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Roberts AH, Moon CW, Faulkner V, Kendall SL, Waddell SJ, Bacon J. EfpA is required for regrowth of Mycobacterium tuberculosis following isoniazid exposure. Antimicrob Agents Chemother 2024; 68:e0026124. [PMID: 39037241 PMCID: PMC11304720 DOI: 10.1128/aac.00261-24] [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: 02/19/2024] [Accepted: 06/02/2024] [Indexed: 07/23/2024] Open
Abstract
Efflux of antibiotics is an important survival strategy in bacteria. Mycobacterium tuberculosis has approximately sixty efflux pumps, but little is known about the role of each pump or the substrates they efflux. The putative efflux pump, EfpA, is a member of the major facilitator superfamily and has been shown to be essential by saturation transposon mutagenesis studies. It has been implicated in the efflux of isoniazid (INH), which is a first-line drug used to treat tuberculosis (TB). This is supported by evidence from transcriptional profiling showing that efpA is induced in response to INH exposure. However, its roles in the physiology and adaptation of M. tuberculosis to antibiotics have yet to be determined. In this study, we describe the repression of efpA in M. tuberculosis, using CRISPR interference (CRISPRi) to knockdown the expression of this essential gene and the direct effect of this on the ability of M. tuberculosis to survive exposure to INH over a 45-day time course. We determined that wild-type levels of efpA were required for recovery of M. tuberculosis following INH exposure and that, after 45 days of INH exposure, only a few viable colonies were recoverable from efpA-repressed M. tuberculosis. We conclude that EfpA is required for recovery of M. tuberculosis following INH exposure, which could reduce the efficacy of INH in vivo, and that EfpA may have a role in the development of resistance during drug therapy.
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Affiliation(s)
- Adam H. Roberts
- Discovery Group, VDEC, UK Health Security Agency, Porton Down, Salisbury, United Kingdom
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Christopher W. Moon
- Discovery Group, VDEC, UK Health Security Agency, Porton Down, Salisbury, United Kingdom
| | - Valwynne Faulkner
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Sharon L. Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Simon J. Waddell
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Joanna Bacon
- Discovery Group, VDEC, UK Health Security Agency, Porton Down, Salisbury, United Kingdom
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2
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Cheng H, Ji Z, Wang Y, Li S, Tang T, Wang F, Peng C, Wu X, Cheng Y, Liu Z, Ma M, Wang J, Huang X, Wang L, Qin L, Liu H, Chen J, Zheng R, Feng CG, Cai X, Qu D, Ye L, Yang H, Ge B. Mycobacterium tuberculosis produces D-serine under hypoxia to limit CD8 + T cell-dependent immunity in mice. Nat Microbiol 2024; 9:1856-1872. [PMID: 38806671 PMCID: PMC11222154 DOI: 10.1038/s41564-024-01701-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/11/2024] [Indexed: 05/30/2024]
Abstract
Adaptation to hypoxia is a major challenge for the survival of Mycobacterium tuberculosis (Mtb) in vivo. Interferon (IFN)-γ-producing CD8+ T cells contribute to control of Mtb infection, in part by promoting antimicrobial activities of macrophages. Whether Mtb counters these responses, particularly during hypoxic conditions, remains unknown. Using metabolomic, proteomic and genetic approaches, here we show that Mtb induced Rv0884c (SerC), an Mtb phosphoserine aminotransferase, to produce D-serine. This activity increased Mtb pathogenesis in mice but did not directly affect intramacrophage Mtb survival. Instead, D-serine inhibited IFN-γ production by CD8+ T cells, which indirectly reduced the ability of macrophages to restrict Mtb upon co-culture. Mechanistically, D-serine interacted with WDR24 and inhibited mTORC1 activation in CD8+ T cells. This decreased T-bet expression and reduced IFN-γ production by CD8+ T cells. Our findings suggest an Mtb evasion mechanism where pathogen metabolic adaptation to hypoxia leads to amino acid-dependent suppression of adaptive anti-TB immunity.
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Affiliation(s)
- Hongyu Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Zhe Ji
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Yang Wang
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Shenzhi Li
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Tianqi Tang
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Fei Wang
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Cheng Peng
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Xiangyang Wu
- Clinical and Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Yuanna Cheng
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Zhonghua Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Mingtong Ma
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Lin Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Haipeng Liu
- Clinical and Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Jianxia Chen
- Clinical and Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Carl G Feng
- Immunology and Host Defense Group, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Tuberculosis Research Program, Centenary Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Xia Cai
- Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, P. R. China
| | - Di Qu
- Biosafety Level 3 Laboratory, Shanghai Medical College, Fudan University, Shanghai, P. R. China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing, P. R. China.
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China.
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, PR China.
- Clinical and Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P. R. China.
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3
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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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4
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Khan H, Paul P, Goar H, Bamniya B, Baid N, Sarkar D. Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by regulating cAMP level. eLife 2024; 13:RP92136. [PMID: 38739431 PMCID: PMC11090507 DOI: 10.7554/elife.92136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024] Open
Abstract
Survival of Mycobacterium tuberculosis within the host macrophages requires the bacterial virulence regulator PhoP, but the underlying reason remains unknown. 3',5'-Cyclic adenosine monophosphate (cAMP) is one of the most widely used second messengers, which impacts a wide range of cellular responses in microbial pathogens including M. tuberculosis. Herein, we hypothesized that intra-bacterial cAMP level could be controlled by PhoP since this major regulator plays a key role in bacterial responses against numerous stress conditions. A transcriptomic analysis reveals that PhoP functions as a repressor of cAMP-specific phosphodiesterase (PDE) Rv0805, which hydrolyzes cAMP. In keeping with these results, we find specific recruitment of the regulator within the promoter region of rv0805 PDE, and absence of phoP or ectopic expression of rv0805 independently accounts for elevated PDE synthesis, leading to the depletion of intra-bacterial cAMP level. Thus, genetic manipulation to inactivate PhoP-rv0805-cAMP pathway decreases cAMP level, stress tolerance, and intracellular survival of the bacillus.
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Affiliation(s)
- Hina Khan
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Partha Paul
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Harsh Goar
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Bhanwar Bamniya
- CSIR, Institute of Microbial TechnologyChandigarhIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Navin Baid
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Dibyendu Sarkar
- CSIR, Institute of Microbial TechnologyChandigarhIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
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5
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Banerjee A, Chakraborty M, Sharma S, Chaturvedi R, Bose A, Biswas P, Singh A, Visweswariah SS. Cyclic AMP binding to a universal stress protein in Mycobacterium tuberculosis is essential for viability. J Biol Chem 2024; 300:107287. [PMID: 38636658 PMCID: PMC11107214 DOI: 10.1016/j.jbc.2024.107287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Mycobacterial genomes encode multiple adenylyl cyclases and cAMP effector proteins, underscoring the diverse ways these bacteria utilize cAMP. We identified universal stress proteins, Rv1636 and MSMEG_3811 in Mycobacterium tuberculosis and Mycobacterium smegmatis, respectively, as abundantly expressed, novel cAMP-binding proteins. Rv1636 is secreted via the SecA2 secretion system in M. tuberculosis but is not directly responsible for the efflux of cAMP from the cell. In slow-growing mycobacteria, intrabacterial concentrations of Rv1636 were equivalent to the concentrations of cAMP present in the cell. In contrast, levels of intrabacterial MSMEG_3811 in M. smegmatis were lower than that of cAMP and therefore, overexpression of Rv1636 increased levels of "bound" cAMP. While msmeg_3811 could be readily deleted from the genome of M. smegmatis, we found that the rv1636 gene is essential for the viability of M. tuberculosis and is dependent on the cAMP-binding ability of Rv1636. Therefore, Rv1636 may function to regulate cAMP signaling by direct sequestration of the second messenger. This is the first evidence of a "sponge" for any second messenger in bacterial signaling that would allow mycobacterial cells to regulate the available intrabacterial "free" pool of cAMP.
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Affiliation(s)
- Arka Banerjee
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Moubani Chakraborty
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Suruchi Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Ruchi Chaturvedi
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Avipsa Bose
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Priyanka Biswas
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Sandhya S Visweswariah
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India.
