koffas1999
koffas1999
koffas1999
01:535–557
Copyright q 1999 by Annual Reviews. All rights reserved
Metabolic Engineering
M. Koffas, C. Roberge, K. Lee, and G. Stephanopoulos
Department of Chemical Engineering, Massachusetts Institute of Technology,
Cambridge, Massachusetts 02139; e-mail: mattheos@mit.edu
tionist paradigm of cellular metabolism, taking instead a holistic view. In this sense,
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CONTENTS
Introduction .....................................................................................
535
Metabolic Fluxes ..............................................................................
537
Primary Metabolites ..........................................................................539
Secondary Metabolites ....................................................................... 542
Cell and Tissue Engineering ............................................................... 545
Biomedical Applications .................................................................... 546
Inborn Errors of Metabolism ............................................................... 547
Cell and Organ Physiology ................................................................. 548
Concluding Remarks ......................................................................... 550
INTRODUCTION
Altering metabolic pathways to improve cell properties and the chances of cell
survival is as old as nature itself. The genomic and metabolic evolution of extre-
mophiles is an example of such a natural adaptation process in bacteria (96). The
1523–9829/99/0820–0535$08.00 535
536 KOFFAS ET AL
ate or enhance desirable attributes has been accomplished with a variety of novel
techniques and applied towards an even greater variety of goals.
In this context, metabolic engineering has emerged as the technological and
scientific discipline dealing with the introduction of specific modifications to met-
abolic pathways to improve cellular properties. Metabolic engineering involves
manipulation of enzymatic, transport, and regulatory functions of the cell by using
recombinant DNA technology (5, 86). First, various analytical techniques are used
to identify and subsequently determine fluxes through critical metabolic pathways
in the cell or tissue of interest. This knowledge provides the rational basis for
applying, in the second step, molecular biological techniques to enhance meta-
bolic flux through a pathway of interest and minimize metabolic flow to undesired
biosynthetically related products. Although a certain sense of direction is inherent
in all strain improvement programs, the directionality of effort is a strong focal
point of metabolic engineering, compared with random mutagenesis, because this
directionality plays a dominant role in enzymatic target selection, experimental
design, and data analysis.
Although various terms have been coined over the past two decades to rep-
resent the increasing activity in pathway modification (pathway engineering, cel-
lular engineering, in vitro evolution, etc) (58, 65), the term metabolic engineering
has succeeded in capturing the ever growing interest in this area. Furthermore,
although initially embodied as a collection of examples from the chemical indus-
try and biomedical research, metabolic engineering is quickly becoming a distinct
scientific field. Its novel contribution lies in its emphasis on complete metabolic
networks rather than individual reactions. To elaborate, as with all traditional
fields of engineering, metabolic engineering too encompasses the two defining
steps of analysis and synthesis. Because metabolic engineering emerged with
DNA recombination as the enabling technology, its initial focus was on synthesis
METABOLIC ENGINEERING 537
olites, the generation of organisms with desirable growth characteristics, and the
manipulation of pathways for the production of chiral compounds as intermedi-
ates in the synthesis of pharmaceutical products (38). Finally, although less widely
appreciated, metabolic engineering techniques can also be applied for studying
physiological systems and isolated whole organs in vivo to elucidate the metabolic
patterns that occur in different physiological states, such as ‘‘fed’’ or ‘‘fasted,’’
as well as in disease (105).
METABOLIC FLUXES
Because metabolic pathways and fluxes are at the core of metabolic engineering,
it is important to elaborate on their definition. A metabolic pathway is defined as
any sequence of feasible and observable biochemical-reaction steps connecting a
specified set of input and output metabolites. The pathway flux is the rate at which
input metabolites are processed to form output metabolites (84). The importance
of feasibility and observability should be noted in the definition, in view of the
diversity and complexity of various metabolic maps. If some metabolic fluxes in
a pathway or metabolic network cannot be determined independently, it is better
to lump these reactions together, because their inclusion provides no additional
information.
