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Applied and Environmental Microbiology, May 2008, p. 3284-3290, Vol. 74, No. 10
0099-2240/08/$08.00+0 doi:10.1128/AEM.02456-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Metabolic Engineering of Escherichia coli for L-Tyrosine Production by Expression of Genes Coding for the Chorismate Mutase Domain of the Native Chorismate Mutase-Prephenate Dehydratase and a Cyclohexadienyl Dehydrogenase from Zymomonas mobilis
María I. Chávez-Béjar,1
Alvaro R. Lara,2,
Hezraí López,1
Georgina Hernández-Chávez,1
Alfredo Martinez,1
Octavio T. Ramírez,2
Francisco Bolívar,1 and
Guillermo Gosset1*
Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62210, México,1
Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62210, México2
Received 31 October 2007/
Accepted 8 March 2008

ABSTRACT
The expression of the feedback inhibition-insensitive enzyme
cyclohexadienyl dehydrogenase (TyrC) from
Zymomonas mobilis and the chorismate mutase domain from native chorismate mutase-prephenate
dehydratase (PheA
CM) from
Escherichia coli was compared to the
expression of native feedback inhibition-sensitive chorismate
mutase-prephenate dehydrogenase (CM-TyrA
p) with regard to the
capacity to produce
L-tyrosine in
E. coli strains modified to
increase the carbon flow to chorismate. Shake flask experiments
showed that TyrC increased the yield of
L-tyrosine from glucose
(
YL-Tyr/Glc) by 6.8-fold compared to the yield obtained with
CM-TyrA
p. In bioreactor experiments, a strain expressing both
TyrC and PheA
CM produced 3 g/liter of
L-tyrosine with a
YL-Tyr/Glc of 66 mg/g. These values are 46 and 48% higher than the values
for a strain expressing only TyrC. The results show that the
feedback inhibition-insensitive enzymes can be employed for
strain development as part of a metabolic engineering strategy
for
L-tyrosine production.

INTRODUCTION
L-Tyrosine (
L-Tyr) is an aromatic amino acid with several applications.
It is used as precursor in the synthesis of some drugs (
39),
biodegradable polymers (
10), melanin (
12), and phenylpropanoids
(
38). The pathway leading to
L-Tyr biosynthesis starts with
the condensation of phosphoenolpyruvate (PEP) and erythrose-4-phosphate
(E4P) in a reaction catalyzed by 3-deoxy-
D-
arabino-heptulosonate-7-phosphate
synthase (DAHPS). Seven reactions are necessary to produce chorismate
(CHA), the common precursor for the synthesis of the three aromatic
amino acids (Fig.
1). For
L-phenylalanine (
L-Phe) and
L-Tyr
biosynthesis, CHA is converted to prephenate (PPA) in a reaction
catalyzed by chorismate mutase (CM). In nature, there are two
distinct pathways that synthesize
L-Tyr. In enteric bacteria,
prephenate dehydrogenase (TyrA
p) catalyzes the conversion of
PPA to
p-hydroxyphenylpyruvate (HPP).
L-Tyr is formed by transamination
of HPP. In plants, PPA is converted to
L-arogenate (
L-AGN) by
transamination. Conversion of
L-AGN into
L-Tyr is catalyzed
by arogenate dehydrogenase (TyrA
a).
Zymomonas mobilis and other
organisms possess enzymes called cyclohexadienyl dehydrogenases
(TyrA
c), which are capable of using either PPA or
L-AGN as a
substrate for
L-Tyr biosynthesis (
47). TyrA
a, TyrA
p, and TyrA
c belong to the TyrA protein family, which includes the group
containing all known dehydrogenases involved in
L-Tyr biosynthesis,
and use NAD
+ or NADP
+ or both dinucleotides as cofactors. Members
of the TyrA protein family are frequently fused to other catalytic
or regulatory domains. Furthermore, compounds like
L-Tyr and
HPP inhibit the activity of some TyrA proteins (
8,
9,
40,
44).