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6
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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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7
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Neo DM, Clatworthy AE, Hung DT. A dual-plasmid CRISPR/Cas9-based method for rapid and efficient genetic disruption in Mycobacterium abscessus. J Bacteriol 2024; 206:e0033523. [PMID: 38319218 PMCID: PMC10955840 DOI: 10.1128/jb.00335-23] [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: 10/15/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Mycobacterium abscessus is increasingly recognized for causing infections that are notoriously difficult to treat, owing to its large arsenal of intrinsic antibiotic resistance mechanisms. Tools for the genetic manipulation of the pathogen are critical for enabling a better understanding of M. abscessus biology, pathogenesis, and antibiotic resistance mechanisms. However, existing methods are largely recombination-based, which are relatively inefficient. Meanwhile, CRISPR/Cas9 has revolutionized the field of genome editing including its recent adaptation for use in mycobacteria. In this study, we report a streamlined and efficient method for rapid genetic disruptions in M. abscessus. Harnessing the CRISPR1 loci from Streptococcus thermophilus, we have developed a dual-plasmid workflow that introduces Cas9 and sgRNA cassettes in separate steps but requires no other additional factors to engineer mutations in single genes or multiple genes simultaneously or sequentially using multiple targeting sgRNAs. Importantly, the efficiency of mutant generation is several orders of magnitude higher than reported for homologous recombination-based methods. This work, thus, reports the first application of CRISPR/Cas9 for gene editing in M. abscessus and is an important tool in the arsenal for the genetic manipulation of this human pathogen. IMPORTANCE Mycobacterium abscessus is an opportunistic pathogen of increasing clinical importance due to its poor clinical outcomes and limited treatment options. Drug discovery and development in this highly antibiotic-resistant species will require further understanding of M. abscessus biology, pathogenesis, and antibiotic resistance mechanisms. However, existing methods for facile genetic engineering are relatively inefficient. This study reports on the first application of CRISPR/Cas9 for gene editing in M. abscessus using a dual-plasmid workflow. We establish that our method is easily programmable, efficient, and versatile for genetic disruptions in M. abscessus. This is a critical advancement to facilitating targeted gene function studies in this emerging pathogen.
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Affiliation(s)
- Donavan Marcus Neo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Anne E. Clatworthy
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Deborah T. Hung
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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8
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Sodani M, Misra CS, Nigam G, Fatima Z, Kulkarni S, Rath D. MSMEG_0311 is a conserved essential polar protein involved in mycobacterium cell wall metabolism. Int J Biol Macromol 2024; 260:129583. [PMID: 38242409 DOI: 10.1016/j.ijbiomac.2024.129583] [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: 11/23/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Cell wall synthesis and cell division are two closely linked pathways in a bacterial cell which distinctly influence the growth and survival of a bacterium. This requires an appreciable coordination between the two processes, more so, in case of mycobacteria with an intricate multi-layered cell wall structure. In this study, we investigated a conserved gene cluster using CRISPR-Cas12 based gene silencing technology to show that knockdown of most of the genes in this cluster leads to growth defects. Investigating conserved genes is important as they likely perform vital cellular functions and the functional insights on such genes can be extended to other mycobacterial species. We characterised one of the genes in the locus, MSMEG_0311. The repression of this gene not only imparts severe growth defect but also changes colony morphology. We demonstrate that the protein preferentially localises to the polar region and investigate its influence on the polar growth of the bacillus. A combination of permeability and drug susceptibility assay strongly suggests a cell wall associated function of this gene which is also corroborated by transcriptomic analysis of the knockdown where a number of cell wall associated genes, particularly iniA and sigF regulon get altered. Considering the gene is highly conserved across mycobacterial species and appears to be essential for growth, it may serve as a potential drug target.
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Affiliation(s)
- Megha Sodani
- Radiation Medicine Centre, Medical Group, Bhabha Atomic Research Centre, Mumbai 400085, 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, Maharashtra, India
| | - Gaurav Nigam
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India; Department of Laboratory Medicine, Faculty of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
| | - Savita Kulkarni
- Radiation Medicine Centre, Medical Group, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India.
| | - Devashish Rath
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, Maharashtra, India; Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India.
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9
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Das M, Sreedharan S, Shee S, Malhotra N, Nandy M, Banerjee U, Kohli S, Rajmani RS, Chandra N, Seshasayee ASN, Laxman S, Singh A. Cysteine desulfurase (IscS)-mediated fine-tuning of bioenergetics and SUF expression prevents Mycobacterium tuberculosis hypervirulence. SCIENCE ADVANCES 2023; 9:eadh2858. [PMID: 38091389 PMCID: PMC10848736 DOI: 10.1126/sciadv.adh2858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
Iron-sulfur (Fe-S) biogenesis requires multiprotein assembly systems, SUF and ISC, in most prokaryotes. M. tuberculosis (Mtb) encodes a complete SUF system, the depletion of which was bactericidal. The ISC operon is truncated to a single gene iscS (cysteine desulfurase), whose function remains uncertain. Here, we show that MtbΔiscS is bioenergetically deficient and hypersensitive to oxidative stress, antibiotics, and hypoxia. MtbΔiscS resisted killing by nitric oxide (NO). RNA sequencing indicates that IscS is important for expressing regulons of DosR and Fe-S-containing transcription factors, WhiB3 and SufR. Unlike wild-type Mtb, MtbΔiscS could not enter a stable persistent state, continued replicating in mice, and showed hypervirulence. The suf operon was overexpressed in MtbΔiscS during infection in a NO-dependent manner. Suppressing suf expression in MtbΔiscS either by CRISPR interference or upon infection in inducible NO-deficient mice arrests hypervirulence. Together, Mtb redesigned the ISC system to "fine-tune" the expression of SUF machinery for establishing persistence without causing detrimental disease in the host.
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Affiliation(s)
- Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
- School of Chemical and Biotechnology, (SASTRA)-Deemed to be University, Thanjavur 613401, India
| | - Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Nitish Malhotra
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Meghna Nandy
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sakshi Kohli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Raju S. Rajmani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
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10
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McManus WR, Schorey JS. Comparison of Ultrastructure, Extracellular Matrix, and Drug Susceptibility in M. avium subs. hominissuis Biofilms. Pathogens 2023; 12:1427. [PMID: 38133310 PMCID: PMC10747021 DOI: 10.3390/pathogens12121427] [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: 10/17/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Pulmonary infections with Mycobacterium avium occur in susceptible individuals following exposure to the bacterium in the environment, where it often persists in biofilms. Many methods have been used to generate biofilms of M. avium, and it is unknown whether different approaches generate similar structures and cell phenotypes. To make a parallel comparison of in vitro biofilm ultrastructure, extracellular matrix (ECM) composition, and the drug susceptibility of biofilm resident bacteria, we used two published methods to generate M. avium biofilms: four-week incubation in M63 medium or 24 h exposure to dithiothreitol (DTT). Scanning electron microscopy revealed differences in the biofilm ultrastructure between the two methods, including variation in the appearance of ECM materials and morphology of resident cells, while light microscopy and staining with calcofluor white indicated that both biofilms contained polysaccharides characteristic of cellulose. Measuring the susceptibility of biofilms to degradation by enzymes suggested differences in structurally important ECM molecules, with DTT biofilms having important protein and, to a lesser extent, cellulose components, and M63 biofilms having moderate protein, cellulose, and DNA components. Both biofilms conferred resistance to the bactericidal effects of amikacin and clarithromycin, with resident cells being killed at greater than 10-fold lower rates than planktonic cells at almost all concentrations. These comparisons indicate differences in biofilm responses by M. avium under differing conditions, but also suggest common features of biofilm formation, including cellulose production and antimicrobial resistance.
