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Archer M, Xu J. Current Practices for Reference Gene Selection in RT-qPCR of Aspergillus: Outlook and Recommendations for the Future. Genes (Basel) 2021; 12:genes12070960. [PMID: 34202507 PMCID: PMC8307107 DOI: 10.3390/genes12070960] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Aspergillus is a genus of filamentous fungi with vast geographic and ecological distributions. Species within this genus are clinically, agriculturally and biotechnologically relevant, leading to increasing interest in elucidating gene expression dynamics of key metabolic and physiological processes. Reverse-transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a sensitive and specific method of quantifying gene expression. A crucial step for comparing RT-qPCR results between strains and experimental conditions is normalisation to experimentally validated reference gene(s). In this review, we provide a critical analysis of current reference gene selection and validation practices for RT-qPCR gene expression analyses of Aspergillus. Of 90 primary research articles obtained through our PubMed query, 17 experimentally validated the reference gene(s) used. Twenty reference genes were used across the 90 studies, with beta-tubulin being the most used reference gene, followed by actin, 18S rRNA and glyceraldehyde 3-phosphate dehydrogenase. Sixteen of the 90 studies used multiple reference genes for normalisation. Failing to experimentally validate the stability of reference genes can lead to conflicting results, as was the case for four studies. Overall, our review highlights the need to experimentally validate reference genes in RT-qPCR studies of Aspergillus.
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Affiliation(s)
| | - Jianping Xu
- Correspondence: ; Tel.: +1-905-525-9140 (ext. 27934); Fax: +1-905-522-6066
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Maeda H, Katase T, Sakai D, Takeuchi M, Kusumoto KI, Amano H, Ishida H, Abe K, Yamagata Y. A novel non-thermostable deuterolysin from Aspergillus oryzae. Biosci Biotechnol Biochem 2016; 80:1813-9. [PMID: 27050120 DOI: 10.1080/09168451.2016.1166933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Three putative deuterolysin (EC 3.4.24.29) genes (deuA, deuB, and deuC) were found in the Aspergillus oryzae genome database ( http://www.bio.nite.go.jp/dogan/project/view/AO ). One of these genes, deuA, was corresponding to NpII gene, previously reported. DeuA and DeuB were overexpressed by recombinant A. oryzae and were purified. The degradation profiles against protein substrates of both enzymes were similar, but DeuB showed wider substrate specificity against peptidyl MCA-substrates compared with DeuA. Enzymatic profiles of DeuB except for thermostability also resembled those of DeuA. DeuB was inactivated by heat treatment above 80° C, different from thermostable DeuA. Transcription analysis in wild type A. oryzae showed only deuB was expressed in liquid culture, and the addition of the proteinous substrate upregulated the transcription. Furthermore, the NaNO3 addition seems to eliminate the effect of proteinous substrate for the transcription of deuB.
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Affiliation(s)
- Hiroshi Maeda
- a Department of Applied Biological Chemistry, The Graduate School of Agriculture , Tokyo University of Agriculture and Technology , Fuchu , Tokyo , Japan
| | - Toru Katase
- b Division of Life Science, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan.,c Amano Enzyme Inc , Nagoya , Japan
| | - Daisuke Sakai
- a Department of Applied Biological Chemistry, The Graduate School of Agriculture , Tokyo University of Agriculture and Technology , Fuchu , Tokyo , Japan
| | - Michio Takeuchi
- a Department of Applied Biological Chemistry, The Graduate School of Agriculture , Tokyo University of Agriculture and Technology , Fuchu , Tokyo , Japan
| | | | | | - Hiroki Ishida
- e Gekkeikan Sake Co., Ltd , Fushimi-ku, Kyoto , Japan
| | - Keietsu Abe
- b Division of Life Science, Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Youhei Yamagata
- a Department of Applied Biological Chemistry, The Graduate School of Agriculture , Tokyo University of Agriculture and Technology , Fuchu , Tokyo , Japan
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