In
Escherichia coli,
L-Tyr inhibits the activity of three enzymes:
the AroF DAHPS isozyme and 3-dehydroquinate synthase in the
common aromatic pathway and the bifunctional enzyme chorismate
mutase-prephenate dehydrogenase (CM-TyrA
p), in the
L-Tyr biosynthetic
pathway (
4,
35) (Fig.
1).
The general strategy used for the development of aromatic amino
acid-overproducing strains has involved the alleviation of control
mechanisms in key pathways (
7,
41). Several different microorganisms
have been modified for
L-Tyr production.
Corynebacterium glutamicum,
Arthrobacter globiformis, and
Brevibacterium lactofermentum L-Tyr-overproducing strains were developed by classical mutagenesis
methods, and they were selected based on their capacity to grow
on toxic aromatic amino acid analogs (
20,
25,
36). Biochemical
analyses of
C. glutamicum strains showed that enzymes like DAHPS
and CM were not inhibited by the aromatic amino acids (Fig.
1), while the TyrA
a of this organism is naturally insensitive
to feedback inhibition by
L-Tyr (
18,
21). The best
C. glutamicum strain obtained by this procedure produced 26 g/liter of
L-Tyr
in 80 h in a fed-batch fermentation (
24). Metabolic engineering
and protein-directed evolution strategies have been used to
construct
E. coli L-Tyr-producing strains (
31,
32; A. Takai,
R. Nishi, Y. Joe, and H. Ito, U.S. patent application 20050277179).
In these studies, feedback inhibition-resistant variants of
CM-TyrA
p were obtained by error-prone PCR of the encoding gene
tyrA and were selected using the toxic analog 3-fluoro-
DL-tyrosine.
Using
E. coli as a host strain, Takai et al. (U.S. patent application
20050277179) and Lütke-Eversloh and Stephanopoulos (
32)
constructed
E. coli L-Tyr producers by overexpression of feedback
inhibition-resistant variants of DAHPS and CM-TyrA
p (
13,
29,
31,
32; Takai et al., U.S. patent application 20050277179).
One of the
E. coli L-Tyr producers, which had additional central
metabolism genetic modifications, produced 9.7 g/liter of
L-Tyr,
with an
L-Tyr yield on glucose (
YL-Tyr/Glc) of 0.10 g/g and
an
L-Tyr-specific production rate (
qL-Tyr) of 73 mg/g (dry weight)/h
in a fed-batch fermentation (
32). Olson et al. (
33) employed
a different approach for construction of an
E. coli L-Tyr producer.
An
L-Phe-producing strain, which was developed by a classical
mutagenesis procedure, was converted into an
L-Tyr-producing
strain by replacing the native promoter of
tyrA with the
trc promoter. This strain produced 55 g/liter of
L-Tyr, with a
YL-Tyr/Glc of 0.3 g/g and a
qL-Tyr of around 57 mg/g (dry weight)/h (
33,
34).
The cyclohexadienyl dehydrogenase (TyrC) of Z. mobilis is not inhibited by L-Tyr or the other two aromatic amino acids (47). Due to this property, this enzyme was used recently for the development of a tunable selection system for mutant prephenate dehydratases. In this system, TyrC diverted PPA into the L-Tyr pathway to avoid the nonenzymatic conversion of PPA into phenylpyruvate in L-Phe biosynthesis (26). On the other hand, CM-prephenate dehydratase (P-protein) from E. coli is involved in L-Phe biosynthesis. When the CM domain (residues 1 to 109) of the P-protein is expressed alone (PheACM), it retains catalytic activity and becomes insensitive to L-Phe inhibition (45, 46). In contrast, the CM domain from CM-TyrAp loses its catalytic activity when it is not fused to the corresponding TyrAp domain (14).