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Affiliation(s)
| | - Jeffrey S. Schorey
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA;
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11
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Singh PR, Goar H, Paul P, Mehta K, Bamniya B, Vijjamarri AK, Bansal R, Khan H, Karthikeyan S, Sarkar D. Dual functioning by the PhoR sensor is a key determinant to Mycobacterium tuberculosis virulence. PLoS Genet 2023; 19:e1011070. [PMID: 38100394 PMCID: PMC10723718 DOI: 10.1371/journal.pgen.1011070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
PhoP-PhoR, one of the 12 two-component systems (TCSs) that empower M. tuberculosis to sense and adapt to diverse environmental conditions, remains essential for virulence, and therefore, represents a major target to develop novel anti-TB therapies. Although both PhoP and PhoR have been structurally characterized, the signal(s) that this TCS responds to remains unknown. Here, we show that PhoR is a sensor of acidic pH/high salt conditions, which subsequently activate PhoP via phosphorylation. In keeping with this, transcriptomic data uncover that acidic pH- inducible expression of PhoP regulon is significantly inhibited in a PhoR-deleted M. tuberculosis. Strikingly, a set of PhoP regulon genes displayed a low pH-dependent activation even in the absence of PhoR, suggesting the presence of non-canonical mechanism(s) of PhoP activation. Using genome-wide interaction-based screening coupled with phosphorylation assays, we identify a non-canonical mechanism of PhoP phosphorylation by the sensor kinase PrrB. To investigate how level of P~PhoP is regulated, we discovered that in addition to its kinase activity PhoR functions as a phosphatase of P~PhoP. Our subsequent results identify the motif/residues responsible for kinase/phosphatase dual functioning of PhoR. Collectively, these results uncover that contrasting kinase and phosphatase functions of PhoR determine the homeostatic mechanism of regulation of intra-mycobacterial P~PhoP which controls the final output of the PhoP regulon. Together, these results connect PhoR to pH-dependent activation of PhoP with downstream functioning of the regulator. Thus, PhoR plays a central role in mycobacterial adaptation to low pH conditions within the host macrophage phagosome, and a PhoR-deleted M. tuberculosis remains significantly attenuated in macrophages and animal models.
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Affiliation(s)
| | - Harsh Goar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Partha Paul
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Khushboo Mehta
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bhanwar Bamniya
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Roohi Bansal
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Hina Khan
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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12
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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: 3.0] [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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13
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Xiao Y, Zhang Y, Xie F, Olsen RH, Shi L, Li L. Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System. Int J Mol Sci 2023; 24:10585. [PMID: 37445761 DOI: 10.3390/ijms241310585] [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: 05/19/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.
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Affiliation(s)
- Yawen Xiao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Yan Zhang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Fengjun Xie
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
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14
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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: 0] [Impact Index Per Article: 0] [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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15
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Gopalakrishna KP, Hillebrand GH, Bhavana VH, Elder JL, D'Mello A, Tettelin H, Hooven TA. Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects. Commun Biol 2023; 6:620. [PMID: 37296208 PMCID: PMC10256743 DOI: 10.1038/s42003-023-04994-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Group B Streptococcus (GBS; S. agalactiae) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial cell. Several recent publications have shown that GBS Cas9 influences genome-wide transcription through a mechanism uncoupled from its function as a specific, RNA-programmable endonuclease. We examine GBS Cas9 effects on genome-wide transcription through generation of several isogenic variants with specific functional defects. We compare whole-genome RNA-seq from Δcas9 GBS with a full-length Cas9 gene deletion; dcas9 defective in its ability to cleave DNA but still able to bind to frequently occurring protospacer adjacent motifs; and scas9 that retains its catalytic domains but is unable to bind protospacer adjacent motifs. Comparing scas9 GBS to the other variants, we identify nonspecific protospacer adjacent motif binding as a driver of genome-wide, Cas9 transcriptional effects in GBS. We also show that Cas9 transcriptional effects from nonspecific scanning tend to influence genes involved in bacterial defense and nucleotide or carbohydrate transport and metabolism. While genome-wide transcription effects are detectable by analysis of next-generation sequencing, they do not result in virulence changes in a mouse model of sepsis. We also demonstrate that catalytically inactive dCas9 expressed from the GBS chromosome can be used with a straightforward, plasmid-based, single guide RNA expression system to suppress transcription of specific GBS genes without potentially confounding off-target effects. We anticipate that this system will be useful for study of nonessential and essential gene roles in GBS physiology and pathogenesis.
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Affiliation(s)
| | - Gideon H Hillebrand
- University of Pittsburgh School of Medicine, Program in Microbiology and Immunology, Pittsburgh, PA, USA
| | - Venkata H Bhavana
- University of Pittsburgh School of Medicine, Department of Pediatrics, Pittsburgh, PA, USA
| | - Jordan L Elder
- The Cleveland Clinic, Clinical Laboratory Services, Cleveland, OH, USA
| | - Adonis D'Mello
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Thomas A Hooven
- University of Pittsburgh School of Medicine, Department of Pediatrics, Pittsburgh, PA, USA.
- Richard King Mellon Institute for Pediatric Research, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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16
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Gopalakrishna KP, Hillebrand GH, Bhavana VH, Elder JL, D'Mello A, Tettelin H, Hooven TA. Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542094. [PMID: 37292749 PMCID: PMC10245859 DOI: 10.1101/2023.05.24.542094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Group B Streptococcus (GBS; S. agalactiae ) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial cell. Several recent publications have shown that GBS Cas9 influences genome-wide transcription through a mechanism uncoupled from its function as a specific, RNA-programmable endonuclease. We examine GBS Cas9 effects on genome-wide transcription through generation of several isogenic variants with specific functional defects. We compare whole-genome RNA-seq from Δ cas9 GBS with a full-length Cas9 gene deletion; dcas9 defective in its ability to cleave DNA but still able to bind to frequently occurring protospacer adjacent motifs; and scas9 that retains its catalytic domains but is unable to bind protospacer adjacent motifs. Comparing scas9 GBS to the other variants, we identify nonspecific protospacer adjacent motif binding as a driver of genome-wide, Cas9 transcriptional effects in GBS. We also show that Cas9 transcriptional effects from nonspecific scanning tend to influence genes involved in bacterial defense and nucleotide or carbohydrate transport and metabolism. While genome-wide transcription effects are detectable by analysis of next-generation sequencing, they do not result in virulence changes in a mouse model of sepsis. We also demonstrate that catalytically inactive dCas9 expressed from the GBS chromosome can be used with a straightforward, plasmid-based, single guide RNA expression system to suppress transcription of specific GBS genes without potentially confounding off-target effects. We anticipate that this system will be useful for study of nonessential and essential gene roles in GBS physiology and pathogenesis.
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17
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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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18
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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: 0] [Impact Index Per Article: 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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19
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Ahmad E, Mitra A, Ahmed W, Mahapatra V, Hegde SR, Sala C, Cole ST, Nagaraja V. Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194923. [PMID: 36822574 DOI: 10.1016/j.bbagrm.2023.194923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
Intrinsic and Rho-dependent transcription termination mechanisms regulate gene expression and recycle RNA polymerase in bacteria. Both the modes are well studied in Escherichia coli, and a few other organisms. The understanding of Rho function is limited in most other bacteria including mycobacteria. Here, we highlight the dominance of Rho-dependent termination in mycobacteria and validate Rho as a key regulatory factor. The lower abundance of intrinsic terminators, high cellular levels of Rho, and its genome-wide association with a majority of transcriptionally active genes indicate the pronounced role of Rho-mediated termination in Mycobacterium tuberculosis (Mtb). Rho modulates the termination of RNA synthesis for both protein-coding and stable RNA genes in Mtb. Concordantly, the depletion of Rho in mycobacteria impact its growth and enhances the transcription read-through at 3' ends of the transcription units. We demonstrate that MtbRho is catalytically active in the presence of RNA with varied secondary structures. These properties suggest an evolutionary adaptation of Rho as the efficient and preponderant mode of transcription termination in mycobacteria.
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Affiliation(s)
- Ezaz Ahmad
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Anirban Mitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Varsha Mahapatra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, India
| | - Claudia Sala
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India.
