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Lin Q, Jiang Z, Zhong B, Chen JQ, Lv ZB, Nie ZM. Unveiling the impact of cryptic plasmids curing on Escherichia coli Nissle 1917: massive increase in Ag43c expression. AMB Express 2024; 14:48. [PMID: 38678482 PMCID: PMC11056357 DOI: 10.1186/s13568-024-01681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 05/01/2024] Open
Abstract
Escherichia coli Nissle 1917 (EcN) is an important chassis strain widely used for the development of live biotherapeutic products (LBPs). EcN strain naturally harbors two cryptic plasmids with unknown function. During the development of LBPs using EcN strain, the cryptic plasmids were cured usually to avoid plasmid incompatibility or alleviate metabolic burdens associated with these cryptic plasmids. While the cryptic plasmids curing in EcN may appear to be a routine procedure, the comprehensive impact of cryptic plasmids curing on the EcN strain remains incompletely understood. In the present study, the effects of cryptic plasmids curing on EcN were investigated using transcriptome sequencing. The results revealed that only a small number of genes showed significant changes in mRNA levels after cryptic plasmid curing (4 upregulated and 6 downregulated genes), primarily involved in amino acid metabolism. Furthermore, the flu gene showed the most significant different expression, encoding Antigen 43 (Ag43) protein, a Cah family adhesin. Mass spectrometry analysis further confirmed the significant increase in Ag43 expression. Ag43 is commonly present in Escherichia coli and mediates the bacterial autoaggregation. However, despite the upregulation of Ag43 expression, no Ag43-mediated cell self-sedimentation was observed in the cured EcN strain. These findings contribute to making informed decisions regarding the curing of the cryptic plasmids when Escherichia coli Nissle 1917 is used as the chassis strain.
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Affiliation(s)
- Qi Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China
| | - Zhuo Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Bo Zhong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jian-Qing Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China
| | - Zheng-Bing Lv
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China
| | - Zuo-Ming Nie
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
- Center for Bioreactor and Protein Drug Research, Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Shaoxing, 312075, China.
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2
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Huang Y, Chen M, Hu G, Wu B, He M. Elimination of editing plasmid mediated by theophylline riboswitch in Zymomonas mobilis. Appl Microbiol Biotechnol 2023; 107:7151-7163. [PMID: 37728624 DOI: 10.1007/s00253-023-12783-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023]
Abstract
Zymomonas mobilis is regarded as a potential chassis for the production of platform chemicals. Genome editing using the CRISPR-Cas system could meet the need for gene modification in metabolic engineering. However, the low curing efficiency of CRISPR editing plasmid is a common bottleneck in Z. mobilis. In this study, we utilized a theophylline-dependent riboswitch to regulate the expression of the replicase gene of the editing plasmid, thereby promoting the elimination of exogeneous plasmid. The riboswitch D (RSD) with rigorous regulatory ability was identified as the optimal candidate by comparing the transformation efficiency of four theophylline riboswitch-based backbone editing plasmids, and the optimal theophylline concentration for inducing RSD was determined to be 2 mM. A highly effective method for eliminating the editing plasmid, cells with RSD-based editing plasmid which were cultured in liquid and solid RM media in alternating passages at 37 °C without shaking, was established by testing the curing efficiency of backbone editing plasmids pMini and pMini-RSD in RM medium with or without theophylline at 30 °C or 37 °C. Finally, the RSD-based editing plasmid was applied to genome editing, resulting in an increase of more than 10% in plasmid elimination efficiency compared to that of pMini-based editing plasmid. KEY POINTS: • An effective strategy for curing CRISPR editing plasmid has been established in Z. mobilis. • Elimination efficiency of the CRISPR editing plasmid was enhanced by 10% to 20% under the regulation of theophylline-dependent riboswitch RSD.
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Affiliation(s)
- Yuhuan Huang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Mao Chen
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China.
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, China.
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3
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Yuan L, Wang D, Chen J, Lyu Y, Feng E, Zhang Y, Liu X, Wang H. Genome Sequence and Phenotypic Analysis of a Protein Lysis-Negative, Attenuated Anthrax Vaccine Strain. BIOLOGY 2023; 12:biology12050645. [PMID: 37237459 DOI: 10.3390/biology12050645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/30/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Bacillus anthracis is a Gram-positive bacterium that causes the zoonotic disease anthrax. Here, we studied the characteristic phenotype and virulence attenuation of the putative No. II vaccine strain, PNO2, which was reportedly introduced from the Pasteur Institute in 1934. Characterization of the strain showed that, compared with the control strain, A16Q1, the attenuated PNO2 (PNO2D1) was phospholipase-positive, with impaired protein hydrolysis and significantly reduced sporulation. Additionally, PNO2D1 significantly extended the survival times of anthrax-challenged mice. An evolutionary tree analysis revealed that PNO2D1 was not a Pasteur strain but was more closely related to a Tsiankovskii strain. A database comparison revealed a seven-base insertion mutation in the nprR gene. Although it did not block nprR transcription, the insertion mutation resulted in the premature termination of protein translation. nprR deletion of A16Q1 resulted in a nonproteolytic phenotype that could not sporulate. The database comparison revealed that the abs gene is also prone to mutation, and the abs promoter activity was much lower in PNO2D1 than in A16Q1. Low abs expression may be an important reason for the decreased virulence of PNO2D1.