The determination of intracellular fluxes, along with analysis of factors affect-
ing flux distributions, is collectively referred to as metabolic flux analysis (MFA).
MFA combines data on uptake and secretion rates, biosynthetic requirements,
metabolic stoichiometry, and quasi–steady-state mass balances on metabolic
intermediates to determine intracellular metabolic fluxes (84). MFA has been the
focus of attention of many researchers in the past and has yielded important
538 KOFFAS ET AL
information on flux distribution and its control in many bacteria. The combination
of analytical methods to quantify fluxes and their control with molecular bio-
logical techniques to implement suggested genetic modifications is the essence
of metabolic engineering. An iterative cycle of genetic change followed by an
analysis of its consequences and design of further modifications, analogous to
that articulated for protein engineering, can also be applied in the development
of an optimized strain (3). The flux thus becomes a focal point of metabolic
engineering and justifies further research for the development of methods for its
determination in vivo.
MFA also reveals the degree of pathway engagement in the overall metabolic
process. Furthermore, elucidation of the control of flux provides a mechanistic
basis for rationalizing observed fluxes and flux distributions at key metabolic
branch points (86). As these fluxes are determined under in vivo conditions, MFA
also allows valid comparisons to be made between in vivo and in vitro enzymatic
behavior. Finally, the flux is a fundamental determinant of cell physiology and a
critical parameter to use when comparing the behavior of strain variants. Even if
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relatively unimportant if the flux distributions around key branch points have not
been altered.
Intracellular fluxes are calculated by MFA with a stoichiometric model for the
internal reactions and mass balances around intracellular metabolites (98).
Required data are obtained from measured extracellular fluxes, such as substrate
uptake rates and metabolite secretion rates (85). Intracellular fluxes from reactions
that are cyclical or that split and later converge may be determined by assaying
asymmetries in the distribution of radio-labeled atoms of intermediate metabolites
(77, 83). The metabolic fluxes determined by MFA provide a comprehensive
perspective of the control system at work in metabolic networks. This control
system can be described in terms of metabolic control coefficients (30, 41). Flux
control coefficients are measures of the degree of control exercised by an enzyme
on the overall network flux and can be determined by measuring flux responses
to metabolic perturbations.
As mentioned in the previous paragraphs, elucidation of the flux control struc-
ture of metabolic pathways offers tremendous opportunities for the rational design
of the optimal genotype of a cellular catalyst. This activity should be viewed as
complementary to molecular biological toolboxes for implementing gene transfers
and other similar modifications. In fact, recombinant technology has advanced so
rapidly in recent years that rational analysis of metabolic pathways for the iden-
tification of target genes and enzymes is the limiting component in the directed
optimization of cellular function. Evidence for this assertion is the observation
that currently, almost 20 years after the pioneering developments in genetic engi-
neering, we have hardly begun to harness the potential of modern biotechnology
in the areas of fuels, chemicals, or materials production.
In the following sections, we review a few illustrative applications of meta-
bolic-pathway manipulation. We organize the various applications of metabolic
METABOLIC ENGINEERING 539
engineering into four basic groups: (a) improving primary metabolite production,
(b) improving secondary metabolite and biopharmaceutical production, (c)
improving cell properties, and (d) improving the biomedical field. We have three
goals in reviewing these applications: first, to provide a sample of the truly broad
range of possibilities for biocatalyst improvement afforded by pathway manipu-
lation and metabolic engineering; second, to alert the reader to the complexity of
metabolic pathways, along with their regulation and need of coordination with
overall metabolism; and, third, to underscore the methods used for effecting
desired changes in cellular systems for industrial use or medical reasons. This
review concludes with some ideas and suggestions for future directions of the
field.
PRIMARY METABOLITES
A large number of mainly industrial applications can be classified as primary
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the production of 1,2-PD in equal amounts in batch and continuous culture. These
results provide the first example of recombinant organisms able to ferment sugars
to 1,2-PD and demonstrate that various strategies for the fermentation of sugars
to 1,3-PD are possible (9).
