different clinical outcome. We combined genome-wide association studies with proteome-wide computational structural modelling to define likely causal variants, and employed direct coupling analysis to identify co-evolving, and therefore potentially epistatic, gene networks. We then used in vivo CRISPR-based silencing to validate our findings and discover clinically relevant M. abscessus virulence factors including a secretion system, thus illustrating how phenogenomics can reveal critical pathways within emerging pathogenic bacteria.
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Affiliation(s)
- Lucas Boeck
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sophie Burbaud
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Marcin Skwark
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Will H Pearson
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Jasper Sangen
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Andreas W Wuest
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Eleanor K P Marshall
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, Cambridge, UK
| | | | - Josephine M Bryant
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Scientific Computing Department, Science and Technology Facilities Council, Harwell, UK
| | - Bridget P Bannerman
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Katrin Kierdorf
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marc S Dionne
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for AI in Medicine, Cambridge, UK.
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK.
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41
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Chaudhary D, Singh A, Marzuki M, Ghosh A, Kidwai S, Gosain TP, Chawla K, Gupta SK, Agarwal N, Saha S, Kumar Y, Thakur KG, Singhal A, Singh R. Identification of small molecules targeting homoserine acetyl transferase from Mycobacterium tuberculosis and Staphylococcus aureus. Sci Rep 2022; 12:13801. [PMID: 35963878 PMCID: PMC9376091 DOI: 10.1038/s41598-022-16468-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
There is an urgent need to validate new drug targets and identify small molecules that possess activity against both drug-resistant and drug-sensitive bacteria. The enzymes belonging to amino acid biosynthesis have been shown to be essential for growth in vitro, in vivo and have not been exploited much for the development of anti-tubercular agents. Here, we have identified small molecule inhibitors targeting homoserine acetyl transferase (HSAT, MetX, Rv3341) from M. tuberculosis. MetX catalyses the first committed step in L-methionine and S-adenosyl methionine biosynthesis resulting in the formation of O-acetyl-homoserine. Using CRISPRi approach, we demonstrate that conditional repression of metX resulted in inhibition of M. tuberculosis growth in vitro. We have determined steady state kinetic parameters for the acetylation of L-homoserine by Rv3341. We show that the recombinant enzyme followed Michaelis-Menten kinetics and utilizes both acetyl-CoA and propionyl-CoA as acyl-donors. High-throughput screening of a 2443 compound library resulted in identification of small molecule inhibitors against MetX enzyme from M. tuberculosis. The identified lead compounds inhibited Rv3341 enzymatic activity in a dose dependent manner and were also active against HSAT homolog from S. aureus. Molecular docking of the identified primary hits predicted residues that are essential for their binding in HSAT homologs from M. tuberculosis and S. aureus. ThermoFluor assay demonstrated direct binding of the identified primary hits with HSAT proteins. Few of the identified small molecules were able to inhibit growth of M. tuberculosis and S. aureus in liquid cultures. Taken together, our findings validated HSAT as an attractive target for development of new broad-spectrum anti-bacterial agents that should be effective against drug-resistant bacteria.
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Affiliation(s)
- Deepika Chaudhary
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Avantika Singh
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Mardiana Marzuki
- Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Saqib Kidwai
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Kiran Chawla
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sonu Kumar Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, West Bengal, 700054, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Amit Singhal
- Infectious Diseases Labs (ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.,Singapore Immunology Network (SIgN), (A*STAR), Singapore, 138648, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, 121001, India. .,Tuberculosis Research Laboratory, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, PO Box # 4, Faridabad, 121001, India.
