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Bei C, Zhu J, Culviner PH, Gan M, Rubin EJ, Fortune SM, Gao Q, Liu Q. Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis. Nat Commun 2024; 15:3088. [PMID: 38600064 PMCID: PMC11006872 DOI: 10.1038/s41467-024-47410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
Transcriptional regulation is a critical adaptive mechanism that allows bacteria to respond to changing environments, yet the concept of transcriptional plasticity (TP) - the variability of gene expression in response to environmental changes - remains largely unexplored. In this study, we investigate the genome-wide TP profiles of Mycobacterium tuberculosis (Mtb) genes by analyzing 894 RNA sequencing samples derived from 73 different environmental conditions. Our data reveal that Mtb genes exhibit significant TP variation that correlates with gene function and gene essentiality. We also find that critical genetic features, such as gene length, GC content, and operon size independently impose constraints on TP, beyond trans-regulation. By extending our analysis to include two other Mycobacterium species -- M. smegmatis and M. abscessus -- we demonstrate a striking conservation of the TP landscape. This study provides a comprehensive understanding of the TP exhibited by mycobacteria genes, shedding light on this significant, yet understudied, genetic feature encoded in bacterial genomes.
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Affiliation(s)
- Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Peter H Culviner
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mingyu Gan
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province, China.
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Bei C, Zhu J, Culviner PH, Rubin EJ, Fortune SM, Gao Q, Liu Q. Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis. RESEARCH SQUARE 2023:rs.3.rs-3303807. [PMID: 37790329 PMCID: PMC10543248 DOI: 10.21203/rs.3.rs-3303807/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Transcriptional regulation is a critical adaptive mechanism that allows bacteria to respond to changing environments, yet the concept of transcriptional plasticity (TP) remains largely unexplored. In this study, we investigate the genome-wide TP profiles of Mycobacterium tuberculosis (Mtb) genes by analyzing 894 RNA sequencing samples derived from 73 different environmental conditions. Our data reveal that Mtb genes exhibit significant TP variation that correlates with gene function and gene essentiality. We also found that critical genetic features, such as gene length, GC content, and operon size independently impose constraints on TP, beyond trans-regulation. By extending our analysis to include two other Mycobacterium species -- M. smegmatis and M. abscessus -- we demonstrate a striking conservation of the TP landscape. This study provides a comprehensive understanding of the TP exhibited by mycobacteria genes, shedding light on this significant, yet understudied, genetic feature encoded in bacterial genomes.
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Affiliation(s)
- Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Peter H Culviner
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen, Guangdong Province, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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Bei C, Zhu J, Culviner PH, Rubin EJ, Fortune SM, Gao Q, Liu Q. Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.553992. [PMID: 37645742 PMCID: PMC10462119 DOI: 10.1101/2023.08.20.553992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Transcriptional regulation is a critical adaptive mechanism that allows bacteria to respond to changing environments, yet the concept of transcriptional plasticity (TP) remains largely unexplored. In this study, we investigate the genome-wide TP profiles of Mycobacterium tuberculosis (Mtb) genes by analyzing 894 RNA sequencing samples derived from 73 different environmental conditions. Our data reveal that Mtb genes exhibit significant TP variation that correlates with gene function and gene essentiality. We also found that critical genetic features, such as gene length, GC content, and operon size independently impose constraints on TP, beyond trans-regulation. By extending our analysis to include two other Mycobacterium species -- M. smegmatis and M. abscessus -- we demonstrate a striking conservation of the TP landscape. This study provides a comprehensive understanding of the TP exhibited by mycobacteria genes, shedding light on this significant, yet understudied, genetic feature encoded in bacterial genomes.
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Affiliation(s)
- Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Peter H Culviner
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen, Guangdong Province, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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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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Liu K, Lin GH, Liu K, Liu YJ, Tao XY, Gao B, Zhao M, Wei DZ, Wang FQ. Multiplexed site-specific genome engineering in Mycolicibacterium neoaurum by Att/Int system. Synth Syst Biotechnol 2022; 7:1002-1011. [PMID: 35782483 PMCID: PMC9213222 DOI: 10.1016/j.synbio.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
Genomic integration of genes and pathway-sized DNA cassettes is often an indispensable way to construct robust and productive microbial cell factories. For some uncommon microbial hosts, such as Mycolicibacterium and Mycobacterium species, however, it is a challenge. Here, we present a multiplexed integrase-assisted site-specific recombination (miSSR) method to precisely and iteratively integrate genes/pathways with controllable copies in the chromosomes of Mycolicibacteria for the purpose of developing cell factories. First, a single-step multi-copy integration method was established in M. neoaurum by a combination application of mycobacteriophage L5 integrase and two-step allelic exchange strategy, the efficiencies of which were ∼100% for no more than three-copy integration events and decreased sharply to ∼20% for five-copy integration events. Second, the R4, Bxb1 and ΦC31 bacteriophage Att/Int systems were selected to extend the available integration toolbox for multiplexed gene integration events. Third, a reconstructed mycolicibacterial Xer recombinases (Xer-cise) system was employed to recycle the selection marker of gene recombination to facilitate the iterative gene manipulation. As a proof of concept, the biosynthetic pathway of ergothioneine (EGT) in Mycolicibacterium neoaurum ATCC 25795 was achieved by remodeling its metabolic pathway with a miSSR system. With six copies of the biosynthetic gene clusters (BGCs) of EGT and pentose phosphate isomerase (PRT), the titer of EGT in the resulting strain in a 30 mL shake flask within 5 days was enhanced to 66 mg/L, which was 3.77 times of that in the wild strain. The improvements indicated that the miSSR system was an effective, flexible, and convenient tool to engineer the genomes of Mycolicibacteria as well as other strains in the Mycobacteriaceae due to their proximate evolutionary relationships.
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Salerno P, Leckenby MW, Humphrey B, Cranenburgh RM. Xer Recombination for the Automatic Deletion of Selectable Marker Genes From Plasmids in Enteric Bacteria. Synth Biol (Oxf) 2022; 7:ysac005. [PMID: 35601876 PMCID: PMC9113270 DOI: 10.1093/synbio/ysac005] [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: 10/05/2021] [Revised: 03/15/2022] [Accepted: 04/12/2022] [Indexed: 11/17/2022] Open
Abstract
Antibiotic resistance genes are widely used to select bacteria transformed with plasmids and to prevent plasmid loss from cultures, yet antibiotics represent contaminants in the biopharmaceutical manufacturing process, and retaining antibiotic resistance genes in vaccines and biological therapies is discouraged by regulatory agencies. To overcome these limitations, we have developed X-mark™, a novel technology that leverages Xer recombination to generate selectable marker gene-free plasmids for downstream therapeutic applications. Using this technique, X-mark plasmids with antibiotic resistance genes flanked by XerC/D target sites are generated in Escherichia coli cytosol aminopeptidase (E. coli pepA) mutants, which are deficient in Xer recombination on plasmids, and subsequently transformed into enteric bacteria with a functional Xer system. This results in rapid deletion of the resistance gene at high resolution (100%) and stable replication of resolved plasmids for more than 40 generations in the absence of antibiotic selective pressure. This technology is effective in both Escherichia coli and Salmonella enterica bacteria due to the high degree of homology between accessory sequences, including strains that have been developed as oral vaccines for clinical use. X-mark effectively eliminates any regulatory and safety concerns around antibiotic resistance carryover in biopharmaceutical products, such as vaccines and therapeutic proteins.