Considering the information described above, an approach not dependent on random mutagenesis for generating a CHA-to-HPP pathway insensitive to feedback inhibition by L-Tyr was evaluated in this work. The strategy reported here was based on expressing genes encoding enzyme domains expected to be insensitive to feedback inhibition by L-Tyr. The tyrC gene from Z. mobilis, which codes for TyrC, was expressed in an E. coli strain previously modified to increase carbon flow to CHA. In addition, to reconstitute the complete CHA-to-HPP pathway, an operon was constructed with the tyrC gene and the region of the pheA gene (pheACM) that codes for the PheACM domain.
Details about the construction of plasmids pTrctyrC, pTrctyrCpheACM, and pTrctyrCpheACMINV are shown in Tables 1 and 2 and Fig. 2. In several experiments, a strain expressing the tyrA gene was used as a control. tyrA was cloned from E. coli JM101 chromosomal DNA (6) into pCR-Blunt II-TOPO to generate plasmid pTOPOtyrA. The tyrA gene was isolated from this plasmid and cloned into plasmid pTrc99A to construct pTrctyrA. The nucleotide sequences of the three genes were determined from plasmids and were found to be identical to those reported previously (Table 2).
Functional complementation assays were performed with
E. coli FA114 (Table
1), which lacks CM, TyrA
p, and prephenate dehydratase
activities. FA114 was transformed with each of the following
plasmids: pTrc99A, pTrc
tyrA, pTrc
tyrCpheACM, and pTrc
tyrCpheACMINV (Table
1). Assays were performed at 30°C in liquid M9 minimal
medium (
37) supplemented with (per liter) 2 g glucose, 20 mg
L-Phe, 20 mg
L-tryptophan, 20 mg
L-leucine, 20 mg
L-isoleucine,
10 mg
p-aminobenzoic acid, 10 mg
p-hydroxybenzoic acid, 10 mg
2,3-dihydroxybenzoic acid, 200 µg ampicillin, and 23.83
mg isopropyl-β-
D-thiogalactopyranoside (IPTG). Only the
cells transformed with plasmid pTrc
tyrA or pTrc
tyrCpheACM were
able to grow in minimal medium (data not shown). This experiment
indicated that the genes were expressed and the enzyme activity
levels of TyrC and PheA
CM were sufficient to give FA114 the
metabolic ability to synthesize
L-Tyr.
In order to determine if L-Tyr inhibited TyrC and PheACM activities, enzymatic assays were performed in the presence or absence of L-Tyr. Strain FA114/pTrctyrCpheACM was grown in LB medium with 23.83 mg/liter of IPTG and 100 mg/liter of carbenicillin. Cultures were started at an optical density at 600 nm (OD600) of 0.03 and incubated at 30°C for 12 h. Cells were washed once with lysis buffer (0.1 M Tris, 1 mM sodium EDTA, 1 mM dithiothreitol, 50 mM KCl; pH 7.5) and disrupted by sonication. PheACM activity was assayed at 30°C by following the consumption of CHA at 290 nm (
290 for CHA, 1.85 x 103 M–1 cm–1). TyrC activity was measured at 30°C by monitoring the appearance of NADH at 340 nm (
340 for NADH plus HPP, 6.4 x 103 M–1 cm–1). The reaction mixtures contained 50 mM Tris, 0.5 mM sodium EDTA, and 0.1 mg/ml bovine serum albumin (pH 7.5) at 30°C. The following concentrations of substrates were used: 2 mM NAD+, 0.2 mM PPA (for TyrC activity), and 1 mM CHA (for PheACM activity) (15, 27). Protein concentrations were determined by the Bradford method (11). One unit of TyrC activity was defined as the amount of enzyme that consumed 1 µmol of CHA per min at 30°C, and 1 U of PheACM activity was defined as the amount of enzyme that produced 1 µmol of NADH per min at 30°C. TyrC had a specific activity of 1.54 ± 0.08 IU/mg protein, while in the presence of 0.6 mM L-Tyr the specific activity was 1.34 ± 0.47 IU/mg protein. These results show that TyrC is not sensitive to L-Tyr inhibition. This is in agreement with the results obtained by Zhao et al. (47), who determined that 2 mM L-Tyr did not inhibit the activity of TyrC. Previous reports have determined that the activity of PheACM is not inhibited by L-Phe (46). However, L-Tyr was not assayed as an inhibitor, because it does not inhibit P-protein activity. To determine the possible sensitivity of the PheACM domain to L-Tyr, assays were carried out as described above. The specific activity of PheACM was 29.4 ± 5.39 IU/mg protein without L-Tyr. The specific activities with 0.6 and 1.1 mM L-Tyr were 34.4 ± 3.09 and 21.0 ± 0.23 IU/mg protein, respectively. In the case of CM-TyrAp, it has been reported that at concentrations higher than 0.5 mM, L-Tyr inhibits TyrAp activity by 90% and CM activity by 45% (23, 43). Our results showed that both TyrC and PheACM are less sensitive to L-Tyr inhibition than corresponding activities of CM-TyrAp.
