Appl Microbiol Biotechnol DOI 10.1007/s00253-013-4988-5 BIOTECHNOLOGICAL PRODUCTS AND PROCESS ENGINEERING Knocking out analysis of tryptophan permeases in Escherichia coli for improving L-tryptophan production Pengfei Gu & Fan Yang & Fangfang Li & Quanfeng Liang & Qingsheng Qi Received: 5 March 2013 / Revised: 3 May 2013 / Accepted: 7 May 2013 # Springer-Verlag Berlin Heidelberg 2013 Abstract Three permeases, Mtr, TnaB, and AroP, are involved in the uptake of L-tryptophan in Escherichia coli. These permeases possess individual function for cell transportation and metabolism, and affect extracellular Ltryptophan accumulation. In this study, by knocking out three tryptophan permeases separately and simultaneously in L-tryptophan-producing strain E. coli GPT1002, we analyzed the effect of permease knock out on L-tryptophan uptake, cell growth, and L-tryptophan production. We found that TnaB is the main transporter that is responsible for the uptake of L-tryptophan. Inactivation of tnaB improved the L-tryptophan production significantly, and inactivation of aroP has an additive effect on tnaB mutant. Quantitative real-time PCR analysis confirmed that knocking out permeases affects gene transcription and cell metabolism in many metabolic pathways. The tryptophan permease-deficient GPT1017 mutant exhibited the highest L-tryptophan production at 2.79 g l−1, which is 51.6 % higher than that produced by the control strain. In 5-l bioreactor fermentation, the L-tryptophan production in GPT1017 reached 16.3 g l−1. Keywords E. coli . L-Tryptophan . TnaB . AroP . Mtr Introduction L-Tryptophan is an important aromatic amino acid that is widely used in food additives, animal feed, and pharmaceutical industries (Berry 1996; Bongaerts et al. 2001; Gosset 2009; P. Gu : F. Yang : F. Li : Q. Liang : Q. Qi State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China Q. Qi (*) National Glycoengineering Research Center, Shandong University, Jinan 250100, People’s Republic of China e-mail: qiqingsheng@sdu.edu.cn Ikeda 2006). Due to the disadvantages of chemical synthesis, microbial fermentation of L-tryptophan has become an attractive alternative. A number of researchers are devoted to improve L-tryptophan production from microorganism via various metabolic engineering methods, including deregulating repression and attenuation on critical enzymes, overexpressing rate-limiting enzymes, blocking competing pathways, and improving precursor levels (Aiba et al. 1982; Chan et al. 1993; Gu et al. 2013; Tribe and Pittard 1979). Through these efforts, Ltryptophan-producing strains with completely defined genetic background were obtained. Another important strategy for improving amino acid production is decreasing the intracellular concentration by transport system engineering. For example, in 2007, Lee et al. constructed recombinant Escherichia coli through deleting transporter TdcC or overexpessing exporter RhtC and increased the L-threonine production by 15.6 and 50.2 %, respectively, compared to the control strains (Lee et al. 2007). Recently, Xie et al. improved the L-isoleucine production significantly in recombinant Corynebacterium glutamicum by deleting the uptake carrier brnQ and overexpressing the export carrier brnFE (Xie et al. 2012). Three tryptophan permeases are present in E. coli: AroP, TnaB, and Mtr. Mtr and TnaB are tryptophan-specific, whereas AroP is a general aromatic amino acid transporter that can also import phenylalanine and tyrosine (Chye et al. 1986; Chye and Pittard 1987; Honore and Cole 1990). Mtr is a high-affinity tryptophan permease (Km of about 3 μM), and it is also responsible for transporting indole, the degradation product of tryptophan (Heatwole and Somerville 1991a; Heatwole and Somerville 1991b; Sarsero and Pittard 1991). TnaB, a low-affinity transporter with a Km of about 70 μM, is essential for cell growth