Genome-wide transcriptome response of Streptomyces tsukubaensis to N-acetylglucosamine: effect on tacrolimus biosynthesis
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Arabolaza, 2010, FasR, a novel class of transcriptional regulator, governs the activation of fatty acid biosynthesis genes in Streptomyces coelicolor, Mol. Microbiol., 78, 47
Ban, 2016, The biosynthetic pathway of FK506 and its engineering: from past achievements to future prospects, J. Ind. Microbiol. Biotechnol., 43, 389, 10.1007/s10295-015-1677-7
Barreiro, 2014, Trends in the biosynthesis and production of the immunosuppressant tacrolimus (FK506), Appl. Microbiol. Biotechnol., 98, 497, 10.1007/s00253-013-5362-3
Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B (Methodological), 57, 289
Brekasis, 2003, A novel sensor of NADH/NAD+ redox poise in Streptomyces coelicolor A3(2), EMBO J., 22, 4856, 10.1093/emboj/cdg453
Chang, 1996, The cutRS signal transduction system of Streptomyces lividans represses the biosynthesis of the polyketide antibiotic actinorhodin, Mol. Microbiol., 21, 1075
Colson, 2007, Conserved cisacting elements upstream of genes composing the chitinolytic system of streptomycetes are DasRresponsive elements, J. Mol. Microbiol. Biotechnol., 12, 60
Colson, 2008, The chitobiose-binding protein, DasA, acts as a link between chitin utilization and morphogenesis in Streptomyces coelicolor, Microbiology, 154, 373, 10.1099/mic.0.2007/011940-0
Craig, 2012, Unsuspected control of siderophore production by N-acetylglucosamine in streptomycetes, Environ. Microbiol. Rep., 4, 512, 10.1111/j.1758-2229.2012.00354.x
Edgar, 2002, Gene expression Omnibus: NCBI gene expression and hybridization array data repository, Nucleic Acids Res., 30, 207, 10.1093/nar/30.1.207
Fowler-Goldsworthy, 2011, The actinobacteriaspecific gene wblA controls major developmental transitions in Streptomyces coelicolor A3(2), Microbiology, 157, 1312, 10.1099/mic.0.047555-0
Hamoen, 2006, SepF, a novel FtsZ-interacting protein required for a late step in cell division, Mol. Microbiol., 59, 989, 10.1111/j.1365-2958.2005.04987.x
Han, 1998, Characterization of β-ketoacyl-acyl carrier protein synthase III from Streptomyces glaucescens and its role in initiation of fatty acid biosynthesis, J. Bacteriol., 180, 4481, 10.1128/JB.180.17.4481-4486.1998
Hopwood, 2007
Hunt, 2005, The bldC developmental locus of Streptomyces coelicolor encodes a member of a family of small DNA-binding proteins related to the DNA binding domains of the MerR family, J. Bacteriol., 187, 716, 10.1128/JB.187.2.716-728.2005
Hutchings, 2004, Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2), Microbiology, 150, 2795, 10.1099/mic.0.27181-0
Ingram, 2009, Impact of topical calcineurin inhibitors on quality of life in patients with atopic dermatitis, Am. J. Clin. Dermatol., 10, 229, 10.2165/00128071-200910040-00003
Kang, 2007, Interspecies DNA microarray analysis identifies WblA as a pleiotropic down-regulator of antibiotic biosynthesis in Streptomyces, J. Bacteriol., 189, 4315, 10.1128/JB.01789-06
Kawamoto, 2001, Molecular and functional analyses of the gene (eshA) encoding the 52-kilodalton protein of Streptomyces coelicolor A3(2) required for antibiotic production, J. Bacteriol., 183, 6009, 10.1128/JB.183.20.6009-6016.2001
Kim, 2012, Negative role of wblA in response to oxidative stress in Streptomyces coelicolor, J. Microbiol. Biotechnol., 22, 736, 10.4014/jmb.1112.12032
