Diversity-oriented production of metabolites derived from chorismate and their use in organic synthesis

Article abstract of DOI:10.1002/anie.201103261

Biosynthesis as a model: Based on the branched structure of biosynthetic pathways, such as the shikimate pathway, the selective bioproduction of a set of diverse metabolites has been achieved by means of metabolic engineering (see scheme). A scale-up for

Full text of DOI:10.1002/anie.201103261

DOI: 10.1002/anie.201103261
Synthetic Biology
Diversity-Oriented Production of Metabolites Derived from
Chorismate and Their Use in Organic Synthesis**
Johannes Bongaerts, Simon Esser, Volker Lorbach, Lꢀay Al-Momani, Michael A. Mꢁller,
Dirk Franke, Christoph Grondal, Anja Kurutsch, Robert Bujnicki, Ralf Takors, Leon Raeven,
Marcel Wubbolts, Roel Bovenberg, Martin Nieger, Melanie Schꢁrmann, Natalie Trachtmann,
Stefan Kozak, Georg A. Sprenger,* and Michael Mꢁller*
Dedicated to Professor Heinz G. Floss
According to Coreyꢀs retrosynthetic approach,[1] the chemical
synthesis of individual target compounds requires the use of
specific starting synthons in most cases. In contrast, the matrix
approach[2] inspired by natureꢀs biosynthetic machinery is
based on a diversity-oriented strategy. Indeed, the in vivo
synthesis of many natural metabolites is subject to a complex
matrix of dependencies and regulations. Thus, natural metab-
olites may generally be biosynthesized by alternative path-
ways, starting either from different or from the same
compounds. The biosynthesis of a metabolite may require
one specific enzymatic transformation or a biotransformation
step that is catalyzed by several enzymes acting together in a
cascade of reactions. Moreover, the activity of some enzymes
may differ from substrate to substrate, some enzymes may
simultaneously be involved in several different pathways, and
other enzymes may be diversified in posttranslational modi-
fication steps.[3] Furthermore, the status of the matrix is
generally controlled on the DNA level by regulating the
enzyme expression, and on the metabolite level by activating
or inhibiting enzyme activities.
The shikimate pathway is one prominent example of a
matrix-based biosynthesis, which is essential in plants, bac-
teria, and fungi,[4] and has been described as a branched
metabolic tree for the synthesis of a wide range of (mostly
aromatic) compounds. Several enzymes that modify choris-
mate exhibit structural and mechanistical similarities. The
biosynthesis of chorismate and its precursors is subject to
complex regulations.[5,6] Some important enzymatic trans-
formations that start from chorismate (1)[7] are depicted in
Scheme 1. The proteinogenic aromatic amino acids, folates,
ubiquinones, menaquinones, enterobactin, and many secon-
dary metabolites are biosynthesized in a few steps starting
from chorismate.[5,8]
[*] S. Esser,[+] M. A. Mꢀller, A. Kurutsch, Prof. M. Mꢀller
Institut fꢀr Pharmazeutische Wissenschaften
Albert-Ludwigs-Universitꢁt Freiburg
Albertstrasse 25, 79104 Freiburg (Germany)
E-mail: michael.mueller@pharmazie.uni-freiburg.de
J. Bongaerts,[+] L. Raeven, M. Wubbolts, R. Bovenberg
Anti-Infectives B.V., DAI-Innovation, Delft (The Netherlands)
V. Lorbach,[+] D. Franke, C. Grondal, R. Bujnicki, M. Schꢀrmann
Institut fꢀr Biotechnologie, Forschungszentrum Jꢀlich (Germany)
Prof. R. Takors
Institut fꢀr Bioverfahrenstechnik, Universitꢁt Stuttgart (Germany)
M. Nieger
Department of Chemistry, University of Helsinki (Finland)
N. Trachtmann, S. Kozak, Prof. G. A. Sprenger
Institut fꢀr Mikrobiologie, Universitꢁt Stuttgart
Allmandring 31, 70569 Stuttgart (Germany)
E-mail: g.sprenger@imb.uni-stuttgart.de
Prof. L. Al-Momani
Tafila Technical University, Tafila (Jordan)
[+] These authors contributed equally to this work.