when tryptophan is used as the sole carbon source (Edwards and Yudkin 1982; Whipp and Pittard 1977; Yanofsky et al. 1991). Despite the information regarding these permeases, the export of L-tryptophan in E. coli has not been thoroughly studied. YddG, an internal membrane Appl Microbiol Biotechnol protein with nine predicted transmembrane domains, can function as an aromatic amino acid exporter, which overexpression enhanced aromatic acid production (Doroshenko et al. 2007). Recently, Liu et al. constructed a recombinant E. coli that exhibited 12.6 % higher L-tryptophan production in fed-batch fermentation than that of the control by modifying the aromatic amino acid transporters, AroP and YddG (Liu et al. 2012). Nevertheless, no L-tryptophan-specific exporter was identified in the study. In our previous work, we constructed recombinant E. coli GPT1002, a L-tryptophan producer that accumulated 10.15 g l−1 L-tryptophan in fed-batch fermentation by metabolic engineering (Gu et al. 2012). However, the effect of L-tryptophan permease knockout was not evaluated. In this study, we separately and simultaneously knocked out the three permeases involved in L-tryptophan importation. The effect of L-tryptophan permease knockout on cell metabolism and L-tryptophan production was also investigated. recombinant E. coli GPT101 was chosen as the parent strain for obtaining tryptophan permease mutants. Recombinant plasmid pTAT with overexpressed feedback-resistant trpEFR, aroGFR, and tktA genes was transformed into mutant strains for the batch and fed-batch fermentation. Gene deletion Three genes, mtr, aroP, and tnaB, were knocked out by the one-step inactivation method (Datsenko and Wanner 2000). Linearized DNA flanked by FLP recognition target sites and homologous sequences were amplified by PCR using pKD3 or pKD4 as template. After DpnI digestion and DNA purification, the PCR product was electroporated into E. coli cells that express the red recombinase. Positive clones were selected by relevant antibiotics and confirmed by PCR analysis. After the elimination of plasmid pKD46, the resistance gene was removed with helper plasmid pCP20, which expresses the FLP recombinase. Temperature-sensitive plasmid pCP20 were removed by overnight growth at 42 °C. Materials and methods Growth conditions Bacterial strains and plasmids The strains, plasmids, and oligonucleotides used in this study are listed in Tables 1 and 2. Previously constructed Strains for cloning were cultivated in Luria-Bertani medium (1 % tryptone, 0.5 % yeast extract, and 1 % NaCl) supplemented with appropriate antibiotics (ampicillin, Table 1 Strains and plasmids used in this study Strains and plasmids Genotype Reference GPT101 W3110 (ΔtrpR::FRT, ΔtnaA::FRT, ΔptsG::FRT)with tryptophan attenuator deletion and trp promoter swapping by 5CPtacs promoter cluster GPT101 (ΔaroP::FRT) GPT101 (ΔtnaB::FRT) GPT101 (Δmtr::FRT) GPT101 (ΔaroP::FRT, ΔtnaB::FRT) GPT101 (ΔaroP::FRT, Δmtr::FRT) GPT101 (ΔtnaB::FRT, Δmtr::FRT) GPT101 (ΔaroP::FRT, ΔtnaB::FRT, Δmtr::FRT) GPT101 containing pTAT GPT201 containing pTAT GPT202 containing pTAT Gu et al. (2012) GPT201 GPT202 GPT203 GPT204 GPT205 GPT206 GPT207 GPT1002 GPT1011 GPT1012 GPT1013 GPT1014 GPT1015 GPT1016 GPT1017 pTAT pKD3 pKD4 pKD46 pCP20 GPT203 containing pTAT GPT204 containing pTAT GPT205 containing pTAT GPT206 containing pTAT GPT207 containing pTAT pCL1920 containing aroGFR, trpEFR, and tktA bla, FRT-kan-FRT bla, FRT-cat-FRT bla, helper plasmid bla and cat, helper plasmid This study This study This study This study This study This study This study Gu et al. (2012) This study This study This This This This This study study study study study Gu et al. (2012) Datsenko and Wanner (2000) Datsenko and Wanner (2000) Datsenko and Wanner (2000) Cherepanov and Wackernagel (1995) Appl Microbiol Biotechnol Table 2 Primers used in this study Primers