Protein expression analysis of a high-demeclocycline producing strain of Streptomyces aureofaciens and the roles of CtcH and CtcJ in demeclocycline biosynthesis
Bioresources and Bioprocessing volume 3, Article number: 46 (2016)
Streptomyces aureofaciens strain A6-9, obtained with traditional mutagenesis, produces elevated levels of 6-DCT. The increased formation of 6-DCT may be attributable to the changes in the expression of some proteins in the 6-DCT biosynthetic pathway. For this reason, we explored the differences in protein expression between A6-9 and wild-type (WT) strains of Streptomyces aureofaciens, and based on the differences (CtcH and CtcJ were overexpressed in A6-9), investigated the roles of CtcH and CtcJ in biosynthesis.
Two-dimensional gel electrophoresis and a Mascot search indicated that some enzymes (including CtcH and CtcJ) involved in the primary and secondary metabolism were more strongly expressed in the high-6-DCT-yielding strain A6-9 than in the WT strain DT1. To examine the roles of CtcH and CtcJ in 6-DCT biosynthesis, ctcH-deleted, ctcJ-deleted, ctcH-overexpressing, and ctcJ-overexpressing mutants and a mutant overexpressing both ctcH and ctcJ were constructed. Compared with WT, 6-DCT production was 50 and 37 % higher in the ctcH-overexpressing and ctcJ-overexpressing strains, respectively, and increased by 60 % in the ctcH–ctcJ-overexpressing strain. The ctcH-deleted and ctcJ-deleted strains produced almost no 6-DCT. Analysis of the metabolic flux distribution indicated that ctcH encodes a hydroxyacyl-CoA dehydrogenase and ctcJ encodes a monooxygenase that are essential for 6-DCT biosynthesis.
Protein expression differs between high-6-DCT-yielding and WT strains, and the enzymes increased in the high-6-DCT-yielding strain explain the increased 6-DCT production. ctcH encodes a hydroxyacyl-CoA dehydrogenase and ctcJ encodes a monooxygenase that are essential for 6-DCT biosynthesis.
Four tetracycline antibiotics, chlortetracycline, tetracycline, demeclocycline (6-DCT), and 6-demethyltetracycline, are secondary metabolites of Streptomyces aureofaciens (Zhu et al. 2001). 6-DCT is produced when the 6-methylation step is blocked in chlortetracycline biosynthesis pathway, and is used for the industrial production of semisynthetic tetracyclines (Nakano et al. 2000). There has been a little research into 6-DCT production, whereas many papers are available concerning the gene clusters and ribosomes involved in the biosynthesis of chlortetracycline and other tetracyclines. Chlortetracycline production depends on the expression of proteins involved in its biosynthetic pathway, so identifying and understanding the corresponding proteins are required for the industrial production of 6-DCT biosynthesis (Mikulik et al. 1983; Li et al. 2001). Streptomyces aureofaciens strain A6-9, obtained with the traditional mutagenesis, produces the elevated levels of 6-DCT. This increased formation of 6-DCT may be attributable to changes in the expression of some proteins in the 6-DCT biosynthetic pathway. Modulating the expression of these proteins may significantly affect 6-DCT biosynthesis.
A type II polyketide synthase (PKS) constructs the skeleton of tetracycline antibiotics, and a series of subsequent reactions modify the skeleton to produce four final products (Nakano et al. 2000). The modification reactions (e.g., chlorination, methylation, and oxidation) are important for the diversity of tetracyclines, and 6-DCT is formed when the 6-methylation step in the pathway is lacking. Above all, oxidation reactions catalyzed by monooxygenases are necessary for the formation of 6-DCT (Fig. 1) (Taguchi et al. 2011; Bentley et al. 2002).