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Affiliation(s)
- Lu Yuan
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Nanhui New City, Shanghai 201306, China
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Dongshu Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
- Laboratory of Advanced Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Jie Chen
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Nanhui New City, Shanghai 201306, China
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yufei Lyu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
- Laboratory of Advanced Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Erling Feng
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yan Zhang
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Nanhui New City, Shanghai 201306, China
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Xiankai Liu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
- Laboratory of Advanced Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Hengliang Wang
- College of Food Science and Technology, Shanghai Ocean University, 999 Hucheng Huan Road, Nanhui New City, Shanghai 201306, China
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
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Prevalence, Antibiotics Resistance and Plasmid Profiling of Vibrio spp. Isolated from Cultured Shrimp in Peninsular Malaysia. Microorganisms 2022; 10:microorganisms10091851. [PMID: 36144453 PMCID: PMC9505939 DOI: 10.3390/microorganisms10091851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 11/21/2022] Open
Abstract
Vibrio is the most common bacterium associated with diseases in crustaceans. Outbreaks of vibriosis pose a serious threat to shrimp production. Therefore, antibiotics are commonly used as preventative and therapeutic measures. Unfortunately, improper use of antibiotics leads to antibiotic resistance. Nevertheless, information on the occurrence of Vibrio spp. and antibiotic use in shrimp, particularly in Malaysia, is minimal. This study aimed to provide information on the occurrence of Vibrio spp., its status of antibiotic resistance and the plasmid profiles of Vibrio spp. isolated from cultured shrimp in Peninsular Malaysia. Shrimp were sampled from seven farms that were located in different geographical regions of Peninsular Malaysia. According to the observations, 85% of the shrimp were healthy, whereas 15% were unhealthy. Subsequently, 225 presumptive Vibrio isolates were subjected to biochemical tests and molecular detection using the pyrH gene. The isolates were also tested for antibiotic susceptibility against 16 antibiotics and were subjected to plasmid profiling. Eventually, 13 different Vibrio spp. were successfully isolated and characterized using the pyrH gene. They were the following: V. parahaemolyticus (55%), V. communis (9%), V. campbellii (8%), V. owensii (7%), V. rotiferianus (5%), Vibrio spp. (4%), V. alginolyticus (3%), V. brasiliensis (2%), V. natriegens (2%), V. xuii (1%), V. harveyi (1%), V. hepatarius (0.4%) and P. damselae (3%). Antibiotic susceptibility profiles revealed that all isolates were resistant to penicillin G (100%), but susceptible to norfloxacin (96%). Furthermore, 16% of the isolates revealed MAR of less than 0.2, while 84% were greater than 0.2. A total of 125 isolates harbored plasmids with molecular weights between 1.0 and above 10 kb, detected among the resistant isolates. The resistant isolates were mediated by both chromosomal and plasmid factors. These findings support the use of surveillance data on the emerging patterns of antimicrobial-resistance and plasmid profiles of Vibrio spp. in shrimp farms. The findings from this study can be used to develop a better disease management strategy for shrimp farming.
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5
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Wang D, Chen G, Lyu Y, Feng E, Zhu L, Pan C, Zhang W, Liu X, Wang H. A CRISPR/Cas12a-based DNAzyme visualization system for rapid, non-electrically dependent detection of Bacillus anthracis. Emerg Microbes Infect 2021; 11:428-437. [PMID: 34842509 PMCID: PMC8812752 DOI: 10.1080/22221751.2021.2012091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
As next-generation pathogen detection methods, CRISPR-Cas-based detection methods can perform single-nucleotide polymorphism (SNP) level detection with high sensitivity and good specificity. They do not require any particular equipment, which opens up new possibilities for the accurate detection and identification of Bacillus anthracis. In this study, we developed a complete detection system for B. anthracis based on Cas12a. We used two chromosomally located SNP targets and two plasmid targets to identify B. anthracis with high accuracy. The CR5 target is completely new. The entire detection process can be completed within 90 min without electrical power and with single-copy level sensitivity. We also developed an unaided-eye visualization system based on G4-DNAzyme for use with our CRISPR-Cas12a detection system. This visualization system has good prospects for deployment in field-based point-of-care detection. We used the antisense nucleic acid CatG4R as the detection probe, which showed stronger resistance to interference from components of the solution. CatG4R can also be designed as an RNA molecule for adaptation to Cas13a detection, thereby broadening the scope of the detection system.
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Affiliation(s)
- Dongshu Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Gang Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Yufei Lyu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Erling Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Chao Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Weicai Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xiankai Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Hengliang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing 100071, China
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6
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Wang T, Weiss A, Ha Y, You L. Predicting plasmid persistence in microbial communities by coarse-grained modeling. Bioessays 2021; 43:e2100084. [PMID: 34278591 DOI: 10.1002/bies.202100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/08/2022]
Abstract
Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.
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Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yuanchi Ha
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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7
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Wang X, Lyu Y, Wang S, Zheng Q, Feng E, Zhu L, Pan C, Wang S, Wang D, Liu X, Wang H. Application of CRISPR/Cas9 System for Plasmid Elimination and Bacterial Killing of Bacillus cereus Group Strains. Front Microbiol 2021; 12:536357. [PMID: 34177818 PMCID: PMC8222586 DOI: 10.3389/fmicb.2021.536357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/19/2021] [Indexed: 11/28/2022] Open
Abstract
The CRISPR-Cas system has been widely applied in prokaryotic genome editing with its high efficiency and easy operation. We constructed some "scissors plasmids" via using the temperature-sensitive pJOE8999 shuttle plasmid, which carry the different 20nt (N20) guiding the Cas9 nuclease as a scissors to break the target DNA. We successfully used scissors plasmids to eliminate native plasmids from Bacillus anthracis and Bacillus cereus, and specifically killed B. anthracis. When curing pXO1 and pXO2 virulence plasmids from B. anthracis A16PI2 and A16Q1, respectively, we found that the plasmid elimination percentage was slightly higher when the sgRNA targeted the replication initiation region (96-100%), rather than the non-replication initiation region (88-92%). We also tried using a mixture of two scissors plasmids to simultaneously eliminate pXO1 and pXO2 plasmids from B. anthracis, and the single and double plasmid-cured rates were 29 and 14%, respectively. To our surprise, when we used the scissor plasmid containing two tandem sgRNAs to cure the target plasmids pXO1 and pXO2 from wild strain B. anthracis A16 simultaneously, only the second sgRNA could guide Cas9 to cleave the target plasmid with high efficiency, while the first sgRNA didn't work in all the experiments we designed. When we used the CRISPR/cas9 system to eliminate the pCE1 mega-virulence plasmid from B. cereus BC307 by simply changing the sgRNA, we also obtained a plasmid-cured isogenic strain at a very high elimination rate (69%). The sterilization efficiency of B. anthracis was about 93%, which is similar to the efficiency of plasmid curing, and there was no significant difference in the efficiency of among the scissors plasmids containing single sgRNA, targeting multi-sites, or single-site targeting and the two tandem sgRNA. This simple and effective curing method, which is applicable to B. cereus group strains, provides a new way to study these bacteria and their virulence profiles.