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42
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Abe T, Hakamata M, Nishiyama A, Tateishi Y, Matsumoto S, Hemmi H, Ueda D, Sato T. Identification and functional analysis of a new type of
Z,E
‐mixed prenyl reductase from mycobacteria. FEBS J 2022; 289:4981-4997. [DOI: 10.1111/febs.16412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/03/2022] [Accepted: 02/22/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Tohru Abe
- Department of Agriculture Faculty of Agriculture and Graduate School of Science and Technology Niigata University Japan
| | - Mariko Hakamata
- Department of Bacteriology Niigata University School of Medicine Japan
| | - Akihito Nishiyama
- Department of Bacteriology Niigata University School of Medicine Japan
| | | | | | - Hisashi Hemmi
- Department of Applied Molecular Bioscience Graduate School of Bioagricultural Sciences Nagoya University Japan
| | - Daijiro Ueda
- Department of Agriculture Faculty of Agriculture and Graduate School of Science and Technology Niigata University Japan
| | - Tsutomu Sato
- Department of Agriculture Faculty of Agriculture and Graduate School of Science and Technology Niigata University Japan
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43
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Kong L, Xiong Z, Song X, Xia Y, Ai L. CRISPR/dCas9-based metabolic pathway engineering for the systematic optimization of exopolysaccharide biosynthesis in Streptococcus thermophilus. J Dairy Sci 2022; 105:6499-6512. [PMID: 35691751 DOI: 10.3168/jds.2021-21409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/05/2022] [Indexed: 12/23/2022]
Abstract
Streptococcus thermophilus is used extensively in the dairy industry and has shown great promise as a chassis cell for the biosynthesis of high-value metabolites. However, metabolic engineering in S. thermophilus lacks effective genetic modification tools to modulate gene expression to relieve metabolic burden and maximize the production of desired compounds. Here, we developed a clustered regularly interspaced short palindromic repeats interference (CRISPRi) system for efficient gene transcriptional modulation in S. thermophilus. Our CRISPRi system typically achieved 66 to 98% knockdown of single or multiple gene expression. We used CRISPRi for the biosynthesis of a new exopolysaccharide (EPS) as a paradigm model. Repression of galK at module of uridine diphosphate glucose sugar metabolism and overexpression of epsA and epsE at EPS synthesis module resulted in an approximately 2-fold increase in EPS titer (277 mg/L) when compared with a control strain. This study demonstrated the effectiveness of CRISPRi as a powerful metabolic engineering tool and synthetic biology strategy for S. thermophilus.
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Affiliation(s)
- Linghui Kong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; School of Pharmacy (School of Enology), Binzhou Medical University, Yantai, 264003, Shandong Province, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yongjun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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Agarwal N, Sharma S, Pal P, Kaushal PS, Kumar N. Era, a GTPase-like protein of the Ras family, does not control ribosome assembly in Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35917161 DOI: 10.1099/mic.0.001200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Era GTPase is universally present in microbes including Mycobacterium tuberculosis (Mtb) complex bacteria. While Era is known to regulate ribosomal assembly in Escherichia coli and predicted to be essential for in vitro growth, its function in mycobacteria remains obscured. Herein, we show that Era ortholog in the attenuated Mtb H37Ra strain, MRA_2388 (annotated as EraMT) is a cell envelope localized protein harbouring critical GTP-binding domains, which interacts with several envelope proteins of Mtb. The purified Era from M. smegmatis (annotated as EraMS) exhibiting ~90 % sequence similarity with EraMT, exists in monomeric conformation. While it is co-purified with RNA upon overexpression in E. coli, the presence of RNA does not modulate the GTPase activity of the EraMS as against its counterpart from other organisms. CRISPRi silencing of eraMT does not show any substantial effect on the in vitro growth of Mtb H37Ra, which suggests a redundant function of Era in mycobacteria. Notably, no effect on ribosome assembly, protein synthesis or bacterial susceptibility to protein synthesis inhibitors was observed upon depletion of EraMT in Mtb H37Ra, further indicating a divergent role of Era GTPase in mycobacteria.
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Affiliation(s)
- Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
| | - Shivani Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
| | - Pramila Pal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India.,Jawaharlal Nehru University, New Mehrauli Road, New Delhi- 110067 (Delhi), India
| | - Prem S Kaushal
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
| | - Naresh Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad- 121001 (Haryana), India
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Abstract
Bacteriophages are the most abundant entities in the biosphere, and many genomes of rare and novel bacteriophages have been sequenced to date. However, bacteriophage functional genomics has been limited by a lack of effective research methods. Clustered regularly interspaced short palindromic repeat/CRISPR-associated gene (CRISPR–Cas) systems provide bacteriophages with a new mechanism for attacking host bacteria as well as new tools for study bacteriophage functional genomics. It has been reported that bacteriophages are not only the driving elements of the evolution of prokaryote CRISPR arrays but also the targets of CRISPR–Cas systems. In this study, a phage genome editing platform based on the heterologous CRISPR–Cas9 system was theoretically designed, and a Vibrio natriegens phage TT4P2 genome editing experiment was carried out in vivo in the host bacterium Vibrio natriegens TT4 to achieve phage gene deletion and replacement. The construction of this phage genome editing platform is expected to solve the problem of insufficient research on phage gene diversity, promote the development of phage synthetic biology and nanotechnology, and even accelerate the discovery of new molecular biology tools. IMPORTANCE Bacteriophages are the most numerous organisms on earth and are known for their diverse lifestyles. Since the discovery of bacteriophages, our knowledge of the wider biological world has undergone immense and unforeseen changes. A variety of V. natriegens phages have been detected, but few have been well characterized. CRISPR was first documented in Escherichia coli in 1987. It has been reported that the CRISPR–Cas system can target and cleave invaders, including bacteriophages, in a sequence-specific manner. Here, we show that the construction of a phage genome editing platform based on the heterologous CRISPR–Cas9 system can achieve V. natriegens phage TT4P2 gene editing and can also improve the efficiency and accuracy of phage TT4P2 gene editing.