Graphical Abstract
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Affiliation(s)
- Paola Salerno
- London Bioscience Innovation Centre, Prokarium Ltd, London, UK
| | - Matthew W Leckenby
- Cobra Biologics Ltd, Stephenson Building, Keele Science Park, Keele, Staffordshire, UK
| | - Bruce Humphrey
- London Bioscience Innovation Centre, Prokarium Ltd, London, UK
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Zhang Z, Yang Z, Zhen J, Xiang X, Liao P, Xie J. Insertion Mutation of MSMEG_0392 Play an Important Role in Resistance of M. smegmatis to Mycobacteriophage SWU1. Infect Drug Resist 2022; 15:347-357. [PMID: 35140480 PMCID: PMC8818766 DOI: 10.2147/idr.s341494] [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: 09/27/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Phage is a new choice for the treatment of multi-drug-resistant bacteria, and phage resistance is also an issue of concern. SWU1 is a mycobacteriophage, and the mechanism of its resistance remain poorly understood. Methods The mutant strains which were stably resistant to SWU1 were screened by transposon mutation library. The stage of phage resistance was observed by transmission electron microscope (TEM). The insertion site of transposon was identified by thermal asymmetric interlaced PCR (TAIL-PCR). The possible relationship between insertion site and phage resistance was verified by gene knockout technique. The fatty acid composition of bacterial cell wall was analyzed by Gas Chromatography-Mass Spectrometer (GC-MS). Through the amplification and sequencing of target genes and gene complement techniques to find the mechanism of SWU1 resistance. Results The transposon mutant M12 which was stably resistant to mycobacteriophage SWU1 was successfully screened. It was confirmed that resistance occurred in the adsorption stage of bacteriophage. It was verified that the insertion site of the transposon was located in the MSMEG_3705 gene, but after knocking out the gene in the wild type M. smegmatis mc2 155, the resistance of the knockout strain to SWU1 was not observed. Through the amplification and sequencing of the target gene MSMEG_0392, it was found that there was an adenine insertion mutation at position 817. After complementing MSMEG_0392 in M12, it was found that M12 returned to sensitivity to SWU1. Conclusion We confirmed that the resistance of M12 to SWU1 was related to the functional inactivation of MSMEG_0392 and this phenomenon may be caused by the change of cell wall of M. smegmatis.
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Affiliation(s)
- Zhen Zhang
- Department of Clinical Laboratory, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, People’s Republic of China
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Three Gorges Eco-Environment and Bioresources, Eco-Environment Key Laboratory of the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People’s Republic of China
| | - Zhulan Yang
- Department of Clinical Laboratory, Southwest Hospital, Army Medical University, Chongqing, People’s Republic of China
| | - Junfeng Zhen
- Department of Clinical Laboratory, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, People’s Republic of China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, People’s Republic of China
| | - Pu Liao
- Department of Clinical Laboratory, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, People’s Republic of China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Three Gorges Eco-Environment and Bioresources, Eco-Environment Key Laboratory of the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People’s Republic of China
- Correspondence: Jianping Xie; Pu Liao, Tel/Fax +8623-68367108, Email ;
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Boldrin F, Manganelli R. Repressible Promoter System to Study Essential Genes in Mycobacteria. Methods Mol Biol 2022; 2377:317-332. [PMID: 34709624 DOI: 10.1007/978-1-0716-1720-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Inducible gene expression systems represent powerful tools for studying essential gene function and for validation of drug targets in bacteria. Even if several regulated promoters have been characterized, only a few of them have been successfully used in Mycobacteria. Here we describe a successful mycobacterial gene regulation system based on the presence of two chromosomally encoded repressors: Pip and TetR, and a tunable promoter (Pptr) that allows a tight regulation of gene expression.
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Affiliation(s)
- Francesca Boldrin
- Department of Molecular Medicine, University of Padova, Padova, Italy
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Cai X, Liu L, Qiu C, Wen C, He Y, Cui Y, Li S, Zhang X, Zhang L, Tian C, Bi L, Zhou ZH, Gong W. Identification and architecture of a putative secretion tube across mycobacterial outer envelope. SCIENCE ADVANCES 2021; 7:7/34/eabg5656. [PMID: 34417177 PMCID: PMC8378821 DOI: 10.1126/sciadv.abg5656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Tuberculosis-causing mycobacteria have thick cell-wall and capsule layers that are formed from complex structures. Protein secretion across these barriers depends on a specialized protein secretion system, but none has been reported. We show that Mycobacterium tuberculosis Rv3705c and its homologous MSMEG_6251 in Mycobacterium smegmatis are tube-forming proteins in the mycobacterial envelope (TiME). Crystallographic and cryo-EM structures of these two proteins show that both proteins form rotationally symmetric rings. Two layers of TiME rings pack together in a tail-to-tail manner into a ring-shaped complex, which, in turn, stacks together to form tubes. M. smegmatis TiME was detected mainly in the cell wall and capsule. Knocking out the TiME gene markedly decreased the amount of secreted protein in the M. smegmatis culture medium, and expression of this gene in knocked-out strain partially restored the level of secreted protein. Our structure and functional data thus suggest that TiME forms a protein transport tube across the mycobacterial outer envelope.