Nucleotide sequence aroP-F aroP-R tnaB-F tnaB-R mtr-F mtr-R aroPtest-F aroPtest-R tnaBtest-F tnaBtest-R mtrtest-F mtrtest-R gltART-F gltART-R zwfRT-F zwfRT-R pgiRT-F 5′-ACTGCGTAGATCAAAAAAACAACCACCGCACGAGGTTTCGTGTAGGCTGGAGCTGCTTC-3′ 5′-TTAATGCGCTTTTACGGCTTTGGCGGTTTTCTCTTTAAAATGGGAATTAGCCATGGTCC-3′ 5′-AATTGGTGGAGGTATGTTTGCTTTACCTGTTGATCTTGCGTGTAGGCTGGAGCTGCTTC-3′ 5′-CTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATATGGGAATTAGCCATGGTCC-3′ 5′-TTCTGGTCAATGGCGGCGCTGATCTTTACCTGGTTCTGTGTGTAGGCTGGAGCTGCTTC-3′ 5′-CAGTGCGTTGCCGACGCCAAACACCAGAATCAGCGCAAT ATGGGAATTAGCCATGGTCC-3′ 5′-CATTCGCTGCCGCATACCATTA-3′ 5′-TTTGCTTCGCTGGGTGATTTCC-3′ 5′-TAGCCACTCTCTTACCCTACATCC-3′ 5′-TGAAAAACGATAACCAACTGGCGA-3′ 5′-CAACGCAGTCGCACTATTTTTCAC-3′ 5′-AGCAGAAATGTCGGATAAGGCACC-3′ 5′-CGATGGGTATTCCGTCTT-3′ 5′-CACTGTGCATTTCGCTCC-3′ 5′-GGTAAAGAAACGGTGCTGAA-3′ 5′-CACTTCTTCTGCCACGGTAA-3′ 5′-CATCTAAAACCTTCACCACT-3′ pgiRT-R gapART-F gapART-R 5′-ATCAATACCAAACTCGCCAA-3′ 5′-AACTGAATGGCAAACTGACTGGTA-3′ 5′-TTTCATTTCGCCTTCAGCAGC-3′ 100 mg l−1; kanamycin, 25 mg l−1; spectinomycin, 50 mg l−1) at 37 °C for 8 to 12 h. The fermentative medium contained (per liter) glucose (20 g), MgSO4·7H2O (5 g), KH2PO4 (2 g), (NH4)2SO4 (4 g), yeast extract (1 g), FeSO4·7H2O (100 mg), and trisodium citrate dehydrate (2 g). Strains were precultured in 5 ml Luria-Bertani medium at 37 °C overnight. The overnight cells (1 ml) were inoculated in 50-ml Luria-Bertani medium and cultured for 8 to 12 h and then 10 % (v/v) seed cultures for batch cultivation were incubated in 50-ml fermentation medium at 37 °C. Isopropyl β-D-1-thiogalactopyranoside (IPTG) was added at a final concentration of 0.2 mM. A stirred 5-l glass vessel with BioFlo310 modular fermentor system (New Brunswick Scientific, USA) was used for bioreactor fermentation. The inoculum ratio was 10 % (v/v) and the initial glucose was 20 g l−1. When glucose concentration in the medium was below 10 g l−1, a feeding solution containing 500 g l−1 of glucose was added to the medium. The incubation temperature was set at 37 °C, and the pH was controlled at 6.8 with NH3·H2O. The dissolved oxygen concentration was kept at 30 % by changing the agitation speed and aeration rate. L-Tryptophan uptake assay The strains for L-tryptophan uptake assay were precultured in Luria-Bertani medium at 37 °C overnight. Exactly 1 ml of the overnight cells was inoculated in 50-ml Luria-Bertani medium and cultured for 8 to 12 h. Cells from the 50-ml cultures were collected by centrifugation and washed three times with phosphate-buffered saline solution (137 mmol NaCl, 2.7 mmol KCl, 10 mmol Na2HPO4, 2 mmol KH2PO4, pH 7.4). The cells were then resuspended in 2-ml phosphatebuffered saline solution and incubated in the 50-ml assay medium at 37 °C with equivalent initial OD600. The assay medium contained (per liter) MgSO4·7H2O (5 g), KH2PO4 (2 g), (NH4)2SO4 (4 g), FeSO4·7H2O (100 mg), trisodium citrate dehydrate (2 g), and L-tryptophan (2 g). LTryptophan was determined using the fluorometric determination method (Iizuka and Yajima 1993). Quantitative real-time PCR analysis Samples for the RNA preparation were cultivated for 4 to 6 h at 37 °C after the addition of IPTG. The total cellular RNA was extracted using the Simple Total RNA Kit (Tiangen, China). Reverse transcription was conducted using random 6-mers primers and oligo dT with the PrimeScript RT Reagent Kit (TaKaRa, China), according to the manufacturer's instructions. RT-PCR was performed with SYBR Premix Ex Taq II (TaKaRa, China) following the protocol of the LightCycler 480 RT-PCR System (Roche, Switzerland). The measurement was repeated three times for each sample. The gene transcript primers are listed in Table 2. The gapA encoding D-glyceraldehyde-3-phosphate dehydrogenase transcript was selected as internal standard. Appl Microbiol Biotechnol At least three tryptophan permease genes are