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Peng F, Zou Y, Liu X, Yang Y, Chen J, Nie J, Huang D, Bai Z. The murein endopeptidase MepA regulated by MtrAB and MprAB participate in cell wall homeostasis. Res Microbiol 2024; 175:104188. [PMID: 38286394 DOI: 10.1016/j.resmic.2024.104188] [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: 04/04/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
The complete genome of Corynebacterium glutamicum contain a gene encoding murein endopeptidase MepA which maintain cell wall homeostasis by regulating peptidoglycan biosynthesis. In this study, we investigate the physiological function, localization and regulator of MepA. The result shows that mepA overexpression lead to peptidoglycan degradation and the defects in cell division. MepA-EGFP was shown to localizes exclusively at the cell cell septum. In addition, mepA overexpression increased cell permeability and reduced the resistance of cells to isoniazid, an antibiotic used to treat Mycobacterium tuberculosis infection. Furthermore, transcription analysis showed that mepA affected cell division and membrane transport pathways, and was coordinately regulated by the two-component systems MtrAB and MprAB(CgtS/R2).
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Affiliation(s)
- Feng Peng
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Yu Zou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Xiuxia Liu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China.
| | - Yankun Yang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Jianqi Nie
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Danni Huang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Zhonghu Bai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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2
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Lin B, He D, Wen W, Lin B, Li Y, Chen X. Whole genome sequencing and functional analysis of porcine-borne Bacillus coagulans LYBC06. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2155568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Biaosheng Lin
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
- Key Laboratory of Fujian Universities Preventive Veterinary Medicine and Biotechnology, Biotechnology and Health products, Engineering Technology Research Center, Longyan University, Longyan, Fujian, PR China
| | - Dingyan He
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
| | - Wenying Wen
- Food Inspection Laboratory, Quality Measurement Inspection and Testing Center, Wuping County Market Supervisory Authority, Wuping, Fujian, PR China
| | - Bin Lin
- Project Management Office, Agricultural and Social Development Section, Longyan Science and Technology Bureau, Longyan, Fujian, PR China
| | - Yan Li
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
| | - Xiaohong Chen
- Department of Biotechnology, College of Life Science, Longyan University, Longyan, Fujian, PR China
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3
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Ju Y, Zhang H, Du X, Wei J, Liu J, Wei L, Liu Q, Xu N. DRAGON: Harnessing the power of DNA repair for accelerating genome evolution in Corynebacterium glutamicum. Metab Eng 2023; 79:182-191. [PMID: 37579915 DOI: 10.1016/j.ymben.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Hypermutation is a robust phenotype characterized by high elevation of spontaneous mutation rates, which has been shown to facilitate rapid adaptation to the stressful environments by hitchhiking with favorable mutations. Accumulating evidence argues that deficient DNA repair can give rise to hypermutation events in bacteria. Here, we provided a comprehensive survey of DNA repair systems to identify promising targets ensuring high DNA fidelity in Corynebacterium glutamicum. Four effective DNA repair factors, including nucS, tag, xpb, and dinP, were found to be strongly associated with the occurrence of hypermutable phenotypes, and these targets were then engineered to establish a CRISPRi-based all-in-one plasmid system for genome mutagenesis. On the basis of these findings, we presented a novel evolutionary engineering method named "DNA repair-assisted genome evolution (DRAGON)". As a proof-of-concept, DRAGON strategy was successfully applied to facilitate rapid acquisition of microbial robustness in C. glutamicum, such as increased tolerances towards kanamycin, acidic pH and high L-serine, showing its promise and potential for rapid strain improvement. Overall, our study will offer new insights into the understanding of DNA repair and evolutionary adaptation in C. glutamicum.
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Affiliation(s)
- Yun Ju
- Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Hongyu Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, PR China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Xiaocong Du
- Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jingxuan Wei
- Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jun Liu
- University of Chinese Academy of Sciences, Beijing, 100049, PR China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Liang Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, PR China.
| | - Qingdai Liu
- Tianjin University of Science and Technology, Tianjin, 300457, PR China.
| | - Ning Xu
- University of Chinese Academy of Sciences, Beijing, 100049, PR China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, PR China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China.
