Biobased production of chemicals – a transformation of a USD3T industry

Publiceret Maj 2017

Human societies evolve around the utilization of material and energy resources, exemplified by historic periods named after them, such as the ‘stone’ age and the ‘bronze age’. Since the industrial revolution, coal, oil, and natural gas have become the primary sources for chemical production and used for the manufacturing of the majority of materials used in common goods. The chemical industry has gone through feedstock shifts in the past. Such shifts continue, and the recent findings of large natural gas reservoirs in North America and China have sent seismic shocks through the industry over the past 5-6 years. The shift from naphtha to liquefied natural gas (LNG) as feedstock for cracking has changed the economic landscape of commodity chemicals dramatically, making smaller molecules cheaper (C1, C2) and larger ones (C3, C4) more expensive. This change in non-renewable feedstock use helps driving another significant burgeoning feedstock change, namely the rise of industrial biotechnology to economically produce a large fraction of the chemicals that society needs from biomass as a renewable feedstock. Although only about 8-10% of the oil produced has been used for chemical synthesis, this change towards biobased production is significant and is likely to play a notable role in our quest towards sustainable lifestyles. The biobased production of chemicals induces a transformation of a 3 trillion US dollar (USD3T) industry.

Biomass as feedstock

Biomass as a feedstock for chemical synthesis has been considered for some time now. During the energy crisis in the early 1980s a comprehensive econometric analysis of the intermediate chemical industry was performed and a systematic assessment of biomass as feedstock was performed (1). The results found that the cost of biomass as a feedstock had to drop by 8-fold in order for it to be cost competitive with fossil feedstock. Since the early 1980s, this economic picture has changed dramatically for two major reasons: 1) advancement of biology enabling better design of biocatalysts and 2) an increasing demand for sustainability in production, mostly with the objective to reduce greenhouse gas emissions.

Since the early 1990s a fortuitous convergence of technologies has occurred. The field of metabolic engineering arose in the early 1990s. Full genome sequences started appearing in the mid 1990s, followed by the development of advanced gene manipulation tools that led to the development of a molecular toolbox for metabolic engineering (2). Simultaneously, genome-scale metabolic models appeared (3) that were found to be useful for generating a cell-wide assessment of metabolic designs.

Currently, DNA sequencing is quite inexpensive, allowing us to sequence new genomes and communities rapidly, leading to metagenomic databases that can potentially find useful genes for metabolic engineering and perform various useful omic profiling, including RNAseq, Chip-seq, and transcription start sites, that together led to the genome-wide definition of transcription units (4). DNA synthesis technology and plasmid construction is advancing, and a growing range of biosensors technologies are being developed (5) for accelerated strain screening purposes.

The convergence of these technologies has led to the engineering and construction of new strains that can produce a wide range of chemicals. Several of these leads have been pursued for industrial scale production, and a growing number of industrial biotechnology companies are being launched, publicly listed, and engaged in deal and partnership making with large chemical companies. Unlike the early days of biotechnology where the start-up companies sought to challenge the existing established infrastructure, the new generation of industrial biotechnology companies is seeking to place themselves within the highly integrated chemical industries.

With the current prices of sugar ($0.30-0.40/kg) and a typical 40-50% mass conversion into fermentation product, the feedstock costs are on the order of $0.80/kg, that in addition to the approximate $0.80/kg processing cost, is leading to about $1.60/kg basis cost for biological production routes to commodity chemicals. Thus, it is likely that most of the biocompatible molecules that currently sell in the marketplace for more than $2.00-2.50/kg can feasibly be replaced with identical molecules made through biological means. Liquid fuels costing about $0.60-1.00/L will remain a challenge for industrial biotech, not only from a straight cost standpoint, but also because of the enormity of the biomass needed to satisfy the huge liquid fuels market.

In the near future, biofuels are likely only to be for small scale, dedicated use. They will only become widely used if the governmental subsidy facilitates the entry of advanced biofuels into the market over sufficient time to ensure expansion of the industry to a level where it can make a significant contribution to the fuel supply. Based on these facts, one can predict that the major impact of industrial biotechnology in the next 10 years will be on producing chemical building blocks that can directly enter the current chemical infrastructure.

It is interesting to note that despite the wide range of microorganisms that can be exploited as biocatalysts, the biotechnology industry is quite conservative and is basically focusing on the use of two cell factory platforms, i.e., Escherichia coli and Saccharomyces cerevisiae. There are a number of factors underlying this choice, but it is mainly due to the presence of well implemented tools for metabolic engineering combined with solid experience on large scale fermentation using these two microorganisms.

Future challenges

This industry will rely on the production and decomposition of biomass into fermentable molecules and the design of microbial cell factories that build the molecules that we wish to manufacture. The field of metabolic engineering has advanced since its inception 20 years ago (2,6). The overall challenge that we now face is to determine the spectrum of industrially relevant chemistries that can be produced biologically, and to shorten the design, construction, and optimization time for production strains. The former is a basic scientific challenge, while the latter is a bioengineering one (Figure 1).

Figure 1. The future challenges of metabolic engineering and industrial biotechnology. A. Improvement of the titer, rate, and yield (TRY) of a given product involves many different engineering strategies. In order to enable a high titer, it is important to ensure that the biocatalyst is tolerant towards the product of interest. To ensure a high rate it is necessary to have efficient enzymes that can sustain a high flux through the pathway that leads to the desired product. Finally, to ensure a high yield, it is necessary to make sure that carbon is not lost to competing pathways. Often optimization of rate and yield goes hand in hand, i.e., an increasing yield may result in an improved rate, but this only holds if the enzymes in the target pathway can support a high flux. Improvement of TRY is costly and takes time, and there is therefore a need for novel technologies that will allow the development of industrial cell factories faster and cheaper. B. Improvement of the TRY involves use of the design-build-test-learn cycle of metabolic engineering.