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20
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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 DOI: 10.1016/j.tube.2022.102292] [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: 08/13/2022] [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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21
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Samukawa N, Yamaguchi T, Ozeki Y, Matsumoto S, Igarashi M, Kinoshita N, Hatano M, Tokudome K, Matsunaga S, Tomita S. An efficient CRISPR interference-based prediction method for synergistic/additive effects of novel combinations of anti-tuberculosis drugs. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748577 DOI: 10.1099/mic.0.001285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is treated by chemotherapy with multiple anti-TB drugs for a long period, spanning 6 months even in a standard course. In perspective, to prevent the emergence of antimicrobial resistance, novel drugs that act synergistically or additively in combination with major anti-TB drugs and, if possible, shorten the duration of TB therapy are needed. However, their combinatorial effect cannot be predicted until the lead identification phase of the drug development. Clustered regularly interspaced short palindromic repeats interference (CRISPRi) is a powerful genetic tool that enables high-throughput screening of novel drug targets. The development of anti-TB drugs promises to be accelerated by CRISPRi. This study determined whether CRISPRi could be applicable for predictive screening of the combinatorial effect between major anti-TB drugs and an inhibitor of a novel target. In the checkerboard assay, isoniazid killed Mycobacterium smegmatis synergistically or additively in combinations with rifampicin or ethambutol, respectively. The susceptibility to rifampicin and ethambutol was increased by knockdown of inhA, which encodes a target molecule of isoniazid. Additionally, knockdown of rpoB, which encodes a target molecule of rifampicin, increased the susceptibility to isoniazid and ethambutol, which act synergistically with rifampicin in the checkerboard assay. Moreover, CRISPRi could successfully predict the synergistic action of cyclomarin A, a novel TB drug candidate, with isoniazid or rifampicin. These results demonstrate that CRISPRi is a useful tool not only for drug target exploration but also for screening the combinatorial effects of novel combinations of anti-TB drugs. This study provides a rationale for anti-TB drug development using CRISPRi.
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Affiliation(s)
- Noriaki Samukawa
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Takehiro Yamaguchi
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Present address: Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Toyama 1-23-1, Shinjuku-ku, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, 60115, Indonesia
| | - Masayuki Igarashi
- Laboratory of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Naoko Kinoshita
- Laboratory of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Masaki Hatano
- Laboratory of Microbiology, Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, Tokyo, Japan
| | - Kentaro Tokudome
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Shinji Matsunaga
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Shuhei Tomita
- Department of Pharmacology, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
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22
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Armianinova DK, Karpov DS, Kotliarova MS, Goncharenko AV. Genetic Engineering in Mycobacteria. Mol Biol 2022. [DOI: 10.1134/s0026893322060036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Genetic tools for targeted modification of the mycobacterial genome contribute to the understanding of the physiology and virulence mechanisms of mycobacteria. Human and animal pathogens, such as the Mycobacterium tuberculosis complex, which causes tuberculosis, and M. leprae, which causes leprosy, are of particular importance. Genetic research opens up novel opportunities to identify and validate new targets for antibacterial drugs and to develop improved vaccines. Although mycobacteria are difficult to work with due to their slow growth rate and a limited possibility to transfer genetic information, significant progress has been made in developing genetic engineering methods for mycobacteria. The review considers the main approaches to changing the mycobacterial genome in a targeted manner, including homologous and site-specific recombination and use of the CRISPR/Cas system.
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23
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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: 0] [Impact Index Per Article: 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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24
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Intrinsic and Rho-dependent termination cooperate for efficient transcription termination at 3’ untranslated regions. Biochem Biophys Res Commun 2022; 628:123-132. [DOI: 10.1016/j.bbrc.2022.08.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/10/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022]
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25
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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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26
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Feng S, Liang L, Shen C, Lin D, Li J, Lyu L, Liang W, Zhong LL, Cook GM, Doi Y, Chen C, Tian GB. A CRISPR-guided mutagenic DNA polymerase strategy for the detection of antibiotic-resistant mutations in M. tuberculosis. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:354-367. [PMID: 35950213 PMCID: PMC9358013 DOI: 10.1016/j.omtn.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
A sharp increase in multidrug-resistant tuberculosis (MDR-TB) threatens human health. Spontaneous mutation in essential gene confers an ability of Mycobacterium tuberculosis resistance to anti-TB drugs. However, conventional laboratory strategies for identification and prediction of the mutations in this slowly growing species remain challenging. Here, by combining XCas9 nickase and the error-prone DNA polymerase A from M. tuberculosis, we constructed a CRISPR-guided DNA polymerase system, CAMPER, for effective site-directed mutagenesis of drug-target genes in mycobacteria. CAMPER was able to generate mutagenesis of all nucleotides at user-defined loci, and its bidirectional mutagenesis at nick sites allowed editing windows with lengths up to 80 nucleotides. Mutagenesis of drug-targeted genes in Mycobacterium smegmatis and M. tuberculosis with this system significantly increased the fraction of the antibiotic-resistant bacterial population to a level approximately 60- to 120-fold higher than that in unedited cells. Moreover, this strategy could facilitate the discovery of the mutation conferring antibiotic resistance and enable a rapid verification of the growth phenotype-mutation genotype association. Our data demonstrate that CAMPER facilitates targeted mutagenesis of genomic loci and thus may be useful for broad functions such as resistance prediction and development of novel TB therapies.
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27
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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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28
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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: 7] [Impact Index Per Article: 3.5] [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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29
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Wan X, Li Q, Olsen RH, Meng H, Zhang Z, Wang J, Zheng H, Li L, Shi L. Engineering a CRISPR interference system targeting AcrAB-TolC efflux pump to prevent multidrug resistance development in Escherichia coli. J Antimicrob Chemother 2022; 77:2158-2166. [PMID: 35642356 DOI: 10.1093/jac/dkac166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES We engineered a CRISPR interference (CRISPRi) system targeting the AcrAB-TolC efflux pump to prevent MDR development in Escherichia coli. METHODS Nine specific single-guide RNAs (sgRNAs) were designed to target the components of the AcrAB-TolC efflux pump, namely AcrA, AcrB and TolC. A total of thirteen CRISPRi recombinant plasmids were constructed with single or clustered sgRNAs. The transcriptional levels of the target genes, MICs of multiple antibiotics and biofilm formation in each CRISPRi strain were tested. RESULTS The CRISPRi system expressing sgRNA clusters targeting acrB and tolC simultaneously exhibited the highest inhibitory effect on AcrAB-TolC efflux pump activity in E. coli HB101, with 78.3%, 90.0% and 65.4% inhibition rates on the transcriptional levels of acrA, acrB and tolC, respectively. The CRISPRi system resulted in ∼2-, ∼8- and 16-fold increased susceptibility to rifampicin, erythromycin and tetracycline, respectively. In addition, the constructed CRISPRi system reduced biofilm formation with inhibition rates in the range of 11.2% to 58.2%. CONCLUSIONS To the best of our knowledge, this is the first report on the construction of an inducible CRISPRi system targeting the AcrAB-TolC efflux pump to prevent MDR development in E. coli. This study provides insights for future regulation and manipulation of AcrAB-TolC activity and bacterial MDR by a CRISPRi system.
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Affiliation(s)
- Xiulin Wan
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingyang Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Zhigang Zhang
- State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
| | - Junlin Wang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Hanyu Zheng
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China.,State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
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30
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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: 70] [Impact Index Per Article: 35.0] [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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31
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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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32
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Hogan AM, Cardona ST. Gradients in gene essentiality reshape antibacterial research. FEMS Microbiol Rev 2022; 46:fuac005. [PMID: 35104846 PMCID: PMC9075587 DOI: 10.1093/femsre/fuac005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
Essential genes encode the processes that are necessary for life. Until recently, commonly applied binary classifications left no space between essential and non-essential genes. In this review, we frame bacterial gene essentiality in the context of genetic networks. We explore how the quantitative properties of gene essentiality are influenced by the nature of the encoded process, environmental conditions and genetic background, including a strain's distinct evolutionary history. The covered topics have important consequences for antibacterials, which inhibit essential processes. We argue that the quantitative properties of essentiality can thus be used to prioritize antibacterial cellular targets and desired spectrum of activity in specific infection settings. We summarize our points with a case study on the core essential genome of the cystic fibrosis pathobiome and highlight avenues for targeted antibacterial development.