The effect of expressing the aroGfbr, tyrA, tyrC, and pheACM genes on L-Tyr production was evaluated in shake flasks cultures. The aroGfbr gene codes for a feedback inhibition-resistant DAHPS mutant; its expression causes an increase in the carbon flux directed into the common aromatic amino acid pathway (3). These experiments were carried out with E. coli strain PB12, which lacks the phosphotransferase system operon genes; therefore, it does not use PEP to transport and phosphorylate glucose (19). In this way, PEP availability for aromatic biosynthesis is increased (2). PB12 was transformed with plasmid pJLBaroGfbr to generate strain PB12G. Strain PB12G was then transformed with plasmid pTrctyrA (PB12A), pTrctyrC (PB12C), or pTrctyrCpheACM (PB12CP) (Table 1). Shake flask cultures were grown at 30°C in M9 liquid medium supplemented with (per liter) 10 g glucose, 23.83 mg IPTG, 30 µg tetracycline, and 100 µg carbenicillin. Growth was monitored by measuring the OD600, and the results were converted to dry weight of cells by assuming that 1 OD600 unit was equivalent to 0.37 g/liter (22). L-Tyr and L-Phe in culture supernatants were quantified using an Agilent 1100 high-performance liquid chromatography system (Agilent Technologies, Palo Alto, CA) equipped with a Phenomenex Synergy Hydro RP18 column (150 by 4.6 mm; 4 µm) attached to an Agilent 1100 electrospray mass spectrometry detection system. Samples were eluted with 10% methanol in 0.1% acetic acid in water at an isocratic flow rate of 0.5 ml/min. UV quantitation was performed at 220 nm. The mass spectrometry conditions for amino acid determination were as follows: electrospray ionization in the positive mode; fragmentor voltage, 90 V; drying gas temperature, 300°C; drying gas flow rate, 13 liters/min; capillary voltage, 4,000 V; and nebulizer pressure, 30 lb/in2. For total scans, (M+1)+ ions were detected and identified for standards and also for samples. The m/z ratios for L-Phe and L-Tyr are 166 and 182, respectively. The glucose content was determined from culture supernatants using an enzymatic analyzer (2700 biochemistry analyzer; YSI, Yellow Springs, OH.).
Compared with PB12G, PB12A had a qL-Tyr and a YL-Tyr/Glc that were 1.6- and 1.1-fold higher, respectively. On the other hand, the qL-Tyr for PB12C and PB12CP were 6.8- and 5.8-fold higher, respectively, than the values for PB12A (Fig. 3 and Table 3). Compared with PB12A, PB12C and PB12CP had YL-Tyr/Glc that were 6.6- and 6.4-fold higher, respectively. These results showed that overexpression of wild-type tyrA (CM-TyrAp) resulted in only a small increase in the L-Tyr production capacity in a strain already expressing a feedback inhibition-resistant version of DAHPS. On the other hand, expression of tyrC resulted in a significant increase in L-Tyr production, and no further enhancement was observed when both tyrC and pheACM were expressed. These results showed that expression of a feedback inhibition-insensitive variant of DAHPS is sufficient to cause E. coli to overproduce L-Tyr. This capacity was not increased considerably by overexpression of CM-TyrAp, most likely because it is subject to feedback inhibition by L-Tyr. This regulatory constraint was overcome in the strains expressing feedback inhibition-insensitive TyrC protein, resulting in a large increase in L-Tyr production. The observed differences in L-Tyr production between PB12A and PB12C indicated that the conversion of PPA to HPP is a limiting step in the pathway that can be overcome by introducing the activity of a feedback inhibition-insensitive TyrA protein, like TyrC.