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Affiliation(s)
- Xiaoying Cai
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Lei Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Chunhong Qiu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Chongzheng Wen
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Yao He
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Siyu Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xuan Zhang
- Institute of Health Science, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China
| | - Longhua Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Changlin Tian
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Lijun Bi
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Weimin Gong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
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Tian X, Gao Y, Wang S, Adnan Hameed HM, Yu W, Fang C, Zhang J, Tan Y, Cao Z, Guan P, Hu J, Liu J, Zhong N, Zhang T. Rapid visualized assessment of drug efficacy in live mice with a selectable marker-free autoluminescent Klebsiella pneumoniae. Biosens Bioelectron 2021; 177:112919. [PMID: 33515974 DOI: 10.1016/j.bios.2020.112919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 12/18/2022]
Abstract
Klebsiella pneumoniae is an opportunistic pathogen that is responsible for community acquired infections and nosocomial infections. Antibiotic-resistant K. pneumoniae and/or hypervirulent K. pneumoniae are emerging as a serious threat to public health. For the sake of alleviating and conquering current dilemma, discovery of effective new drugs against K. pneumoniae is a tough challenge. However, traditional anti-K. pneumoniae drug discovery methods cost considerable amount of time, animals, labor and so on. So an efficient technique for in vitro and in vivo drug screening with the least time duration, animals and labor cost is highly needed for the discovery of new effective compounds. Hence, in this study we constructed a selectable marker-free autoluminescent K. pneumoniae (SfAlKp) harboring luxCDABE by combining Tn7 transposon and Xer-dif system. SfAlKp can be used for discovery of new drugs via detecting luminescence intensity as a surrogate marker. The energy-consuming autoluminescent reaction catalyzed by the LuxAB enzymes which use the substrates produced by LuxCDE using the metabolites of the bacteria. Tn7 can insert exogenous genes into the bacterial genome and the DNA fragment in between dif sequences can be recognized and removed by endogenous XerCD recombinases of K. pneumoniae. The drug susceptibility and growth rate of SfAlKp are identical to its parent strain, meanwhile the luminescence intensity and stability are also significant characteristics of SfAlKp. Compared to conventional techniques, the autoluminescence-based measurement is more applicable to high throughput screening for compounds both in vitro as well as in vivo in animal model.
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Affiliation(s)
- Xirong Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Yu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingran Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Zhizhong Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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11
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Borgers K, Vandewalle K, Van Hecke A, Michielsen G, Plets E, van Schie L, Vanmarcke S, Schindfessel L, Festjens N, Callewaert N. Development of a Counterselectable Transposon To Create Markerless Knockouts from an 18,432-Clone Ordered Mycobacterium bovis Bacillus Calmette-Guérin Mutant Resource. mSystems 2020; 5:e00180-20. [PMID: 32788404 PMCID: PMC7426150 DOI: 10.1128/msystems.00180-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/20/2020] [Indexed: 12/02/2022] Open
Abstract
Mutant resources are essential to improve our understanding of the biology of slow-growing mycobacteria, which include the causative agents of tuberculosis in various species, including humans. The generation of deletion mutants in slow-growing mycobacteria in a gene-by-gene approach in order to make genome-wide ordered mutant resources is still a laborious and costly approach, despite the recent development of improved methods. On the other hand, transposon mutagenesis in combination with Cartesian pooling-coordinate sequencing (CP-CSeq) allows the creation of large archived Mycobacterium transposon insertion libraries. However, such mutants contain selection marker genes with a risk of polar gene effects, which are undesired both for research and for use of these mutants as live attenuated vaccines. In this paper, a derivative of the Himar1 transposon is described which allows the generation of clean, markerless knockouts from archived transposon libraries. By incorporating FRT sites for FlpE/FRT-mediated recombination and I-SceI sites for ISceIM-based transposon removal, we enable two thoroughly experimentally validated possibilities to create unmarked mutants from such marked transposon mutants. The FRT approach is highly efficient but leaves an FRT scar in the genome, whereas the I-SceI-mediated approach can create mutants without any heterologous DNA in the genome. The combined use of CP-CSeq and this optimized transposon was applied in the BCG Danish 1331 vaccine strain (WHO reference 07/270), creating the largest ordered, characterized resource of mutants in a member of the Mycobacterium tuberculosis complex (18,432 clones, mutating 83% of the nonessential M. tuberculosis homologues), from which markerless knockouts can be easily generated.IMPORTANCE While speeding up research for many fields of biology (e.g., yeast, plant, and Caenorhabditis elegans), genome-wide ordered mutant collections are still elusive in mycobacterial research. We developed methods to generate such resources in a time- and cost-effective manner and developed a newly engineered transposon from which unmarked mutants can be efficiently generated. Our library in the WHO reference vaccine strain of Mycobacterium bovis BCG Danish targets 83% of all nonessential genes and was made publicly available via the BCCM/ITM Mycobacteria Collection. This resource will speed up Mycobacterium research (e.g., drug resistance research and vaccine development) and paves the way to similar genome-wide mutant collections in other strains of the Mycobacterium tuberculosis complex. The stretch to a full collection of mutants in all nonessential genes is now much shorter, with just 17% remaining genes to be targeted using gene-by-gene approaches, for which highly effective methods have recently also been described.
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Affiliation(s)
- Katlyn Borgers
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kristof Vandewalle
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Annelies Van Hecke
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Gitte Michielsen
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Evelyn Plets
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Loes van Schie
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sandrine Vanmarcke
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Nele Festjens
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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12
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Wang S, Yu W, Liu Z, Cai X, Zeng S, Zhang J, Gao Y, Tan Y, Cao Z, Guo L, Hameed HMA, Khan SA, Khan Z, Tian X, Fang C, Islam MM, Sapkota S, Guan P, Hu J, Liu J, Zhong N, Zhang T. Rapid, serial, non-invasive quantification of Pseudomonas aeruginosa in live mice with a selectable marker-free autoluminescent strain. Biosens Bioelectron 2020; 165:112396. [PMID: 32729517 DOI: 10.1016/j.bios.2020.112396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/26/2020] [Accepted: 06/15/2020] [Indexed: 01/07/2023]
Abstract
Pseudomonas aeruginosa is an increasingly prevalent pathogen that has become a serious health concern due to an increasing incidence of multidrug-resistant (MDR) hospital-acquired infections. The emergence of MDR-P. aeruginosa coupled with shrinking antibiotic pipelines has increased the demand for new antimicrobials and therapeutics. An effective tool for drug screening both in vitro and in vivo can facilitate the discovery of drugs and regimens for treating P. aeruginosa infection. Here, for the first time, we combined the mini-Tn7 system and Xer/dif recombinase system to construct a stable and selectable marker-free autoluminescent P. aeruginosa (SfAlPa) by one step. Afterwards, in vitro and in vivo activities of several antibiotics including amikacin, biapenem, levofloxacin and polymyxin B were assessed using SfAlPa. This study demonstrated that the use of SfAlPa could significantly facilitate rapid real-time evaluating the activities of compounds. Compared to prevailing methods, this method reduces the time, effort, animals and costs consumed in the discovery of new drugs against P. aeruginosa. Additionally, the methodology described in this study could be easily modified for construction of selectable marker-free reporter strain in other Gram-negative bacteria.