Although certain features of the secondary metabolism of Streptomyces have been studied in detail, including the synthesis of antibiotics and its differentiation processes, its primary metabolism has not been (Al-Shamma et al. 1983; Hensel et al. 1991). Hydroxyacyl-CoA dehydrogenase is involved in the β-oxidation of fatty acids, which is essential for the whole metabolism of the microorganism (Fujita et al. 2007; Rock and Cronan 1996; DiRusso and Nystrom 1998; Schujman et al. 2003; Lu and Rock 2006). Hydroxyacyl-CoA is oxidized by hydroxyacyl-CoA dehydrogenase to generate acetyl-CoA, NADH, and H+, which are essential for the biosynthesis of 6-DCT (Fig. 2).
In this study, we examined the differences in protein expression between A6-9 and the parental wild-type (WT) strain to identify the enzymes that are important for 6-DCT biosynthesis, using two-dimensional (2D) gel electrophoresis and mass spectrometry. Based on the results, the roles of CtcH (hydroxyacyl-CoA dehydrogenase) and CtcJ (monooxygenase) in 6-DCT biosynthesis were examined by inactivating or overexpressing them individually and together in DT1.
Microbial strains and plasmids
The strains and plasmids used in this study are listed in Table 1.
Media and culture conditions
Escherichia coli DH5α and its derivatives were routinely grown aerobically in LB medium (37 °C, 180 rpm) (Jian et al. 2010; Zhang et al. 2006). ISP4-containing 80 mmol l−1 MgCl2 was used for E.coli ET12567/pUZ8002-Streptomyces conjugative medium (Liu et al. 2015).
The mycelia of S. aureofaciens were stored in 20 % glycerol solution at −80 °C. A 250-ml shaker flask containing 30 ml of seed medium was inoculated with 3 ml of mycelial solution. After incubation for 48 h at 27 °C, a 250-ml fermentation flask containing 30 ml of fermentation medium was inoculated with 3 ml of seed medium, and shaken at 27 °C and 240 rpm for 148 h. All experiments were performed in triplicate. The seed medium and fermentation medium were adjusted to pH 6.5.
Generation of gene-inactivated and gene-overexpressing strains
Genes ctcH and ctcJ were deleted with the non-replicating plasmid pOJ260-neo, which produced deletion mutants substituted with a kanamycin-resistance gene cassette. The transformants (ΔctcH and ΔctcJ) were grown on ISP4 plates-containing kanamycin and nalidixic acid, selected on MS plates-containing kanamycin and apramycin, and verified with DNA sequencing and PCR. All primers used in this study are shown in Additional file 1: Online Resource 1 and the plasmid used for the gene-overexpressing constructs is shown in Additional file 2: Online Resource 2.
Genes ctcH and ctcJ were overexpressed individually or both genes were overexpressed simultaneously with an integrative plasmid, pIB139, containing a strong promoter from the erythromycin-resistance gene and the ϕC31 attp site, which can integrate into the attB site of Streptomyces. A 719-bp DNA fragment containing ctcH was cloned and inserted into pIB139 to generate pIB139-H, and a 763-bp DNA fragment containing ctcJ was inserted into pIB139 to generate pIB139-J. The two fragments were inserted into pIB139 to generate pIB139-H-J. The genotypes of WT and the overexpressing mutants are shown in Fig. 5a. The transformants (ctcH+, ctcJ+, and ctcH–ctcJ+) were isolated on ISP4 plates under apramycin and nalidixic acid selection, cloned on MS plates, and verified with PCR and a transcription analysis.
Determination of 6-DCT
The production of 6-DCT was determined with high-performance liquid chromatography (HPLC), using the linear regression equation: U = 3 × 10−4 A − 10.98, r 2 = 0.9956, where U and A represent the concentration of 6-DCT and the peak area, respectively. Samples (1, 2, 3, 4, or 5 µl) of a standard 6-DCT solution (4000 µg/ml) were injected and eluted after 15 min, and the peak areas were calculated. The linear regression equation was obtained and plotted, with the concentration of 6-DCT on the horizontal axis and the peak area on the vertical axis. As a control, WT DT1 was processed under the same fermentation conditions.
