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Hu WF, Yang JY, Wang JJ, Yuan SF, Yue XJ, Zhang Z, Zhang YQ, Meng JY, Li YZ. Characteristics and immune functions of the endogenous CRISPR-Cas systems in myxobacteria. mSystems 2024; 9:e0121023. [PMID: 38747603 PMCID: PMC11237760 DOI: 10.1128/msystems.01210-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/15/2024] [Indexed: 06/19/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The cas genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in Myxococcus xanthus DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery. IMPORTANCE Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials. Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in myxobacteria but also their potential applications.
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Affiliation(s)
- Wei-Feng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jiang-Yu Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Fei Yuan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Ya-Qi Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jun-Yan Meng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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de Araújo HK, de Oliveira Castro S, da Silva Valejo MJA, da Costa Lima Junior MS, Neitzke-Abreu HC. LIMITATION OF PRIMERS USED IN PCR FOR THE CHARACTERIZATION OF LEISHMANIA INFANTUM. J Parasitol 2023; 109:445-449. [PMID: 37668295 DOI: 10.1645/21-130] [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: 09/06/2023] Open
Abstract
Conventional PCR provides Leishmania species characterization with even a small amount of biological material. Species-specific primers have been a widely used alternative; however, nonspecific amplifications are a reality, interfering with PCR efficiency. In endemic areas with multiple etiological agents for leishmaniasis, there is a requirement for higher specificity of primers. This study evaluates 3 pairs of primers described for the identification and characterization of Leishmania infantum. Primers RV1/RV2, LEISH1/LEISH2, and FLC2/RLC2 were used with the DNA of L. infantum, Leishmania amazonensis, and Leishmania braziliensis. An initial temperature curve was performed (52-62 C) to determine the optimal annealing temperature, followed by a dilution curve of Leishmania DNA (500 pg/μl, 50 pg/μl, 5 pg/μl, 500 fg/μl, 50 fg/μl, 5 fg/μl, and 0.5 fg/μl) to be used for analytical sensitivity. RV1/RV2 PCR amplified L. infantum and L. amazonensis at all analyzed temperatures; LEISH1/LEISH2 PCR amplified all 3 species of Leishmania, although at some temperatures L. infantum was specifically amplified, and, finally, FLC2/RLC2 PCR amplified only L. infantum at all temperatures analyzed. In terms of sensitivity, RV1/RV2 PCR detected 1 fg of L. infantum DNA and 100 pg of L. amazonensis DNA; LEISH1/LEISH2 PCR detected 1 fg of L. infantum DNA, 100 fg of L. amazonensis DNA, and 10 fg of L. braziliensis DNA; and FLC2/RLC2 PCR detected 10 fg of L. infantum DNA. Thus, PCR with FLC2/RLC2 primers is best suited for the molecular characterization of L. infantum, especially in areas where there is an incidence of more than 1 Leishmania species, such as South America.
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Affiliation(s)
- Helton Krisman de Araújo
- Faculty of Health Sciences, Universidade Federal da Grande Dourados (UFGD), 79804-070, Dourados, Mato Grosso do Sul State, Brazil
| | - Silvana de Oliveira Castro
- Faculty of Health Sciences, Universidade Federal da Grande Dourados (UFGD), 79804-070, Dourados, Mato Grosso do Sul State, Brazil
| | - Maria Joelma Alves da Silva Valejo
- Postgraduate Program in Health Sciences, Universidade Federal da Grande Dourados (UFGD), 79804-070, Dourados, Mato Grosso do Sul State, Brazil
| | | | - Herintha Coeto Neitzke-Abreu
- Faculty of Health Sciences, Universidade Federal da Grande Dourados (UFGD), 79804-070, Dourados, Mato Grosso do Sul State, Brazil
- Postgraduate Program in Health Sciences, Universidade Federal da Grande Dourados (UFGD), 79804-070, Dourados, Mato Grosso do Sul State, Brazil
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Direct and Rapid Identification of Vibrio Cholerae Serogroup and Toxigenicity by a Novel Multiplex Real-Time Assay. Pathogens 2022; 11:pathogens11080865. [PMID: 36014986 PMCID: PMC9416260 DOI: 10.3390/pathogens11080865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/27/2022] Open
Abstract
Molecular diagnostic assays for cholera detection have superior sensitivity to conventional assays and are now being accepted as the new standard method, especially the real-time PCR/RT-PCR. However, limited throughput capacity and long detection duration prevent them from detecting more specimens and more targets in one turnaround time simultaneously. In this study, we utilized nucleic acid extraction-free, direct RT-PCR and high-speed amplification to develop a novel multiplex assay, a quadplex direct one-tube real-time RT-PCR assay, for rapid detection of the serogroup and cholera toxin toxigenicity of Vibrio cholerae targeting the epsM, ctxA, rfb-O1, and rfb-O139 genes. Performance of the multiplex assay was evaluated by comparison with the monoplex real-time PCR assay according to the China Cholera Prevention Manual. Detection data from clinical specimens showed that the new assay had good diagnostic sensitivities for epsM (100%, n = 301), ctxA (100%, n = 125), rfb-O1 (100%, n = 85), and rfb-O139 (97.87%, n = 49). Analysis of the analytical sensitivities with serial dilutions of positive standards showed that the detection limits of the new assay for Vibrio cholerae epsM,ctxA,rfb-O1, and rfb-O139 were up to 200, 590, 115, and 1052 copies per mL lower than the monoplex real-time PCR (910, 345, and 1616 copies/mL respectively, for ctxA,rfb-O1, and rfb-O139). The results indicate that the multiplex assay is a rapid, sensitive, specific, and easy-to-use detection tool for Vibrio cholerae, especially suitable for rapid identification and screening detection of mass specimens.
