Abstract
Global regulator BldA, the only tRNA for a rare leucine codon UUA, is best known for its ability to affect morphological differentiation and secondary metabolism in the genus Streptomyces. In this study, we confirmed the regulatory function of the bldA gene (Genbank accession no. EU124663.1) in Streptomyces lincolnensis. Disruption of bldA hinders the sporulation and lincomycin production, that can recur when complemented with a functional bldA gene. Western blotting assays demonstrate that translation of the lmbB2 gene which encodes a L-tyrosine hydroxylase is absolutely dependent on BldA; however, mistranslation of the lmbU gene which encodes a cluster-situated regulator (CSR) is observed in a bldA mutant. Intriguingly, when the preferential cognate codon CTG was used, the expression level of LmbU was not the highest compared to the usage of rare codon TTA or CTA, indicating the rare codon in this position is significant for the regulation of lmbU expression. Moreover, replacement of TTA codons in both genes with another leucin codon in the bldA mutant did not restore lincomycin production. Thus, we believe that the bldA gene regulates lincomycin production via controlling the translation of not only lmbB2 and lmbU, but also the other TTA-containing genes. In conclusion, the present study demonstrated the importance of the bldA gene in morphological differentiation and lincomycin production in S. lincolnensis.
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References
Bierman M, Logan R, O’Brien K, Seno ET, Rao RN, Schoner BE (1992) Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene 116:43–49. https://doi.org/10.1016/0378-1119(92)90627-2
Bignell DR, Tahlan K, Colvin KR, Jensen SE, Leskiw BK (2005) Expression of ccaR, encoding the positive activator of cephamycin C and clavulanic acid production in Streptomyces clavuligerus, is dependent on bldG. Antimicrob Agents Chemother 49:1529–1541. https://doi.org/10.1128/AAC.49.4.1529-1541.2005
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
Chater KF (1998) Taking a genetic scalpel to the Streptomyces colony. Microbiol 144:1465–1478
Chater KF (2001) Regulation of sporulation in Streptomyces coelicolor A3(2): a checkpoint multiplex? Curr Opin Microbiol 4:667–673. https://doi.org/10.1016/S1369-5274(01)00267-3
Chater KF (2006) Streptomyces inside-out: a new perspective on the bacteria that provide us with antibiotics. Philos Trans R Soc Lond Ser B Biol Sci 361:761–768. https://doi.org/10.1098/rstb.2005.1758
Chater KF, Chandra G (2006) The evolution of development in Streptomyces analysed by genome comparisons. FEMS Microbiol Rev 30:651–672. https://doi.org/10.1111/j.1574-6976.2006.00033.x
Chater KF, Chandra G (2008) The use of the rare UUA codon to define “expression space” for genes involved in secondary metabolism, development and environmental adaptation in Streptomyces. J Microbiol 46:1–11. https://doi.org/10.1007/s12275-007-0233-1
Chen GF, Inouye M (1990) Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the Escherichia coli genes. Nucleic Acids Res 18:1465–1473
Ferguson NL, Peña-Castillo L, Moore MA, Bignell DR, Tahlan K (2016) Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus. J Ind Microbiol Biotechnol 43:537–555. https://doi.org/10.1007/s10295-016-1733-y
Fernández-Moreno MA, Caballero JL, Hopwood DA, Malpartida F (1991) The act cluster contains regulatory and antibiotic export genes, direct targets for translational control by the bldA tRNA gene of Streptomyces. Cell 66:769–780. https://doi.org/10.1016/0092-8674(91)90120-N
Guthrie EP, Flaxman CS, White J, Hodgson DA, Bibb MJ, Chater KF (1998) A response-regulator-like activator of antibiotic synthesis from Streptomyces coelicolor A3(2) with an amino-terminal domain that lacks a phosphorylation pocket. Microbiol 144:727–738. https://doi.org/10.1099/00221287-144-3-727
Hackl S, Bechthold A (2015) The gene bldA, a regulator of morphological differentiation and antibiotic production in Streptomyces. Arch Pharm (Weinheim) 348:455–462. https://doi.org/10.1002/ardp.201500073
Hesketh A, Bucca G, Laing E, Flett F, Hotchkiss G, Smith CP, Chater KF (2007) New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures. BMC Genomics 8:261. https://doi.org/10.1186/1471-2164-8-261