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Affiliation(s)
- Xiaojing Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yufei Lyu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Siya Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- Experimental Teaching Center, Shenyang Normal University, Shenyang, China
| | - Qingfang Zheng
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- College of Food Science and Technology, Shanghai Ocean University, Ministry of Agriculture Shanghai Engineering Research Center of Aquatic Product Processing & Preservation, Laboratory of Quality & Safety Risk Assessment for Aquatic Product on Storage and Preservation, Shanghai, China
| | - Erling Feng
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Li Zhu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Chao Pan
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Shenghou Wang
- Experimental Teaching Center, Shenyang Normal University, Shenyang, China
| | - Dongshu Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xiankai Liu
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hengliang Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
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Obtaining Specific Sequence Tags for Yersinia pestis and Visually Detecting Them Using the CRISPR-Cas12a System. Pathogens 2021; 10:pathogens10050562. [PMID: 34066578 PMCID: PMC8148545 DOI: 10.3390/pathogens10050562] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022] Open
Abstract
Three worldwide historical plague pandemics resulted in millions of deaths. Yersinia pestis, the etiologic agent of plague, is also a potential bioterrorist weapon. Simple, rapid, and specific detection of Y. pestis is important to prevent and control plague. However, the high similarity between Y. pestis and its sister species within the same genus makes detection work problematic. Here, the genome sequence from the Y. pestis CO92 strain was electronically separated into millions of fragments. These fragments were analyzed and compared with the genome sequences of 539 Y. pestis strains and 572 strains of 20 species within the Yersinia genus. Altogether, 97 Y. pestis-specific tags containing two or more single nucleotide polymorphism sites were screened out. These 97 tags efficiently distinguished Y. pestis from all other closely related species. We chose four of these tags to design a Cas12a-based detection system. PCR–fluorescence methodology was used to test the specificity of these tags, and the results showed that the fluorescence intensity produced by Y. pestis was significantly higher than that of non-Y. pestis (p < 0.0001). We then employed recombinase polymerase amplification and lateral flow dipsticks to visualize the results. Our newly developed plasmid-independent, species-specific library of tags completely and effectively screened chromosomal sequences. The detection limit of our four-tag Cas12a system reached picogram levels.
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Sheng D, Chen X, Li Y, Wang J, Zhuo L, Li Y. ParC, a New Partitioning Protein, Is Necessary for the Active Form of ParA From Myxococcus pMF1 Plasmid. Front Microbiol 2021; 11:623699. [PMID: 33519784 PMCID: PMC7843461 DOI: 10.3389/fmicb.2020.623699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
The ParABS partitioning system, a main driver of DNA segregation in bacteria, employs two proteins, ParA and ParB, for plasmid partition. The pMF1 plasmid from Myxococcus fulvus 124B02 has a par operon encoding a small acidic protein, ParC, in addition to type I ParA and ParB homologs. Here, we show that expression of parC upstream of parA (as in the natural case), but not ectopic expression, is essential for the plasmid inheritance in Myxococcus cells. Co-expression of parC upstream of parA was determined to form a soluble ParC-ParA heterodimer at a 1:1 ratio, while individual expression of parA or co-expression of parA with ectopic parC formed insoluble ParA proteins. Purified ParA proteins alone had no ATPase activity and was easily dimerized, while mixing ParA with ParC formed the ParC-ParA heterodimer with the ATPase and polymerization activities. Fusing ParC and ParA also produced soluble proteins and some chimeras restored the ATPase activity and plasmid inheritance. The results highlight that proximal location of parC before parA is critical to realize the functions of ParA in the partition of Myxococcus plasmid pMF1 and shed light on a new mechanism to realize a protein function by two separate proteins.
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Affiliation(s)
- Duohong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaojing Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yajie Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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10
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Liu LP, Yang X, Zhao XJ, Zhang KY, Li WC, Xie YY, Jia SR, Zhong C. A Lambda Red and FLP/FRT-Mediated Site-Specific Recombination System in Komagataeibacter xylinus and Its Application to Enhance the Productivity of Bacterial Cellulose. ACS Synth Biol 2020; 9:3171-3180. [PMID: 33048520 DOI: 10.1021/acssynbio.0c00450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Komagataeibacter xylinus has received increasing attention as an important microorganism for the conversion of several carbon sources to bacterial cellulose (BC). However, BC productivity has been impeded by the lack of efficient genetic engineering techniques. In this study, a lambda Red and FLP/FRT-mediated site-specific recombination system was successfully established in Komagataeibacter xylinus. Using this system, the membrane bound gene gcd, a gene that encodes glucose dehydrogenase, was knocked out to reduce the modification of glucose to gluconic acid. The engineered strain could not produce any gluconic acid and presented a decreased bacterial cellulose (BC) production due to its restricted glucose utilization. To address this problem, the gene of glucose facilitator protein (glf; ZMO0366) was introduced into the knockout strain coupled with the overexpression of the endogenous glucokinase gene (glk). The BC yield of the resultant strain increased by 63.63-173.68%, thus reducing the production cost.