[**] This work was financially supported by the German Federal Ministry
of Education and Research (BMBF) as part of the CHORUS (BMBF
0312688) project. Technical assistance by Petra Geilenkirchen,
Ursula Degner, Susanne Kremer, Sonja Orf, and Dick Schippers is
gratefully acknowledged.
Scheme 1. Recently described metabolites derived from chorismate
(1). ADIC=2-amino-2-deoxyisochorismate, ADC=4-amino-4-deoxy-
chorismate, CHD=cyclohexadienediol carboxylate, CHA=cyclohexa-
dieneaminoalcohol carboxylate, SHCHC=(1R,6R)-2-succinyl-6-hydroxy-
2,4-cyclohexadiene carboxylate.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201103261.
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The aim herein was to use the biosynthetic strategy as a
model for producing diverse compounds based on one major
biosynthesis pathway. To exemplify this strategy, we chose the
shikimate pathway with chorismate as the branching point for
the production of a broad array of non-aromatic compounds
(Scheme 1). In theory, however, this approach is not restricted
to these compounds.
As it has been shown by Leistner and co-workers,[9] strains
of Klebsiella pneumoniae with deficiencies in the aromatic
amino acid pathway excrete (5S,6S)-5,6-dihydroxycyclohexa-
1,3-dienecarboxylic acid (2,3-trans-CHD, 5) and (3R,4R)-3,4-
dihydroxycyclohexa-1,5-dienecarboxylic acid (3,4-trans-
CHD, 9) when enzymes catalyzing the conversion of choris-
mate (1) towards these metabolites are overproduced. We
have previously described microbial access to 5 and 9 with
recombinant E. coli strains.[10,11] Improvement in the genetic
construction of the relevant strains (deletion of competing
metabolic pathways towards phenylalanine and tyrosine,
deregulation of precursor flux through the shikimate pathway,
enhancement of enzyme activities for the chorismate-con-
verting enzymes EntB and EntC for 5, enhancement of the
activity for EntB, deletion of the entC gene for 9) and
improvements of the fermentation process (that is, applica-
tion of closed-loop control of glucose supply and indirect
control for optimum tyrosine and phenylalanine feed during
cell growth in 7.5 L or 42 L fed-batch fermentations, respec-
tively) ultimately resulted in a high final concentration of the
product of more than 15 gLÀ1 for both metabolites together
with only low acetate titers. By means of a 300 L fed-batch
approach, both compounds were produced on a kilogram
scale, and could also be separated by in situ product recovery
(ISPR) using reactive extraction.[12] Enantiopure 5 and 9, as
well as the other compounds shown in Scheme 1, are hardly
accessible by chemical synthesis. Thus, 5 and 9 became
available for subsequent chemical modifications for the
synthesis of natural products and pharmaceutically relevant
compounds.
The first chemical conversions aimed at the synthesis of
structurally related cyclitols. We showed in earlier work that
2,3-trans-CHD (5) is a beneficial building block for the
synthesis of natural product derivatives by stereo- and
regioselective epoxidation and dihydroxylation.[13,14] In a
similar approach, 3,4-trans-CHD (9) was regio- and stereose-
lectively functionalized on each of the two carbon–carbon
double bonds. Steric hindrance and induced preferential
conformations are the key issues for stereoselectivity. Thus,
the hydroxy groups of 3,4-trans-CHD methyl ester (10) were
protected with either sterically demanding tert-butyldimetyl-
silyl (TBS) groups (11), or by derivatization to a conforma-
tionally rigid [1,3,5]-trioxepine system (12; Scheme 2). Sub-
sequent oxidation of 11 with N-bromoacetamide took selec-
tively place at the less substituted double bond and resulted in
the formation of two isomeric brominated compounds with a
ratio of 3:1. Treatment of a methanolic solution of a mixture
of both compounds with solid sodium carbonate led to the
formation of epoxide 13 and the brominated 3,4-trans-CHD
derivative 14. The oxidation of the bicyclic diene 12 with N-
bromoacetamide in the presence of silver(I) and acetic acid
yielded exclusively in one product 15. The configuration of 15
Scheme 2. 3,4-trans-CHD (9) as a building block in a diversity-oriented
synthesis. The molecular structure of 16 was determined by X-ray
structure analysis (see the Supporting Information). MOM=methox-
ymethyl, TBS=tert-butyldimethylsilyl, DMP=2,2-dimethoxypropane,
NMO=4-methylmorpholine 4-oxide, DIBAL-H=diisobutylaluminum
hydride.