After fermentation for 7 days, the pH of the culture broth was adjusted to 1.8–2.0 with oxalic acid. The filtration supernatant was assayed with HPLC using an Extend-C18 reverse phase column (4.6 mm × 150 mm, 5 μm; Agilent, USA) at 350 nm with 0.01-M oxalic acid–0.08-M ammonium oxalate solution and 40 % methanol/acetonitrile/water as the mobile phase at a flow rate of 0.4 ml/min. The column temperature was at 25 °C.
2D gel electrophoresis and Mascot search
The mycoproteins were extracted with ultrasonication and their concentrations determined with Coomassie Brilliant Blue. The mycelia were washed in low-salt buffer (2.5 mM KH2PO4, 5 mM NaH2PO4) precooled to 4 °C, and then resuspended in 1 ml of lysis buffer (8 M carbamide, 1 % IPG buffer, 2 % dithiothreitol). Protein sample preparation and 2D gel electrophoresis were performed as previously described (Helmel et al. 2014; Jan et al. 2014). (All chemicals were from Sigma-Aldrich, St. Louis, MO, USA). A Mascot search was performed by Shanghai Bo-Yuan Biological Technology Co., Ltd.
RNA isolation and quantitative real-time reverse transcription-PCR (RT-qPCR)
The transcription levels of ctcH and ctcJ were assayed with RT-qPCR (Bio-Rad CFX96). Sample preparation, RNA isolation, and the PCR were all conducted according to a previous study (Zhu et al. 2013). RT-qPCR was performed with the SYBR Green Two-Step RT-qPCR SuperMix (Takara). The transcription levels were normalized to the expression of 16S rRNA. RT-qPCR was performed in three independent experiments, each in triplicate.
Differences in protein expression by S. aureofaciens strains A6-9 and DT1
A high-6-DCT-yield S. aureofaciens strain A6-9 was generated with the traditional mutagenesis. Compared with the parental strain under the same flask fermentation conditions, A6-9 showed a 20 % increase in 6-DCT production, which might be attributable to changes in protein expression. For this reason, 2D gel electrophoresis and a Mascot search were used to explore the differences in protein expression between the mutant A6-9 and the parental strain DT1.
Seven differentially expressed proteins were identified with mass spectrometry using the PDquest software (Fig. 3; Table 2). Malate dehydrogenase, glutamine synthetase, 6-hydroxylation enzyme, CtcH, and CtcJ were expressed more strongly and ATP synthetase less strongly in A6-9 than in DT1.
6-DCT biosynthesis requires CtcH and CtcJ
The proteins expressed more strongly in A6-9, according to 2D gel electrophoresis and the Mascot search, might explain, at least in part, the increase in 6-DCT production. CtcH and CtcJ are encoded by ctcH and ctcJ, respectively, which belong to the chlortetracycline biosynthesis gene cluster, and occur near one another on the S. aureofaciens chromosome, but have not yet been investigated. Therefore, their roles in 6-DCT biosynthesis were examined first, and the other enzymes upregulated in A6-9 will be explored in a future study. ctcH and ctcJ were knocked out individually to study their effects on 6-DCT biosynthesis.
The ctcH and ctcJ deletion mutants of S. aureofaciens DT1 were generated by in-frame deletion (Fig. 4a) and confirmed with PCR (Fig. 4b). The mutants and WT were grown in fermentation culture for 7 days and the 6-DCT concentrations detected with HPLC. Less 6-DCT was detected in ΔctcH, and no 6-DCT was detected in ΔctcJ (Fig. 4c). The HPLC analyses of the mutants and WT are shown in Additional file 3: Online Resource 3.