Another example of converting native metabolic intermediates to desirable end
products is the production of the b-carotene precursor to vitamin A. By intro-
ducing the three carotenogenic genes required for lycopene synthesis from farenyl
diphosphate under the control of Candida utilis, a C. utilis strain producing 1.1
mg of lycopene/g (dry weight) of cells has been generated. By using concepts of
metabolic engineering with C. utilis, carbon flux in this yeast strain was redirected
away from ergosterol formation for potential use by the carotenoid pathway. The
influential steps in the pathway that were manipulated were 3-hydroxy methyl-
glutaryl (HMG)-coenzyme A (CoA) reductase, encoded by the HMG gene, and
squalene synthase, encoded by the ERG9 gene. A combination of ERG9 gene
disruption and the overexpression of the HMG catalytic domain gave the highest
lycopene yield. These findings illustrate how modifications in related biochemical
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observed decrease in the NADH/NAD ratio under aerobic conditions. This engi-
neered system could be used to provoke a shift from homolactic to mixed-acid
fermentation during aerobic glucose catabolism. The magnitude of this shift was
directly dependent on the level of NADH oxidase overproduced. These results
indicate that the observed shift from homolactic to mixed-acid fermentation under
aerobic conditions is mainly modulated by the level of NADH oxidation resulting
in low NADH/NAD ratios in the cells (57).
SECONDARY METABOLITES
The challenges associated with engineering the biosynthesis of secondary metab-
olites are qualitatively different from those associated with the production of
commodity bulk chemicals. Products of interest are often complex molecules that
are necessarily derived from biological sources. In this arena, pathway engineer-
ing may increase the efficiency of existing production methods but may also lead
to the development of new products. The relatively high value of these products
shifts the emphasis from economics and efficiency to innovation.
An interesting example is the production of antibiotics. Antibiotics are made
by secondary metabolic pathways that use common metabolites in less specific
and, sometimes, more intricate ways than metabolites are used in primary metab-
olism. Recently, it has become apparent that yields of secondary metabolites,
including antibiotics, can also be improved by overcoming rate-controlling bio-
synthetic steps through genetic techniques. In addition, metabolic engineering
techniques are applied to modify known antibiotics to improve their properties
and also to synthesize new product forms.
Among various antibiotic producers of industrial importance, Streptomyces
species rank near the top. Actinorhodin biosynthesis genes were transferred from
METABOLIC ENGINEERING 543
strains without the hemoglobin gene. This result clearly demonstrates the com-
plications that can arise in using bacterial hemoglobins as metabolic engineering
tools.
In the area of cell cycle improvements, some of the most complex and impor-
tant regulatory mechanisms of eukaryotic cells are those that govern cell division.
Effective reprogramming of the complex regulatory apparatus to achieve biopro-
cess goals, such as cessation of proliferation at high cell density to allow an
extended period of high production, can require coordinated manipulation of mul-
tiple genes. The overexpression of the cyclin-dependent kinase inhibitors p21 and
p27 has already proven to be effective in cancer therapy. In a stable genetic
configuration, only regulated overexpression of p27 was successful in inducing
a sustained Chinese hamster ovary cell growth arrest in G1 phase, which also
resulted in a 10-fold increase in per-cell secreted alkaline phospatase, a model
heterologous protein used during these studies. Stable overexpression of p21
alone did not result in growth arrest. Recently, by tetracycline-regulated coex-
pression of p21 and the differentiation factor CCAAT/enhancer-binding protein
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cell cycle arrest. Production of secreted alkaline phospatase has been increased
10- to 15-fold, on a per cell basis, relative to an isogenic control cell line. Because
the activation of apoptosis response is a possible complication in a proliferation-
arrested culture, the survival gene bcl-xL was coexpressed with another CDI, p27,
found to enable CHO cell cycle arrest predominantly in G1 phase. CHO cells
stably transfected with a tricistronic construct containing the genes for these pro-
teins and for secreted alkaline phospatase showed 30-fold higher secreted alkaline
phospatase expression than control cells (25).
