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Pan Y, Zhao Y, Zeng HR, Wu JQ, Song YY, Rao YH, Li GQ, Jin L. Reference Genes for Expression Analyses by qRT-PCR in Enterobacter cancerogenus. Microorganisms 2024; 12:1024. [PMID: 38792853 PMCID: PMC11123693 DOI: 10.3390/microorganisms12051024] [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: 03/25/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
The Enterobacter cancerogenus strain EcHa1 was isolated from the dead larvae of Helicoverpa armigera, and has the potential for biocontrol of some Lepidoptera insects. In order to screen insecticidal-related genes by qRT-PCR, stable endogenous reference genes used for normalizing qRT-PCR data were selected and evaluated from 13 housekeeping genes (HKGs). The expression levels of the HKGs were determined using qRT-PCR under different experimental conditions, including two culture temperatures and three bacterial OD values. Five stability analysis methods (Ct, BestKeeper, NormFinder, geNorm, and RefFinder) were used to comprehensively rank the candidate genes. The results showed that the optimal reference genes varied under different experimental conditions. The combination of gyrA and gyrB was recommended as the best reference gene combination at 28 °C, while gyrA and rpoB was the best combination at 37 °C. When the OD values were 0.5, 1.0 and 2.0, the recommended reference gene combinations were ftsZ and gyrA, rpoB and gyrB, and gyrA and pyk, respectively. The most suitable reference genes were gyrA and gyrB under all experimental conditions. Using gyrA and gyrB as the reference genes for qRT-PCR, EcHa1 was found to invade all tissues of the H. armigera larvae, and expressed a candidate pathogenic factor Hcp at high levels in gut, Malpighian tubules, and epidermis tissues. This study not only establishes an accurate and reliable normalization for qRT-PCR in entomopathogenic bacteria but also lays a solid foundation for further study of functional genes in E. cancerogenus.
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Affiliation(s)
| | | | | | | | | | | | | | - Lin Jin
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.P.); (Y.Z.); (H.-R.Z.); (J.-Q.W.); (Y.-Y.S.); (Y.-H.R.); (G.-Q.L.)
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2
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Pizarro L, Magalhães C, Almeida CMR, Carvalho MDF, Semedo M. Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4. FEMS Microbiol Lett 2023; 370:fnad047. [PMID: 37279908 PMCID: PMC10337742 DOI: 10.1093/femsle/fnad047] [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: 01/31/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.
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Affiliation(s)
- Leonor Pizarro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Faculty of Biotechnology, Catholic University of Portugal, Porto 4169-005, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Biology, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - Maria de Fátima Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
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3
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Sánchez-Osuna M, Cortés P, Lee M, Smith AT, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Res 2021; 49:11050-11066. [PMID: 34614190 PMCID: PMC8565304 DOI: 10.1093/nar/gkab773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/18/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transcriptional repressor, which controls genes involved in DNA repair, mutagenesis and cell-cycle control. To date, the SOS response has been characterized in most major bacterial groups, with the notable exception of the Bacteroidetes. No LexA homologs had been identified in this large, diverse and ecologically important phylum, suggesting that it lacked an inducible mechanism to address DNA damage. Here, we report the identification of a novel family of transcriptional repressors in the Bacteroidetes that orchestrate a canonical response to DNA damage in this phylum. These proteins belong to the S24 peptidase family, but are structurally different from LexA. Their N-terminal domain is most closely related to CI-type bacteriophage repressors, suggesting that they may have originated from phage lytic phase repressors. Given their role as SOS regulators, however, we propose to designate them as non-canonical LexA proteins. The identification of a new class of repressors orchestrating the SOS response illuminates long-standing questions regarding the origin and plasticity of this transcriptional network.