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Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
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33
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Moraes L, Trentini MM, Fousteris D, Eto SF, Chudzinski-Tavassi AM, Leite LCDC, Kanno AI. CRISPR/Cas9 Approach to Generate an Auxotrophic BCG Strain for Unmarked Expression of LTAK63 Adjuvant: A Tuberculosis Vaccine Candidate. Front Immunol 2022; 13:867195. [PMID: 35432328 PMCID: PMC9005855 DOI: 10.3389/fimmu.2022.867195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/09/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis is one of the deadliest infectious diseases and a huge healthcare burden in many countries. New vaccines, including recombinant BCG-based candidates, are currently under evaluation in clinical trials. Our group previously showed that a recombinant BCG expressing LTAK63 (rBCG-LTAK63), a genetically detoxified subunit A of heat-labile toxin (LT) from Escherichia coli, induces improved protection against Mycobacterium tuberculosis (Mtb) in mouse models. This construct uses a traditional antibiotic resistance marker to enable heterologous expression. In order to avoid the use of these markers, not appropriate for human vaccines, we used CRISPR/Cas9 to generate unmarked mutations in the lysA gene, thus obtaining a lysine auxotrophic BCG strain. A mycobacterial vector carrying lysA and ltak63 gene was used to complement the auxotrophic BCG which co-expressed the LTAK63 antigen (rBCGΔ-LTAK63) at comparable levels to the original construct. The intranasal challenge with Mtb confirmed the superior protection induced by rBCGΔ-LTAK63 compared to wild-type BCG. Furthermore, mice immunized with rBCGΔ-LTAK63 showed improved lung function. In this work we showed the practical application of CRISPR/Cas9 in the tuberculosis vaccine development field.
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Affiliation(s)
- Luana Moraes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil.,Programa de Pós-Graduação Interunidades em Biotecnologia Universidade de São Paulo - Instituto de Pesquisas Tecnológicas - Instituto Butantan (USP-IPT-IB), São Paulo, Brazil
| | | | - Dimitrios Fousteris
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil.,UnivLyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Silas Fernandes Eto
- Development and Innovation Laboratory, Instituto Butantan, São Paulo, Brazil
| | - Ana Marisa Chudzinski-Tavassi
- Development and Innovation Laboratory, Instituto Butantan, São Paulo, Brazil.,Center of Excellence in New Target Discovery (CENTD) Special Laboratory, Instituto Butantan, São Paulo, Brazil
| | | | - Alex Issamu Kanno
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, Brazil
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34
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Kon OM, Beare N, Connell D, Damato E, Gorsuch T, Hagan G, Perrin F, Petrushkin H, Potter J, Sethi C, Stanford M. BTS clinical statement for the diagnosis and management of ocular tuberculosis. BMJ Open Respir Res 2022; 9:9/1/e001225. [PMID: 35379660 PMCID: PMC9021811 DOI: 10.1136/bmjresp-2022-001225] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/03/2022] Open
Abstract
The BTS clinical statement for the diagnosis and management of ocular tuberculosis (TB) draws on the expertise of both TB and and ophthalmic specialists to outline the current understanding of disease pathogenesis, diagnosis and management in adults. Published literature lacks high-quality evidence to inform clinical practice and there is also a paucity of data from animal models to elucidate mechanisms of disease. However, in order to improve and standardise patient care, this statement provides consensus points with the currently available data and agreed best practice.
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Affiliation(s)
- Onn Min Kon
- Chest and Allergy Clinic, Imperial College Healthcare NHS Trust, London, UK
- National Heart and Lung Institute, Imperial College, London, UK
| | - Nicholas Beare
- St Paul's Eye Unit, Liverpool University Hospitals, Liverpool, UK
- Department of Eye and Vision Research, University of Liverpool, Liverpool, UK
| | - David Connell
- Respiratory Medicine, Ninewells Hospital and Medical School, NHS Tayside, Dundee, UK
| | - Erika Damato
- Ophthalmology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Thomas Gorsuch
- Department of Respiratory Medicine, Manchester Royal Infirmary, Manchester, UK
| | - Guy Hagan
- Respiratory Medicine, City Hospital, Birmingham, UK
| | - Felicity Perrin
- Department of Respiratory Medicine, King's College Hospital NHS Foundation Trust, London, UK
| | - Harry Petrushkin
- Ophthalmology, Moorfields Eye Hospital City Road Campus, London, UK
| | - Jessica Potter
- Respiratory Medicine, North Middlesex University Hospital NHS Trust, London, UK
| | - Charanjit Sethi
- Ophthalmology, Hillingdon Hospitals NHS Foundation Trust, Uxbridge, UK
| | - Miles Stanford
- Ophthalmology, Guy's and St Thomas' Hospitals NHS Trust, London, UK
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35
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Tripathi A, Anand K, Das M, O'Niel RA, P S S, Thakur C, R L RR, Rajmani RS, Chandra N, Laxman S, Singh A. Mycobacterium tuberculosis requires SufT for Fe-S cluster maturation, metabolism, and survival in vivo. PLoS Pathog 2022; 18:e1010475. [PMID: 35427399 PMCID: PMC9045647 DOI: 10.1371/journal.ppat.1010475] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/27/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Iron-sulfur (Fe-S) cluster proteins carry out essential cellular functions in diverse organisms, including the human pathogen Mycobacterium tuberculosis (Mtb). The mechanisms underlying Fe-S cluster biogenesis are poorly defined in Mtb. Here, we show that Mtb SufT (Rv1466), a DUF59 domain-containing essential protein, is required for the Fe-S cluster maturation. Mtb SufT homodimerizes and interacts with Fe-S cluster biogenesis proteins; SufS and SufU. SufT also interacts with the 4Fe-4S cluster containing proteins; aconitase and SufR. Importantly, a hyperactive cysteine in the DUF59 domain mediates interaction of SufT with SufS, SufU, aconitase, and SufR. We efficiently repressed the expression of SufT to generate a SufT knock-down strain in Mtb (SufT-KD) using CRISPR interference. Depleting SufT reduces aconitase's enzymatic activity under standard growth conditions and in response to oxidative stress and iron limitation. The SufT-KD strain exhibited defective growth and an altered pool of tricarboxylic acid cycle intermediates, amino acids, and sulfur metabolites. Using Seahorse Extracellular Flux analyzer, we demonstrated that SufT depletion diminishes glycolytic rate and oxidative phosphorylation in Mtb. The SufT-KD strain showed defective survival upon exposure to oxidative stress and nitric oxide. Lastly, SufT depletion reduced the survival of Mtb in macrophages and attenuated the ability of Mtb to persist in mice. Altogether, SufT assists in Fe-S cluster maturation and couples this process to bioenergetics of Mtb for survival under low and high demand for Fe-S clusters.
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Affiliation(s)
- Ashutosh Tripathi
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Kushi Anand
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Mayashree Das
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Ruchika Annie O'Niel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Sabarinath P S
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Raghunatha Reddy R L
- Regional Horticultural Research and Extension Centre (RHREK), GKVK, Bengaluru, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Amit Singh
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
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A Feedback Regulatory Loop Containing McdR and WhiB2 Controls Cell Division and DNA Repair in Mycobacteria. mBio 2022; 13:e0334321. [PMID: 35357209 PMCID: PMC9040748 DOI: 10.1128/mbio.03343-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell division must be coordinated with DNA repair, which is strictly regulated in response to different drugs and environmental stresses in bacteria. However, the mechanisms by which mycobacteria orchestrate these two processes remain largely uncharacterized. Here, we report a regulatory loop between two essential mycobacterial regulators, McdR (Rv1830) and WhiB2, in coordinating the processes of cell division and DNA repair. McdR inhibits cell division-associated whiB2 expression by binding to the AATnACAnnnnTGTnATT motif in the promoter region. Furthermore, McdR overexpression simultaneously activates imuAB and dnaE2 expression to promote error-prone DNA repair, which facilitates genetic adaptation to stress conditions. Through a feedback mechanism, WhiB2 activates mcdR expression by binding to the cGACACGc motif in the promoter region. Importantly, analyses of mutations in clinical Mycobacterium tuberculosis strains indicate that disruption of this McdR-WhiB2 feedback regulatory loop influences expression of both cell growth- and DNA repair-associated genes, which further supports the contribution of McdR-WhiB2 regulatory loop in regulating mycobacterial cell growth and drug resistance. This highly conserved feedback regulatory loop provides fresh insight into the link between mycobacterial cell growth control and stress responses. IMPORTANCE Drug-resistant M. tuberculosis poses a threat to the control and prevention of tuberculosis (TB) worldwide. Thus, there is a need to identify the mechanisms enabling M. tuberculosis to adapt and grow under drug-induced stress. Rv1830 has been shown to be associated with drug resistance in M. tuberculosis, but its mechanisms have not yet been elucidated. Here, we reveal a regulatory role of Rv1830, which coordinates cell division and DNA repair in mycobacteria, and rename it McdR (mycobacterial cell division regulator). An increase in McdR levels represses the expression of cell division-associated whiB2 but activates the DNA repair-associated, error-prone enzymes ImuA/B and DnaE2, which in turn facilitates adaptation to stress responses and drug resistance. Furthermore, WhiB2 activates the transcription of mcdR to form a conserved regulatory loop. These data provide new insights into the mechanisms controlling mycobacterial cell growth and stress responses.
