The Locks and Keys To Industrial Biotechnology: Roland Wohlgemuth
The Locks and Keys To Industrial Biotechnology: Roland Wohlgemuth
The Locks and Keys To Industrial Biotechnology: Roland Wohlgemuth
Review
biotechnology
Roland Wohlgemuth
The sustainable use of resources by Nature to synthesize the required products at the right place, when
they are needed, continues to be the role model for total synthesis and production in general. The
combination of molecular and engineering science and technology in the biotechnological approach
needs no protecting groups at all and has therefore been established for numerous large-scale routes to
both natural and synthetic products in industry. The use of biobased raw materials for chemical
synthesis, and the economy of molecular transformations like atom economy and step economy are of
growing importance. As safety, health and environmental issues are key drivers for process
improvements in the chemical industry, the development of biocatalytic reactions or pathways
replacing hazardous reagents is a major focus. The integration of the biocatalytic reaction and
downstream processing with product isolation has led to a variety of in situ product recovery techniques
and has found numerous successful applications. With the growing collection of biocatalytic reactions,
the retrosynthetic thinking can be applied to biocatalysis as well. The introduction of biocatalytic
reactions is uniquely suited to cost reductions and higher quality products, as well as to more sustainable
processes. The transfer of Nature’s simple and robust sensing and control principles as well as its reaction
and separation organization into useful technical systems can be applied to different fermentations,
biotransformations and downstream processes. Biocatalyst and pathway discovery and development is
the key towards new synthetic transformations in industrial biotechnology.
Introduction chemist Berzelius [1] and the discovery by Liebig and Wöhler
The evolution of biobased technology has been a constant that almond extract emulsion was able to split amygdalin into
driving force for sustainable development in human history glucose, benzaldehyde and cyanide, sparked early interest in
for thousands of years. The preparation and stabilization of food biocatalytic processes [2]. With fundamental progress coming
and beverages were developed long before industrialization and from the chemical concept of a reaction rate and studies on
without the modern concepts of biotechnology and chemistry. catalytic processes [3] with measurable reaction times, the nature
The industrialization of the 19th century, with the concomitant of catalysts was then sought in the acceleration of a reaction [4].
initiative in fundamental and applied research, illustrated not The foundation and growth of many industries in the 19th and
only the potential key issues of using biotransformations for 20th centuries and modern life have been influenced in many
chemical transformations, but also the difficulties and obstacles ways by the development of catalytic processes. The production
of moving ahead without an understanding of the enzymes and of chemicals, fuels, pharmaceuticals, flavours and fragrances
reagents that determine the outcome of a chemical reaction. The today is routinely performed with catalytic tools such as
creation of the concept of catalysis and catalysts by the Swedish enzymes, inorganic and organic catalysts [5], whereby in tech-
nical reactions the reaction of molecules with solid surfaces is
E-mail address: [email protected]. often decisive [6].
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Although the field of organic synthesis has achieved outstand- Raw materials for further transformations and processing are key
ing success in the total synthesis of complex molecules since areas for advancing biobased processes that will be very different
Wöhler’s urea synthesis, present state-of-the-art processes for from current processes based on fossil feedstock [22–23]. New
synthesis of chemical products are considered highly inefficient bioprocesses might even be of interest in the utilization of certain
by Li and Trost [7]. The exact build-up of functional groups within fossil feedstock. Close interaction of biocatalytic and heteroge-
a complex molecule still represents a challenge and lock to access neous catalytic processes has been proposed as the best concept for
complex structures without using auxiliaries, activating and pro- the utilization of renewable raw materials [24]. The global value of
tecting groups that increase stoichiometrically the amount of renewable raw materials provided annually by the entire bio-
waste per unit of product, the E-factor [8]. Although the first sphere, which has been estimated to be only about one third of
aim in total synthesis is to find a way of constructing the target the corresponding value for waste treatment [25], could be
molecule in the required quality, the second aim of designing a increased tremendously, if new raw materials from the global
synthetic route with a low E-factor depends very much on the biodiversity are discovered before the species becomes extinct.