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Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Mark Lee
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Ivan Erill
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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Bao X, Wang F, Yang R, Zhang Y, Fu L, Wang Y. Ornithine Decarboxylation System of Shewanella baltica Regulates Putrescine Production and Acid Resistance. J Food Prot 2021; 84:303-309. [PMID: 33003195 DOI: 10.4315/jfp-20-227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/30/2020] [Indexed: 01/18/2023]
Abstract
ABSTRACT Shewanella baltica, one of the dominant spoilers of seafoods, can synthesize putrescine from ornithine under acidic conditions, which could result in food spoilage and health problems. We identified three regulatory enzymes (SpeC, SpeF, and PotE) in the ornithine decarboxylation (ODC) pathway of S. baltica by searching the NCBI database and exploring their functional roles through gene knock-out technology. The ornithine decarboxylase SpeC is an auxiliary adjustor of the ODC system, whereas the ornithine-putrescine transporter SpeE and ornithine decarboxylase SpeF participate in the production of extracellular putrescine. Exogenous addition of ornithine and putrescine promotes the extracellular secretion of putrescine by upregulating the expression of speF and potE. The putrescine biosynthesis and alkalization of cytoplasm is enhanced at weak acidic pH compared with neutral pH, especially at pH 6.0. The maximum upregulation of ODC genes and the optimum decarboxylation activity of SpeF are achieved in a weak acidic environment (pH 6.0), suggesting that the ODC pathway plays an important role in putrescine production and the cytoplasmic acid counteraction of S. baltica. This study contributes to a wider understanding of spoilage mechanisms in food systems and provides theoretical support for developing novel seafood preservation methods. HIGHLIGHTS
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Affiliation(s)
- Xingyue Bao
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, People's Republic of China
| | - Feifei Wang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, People's Republic of China
| | - Rendi Yang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, People's Republic of China
| | - Yan Zhang
- Hebei Food Inspection and Research Institute, Shijiazhuang 050091, People's Republic of China
| | - Linglin Fu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, People's Republic of China
| | - Yanbo Wang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, People's Republic of China
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Wang H, Lv Y, Wang C, Leng D, Yan Y, Blessing Fasae M, Madiha Zahra S, Jiang Y, Wang Z, Yang B, Bai Y. Systematic Analysis of Intestinal MicroRNAs Expression in HCC: Identification of Suitable Reference Genes in Fecal Samples. Front Genet 2019; 10:687. [PMID: 31456816 PMCID: PMC6700738 DOI: 10.3389/fgene.2019.00687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 07/01/2019] [Indexed: 01/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is an extremely fatal malignancy. Intestinal microRNAs, which can be detected in fecal samples in humans may be involved in the pathological process of HCC. Therefore, screening for functional intestinal microRNAs in fecal samples and investigating their potential roles in the molecular progression of HCC are necessary. Quantitative real-time PCR (qRT-PCR) has been widely used in microRNA expression studies. However, few genes have been reported as reference genes for intestinal microRNAs in fecal samples. In order to obtain a more accurately analyzed intestinal microRNAs expression, we first searched for reliable reference genes for intestinal microRNAs expression normalization during qRT-PCR, using three software packages (GeNorm, NormFinder, and Bestkeeper). Next we screened and predicted the target genes of the differentially intestinal microRNAs of control and HCC mice through quantitative RT-PCR or miRtarBase. Finally, we also analyzed the mRNA targets for enrichment of Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using the DAVID Bioinformatic Resources database. This study has successfully screened relatively suitable reference genes and we have discovered that the differential intestinal microRNAs play significant roles in the development of HCC. The top reference genes identified in this study could provide a theoretical foundation for the reasonable selection of a suitable reference gene. Furthermore, the detection of intestinal microRNAs expression may serve as a promising therapeutic target for the diagnosis and treatment of HCC.
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Affiliation(s)
- Hui Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yuan Lv
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Cao Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Dongjing Leng
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yan Yan
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Moyondafoluwa Blessing Fasae
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Syeda Madiha Zahra
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yanan Jiang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China.,Chronic Disease Research Institute, Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Zhiguo Wang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Baofeng Yang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China.,Chronic Disease Research Institute, Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yunlong Bai
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Medicine Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China.,Chronic Disease Research Institute, Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
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Reference genes for real-time RT-PCR expression studies in an Antarctic Pseudomonas exposed to different temperature conditions. Extremophiles 2019; 23:625-633. [DOI: 10.1007/s00792-019-01109-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022]
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7
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Casagrande Pierantoni D, Corte L, Roscini L, Cardinali G. High-Throughput Rapid and Inexpensive Assay for Quantitative Determination of Low Cell-Density Yeast Cultures. Microorganisms 2019; 7:E32. [PMID: 30682881 PMCID: PMC6406537 DOI: 10.3390/microorganisms7020032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/12/2019] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
A procedure for microbial cell density determination with a high-throughput densitometric assay was developed to allow a precise quantification of both free and sessile cells, such as those of a biofilm, with a large range from low to high cell densities. Densitometry was chosen because it allows fast, rapid and cost-effective measures; it is non-disruptive; and has an easy learning curve. The method setup, and the further validation, was carried out with strains of Candida albicans, C. tropicalis and C. parapsilosis. Equations were developed at the level of the single strains, of the three species and finally a general one applicable to all three species. In the cross validation, with strains absent from the training set, the method was shown to be robust and flexible. The best results were obtained with species specific equations, although the global equation performed almost as well in terms of correlation between real and estimated density values. In all cases, a correlation around 0.98 between effective and predicted density was obtained with figures ranging from 10² to 10⁸ cells mL-1. The entire analytical part of the procedure can be accomplished with a MS Excel macro provided free of charge.
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Affiliation(s)
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy.
| | - Luca Roscini
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials, Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy.
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy.
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