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Affiliation(s)
- Ling-Pu Liu
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
| | - Xue Yang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
| | - Xiang-Jun Zhao
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
| | - Kai-Yue Zhang
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
| | - Wen-Chao Li
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
| | - Yan-Yan Xie
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
| | - Shi-Ru Jia
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
| | - Cheng Zhong
- State Key Laboratory of Food Nutrition & Safety, Tianjin University of Science & Technology, Tianjin 300072, PR China
- Key Laboratory of Industrial Fermentation Microbiology, (Ministry of Education), Tianjin University of Science & Technology, Tianjin 300072, PR China
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11
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Antibiotic-resistant Enterobacteriaceae from diseased freshwater goldfish. Arch Microbiol 2020; 203:219-231. [PMID: 32803348 DOI: 10.1007/s00203-020-02021-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
Goldfish farming gained more attention among the ornamental fishes in aquaculture industry. The occurrence of bacterial infections and further antimicrobial treatment lead to the major crisis of antibiotic resistance in aquaculture. We have isolated diverse enterobacteriaceae groups which affect the goldfish and identified their response towards 46 antimicrobials of 15 different classes. Thirteen significant bacterial isolates such as Edwardsiella tarda, Serratia marcescens, Klebsiella aerogenes, Proteus penneri, P. hauseri, Enterobacter cloacae, E. cancerogenus, E. ludwigii, Citrobacter freundii, E. coli, Kluyvera cryocrescens, Plesiomonas shigelloides and Providencia vermicola were recovered from the infected fish with the Shannon-wiener diversity index of 2.556. Multiple antibiotic resistance (MAR) index was found to be maximum for P. penneri (0.87) and minimum for C. freundii and E. cloacae (0.22), highlighting the hyper antibiotic selection pressure in the farm. The minimum concentration of antibiotics required to inhibit most of the resistant isolates was found to be > 256 mcg/ml. All the isolates were susceptible towards ciprofloxacin. Plasmid curing and further AMR tests could reveal the location of antibiotic resistance genes mainly as plasmids which determine the large extent of AMR spread through horizontal gene transfer. This study is the first of its kind to investigate the antimicrobial resistance profile of enterobacteriaceae recovered from goldfish, before and after plasmid curing.
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
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Chen XJ, Zhang Z, Li YJ, Zhuo L, Sheng DH, Li YZ. Insights into the persistence and phenotypic effects of the endogenous and cryptic plasmid pMF1 in its host strain Myxococcus fulvus 124B02. FEMS Microbiol Ecol 2020; 96:5698802. [PMID: 31917409 DOI: 10.1093/femsec/fiaa001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 01/08/2020] [Indexed: 11/12/2022] Open
Abstract
Many endogenous plasmids carry no noticeable benefits for their bacterial hosts, and the persistence of these 'cryptic plasmids' and their functional impacts are mostly unclear. In this study, we investigated these uncertainties using the social bacterium Myxococcus fulvus 124B02 and its endogenous plasmid pMF1. pMF1 possesses diverse genes that originated from myxobacteria, suggesting a longstanding co-existence of the plasmid with various myxobacterial species. The curing of pMF1 from 124B02 had almost no phenotypic effects on the host. Laboratory evolution experiments showed that the 124B02 strain retained pMF1 when subcultured on dead Escherichia coli cells but lost pMF1 when subcultured on living E. coli cells or on casitone medium; these results indicated that the persistence of pMF1 in 124B02 was environment-dependent. Curing pMF1 caused the mutant to lose the ability to predate and develop fruiting bodies more quickly than the pMF1-containing strain after they were subcultured on dead E. coli cells, which indicated that the presence of pMF1 in M. fulvus 124B02 has some long-term effects on its host. The results provide some new insights into the persistence and impacts of cryptic plasmids in their natural bacterial cells.
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Affiliation(s)
- Xiao-Jing Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.,Institute of Medical Sciences, The Second Hospital of Shandong University, Jinan, Shandong, 250033, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Ya-Jie Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Duo-Hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
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Amalina NZ, Santha S, Zulperi D, Amal MNA, Yusof MT, Zamri-Saad M, Ina-Salwany MY. Prevalence, antimicrobial susceptibility and plasmid profiling of Vibrio spp. isolated from cultured groupers in Peninsular Malaysia. BMC Microbiol 2019; 19:251. [PMID: 31711432 PMCID: PMC6849203 DOI: 10.1186/s12866-019-1624-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/24/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Numerous prevalence studies of Vibrio spp. infection in fish have been extensively reported worldwide, including Malaysia. Unfortunately, information on the prevalence of Vibrio spp. in groupers (Epinephelus spp.) is limited. In this study, groupers obtained from nine farms located at different geographical regions in Malaysia were sampled for the presence of pathogenic Vibrio spp. and their susceptibility profiles against seven antibiotics. RESULTS Out of 270 grouper samples, 195 (72%) were detected with the presence of Vibrio spp. Vibrio communis showed highest prevalence in grouper (28%), followed by V. parahaemolyticus (25%), V. alginolyticus (19%), V. vulnificus (14%), V. rotiferianus (3%), Vibrio sp. (3%), V. campbellii (2%), V. mytili (2%), V. furnissii (2%), V. harveyi (1%), V. tubiashii (1%), V. fluvialis (0.3%) and V. diabolicus (0.3%). Assessment on the antibiotic susceptibility profiles of the Vibrio spp. revealed that majority of the isolates were susceptible to tetracycline, streptomycin, erythromycin and bacitracin, but resistance to ampicillin, penicillin G and vancomycin. The mean MAR index of the Vibrio isolates was 0.51, with 85% of the isolates showed MAR index value of higher than 0.2. Results indicate that the Vibrio spp. were continuously exposed to antibiotics. Furthermore, the plasmid profiles of Vibrio spp. showed that 38.7% of the isolates harbored plasmid with molecular weight of more than 10 kb, while 61.3% were without plasmid. During curing process, Vibrio spp. lost their plasmid, but remained resistant to ampicillin, penicillin G, bacitracin and vancomycin while a few isolates remained resistant to erythromycin, streptomycin and tetracycline. The results suggested that the resistance to antibiotics in isolated Vibrio spp. might be due to chromosomal and plasmid borne. CONCLUSIONS This study demonstrates the prevalence of Vibrio spp. in groupers and the distribution of multidrug resistance strains that could be of concern to the farmers in Malaysia. In addition, data from this study can be further used in fish disease management plan.