selectivities of the usable reactions. Inspiration from biosynthetic The change from a fossil-based supply chain to a biobased raw
Review
pathways and the natural reactivity of functional groups within a material supply chain shown in Figure 1 will require work in the
complex setup have been used constructively in new approaches domains of biosynthetic and photosynthetic processes, isolation,
to chemical synthesis of marine natural products without protect- conversion and purification processes as well as biodegradation
ing groups [9]. While this approach for certain classes of molecules processes. New processes and applications for existing renewable
might always require some level of protection owing to the lack of raw materials as well as waste conversion into raw materials as in
reaction selectivity and practical issues of purification and char- self-sufficient ecospheres will be of major interest. A substantial
acterization [9], the biotechnological approach needs no protect- fraction of the pharmaceuticals that are currently in use for clinical
ing groups at all and has therefore provided numerous large-scale treatments are of natural product origin with a significant number
routes to both natural and synthetic products in industry. The being produced by microbes [26]. Complex three-dimensional
economic use of raw materials by Nature to synthesize its required structures from Nature’s selection process for optimized activity
products by biocatalytic transformations continues to be the role towards a biological target might be an inexpensive supply of raw
model for total synthesis. materials for the semisynthesis of new medicines.
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Review
FIGURE 1
Biobased raw material supply chain.
development [38]. Strain improvement programmes have integration of the biocatalytic reaction and the downstream pro-
decreased costs tremendously by increasing productivity for the cessing with product isolation has led to a variety of in situ product
target product and eliminating undesirable side-products or ana- recovery techniques and has found numerous successful applica-
logues [39]. tions [43–45]. As organic solvents have been the most common
The development of industrial biocatalytic steps aims at high tools for extracting the product from the biocatalytic reaction
space-time yield for the products, which will necessitate also high mixture, the influence of organic solvents not only on the extrac-
substrate concentrations, either of which may inhibit a reaction or tion but also on the biocatalytic conversion itself have been of
be toxic to the biocatalyst. To overcome these limitations, both both fundamental and practical interest [46–48]. This type of
molecular biological and biochemical engineering approaches integrated process was called extractive bioconversion [49–50].
have been used. Enzyme properties towards inhibitory concentra- Non-aqueous media like organic solvents are also of much interest
tions of substrate and product have been improved by protein as reaction medium, because thermodynamic equilibria favour
engineering. To design the process with a given enzyme, separa- synthesis over hydrolysis and water-dependent side-reactions
tion tools such as membranes and auxiliary phases such as extrac- can be suppressed [51–53]. Other process designs included the
tants or adsorbents [40] have been developed. use of aqueous two-phase systems and membrane reactors [54] in
One process concept of creating a reaction space that is effective extractive bioconversions. The use of solid adsorbers instead of
both for a high space-time yield as well as for a robust and rapid liquid extractants was already used in different biocatalytic reduc-
isolation and purification of the product is the confinement of the tions. It has, however, been difficult to design new biocatalytic
enzyme. Immobilization of the enzyme [41] and membrane reac- reactions with the choice of the best adsorber for a given reaction.
tors [42] have been useful in biocatalytic resolutions of racemic The in situ substrate feed and product recovery (SFPR), where the
compounds, use of precious enzymes and substrate and product free enzyme is used and the substrate and product bound to an
solubility incompatibilities with the enzyme. The reverse concept adsorber, has proven its potential in biocatalytic asymmetric
to the confinement of the enzyme is the confinement of the oxidations [55–58]. The separation of stereoisomeric mixtures
substrate and product. This has in the past been focused mainly can be greatly facilitated by a preceding biocatalytic step.
on the product perspective, since product inhibition and product The linear or convergent synthesis of complex organic com-
instability are common limitations in many bioprocesses. The pounds depends on a sequence of several synthetic steps, usually
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FIGURE 2
Biocatalytic multi-step reactions 1–12 from aminolevulinic acid (ALA) to hydrogenobyrinic acid by the use of the following biocatalysts: 1 ALA dehydratase (hemB),
2 PBG deaminase (hemC), 3 Urogen III synthase (hemD), 4 Urogen methylase M-1 (cysG/CobA), 5 Urogen methylase M-2 (CobI, cbiL), 6 Precorrin-3 synthase
(cobG), 7 Ring contractase/17 methyl transferase M-3(cobJ), 8 Methyltransferase M-4 (cobM), 9 Methyltransferase M-5 (cobF), 10 Reductase (cobK), 11 Precorrin-8
synthase (Methyltransferase M-6/decarboxylase), 12 [1,5]-sigmatropic shiftase (cobH). The subsequent chemical reactions 13–16 involve: 13 the insertion of Co, 14
Esterification, 15 Nucleotide Addition and 16 Ammonolysis, which ultimately leads to the final product vitamin B12.