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Affiliation(s)
- Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Yu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoyin Cai
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng Zeng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jingran Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Zhizhong Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Lingmin Guo
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shahzad Akbar Khan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Laboratory of Pathology, Department of Pathobiology, University of the Poonch, Rawalakot, 12350, Pakistan
| | - Zafran Khan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xirong Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sanjeep Sapkota
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, 510095, China
| | - Nanshan Zhong
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510095, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510095, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Assessment of Clofazimine and TB47 Combination Activity against Mycobacterium abscessus Using a Bioluminescent Approach. Antimicrob Agents Chemother 2020; 64:AAC.01881-19. [PMID: 31843996 DOI: 10.1128/aac.01881-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/10/2019] [Indexed: 01/02/2023] Open
Abstract
Mycobacterium abscessus is intrinsically resistant to most antimicrobial agents. The emerging infections caused by M. abscessus and the lack of effective treatment call for rapid attention. Here, we intended to construct a selectable marker-free autoluminescent M. abscessus strain (designated UAlMab) as a real-time reporter strain to facilitate the discovery of effective drugs and regimens for treating M. abscessus The UAlMab strain was constructed using the dif/Xer recombinase system. In vitro and in vivo activities of several drugs, including clofazimine and TB47, a recently reported cytochrome bc 1 inhibitor, were assessed using UAlMab. Furthermore, the efficacy of multiple drug combinations, including the clofazimine and TB47 combination, were tested against 20 clinical M. abscessus isolates. The UAlMab strain enabled us to evaluate drug efficacy both in vitro and in live BALB/c mice in a real-time, noninvasive fashion. Importantly, although TB47 showed marginal activity either alone or in combination with clarithromycin, amikacin, or roxithromycin, the drug markedly potentiated the activity of clofazimine, both in vitro and in vivo This study demonstrates that the use of the UAlMab strain can significantly facilitate rapid evaluation of new drugs and regimens. The clofazimine and TB47 combination is effective against M. abscessus, and dual/triple electron transport chain (ETC) targeting can be an effective therapeutic approach for treating mycobacterial infections.
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14
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Castañeda-García A, Martín-Blecua I, Cebrián-Sastre E, Chiner-Oms A, Torres-Puente M, Comas I, Blázquez J. Specificity and mutagenesis bias of the mycobacterial alternative mismatch repair analyzed by mutation accumulation studies. SCIENCE ADVANCES 2020; 6:eaay4453. [PMID: 32095527 PMCID: PMC7015689 DOI: 10.1126/sciadv.aay4453] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/25/2019] [Indexed: 05/09/2023]
Abstract
The postreplicative mismatch repair (MMR) is an almost ubiquitous DNA repair essential for maintaining genome stability. It has been suggested that Mycobacteria have an alternative MMR in which NucS, an endonuclease with no structural homology to the canonical MMR proteins (MutS/MutL), is the key factor. Here, we analyze the spontaneous mutations accumulated in a neutral manner over thousands of generations by Mycobacterium smegmatis and its MMR-deficient derivative (ΔnucS). The base pair substitution rates per genome per generation are 0.004 and 0.165 for wild type and ΔnucS, respectively. By comparing the activity of different bacterial MMR pathways, we demonstrate that both MutS/L- and NucS-based systems display similar specificity and mutagenesis bias, revealing a functional evolutionary convergence. However, NucS is not able to repair indels in vivo. Our results provide an unparalleled view of how this mycobacterial system works in vivo to maintain genome stability and how it may affect Mycobacterium evolution.
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Affiliation(s)
- A. Castañeda-García
- Centro Nacional de Biotecnología–CSIC, Madrid, Spain
- Corresponding author. (A.C.-G.); (J.B.)
| | | | | | - A. Chiner-Oms
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, Spain
| | | | - I. Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, Spain
- CIBER in Epidemiology and Public Health
| | - J. Blázquez
- Centro Nacional de Biotecnología–CSIC, Madrid, Spain
- Corresponding author. (A.C.-G.); (J.B.)
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15
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An improved Xer-cise technology for the generation of multiple unmarked mutants in Mycobacteria. Biotechniques 2020; 68:106-110. [PMID: 31937110 DOI: 10.2144/btn-2019-0119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Xer-cise is a technique using antibiotic resistance cassettes flanked by dif sites allowing spontaneous and accurate excision from bacterial chromosomes with a high frequency through the action of the cellular recombinase XerCD. Here, we report a significant improvement of Xer-cise in Mycobacteria. Zeocin resistance cassettes flanked by variants of the natural Mycobacterium tuberculosis dif site were constructed and shown to be effective tools to construct multiple unmarked mutations in M. tuberculosis and in the model species Mycobacterium smegmatis. The dif site variants harbor mutations in the central region and can therefore not recombine with the wild-type or other variants, resulting in mutants of increased genetic stability. The herein described method should be generalizable to virtually any transformable bacterial species.
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16
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L-Alanine specifically potentiates fluoroquinolone efficacy against Mycobacterium persisters via increased intracellular reactive oxygen species. Appl Microbiol Biotechnol 2020; 104:2137-2147. [PMID: 31940082 DOI: 10.1007/s00253-020-10358-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/23/2019] [Accepted: 01/05/2020] [Indexed: 02/01/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis remains a major global health concern; M. tuberculosis drug resistance and persistence further fueled the situation. Nutrient supportive therapy was intensively pursued to complement the conventional treatment, as well as their synergy with current antibiotics. To explore whether L-alanine can synergize with fluoroquinolones against M. tuberculosis, M. smegmatis was used as a surrogate in this study. We found that L-alanine can boost the bactericidal efficacy of fluoroquinolones, increasing the production of intracellular reactive oxygen species. This effect is very significant for persisters. Accelerated tricarboxylic acid cycle and/or nucleotide metabolism were observed after the addition of L-alanine. M. smegmatis MSMEG2660 is a homolog of the alanine dehydrogenase (Rv2780, MSMEG2659) negative regulator Rv2779c and involved in the L-alanine potentiation of fluoroquinolone via funneling more alanine into tricarboxylic acid. Deletion mutant of the MSMEG2660 (∆Ms2660) became more susceptible, and more readily revived from persistence. We firstly found that L-alanine can synergize with fluoroquinolones against Mycobacterium, especially the persisters via promoting metabolism. This will inspire new avenue to eliminate Mycobacterium persisters.
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17
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Borgers K, Vandewalle K, Festjens N, Callewaert N. A guide to Mycobacterium mutagenesis. FEBS J 2019; 286:3757-3774. [PMID: 31419030 DOI: 10.1111/febs.15041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/05/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
Abstract
The genus Mycobacterium includes several pathogens that cause severe disease in humans, like Mycobacterium tuberculosis (M. tb), the infectious agent causing tuberculosis. Genetic tools to engineer mycobacterial genomes, in a targeted or random fashion, have provided opportunities to investigate M. tb infection and pathogenesis. Furthermore, they have allowed the identification and validation of potential targets for the diagnosis, prevention, and treatment of tuberculosis. This review describes the various methods that are available for the generation of mutants in Mycobacterium species, focusing specifically on tools for altering slow-growing mycobacteria from the M. tb complex. Among others, it incorporates the recent new molecular biological technologies (e.g. ORBIT) to rapidly and/or genome-wide comprehensively obtain targeted mutants in mycobacteria. As such, this review can be used as a guide to select the appropriate genetic tools to generate mycobacterial mutants of interest, which can be used as tools to aid understanding of M. tb infection or to help developing TB intervention strategies.