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Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses. Diagnostics (Basel) 2021; 11:diagnostics11061084. [PMID: 34199257 PMCID: PMC8231941 DOI: 10.3390/diagnostics11061084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81-104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland-Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.
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Xu L, Qi J, Wen Y, Liang W, Wang L, Yang Z, Yang X, Qi Y, Duan M, Zhao K, Gu J, Shen Y, Rao P, Ding M, Ren S, Li L, Liu G. A polyA DNA probe-based ultra-sensitive and structure-distinguishable electrochemical biosensor for the analysis of RNAi transgenic maize. Analyst 2021; 146:3526-3533. [PMID: 33881427 DOI: 10.1039/d1an00313e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Since the application of RNA interference (RNAi) is rapidly developing in GMO technology, accurate and sensitive detection of functional RNA molecules was urgently needed, for the safety and functional assessment of RNAi crops. In this work, we developed an electrochemical biosensor for transgene-derived long RNA based on a poly-adenine (polyA) DNA capture probe. The polyA self-assembling monolayer (SAM) provided enhanced interface stability and optimized surface density for the subsequent hybridization of the long RNA molecule. A multiple reporter probe system (MRP) containing 12 reporter probes (RPs) and 2 spacers was applied to open the complex molecular secondary structure and hybridize with the long RNA, with the critical assistance of dimethyl sulfoxide (DMSO). By using 3 addressable RPs, structural recognition was performed among long stem-loop RNA, long dsRNA (no loop), and siRNA. Excellent selectivity was achieved when the extracted total RNA samples were directly analyzed. When reverse transcription recombinase polymerase amplification (RT-RPA) technology was combined, the sensitivity was improved to 10 aM. To the best of our knowledge, this is the first electrochemical biosensor with the excellent capability of quantification and structural analysis of the long RNA of the RNAi GMO. Our work shows great potential in a wide range of RNAi GMO samples.
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Affiliation(s)
- Li Xu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Jiawei Qi
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China. and College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, P.R. China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Wen Liang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Lele Wang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Zhenzhou Yang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Xue Yang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Yu Qi
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Manlei Duan
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Keke Zhao
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Jie Gu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Yiji Shen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Pinhua Rao
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, P.R. China
| | - Min Ding
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Shuzhen Ren
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
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Zhu H, Zhang H, Xu Y, Laššáková S, Korabečná M, Neužil P. PCR past, present and future. Biotechniques 2020; 69:317-325. [PMID: 32815744 PMCID: PMC7439763 DOI: 10.2144/btn-2020-0057] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.
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Affiliation(s)
- Hanliang Zhu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Haoqing Zhang
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Ying Xu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Soňa Laššáková
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Marie Korabečná
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Pavel Neužil
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
- Brno University of Technology, Central European Institute
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Electrical
Engineering and Communications, Technická 3058/10, 616 00 Brno,
Czech Republic
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Fleming AM, Burrows CJ. Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters. J Am Chem Soc 2020; 142:1115-1136. [PMID: 31880930 PMCID: PMC6988379 DOI: 10.1021/jacs.9b11050] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living in an oxygen atmosphere demands an ability to thrive in the presence of reactive oxygen species (ROS). Aerobic organisms have successfully found solutions to the oxidative threats imposed by ROS by evolving an elaborate detoxification system, upregulating ROS during inflammation, and utilizing ROS as messenger molecules. In this Perspective, recent studies are discussed that demonstrate ROS as signaling molecules for gene regulation by combining two emergent properties of the guanine (G) heterocycle in DNA, namely, oxidation sensitivity and a propensity for G-quadruplex (G4) folding, both of which depend upon sequence context. In human gene promoters, this results from an elevated 5'-GG-3' dinucleotide frequency and GC enrichment near transcription start sites. Oxidation of DNA by ROS drives conversion of G to 8-oxo-7,8-dihydroguanine (OG) to mark target promoters for base excision repair initiated by OG-glycosylase I (OGG1). Sequence-dependent mechanisms for gene activation are available to OGG1 to induce transcription. Either OGG1 releases OG to yield an abasic site driving formation of a non-canonical fold, such as a G4, to be displayed to apurinic/apyrimidinic 1 (APE1) and stalling on the fold to recruit activating factors, or OGG1 binds OG and facilitates activator protein recruitment. The mechanisms described drive induction of stress response, DNA repair, or estrogen-induced genes, and these pathways are novel potential anticancer targets for therapeutic intervention. Chemical concepts provide a framework to discuss the regulatory or possible epigenetic potential of the OG modification in DNA, in which DNA "damage" and non-canonical folds collaborate to turn on or off gene expression. The next steps for scientific discovery in this growing field are discussed.
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Affiliation(s)
- Aaron M. Fleming
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J. Burrows
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
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Green MR, Sambrook J. Polymerase Chain Reaction. Cold Spring Harb Protoc 2019; 2019:2019/6/pdb.top095109. [PMID: 31160389 DOI: 10.1101/pdb.top095109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The polymerase chain reaction (PCR) underlies almost all of modern molecular cloning. Using PCR, a defined target sequence that occurs once within a DNA of high complexity and large size-an entire mammalian genome, for example-can be rapidly and selectively amplified in a quasi-exponential chain reaction that generates millions of copies. The reaction is simple to set up, cheap, and undemanding, the only requirement being some knowledge of the nucleotide sequences of the target. In addition to its simplicity, PCR is robust, speedy, flexible, and sensitive.
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