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Review
talysis, biosynthesis or fermentation, depending on the number of
steps involved. The engineering of part of or a whole pathway in a
suitable microbial host strain is of interest not only in the produc-
tion of the final products like fine chemicals, vitamins and anti-
biotics, but also towards the modular setup of biocatalytic multi-
step reactions. The most striking example of biocatalytic multi-
step reactions is the one-pot reaction for the synthesis of hydro-
genobyrinic acid as shown in Figure 2, involving 12 overproduced
enzymes [60] working together sequentially. This illustrates the
importance of analyzing step by step the complex molecular
mechanisms [61] and is used in the microbial large-scale produc-
tion of vitamin B12. The chemical rationalization and synthesis of
the B12 structure via cobyric acid has been realized by two different
routes, by the groups of Eschenmoser at ETH and Woodward at
Harvard, and represents a milestone of total synthesis [62].
The engineering of regulatory, metabolic and other cellular
networks in an integrated manner and consideration of fermenta-
tion and downstream processing at early stages are promising for
the development of bioprocesses and strains [63]. The scale-down
and parallelization of process technology and equipment in com-
bination with miniaturized process analytical technology, such as
FIGURE 3
sensors and actuators, open up fascinating new opportunities for
Schematic interactions and reaction interfaces of industrial biotechnology
establishing and improving industrial processes by performing
with organic chemistry.
bioprocess research and development on the microscale [64–66].
Interfacing synthetic organic reactions with technologies. In any case, the open scientific communication of
biocatalytic reactions dead ends and locks between chemistry, biology and engineering
Between the two extremes of a total synthesis without any bioca- is important and a key to the development of a better chemoenzy-
talytic reaction and a biocatalytic reaction cascade or fermentation matic synthesis of the final product-in-the-bottle. If, in the last
without any synthetic organic reactions, all kinds of combinations step of a long total synthesis, the protecting group cannot be
of reactions occur. The historical vitamin C-synthesis starting cleaved off without damage to the product, or in the case where
from D-(+)-glucose by the 6-step Reichstein–Grüssner route makes the modification of a complex natural product from a biosynthetic
use of only one biocatalytic step achieving the important selective approach is not known to occur by a biocatalytic reaction, a whole
oxidation of D-sorbitol to L-sorbose [67]. Many successful examples synthetic route might become a dead end.
of single biocatalytic reaction steps, as a replacement of proble- The search for novel reaction methodologies is therefore highly
matic chemical reactions or as the only practical way for an relevant, but represents a major challenge and lock for further
intended reaction, have been established in industry on large- advances. Whether the successful problem solution will come
scale [68]. The pace of new and highly efficient sequences of from engineering substrates, reaction media, process conditions
reactions in large-scale syntheses, for example, of active pharma- or from the expanding applications of known biocatalysts, pro-
ceutical ingredients, has been increasing owing to interaction gress in the understanding of the molecular mechanisms of
between chemical and biocatalytic research already in the plan- enzyme action will be key for the further development of the
ning phase [69–72]. Whether the emphasis is more on the che- science of synthesis with its challenges towards the more difficult
mical or the biocatalytic reaction side, illustrated by the schematic and more complex target molecules. With the growing collection
interactions and interfaces in Figure 3, may well depend on the of biocatalytic reactions, the successful retrosynthetic thinking
research and development history or on established platform [73] can be applied to biocatalysis as well. The introduction of
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biocatalytic reactions into synthetic organic reaction sequences is Product purification technology
uniquely suited for cost reductions and quality improvements and The success in bioprocesses has led to challenges and locks on the
offers opportunities for making pharmaceutical processes more downstream processing and product purification side, shown
sustainable [74]. schematically in Figure 4, where usually the majority of the efforts
in production are needed and therefore technology innovations
Process analytical technology have a substantial economic impact. Centrifugation and mem-
The lock and challenge in the analysis and control of bioprocesses brane technology constitute the main primary recovery steps [89],
is the transfer of Nature’s simple and robust sensing and control if biomass and liquid media have to be separated. Microscale
principles into useful technical systems that can be applied to the techniques have been established for the automated high-
analysis and control of different fermentations, biotransforma- throughput microfiltration of complex biological feed streams,
tions and downstream processes [75]. The ongoing miniaturiza- which allow rapid evaluation of the influence of parameters such
tion and automation of preparative and analytical equipment as harvest time, buffers and media components [90]. Depending
enables new approaches for faster process development with less on the localization of the desired products in the intracellular,
Review
starting material and more analytical information. Although phy- membrane, cell wall or extracellular space, different recovery parts,
sical parameters can be routinely analysed by sensors in real-time for example, pellet/retentate or supernatant/filtrate, are utilized
without sampling, the range of sensors for chemical, biochemical for further purification. If the desired product is produced in
and biological parameters is more limited, and most often sam- particulate form, as crystal or inclusion body, selective particle
pling and offline analysis is required [76]. No matter whether the harvesting is an attractive form of recovery [91]. In the area of
analysis is performed online or offline, the key requirement is that biotransformations, high-performance particle sieving has been
the analytical response time is compatible with the time scale of successful in the particle-particle separation of adsorbers and cells
the bioprocess of interest. The different biological time scales of in the SFPR technology [57].