present in E. coli chromosomes. To study the function of individual permeases, we separately knocked out aroP, tnaB, and mtr in Ltryptophan-producing strain GPT101, generating E. coli GPT201, GPT202, and GPT203. The three mutants were then subjected to L-tryptophan uptake assay. L-Tryptophan (2 g l−1) was employed as substrate in the assay medium. Thus, the rate of L-tryptophan uptake was calculated on the basis of L-tryptophan utilization rate and cell density (Table 3). Knocking out aroP or mtr did not significantly affect the L-tryptophan utilization rate. By contrast, the utilization rates of L-tryptophan in GPT201 and GPT203 were slightly increased. Knock out of TnaB decreased Ltryptophan utilization from 0.058 to 0.054 g l−1 h−1 per OD600. This result indicates that TnaB is the main transporter responsible for L-tryptophan uptake in E. coli. The inactivation of TnaB may improve L-tryptophan accumulation in L-tryptophan-producing strains. However, the effect of permease knockout on the host requires evaluation. this end, plasmid pTAT, which we previously constructed by overexpressing the tktA, aroGFR, and trpEFR genes, was introduced into single permease mutant GPT201, GPT202, and GPT203, and generated E. coli GPT1011, GPT1012, and GPT1013. These strains were then cultivated in medium using glucose as substrate (Table 4). GPT1011 and GPT1012 exhibited similar cell growth and glucose consumption compared with the control GPT1002, indicating that AroP or TnaB inactivation has a negligible effect on cell growth. However, the GPT1013 strain with inactive Mtr showed poor cell growth and glucose consumption. The maximum OD600 of GPT1013 was only 5.1, which is about half that of the control. GPT1012 exhibited the highest Ltryptophan production at 2.05 g l−1. This result is consistent with the L-tryptophan uptake assay, confirming that TnaB is the main transporter responsible for L-tryptophan uptake in E. coli. The double mutants of L-tryptophan permeases, E. coli GPT1014, GPT1015, and GPT1016, were constructed to further elucidate tryptophan permease function. The cultivation of these mutants showed that they all exhibited poor growth compared with the control (Table 4). The maximum OD600 of the three mutants were 5.65, 4.32, and 6.24, respectively. GPT1014, which is characterized by AroP and TnaB double inactivation, showed the highest Ltryptophan production at 2.44 g l−1. This value is 19.02 % higher than that generated by TnaB single mutant GPT1012 and 32.6 % higher than achieved by the control. GPT1015 and GPT1016 produced low levels of L-tryptophan at 60 to 70 mg l−l. Metabolite analysis shows that the acetate secretion in GPT1015 and GPT1016 increased to 8.12 and 8.44 g l−1, respectively. These values are approximately seven times higher than that observed in GPT1014. Both GPT1015 and GPT1016 exhibit Mtr mutation. Given that the single inactivation of Mtr also affected cell growth, this result indicates that the metabolic flux in GPT1015 and GPT1016 may have been severely affected by the knockout of Mtr. Effect of L-tryptophan permease knockout on cell physiology Production of L-tryptophan from tryptophan permease-deficient mutants The growth of the L-tryptophan permease mutants were compared under L-tryptophan accumulating conditions. To The triple mutant of L-tryptophan permeases was constructed by knocking out the AroP, TnaB, and Mtr genes, Analytical method Cell growth was monitored by optical density at 600 nm (OD600) using a spectrophotometer (Shimadzu, Japan). Glucose was quantitatively analyzed with a highperformance liquid chromatography instrument (Shimadzu, Japan) equipped with a column of Aminex HPX-87H ion exclusion particles (300 mm×7.8 mm, Bio-Rad, USA). The samples were centrifuged at 12,000 rpm for 5 min and filtrated with a 0.22-μm aqueous membrane. The mobile phase was 5 mM sulfuric acid (in