To further characterize the best
L-Tyr-producing strains, PB12C
and PB12CP were grown using media and fermentation conditions
similar to those employed for biotechnological processes. Cultures
were grown in 1-liter bioreactors (BioFlo 110 modular fermentor
system; New Brunswick Scientific, New Jersey). Operation parameters
were controlled by the AFS-Biocommand bioprocessing software
(New Brunswick Scientific, New Jersey). The culture conditions
were as follows: working volume, 0.6 liter; temperature, 37°C;
airflow rate, 0.6 liter/min; dissolved oxygen level maintained
above 30% air saturation by increasing the stirrer speed (500
to 1200 rpm); and pH controlled at 7.0 by addition of 15% NH
4OH.
The culture medium contained (per liter) 50 g glucose, 6 g Na
2HPO
4,
3 g KH
2PO
4, 5 g (NH
4)
2SO
4, 2 g sodium citrate·2H
2O, 10
g yeast extract, 1.5 g MgSO
4·7H
2O, 550 mg CaCl
2, 40 mg
thiamine-HCl, 30 µg tetracycline, 100 µg carbenicillin,
and 23.83 mg IPTG. A trace element solution contained (per liter)
8.74 µg Na-EDTA·2H
2O, 1.55 µg CoCl
2·6H
2O,
9.30 µg MnCl
2, 0.93 µg CuCl
2, 1.30 µg Na
2MoO
4·2H
2O,
20.96 µg zinc acetate·H
2O, 62.49 µg Fe(III)
citrate, and 1.86 µg H
3BO
3. The cell glucose,
L-Tyr, and
L-Phe contents were determined as described above. Acetic acid,
3-dehydroshikimic acid (DHS), and shikimic acid (SHIK) were
quantified as described elsewhere (
3).
L-Tyr is insoluble in
water at concentrations above 0.4 g/liter at neutral pH; for
this reason, 1-ml portions of fermentation samples were treated
with 50 µl of 6 N HCl, mixed, and incubated 30 min at
42°C, samples were centrifuged at 12,000 rpm to remove the
cells (Eppendorf 5410), and supernatants were filtered and diluted
for high-performance liquid chromatography analysis.
After 21 and 27 h of incubation, strains PB12C and PB12CP reached final biomass concentrations of 13.9 ± 0.8 and 11.1 ± 2.1 g (dry weight)/liter, respectively. Differences in several parameters related to L-Tyr production were observed between these strains (Table 4). PB12CP, which expresses the tyrC and pheACM genes, produced an L-Tyr titer that was 46% higher than that of PB12C. For PB12CP the amount of L-Tyr produced per gram (dry weight) of cells and the YL-Tyr/Glc were 85 and 48% higher than the values for PB12C, respectively. The YL-Tyr/Glc for PB12C and PB12CP corresponded to 7.7 and 11.9%, respectively, of the maximum theoretical yield (0.553 g/g) (32). Finally, the qL-Tyr for PB12CP was 36% higher than that for PB12C. Under these culture conditions, strain PB12CP displayed the highest L-Tyr yields and titer. Based on these results, it is clear that a strain expressing both tyrC and pheACM is a better L-Tyr producer than a strain expressing only tyrC. However, considering the results observed in shake flask experiments, the positive effect of expressing both tyrC and pheACM appears to be dependent on the culture conditions.