was determined by subsequent reduction with DIBAL-H and
single-crystal X-ray structure analysis of the resulting diol 16
(see the Supporting Information). The cis-selective dihydrox-
ylation of 11 with a mixture of 4-methylmorpholine-4-oxide
and catalytic amounts of potassium osmate(VI) occurs
predominantly at the more highly substituted double bond.
Two regioisomers were obtained in a ratio of 4:1 and 70%
yield. Subsequent acid-catalyzed conversion of the mixture of
both diols with 2,2-dimethoxypropane (DMP) resulted in the
formation of the two acetonides 17 and 18. The relative
stereochemistry of 17 was shown by cleavage of the TBS
ethers, which resulted in a compound described by Myers
et al.[15] The relative stereochemistry of 18 was elucidated by
NOE-NMR experiments after cleavage of the TBS ethers.
Surprisingly, and in contrast to our experience with 2,3-trans-
CHD (5), the major products of all reactions examined to
date result from an attack cis to the adjacent allylic TBS ether
of 11 (Scheme 2).
Combined, the microbial access to 2,3-trans-CHD (5) and
3,4-trans-CHD (9) enables the efficient synthesis of a variety
of different cyclitols and derivatives thereof within a few
synthetic steps. The complementary of 5 and 9 was empha-
sized by the synthesis of both enantiomers of the natural
product valienone (19) starting from these compounds
(Scheme 3).[16]
1,2-Amino alcohols are prevalent in natural products and
pharmaceuticals, for example in adrenaline and beta blockers.
Furthermore, they serve as chiral auxiliaries and ligands for
organic synthesis. Amino acids are another group of com-
pounds that are omnipresent in nature. Besides proteinogenic
a-amino acids, which are ubiquitous building blocks in nature,
numerous bioactive compounds are amino acids, such as the
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Scheme 3. Synthesis of both enantiomers of valienone (19) starting
from dienes 5 and 9.[16]
inhibitory neurotransmitter GABA (g-aminobutyric acid)
and l-DOPA.
Scheme 4. 2,3-trans-CHA (3) as a starting compound for cycloaddi-
tions. DMAP=4-(dimethylamino)pyridine, Bz=benzoyl.
Both structural features of a 1,2-amino alcohol and amino
acid are combined in the aminocyclitols (5S,6S)-6-amino-5-
hydroxy-cyclohexa-1,5-dienecarboxylic acid (2,3-trans-CHA,
3) and (3R,4R)-4-amino-3-hydroxy-cyclohexa-1,5-diene car-
boxylic acid (3,4-trans-CHA, 8). Thus, besides the two diols 5
and 9, access to these related amino alcohols 3 and 8 expands
the range of enantiopure building blocks considerably. Micro-
bial access to 3 has been described previously by McCormick
et al. using an uncharacterized mutant of Streptomyces
aureofaciens.[17] Here, strain improvement using a recombi-
nant E. coli strain resulted in the microbial production of 3, 8,
and 4-amino-4-deoxychorismate (ADC, 7). Moreover, high
product concentration facilitated isolation on a preparative
scale.