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Affiliation(s)
- Nor Zulkiply Amalina
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Silvaraj Santha
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Dzarifah Zulperi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohammad Noor Azmai Amal
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohd Termizi Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohd Zamri-Saad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Md Yasin Ina-Salwany
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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Buckner MMC, Ciusa ML, Piddock LJV. Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing. FEMS Microbiol Rev 2018; 42:781-804. [PMID: 30085063 PMCID: PMC6199537 DOI: 10.1093/femsre/fuy031] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/25/2018] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global problem hindering treatment of bacterial infections, rendering many aspects of modern medicine less effective. AMR genes (ARGs) are frequently located on plasmids, which are self-replicating elements of DNA. They are often transmissible between bacteria, and some have spread globally. Novel strategies to combat AMR are needed, and plasmid curing and anti-plasmid approaches could reduce ARG prevalence, and sensitise bacteria to antibiotics. We discuss the use of curing agents as laboratory tools including chemicals (e.g. detergents and intercalating agents), drugs used in medicine including ascorbic acid, psychotropic drugs (e.g. chlorpromazine), antibiotics (e.g. aminocoumarins, quinolones and rifampicin) and plant-derived compounds. Novel strategies are examined; these include conjugation inhibitors (e.g. TraE inhibitors, linoleic, oleic, 2-hexadecynoic and tanzawaic acids), systems designed around plasmid incompatibility, phages and CRISPR/Cas-based approaches. Currently, there is a general lack of in vivo curing options. This review highlights this important shortfall, which if filled could provide a promising mechanism to reduce ARG prevalence in humans and animals. Plasmid curing mechanisms which are not suitable for in vivo use could still prove important for reducing the global burden of AMR, as high levels of ARGs exist in the environment.
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Affiliation(s)
- Michelle M C Buckner
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham B15 2TT, UK
| | - Maria Laura Ciusa
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham B15 2TT, UK
| | - Laura J V Piddock
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham B15 2TT, UK
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Song X, Huang H, Xiong Z, Xia Y, Wang G, Yin B, Ai L. Characterization of a cryptic plasmid isolated from Lactobacillus casei CP002616 and construction of shuttle vectors based on its replicon. J Dairy Sci 2018; 101:2875-2886. [PMID: 29428762 DOI: 10.3168/jds.2017-13771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/19/2017] [Indexed: 11/19/2022]
Abstract
The cryptic plasmid pLC2W was isolated from Lactobacillus casei CP002616. Nucleotide sequence analysis revealed that 4 putative open reading frames (ORF) were responsible for DNA replication. Four Escherichia coli-Lactobacillus shuttle vectors were constructed using different lengths of the pLC2W replicon to identify the shortest functional replicon. The length of the pLC2W replicon did not affect the stability of the plasmids. Green fluorescent protein (GFP) as a reporter was expressed successfully in several lactobacilli using our constructed vectors. The results suggested that the expression vectors pUE-F0GFP and pUE-F1GFP are potential molecular tools for heterologous gene cloning and expression in lactobacilli. Moreover, 2 plasmid-curing methods were used to eliminate pLC2W from L. casei. We detected no difference between L. casei CP002616 and L. casei CP002616 pLC2WΔ-IC (mutant strain cured by plasmid incompatibility method) in production of exopolysaccharide (EPS) or acid. However, EPS and acid production were both reduced in L. casei CP002616 pLC2WΔ-HT (mutant strain cured by high-temperature heat treatment method), demonstrating a difference between these 2 curing methods. Sequence analysis of pLC2W and plasmid curing data suggest that plasmid pLC2W is not involved in EPS synthesis.
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Affiliation(s)
- Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - He Huang
- Key Lab of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yongjun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Guangqiang Wang
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Boxing Yin
- Kangyuan Dairy Co. Ltd., Yangzhou University, Yangzhou 225004, China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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17
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Wang P, Zhu Y, Shang H, Deng Y, Sun M. A minireplicon of plasmid pBMB26 represents a new typical replicon in the megaplasmids of Bacillus cereus group. J Basic Microbiol 2017; 58:263-272. [PMID: 29243837 DOI: 10.1002/jobm.201700525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/02/2017] [Accepted: 11/19/2017] [Indexed: 11/11/2022]
Abstract
A new minireplicon (rep26 minireplicon) from pBMB26, the 188 kb indigenous plasmid related to spore-crystal association (SCA) phenotype in Bacillus thuringiensis strain YBT-020, was characterized. A 12 kb EcoRI fragment, which encoded 10 putative open reading frames (ORFs), was capable of supporting replication when cloned in a replication probe vector. Deletion and frame shift mutation analysis showed that a 4.1 kb region encompassing two putative ORFs (orf21 and orf22) was essential for the plasmid replication in B. thuringiensis. Gene orf21 encoding a 49.8 kDa protein (named Rep26) with a helix-turn-helix motif showed no homology with known replication proteins and gene orf22 encoding a protein of 82.6 kDa showed homology to bacterial PcrA helicase. The replication origin of rep26 minireplicon was proved to be located in the coding region of orf21. Plasmid stability experiments indicated that the recombinant plasmid containing rep26 minireplicon has excellent segregational stability. BLASTP analysis revealed that amino acid sequences of ORF21 and ORF22 were well conserved among Bacillus cereus group strains. The rep26 minireplicon was widely distributed and could be defined as a new typical replicon in the megaplasmids of B. cereus group.