Overexpression of ctcH- and/or ctcJ-enhanced 6-DCT production
The results of ctcH or ctcJ deletion suggested that the production of 6-DCT may increase when the genes are overexpressed. To improve 6-DCT production and explore the effect of each gene on it, ctcH and ctcJ were overexpressed individually and together in DT1 (Fig. 5b). As predicted, the ctcH+, ctcJ+, and ctcH–ctcJ+ mutants expressed considerably more 6-DCT than did DT1, with increases of ca. 50, 37, and 60 %, respectively. Compared with the 3164-µg/ml 6-DCT produced by DT1, ctcH+ produced 4715 µg/ml, ctcJ+ produced 4332 µg/ml, and ctcH–ctcJ+ produced 5075 µg/ml (Fig. 5c). The transcription levels of ctcH and ctcJ were also high in the mutants (Fig. 5d), indicating that the overexpression of these genes caused the increase in 6-DCT production. The HPLC analysis of the mutants and WT is shown in Additional file 3: Online Resource 3.
In recent years, engineering the primary metabolism has been used to supply more precursors for the production of the secondary metabolites of Streptomyces and rationally engineering the secondary metabolism has shown potential utility in strain improvement, allowing the production of high levels of antibiotics and to reduce the byproducts (Pang et al. 2015; Zhuo et al. 2010; Zhang et al. 2008). Gene overexpression has been an effective way to enhance antibiotic production (Liu et al. 2015; Du et al. 2013; Yuan et al. 2011; Malla et al. 2010). In this study, the overexpression of some key enzymes involved in the 6-DCT biosynthetic pathway in the high-yield strain A6-9 explained the enhanced production of 6-DCT.
ctcH is an endogenous gene that encodes a 3-hydroxylacyl-CoA dehydrogenase, an NADH-dependent enzyme that also has Δ3-cis, Δ2-trans-enoyl-CoA isomerase and (S)/(R)-epimerase activities. It is responsible for the oxidation of 3-hydroxyacyl-CoA, generating NADH, H+, and β-ketoacyl-CoA, which can also generate acetyl-CoA when it is catalyzed by thiolase during the β-oxidation of fatty acids (Fig. 2) (Volodina and Steinbuchel 2014; Fujita et al. 2007; Kunau et al. 1995; Black and DiRusso 1994; Pramanik et al. 1979). Here, the results of modulating ctcH can be explained by the requirement for NADH, H+, and acetyl-CoA in 6-DCT biosynthesis. First, the regulation of ctcH expression has a direct effect on the generation of NADH and H+, which are the major reductants in the 6-DCT biosynthetic pathway, and second, it affects the amount of acetyl-CoA, a major source of the precursors of 6-DCT.
In ΔctcH, 3-hydroxyacyl-CoA could not be oxidized to a keto group, so the mutation of ctcH reduced the generation of NADH, H+, and acetyl-CoA, further reducing 6-DCT production. One cycle of β-oxidation produces one molecule each of NADH, H+, and acetyl-CoA, which are necessary for the 6-DCT biosynthesis (Fig. 2). However, in ctcH+ and ctcH–ctcJ+, the reaction catalyzed by 3-hydroxylacyl-CoA dehydrogenase was enhanced, increasing the amounts of NADH, H+, and acetyl-CoA, and thus increasing 6-DCT production.
ctcJ encodes a monooxygenase involved in antibiotic biosynthesis, and is also involved in the monooxygenation of intermediates in the macrolide biosynthetic pathways (Gaisser et al. 2002). These oxygenases belong to the so-called post-PKS-modifying (tailoring) enzymes, which play crucial roles in the formation of interesting and unique molecular structures. The monooxygenases are representative, tailoring enzymes that are especially important in providing the structural elements essential for the special biological activity of these structures (Taguchi et al. 2011; Faust et al. 2000).
In ΔctcJ, no 6-DCT was formed, and instead, an unknown chemical was produced that was also produced in DT1. These results indicate that ΔctcJ is unable to catalyze the oxidation steps (Fig. 1) required in the 6-DCT biosynthetic pathway. In ctcJ+ and ctcH–ctcJ+, the oxidation steps involving CtcJ in the 6-DCT biosynthesis pathway were enhanced.