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Yu X, Li S, Feng H, Liao X, Xing XH, Bai Z, Liu X, Zhang C. CRISPRi-microfluidics screening enables genome-scale target identification for high-titer protein production and secretion. Metab Eng 2023; 75:192-204. [PMID: 36572334 DOI: 10.1016/j.ymben.2022.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/25/2022]
Abstract
Genome-scale target identification promises to guide microbial cell factory engineering for higher-titer production of biomolecules such as recombinant proteins (r-protein), but challenges remain due to the need not only for comprehensive genotypic perturbation but also in conjunction with high-throughput phenotypic screening strategies. Here, we developed a CRISPRi-microfluidics screening platform to systematically identify crucial gene targets that can be engineered to enhance r-protein secretion in Corynebacterium glutamicum. We created a CRISPR interference (CRISPRi) library containing 46,549 single-guide RNAs, where we aimed to unbiasedly target all genes for repression. Meanwhile, we developed a highly efficient droplet-based microfluidics system integrating the FlAsH-tetracysteine assay that enables screening of millions of strains to identify potential knockdowns conducive to nanobody VHH secretion. Among our highest-ranking candidates are a slew of previously unknown targets involved in transmembrane transport, amino-acid metabolism and redox regulation. Guided by these findings, we eventually constructed a hyperproducer for multiple proteins via combinatorial engineering of redox-response transcription factors. As the near-universal applicability of CRISPRi technology and the FlAsH-based screening platform, this procedure might be expanded to include a varied variety of microbial species and recombinant proteins.
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Affiliation(s)
- Xinyu Yu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Shuang Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xihao Liao
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Zhonghu Bai
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiuxia Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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5
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Development of a novel platform for recombinant protein production in Corynebacterium glutamicum on ethanol. Synth Syst Biotechnol 2022; 7:765-774. [PMID: 35387228 PMCID: PMC8942793 DOI: 10.1016/j.synbio.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/04/2022] [Accepted: 03/15/2022] [Indexed: 02/03/2023] Open
Abstract
Corynebacterium glutamicum represents an emerging recombinant protein expression factory due to its ideal features for protein secretion, but its applicability is harmed by the lack of an autoinduction system with tight regulation and high yield. Here, we propose a new recombinant protein manufacturing platform that leverages ethanol as both a delayed carbon source and an inducer. First, we reanalysed the native inducible promoter PICL from the acetate uptake operon and found that its limited capacity is the result of the inadequate translation initial architecture. The two strategies of bicistronic design and ribozyme-based insulator can ensure the high activity of this promoter. Next, through transcriptional engineering that alters transcription factor binding sites (TFBSs) and the first transcribed sequence, the truncated promoter PA256 with a dramatically higher transcription level was generated. When producing the superfolder green fluorescent protein (sfGFP) under 1% ethanol conditions, PA256 exhibited substantially lower protein accumulation in prophase but an approximately 2.5-fold greater final yield than the strong promoter PH36. This superior expression mode was further validated using two secreted proteins, camelid antibody fragment (VHH) and endoxylanase (XynA). Furthermore, utilizing CRISPRi technology, ethanol utilization blocking strains were created, and PA256 was shown to be impaired in the phosphotransacetylase (PTA) knockdown strains, indicating that ethanol metabolism into the tricarboxylic acid cycle is required for PA256 upregulation. Finally, this platform was applied to produce the “de novo design” protein NEO-2/15, and by introducing the N-propeptide of CspB, NEO-2/15 was effectively secreted with the accumulation 281 mg/L obtained after 24 h of shake-flask fermentation. To the best of our knowledge, this is the first report of NEO-2/15 secretory overexpression.
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Amoah OJ, Nguyen HT, Sohng JK. N-Glucosylation in Corynebacterium glutamicum with YdhE from Bacillus lichenformis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113405. [PMID: 35684346 PMCID: PMC9182490 DOI: 10.3390/molecules27113405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/23/2022]
Abstract
Corynebacterium glutamicum is traditionally known as a food-grade microorganism due to its high ability to produce amino acids and its endotoxin-free recombinant protein expression factory. In recent years, studies to improve the activities of useful therapeutics and pharmaceutical compounds have led to the engineering of the therapeutically advantageous C. glutamicum cell factory system. One of the well-studied ways to improve the activities of useful compounds is glucosylation with glycosyltransferases. In this study, we successfully and efficiently glycosylated therapeutic butyl-4-aminobenzoate and other N-linked compounds in C. glutamicum using a promiscuous YdhE, which is a glycosyltransferase from Bacillus lichenformis. For efficient glucosylation, components, such as promoter, codons sequence, expression temperatures, and substrate and glucose concentrations were optimized. With glucose as the sole carbon source, we achieved a conversion rate of almost 96% of the glycosylated products in the culture medium. The glycosylated product of high concentration was successfully purified by a simple purification method, and subjected to further analysis. This is a report of the in vivo cultivation and glucosylation of N-linked compounds in C. glutamicum.
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Affiliation(s)
- Obed Jackson Amoah
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si 31460, Chungnam, Korea; (O.J.A.); (H.T.N.)
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si 31460, Chungnam, Korea; (O.J.A.); (H.T.N.)
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si 31460, Chungnam, Korea; (O.J.A.); (H.T.N.)