Milli-Q water) with a flow rate of 0.6 ml min−1. Column temperature was maintained at 65 °C. Results Effect of L-tryptophan permease knockout on L-tryptophan uptake Table 3 L-Tryptophan uptake assay of single permease mutants Each data represented the average value of three independent experiments Strains Permease deletion Maximum OD600 L-Tryptophan consumption rate (g l−1 h−1) L-Tryptophan consumption rate/OD600 (g l−1 h−1) GPT101 GPT201 GPT202 GPT203 – aroP tnaB mtr 1.07±0.011 0.95±0.021 0.98±0.016 1.10±0.030 0.062±0.002 0.061±0.001 0.053±0.0001 0.080±0.001 0.058±0.002 0.064±0.0003 0.054±0.001 0.072±0.0008 Appl Microbiol Biotechnol Table 4 Fermentation parameters of L-Tryptophan permease mutants Strains Permease inactivation Maximum OD600 Glucose consumption rate (g l−1 h−1) Maximum L-Tryptophan titer (g l−1) Acetate (g l−1) GPT1002 GPT1011 GPT1012 GPT1013 – aroP tnaB mtr 10.39±1.31 12.40±0.60 11.60±0.40 5.10±0.82 0.31±0.05 0.32±0.08 0.32±0.07 0.13±0.03 1.84±0.009 1.81±0.04 2.05±0.10 1.75±0.03 1.05±0.17 1.12±0.23 1.08±0.12 0.96±0.17 GPT1014 GPT1015 GPT1016 aroP tnaB aroP mtr tnaB mtr 5.65±0.77 4.32±0.36 6.24±0.29 0.42±0.014 0.59±0.0001 0.54±0.07 2.44±0.29 0.06±0.003 0.07±0.005 1.22±0.16 8.12±0.24 8.44±0.28 Batch cultivation was performed in 50-ml fermentative medium at 250 rpm and 37 °C for 54 h. Each data represented the average value of three independent experiments thereby improving L-tryptophan production in recombinant E. coli. GPT1017 exhibited restored cell growth compared with the double mutant of tryptophan permeases despite the presence of Mtr. The maximum OD600 was 12.89, which is higher than that achieved with the GPT1002. The Ltryptophan production of GPT1017 was 2.79 g l−1 in batch cultivation, a value 51.6 % higher than that produced by the control strain (Fig. 1). Only 1.02 g l−1 acetate was detected in GPT1017 after 54-h cultivation, a value 87.4 and 87.9 % lower than those produced in GPT1015 and GPT1016, respectively. GPT1017 was then investigated for L-tryptophan production potential in fed-batch fermentation (Fig. 2). It exhibited a long lag growth phase of 24 h. Glucose was consumed slowly during this period, and the cell entered the exponential phase after 24 h. A maximum OD600 of 44.7 occurred at 45 h. L-Tryptophan accumulated at the beginning of the fermentation at a relatively constant speed. The maximum L-tryptophan production was 16.3 g l−1 at 66 h. Compared with the GPT1002, To investigate the effect of knocking out L-tryptophan permeases on L-tryptophan production and metabolism flux at the genetic level, we performed RT-PCR analysis of three key genes: citrate synthase, glucose-6-phosphate dehydrogenase, and glucosephosphate isomerase, which are involved in the tricarboxylic acid cycle, pentose phosphate pathway, and glycolysis in E. coli, respectively (Fig. 3). These genes showed decreased transcription in all mutants, especially in GPT1015 and GPT1016, in which they were downregulated to 0.01– 0.08-fold of the level in GPT1002. This result indicates that the inactivation of L-tryptophan permeases influences the metabolic pathway and metabolic flux, thereby resulting in poor cell growth of mutants. However, Fig. 1 Batch cultivation of tryptophan permease-deficient mutant GPT1017. Each data represented the average value of three independent experiments and the error bars represent standard deviations Fig. 2 Fed-batch fermentation of GPT1017. The error bars represent standard deviations from three measurements GPT1017 produced approximately 50 % more L-tryptophan under similar condition. This result indicates potential application in industry. Transcriptional analysis of L-tryptophan permease mutants Appl Microbiol Biotechnol Fig. 3 Relative gene transcription of L-tryptophan permease mutants comparing to the parent strain GPT1002. gapA transcripts were selected as standard and each