materials for the synthesis of non-natural peptides.[20] Fur-
thermore, 3 can serve as a chiral catalyst for asymmetric
synthesis, as is known for a-amino acids such as proline. For
example, by using Zn2+-CHA complex 23 as a catalyst in
aqueous solution, we converted 4-nitrobenzaldehyde and
acetone[21] into the corresponding aldol product with an
enantiomeric excess of up to 88% (Scheme 5).[22] This result
Microbial access to 3 was made possible by expression of
the phzDE genes from the biosynthesis of phenazines as they
occur in Pseudomonas strains.[18] Expression of the two genes
in E. coli cells, which had been improved in the chorismate
supply while deleting competing aromatic amino acid path-
ways, allowed production of up to 12 gLÀ1 of 2,3-trans-CHA
(3) in a 2 L scale, l-tyrosine-limited fed-batch process. By
using a 300 L fed-batch approach, 3 was produced on a
kilogram scale.[12] Isolation of 3 was performed efficiently by
concentration of the cell-free fermentation broth and crys-
tallization from water at 48C to obtain 3 in 80% yield (purity
> 95%). The relative configuration of 3 was verified by
single-crystal X-ray structure analysis of the corresponding
bisacetyl-protected methylester 20 (see the Supporting Infor-
mation). Steel et al.[19] recently reported that 3, synthesized in
racemic form, can be oxidized stereoselectively analogous to
the oxidation of the diols 5 and 9. Furthermore, 3 and
derivatives thereof have been used in cycloaddition reactions.
Scheme 5. Asymmetric aldol reaction catalyzed by Zn(2,3-trans-CHA)2
23.
shows the potential of b-amino acids as chiral catalysts, which
is at present underrepresented. In comparison to many other
amino acids, 3 allows flexible regio- and stereoselective
functionalization, thus facilitating the optimization of puta-
tive catalytic properties.
ADC (7), an intermediate on the way from chorismate (1)
to amino acid 8, was produced to investigate the biosynthesis
of 8. For the production of 7, the naturally occurring pabAB
gene fusion from Corynebacterium glutamicum[23] was
expressed in a recombinant E. coli strain with improved flux
through the shikimate pathway and with deletions of pheA
and tyrA genes to avoid any drain of chorismate.[24] Com-
pound 7 was produced at up to 7 gLÀ1 in a 2 L scale fed-batch
reactor with l-tyrosine limitation; by-products were choris-
mate and aminodeoxyprephenate. Compound 7 was isolated
from the fermentation broth by cation-exchange chromatog-
raphy.
Although a homomolecular Diels–Alder reaction of
3
requires more drastic conditions compared to 5, dimerization
was achieved by heating a concentrated aqueous solution of 3
for a period of several days. Single-crystal X-ray structure
analysis was used to determine the structure of the dimer 21
and putatively also displays the arrangement of the corre-
sponding dimeric compound of 2,3-trans-CHD methyl ester
(see the Supporting Information). Moreover, we used 5 and 3
as enophiles in a set of different hetero-Diels–Alder reactions.
All of the reactions tested proceeded with high stereoselec-
tivity, and the stereochemistry of the reactions such as that
leading to 22 was not dependent on the presence or type of
protecting groups (Scheme 4).
A culture medium concentration of more than 1.7 gLÀ1 of
3,4-trans-CHA (8) was obtained by combining pabAB gene[25]
from C. glutamicum and the phzD gene from P. aeruginosa on
one plasmid in a recombinant E. coli strain with improved
chorismate supply and cultivation of this strain in a 2 L scale
l-tyrosine-limited fed-batch process. A by-product was 3,4-
trans-CHD (9), with a final titer of 5.4 gLÀ1. Compound 8 has
not yet been described as a metabolite with biological
2,3-trans-CHA (3) is a new member of the class of cyclic b-
amino acids, which are of increasing interest as starting
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Communications
function. In analogy to 7, this compound was isolated from
fermentation broth by cation exchange chromatography.
Similar to the b-amino acid 3, d-amino acid 8 promises
diverse applications as a chiral building block. A prominent
example of a structurally related compound is the neurami-
nidase inhibitor oseltamivir (GS4104),[26] and selective modi-
fications of 8 towards the synthesis of this compound were
investigated (Scheme 6).
Scheme 7. Microbial synthesis of natural SHCHC (6) and enzymatic
in vitro synthesis of 28, a novel non-natural chiral building block.
ThDP=thiamine diphosphate.