Kino, 1987, FK-506, a novel immunosuppressant isolated from a Streptomyces. I. Fermentation, isolation, and physico-chemical and biological characteristics, J. Antibiot. (Tokyo), 40, 1249, 10.7164/antibiotics.40.1249
Kino, 1987, FK-506, a novel immunosuppressant isolated from a Streptomyces. II. Immunosuppressive effect of FK-506 in vitro, J. Antibiot. (Tokyo), 40, 1256, 10.7164/antibiotics.40.1256
Kormanec, 1993, Differential expression of principal sigma factor homologues of Streptomyces aureofaciens correlates with the developmental stage, Nucleic Acids Res., 21, 3647, 10.1093/nar/21.16.3647
Magasanik, 1961, Catabolite repression, Cold Spring Harb. Symp. Quant. Biol., 26, 249, 10.1101/SQB.1961.026.01.031
Martín, 2004, Phosphate control of the biosynthesis of antibiotics and other secondary metabolites is mediated by the PhoR-PhoP system: an unfinished story, J. Bacteriol., 186, 5197, 10.1128/JB.186.16.5197-5201.2004
Martín, 2010, Engineering of regulatory cascades and networks controlling antibiotic biosynthesis in Streptomyces, Curr. Opin. Microbiol., 13, 263, 10.1016/j.mib.2010.02.008
Martín, 2012, Two component systems in streptomyces
Martín, 2016, Cross-talk of global regulators in streptomyces
Martínez-Castro, 2013, Taxonomy and chemically semi-defined media for the analysis of the tacrolimus producer 'Streptomyces tsukubaensis, Appl. Microbiol. Biotechnol., 97, 2139, 10.1007/s00253-012-4364-x
Martín-Martín, 2017, Self-control of the PHO regulon: the PhoP-dependent protein PhoU controls negatively expression of genes of PHO regulon in Streptomyces coelicolor, J. Antibiot. (Tokyo)
McBride, 1987, Effects of intracellular trehalose content on Streptomyces griseus spores, J. Bacteriol., 169, 4995, 10.1128/jb.169.11.4995-5001.1987
McCormack, 2006, Tacrolimus: in heart transplant recipients, Drugs, 66, 2269, 10.2165/00003495-200666170-00010
McKenzie, 2007, Phosphorylated AbsA2 negatively regulates antibiotic production in Streptomyces coelicolor through interactions with pathway-specific regulatory gene promoters, J. Bacteriol., 189, 5284, 10.1128/JB.00305-07
Mehra, 2006, A framework to analyze multiple time series data: a case study with Streptomyces coelicolor, J. Ind. Microbiol. Biotechnol., 33, 159, 10.1007/s10295-005-0034-7
Meier-Kriesche, 2006, Immunosuppression: evolution in practice and trends, 1994-2004, Am. J. Transplant., 6, 1111, 10.1111/j.1600-6143.2006.01270.x
Miyashita, 2000, Induction and repression of a Streptomyces lividans chitinase gene promoter in response to various carbon sources, Biosci. Biotechnol. Biochem., 64, 39, 10.1271/bbb.64.39
Nazari, 2011, High expression levels of chitinase genes in Streptomyces coelicolor A3(2) grown in soil, FEMS Microbiol. Ecol., 77, 623, 10.1111/j.1574-6941.2011.01143.x
Nazari, 2013, Chitin-induced gene expression in secondary metabolic pathways of Streptomyces coelicolor A3(2) grown in soil, Appl. Environ. Microbiol., 79, 707, 10.1128/AEM.02217-12
Nodwell, 1996, An oligopeptide permease responsible for the import of an extracellular signal governing aerial mycelium formation in Streptomyces coelicolor, Mol. Microbiol., 22, 881, 10.1046/j.1365-2958.1996.01540.x
Nothaft, 2003, The phosphotransferase system of Streptomyces coelicolor is biased for N-acetylglucosamine metabolism, J. Bacteriol., 185, 7019, 10.1128/JB.185.23.7019-7023.2003