living organisms, from physiological response over development The extent and type of primary solid–liquid separation can
to evolution, have different requirements for the analytical tech- affect the performance of subsequent steps, as shown by the
nology used.
The goal of process analytical technology (PAT) as defined by
the food and drug administration (FDA) is to ensure final product
quality by timely measurements of crucial quality and perfor-
mance parameters [77]. Even if new analytical technologies are
not readily adopted by industry, maximizing the value of existing
analysers can lead to significant improvements [78]. Making use of
established analytical technology can lead the way to better yields,
higher quality and even new industrial bioprocesses [79]. Fermen-
tation and downstream processing can be guided by size-adapted
analytical instruments like monitoring growth by optical sensors
for dissolved oxygen and pH [80] or decision-making about pool-
ing in chromatography by HPLC [81].
Many analytical chemistry applications are of potential interest
to process analytical technology [82], but separation technology
coupled to MS-spectroscopy and NMR-spectroscopy identification
can be applied more widely than specific sensors. Capillary elec-
trophoresis, HPLC or GC coupled with high-sensitivity mass spec-
trometry are combining speed with high sensitivity and resolution
[83]. The combination of high-performance chromatographic
separations with the high sensitivity of mass spectrometry and
direct infusion techniques makes it possible to investigate the
influence of reaction parameters on bioprocesses to complex
natural products [84]. Direct mass spectrometry methods without
any sample preparation steps have developed rapidly since the
introduction of desorption electrospray ionization (DESI) [85] and
the direct analysis in real time (DART) [86]. NMR has provided rich
structural information, is particularly amenable to compounds
that are less detectable by mass spectrometry and permits the
identification of novel molecular entities without the need of
derivatization [87]. While process analysis in terms of balances
and kinetics has been extensively used in biotechnology, measure-
ments on the thermodynamics of biotechnological processes have
been rare but offer bridges to chemical processes and opportunities FIGURE 4
for thorough optimizations [88]. Downstream processing and product purification technologies.
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impact of the clarification on hydrophobic interaction chromato- functions. Activity-based protein profiling (ABPP) has been useful
graphy [92]. The number and type of further purification processes for the assignment of functions to enzymes [112]. Directed evolu-
depend not only on product and impurity properties like size, tion strategies for the optimization of enzyme properties like
charge and solubility, but also on quality requirements and eco- enantioselectivity have led to impressive improvements [113–
nomic factors such as product value. In addition to adsorption, 115]. Excellent progress has been achieved in the mechanistic
other preferred primary product isolation steps are solvent extrac- understanding of enzyme reactions [116] and in the design of
tion, crystallization, precipitation or ultrafiltration. The rapid Kemp elimination catalysts by a combination of computation with
evaluation of large-scale separations by microscale HPLC [93] directed evolution [117].
and high-throughput screening of ion-exchange chromatography The discovery of truly novel enzyme functions is, however, still
[94] provide a general, fast and relatively inexpensive technology a challenge and lock and the discoveries of enzymes judged as
for many otherwise difficult purifications. Simulated moving bed novel by a new EC number over the past decades is shown in
chromatography, both as a separate unit operation for purification Figure 5. The de novo design of biocatalysts with a minimum
as well as in combination with a biotransformation step, is a very number of amino acid building blocks, the rational engineering
Review
attractive option for high-performance purications with decreased of an enzyme to enhance activity or stereoselectivity [118] as well
solvent use [95–96]. as selection and evolution of enzymes from a non-catalytic scaf-
As product purification is an essential part of the bioprocess, it is fold [119] offer interesting approaches. Because only a minority of
also evident that the development and optimization of this part microorganisms are cultivable, the isolation and cloning of com-
has to be performed in an integral way together with other key plete microbial genomes in a particular environment, the meta-
elements like biotransformation, fermentation or biocatalyst genome, broadens access to the habitats of the global microbial
development. Changes in the bioprocess itself or in the reaction universe, whether the microbes are cultivable or noncultivable
conditions like pH, temperature and solvent, can have a decisive [120–124]. The tremendous genetic resources for biocatalysts are
influence on the crystallization, phase separation, extraction or illustrated by the research expeditions into marine environments
adsorption behaviour of product and impurities [45,97–101]. The [125,126].