Metabolites of
L-Phe and common aromatic pathways were also
measured (
L-Phe, DHS, and SHIK) (Fig.
1 and Table
4).
L-Phe
was not detected in culture supernatants from either of the
two strains (data not shown). On the other hand, accumulation
of DHS and SHIK in the culture medium indicated the presence
of rate-limiting steps in the common aromatic pathway (
3,
16,
30). This suggests that the TyrC and PheA
CM enzymes efficiently
compete for carbon with the
L-Phe pathway. The amounts of
L-Tyr
produced by PB12C and PB12CP represent 45 and 42%, respectively,
of the sum of the amounts of the measured metabolites (DHS,
SHIK, and Tyr). Finally, acetic acid was not detected in culture
supernatants. Strains with an inactive phosphotransferase system
display very low acetic acid production, even with elevated
glucose concentrations (
28).
Previous studies of microbial production of L-Tyr employed classical mutagenesis methods for the generation of strains that overproduce this amino acid. More recently, mutagenesis of genes encoding specific enzymes that are feedback inhibited by L-Tyr has proven to be a successful approach for generating production strains. Despite the utility of these approaches, their application involves a requirement to generate and screen a large number of mutants to find strains with an increased capacity to overproduce L-Tyr (or L-Phe) or feedback inhibition-resistant enzymes that retain their catalytic activity. In this work, we took advantage of the natural diversity in the TyrA family of enzymes and designed a rational strategy to overcome feedback inhibition regulation in the L-Tyr pathway in E. coli. TyrC from Z. mobilis is not inhibited by L-Tyr; thus, by expressing TyrC in E. coli it was possible to reduce considerably the negative control that L-Tyr exerts in its terminal pathway. Our results showed that this approach greatly increased carbon flow to the L-Tyr pathway. On the other hand, in enzymatic assays it was found that the PheACM domain of P-protein was weakly inhibited by L-Tyr. In bioreactor cultures it was determined that expression of this domain increases the L-Tyr production capacity in a strain also expressing TyrC. The strains generated in this study are not final production strains; they can be further improved with additional genetic alterations. If all the metabolic bottlenecks in the common aromatic pathway could be alleviated, it would be possible to increase the amount L-Tyr produced by PB12C and PB12CP twofold. The modifications needed to meet this goal are overexpression of the aroL and ydiB genes in the common aromatic pathway (30; Takai et al., U.S. patent application 20050277179). In addition, it should be possible to further improve these strains by expression of the tktA gene to increase E4P availability (17) and by inactivation of the transcriptional regulator TyrR (32; Takai et al., U.S. patent application 20050277179). The approach described here is one of the strategies that can be used to eliminate the regulation in the L-Tyr biosynthetic pathway, with the purpose of producing L-Tyr and compounds derived from L-Tyr. Finally, the results obtained in this study show that a metabolic engineering strategy, based on the utilization of natural diversity, is a viable rational alternative to approaches based on random mutagenesis.

ACKNOWLEDGMENTS
This work was supported in part by CONACyT grants D432432 and
44126. María I. Chávez-Béjar was supported
by fellowships from CONACyT and DGEP/UNAM.
We thank Roy Jensen for critically reading the manuscript and Joel Osuna from Instituto de Biotecnología/Universidad Nacional Autónoma de México for the gift of E. coli FA114. We thank Mercedes Enzaldo and Shirley Ainsworth for technical assistance.

FOOTNOTES
* Corresponding author. Mailing address: Instituto de Biotecnología, Universidad Nacional Autónoma de México (U.N.A.M.), Apdo. Postal 510-3, Cuernavaca, Morelos 62210, México. Phone: 52-777-3291601. Fax: 52-777-3172388. E-mail:
gosset{at}ibt.unam.mx 
Published ahead of print on 14 March 2008. 
Present address: Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, México City, México. 

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Applied and Environmental Microbiology, May 2008, p. 3284-3290, Vol. 74, No. 10
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