De novo biosynthetic pathways: rational design of microbial chemical factories

Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions

Engineered bacteria could perform many functions in the environment, for example, to remediate pollutants, deliver nutrients to crops or act as in-field biosensors. Model organisms can be unreliable in the field, but selecting an isolate from the thousands that naturally live there and genetically manipulating them to carry the desired function is a slow and uninformed process. Here, we demonstrate the parallel engineering of isolates from environmental samples by using the broad-host-range XPORT conjugation system (Bacillus subtilis mini-ICEBs1) to transfer a genetic payload to many isolates in parallel. Bacillus and Lysinibacillus species were obtained from seven soil and water samples from different locations in Israel. XPORT successfully transferred a genetic function (reporter expression) into 25 of these isolates. They were then screened to identify the best-performing chassis based on the expression level, doubling time, functional stability in soil, and environmentally-relevant traits of its closest annotated reference species, such as the ability to sporulate and temperature tolerance. From this library, we selected Bacillus frigoritolerans A3E1, re-introduced it to soil, and measured function and genetic stability in a contained environment that replicates jungle conditions. After 21 months of storage, the engineered bacteria were viable, could perform their function, and did not accumulate disruptive mutations.

Augmentation of an Engineered Bacterial Strain Potentially Improves the Cleanup of PCB Water Pollution

Polychlorinated biphenyls (PCBs) are recalcitrant organohalide pollutants, consisting of 209 congeners. PCB cleanup in natural landscapes is expected to be achieved by the metabolic activity of microorganisms, but aerobic PCB-degrading bacteria that inhabit sites polluted by PCBs cannot degrade all PCB congeners due to the specificity of their enzymes. In this study, we investigated the degradability of PCBs when a genetically modified PCB-degrading bacterium was compounded with wild-type PCB-degrading bacteria. We used two bacterial strains, Comamonas testosteroni YAZ2 isolated from a PCB-uncontaminated natural landscape and Escherichia coli BL21(DE3) transformed with a biphenyl dioxygenase (BphA) gene from a well-known PCB degrader, Burkholderia xenovorans LB400. The enzymatic specificities of BphA were 2,3-dioxygenation in the YAZ2 and 2,3- and 3,4-dioxygenations in the recombinant E. coli. For the PCB-degrading experiment, a dedicated bioreactor capable of generating oxygen microbubbles was prototyped and used. The combined cells of the recombinant and the wild-type strains with an appropriate composite ratio degraded 40 mg/L of Kaneclor KC-300 to 0.3 ± 0.1 mg/L within 24 h. All of the health-toxic coplanar PCB congeners in KC-300 were degraded. This study suggested that the augmentation of an engineered bacterial strain could improve the cleanup of PCB water pollution. It also revealed the importance of the ratio of the strains with different PCB-degrading profiles to efficient degradation and that the application of oxygen microbubbles could rapidly accelerate the cleanup. IMPORTANCE PCB cleanup technique in a natural environment relies on the use of enzymes from microorganisms, primarily biphenyl dioxygenase and dehalogenase. Herein, we focused on biphenyl dioxygenase and created a recombinant PCB-degrading E. coli strain. Despite the development of environments for the field use of transgenic microbial strains around the world, verification of the applicability of transgenic microbial strains for PCB cleanup in the field has not yet been reported. We tentatively verified the extent to which degradability could be obtained by an augmentation model of a transgenic strain, the enzyme expression of which is easily regulated in rivers and lakes with PCB pollution. Our experiments used a dedicated bioreactor to model the natural landscape and produced results superior to those of bioremediation or biostimulation methods. The application of micro-nano bubbles, which has recently been discussed, to the cleanup of environmental pollution was also found to be useful in this study.

Implementation of Synthetic Pathways to Foster Microbe-Based Production of Non-Naturally Occurring Carboxylic Acids and Derivatives

Microbially produced carboxylic acids (CAs) are considered key players in the implementation of more sustainable industrial processes due to their potential to replace a set of oil-derived commodity chemicals. Most CAs are intermediates of microbial central carbon metabolism, and therefore, a biochemical production pathway is described and can be transferred to a host of choice to enable/improve production at an industrial scale. However, for some CAs, the implementation of this approach is difficult, either because they do not occur naturally (as is the case for levulinic acid) or because the described production pathway cannot be easily ported (as it is the case for adipic, muconic or glucaric acids). Synthetic biology has been reshaping the range of molecules that can be produced by microbial cells by setting new-to-nature pathways that leverage on enzyme arrangements not observed in vivo, often in association with the use of substrates that are not enzymes’ natural ones. In this review, we provide an overview of how the establishment of synthetic pathways, assisted by computational tools for metabolic retrobiosynthesis, has been applied to the field of CA production. The translation of these efforts in bridging the gap between the synthesis of CAs and of their more interesting derivatives, often themselves non-naturally occurring molecules, is also reviewed using as case studies the production of methacrylic, methylmethacrylic and poly-lactic acids.

Microbial factories: monitoring vitamin B2 production by Escherichia coli in microfluidic cultivation chambers

Microbial cells represent a standard production host for various important biotechnological products. Production yields can be increased by optimising strains and growth conditions and understanding deviations in production rates over time or within the microbial population. We introduce here microfluidic cultivation chambers for highly parallel studies on microbial cultures, enabling continuous biosynthesis monitoring of the industrially relevant product by Escherichia coli cells. The growth chambers are defined by ring-valves that encapsulate a volume of 200 pL when activated. Bacterial cells, labelled with magnetic beads, are inoculated in a small magnetic trap, positioned in the centre of each chamber. Afterwards, the ring-valves are partially activated, allowing for exchange reagents, such as the addition of fresh media or specific inducers of biosynthesis, while the bacterial cells and their progeny are maintained inside. On this platform, we monitor the production of riboflavin (vitamin B₂). We used different variants of a riboflavin-overproducing bacterial strain with different riboflavin production levels and could distinguish them on the level of individual micro-colonies. In addition, we could also observe differences in the bacterial morphology with respect to the production. The presented platform represents a flexible microfluidic tool for further studies of microbial cell factories.