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Dubey AK, Kumar Gupta V, Kujawska M, Orive G, Kim NY, Li CZ, Kumar Mishra Y, Kaushik A. Exploring nano-enabled CRISPR-Cas-powered strategies for efficient diagnostics and treatment of infectious diseases. JOURNAL OF NANOSTRUCTURE IN CHEMISTRY 2022; 12:833-864. [PMID: 35194511 PMCID: PMC8853211 DOI: 10.1007/s40097-022-00472-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/23/2022] [Indexed: 05/02/2023]
Abstract
Biomedical researchers have subsequently been inspired the development of new approaches for precisely changing an organism's genomic DNA in order to investigate customized diagnostics and therapeutics utilizing genetic engineering techniques. Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR) is one such technique that has emerged as a safe, targeted, and effective pharmaceutical treatment against a wide range of disease-causing organisms, including bacteria, fungi, parasites, and viruses, as well as genetic abnormalities. The recent discovery of very flexible engineered nucleic acid binding proteins has changed the scientific area of genome editing in a revolutionary way. Since current genetic engineering technique relies on viral vectors, issues about immunogenicity, insertional oncogenesis, retention, and targeted delivery remain unanswered. The use of nanotechnology has the potential to improve the safety and efficacy of CRISPR/Cas9 component distribution by employing tailored polymeric nanoparticles. The combination of two (CRISPR/Cas9 and nanotechnology) offers the potential to open new therapeutic paths. Considering the benefits, demand, and constraints, the goal of this research is to acquire more about the biology of CRISPR technology, as well as aspects of selective and effective diagnostics and therapies for infectious illnesses and other metabolic disorders. This review advocated combining nanomedicine (nanomedicine) with a CRISPR/Cas enabled sensing system to perform early-stage diagnostics and selective therapy of specific infectious disorders. Such a Nano-CRISPR-powered nanomedicine and sensing system would allow for successful infectious illness control, even on a personal level. This comprehensive study also discusses the current obstacles and potential of the predicted technology. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40097-022-00472-7.
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Affiliation(s)
- Ankit Kumar Dubey
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, 600036, Chennai, Tamil Nadu India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Małgorzata Kujawska
- Department of Toxicology, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznań, Poland
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- CIBER Bioengineering, Biomaterials and Nanomedicine (CIBERBBN), Institute of Health Carlos III, Madrid, Spain
- Bioaraba Health Research Institute, Nanobiocel Research Group, Vitoria-Gasteiz, Spain
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria-Gasteiz, Spain
- Singapore Eye Research Institute, Singapore, Singapore
| | - Nam-Young Kim
- Department of Electronics Engineering, RFIC Bio Centre, NDAC Centre, RFIC Bio Centre, NDAC Centre, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul, 01897 South Korea
| | - Chen-zhong Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112 USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112 USA
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alison 2, 6400 Sønderborg, Denmark
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Health System Engineering, Department of Natural Sciences, Florida Polytechnic University, Lakeland, FL-33805 USA
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Li X, Chen F, Liu X, Xiao J, Andongma BT, Tang Q, Cao X, Chou SH, Galperin MY, He J. Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response. eLife 2022; 11:73347. [PMID: 35080493 PMCID: PMC8820732 DOI: 10.7554/elife.73347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/25/2022] [Indexed: 12/02/2022] Open
Abstract
Under starvation conditions, bacteria tend to slow down their translation rate by reducing rRNA synthesis, but the way they accomplish that may vary in different bacteria. In Mycobacterium species, transcription of rRNA is activated by the RNA polymerase (RNAP) accessory transcription factor CarD, which interacts directly with RNAP to stabilize the RNAP-promoter open complex formed on rRNA genes. The functions of CarD have been extensively studied, but the mechanisms that control its expression remain obscure. Here, we report that the level of CarD was tightly regulated when mycobacterial cells switched from nutrient-rich to nutrient-deprived conditions. At the translational level, an antisense RNA of carD (AscarD) was induced in a SigF-dependent manner to bind with carD mRNA and inhibit CarD translation, while at the post-translational level, the residual intracellular CarD was quickly degraded by the Clp protease. AscarD thus worked synergistically with Clp protease to decrease the CarD level to help mycobacterial cells cope with the nutritional stress. Altogether, our work elucidates the regulation mode of CarD and delineates a new mechanism for the mycobacterial starvation response, which is important for the adaptation and persistence of mycobacterial pathogens in the host environment.
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Affiliation(s)
- Xinfeng Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fang Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoyu Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinfeng Xiao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Binda T Andongma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing Tang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Cao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shan-Ho Chou
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jin He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Perveen S, Sharma R. Screening approaches and therapeutic targets: The two driving wheels of tuberculosis drug discovery. Biochem Pharmacol 2022; 197:114906. [PMID: 34990594 DOI: 10.1016/j.bcp.2021.114906] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease, infecting a quarter of world's population. Drug resistant TB further exacerbates the grim scenario of the drying TB drug discovery pipeline. The limited arsenal to fight TB presses the need for thorough efforts for identifying promising hits to combat the disease. The review highlights the efforts in the field of tuberculosis drug discovery, with an emphasis on massive drug screening campaigns for identifying novel hits against Mtb in both industry and academia. As an intracellular pathogen, mycobacteria reside in a complicated intracellular environment with multiple factors at play. Here, we outline various strategies employed in an effort to mimic the intracellular milieu for bringing the screening models closer to the actual settings. The review also focuses on the novel targets and pathways that could aid in target-based drug discovery in TB. The recent high throughput screening efforts resulting in the identification of potent hits against Mtb has been summarized in this article. There is a pressing need for effective screening strategies and approaches employing innovative tools and recent technologies; including nanotechnology, gene-editing tools such as CRISPR-cas system, host-directed bacterial killing and high content screening to augment the TB drug discovery pipeline with safer and shorter drug regimens.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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40
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Gibson AJ, Passmore IJ, Faulkner V, Xia D, Nobeli I, Stiens J, Willcocks S, Clark TG, Sobkowiak B, Werling D, Villarreal-Ramos B, Wren BW, Kendall SL. Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq. Front Vet Sci 2021; 8:760717. [PMID: 35004921 PMCID: PMC8739905 DOI: 10.3389/fvets.2021.760717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Members of the Mycobacterium tuberculosis complex (MTBC) show distinct host adaptations, preferences and phenotypes despite being >99% identical at the nucleic acid level. Previous studies have explored gene expression changes between the members, however few studies have probed differences in gene essentiality. To better understand the functional impacts of the nucleic acid differences between Mycobacterium bovis and Mycobacterium tuberculosis, we used the Mycomar T7 phagemid delivery system to generate whole genome transposon libraries in laboratory strains of both species and compared the essentiality status of genes during growth under identical in vitro conditions. Libraries contained insertions in 54% of possible TA sites in M. bovis and 40% of those present in M. tuberculosis, achieving similar saturation levels to those previously reported for the MTBC. The distributions of essentiality across the functional categories were similar in both species. 527 genes were found to be essential in M. bovis whereas 477 genes were essential in M. tuberculosis and 370 essential genes were common in both species. CRISPRi was successfully utilised in both species to determine the impacts of silencing genes including wag31, a gene involved in peptidoglycan synthesis and Rv2182c/Mb2204c, a gene involved in glycerophospholipid metabolism. We observed species specific differences in the response to gene silencing, with the inhibition of expression of Mb2204c in M. bovis showing significantly less growth impact than silencing its orthologue (Rv2182c) in M. tuberculosis. Given that glycerophospholipid metabolism is a validated pathway for antimicrobials, our observations suggest that target vulnerability in the animal adapted lineages cannot be assumed to be the same as the human counterpart. This is of relevance for zoonotic tuberculosis as it implies that the development of antimicrobials targeting the human adapted lineage might not necessarily be effective against the animal adapted lineage. The generation of a transposon library and the first reported utilisation of CRISPRi in M. bovis will enable the use of these tools to further probe the genetic basis of survival under disease relevant conditions.