Higo A, Horinouchi S, Ohnishi Y (2011) Strict regulation of morphological differentiation and secondary metabolism by a positive feedback loop between two global regulator AdpA and BldA in Streptomyces griseus. Mol Microbiol 81:1607–1622. https://doi.org/10.1111/j.1365-2958.2011.07795.x
Hopwood DA (1960) Phase-contrast observations on Streptomyces coelicolor. J Gen Microbiol 22:295–302. https://doi.org/10.1099/00221287-22-1-295
Hou B, Lin Y, Wu H, Guo M, Petkovic H, Tao L, Zhu X, Ye J, Zhang H (2018) The novel transcriptional regulator LmbU promotes lincomycin biosynthesis through regulating expression of its target genes in Streptomyces lincolnensis. J Bacteriol 200:e00447–e00417. https://doi.org/10.1128/JB.00447-17
Huang H, Grove A (2013) The transcriptional regulator TamR from Streptomyces coelicolor controls a key step in central metabolism during oxidative stress. Mol Microbiol 87:1151–1161. https://doi.org/10.1111/mmi.12156
Jiraskova PS, Novotna J, Kuzma M, Janata J (2016) New concept of the biosynthesis of 4-alkyl-L-proline precursors of lincomycin, hormaomycin, and pyrrolobenzodiazepines: could a -glutamytransferase cleave the C-C bond? Front Microbiol 7:276. https://doi.org/10.3389/fmicb.2016.00276
Ju KS, Zhang X, Elliot MA (2018) New kid on the block: LmbU expands the repertoire of specialized metabolic regulators in Streptomyces. J Bacteriol 200:e00559–e00517. https://doi.org/10.1128/JB.00559-17
Kalan L, Gessner A, Thaker MN, Waglechner N, Zhu X, Szawiola A, Bechthold A, Wright GD, Zechel DL (2013) A cryptic polyene biosynthetic gene cluster in Streptomyces calvus is expressed upon complementation with a functional bldA gene. Chem Biol 20:1214–1224. https://doi.org/10.1016/j.chembiol.2013.09.006
Kelemen GH, Buttner MJ (1998) Initiation of aerial mycelium formation in Streptomyces. Curr Opin Microbiol 1:656–662. https://doi.org/10.1016/S1369-5274(98)80111-2
Kim DW, Chater K, Lee KJ, Hesketh A (2005) Changes in the extracellular proteome caused by the absence of the bldA gene product, a developmentally significant tRNA, reveal a new target for the pleiotropic regulator AdpA in Streptomyces coelicolor. J Bacterial 187:2957–2966. https://doi.org/10.1128/JB.187.9.2957-2966.2005
Koshla O, Lopatniuk M, Rokytskyy I, Yushchuk O, Dacyuk Y, Fedorenko V, Luzhetskyy A, Ostash B (2017) Properties of Streptomyces albus J1074 mutant deficient in tRNALeu UAA gene bldA. Arch Microbiol 199:1175–1183. https://doi.org/10.1007/s00203-017-1389-7
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Li W, Wu J, Tao W, Zhao C, Wang y HX, Chandra G, Zhou X, Deng Z, Chater KF, Tao M (2007) A genetic and bioinformatic analysis of Streptomyces coelicolor genes containing TTA codons, possible targets for regulation by a developmentally significant tRNA. FEMS Microbiol Lett 266:20–28. https://doi.org/10.1111/j.1574-6968.2006.00494.x
Liu F, Xu D, Zhang Y, Zhu Y, Ye J, Zhang H (2015) Identification of BagI as a positive transcriptional regulator of bagremycin biosynthesis in engineered Streptomyces sp. Tü 4128. Microbiol Res 173:18–24. https://doi.org/10.1016/j.micres.2015.01.011
Liu G, Chater KF, Chandra G, Niu G, Tan H (2013a) Molecular regulation of antibiotic biosynthesis in Streptomyces. Microbiol Mol Biol Rev 77:112–143. https://doi.org/10.1128/MMBR.00054-12
Liu J, Li J, Dong H, Chen Y, Wang Y, Wu H, Li C, Weaver DT, Zhang L, Zhang B (2017) Characterization of an Lrp/AsnC family regulator SCO3361, controlling actinorhodin production and morphological development in Streptomyces coelicolor. Appl Microbiol Biotechnol 101:5773–5783. https://doi.org/10.1007/s00253-017-8339-9
Liu YP, Yan TT, Jiang LB, Wen Y, Song Y, Chen Z, Li JL (2013b) Characterization of SAV7471, a TetR-family transcriptional regulator involved in the regulation of coenzyme a metabolism in Streptomyces avermitilis. J Bacteriol 195:4365–4372. https://doi.org/10.1128/JB.00716-13
López-García MT, Santamarta I, Liras P (2010) Morphological differentiation and clavulanic acid formation are affected in a Streptomyces clavuligerus adpA-deleted mutant. Microbiology 156:2354–2365. https://doi.org/10.1099/mic.0.035956-0
Mao XM, Luo S, Zhou RC, Wang F, Yu P, Sun N, Chen XX, Tang Y, Li YQ (2015) Transcriptional regulation of the daptomycin gene cluster in Streptomyces roseosporus by an autoregulator, AtrA. J Biol Chem 290:7992–8001. https://doi.org/10.1074/jbc.M114.608273