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Affiliation(s)
- Katlyn Borgers
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Kristof Vandewalle
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Nele Festjens
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Nico Callewaert
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
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18
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Duan W, Li X, Ge Y, Yu Z, Li P, Li J, Qin L, Xie J. Mycobacterium tuberculosis Rv1473 is a novel macrolides ABC Efflux Pump regulated by WhiB7. Future Microbiol 2018; 14:47-59. [PMID: 30539658 DOI: 10.2217/fmb-2018-0207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIM To characterize a novel macrolide ATP binding cassette efflux pump encoding gene Rv1473 which might be involved in antibiotic resistance. METHODS Mycobacterium smegmatis was used as a surrogate model for pathogenic mycobacteria, drug susceptibility assays and ethidium bromide accumulation assay were harnessed to verify drug resistance. The real-time quantitative PCR was used to evaluate the transcription levels of WhiB7 and Ms3140 upon exposure to macrolides. RESULTS Rv1473 contributes to macrolides resistance via efflux mechanisms, and was positively regulated by the transcription factor WhiB7 upon macrolides exposure. CONCLUSION Rv1473 is a novel ATP binding cassette efflux pump involved in mycobacterium intrinsic antibiotics resistance via efflux mechanism. This finding will facilitate novel antibiotic discovery and the treatment of pathogen, especially for nontuberculous mycobacteria.
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Affiliation(s)
- Wei Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Xue Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Yan Ge
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Zhaoxiao Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Ping Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Jiang Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai 200433, PR China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
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19
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Kilpeläinen A, Maya-Hoyos M, Saubí N, Soto CY, Joseph Munne J. Advances and challenges in recombinant Mycobacterium bovis BCG-based HIV vaccine development: lessons learned. Expert Rev Vaccines 2018; 17:1005-1020. [PMID: 30300040 DOI: 10.1080/14760584.2018.1534588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Human Immunodeficiency Virus/Acquired Immune Deficiency Syndrome, tuberculosis, and malaria are responsible for most human deaths produced by infectious diseases worldwide. Vaccination against HIV requires generation of memory T cells and neutralizing antibodies, mucosal immunity, and stimulation of an innate immune responses. In this context, the use of Mycobacterium bovis bacillus Calmette-Guérin (BCG) as a live vaccine vehicle is a promising approach for T-cell induction. AREAS COVERED In this review, we provide a comprehensive summary of the literature regarding immunogenicity studies in animal models performed since 2005. Furthermore, we provide expert commentary and 5-year view on how the development of potential recombinant BCG-based HIV vaccines involves careful selection of the HIV antigen, expression vectors, promoters, BCG strain, preclinical animal models, influence of preexisting immunity, and safety issues, for the rational design of recombinant BCG:HIV vaccines to prevent HIV transmission in the general population. EXPERT COMMENTARY The three critical issues to be considered when developing a rBCG:HIV vaccine are codon optimization, antigen localization, and plasmid stability in vivo. The use of integrative expression vectors are likely to improve the mycobacterial vaccine stability and immunogenicity to develop not only recombinant BCG-based vaccines expressing second generation of HIV-1 immunogens but also other major pediatric pathogens to prime protective responses shortly following birth.
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Affiliation(s)
- Athina Kilpeläinen
- a Catalan Center for HIV Vaccine Research and Development, AIDS Research Unit, Infectious Diseases Department, Hospital Clínic/IDIBAPS, School of Medicine , University of Barcelona , Barcelona , Spain
| | - Milena Maya-Hoyos
- b Chemistry Department, Faculty of Sciences , Universidad Nacional de Colombia, Ciudad Universitaria , Bogotá , Colombia
| | - Narcís Saubí
- a Catalan Center for HIV Vaccine Research and Development, AIDS Research Unit, Infectious Diseases Department, Hospital Clínic/IDIBAPS, School of Medicine , University of Barcelona , Barcelona , Spain
| | - Carlos Y Soto
- b Chemistry Department, Faculty of Sciences , Universidad Nacional de Colombia, Ciudad Universitaria , Bogotá , Colombia
| | - Joan Joseph Munne
- a Catalan Center for HIV Vaccine Research and Development, AIDS Research Unit, Infectious Diseases Department, Hospital Clínic/IDIBAPS, School of Medicine , University of Barcelona , Barcelona , Spain
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20
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Chhotaray C, Tan Y, Mugweru J, Islam MM, Adnan Hameed HM, Wang S, Lu Z, Wang C, Li X, Tan S, Liu J, Zhang T. Advances in the development of molecular genetic tools for Mycobacterium tuberculosis. J Genet Genomics 2018; 45:S1673-8527(18)30114-0. [PMID: 29941353 DOI: 10.1016/j.jgg.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference (CRISPRi), a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.
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Affiliation(s)
- Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, P.O Box 6 -60100, Embu, Kenya
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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21
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Zhang R, Liu X, Wang Y, Han Y, Sun J, Shi J, Zhang B. Identification, function, and application of 3-ketosteroid Δ1-dehydrogenase isozymes in Mycobacterium neoaurum DSM 1381 for the production of steroidic synthons. Microb Cell Fact 2018; 17:77. [PMID: 29776364 PMCID: PMC5960168 DOI: 10.1186/s12934-018-0916-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/03/2018] [Indexed: 12/18/2022] Open
Abstract
Background 3-Ketosteroid-Δ1-dehydrogenase (KstD) is a key enzyme in the metabolic pathway for chemical modifications of steroid hormones. Only a few KstDs have thus far been characterized biochemically and applied for the production of steroidal pharmaceutical intermediates. Three KstDs, KstD1, KstD2, and KstD3, were identified in Mycobacterium neoaurum DSM 1381, and they shared up to 99, 85 and 97% amino acid identity with previously reported KstDs, respectively. In this paper, KstDs from M. neoaurum DSM 1381 were investigated and exemplified their potential application for industrial steroid transformation. Results The recombinant KstD2 from Bacillus subtilis exhibited higher enzymatic activity when 4-androstene-3,17-dione (AD) and 22-hydroxy-23, 24-bisnorchol-4-ene-3-one (4HP) were used as the substrates, and resulted in specific activities of 22.40 and 19.19 U mg−1, respectively. However, the specific activities of recombinant KstD2 from Escherichia coli, recombinant KstD1 from B. subtilis and E. coli, and recombinant KstD3, also fed with AD and 4HP, had significantly lower specific activities. We achieved up to 99% bioconversion rate of 1,4-androstadiene-3,17-dione (ADD) from 8 g L−1 AD after 15 h of fermentation using E. coli transformant BL21-kstD2. And in vivo transcriptional analysis revealed that the expression of kstD1 in M. neoaurum DSM 1381 increased by 60.5-fold with phytosterols as the substrate, while the mRNA levels of kstD2 and kstD3 were bearly affected by the phytosterols. Therefore, we attempted to create a 4HP producing strain without kstD1, which could covert 20 g L−1 phytosterols to 14.18 g L−1 4HP. Conclusions In vitro assay employing the recombinant enzymes revealed that KstD2 was the most promising candidate for biocatalysis in biotransformation of AD. However, in vivo analysis showed that the cellular regulation of kstD1 was much more active than those of the other kstDs in response to the presence of phytosterols. Based on the findings above, we successfully constructed E. coli transformant BL21-kstD2 for ADD production from AD and M. neoaurum DSM 1381 ΔkstD1 strain for 4HP production using phytosterols as the substrate. Electronic supplementary material The online version of this article (10.1186/s12934-018-0916-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruijie Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangcen Liu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, 201210, Shanghai, China
| | - Yushi Wang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, 201210, Shanghai, China
| | - Yuchang Han
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, 201210, Shanghai, China
| | - Junsong Sun
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, 201210, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Baoguo Zhang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, 201210, Shanghai, China.