This study mainly focused on the differences in protein expression between S. aureofaciens strains A6-9 and DT1 and the effects of CtcH and CtcJ on the production of 6-DCT in S. aureofaciens. Our experiments demonstrate that CtcH and CtcJ play important roles in the formation of 6-DCT. Further exploration of all the enzymes overexpressed in A6-9 will allow us to clarify the 6-DCT biosynthetic pathway. Our findings should be useful in controlling this metabolic node and modifying the metabolic pathway to increase the production of 6-DCT in an industrial strain.
Al-Shamma KJ, Karim KH, Al-Genno GM (1983) Biological effects of inhaled welding fumes from flux-coated electrodes (OK 46.00). Dev Toxicol Environ Sci 11:487–490
Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147
Black PN, DiRusso CC (1994) Molecular and biochemical analyses of fatty acid transport, metabolism, and gene regulation in Escherichia coli. Biochim Biophys Acta 1210:123–145
DiRusso CC, Nystrom T (1998) The fats of Escherichia coli during infancy and old age: regulation by global regulators, alarmones and lipid intermediates. Mol Microbiol 27:1–8
Du D, Zhu Y, Wei J, Tian Y, Niu G (2013) Improvement of gougerotin and nikkomycin production by engineering their biosynthetic gene clusters. Appl Microbiol Biotechnol 97:6383–6396
Faust B, Hoffmeister D, Weitnauer G, Westrich L, Haag S (2000) Two new tailoring enzymes, a glycosyltransferase and an oxygenase, involved in biosynthesis of the angucycline antibiotic urdamycin A in Streptomyces fradiae Tu2717. Microbiology 146:147–154
Fujita Y, Matsuoka H, Hirooka K (2007) Regulation of fatty acid metabolism in bacteria. Mol Microbiol 66:829–839
Gaisser S, Lill R, Staunton J, Mendez C, Salas J (2002) Parallel pathways for oxidation of 14-membered polyketide macrolactones in Saccharopolyspora erythraea. Mol Microbiol 44:771–781
Helmel M, Posch A, Herwig C, Allmaier G, Marchetti-Deschmann M (2014) Proteome profiling illustrated by a large-scale fed-batch fermentation of Penicillium chrysogenum. EuPA 4:113–120
Hensel M, Deckers-Hebestreit G, Altendorf K (1991) Purification and characterization of the F1 portion of the ATP synthase (F1Fo) of Streptomyces lividans. Eur J Biochem 202:1313–1319
Jan K, Renata N, Eric M, Lubomira F (2014) Intriguing properties of the angucyclineantibiotic auricin and complex regulation of its biosynthesis. Appl Microbiol Biotechnol 98:45–60
Jian J, Zhang SQ, Shi ZY, Wang W, Chen GQ (2010) Production of polyhydroxyalkanoates by Escherichia coli mutants with defected mixed acid fermentation pathways. Appl Microbiol Biotechnol 87:2247–2256
Kunau WH, Dommes V, Schulz H (1995) Beta-oxidation of fatty acids in mitochondria, peroxisomes, and bacteria: a century of continued progress. Prog Lipid Res 34:267–342
Li XM, Novotna J, Vohradsky J, Weiser J (2001) Major proteins related to chlortetracycline biosynthesis in a Streptomyces aureofaciens production strain studied by quantitative proteomics. Appl Microbiol Biotechnol 57:717–724
Liu F, Xu D, Zhang Y, Zhu Y, Ye J (2015) Identification of BagI as a positive transcriptional regulator of bagremycin biosynthesis in engineered Streptomyces sp. Tu 4128. Microbiol Res 173:18–24
Lu YJ, Rock CO (2006) Transcriptional regulation of fatty acid biosynthesis in Streptococcus pneumoniae. Mol Microbiol 59:551–566
Malla S, Niraula NP, Liou K, Sohng JK (2010) Self-resistance mechanism in Streptomyces peucetius: overexpression of drrA, drrB and drrC for doxorubicin enhancement. Microbiol Res 165:259–267