BIOMEDICAL APPLICATIONS
Besides manufacturing applications, metabolic engineering is having a significant
impact on the medical field. The main focus here is the design of new therapies
by identifying specific targets for drug development and by contributing to the
design of gene therapies. Such approaches currently target a specific single enzy-
matic step implicated in a particular disease. There is no assurance, however, that
the manipulation of a single reaction will translate to systematic responses in the
human body. Although mammalian intermediary metabolism was defined in bio-
chemical terms many years ago, it is important to remember that much of this
information accrued from studies in vitro. We have less understanding of the
organization in vivo. Furthermore, the intersections of the central pathways of
metabolism, such as glycolysis, gluconeogenesis, urea synthesis, tricarboxylic
acid cycle, etc, cause changes in one pathway, owing to inborn error or disease,
to affect pathways that may seem remote from the initial metabolic defect (73).
In this regard, medical applications are no different from the ones mentioned
earlier in an industrial context, and, as such, they will benefit from developments
METABOLIC ENGINEERING 547
Once inherited disorders of metabolism are diagnosed and the affected bio-
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chemical pathways have been identified, these diseases may be treated by using
genetic-engineering tools. The therapy for many inherited liver enzyme deficien-
cies requires the removal of toxic intermediate metabolites from the blood of
affected individuals. Recent research tries to focus on the removal of circulating
toxins by expressing the missing enzymes in tissues other than the liver. This will
hopefully positively influence the disease phenotype. Harding et al (29) success-
fully expressed the phenylalanine hydroxylase (PAH) activity in skeletal and car-
diac muscle of mice under the control of the mouse muscle creatine kinase
promoter. When they bred the muscle PAH-expressing mice with liver PAH-
deficient mice, a progeny was created that lacked PAH activity in liver but
expressed PAH in muscle. These mice exhibited hyperphenylalaninemia at base-
line, but serum phenylalanine levels decreased significantly when the mice were
supplemented with tetrahydrobiopterin, a required cofactor for PAH. This result
suggests that gene therapy targeted to heterologous tissue, such as muscle, will
be an effective treatment of selected inborn errors of metabolism.
use for de novo lipogenesis, leading to greater capacity for fat storage, which
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extracted into the liver from portal circulation. Coined as ‘‘chemical biopsy’’ by
DiDonato et al (17), these noninvasive organ-monitoring protocols used in con-
junction with 13C-labeling experiments could become an important research and
diagnostic tool, providing a more detailed assessment of the metabolic state of
liver in human metabolic disorders.
CONCLUDING REMARKS
in the study of the interactions of signal transduction pathways and the elucidation
of the complex mechanisms by which external stimuli control gene expression.
Metabolic engineering is the science aiming at a holistic understanding of
metabolic functions and cellular physiology. As such it provides a much needed
framework for analyzing measurements of differential gene expression obtained
through the application of emerging technologies such as DNA microarray
hybridization. These data, in combination with detailed flux measurements
obtained by available methods and others under development, offer the best prom-
ise for a systematic study and elucidation of metabolic networks. As accurate
measurements of gene expression, protein content, and in vivo fluxes become
readily available, intricate regulatory structures at the genetic and metabolic levels
will be gradually better understood using the principles of metabolic engineering.
This will have profound implications for the rational modification of metabolic
and signaling pathways both in a biotechnological context and in refining current
methods for target selection in drug development and gene therapy.
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CONTENTS
A Dedication in Memoriam of Dr. Richard Skalak, Thomas C. Skalak 1
153
Diabetes, Adam Heller
Injectable Electronic Identification, Monitoring, and Stimulation Systems,
177
Philip R. Troyk