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Affiliation(s)
- Pengxia Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Yiguang Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Hui Shang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Yun Deng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
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18
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Chen Y, Taton A, Go M, London RE, Pieper LM, Golden SS, Golden JW. Self-replicating shuttle vectors based on pANS, a small endogenous plasmid of the unicellular cyanobacterium Synechococcus elongatus PCC 7942. Microbiology (Reading) 2016; 162:2029-2041. [DOI: 10.1099/mic.0.000377] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- You Chen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Arnaud Taton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Michaela Go
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ross E. London
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lindsey M. Pieper
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Susan S. Golden
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - James W. Golden
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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19
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Letchumanan V, Pusparajah P, Tan LTH, Yin WF, Lee LH, Chan KG. Occurrence and Antibiotic Resistance of Vibrio parahaemolyticus from Shellfish in Selangor, Malaysia. Front Microbiol 2015; 6:1417. [PMID: 26697003 PMCID: PMC4678184 DOI: 10.3389/fmicb.2015.01417] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/27/2015] [Indexed: 01/19/2023] Open
Abstract
High consumer demand for shellfish has led to the need for large-scale, reliable shellfish supply through aquaculture or shellfish farming. However, bacterial infections which can spread rapidly among shellfish poses a major threat to this industry. Shellfish farmers therefore often resort to extensive use of antibiotics, both prophylactically and therapeutically, in order to protect their stocks. The extensive use of antibiotics in aquaculture has been postulated to represent a major contributing factor in the rising incidence of antimicrobial resistant pathogenic bacteria in shellfish. This study aimed to investigate the incidence of pathogenic Vibrio parahaemolyticus and determine the antibiotic resistance profile as well as to perform plasmid curing in order to determine the antibiotic resistance mediation. Based on colony morphology, all 450 samples tested were positive for Vibrio sp; however, tox-R assay showed that only 44.4% (200/450) of these were V. parahaemolyticus. Out of these 200 samples, 6.5% (13/200) were trh-positive while none were tdh-positive. Antibiotic resistance was determined for all V. parahaemolyticus identified against 14 commonly used antibiotics and the multiple antibiotic resistance index (MAR) was calculated. The isolates demonstrated high resistance to several antibiotics tested- including second and third-line antibiotics- with 88% resistant to ampicillin, 81% to amikacin,70.5% to kanamycin, 73% to cefotaxime, and 51.5% to ceftazidime. The MAR index ranged from 0.00 to 0.79 with the majority of samples having an index of 0.36 (resistant to five antibiotics). Among the 13 trh-positive strains, almost 70% (9/13) demonstrated resistance to 4 or more antibiotics. Plasmid profiling for all V. parahaemolyticus isolates revealed that 86.5% (173/200) contained plasmids - ranging from 1 to 7 plasmids with DNA band sizes ranging from 1.2 kb to greater than 10 kb. 6/13 of the pathogenic V. pathogenic strains contained plasmid. After plasmid curing, the plasmid containing pathogenic strains isolated in our study have chromosomally mediated ampicillin resistance while the remaining resistance phenotypes are plasmid mediated. Overall, our results indicate that while the incidence of pathogenic V. parahaemolyticus in shellfish in Selangor still appears to be at relatively reassuring levels, antibiotic resistance is a real concern and warrants ongoing surveillance.
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Affiliation(s)
- Vengadesh Letchumanan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia ; Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Priyia Pusparajah
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Loh Teng-Hern Tan
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
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D'Amelio E, Gentile B, Lista F, D'Amelio R. Historical evolution of human anthrax from occupational disease to potentially global threat as bioweapon. ENVIRONMENT INTERNATIONAL 2015; 85:133-146. [PMID: 26386727 DOI: 10.1016/j.envint.2015.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 06/05/2023]
Abstract
PURPOSE Anthrax is caused by Bacillus anthracis, which can naturally infect livestock, wildlife and occupationally exposed humans. However, for its resistance due to spore formation, ease of dissemination, persistence in the environment and high virulence, B. anthracis has been considered the most serious bioterrorism agent for a long time. During the last century anthrax evolved from limited natural disease to potentially global threat if used as bioweapon. Several factors may mitigate the consequences of an anthrax attack, including 1. the capability to promptly recognize and manage the illness and its public health consequences; 2. the limitation of secondary contamination risk through an appropriate decontamination; and 3. the evolution of genotyping methods (for microbes characterization at high resolution level) that can influence the course and/or focus of investigations, impacting the response of the government to an attack. METHODS A PubMed search has been done using the key words “bioterrorism anthrax”. RESULTS Over one thousand papers have been screened and the most significant examined to present a comprehensive literature review in order to discuss the current knowledge and strategies in preparedness for a possible deliberate release of B. anthracis spores and to indicate the most current and complete documents in which to deepen. CONCLUSIONS The comprehensive analysis of the two most relevant unnatural anthrax release events, Sverdlovsk in the former Soviet Union (1979) and the contaminated letters in the USA (2001), shows that inhalational anthrax may easily and cheaply be spread resulting in serious consequences. The damage caused by an anthrax attack can be limited if public health organization, first responders, researchers and investigators will be able to promptly manage anthrax cases and use new technologies for decontamination methods and in forensic microbiology.
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Affiliation(s)
| | - Bernardina Gentile
- Histology and Molecular Biology Section, Army Medical Research Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
| | - Florigio Lista
- Histology and Molecular Biology Section, Army Medical Research Center, Via Santo Stefano Rotondo 4, 00184 Rome, Italy
| | - Raffaele D'Amelio
- Sapienza University of Rome, Department of Clinical and Molecular Medicine, S. Andrea University Hospital, Via di Grottarossa 1039, 00189 Rome, Italy.