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22
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Deng Q, Meng J, Guan Y, Liu Y, Xiao C. Plasmid to generate Mycobacteria mutants. AMB Express 2018; 8:13. [PMID: 29392444 PMCID: PMC5794715 DOI: 10.1186/s13568-018-0537-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/15/2018] [Indexed: 11/30/2022] Open
Abstract
The generation of conditional mutants has been an effective approach to studying bacteria and validating drug targets, and mutants of Mycobacteria are no exception. However unlike other bacteria, there is still a paucity of available tools for Mycobacteria. We constructed a new plasmid containing tetracycline-repressive expression system (TetRr1.7) and Xer Site-Specific recombinase system to generate label-free controllable expression strains. The plasmid was subsequently used to construct a strain of M. tuberculosis expressing the only copy of d-alanine:d-alanine ligase under the control of the tetracycline-repressive promoter. The results showed that the mutant strain lost the ability of colony formation, became more sensitive to d-cycloserine and the cell wall of the mutant strain was disrupted when anhydrotetracycline was added to the medium. Taken together these observations, confirmed that the expression of d-alanine:d-alanine ligase was tightly controlled by the promoter. In conclusion, the new plasmid is a convenient tool for constructing stable conditional mutant strains in Mycobacteria and can be used for future target identification.
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23
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Boldrin F, Degiacomi G, Serafini A, Kolly GS, Ventura M, Sala C, Provvedi R, Palù G, Cole ST, Manganelli R. Promoter mutagenesis for fine-tuning expression of essential genes in Mycobacterium tuberculosis. Microb Biotechnol 2017; 11:238-247. [PMID: 29076636 PMCID: PMC5743821 DOI: 10.1111/1751-7915.12875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/05/2017] [Accepted: 09/25/2017] [Indexed: 02/04/2023] Open
Abstract
A range of regulated gene expression systems has been developed for mycobacteria in the last few years to facilitate the study of essential genes, validate novel drug targets and evaluate their vulnerability. Among these, the TetR/Pip-OFF repressible promoter system was successfully used in several mycobacterial species both in vitro and in vivo. In the first version of the system, the repressible promoter was Pptr , a strong Pip-repressible promoter of Streptomyces pristinaespiralis, which might hamper effective downregulation of genes with a low basal expression level. Here, we report an enhanced system that allows more effective control of genes expressed at low level. To this end, we subjected Pptr to targeted mutagenesis and produced 16 different promoters with different strength. Three of them, weaker than the wild-type promoter, were selected and characterized showing that they can indeed improve the performances of TetR/Pip-OFF repressible system both in vitro and in vivo increasing its stringency. Finally, we used these promoters to construct a series of bacterial biosensors with different sensitivity to DprE1 inhibitors and developed a whole-cell screening assay to identify inhibitors of this enzyme.
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Affiliation(s)
- Francesca Boldrin
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Giulia Degiacomi
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Agnese Serafini
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Gaëlle S Kolly
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015, Lausanne, Switzerland
| | - Marcello Ventura
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Claudia Sala
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015, Lausanne, Switzerland
| | - Roberta Provvedi
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Stewart T Cole
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, 1015, Lausanne, Switzerland
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
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24
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Mugweru J, Makafe G, Cao Y, Zhang Y, Wang B, Huang S, Njire M, Chhotaray C, Tan Y, Li X, Liu J, Tan S, Deng J, Zhang T. A Cassette Containing Thiostrepton, Gentamicin Resistance Genes, and dif sequences Is Effective in Construction of Recombinant Mycobacteria. Front Microbiol 2017; 8:468. [PMID: 28392781 PMCID: PMC5364183 DOI: 10.3389/fmicb.2017.00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/07/2017] [Indexed: 11/24/2022] Open
Abstract
The genetic manipulation of Mycobacterium tuberculosis genome is limited by the availability of selection markers. Spontaneous resistance mutation rate of M. tuberculosis to the widely used kanamycin is relatively high which often leads to some false positive transformants. Due to the few available markers, we have created a cassette containing thiostrepton resistance gene (tsr) for selection in M. tuberculosis and M. bovis BCG, and gentamicin resistance gene (aacC1) for Escherichia coli and M. smegmatis mc2155, flanked with dif sequences recognized by the Xer system of mycobacteria. This cassette adds to the limited available selection markers for mycobacteria.
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Affiliation(s)
- Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Gaelle Makafe
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yuanyuan Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Yang Zhang
- Key Laboratory of Biotechnology of Antibiotics, Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Shaobo Huang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Moses Njire
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
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25
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Zeng J, Deng W, Yang W, Luo H, Duan X, Xie L, Li P, Wang R, Fu T, Abdalla AE, Xie J. Mycobacterium tuberculosis Rv1152 is a Novel GntR Family Transcriptional Regulator Involved in Intrinsic Vancomycin Resistance and is a Potential Vancomycin Adjuvant Target. Sci Rep 2016; 6:28002. [PMID: 27349953 PMCID: PMC4923875 DOI: 10.1038/srep28002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 05/27/2016] [Indexed: 12/16/2022] Open
Abstract
Novel factors involved in Mycobacteria antibiotics resistance are crucial for better targets to combat the ever-increasing drug resistant strains. Mycobacterium tuberculosis Rv1152, a novel GntR family transcriptional regulator and a promising vancomycin adjuvant target, was firstly characterized in our study. Overexpression of Rv1152 in Mycobacterium smegmatis decreased bacterial susceptibility to vancomycin. Moreover, a deficiency in MSMEG_5174, an Rv1152 homolog made M. smegmatis more sensitive to vancomycin, which was reverted by complementing the MSMEG_5174 deficiency with Rv1152 of M. tuberculosis. Rv1152 negatively regulated four vancomycin responsive genes, namely genes encoding the ribosome binding protein Hsp, small unit of sulfate adenylyltransferase CysD, L-lysine-epsilon aminotransferase Lat, and protease HtpX. Taken together, Rv1152 controls the expression of genes required for the susceptibility to vancomycin. This is the first report that links the GntR family transcriptional factor with vancomycin susceptibility. Inhibitors of Rv1152 might be ideal vancomycin adjuvants for controlling multi-drug resistant Mycobacterial infections.