Microbial access to all of the compounds depicted in
Scheme 1 (except ADIC (2))[18,33] was realized, and trans-
CHD 5 and 9 as well as 2,3-trans-CHA (3) were produced on a
kilogram scale. Interestingly, the activity of PhzD towards
ADC (7) enables the bioproduction of 8 and is significantly
higher (KM = (1.5 Æ 0.3) mmolLÀ1, kcat = (4.1 Æ 0.12) sÀ1, kcat
/
KM = 2.7 ꢁ 103 LmolÀ1 sÀ1)[24b] than found by Parsons et al.
Scheme 6. Application of 3,4-trans-CHA (8) as a chiral building block.
KM = (0.59 Æ 0.14) mmolLÀ1,
k
cat = (0.02 Æ 0.002) sÀ1, kcat
/
KM = (34 Æ 24) LmolÀ1 sÀ1).[34] One reason for this discrep-
ancy might be the influence of the different buffers used for
the measurements of the enzyme kinetics.[35] In comparison,
EntB[36] shows ADC hydrolase activity similar to PhzD (KM =
Starting from 8, we synthesized TBS-protected cyclo-
hexene 25 in 7 steps (11% yield). 25, which already possesses
the fully functionalized skeleton of oseltamivir, was depro-
tected towards the known amino alcohol 26 (Scheme 6).[27]
Apart from the obvious structural relationship of 8 and
oseltamivir, natural products such as the monocillinols A
and B might be derived and/or synthesized starting from 8.[28]
Moreover, analogous to 3, the rigid d-amino acid 8 allows the
synthesis of non-natural peptides with new properties through
selective modifications of the cyclic system and specific tuning
of the conformation.
All of the compounds derived from chorismate (1)
presented to date combine a cyclohexadiene system with
stereogenic centers of secondary alcohols and amines, respec-
tively. By conversion of isochorismate (4) into (1R,6R)-2-(3-
carboxypropanoyl)-6-hydroxycyclohexa-2,4-dienecarboxylic
acid (SHCHC, 6), which is a metabolite of the menaquinone
pathway,[29] the carbon skeleton is expanded by the addition
of a succinyl residue, and a chiral tertiary carbon center is
generated selectively. Microbial access to 6 was facilitated by
expression of the genes entC and menD[30] from E. coli in a
recombinant E. coli strain with deficiencies in the biosynthe-
ses of the aromatic amino acids phenylalanine and tyrosine
and a lack of MenC activity. Compound 6 was produced with
product titers of up to 8.6 gLÀ1 in a 2 L scale fed-batch reactor
with l-tyrosine limitation, and isolated by anion-exchange
chromatography; by-products were chorismate (1) and iso-
chorismate (4).[31] In vitro experiments starting from 2,3-
trans-CHD (5), 2-ketoglutarate, and MenD resulted in the
formation of 27, which upon isolation tautomerized towards
the non-natural new chiral building block 28 (Scheme 7).[32]
(1.4 Æ 0.3) mmolLÀ1,
k
cat = (2 Æ 0.05) sÀ1,
kcat/KM = 1.8 ꢁ
103 LmolÀ1 sÀ1), but a higher chorismatase activity (KM =
(1.1 Æ 0.15) mmolLÀ1
,
k
cat = (56 Æ 3) sÀ1,
kcat/KM = 40 ꢁ
103 LmolÀ1 sÀ1), making EntB less appropriate for the con-
version of ADC (7) into 3,4-trans-CHA (8). The bioproduc-
tion of 3,4-trans-CHA (8) and SHCHC (6) has not yet been
optimized with respect to bioreaction engineering.
The versatility of these bioproducts has been demon-
strated in natural product syntheses and their value as
enantiopure chiral building blocks has been shown. The
synthesis of either enantiomer of valienone starting from 5
and 9, respectively, has been shown exemplarily. Complex
chiral structures have been generated selectively by using
cycloadditions. Their application as chiral catalysts, as starting
materials for chiral ligands, or their use as conformationally
rigid amino acids in peptide chemistry are just a few examples
of the variety of possibilities.