combination of fermentation/biotransformation with in situ On the side of the completely sequenced genomes (www.geno-
recovery techniques continues to be of much importance [44– mesonline.org) the large fraction of genes encoding enzymes of
45,102–103]. Tabletop centrifugal contact separators have been unknown biochemical function has led to an interest in coupling
shown to be highly advantageous for the lipase-catalyzed ester- genomics and enzymology. The function of an enzyme of
ification of oleic acid with 1-butanol [104]. Phenol production was unknown activity has been successfully predicted from structure
increased more than 4-fold using resins as in situ product recovery by docking high-energy intermediate forms of thousands of can-
tools [105]. Activated carbon could be used as an efficient adsorber didate metabolites, the function being an S-Adenosylhomocys-
in an integrated process for the production surfactin [106]. teine deaminase, with three adenine analogues accepted as
The final step to obtaining the correct product in the required substrates [127].
quality consists of polishing steps towards the right solid or liquid As the endogenous substrate of an enzymatic reaction is con-
form of the product. The definition of the final product quality verted to its product, which is in turn a substrate for the next
requires, in addition to standard quality control methods, the enzyme in a pathway, global metabolomics approaches have
development of analytical methods to test for parameters respon- become attractive for enzyme discovery [128–131]. Although a
sible for the ultimate functional suitability in the product applica- substantial number of endogenous substrates are available for such
tion. studies, the synthesis of enzyme substrates having the correct
stereochemistry continues to be an important cornerstone for
Biocatalyst development the assay of enzyme functions no matter how the novel enzyme
Many new biocatalysts for the large-scale production of chemicals has been prepared. The development of new applications of exist-
have been discovered by extensive and persistent screening of ing and improved biocatalysts following the metabolic paths but
large numbers of microorganisms from Nature [107–108]. In view
of the global importance of safety, health and environmental
issues, biocatalyst and pathway discovery and development is
key towards the development of new synthetic transformations
in industrial biotechnology.
Although classical microbial enrichment and acclimation cul-
ture together with screening has led to many established industrial
biocatalysts, the development of miniaturized disposable micro-
bial culture chips [109–110] in combination with highly sensitive
fluorogenic enzyme substrates or fluorescent detection of enzyme
action offer key improvements for full automation and multi-
plexing of microbial culturing, screening, counting and selection
in a high-throughput mode. Generalised, fast, selective and sensi-
tive activity assay technologies [111] are the keys to discovery and
optimization of novel biocatalysts as well as for the identification FIGURE 5
of the physiological enzyme substrates for proteins with unknown Development of novel biocatalysts by EC numbers as a function of time.
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pushing towards completion of the reactions is therefore of much biocatalytic reaction methodologies is not only key to industrial
interest for production of such substrates, especially where classi- biotechnology, but also of fundamental scientific interest in our
cal methods of organic chemistry are challenging [132–134]. understanding of the various proteins without known functions
and the regulation of these functions. The further development of
Outlook modular and scalable biocatalytic reaction steps [135] is compa-
Safety, health, renewable resources, energy conservation and tible with the development of chemical reactions. Multi-step
waste minimization are issues of both global and local concern. reaction sequences are of much fundamental interest to overcome
Therefore, it is not surprising that initiatives for process improve- limitations in one reaction step and avoid intermediate product
ments have appeared in different scientific disciplines, geographic purification, by analogy with cellular metabolic pathways.
areas and industrial activities. In chemistry, the aims of green or The production of bulk chemicals using industrial biotechnol-
sustainable chemistry have been established. In biotechnology, ogy has been estimated to make a significant contribution to
the creation of the notion of white or industrial biotechnology has solving two of the most urgent environmental problems, climate
been established later, but enjoys a very high acceptance. change and the depletion of fossil energy [136]. The scientific and
Review
The scientific and technological advances in the areas of bio- technological progress of industrial biotechnology will therefore
catalyst development, bioprocess design and interfacing with offer excellent opportunities for global scientific cooperation to
organic reactions, process analysis and product purification tech- bring economy and ecology into harmony and to make funda-
nology have created the proper mindset today for a bright future mental and substantial contributions in sustainable real value
for industrial biotechnology. The research and development on creation.
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