1
|
Nguyen MT, Kim SA, Cheng YY, Hong SH, Jin YS, Han NS. A qPCR Method to Assay Endonuclease Activity of Cas9-sgRNA Ribonucleoprotein Complexes. J Microbiol Biotechnol 2023; 33:1228-1237. [PMID: 37415091 PMCID: PMC10580886 DOI: 10.4014/jmb.2305.05010] [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: 05/10/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
The CRISPR-Cas system has emerged as the most efficient genome editing technique for a wide range of cells. Delivery of the Cas9-sgRNA ribonucleoprotein complex (Cas9 RNP) has gained popularity. The objective of this study was to develop a quantitative polymerase chain reaction (qPCR)-based assay to quantify the double-strand break reaction mediated by Cas9 RNP. To accomplish this, the dextransucrase gene (dsr) from Leuconostoc citreum was selected as the target DNA. The Cas9 protein was produced using recombinant Escherichia coli BL21, and two sgRNAs were synthesized through in vitro transcription to facilitate binding with the dsr gene. Under optimized in vitro conditions, the 2.6 kb dsr DNA was specifically cleaved into 1.1 and 1.5 kb fragments by both Cas9-sgRNA365 and Cas9-sgRNA433. By monitoring changes in dsr concentration using qPCR, the endonuclease activities of the two Cas9 RNPs were measured, and their efficiencies were compared. Specifically, the specific activities of dsr365RNP and dsr433RNP were 28.74 and 34.48 (unit/μg RNP), respectively. The versatility of this method was also verified using different target genes, uracil phosphoribosyl transferase (upp) gene, of Bifidobacterium bifidum and specific sgRNAs. The assay method was also utilized to determine the impact of high electrical field on Cas9 RNP activity during an efficient electroporation process. Overall, the results demonstrated that the qPCR-based method is an effective tool for measuring the endonuclease activity of Cas9 RNP.
Collapse
Affiliation(s)
- Minh Tri Nguyen
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
- Faculty of Biology, Dalat University, 01- Phu Dong Thien Vuong, Dalat, Vietnam
| | - Seul-Ah Kim
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ya-Yun Cheng
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sung Hoon Hong
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nam Soo Han
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| |
Collapse
|
2
|
Kim SA, Lee DH, Ryu BH, Han NS. Strain-specific barcode PCR and quantitative PCR assay for identification and enumeration of kimchi starter, Leuconostoc mesenteroides DRC1506. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
3
|
Gumustop I, Ortakci F. Comparative genomics of Leuconostoc lactis strains isolated from human gastrointestinal system and fermented foods microbiomes. BMC Genom Data 2022; 23:61. [PMID: 35918643 PMCID: PMC9344693 DOI: 10.1186/s12863-022-01074-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background Leuconostoc lactis forms a crucial member of the genus Leuconostoc and has been widely used in the fermentation industry to convert raw material into acidified and flavored products in dairy and plant-based food systems. Since the ecological niches that strains of Ln. lactis being isolated from were truly diverse such as the human gut, dairy, and plant environments, comparative genome analysis studies are needed to better understand the strain differences from a metabolic adaptation point of view across diverse sources of origin. We compared eight Ln. lactis strains of 1.2.28, aa_0143, BIOML-A1, CBA3625, LN19, LN24, WIKIM21, and WiKim40 using bioinformatics to elucidate genomic level characteristics of each strain for better utilization of this species in a broad range of applications in food industry. Results Phylogenomic analysis of twenty-nine Ln. lactis strains resulted in nine clades. Whole-genome sequence analysis was performed on eight Ln. lactis strains representing human gastrointestinal tract and fermented foods microbiomes. The findings of the present study are based on comparative genome analysis against the reference Ln. lactis CBA3625 genome. Overall, a ~ 41% of all CDS were conserved between all strains. When the coding sequences were assigned to a function, mobile genetic elements, mainly insertion sequences were carried by all eight strains. All strains except LN24 and WiKim40 harbor at least one intact putative prophage region, and two of the strains contained CRISPR-Cas system. All strains encoded Lactococcin 972 bacteriocin biosynthesis gene clusters except for CBA3625. Conclusions The findings in the present study put forth new perspectives on genomics of Ln. lactis via complete genome sequence based comparative analysis and further determination of genomic characteristics. The outcomes of this work could potentially pave the way for developing elements for future strain engineering applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01074-6.