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Call SN, Andrews LB. CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. Front Genome Ed 2022; 4:892304. [PMID: 35813973 PMCID: PMC9260158 DOI: 10.3389/fgeed.2022.892304] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 01/08/2023] Open
Abstract
CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) have become ubiquitous approaches to control gene expression in bacteria due to their simple design and effectiveness. By regulating transcription of a target gene(s), CRISPRi/a can dynamically engineer cellular metabolism, implement transcriptional regulation circuitry, or elucidate genotype-phenotype relationships from smaller targeted libraries up to whole genome-wide libraries. While CRISPRi/a has been primarily established in the model bacteria Escherichia coli and Bacillus subtilis, a growing numbering of studies have demonstrated the extension of these tools to other species of bacteria (here broadly referred to as non-model bacteria). In this mini-review, we discuss the challenges that contribute to the slower creation of CRISPRi/a tools in diverse, non-model bacteria and summarize the current state of these approaches across bacterial phyla. We find that despite the potential difficulties in establishing novel CRISPRi/a in non-model microbes, over 190 recent examples across eight bacterial phyla have been reported in the literature. Most studies have focused on tool development or used these CRISPRi/a approaches to interrogate gene function, with fewer examples applying CRISPRi/a gene regulation for metabolic engineering or high-throughput screens and selections. To date, most CRISPRi/a reports have been developed for common strains of non-model bacterial species, suggesting barriers remain to establish these genetic tools in undomesticated bacteria. More efficient and generalizable methods will help realize the immense potential of programmable CRISPR-based transcriptional control in diverse bacteria.
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Affiliation(s)
- Stephanie N. Call
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, United States
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Li S, Poulton NC, Chang JS, Azadian ZA, DeJesus MA, Ruecker N, Zimmerman MD, Eckartt KA, Bosch B, Engelhart CA, Sullivan DF, Gengenbacher M, Dartois VA, Schnappinger D, Rock JM. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat Microbiol 2022; 7:766-779. [PMID: 35637331 PMCID: PMC9159947 DOI: 10.1038/s41564-022-01130-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Mycobacterium tuberculosis (Mtb) infection is notoriously difficult to treat. Treatment efficacy is limited by Mtb's intrinsic drug resistance, as well as its ability to evolve acquired resistance to all antituberculars in clinical use. A deeper understanding of the bacterial pathways that influence drug efficacy could facilitate the development of more effective therapies, identify new mechanisms of acquired resistance, and reveal overlooked therapeutic opportunities. Here we developed a CRISPR interference chemical-genetics platform to titrate the expression of Mtb genes and quantify bacterial fitness in the presence of different drugs. We discovered diverse mechanisms of intrinsic drug resistance, unveiling hundreds of potential targets for synergistic drug combinations. Combining chemical genetics with comparative genomics of Mtb clinical isolates, we further identified several previously unknown mechanisms of acquired drug resistance, one of which is associated with a multidrug-resistant tuberculosis outbreak in South America. Lastly, we found that the intrinsic resistance factor whiB7 was inactivated in an entire Mtb sublineage endemic to Southeast Asia, presenting an opportunity to potentially repurpose the macrolide antibiotic clarithromycin to treat tuberculosis. This chemical-genetic map provides a rich resource to understand drug efficacy in Mtb and guide future tuberculosis drug development and treatment.