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Affiliation(s)
- Amanda J. Gibson
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Ian J. Passmore
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Valwynne Faulkner
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Dong Xia
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ben Sobkowiak
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dirk Werling
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | | | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sharon L. Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom,*Correspondence: Sharon L. Kendall
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41
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Reprogramming Mycobacterium tuberculosis CRISPR System for Gene Editing and Genome-wide RNA Interference Screening. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 20:1180-1196. [PMID: 34923124 DOI: 10.1016/j.gpb.2021.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/29/2020] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), which is still the leading cause of mortality from a single infectious disease worldwide. The development of novel anti-TB drugs and vaccines is severely hampered by the complicated and time-consuming genetic manipulation techniques for M. tuberculosis. Here, we harnessed an endogenous type III-A CRISPR/Cas10 system of M. tuberculosis for efficient gene editing and RNA interference (RNAi). This simple and easy method only needs to transform a single mini-CRISPR array plasmid, thus avoiding the introduction of exogenous protein and minimizing proteotoxicity. We demonstrated that M. tuberculosis genes can be efficiently and specifically knocked in/out by this system as confirmed by DNA high-throughput sequencing. This system was further applied to single- and multiple-gene RNAi. Moreover, we successfully performed genome-wide RNAi screening to identify M. tuberculosis genes regulating in vitro and intracellular growth. This system can be extensively used for exploring the functional genomics of M. tuberculosis and facilitate the development of novel anti-TB drugs and vaccines.
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42
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Novel gene similar to nitrite reductase (NO forming) plays potentially important role in the latency of tuberculosis. Sci Rep 2021; 11:19813. [PMID: 34615967 PMCID: PMC8494734 DOI: 10.1038/s41598-021-99346-1] [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: 02/27/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
The development of the latent phenotype of Mycobacterium tuberculosis (Mtb) in the human lungs is the major hurdle to eradicate Tuberculosis. We recently reported that exposure to nitrite (10 mM) for six days under in vitro aerobic conditions completely transforms the bacilli into a viable but non-cultivable phenotype. Herein, we show that nitrite (beyond 5 mM) treated Mtb produces nitric oxide (NO) within the cell in a dose-dependent manner. Our search for the conserved sequence of NO synthesizing enzyme in the bacterial system identified MRA2164 and MRA0854 genes, of which the former was found to be significantly up regulated after nitrite exposure. In addition, the purified recombinant MRA2164 protein shows significant nitrite dependent NO synthesizing activity. The knockdown of the MRA2164 gene at mRNA level expression resulted in a significantly reduced NO level compared to the wild type bacilli with a simultaneous return of its replicative capability. Therefore, this study first time reports that nitrite induces dormancy in Mtb cells through induced expression of the MRA2164 gene and productions of NO as a mechanism for maintaining non-replicative stage in Mtb. This observation could help to control the Tuberculosis disease, especially the latent phenotype of the bacilli.
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43
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Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell 2021; 184:4579-4592.e24. [PMID: 34297925 PMCID: PMC8382161 DOI: 10.1016/j.cell.2021.06.033] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/13/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Antibacterial agents target the products of essential genes but rarely achieve complete target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic approaches fails to discern the most attractive bacterial targets: those whose incomplete inhibition results in major fitness costs. In contrast, gene "vulnerability" is a continuous, quantifiable trait that relates the magnitude of gene inhibition to the effect on bacterial fitness. We developed a CRISPR interference-based functional genomics method to systematically titrate gene expression in Mycobacterium tuberculosis (Mtb) and monitor fitness outcomes. We identified highly vulnerable genes in various processes, including novel targets unexplored for drug discovery. Equally important, we identified invulnerable essential genes, potentially explaining failed drug discovery efforts. Comparison of vulnerability between the reference and a hypervirulent Mtb isolate revealed incomplete conservation of vulnerability and that differential vulnerability can predict differential antibacterial susceptibility. Our results quantitatively redefine essential bacterial processes and identify high-value targets for drug development.
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Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sophie Lavalette
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joshua B Wallach
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.
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Schuller M, Butler RE, Ariza A, Tromans-Coia C, Jankevicius G, Claridge TDW, Kendall SL, Goh S, Stewart GR, Ahel I. Molecular basis for DarT ADP-ribosylation of a DNA base. Nature 2021; 596:597-602. [PMID: 34408320 DOI: 10.1038/s41586-021-03825-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
ADP-ribosyltransferases use NAD+ to catalyse substrate ADP-ribosylation1, and thereby regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria2-4. Reversible ADP-ribosylation has traditionally been considered a protein-specific modification5, but recent in vitro studies have suggested nucleic acids as targets6-9. Here we present evidence that specific, reversible ADP-ribosylation of DNA on thymidine bases occurs in cellulo through the DarT-DarG toxin-antitoxin system, which is found in a variety of bacteria (including global pathogens such as Mycobacterium tuberculosis, enteropathogenic Escherichia coli and Pseudomonas aeruginosa)10. We report the structure of DarT, which identifies this protein as a diverged member of the PARP family. We provide a set of high-resolution structures of this enzyme in ligand-free and pre- and post-reaction states, which reveals a specialized mechanism of catalysis that includes a key active-site arginine that extends the canonical ADP-ribosyltransferase toolkit. Comparison with PARP-HPF1, a well-established DNA repair protein ADP-ribosylation complex, offers insights into how the DarT class of ADP-ribosyltransferases evolved into specific DNA-modifying enzymes. Together, our structural and mechanistic data provide details of this PARP family member and contribute to a fundamental understanding of the ADP-ribosylation of nucleic acids. We also show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin (functioning as a noncanonical DNA repair factor) are used not only for targeted DNA damage to induce toxicity, but also as a signalling strategy for cellular processes. Using M. tuberculosis as an exemplar, we show that DarT-DarG regulates growth by ADP-ribosylation of DNA at the origin of chromosome replication.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel E Butler
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Biozentrum, University of Basel, Basel, Switzerland
| | - Tim D W Claridge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Sharon L Kendall
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Shan Goh
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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45
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Nadolinskaia NI, Zamakhaev MV, Shumkov MS, Armianinova DK, Karpov DS, Goncharenko AV. CRISPR Interference of Adenylate Cyclases from Mycobacterium tuberculosis. APPL BIOCHEM MICRO+ 2021; 57:421-425. [PMID: 34334794 PMCID: PMC8315726 DOI: 10.1134/s0003683821040128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/20/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
This work describes a modification of the pRH2521 vector of the pRH2502/pRH2521 system for CRISPR-dCas9-mediated RNA interference. The modification enabled an increase in the cloning efficiency of guide RNA spacers. The ability of the modified pRH2502/pRH2521 system to suppress the transcription of certain genes was evaluated with the use of genes of Mycobacterium tuberculosis adenylate cyclases. The results revealed the limitations of the pRH2502/pRH2521 system for CRISPR interference associated with the probability of the detection of a protospacer adjacent motif (PAM) in the gene promoter region.
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Affiliation(s)
- N I Nadolinskaia
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - M V Zamakhaev
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - M S Shumkov
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - D K Armianinova
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
| | - D S Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Goncharenko
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 119071 Moscow, Russia
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46
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Fleck N, Grundner C. A Cas12a-based CRISPR interference system for multigene regulation in mycobacteria. J Biol Chem 2021; 297:100990. [PMID: 34298016 PMCID: PMC8363830 DOI: 10.1016/j.jbc.2021.100990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
Mycobacteria are responsible for a heavy global disease burden, but their relative genetic intractability has long frustrated research efforts. The introduction of clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) has made gene repression in mycobacteria much more efficient, but limitations of the prototypical Cas9-based platform, for example, in multigene regulation, remain. Here, we introduce an alternative CRISPRi platform for mycobacteria that is based on the minimal type V Cas12a enzyme in combination with synthetic CRISPR arrays. This system is simple, tunable, reversible, can efficiently regulate essential genes and multiple genes simultaneously, and works as efficiently in infected macrophages as it does in vitro. Together, Cas12a-based CRISPRi provides a facile tool to probe higher-order genetic interactions in mycobacteria including Mycobacterium tuberculosis (Mtb), which will enable the development of synthetically lethal drug targets and the study of genes conditionally essential during infection.
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Affiliation(s)
- Neil Fleck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA; Department of Pediatrics, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA.