Mikulik K, Jiranova K, Janda I, Weiser J (1983) Susceptibility of ribosomes of the tetracycline-producing strain of Streptomyces aureofaciens to tetracyclines. FEBS Lett 152:125–130
Nakano T, Miyake K, Ikeda M, Mizukami T, Katsumata R (2000) Mechanism of the incidental production of a melanin-like pigment during 6-demethylchlortetracycline production in Streptomyces aureofaciens. Appl Environ Microbiol 66:1400–1404
Pang AP, Du L, Lin CY, Qiao J, Zhao GR (2015) Co-overexpression of lmbW and metK led to increased lincomycin A production and decreased by product lincomycin B content in an industrial strain of Streptomyces lincolnensis. J Appl Microbiol 119:1064–1074
Pramanik A, Pawar S, Antonian E, Schulz H (1979) Five different enzymatic activities are associated with the multienzyme complex of fatty acid oxidation from Escherichia coli. J Bacteriol 137:469–473
Rock CO, Cronan JE (1996) Escherichia coli as a model for the regulation of dissociable (type II) fatty acid biosynthesis. Biochim Biophys Acta 1302:1–16
Schujman GE, Paoletti L, Grossman AD, Mendoza D (2003) FapR, a bacterial transcription factor involved in global regulation of membrane lipid biosynthesis. Dev Cell 4:663–672
Taguchi T, Okamoto S, Hasegawa K, Ichinose K (2011) Epoxyquinone formation catalyzed by a two-component flavin-dependent monooxygenase involved in biosynthesis of the antibiotic actinorhodin. ChemBioChem 12:2767–2773
Volodina E, Steinbuchel A (2014) (S)-3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase (FadB’) from fatty acid degradation operon of Ralstonia eutropha H16. AMB Express 4:69
Yuan T, Yin C, Zhu C, Zhu B, Hu Y (2011) Improvement of antibiotic productivity by knock-out of dauW in Streptomyces coeruleobidus. Microbiol Res 166:539–547
Zhang Y, Li Y, Du C, Liu M, Cao Z (2006) Inactivation of aldehyde dehydrogenase: a key factor for engineering 1,3-propanediol production by Klebsiella pneumoniae. Metab Eng 8:578–586
Zhang X, Fen M, Shi X, Bai L, Zhou P (2008) Overexpression of yeast S-adenosylmethionine synthetase metK in Streptomyces actuosus leads to increased production of nosiheptide. Appl Microbiol Biotechnol 78:991–995
Zhu J, Snow DD, Cassada DA, Monson SJ, Spalding RF (2001) Analysis of oxytetracycline, tetracycline, and chlortetracycline in water using solid-phase extraction and liquid chromatography-tandem mass spectrometry. J Chromatogr A 928:177–186
Zhu YX, Xu DK, Liao SY, Ye J, Zhang HZ (2013) Cloning and characterization of bagB and bagC, two co-transcribed genes involved in bagremycin biosynthesis in Streptomyces sp Tu 4128. Ann Microbiol 63:167–172
Zhuo Y, Zhang W, Chen D, Gao H, Tao J (2010) Reverse biological engineering of hrdB to enhance the production of avermectins in an industrial strain of Streptomyces avermitilis. Proc Natl Acad Sci USA 107:11250–11254
All authors have participated in the interpretation of results during preparation of the manuscript. All authors read and approved the final manuscript.
This work was financially supported by Topfond Pharmaceutical Co., Ltd., Henan, China.
The authors declare that they have no competing interests.
About this article
Cite this article
Li, H., Ye, R., Lin, G. et al. Protein expression analysis of a high-demeclocycline producing strain of Streptomyces aureofaciens and the roles of CtcH and CtcJ in demeclocycline biosynthesis. Bioresour. Bioprocess. 3, 46 (2016). https://doi.org/10.1186/s40643-016-0123-7