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Affiliation(s)
- Jie Zeng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Wanyan Deng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Wenmin Yang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Hongping Luo
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xiangke Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Ping Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Rui Wang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Tiwei Fu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Abualgasim Elgaili Abdalla
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China.,Department of Clinical Microbiology, College of Medical Laboratory Sciences, Omdurman Islamic University, Omdurman, Khartoum, Sudan
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
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26
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Wang P, Zhu Y, Zhang Y, Zhang C, Xu J, Deng Y, Peng D, Ruan L, Sun M. Mob/oriT, a mobilizable site-specific recombination system for unmarked genetic manipulation in Bacillus thuringiensis and Bacillus cereus. Microb Cell Fact 2016; 15:108. [PMID: 27286821 PMCID: PMC4902927 DOI: 10.1186/s12934-016-0492-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/23/2016] [Indexed: 11/29/2022] Open
Abstract
Background Bacillus thuringiensis and Bacillus cereus are two important species in B. cereus group. The intensive study of these strains at the molecular level and construction of genetically modified bacteria requires the development of efficient genetic tools. To insert genes into or delete genes from bacterial chromosomes, marker-less manipulation methods were employed. Results We present a novel genetic manipulation method for B. thuringiensis and B. cereus strains that does not leave selection markers. Our approach takes advantage of the relaxase Mob02281 encoded by plasmid pBMB0228 from Bacillus thuringiensis. In addition to its mobilization function, this Mob protein can mediate recombination between oriT sites. The Mob02281 mobilization module was associated with a spectinomycin-resistance gene to form a Mob-Spc cassette, which was flanked by the core 24-bp oriT sequences from pBMB0228. A strain in which the wild-type chromosome was replaced with the modified copy containing the Mob-Spc cassette at the target locus was obtained via homologous recombination. Thus, the spectinomycin-resistance gene can be used to screen for Mob-Spc cassette integration mutants. Recombination between the two oriT sequences mediated by Mob02281, encoded by the Mob-Spc cassette, resulted in the excision of the Mob-Spc cassette, producing the desired chromosomal alteration without introducing unwanted selection markers. We used this system to generate an in-frame deletion of a target gene in B. thuringiensis as well as a gene located in an operon of B. cereus. Moreover, we demonstrated that this system can be used to introduce a single gene or an expression cassette of interest in B. thuringiensis. Conclusion The Mob/oriT recombination system provides an efficient method for unmarked genetic manipulation and for constructing genetically modified bacteria of B. thuringiensis and B. cereus. Our method extends the available genetic tools for B. thuringiensis and B. cereus strains. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0492-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengxia Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yiguang Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuyang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chunyi Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianyi Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.
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27
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Efficient and simple generation of multiple unmarked gene deletions in Mycobacterium smegmatis. Sci Rep 2016; 6:22922. [PMID: 26972108 PMCID: PMC4789726 DOI: 10.1038/srep22922] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 11/27/2022] Open
Abstract
Research on mycobacterial genetics relies heavily on techniques for directed gene mutation, but genetic studies are often hampered by the difficulty of generating gene deletions in mycobacteria. We developed an efficient and improved deletion system, described here in detail, which can be used to construct multiple unmarked recombinants in mycobacteria. We tested this system by using it to sequentially delete four pairs of toxin-antitoxin genes in Mycobacterium smegmatis.
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28
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pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence. Nat Microbiol 2016; 1:15019. [PMID: 27571976 DOI: 10.1038/nmicrobiol.2015.19] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/19/2015] [Indexed: 01/09/2023]
Abstract
Mycobacterium tuberculosis is a major, globally spread, aerosol-transmitted human pathogen, thought to have evolved by clonal expansion from a Mycobacterium canettii-like progenitor. In contrast, extant M. canettii strains are rare, genetically diverse, and geographically restricted mycobacteria of only marginal epidemiological importance. Here, we show that the contrasting evolutionary success of these two groups is linked to loss of lipooligosaccharide biosynthesis and subsequent morphotype changes. Spontaneous smooth-to-rough M. canettii variants were found to be mutated in the polyketide-synthase-encoding pks5 locus and deficient in lipooligosaccharide synthesis, a phenotype restored by complementation. Importantly, these rough variants showed an altered host-pathogen interaction and increased virulence in cellular- and animal-infection models. In one variant, lipooligosaccharide deficiency occurred via homologous recombination between two pks5 genes and removal of the intervening acyltransferase-encoding gene. The resulting single pks5 configuration is similar to that fixed in M. tuberculosis, which is known to lack lipooligosaccharides. Our results suggest that pks5-recombination-mediated bacterial surface remodelling increased virulence, driving evolution from putative generalist mycobacteria towards professional pathogens of mammalian hosts.
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29
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Li Q, Fu T, Li C, Fan X, Xie J. Mycobacterial IclR family transcriptional factor Rv2989 is specifically involved in isoniazid tolerance by regulating the expression of catalase encoding gene katG. RSC Adv 2016. [DOI: 10.1039/c6ra07733a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Transcriptional factors are essential for bacteria to adapt diverse environmental stresses, especially upon exposure to antibiotics.