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Affiliation(s)
- Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Jesseon S Chang
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Kathryn A Eckartt
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Daniel F Sullivan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA
| | - Véronique A Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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Gene–drug potency screening in M. tuberculosis. Nat Microbiol 2022; 7:743-744. [DOI: 10.1038/s41564-022-01139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fernandes LGV, Nascimento ALTO. A Novel Breakthrough in Leptospira spp. Mutagenesis: Knockout by Combination of CRISPR/Cas9 and Non-homologous End-Joining Systems. Front Microbiol 2022; 13:915382. [PMID: 35722349 PMCID: PMC9199861 DOI: 10.3389/fmicb.2022.915382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/28/2022] [Indexed: 12/28/2022] Open
Abstract
Leptospirosis is of general concern as it is a widespread zoonotic disease caused by pathogenic species of the genus Leptospira, although this genus also includes free-living saprophytic strains. Understanding the pathophysiology of leptospirosis is still in its infancy even after several years of its discovery, because of the lack of effective genetic tools. The use of the Streptococcus pyogenes CRISPR/Cas9 system and its variations have pushed the leptospirosis research forward, relying on the simplicity of the technique. However, the lethality of double-strand breaks (DSB) induced by the RNA-guided Cas9 enzyme has limited the generation of knockout mutants. In this work, we demonstrated sustained cell viability after concurrent expression of CRISPR/Cas9 and Mycobacterium tuberculosis non-homologous end-joining components in a single-plasmid strategy in L. biflexa. Scarless mutations resulting in null phenotypes could be observed in most of the colonies recovered, with deletions in the junctional site ranging from 3 to almost 400 bp. After plasmid curing by in vitro passages in a medium without antibiotic, selected marker-free and targeted mutants could be recovered. Knockout mutants for LipL32 protein in the pathogen L. interrogans could be obtained using M. smegmatis NHEJ machinery, with deletions ranging from 10 to 345 bp. In conclusion, we now have a powerful genetic tool for generating scarless and markerless knockout mutants for both saprophytic and pathogenic strains of Leptospira.
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Affiliation(s)
- Luis G. V. Fernandes
- Laboratorio de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- *Correspondence: Luis G. V. Fernandes,
| | - Ana L. T. O. Nascimento
- Laboratorio de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
- Programa de Pos-Graduacao Interunidades em Biotecnologia, Instituto de Ciencias Biomedicas, São Paulo, Brazil
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50
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Barman A, Patra MM, Das Gupta SK. The respiratory lipoquinone, menaquinone, functions as an inducer of genes regulated by the Mycobacterium smegmatis repressor MSMEG_2295. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35575764 DOI: 10.1099/mic.0.001192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A previous study reported that the Mycobacterium smegmatis (Msm) protein MSMEG_2295 is a repressor controlling the expression of several genes, including that for MSMEG_5125, a putative isoprenoid binding protein belonging to the YceI family, and DinB2, a DNA damage repair enzyme. This repressor is encoded by the first gene of the operon that also expresses the gene for DinB2. Targeted inhibition of MSMEG_5125 using CRISPRi technology resulted in a significant loss of Msm's respiratory activity and viability. Since this protein has been predicted to be an isoprenoid binding protein, we suspected a role of menaquinones, which are isoprenoid naphthoquinones, in the observed phenomenon. Accordingly, we tested whether MSMEG_5125's deficiency-induced lethality could be reversed by adding menaquinone. The result was positive, implying cooperation between MSMEG_5125 and menaquinone in bringing about respiration. Inhibition of MSMEG_5125 expression led to the induction of MSMEG_0089 and 2296, two hallmark genes of the MSMEG_2295 regulon. This result suggests that when MSMEG_5125 becomes limiting, a feedback-loop derepresses the MSMEG_2295 regulon genes, including its own. Interestingly, menaquinone functioned as an inducer of MSMEG_5125, indicating that it is likely to mediate the feedback mechanism. This result also strengthens our hypothesis that the functions of menaquinone and MSMEG_5125 are interrelated. Menaquinone also induced the MSMEG_2295-controlled operon MSMEG_2295-2294 (dinB2) not induced following the inactivation of MSMEG_5125. Therefore, the activation mechanism of MSMEG_2295-regulated genes may not be the same for all, although derepression is likely to be a common feature. In vitro, menaquinone abolished MSMEG_2295's DNA binding activity by interacting with it, confirming its role as an inducer. Therefore, a menaquinone-MSMEG_5125-regulated gene expression circuit controls Msm respiration and possibly oxidative stress-induced DNA damage repair.
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Affiliation(s)
- Anik Barman
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Madhu Manti Patra
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Sujoy K Das Gupta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
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