Nothaft, 2010, The permease gene nagE2 is the key to N-acetylglucosamine sensing and utilization in Streptomyces coelicolor and is subject to multi-level control, Mol. Microbiol., 75, 1133, 10.1111/j.1365-2958.2009.07020.x
Okamoto, 1998, An essential GTP-binding protein functions as a regulator for differentiation in Streptomyces coelicolor, Mol. Microbiol., 30, 107, 10.1046/j.1365-2958.1998.01042.x
Ordóñez-Robles, 2016, Target genes of the Streptomyces tsukubaensis FkbN regulator includemost of the tacrolimus biosynthesis genes, a phosphopantetheinyl transferase and other PKS genes, Appl. Microbiol. Biotechnol., 100, 8091, 10.1007/s00253-016-7696-0
Ordóñez-Robles, 2017, Analysis of the pho regulon in Streptomyces tsukubaensis, Microbiol. Res., 205, 80, 10.1016/j.micres.2017.08.010
Ordóñez-Robles, 2017, Streptomyces tsukubaensis as a new model for carbon repression: transcriptomic response to tacrolimus repressing carbon sources, Appl. Microbiol. Biotechnol., 101, 8181, 10.1007/s00253-017-8545-5
Ortiz de Orué Lucana, 2009, The three-component signalling system HbpS-SenS-SenR as an example of a redox sensing pathway in bacteria, Amino Acids, 37, 479, 10.1007/s00726-009-0260-9
Rabyk, 2011, Streptomyces ghanaensis pleiotropic regulatory gene wblAgh influences morphogenesis and moenomycin production, Biotechnol. Lett., 33, 2481, 10.1007/s10529-011-0728-z
Remitz, 2009, Long-term safety of tacrolimus ointment in atopic dermatitis, Expert Opin. Drug Saf., 8, 501, 10.1517/14740330902969441
Revill, 2001, β, J. Bacteriol., 183, 3526, 10.1128/JB.183.11.3526-3530.2001
Rexer, 2006, Investigation of the functional properties and regulation of three glutamine synthetase-like genes in Streptomyces coelicolor A3(2), Arch. Microbiol., 186, 447, 10.1007/s00203-006-0159-8
Rigali, 2002, Subdivision of the helix–turn–helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies, J. Biol. Chem., 277, 12507, 10.1074/jbc.M110968200
Rigali, 2004, Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships, Nucleic Acids Res., 32, 3418, 10.1093/nar/gkh673
Rigali, 2006, The sugar phosphotransferase system of Streptomyces coelicolor is regulated by the GntR-family regulator DasR and links N-acetylglucosamine metabolism to the control of development, Mol. Microbiol., 61, 1237, 10.1111/j.1365-2958.2006.05319.x
Rigali, 2008, Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces, EMBO Rep., 9, 670, 10.1038/embor.2008.83
Romero-Rodríguez, 2016, Carbon catabolite regulation of secondary metabolite formation and morphological differentiation in Streptomyces coelicolor, Appl. Biochem. Biotechnol., 180, 1152, 10.1007/s12010-016-2158-9
Saito, 2006, EshA accentuates ppGpp accumulation and is conditionally required for antibiotic production in Streptomyces coelicolor A3(2), J. Bacteriol., 188, 4952, 10.1128/JB.00343-06
Saito, 2007, The dasABC gene cluster, adjacent to dasR, encodes a novel ABC transporter for the uptake of N,N'-diacetylchitobiose in Streptomyces coelicolor A3(2), Appl. Environ. Microbiol., 73, 3000, 10.1128/AEM.02612-06
Saito, 2008, The msiK gene, encoding the ATP hydrolysing component of N,N'-diacetylchitobiose ABC transporters, is essential for induction of chitinase production in Streptomyces coelicolor A3(2), Microbiology, 154, 3358, 10.1099/mic.0.2008/019612-0
San Paolo, 2006, raggenes: novel components of the RamR regulon that trigger morphological differentiation in Streptomyces coelicolor, Mol. Microbiol., 61, 1167, 10.1111/j.1365-2958.2006.05304.x
Sánchez, 2010, Carbon source regulation of antibiotic production, J. Antibiot. (Tokyo), 63, 442, 10.1038/ja.2010.78
