rpoB and efp are stable candidate reference genes for quantitative real-time PCR analysis in Saccharopolyspora spinosa

References

• Kirst HA. The spinosyn family of insecticides: realizing the potential of natural products research. J Antibiot (Tokyo). 2010;63(3):101–111.
   PubMed Web of Science ®Google Scholar
• Sanon A, Ba NM, Binso-Dabire CL, et al. Effectiveness of spinosad (naturalytes) in controlling the cowpea storage pest, Callosobruchus maculatus (Coleoptera: Bruchidae). J Econ Entomol. 2010;103(1):203–210.
   PubMed Web of Science ®Google Scholar
• Tao H, Zhang Y, Deng Z, et al. Strategies for enhancing the yield of the potent insecticide spinosad in actinomycetes. Biotechnol J. 2019;14(1):1700769.
   Web of Science ®Google Scholar
• Williams T, Valle J, Viñuela E. Is the naturally derived insecticide spinosad® compatible with insect natural enemies? Biocontrol Sci Techn. 2003;13(5):459–475.
   Web of Science ®Google Scholar
• Huang KX, Xia L, Zhang Y, et al. Recent advances in the biochemistry of spinosyns. Appl Microbiol Biotechnol. 2009;82(1):13–23.
   PubMed Web of Science ®Google Scholar
• Pan YL, Yang XY, Li J, Zhang RF, et al. Genome sequence of the spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395. J Bacteriol. 2011;193(12):3150–3151.
   PubMed Web of Science ®Google Scholar
• Derveaux S, Vandesompele J, Hellemans J. How to do successful gene expression analysis using real-time PCR. Methods. 2010;50(4):227–230.
   PubMed Web of Science ®Google Scholar
• Huggett JF, Dheda K, Bustin SA, et al. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005;6(4):279–284.
   PubMed Web of Science ®Google Scholar
• Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat Protoc. 2006;1(3):1559–1582.
   PubMed Web of Science ®Google Scholar
• Florindo C, Ferreira R, Borges V, et al. Selection of reference genes for real-time expression studies in Streptococcus agalactiae. J Microbiol Methods. 2012;90(3):220–227.
   PubMed Web of Science ®Google Scholar
• Løvdal T, Saha A. Reference gene selection in Carnobacterium maltaromaticum, Lactobacillus curvatus, and Listeria innocua subjected to temperature and salt stress. Mol Biotechnol. 2014;56(3):210–222.
   PubMed Web of Science ®Google Scholar
• Mcmillan M, Pereg L. Evaluation of reference genes for gene expression analysis using quantitative RT-PCR in Azospirillum brasilense. Plos One. 2014;9(5):e98162.
   PubMed Web of Science ®Google Scholar
• Sun Z, Deng J, Wu H, et al. Selection of stable reference genes for real-time quantitative PCR analysis in Edwardsiella tarda. J Microbiol Biotechnol. 2017;27(1):112–121.
   PubMed Web of Science ®Google Scholar
• Wen S, Chen X, Xu F, et al. Validation of reference genes for real-time quantitative PCR (qPCR) analysis of Avibacterium paragallinarum. PLoS One. 2016;11(12):e0167736.
   PubMed Web of Science ®Google Scholar
• Huang Y, Zhang X, Zhao C, et al. Improvement of spinosad production upon utilization of oils and manipulation of β-oxidation in a high-producing Saccharopolyspora spinosa strain. J Mol Microbiol Biotechnol. 2018;28(2):53–64.
   PubMed Web of Science ®Google Scholar
• Luo Y, Ding X, Xia L, et al. Comparative proteomic analysis of Saccharopolyspora spinosa SP06081 and PR2 strains reveals the differentially expressed proteins correlated with the increase of spinosad yield. Proteome Sci. 2011;9:40.