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47
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Marques-Neto LM, Piwowarska Z, Kanno AI, Moraes L, Trentini MM, Rodriguez D, Silva JLSC, Leite LCC. Thirty years of recombinant BCG: new trends for a centenary vaccine. Expert Rev Vaccines 2021; 20:1001-1011. [PMID: 34224293 DOI: 10.1080/14760584.2021.1951243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Global perception of the potential for Bacille Calmette-Guérin (BCG), and consequently recombinant BCG (rBCG), in a variety of prophylactic and therapeutic applications has been increasing. A century of information on BCG, and three decades of experience with rBCG, has generated solid knowledge in this field.Area covered: Here, we review the current state of knowledge of BCG and rBCG development. Molecular tools have facilitated the expression of a variety of molecules in BCG, with the aim of improving its efficacy as a tuberculosis vaccine, generating polyvalent vaccines against other pathogens, including viruses, bacteria, and parasites, and developing immunotherapy approaches against noninvasive bladder cancer. BCG's recently appraised heterologous effects and prospects for expanding its application to other diseases are also addressed.Expert opinion: There are high expectations for new tuberculosis vaccines currently undergoing advanced clinical trials, which could change the prospects of the field. Systems biology could reveal effective biomarkers of protection, which would greatly support vaccine development. The development of appropriate large-scale production processes would further support implementation of new vaccines and rBCG products. The next few years should consolidate the broader applications of BCG and produce insights into improvements using the recombinant BCG technology.
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Affiliation(s)
| | - Zuzanna Piwowarska
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil.,UnivLyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Alex I Kanno
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Luana Moraes
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil.,Programa De Pós-Graduação Interunidades Em Biotecnologia USP-Instituto Butantan-IPT, São Paulo, Brazil
| | - Monalisa M Trentini
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Dunia Rodriguez
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Jose L S C Silva
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil.,Programa De Pós-Graduação Interunidades Em Biotecnologia USP-Instituto Butantan-IPT, São Paulo, Brazil
| | - Luciana C C Leite
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
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48
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Anand K, Tripathi A, Shukla K, Malhotra N, Jamithireddy AK, Jha RK, Chaudhury SN, Rajmani RS, Ramesh A, Nagaraja V, Gopal B, Nagaraju G, Narain Seshayee AS, Singh A. Mycobacterium tuberculosis SufR responds to nitric oxide via its 4Fe-4S cluster and regulates Fe-S cluster biogenesis for persistence in mice. Redox Biol 2021; 46:102062. [PMID: 34392160 PMCID: PMC8371249 DOI: 10.1016/j.redox.2021.102062] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
The persistence of Mycobacterium tuberculosis (Mtb) is a major problem in managing tuberculosis (TB). Host-generated nitric oxide (NO) is perceived as one of the signals by Mtb to reprogram metabolism and respiration for persistence. However, the mechanisms involved in NO sensing and reorganizing Mtb's physiology are not fully understood. Since NO damages iron-sulfur (Fe-S) clusters of essential enzymes, the mechanism(s) involved in regulating Fe-S cluster biogenesis could help Mtb persist in host tissues. Here, we show that a transcription factor SufR (Rv1460) senses NO via its 4Fe-4S cluster and promotes persistence of Mtb by mobilizing the Fe-S cluster biogenesis system; suf operon (Rv1460-Rv1466). Analysis of anaerobically purified SufR by UV-visible spectroscopy, circular dichroism, and iron-sulfide estimation confirms the presence of a 4Fe-4S cluster. Atmospheric O2 and H2O2 gradually degrade the 4Fe-4S cluster of SufR. Furthermore, electron paramagnetic resonance (EPR) analysis demonstrates that NO directly targets SufR 4Fe-4S cluster by forming a protein-bound dinitrosyl-iron-dithiol complex. DNase I footprinting, gel-shift, and in vitro transcription assays confirm that SufR directly regulates the expression of the suf operon in response to NO. Consistent with this, RNA-sequencing of MtbΔsufR demonstrates deregulation of the suf operon under NO stress. Strikingly, NO inflicted irreversible damage upon Fe-S clusters to exhaust respiratory and redox buffering capacity of MtbΔsufR. Lastly, MtbΔsufR failed to recover from a NO-induced non-growing state and displayed persistence defect inside immune-activated macrophages and murine lungs in a NO-dependent manner. Data suggest that SufR is a sensor of NO that supports persistence by reprogramming Fe-S cluster metabolism and bioenergetics.
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Affiliation(s)
- Kushi Anand
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Ashutosh Tripathi
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Kaustubh Shukla
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Nitish Malhotra
- National Centre for Biological Science, Bangalore, 560065, India
| | | | - Rajiv Kumar Jha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Arati Ramesh
- National Centre for Biological Science, Bangalore, 560065, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | | | - Amit Singh
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India; Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.
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49
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Direct Interaction of Polar Scaffolding Protein Wag31 with Nucleoid-Associated Protein Rv3852 Regulates Its Polar Localization. Cells 2021; 10:cells10061558. [PMID: 34203111 PMCID: PMC8233713 DOI: 10.3390/cells10061558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/12/2021] [Accepted: 06/16/2021] [Indexed: 11/25/2022] Open
Abstract
Rv3852 is a unique nucleoid-associated protein (NAP) found exclusively in Mycobacterium tuberculosis (Mtb) and closely related species. Although annotated as H-NS, we showed previously that it is very different from H-NS in its properties and is distinct from other NAPs, anchoring to cell membrane by virtue of possessing a C-terminal transmembrane helix. Here, we investigated the role of Rv3852 in Mtb in organizing architecture or synthesis machinery of cell wall by protein–protein interaction approach. We demonstrated a direct physical interaction of Rv3852 with Wag31, an important cell shape and cell wall integrity determinant essential in Mtb. Wag31 localizes to the cell poles and possibly acts as a scaffold for cell wall synthesis proteins, resulting in polar cell growth in Mtb. Ectopic expression of Rv3852 in M. smegmatis resulted in its interaction with Wag31 orthologue DivIVAMsm. Binding of the NAP to Wag31 appears to be necessary for fine-tuning Wag31 localization to the cell poles, enabling complex cell wall synthesis in Mtb. In Rv3852 knockout background, Wag31 is mislocalized resulting in disturbed nascent peptidoglycan synthesis, suggesting that the NAP acts as a driver for localization of Wag31 to the cell poles. While this novel association between these two proteins presents one of the mechanisms to structure the elaborate multi-layered cell envelope of Mtb, it also exemplifies a new function for a NAP in mycobacteria.
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50
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Feng S, Hong Z, Zhang G, Li J, Tian GB, Zhou H, Huang X. Mycobacterium PPE31 Contributes to Host Cell Death. Front Cell Infect Microbiol 2021; 11:629836. [PMID: 33928042 PMCID: PMC8078103 DOI: 10.3389/fcimb.2021.629836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/23/2021] [Indexed: 12/03/2022] Open
Abstract
Genome scale mutagenesis identifies many genes required for mycobacterial infectivity and survival, but their contributions and mechanisms of action within the host are poorly understood. Using CRISPR interference, we created a knockdown of ppe31Mm gene in Mycobacterium marinum (M. marinum), which reduced the resistance to acid medium. To further explore the function of PPE31, the ppe31 mutant strain was generated in M. marinum and Mycobacterium tuberculosis (M. tuberculosis), respectively. Macrophages infected with the ppe31Mm mutant strain caused a reduced inflammatory mediator expressions. In addition, macrophages infected with M. marinum Δppe31Mm had decreased host cell death dependent on JNK signaling. Consistent with these results, deletion of ppe31Mtb from M. tuberculosis increased the sensitivity to acid medium and reduced cell death in macrophages. Furthermore, we demonstrate that both ppe31 mutants from M. marinum and M. tuberculosis resulted in reduced survival in macrophages, and the survivability of M. marinum was deceased in zebrafish due to loss of ppe31Mm. Our findings confirm that PPE31 as a virulence associated factor that modulates innate immune responses to mycobacterial infection.
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Affiliation(s)
- Siyuan Feng
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Zhongsi Hong
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
| | - Guoliang Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Jiachen Li
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Guo-Bao Tian
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Haibo Zhou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Xi Huang
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.,The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China.,Sino-French Hoffmann Institute of Immunology, College of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
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