Santos-Beneit, 2013, Identification of different promoters in the absA1absA2 two-component system, a negative regulator of antibiotic production in Streptomyces coelicolor, Mol. Genet. Genomics, 288, 39, 10.1007/s00438-012-0728-2
Schlösser, 1997, The Streptomyces ATP-binding component MsiK assists in cellobiose and maltose transport, J. Bacteriol., 179, 2092, 10.1128/jb.179.6.2092-2095.1997
Sidders, 2007, Quantification of global transcription patterns in prokaryotes using spotted microarrays, Genome Biol., 8, R265, 10.1186/gb-2007-8-12-r265
Singh, 2009, Regulation of tacrolimus production by altering primary source of carbons and amino acids, Lett. Appl. Microbiol., 49, 254, 10.1111/j.1472-765X.2009.02652.x
Smyth, 2004, Linear models and empirical Bayes methods for assessing differential expression in microarray experiments, Stat. Appl. Genet. Mol. Biol., 1
Sola-Landa, 2003, The two-component PhoR-PhoP system controls both primary metabolism and secondary metabolite biosynthesis in Streptomyces lividans, Proc. Natl. Acad. Sci. U. S. A., 100, 6133, 10.1073/pnas.0931429100
Sola-Landa, 2005, Binding of PhoP to promoters of phosphate-regulated genes in Streptomyces coelicolor: identification of PHO boxes, Mol. Microbiol., 56, 1373, 10.1111/j.1365-2958.2005.04631.x
Sola-Landa, 2013, Competition between the GlnR and PhoP regulators for the glnA and amtB promoters in Streptomyces coelicolor, Nucleic Acids Res., 41, 1767, 10.1093/nar/gks1203
Świątek, 2012, Functional analysis of the N-acetylglucosamine metabolic genes of Streptomyces coelicolor and role in control of development and antibiotic production, J. Bacteriol., 194, 1136, 10.1128/JB.06370-11
Świątek, 2013, The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in Streptomyces coelicolor, J. Bacteriol., 195, 1236, 10.1128/JB.02191-12
Świątek-Połatyńska, 2015, Genome-wide analysis of in vivo binding of the master regulator DasR in Streptomyces coelicolor identifies novel non-canonical targets, PLoS One, 10, e0122479, 10.1371/journal.pone.0122479
Tenconi, 2015, Multiple allosteric effectors control the affinity of DasR for its target sites, Biochem. Biophys. Res. Commun., 464, 324, 10.1016/j.bbrc.2015.06.152
Tseng, 1991, A cloned ompR-like gene of Streptomyces lividans 66 suppresses defective melC1, a putative copper-transfer gene, Mol. Microbiol., 5, 1187, 10.1111/j.1365-2958.1991.tb01892.x
Uguru, 2005, Transcriptional activation of the pathway-specific regulator of the actinorhodin biosynthetic genes in Streptomyces coelicolor, Mol. Microbiol., 58, 131, 10.1111/j.1365-2958.2005.04817.x
Vujaklija, 1993, Detection of an A-factor-responsive protein that binds to the upstream activation sequence of strR, a regulatory gene for streptomycin biosynthesis in Streptomyces griseus, J. Bacteriol., 175, 2652, 10.1128/jb.175.9.2652-2661.1993
Wang, 2013, Identification of two component system AfsQ1/Q2 regulon and its cross-regulation with GlnR in Streptomyces coelicolor, Mol. Microbiol., 87, 30, 10.1111/mmi.12080
Wang, 2016, Characterization of discrete phosphopantetheinyl transferases in Streptomyces tsukubaensis L19 unveils a complicate phosphopantetheinylation network, Sci. Rep., 6, 24255, 10.1038/srep24255
Xiao, 2002, The novel Streptomyces olivaceoviridis ABC transporter Ngc mediates uptake of N-acetylglucosamine and N,N’diacetylchitobiose, Mol. Genet. Genomics, 267, 429, 10.1007/s00438-002-0640-2