   PubMed Web of Science ®Google Scholar
• Tang Y, Xia L, Ding X, et al. Duplication of partial spinosyn biosynthetic gene cluster in Saccharopolyspora spinosa enhances spinosyn production. FEMS Microbiol Lett. 2011;325(1):22–29.
   PubMed Web of Science ®Google Scholar
• Rang J, He H, Yuan S, et al. Deciphering the metabolic pathway difference between Saccharopolyspora pogona and Saccharopolyspora spinosa by comparative proteomics and metabonomics. Front Microbiol. 2020;11:396.
   PubMed Web of Science ®Google Scholar
• Yang Q, Ding X, Liu X, et al. Differential proteomic profiling reveals regulatory proteins and novel links between primary metabolism and spinosad production in Saccharopolyspora spinosa. Microb Cell Fact. 2014;13(1):27.
   PubMedGoogle Scholar
• Zhang X, Xue C, Zhao F, et al. Suitable extracellular oxidoreduction potential inhibit rex regulation and effect central carbon and energy metabolism in Saccharopolyspora spinosa. Microb Cell Fact. 2014;13:98.
   PubMed Web of Science ®Google Scholar
• Zhao C, Huang Y, Guo C, et al. Heterologous expression of spinosyn biosynthetic gene cluster in Streptomyces species is dependent on the expression of rhamnose biosynthesis genes. J Mol Microbiol Biotechnol. 2017;27(3):190–198.
   PubMed Web of Science ®Google Scholar
• Zhang C, Xue C, Shen Y, et al. Selection of reference genes in Saccharopolyspora Spinosa for real-time PCR. Trans Tianjin Univ. 2015;21(5):461–467.
   Google Scholar
• Rio DC, Ares M, Hannon GJ, et al. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harb Protoc. 2010;2010(6):pdb.prot5439.
   PubMedGoogle Scholar
• Li S, Wang W, Li X, et al. Genome-wide identification and characterization of reference genes with different transcript abundances for Streptomyces coelicolor. Sci Rep. 2015;5:15840.
   PubMed Web of Science ®Google Scholar
• Tanaka Y, Komatsu M, Okamoto S, et al. Antibiotic overproduction by rpsL and rsmG mutants of various actinomycetes. Appl Environ Microbiol. 2009;75(14):4919–4922.
   PubMed Web of Science ®Google Scholar
• Saddhe AA, Malvankar MR, Kumar K. Selection of reference genes for quantitative real-time PCR analysis in halophytic plant Rhizophora apiculata. Peer J. 2018;6:e5226.
   PubMed Web of Science ®Google Scholar
• Sinha P, Singh VK, Suryanarayana L, et al. Evaluation and validation of housekeeping genes as reference for gene expression studies in pigeonpea (Cajanus cajan) under drought stress conditions. PLoS One. 2015;10(4):e0122847.
   PubMed Web of Science ®Google Scholar
• Andersen CL, Jensen JL, Rntoft TF. Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004;64(15):5245–5250.
   PubMed Web of Science ®Google Scholar
• Pfaffl MW, Tichopad A, Prgomet C, et al. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol Lett. 2004;26(6):509–515.
   PubMed Web of Science ®Google Scholar
• Vandesompele J, De Preter K, Pattyn F, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3(7):RESEARCH0034.1.
   Web of Science ®Google Scholar
• Bustin SA, Benes V, Garson JA, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55(4):611–622.
   PubMed Web of Science ®Google Scholar
• Bustin SA, Benes V, Nolan T, et al. Quantitative real-time RT-PCR-a perspective. J Mol Endocrinol. 2005;34(3):597–601.
   PubMed Web of Science ®Google Scholar
• Niu X, Chen M, Huang X, et al. Reference gene selection for qRT-PCR normalization analysis in kenaf (Hibiscus cannabinus L.) under abiotic stress and hormonal stimuli. Front Plant Sci. 2017;8:771.