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The Native Plasmid pML21 Plays a Role in Stress Tolerance in Enterococcus faecalis ML21, as Analyzed by Plasmid Curing Using Plasmid Incompatibility. Appl Biochem Biotechnol 2015; 178:451-61. [PMID: 26519343 DOI: 10.1007/s12010-015-1886-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 10/04/2015] [Indexed: 10/22/2022]
Abstract
To investigate the role of the native plasmid pML21 in Enterococcus faecalis ML21's response to abiotic stresses, the plasmid pML21 was cured based on the principle of plasmid incompatibility and segregational instability, generating E. faecalis mutant strain ML0. The mutant and the wild strains were exposed to abiotic stresses: bile salts, low pH, H2O2, ethanol, heat, and NaCl, and their survival rate was measured. We found that curing of pML21 lead to reduced tolerance to stress in E. faecalis ML0, especially oxidative and osmotic stress. Complementation analysis suggested that the genes from pML21 played different role in stress tolerance. The result indicated that pML21 plays a role in E. faecalis ML21's response to abiotic stresses.
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22
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Derzelle S, Girault G, Kokotovic B, Angen Ø. Whole Genome-Sequencing and Phylogenetic Analysis of a Historical Collection of Bacillus anthracis Strains from Danish Cattle. PLoS One 2015; 10:e0134699. [PMID: 26317972 PMCID: PMC4552859 DOI: 10.1371/journal.pone.0134699] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/13/2015] [Indexed: 11/28/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is known as one of the most genetically monomorphic species. Canonical single-nucleotide polymorphism (SNP) typing and whole-genome sequencing were used to investigate the molecular diversity of eleven B. anthracis strains isolated from cattle in Denmark between 1935 and 1988. Danish strains were assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4), A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and A.Br.Aust94 (n = 1). The match with the A.Br.Ames lineage is of particular interest as the occurrence of such lineage in Europe is demonstrated for the first time, filling an historical gap within the phylogeography of the lineage. Comparative genome analyses of these strains with 41 isolates from other parts of the world revealed that the two Danish A.Br.008/011 strains were related to the heroin-associated strains responsible for outbreaks of injection anthrax in drug users in Europe. Eight novel diagnostic SNPs that specifically discriminate the different sub-groups of Danish strains were identified and developed into PCR-based genotyping assays.
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Affiliation(s)
- Sylviane Derzelle
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Guillaume Girault
- University Paris-Est, Anses, Animal Health Laboratory, Maisons-Alfort, France
| | - Branko Kokotovic
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Øystein Angen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
- * E-mail:
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Letchumanan V, Chan KG, Lee LH. An insight of traditional plasmid curing in Vibrio species. Front Microbiol 2015; 6:735. [PMID: 26347714 PMCID: PMC4544227 DOI: 10.3389/fmicb.2015.00735] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/06/2015] [Indexed: 12/20/2022] Open
Abstract
As the causative agent of foodborne related illness, Vibrio species causes a huge impact on the public health and management. Vibrio species is often associated with seafood as the latter plays a role as a vehicle to transmit bacterial infections. Hence, antibiotics are used not to promote growth but rather to prevent and treat bacterial infections. The extensive use of antibiotics in the aquaculture industry and environment has led to the emerging of antibiotic resistant strains. This phenomenon has triggered an alarming public health concern due to the increase number of pathogenic Vibrio strains that are resistant to clinically used antibiotics and is found in the environment. Antibiotic resistance and the genes location in the strains can be detected through plasmid curing assay. The results derived from plasmid curing assay is fast, cost effective, sufficient in providing insights, and influence the antibiotic management policies in the aquaculture industry. This presentation aims in discussing and providing insights on various curing agents in Vibrio species. To our best of knowledge, this is a first review written discussing on plasmid curing in Vibrio species.
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Affiliation(s)
- Vengadesh Letchumanan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway Malaysia ; Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway Malaysia
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Albuquerque Costa R, Araújo RL, Souza OV, Vieira RHSDF. Antibiotic-resistant vibrios in farmed shrimp. BIOMED RESEARCH INTERNATIONAL 2015; 2015:505914. [PMID: 25918714 PMCID: PMC4396125 DOI: 10.1155/2015/505914] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/13/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022]
Abstract
Antimicrobial susceptibility pattern was determined in 100 strains of Vibrio isolated from the Litopenaeus vannamei shrimp and identified phenotypically. A high antibiotic-resistance index (75%) was observed, with the following phenotypic profiles: monoresistance (n = 42), cross-resistance to β-lactams (n = 20) and multiple resistance (n = 13). Plasmid resistance was characterized for penicillin (n = 11), penicillin + ampicillin (n = 1), penicillin + aztreonam (n = 1), and ampicillin (n = 1). Resistance to antimicrobial drugs by the other strains (n = 86) was possibly mediated by chromosomal genes. The findings of this study support the conclusion that the cultured shrimps can be vehicles of vibrios resistant to β-lactam and tetracycline.