As the fermentation procedures can be scaled up easily,
production of these metabolites can be achieved on a
technical scale. The bioproduction of 3, 5, and 9 on a 300 L
scale yielded more than 15% product with respect to the
glucose consumed during the fermentation process. Apart
from their use as fine chemicals, all these compounds promise
easy aromatization directly from fermentation broth, as has
been shown for dehydroshikimate and dehydroquinate,[37]
which would demonstrate their potential as platform chem-
icals accessible from renewable sources.
The application of 13C- or 15N-labeled substrates results in
the formation of specifically labeled metabolites (results not
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SHCHC = (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene carbox-
ylate, IPTG = isopropyl thio-ß-galactopyranoside.
shown), which are valuable in elucidating as yet unexplored
branches derived from the shikimate/chorismate pathway.[38]
The microbial production of uncommon structures derived
from chorismate (such as echinosporin)[39] becomes feasible
as demonstrated by the thiamine diphosphate (ThDP)-
Received: May 12, 2011
Published online: July 7, 2011
À
dependent MenD-catalyzed C C bond formation resulting
Keywords: asymmetric synthesis · isochorismate ·
metabolic engineering · shikimate pathway ·
sustainable chemistry
in the production of 6. Given the multipurpose activity and
broad substrate range of ThDP-dependent enzymes,[40] it is
justified to suppose that MenD variants or other ThDP-
dependent enzymes will accept chorismate, isochorismate,
and derivatives as a substrate. This will result in the formation
of natural and novel non-natural metabolites such as 27.
We have demonstrated that single pathways or parts of a
biosynthetic matrix can be successfully amplified or sup-
pressed. In this way, the modified matrix becomes an efficient
tool for the directed biosynthesis of a valuable single
metabolite. Along with the possibility of using the metabolite
produced from the biomimetic approach as a renewable
resource in diversity-oriented synthesis,[41] the metabolites
have another intrinsic advantage: products derived from
natural products are privileged structures with regard to
biological activity.[42] This method thus enables a smooth
development and seamless scale-up, which is desirable for
new pharmaceutical approaches.
.
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Experimental Section
Genes of interest (entB, entC, phzDE, pabAB) were amplified and
cloned by standard PCR and cloning techniques[43] using suitable
plasmid cloning and expression vectors (for example pJF119EH)[44]
for expression in recombinant E. coli K-12 host strains, which had
been improved for chorismate supply by enhancing genes of the
general aromatic amino acid pathway and by deleting competing
pathways for chorismate. All amplified genes were checked for
sequence identity. Competing metabolic pathways were eliminated by
disruption or deletion of the cognate genes (pheA, tyrA, entC) using
standard procedures.[45] Genes phzDE from the phenazine biosyn-
thetic pathway[34,46] were amplified from Pseudomonas aeruginosa,
and the gene pabAB encoding ADC synthase was cloned from
Corynebacterium glutamicum using genomic data of this organism.[23]
Details of cloning and strain constructions will be presented else-
where. entB or entB/C genes were combined with aroF, aroB, and
aroL genes from E. coli K-12 on plasmid pJF119EH.
Recombinant E. coli strains were incubated in 7.5, 42, and 300 L
reactors at 378C with a starting aeration of 0.5 volume per volume per
minute (vvm). Induction was at an optical density of 6–8 at 620 nm
with 0.1 mm IPTG (final concentration). Incubation was carried on
for approximately 50 h.
CCDC 641767 (16), 641768 (20), and 641769 (21) contain the
supplementary crystallographic data for this paper. These data can be
obtained free of charge from The Cambridge Crystallographic Data
Centre via www.ccdc.cam.ac.uk/data_request/cif.
Abbreviations: EntB = isochorismatase from E. coli, EntC = iso-
chorismate synthase from E. coli, PhzD = isochorismatase from
P. aeruginosa, PhzE = 2-amino-2-deoxyisochorismate synthase from
P. aeruginosa, PabAB = 4-amino-4-deoxychorismate synthase from
C. glutamicum, MenD = 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclo-
hexene-1-carboxylate synthase, ADIC = 2-amino-2-deoxyisochoris-
mate, ADC = 4-amino-4-deoxychorismate, CHD = cyclohexadiene-
diol carboxylate, CHA = cyclohexadieneaminoalcohol carboxylate,
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