Neusser D, Schmidt H, Spizèk J, Novotnà J, Peschke U, Kaschabeck S, Tichy P, Piepersberg W (1998) The genes lmbB1 and lmbB2 of Streptomyces lincolnensis encode enzymes involved in the conversion of L-tyrosine to propylproline during the biosynthesis of the antibiotic lincomycin A. Arch Microbiol 169:322–332
O’Rourke S, Wietzorrek A, Fowler K, Corre C, Challis GL, Chater KF (2009) Extracellular signalling, translational control, two repressors and an activator all contribute to the regulation of methylenomycin production in Streptomyces coelicolor. Mol Microbiol 71:763–778. https://doi.org/10.1111/j.1365-2958.2008.06560.x
Shi Y, Pan C, Auckloo BN, Chen X, Chen CA, Wang K, Wu X, Ye Y, Wu B (2017) Stress-driven discovery of a cryptic antibiotic produced by Streptomyces sp. WU20 from Kueishantao hydrothermal vent with an integrated metabolomics strategy. Appl Microbiol Biotechnol 101:1395–1408. https://doi.org/10.1007/s00253-016-7823-y
Soliveri JA, Gomez J, Bishai WR, Chater KF (2000) Multiple paralogous genes related to the Streptomyces coelicolor developmental regulatory gene whiB are present in Streptomyces and other actinomycetes. Microbiology 146:333–343. https://doi.org/10.1099/00221287-146-2-333
Spízek J, Rezanka T (2004) Lincomycin, cultivation of producing strains and biosynthesis. App Microbiol Biotechnol 63:510–519. https://doi.org/10.1007/s00253-003-1431-3
Takano E, Tao M, Long F, Bibb MJ, Wang L, Li W, Buttner MJ, Bibb MJ, Deng ZX, Chater KF (2003) A rare leucine codon in adpA is implicated in the morphological defect of bldA mutants of Streptomyces coelicolor. Mol Microbiol 50:475–486. https://doi.org/10.1046/j.1365-2958.2003.03728.x
Takano H, Nishiyama T, Amano S, Beppu T, Kobayashi M, Ueda K (2016) Streptomyces metabolites in divergent microbial interactions. J Ind Microbiol Biotechnol 43:143–148. https://doi.org/10.1007/s10295-015-1680-z
Trepanier NK, Jensen SE, Alexander DC, Leskiw BK (2002) The positive activator of cephamycin C and clavulanic acid production in Streptomyces clavuligerus is mistranslated in a bldA mutant. Microbiology 148:643–656. https://doi.org/10.1099/00221287-148-3-643
Wang J, Schully KL, Pettis GS (2009) Growth-regulated expression of a bacteriocin, produced by the sweet potato pathogen Streptomyces ipomoeae, that exhibits interstrain inhibition. Appl Environ Microbiol 75:1236–1242. https://doi.org/10.1128/AEM.01598-08
White J, Bibb M (1997) bldA dependence of undecylprodigiosin production in Streptomyces coelicolor A3(2) involves a pathway-specific regulatory cascade. J Bacteriol 179:627–633. https://doi.org/10.1128/jb.179.3.627-633.1997
Wilkinson CJ, Hughes-Thomas ZA, Martin CJ, Böhm I, Mironenko T, Deacon M, Wheatcroft M, Wirtz G, Staunton J, Leadlay PF (2002) Increasing the efficiency of heterologous promoters in Actinomycetes. J Mol Microbiol Biotechnol 4:417–426
Xu J, Zhang J, Zhuo J, Li Y, Tian Y, Tan H (2017) Activation and molecular mechanism of a cryptic oviedomycin biosynthetic gene cluster via the disruption of a global regulatory gene—adpA in Streptomyces ansochromogenes. J Biol Chem 292:19708–19720. https://doi.org/10.1074/jbc.M117.809145
Xu W, Huang J, Lin R, Shi J, Cohen SN (2010) Regulation of morphological differentiation in S. coelicolor by RNase III (AbsB) cleavage of mRNA encoding the AdpA transcription factor. Mol Microbiol 75:781–791. https://doi.org/10.1111/j.1365-2958.2009.07023.x
Zhu XM, Hackl S, Thaker MN, Kalan L, Weber C, Urgast DS, Krupp EM, Brewer A, Vanner S, Szawiola A, Yim G, Feldmann J, Bechthold A, Wright GD, Zechel DL (2015) Biosynthesis of the fluorinated natural product nucleocidin in Streptomyces calvus is dependent on the bldA-specified Leu-tRNA(UUA) molecule. Chembiochem 16:2498–2506. https://doi.org/10.1002/cbic.201500402
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This work was supported by the National Natural Science Foundation of China (NSFS) (3120026).
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Hou, B., Tao, L., Zhu, X. et al. Global regulator BldA regulates morphological differentiation and lincomycin production in Streptomyces lincolnensis. Appl Microbiol Biotechnol 102, 4101–4115 (2018). https://doi.org/10.1007/s00253-018-8900-1
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DOI: https://doi.org/10.1007/s00253-018-8900-1