measurement was repeated three times. The error bars indicate standard deviations the transcription of gltA, zwf, and pgi was restored in the tryptophan permease-deficient mutant GPT1017. The transcription of gltA in GPT1017, which is the key gene in the TCA cycle, increased by 40-fold over the levels observed in GPT1015 and GPT1016. Discussion Transport system engineering is an efficient strategy for regulating the metabolic flux towards high-yield amino acid production (Morbach et al. 1996). Many studies on transport system have been carried out in C. glutamicum, a model organism widely used for amino acid production. In 1994, Ikeda et al. analyzed the uptake of aromatic amino acid in C. glutamicum and improved the amino acid production by decreasing uptake activity (Ikeda and Katsumata 1994). Later, they obtained a C. glutamicum strain with decreased L-tryptophan assimilation ability by multiple rounds of random mutagenesis. This strain produced 10–20 % more L-tryptophan than the control. However, it was difficult to verify if unexpected mutations at other sites led to the increased L-tryptophan (Ikeda and Katsumata 1995). In 2011, Zhao et al. identified a gene ncgl1108 (PhePCg), encoding a new Lphenylalanine transporter, in C. glutamicum RES167 (Zhao et al. 2011). In this study, we investigated the effect of L-tryptophan permeases on the cell metabolism and L-tryptophan production of E. coli by constructing a series of knockout mutants. Knocking out tnaB decreased the rate of L-tryptophan utilization, indicating that TnaB is the main transporter responsible for the uptake of L-tryptophan in E. coli. All the mutants that contain inactive TnaB showed increased L-tryptophan production. This result is inconsistent with the report of Zhao et al., who showed that knocking out mtr more efficiently improves L-tryptophan production (Zhao et al. 2012). By contrast, we found that mtr inactivation severely influenced cell growth and L-tryptophan production. GPT1015 and GPT1016, which both contain inactive mtr, produced almost no L-tryptophan. Mtr is a highaffinity tryptophan permease, of which the expression is repressed in the presence of tryptophan (Heatwole and Somerville 1991b; Sarsero et al. 1991), whereas TnaB is a low-affinity transporter responsible for the tryptophan uptake from the medium (Yanofsky et al. 1991). Therefore, Mtr should be repressed in a tryptophan-producing strain and cannot play a key role in reutilization of tryptophan. In this case, TnaB shall be the main tryptophan importer, and inactivation of TnaB shall prevent the reutilization of tryptophan and improve the tryptophan production. Our experimental result confirmed this expectation. RT-PCR analysis showed that the key genes, gltA, zwf, and pgi, which are involved in tricarboxylic acid cycle, pentose phosphate pathway, and glycolysis, were downregulated to 0.01–0.08-fold over the level achieved with the control. The effect of mtr knockout on cell growth has not been comprehensively investigated, but previous studies showed that Mtr transports both Ltryptophan and indole. Indole has several diverse roles in bacterial signaling (Lacour and Landini 2004; PineroFernandez et al. 2011). Indole behavior is, in many respects, similar to the signaling component of a quorum-sensing system. Knocking out mtr may affect indole transport and, therefore, affect some important cell physiological processes. Triple-gene knockout mutant E. coli GPT1017 exhibited restored cell growth, reduced acetate secretion, and increased L-tryptophan production. The RT-PCR analysis suggests that this finding is attributed to the restored transcription of the key genes in central metabolic pathways. Further experiments should be conducted to determine the exact regulation mechanism of L-tryptophan permeases on cell metabolism. 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