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si 31460, Chungnam, Korea
- Correspondence: ; Tel.: +82-(41)-530-2246; Fax: +82-(41)-530-8229
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7
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Ye Y, Zhong M, Zhang Z, Chen T, Shen Y, Lin Z, Wang Y. Genomic Iterative Replacements of Large Synthetic DNA Fragments in Corynebacterium glutamicum. ACS Synth Biol 2022; 11:1588-1599. [PMID: 35290032 DOI: 10.1021/acssynbio.1c00644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic genomics will advance our understanding of life and allow us to rebuild the genomes of industrial microorganisms for enhancing performances. Corynebacterium glutamicum, a Gram-positive bacterium, is an important industrial workhorse. However, its genome synthesis is impeded by the low efficiencies in DNA delivery and in genomic recombination/replacement. In the present study, we describe a genomic iterative replacement system based on RecET recombination for C. glutamicum, involving the successive integration of up to 10 kb DNA fragments obtained in vitro, and the transformants are selected by the alternative use of kanR and speR selectable markers. As a proof of concept, we systematically redesigned and replaced a 54.3 kb wild-type sequence of C. glutamicumATCC13032 with its 55.1 kb synthetic counterpart with several novel features, including decoupled genes, the standard PCRTags, and 20 loxPsym sites, which was for the first time incorporated into a bacterial genome. The resulting strain semi-synCG-A1 had a phenotype and fitness similar to the wild-type strain under various stress conditions. The stability of the synthetic genome region faithfully maintained over 100 generations of nonselective growth. Genomic deletions, inversions, and translocations occurred in the synthetic genome region upon induction of synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE), revealing potential genetic flexibility for C. glutamicum. This strategy can be used for the synthesis of a larger region of the genome and facilitate the endeavors for metabolic engineering and synthetic biology of C. glutamicum.
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Affiliation(s)
- Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou 510006, China
| | - Minmin Zhong
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou 510006, China
| | - Zhanhua Zhang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou 510006, China
| | - Tai Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, University Park, Guangzhou 510006, China
| | - Yun Wang
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
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8
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Dai Y, Kou H, Guo X, Gong Z, Liu H, Liu Y, Wang H, Guo Y. Identification and validation of reference genes for RT-qPCR analysis in fetal rat pancreas. Reprod Toxicol 2021; 105:211-220. [PMID: 34537367 DOI: 10.1016/j.reprotox.2021.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/20/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022]
Abstract
The choice of reference gene is crucial for quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) assay. To screen and determine the suitable reference genes in fetal rat pancreas, we selected eight candidate reference genes (Gapdh, Actb, Rn18 s, B2m, Rpl13a, Tbp, Ywhaz and Ubc), and evaluated the constancy of gene expression from fetal rat pancreases in non-pathological situation and prenatal dexamethasone exposure (PDE) model, using four algorithms: GeNorm, NormFinder, Bestkeeper and Comparative ΔCt method. In addition, the alteration of mRNA levels of pancreatic insulin was compared between control and PDE groups to validate the reliability of selected reference genes for data normalization of RT-qPCR. The comprehensive ranking of reference genes under physiological condition was as follow: Gapdh > Actb > Ywhaz > Ubc > Rn18s > Rpl13a > B2m > Tbp (female); Actb > Ywhaz > Gapdh > Ubc > B2m > Rpl13a > Rn18 s | Tbp (male). The top ranking reference genes were also stably expressed in PDE fetal pancreas. The best reference gene combinations are: Ywhaz+Actb for female and Ywhaz+Gapdh for male fetal rat pancreas, respectively. Compared with low ranking or single reference gene, the change trend of insulin mRNA normalized by the best reference gene combination between control and PDE groups was more significant and consistent with that of serum insulin level. In conclusion, our results provided the optimal combination of stable reference genes for RT-qPCR assay in pancreatic developmental toxicity study.
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Affiliation(s)
- Yongguo Dai
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Hao Kou
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China; Department of Pharmacy, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Xiaoling Guo
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Zheng Gong
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Heze Liu
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Yi Liu
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Hui Wang
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China.
| | - Yu Guo
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, Hubei Province, People's Republic of China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei Province, People's Republic of China.