Collapse
|
4
|
Shi Z, Li X, Fan X, Xu J, Liu Q, Wu Z, Pan D. PMA-qPCR method for the selective quantitation of viable lactic acid bacteria in fermented milk. Front Microbiol 2022; 13:984506. [PMID: 36160254 PMCID: PMC9491339 DOI: 10.3389/fmicb.2022.984506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
The number of viable lactic acid bacteria (LAB) is a key indicator of the quality of fermented milk. Currently, the combination of propidium monoazide (PMA) and qPCR has been applied in the quantification of viable bacteria in various matrices. In this research, the PMA-qPCR method was used to detect the number of viable bacteria of each LAB species in fermented milk. By analyzing pheS gene and 16S rRNA gene sequence similarities in five species of LAB, namely Lactobacillus delbrueckii subsp. bulgaricus, Lactiplantibacillus plantarum, Streptococcus thermophilus, Lactobacillus helveticus, and Lactococcus lactis subsp. lactis, the pheS gene resolved species identities better and was thus selected to design specific primers and probes. The pheS gene was cloned into the pUC19 vector and used to construct a standard curve for absolute quantification. Standard curves for quantification were constructed for each LAB species for serial dilutions between 1011 and 106 CFU/mL, with R2 > 0.99. The number of viable bacteria in the fermented milk detected by PMA-qPCR was significantly lower than that of qPCR (P < 0.05), indicating that PMA inhibited the amplification of DNA from dead cells. This was corroborated by the results from bacterial staining and plate count experiments. The proposed PMA-qPCR method provided rapid qualitative and quantitative determination of the number of viable bacteria for each LAB species in fermented milk within 3 h.
Collapse
Affiliation(s)
- Zihang Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Xiefei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Xiankang Fan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jue Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Qing Liu
- Nanjing Dairy Group, Nanjing, China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- *Correspondence: Zhen Wu,
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- Daodong Pan,
| |
Collapse
|
5
|
Premjit Y, Mitra J. Optimization of Electrospray-Assisted Microencapsulation of Probiotics (Leuconostoc lactis) in Soy Protein Isolate-Oil Particles Using Box-Behnken Experimental Design. FOOD BIOPROCESS TECH 2021. [DOI: 10.1007/s11947-021-02670-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
6
|
Xie X, Liu Z. Simultaneous enumeration of Cronobacter sakazakii and Staphylococcus aureus in powdered infant foods through duplex TaqMan real-time PCR. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
7
|
Su Z, Li Y, Pan L, He Z, Liu L, Zhang M. Nitrogen removal performance, quantitative detection and potential application of a novel aerobic denitrifying strain, Pseudomonas sp. GZWN4 isolated from aquaculture water. Bioprocess Biosyst Eng 2021; 44:1237-1251. [PMID: 33599872 DOI: 10.1007/s00449-021-02523-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/28/2021] [Indexed: 11/25/2022]
Abstract
A novel Pseudomonas sp. GZWN4 with the aerobic nitrogen removal ability was isolated from aquaculture water, whose removal efficiency of NO2--N, NO3--N and NH4+-N was 99.72%, 82.54% and 98.62%, respectively. The key genes involved in nitrogen removal, nxr, napA, narI, nirS, norB and nosZ, were successfully amplified and by combination with the results of nitrogen balance analysis, it was inferred that the denitrification pathway of strain GZWN4 was NO3--N → NO2--N → NO → N2O → N2. The strain GZWN4 had excellent nitrite removal performance at pH 7.0-8.5, temperature 25-30 ℃, C/N ratio 5-20, salinity 8-32‰ and dissolved oxygen concentration 2.52-5.73 mg L-1. The receivable linear correlation (R2 = 0.9809) was obtained with the range of quantification between l03 and 108 CFU mL-1 of the strain by enzyme-linked immunosorbent assay. Strain GZWN4 could maintain high abundance in the actual water and wastewater of mariculture and the removal efficiency of TN were 52.57% and 63.64%, respectively. The safety evaluation experiment showed that the strain GZWN4 had no hemolysis and high biosecurity toward shrimp Litopenaeus vannamei. The excellent nitrogen removal ability and adaptability to aquaculture environment made strain GZWN4 a promising candidate for treatment of water and wastewater in aquaculture.
Collapse
Affiliation(s)
- Zhaopeng Su
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, Shandong, China
| | - Yun Li
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, Shandong, China.
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, Shandong, China
| | - Ziyan He
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, Shandong, China
| | - Liping Liu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, Shandong, China
| | - Mengyu Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, Shandong, China
| |
Collapse
|
8
|
A Species-Specific qPCR Method for Enumeration of Lactobacillus sanfranciscensis, Lactobacillus brevis, and Lactobacillus curvatus During Cocultivation in Sourdough. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01920-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|