   PubMed Web of Science ®Google Scholar
• Pinto F, Pacheco CC, Ferreira D, et al. Selection of suitable reference genes for RT-qPCR analyses in cyanobacteria. PLoS One. 2012;7(4):e34983.
   PubMed Web of Science ®Google Scholar
• Hampton TH, Koeppen K, Bashor L, et al. Selection of reference genes for quantitative PCR: identifying reference genes for airway epithelial cells exposed to Pseudomonas aeruginosa. Am J Physiol Lung Cellular Mol Physiol. 2020;319:256–265.
   Web of Science ®Google Scholar
• Li Y, Yu Z, Zhu Y, et al. Selection of nitrite-degrading and biogenic amine-degrading strains and its involved genes. Food Qual Saf. 2020;4:225–235.
   Google Scholar
• Cankorur-Cetinkaya A, Dereli E, Eraslan S, et al. A novel strategy for selection and validation of reference genes in dynamic multidimensional experimental design in yeast. PLoS One. 2012;7(6):e38351.
   PubMed Web of Science ®Google Scholar
• Sun ZB, Li SD, Sun MH. Selection of reliable reference genes for gene expression studies in Clonostachys rosea 67-1 under sclerotial induction. J Microbiol Methods. 2015;114:62–65.
   PubMed Web of Science ®Google Scholar
• Bao Z, Zhang K, Lin H, et al. Identification and selection of reference genes for quantitative transcript analysis in Corydalis yanhusuo. Genes. 2020;11(2):130.
   PubMed Web of Science ®Google Scholar
• Long X, Lu J, Kav NNV, et al. Identification and evaluation of suitable reference genes for gene expression analysis in rubber tree leaf. Mol Biol Rep. 2020;47:7.
   Web of Science ®Google Scholar
• Miao L, Qin X, Gao LH, et al. Selection of reference genes for quantitative real-time PCR analysis in cucumber (Cucumis sativus L.), pumpkin (Cucurbita moschata Duch.) and cucumber-pumpkin grafted plants. PeerJ. 2019;7:e6536.
   PubMed Web of Science ®Google Scholar
• Turroni S, Bendazzoli C, Dipalo SCF, et al. Oxalate-degrading activity in Bifidobacterium animalis subsp. lactis: impact of acidic conditions on the transcriptional levels of the oxalyl coenzyme A (CoA) decarboxylase and formyl-CoA transferase genes. Appl Environ Microbiol. 2010;76(16):5609–5620.
   PubMed Web of Science ®Google Scholar
• Bujold AR, Macinnes JI. Validation of reference genes for quantitative real-time PCR (qPCR) analysis of Actinobacillus suis. BMC Res Notes. 2015;8:86.
   PubMedGoogle Scholar
• Jacob TR, Laia ML, Ferro JA, et al. Selection and validation of reference genes for gene expression studies by reverse transcription quantitative PCR in Xanthomonas citri subsp. citri during infection of Citrus sinensis. Biotechnol Lett. 2011;33(6):1177–1184.
   PubMed Web of Science ®Google Scholar
• Sihto H-M, Tasara T, Stephan R, et al. Validation of reference genes for normalization of qPCR mRNA expression levels in Staphylococcus aureus exposed to osmotic and lactic acid stress conditions encountered during food production and preservation. FEMS Microbiol Lett. 2014;356(1):134–140.
   PubMed Web of Science ®Google Scholar
• Taurai T, Roger S. Evaluation of housekeeping genes in Listeria monocytogenes as potential internal control references for normalizing mRNA expression levels in stress adaptation models using real-time PCR. FEMS Microbiol Lett. 2007;269:265–272.
   PubMed Web of Science ®Google Scholar
• Guerra SM, Rodríguez-García A, Santos-Aberturas J, et al. LAL regulators SCO0877 and SCO7173 as pleiotropic modulators of phosphate starvation response and actinorhodin biosynthesis in Streptomyces coelicolor. PLoS One. 2012;7(2):e31475.
   PubMed Web of Science ®Google Scholar