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9
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Zhao X, Chen H, Zhu Y, Liu Y, Gao L, Wang H, Ao Y. The selection and identification of compound housekeeping genes for quantitative real-time polymerase chain reaction analysis in rat fetal kidney. J Appl Toxicol 2021; 42:360-370. [PMID: 34374451 DOI: 10.1002/jat.4221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/12/2021] [Accepted: 07/05/2021] [Indexed: 11/06/2022]
Abstract
During quantitative real-time polymerase chain reaction (RT-qPCR) data analysis, the selection of optimal housekeeping gene is necessary to ensure the accuracy of results. It is noteworthy that housekeeping genes commonly used in adult studies may not be applicable for fetus. However, the stability analysis of housekeeping gene in fetal kidney has not been reported. This study intends to screen the applicable compound housekeeping genes in rat fetal kidney. In this study, eight housekeeping genes used in kidney studies based on literature reports (GAPDH, ACTB, 18S, HPRT, YWHAZ, HMBS, PPIA, and TBP) were selected as the research object. Their expression levels in the rat fetal kidney in physiological condition and the intrauterine growth retardation (IUGR) model induced by prenatal dexamethasone exposure (PDE) (0.2 mg/kg·day from gestation Days 9 to 20) was measured. Furthermore, these eight housekeeping genes were used to conduct relative quantitative analysis of nephrin expression in the fetal kidney in PDE-induced IUGR model, to compare the influence of choosing different housekeeping gene on data analysis of nephrin expression and to verify the reliability of selected compound housekeeping genes. In this study, stable housekeeping genes of fetal kidney tissues in PDE-induced IUGR model were identified: ACTB, GAPDH, TBP, and HMBS for males; ACTB, YWHAZ, and GAPDH for females. Besides, our results suggest that ACTB + GAPDH were the best compound housekeeping genes for normalization analysis in male fetal kidney studies, and ACTB + YWHAZ in females. This study will provide an experimental evidence basis for the selection of housekeeping genes in the RT-qPCR experiment in renal development toxicology-related models.
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Affiliation(s)
- Xiaoqi Zhao
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China
| | - Haiyun Chen
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China
| | - Yanan Zhu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China
| | - Yi Liu
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China
| | - Lili Gao
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China
| | - Hui Wang
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China
| | - Ying Ao
- Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China
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10
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Toorani T, Mackie PM, Mastromonaco GF. Validation of reference genes for use in untreated bovine fibroblasts. Sci Rep 2021; 11:10253. [PMID: 33986374 PMCID: PMC8119449 DOI: 10.1038/s41598-021-89657-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/27/2021] [Indexed: 12/20/2022] Open
Abstract
Proper normalization of RT-qPCR data is pivotal to the interpretation of results and accuracy of scientific conclusions. Though different approaches may be taken, normalization against multiple reference genes is now standard practice. Genes traditionally used and deemed constitutively expressed have demonstrated variability in expression under different experimental conditions, necessitating the proper validation of reference genes prior to utilization. Considering the wide use of fibroblasts in research and scientific applications, it is imperative that suitable reference genes for fibroblasts of different animal origins and conditions be elucidated. Previous studies on bovine fibroblasts have tested limited genes and/or samples. Herein, we present an extensive study investigating the expression stability of 16 candidate reference genes across 7 untreated bovine fibroblast cell lines subjected to controlled conditions. Data were analysed using various statistical tools and algorithms, including geNorm, NormFinder, BestKeeper, and RefFinder. A combined use of GUSB and RPL13A was determined to be the best approach for data normalization in untreated bovine fibroblasts.
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Affiliation(s)
- T Toorani
- Reproductive Sciences, Toronto Zoo, Scarborough, ON, M1B 5K7, Canada
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - P M Mackie
- Reproductive Sciences, Toronto Zoo, Scarborough, ON, M1B 5K7, Canada
| | - G F Mastromonaco
- Reproductive Sciences, Toronto Zoo, Scarborough, ON, M1B 5K7, Canada.
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Validation of stable reference genes in Staphylococcus aureus to study gene expression under photodynamic treatment: a case study of SEB virulence factor analysis. Sci Rep 2020; 10:16354. [PMID: 33004977 PMCID: PMC7530716 DOI: 10.1038/s41598-020-73409-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022] Open
Abstract
Staphylococcal enterotoxin B (SEB), encoded by the seb gene, is a virulence factor produced by Staphylococcus aureus that is involved mainly in food poisoning and is known to act as an aggravating factor in patients with atopic dermatitis. Research results in animal infection models support the concept that superantigens, including SEB contribute to sepsis and skin and soft tissue infections. In contrast to antibiotics, antimicrobial photodynamic inactivation (aPDI) is a promising method to combat both bacterial cells and virulence factors. The main aims of this research were to (1) select the most stable reference genes under sublethal aPDI treatments and (2) evaluate the impact of aPDI on seb. Two aPDI combinations were applied under sublethal conditions: rose bengal (RB) and green light (λmax = 515 nm) and new methylene blue (NMB) and red light (λmax = 632 nm). The stability of ten candidate reference genes (16S rRNA, fabD, ftsZ, gmk, gyrB, proC, pyk, rho, rpoB and tpiA) was evaluated upon aPDI using four software packages—BestKeeper, geNorm, NormFinder and RefFinder. Statistical analyses ranked ftsZ and gmk (RB + green light) and ftsZ, proC, and fabD (NMB + red light) as the most stable reference genes upon photodynamic treatment. Our studies showed downregulation of seb under both aPDI conditions, suggesting that aPDI could decrease the level of virulence factors.
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