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Affiliation(s)
- Renata Albuquerque Costa
- Sea Science Institute, Federal University of Ceará, Avenida Abolição 3207, 60165-081 Fortaleza, CE, Brazil
- Fisheries Engineering Department, Federal University of Ceará, 60440-900 Fortaleza, CE, Brazil
| | - Rayza Lima Araújo
- Sea Science Institute, Federal University of Ceará, Avenida Abolição 3207, 60165-081 Fortaleza, CE, Brazil
- Fisheries Engineering Department, Federal University of Ceará, 60440-900 Fortaleza, CE, Brazil
| | - Oscarina Viana Souza
- Sea Science Institute, Federal University of Ceará, Avenida Abolição 3207, 60165-081 Fortaleza, CE, Brazil
- Fisheries Engineering Department, Federal University of Ceará, 60440-900 Fortaleza, CE, Brazil
| | - Regine Helena Silva dos Fernandes Vieira
- Sea Science Institute, Federal University of Ceará, Avenida Abolição 3207, 60165-081 Fortaleza, CE, Brazil
- Fisheries Engineering Department, Federal University of Ceará, 60440-900 Fortaleza, CE, Brazil
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25
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Letchumanan V, Yin WF, Lee LH, Chan KG. Prevalence and antimicrobial susceptibility of Vibrio parahaemolyticus isolated from retail shrimps in Malaysia. Front Microbiol 2015; 6:33. [PMID: 25688239 PMCID: PMC4311705 DOI: 10.3389/fmicb.2015.00033] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/11/2015] [Indexed: 12/21/2022] Open
Abstract
Vibrio parahaemolyticus is a marine and estuarine bacterium that has been the leading cause of foodborne outbreaks which leads to a significant threat to human health worldwide. Consumption of seafood contaminated with V. parahaemolyticus causes acute gastroenteritis in individuals. The bacterium poses two main virulence factor including the thermostable direct hemolysin (tdh) which is a pore-forming protein that contributes to the invasiveness of the bacterium in humans and TDH-related hemolysin (trh), which plays a similar role as tdh in the disease pathogenesis. This study aimed to investigate the antimicrobial resistance V. parahaemolyticus strains in shrimps purchased from wetmarkets and supermarkets. The toxR-based PCR assay indicated that a total of 57.8% (185/320) isolates were positive for V. parahaemolyticus. Only 10% (19/185) toxR-positive isolate exhibit the trh gene and none of the isolates were tested positive for tdh. The MAR index was measured for 14 common antimicrobial agents. The results indicated 98% of the isolates were highly susceptible to imipenem, ampicillin sulbactam (96%), chloramphenicol (95%), trimethoprim-sulfamethoxazole (93%), gentamicin (85%), levofloxacin (83%), and tetracycline (82%). The chloramphenicol (catA2) and kanamycin (aphA-3) resistance genes were detected in the resistant V. parahaemolyticus isolates. Our results demonstrate that shrimps are contaminated with V. parahaemolyticus, some of which carry the trh-gene thus being potential to cause food borne illness. The occurrence of multidrug resistance strains in the environment could be an indication of excessive usage of antibiotics in agriculture and aquaculture fields.
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Affiliation(s)
- Vengadesh Letchumanan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia ; Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
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26
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Encinas D, Garcillán-Barcia MP, Santos-Merino M, Delaye L, Moya A, de la Cruz F. Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria. J Bacteriol 2014; 196:1551-9. [PMID: 24509315 PMCID: PMC3993370 DOI: 10.1128/jb.01464-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Comparative genomics have shown that 5% of Synechococcus elongatus PCC 7942 genes are of probable proteobacterial origin. To investigate the role of interphylum conjugation in cyanobacterial gene acquisition, we tested the ability of a set of prototype proteobacterial conjugative plasmids (RP4, pKM101, R388, R64, and F) to transfer DNA from Escherichia coli to S. elongatus. A series of BioBrick-compatible, mobilizable shuttle vectors was developed. These vectors were based on the putative origin of replication of the Synechococcus resident plasmid pANL. Not only broad-host-range plasmids, such as RP4 and R388, but also narrower-host-range plasmids, such as pKM101, all encoding MPFT-type IV secretion systems, were able to transfer plasmid DNA from E. coli to S. elongatus by conjugation. Neither MPFF nor MPFI could be used as interphylum DNA delivery agents. Reciprocally, pANL-derived cointegrates could be introduced in E. coli by electroporation, where they conferred a functional phenotype. These results suggest the existence of potentially ample channels of gene flow between proteobacteria and cyanobacteria and point to MPFT-based interphylum conjugation as a potential mechanism to explain the proteobacterial origin of a majority of S. elongatus xenologous genes.
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Affiliation(s)
- David Encinas
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
| | - M. Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
| | - María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
| | - Luis Delaye
- Departamento de Ingeniería Genética CINVESTAV-Irapuato, Irapuato, Guanajuato, Mexico
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC, CSIC–Universidad de Cantabria-SODERCAN, Santander, Spain
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Zheng J, Peng D, Ruan L, Sun M. Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group. BMC Evol Biol 2013; 13:262. [PMID: 24295128 PMCID: PMC4219350 DOI: 10.1186/1471-2148-13-262] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 11/25/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. However, the origin and evolution of most plasmids remains unclear, especially for megaplasmids. Strains of the Bacillus cereus group contain up to 13 plasmids with genome sizes ranging from 2 kb to 600 kb, and thus can be used to study plasmid dynamics and evolution. RESULTS This work studied the origin and evolution of 31 B. cereus group megaplasmids (>100 kb) focusing on the most conserved regions on plasmids, minireplicons. Sixty-five putative minireplicons were identified and classified to six types on the basis of proteins that are essential for replication. Twenty-nine of the 31 megaplasmids contained two or more minireplicons. Phylogenetic analysis of the protein sequences showed that different minireplicons on the same megaplasmid have different evolutionary histories. Therefore, we speculated that these megaplasmids are the results of fusion of smaller plasmids. All plasmids of a bacterial strain must be compatible. In megaplasmids of the B. cereus group, individual minireplicons of different megaplasmids in the same strain belong to different types or subtypes. Thus, the subtypes of each minireplicon they contain may determine the incompatibilities of megaplasmids. A broader analysis of all 1285 bacterial plasmids with putative known minireplicons whose complete genome sequences were available from GenBank revealed that 34% (443 plasmids) of the plasmids have two or more minireplicons. This indicates that plasmid fusion events are general among bacterial plasmids. CONCLUSIONS Megaplasmids of B. cereus group are fusion of smaller plasmids, and the fusion of plasmids likely occurs frequently in the B. cereus group and in other bacterial taxa. Plasmid fusion may be one of the major mechanisms for formation of novel megaplasmids in the evolution of bacteria.
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Affiliation(s)
- Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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