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Affiliation(s)
- Qiming Li
- Institute of Modern Biopharmaceuticals
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region
- Ministry of Education
- School of Life Sciences
| | - Tiwei Fu
- Institute of Modern Biopharmaceuticals
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region
- Ministry of Education
- School of Life Sciences
| | - Chunyan Li
- Institute of Modern Biopharmaceuticals
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region
- Ministry of Education
- School of Life Sciences
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region
- Ministry of Education
- School of Life Sciences
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region
- Ministry of Education
- School of Life Sciences
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30
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Yang F, Njire MM, Liu J, Wu T, Wang B, Liu T, Cao Y, Liu Z, Wan J, Tu Z, Tan Y, Tan S, Zhang T. Engineering more stable, selectable marker-free autoluminescent mycobacteria by one step. PLoS One 2015; 10:e0119341. [PMID: 25760622 PMCID: PMC4356594 DOI: 10.1371/journal.pone.0119341] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/05/2015] [Indexed: 12/02/2022] Open
Abstract
In our previous study, we demonstrated that the use of the autoluminescent Mycobacterium tuberculosis as a reporter strain had the potential to drastically reduce the time, effort, animals and costs consumed in evaluation of the activities of drugs and vaccines in live mice. However, the strains were relatively unstable and lost reporter with time without selection. The kanamycin selection marker used wasn’t the best choice as it provides resistance to amino glycosides which are an important class of second line drugs used in tuberculosis treatment. In addition, the marker could limit utility of the strains for screening of new potential drugs or evaluating drug combinations for tuberculosis treatment. Limited selection marker genes for mycobacterial genetic manipulation is a major drawback for such a marker-containing strain in many research fields. Therefore, selectable marker-free, more stable autoluminescent mycobacteria are highly needed. After trying several strategies, we created such mycobacterial strains successfully by using an integrative vector and removing both the resistance maker and integrase genes by Xer site-specific recombination in one step. The corresponding plasmid vectors developed in this study could be very convenient in constructing other selectable marker-free, more stable reporter mycobacteria with diverse applications.
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Affiliation(s)
- Feng Yang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Moses M. Njire
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Jia Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Tian Wu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Tianzhou Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yuanyuan Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Junting Wan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Zhengchao Tu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou, Guangdong, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou, Guangdong, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- * E-mail:
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Zhang Z, Wang R, Xie J. Mycobacterium smegmatis MSMEG_3705 Encodes a Selective Major Facilitator Superfamily Efflux Pump with Multiple Roles. Curr Microbiol 2015; 70:801-9. [DOI: 10.1007/s00284-015-0783-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 12/15/2014] [Indexed: 11/30/2022]
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Yang F, Tan Y, Liu J, Liu T, Wang B, Cao Y, Qu Y, Lithgow T, Tan S, Zhang T. Efficient construction of unmarked recombinant mycobacteria using an improved system. J Microbiol Methods 2014; 103:29-36. [DOI: 10.1016/j.mimet.2014.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 05/03/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
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Serafini A, Pisu D, Palù G, Rodriguez GM, Manganelli R. The ESX-3 secretion system is necessary for iron and zinc homeostasis in Mycobacterium tuberculosis. PLoS One 2013; 8:e78351. [PMID: 24155985 PMCID: PMC3796483 DOI: 10.1371/journal.pone.0078351] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/18/2013] [Indexed: 12/25/2022] Open
Abstract
ESX-3 is one of the five type VII secretion systems encoded by the Mycobacterium tuberculosis genome. We recently showed the essentiality of ESX-3 for M. tuberculosis viability and proposed its involvement in iron and zinc metabolism. In this study we confirmed the role of ESX-3 in iron uptake and its involvement in the adaptation to low zinc environment in M. tuberculosis. Moreover, we unveiled functional differences between the ESX-3 roles in M. tuberculosis and M. smegmatis showing that in the latter ESX-3 is only involved in the adaptation to iron and not to zinc restriction. Finally, we also showed that in M. tuberculosis this secretion system is essential for iron and zinc homeostasis not only in conditions in which the concentrations of these metals are limiting but also in metal sufficient conditions.
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Affiliation(s)
- Agnese Serafini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Davide Pisu
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G. Marcela Rodriguez
- Public Health Research Institute - Rutgers, the State University of New Jersey, Newark, New Jersey, United States of America
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
- * E-mail:
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Personne Y, Parish T. Mycobacterium tuberculosis possesses an unusual tmRNA rescue system. Tuberculosis (Edinb) 2013; 94:34-42. [PMID: 24145139 DOI: 10.1016/j.tube.2013.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 12/31/2022]
Abstract
Trans-translation is a key process in bacteria which recycles stalled ribosomes and tags incomplete nascent proteins for degradation. This ensures the availability of ribosomes for protein synthesis and prevents the accumulation of dysfunctional proteins. The tmRNA, ssrA, is responsible for both recovering stalled ribosomes and encodes the degradation tag; ssrA associates and functions with accessory proteins such as SmpB. Although ssrA and smpB are ubiquitous in bacteria, they are not essential for the viability of many species. The Mycobacterium tuberculosis genome has homologues of both ssrA and smpB. We demonstrated that ssrA is essential in M. tuberculosis, since the chromosomal copy of the gene could only be deleted in the presence of a functional copy integrated elsewhere. However, we were able to delete the proteolytic tagging function by constructing strains carrying a mutant allele (ssrADD). This demonstrates that ribosome rescue by ssrA is the essential function in M. tuberculosis, SmpB was not required for aerobic growth, since we were able to construct a deletion strain. However, the smpBΔ strain was more sensitive to antibiotics targeting the ribosome. Strains with deletion of smpB or mutations in ssrA did not show increased sensitivity (or resistance) to pyrazinamide suggesting that this antibiotic does not directly target these components of the tmRNA tagging system.
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Affiliation(s)
- Yoann Personne
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, UK
| | - Tanya Parish
- Queen Mary University of London, Barts & The London School of Medicine and Dentistry, London E1 2AT, UK.
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Du QL, Fan XY, Mao JX, Xie JP. [Progression on genetic knockout tools in Mycobacterium]. YI CHUAN = HEREDITAS 2012; 34:857-62. [PMID: 22805211 DOI: 10.3724/sp.j.1005.2012.00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pathogenic mycobacteria were and remain a heavy burden to public health. Unfortunately, genetic manipulation including knockout technologies of Mycobacterium is difficult compared with other traditional model organisms. To overcome this obstacle, achievements in Mycobacterium knockout technologies were summarized, including delivery vector, sequence-specific recombination system, as well as the recently developed recombinogenic engineering and its application. The future for this tool innovation is also addressed.
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Affiliation(s)
- Qin-Lin Du
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Madyagol M, Al-Alami H, Levarski Z, Drahovská H, Turňa J, Stuchlík S. Gene replacement techniques for Escherichia coli genome modification. Folia Microbiol (Praha) 2011; 56:253-63. [PMID: 21614539 DOI: 10.1007/s12223-011-0035-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/04/2011] [Indexed: 11/24/2022]
Abstract
The subject of this review covers modern experimental procedures for chromosomal gene replacement in Escherichia coli and related bacteria, which enable the specific substitution of targeted genome sequences with copies of those carrying defined mutations. Two principal methods for gene replacement were established. The first "in-out" method is based on integration of plasmid into bacterial chromosome and subsequent resolving of the cointegrate. The "linear fragment" method (recombineering) is based on homologous recombination mediated by short homology arms at the ends of linear DNA molecule. Many new protocols and improvements in targeted gene replacement were introduced during the last 10 years. These methods are well suited for high-throughput functional gene studies and for many biotechnological applications.
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Affiliation(s)
- Mahesh Madyagol
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 842 15, Bratislava, Slovak Republic
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