Evaluation of the industrially relevant chemistries that can be produced biologically requires a thorough analysis and archiving of all possible enzyme catalyzed reactions. Currently a very large number of enzymes have been identified from many different organisms, and repositories like KEGG and UniProt provide information on many of these enzymes. Furthermore, with the advancement of metagenome sequencing, new genomic information is constantly being added. This rapidly expands the database of available sequences that encode for different types of enzymes, and these sequences can subsequently be evaluated in appropriate hosts for their catalytic properties.

Besides gaining access to new sources for different enzymes there is also much development on identifying possible new pathway routes for biosynthesis of specific molecules, e.g., BNICE (7), which enables identification of specific enzymes required for a given pathway. Such enzymes can subsequently be identified from general databases, or by using a scaffold enzyme they can be evolved to have the desired properties using directed evolution.

Following implementation of a biosynthetic pathway for production of a given chemical it is necessary to improve the TRY. This is generally difficult as metabolism in any organism has evolved to fit the specific requirement of the organism, and redirection of carbon fluxes towards the product of interest therefore requires extensive engineering that overcomes regulatory structures (2). With recent development in genome editing technologies, such as CRISPR-Cas9, and tools for rapidly screening of strain libraries, such as biosensors that can detect the intracellular level of specific metabolites, it has, however, become possible to build and test a very large number of designs quite rapidly. Focus is therefore currently on improving the design of cell factories, e.g., through the use of advanced mathematical models (2).


1,3 Propanediol used for production of the polymer Sorona® and produced by E. coli. The biocatalyst was developed through a close collaboration between Dupont and Genencor (lasting several years) and the process was developed through collaboration with Tate&Lyle.

Lactic acid used for production of polylactate that finds application as a polymer used in fabrics and packaging materials and produced by an engineered yeast strain. Cargill identified a low pH tolerant yeast strain that it engineered for efficient lactic acid production. By using yeast, they culd use a minimal medium and operate the fermentation process at a low pH, saving costs in the purification of lactic acid.

Succinic acid used for the production of polymer resins and solvents and produced by several different microorganisms. DSM and Roquette formed the joint-venture Reverdia that uses an engineered strain of S. cerevisiae for succinic acid production. BASF uses a bacterium, Basfia succiniciproducens, that has a capacity to produce succinic acid at very high rates in their production process, which is now operated by Succinity, a joint venture with Corbion. Finally, BioAmber developed a succinic acid process based on engineering the low-pH tolerant yeast strain used by Cargill for lactic acid production for high-level succinic acid production.

1,4 Butanediol used for production of polymer resins and produced by an engineered E. coli developed by Genomatica. The fermentation process was developed in close collaboration with Novamont.

Isobutanol used as a biofuel with improved properties over ethanol, but can also be used for chemical synthesis of branched hydrocarbons that are well suited for use in jet fuels. GEVO engineered S. cerevisiae for production of isobutanol and retrofitted ethanol plants for the production. Since isobutanol is far more toxic than ethanol they developed a system for integrated process separation. Butamax, a joint-venture between Dupont and BP, also developed a yeast based process for isobutanol production.

Farnesene used as a drop-in diesel fuel, jet fuel, or chemical for production of squalene and produced by an engineered strain of S. cerevisiae by Amyris.

L-Methionine used as a feed additive and produced by an engineered E. coli by MetabolicExplorer. This new product replaces DL-methionine traditionally produced by chemical synthesis.

Global impacts

Thus, there appears to be a global change in store for the chemical industry. This industry is massive, with about $3T in sales per year. This number should be viewed in light of the world’s GNP that currently stands at about $55-60T/year. The chemical industries thus represent about 5% of the world’s GNP. Interestingly, the chemical industry built over the past 100 years was primarily built by a relatively small group of scientists and engineers. In Europe, these developments took place through mechanical and process engineering on one hand and industrial chemistry on the other.

In contrast, in the United States and Britain, a separate discipline, chemical engineering, emerged in engineering schools. It differed from other engineering disciplines in its strong scientific content and character. Although not widely known or appreciated, the expansion of the chemical industry has had an enormous socioeconomic impact. One example is provided by the Haber-Bosch process, that fixes nitrogen from the atmosphere to make ammonia used in fertilizer which is responsible for over 40% of nitrogen atoms found in humans (8). In other words, biological fixation of nitrogen on the planet alone could not sustain our current population and it can be similarly argued that it is only through novel, sustainable production routes that our planet will be able to accommodate the predicted 10 billion people by 2050.

One can now foresee similar developments of a bioengineering discipline over the coming decades. It will have to span basic natural sciences, in terms of genomics, biochemistry, and microbiology to engineering, in terms of physical rate processes and processing/design issues. The new biologically-based chemical processing industry will be created, operated, and run by a new generation of bioengineers. The impact is expected to be enormous.

It is noteworthy to contrast the size of this effort to the current biotechnology industry that is primarily focused on health care related products. In the US, the size of the healthcare industry is about $2.5T. Physicians, insurance companies, lawyers, and hospital administrators dominate this industry. Only about 8-10% is the cost of pharmaceuticals where the biotech industry has historically focused its efforts. About 5% is in materials, instrumentation, and devices where classical bioengineering has played a role. Thus, the new bioengineering challenge outlined above is expected to be notably larger in its socio economic footprint than traditional biotechnology.

Chemical production depends on available feedstocks. Changes in feedstock availability, price, geographical distribution, and socio-economic pressures tremendously impact the processing technology used at any given time. The chemical industry has gone through multiple feedstock shifts in its history. Based on what we have presented above, we predict that another shift will unfold over the coming couple of decades with significant impacts on the chemical industry.


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