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quantify. Here we review the major sources of uncertainty and survey existing approaches developed for representing and addressing them. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity.

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.

Applying Non-canonical Redox Cofactors in Fermentation Processes

Fermentation processes are used to sustainably produce chemicals and as such contribute to the transition to a circular economy. The maximum theoretical yield of a conversion can only be approached if all electrons present in the substrate end up in the product. Control over the electrons is therefore crucial. However, electron transfer via redox cofactors results in a diffuse distribution of electrons over metabolism. To overcome this challenge, we propose to apply non-canonical redox cofactors (NRCs) in metabolic networks: cofactors that channel electrons exclusively from substrate to product, forming orthogonal circuits for electron transfer.

Metabolic pathway engineering: Perspectives and applications

BACKGROUND

Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering.

CONCLUSION

In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.

Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable

Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner. This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments. Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays. These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules. In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data. In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework.

MAPPS: A Web-Based Tool for Metabolic Pathway Prediction and Network Analysis in the Postgenomic Era

Comparative and evolutionary analyses of metabolic networks have a wide range of applications, ranging from research into metabolic evolution through to practical applications in drug development, synthetic biology, and biodegradation. We present MAPPS: Metabolic network Analysis and Pathway Prediction Server (https://mapps.lums.edu.pk), a web-based tool to study functions and evolution of metabolic networks using traditional and 'omics data sets. MAPPS provides diverse functionalities including an interactive interface, graphical visualization of results, pathway prediction and network comparison, identification of potential drug targets, in silico metabolic engineering, host-microbe interactions, and ancestral network building. Importantly, MAPPS also allows users to upload custom data, thus enabling metabolic analyses on draft and custom genomes, and has an 'omics pipeline to filter pathway results, making it relevant in today's postgenomic era.

RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

Background

The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical in a chassis organism is computationally intractable. Many current methods provide a single solution to this problem, but fail to provide all optimal pathways, optional sub-optimal solutions or hybrid biological/non-biological solutions.

Results

Here we present RetSynth, software with a novel algorithm for determining all optimal biological pathways given a starting biological chassis and target chemical. By dynamically selecting constraints, the number of potential pathways scales by the number of fully independent pathways and not by the number of overall reactions or size of the metabolic network. This feature allows all optimal pathways to be determined for a large number of chemicals and for a large corpus of potential chassis organisms. Additionally, this software contains other features including the ability to collect data from metabolic repositories, perform flux balance analysis, and to view optimal pathways identified by our algorithm using a built-in visualization module. This software also identifies sub-optimal pathways and allows incorporation of non-biological chemical reactions, which may be performed after metabolic production of precursor molecules.

Conclusions

The novel algorithm designed for RetSynth streamlines an arduous and complex process in metabolic engineering. Our stand-alone software allows the identification of candidate optimal and additional sub-optimal pathways, and provides the user with necessary ranking criteria such as target yield to decide which route to select for target production. Furthermore, the ability to incorporate non-biological reactions into the final steps allows determination of pathways to production for targets that cannot be solely produced biologically. With this comprehensive suite of features RetSynth exceeds any open-source software or webservice currently available for identifying optimal pathways for target production.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-3025-9) contains supplementary material, which is available to authorized users.

The phage T4 DNA ligase in vivo improves the survival-coupled bacterial mutagenesis

Background

Microbial mutagenesis is an important avenue to acquire microbial strains with desirable traits for industry application. However, mutagens either chemical or physical used often leads narrow library pool due to high lethal rate. The T4 DNA ligase is one of the most widely utilized enzymes in modern molecular biology. Its contribution to repair chromosomal DNA damages, therefore cell survival during mutagenesis will be discussed.

Results

Expression of T4 DNA ligase in vivo could substantially increase cell survival to ionizing radiation in multiple species. A T4 mediated survival-coupled mutagenesis approach was proposed. When polyhydroxybutyrate (PHB)-producing E. coli with T4 DNA ligase expressed in vivo was subjected to ionizing radiation, mutants with improved PHB production were acquired quickly owing to a large viable mutant library generated. Draft genome sequence analysis showed that the mutants obtained possess not only single nucleotide variation (SNV) but also DNA fragment deletion, indicating that T4 DNA ligase in vivo may contribute to the repair of DNA double strand breaks.

Conclusions

Expression of T4 DNA ligase in vivo could notably enhance microbial survival to excess chromosomal damages caused by various mutagens. Potential application of T4 DNA ligase in microbial mutagenesis was explored by mutating and screening PHB producing E. coli XLPHB strain. When applied to atmospheric and room temperature plasma (ARTP) microbial mutagenesis, large survival pool was obtained. Mutants available for subsequent screening for desirable features. The use of T4 DNA ligase we were able to quickly improve the PHB production by generating a larger viable mutants pool. This method is a universal strategy can be employed in wide range of bacteria. It indicated that traditional random mutagenesis became more powerful in combine with modern genetic molecular biology and has exciting prospect.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1160-7) contains supplementary material, which is available to authorized users.

An alternative genome-integrated method for undomesticated Bacillus subtilis and related species

Given their applicability in genetic engineering, undomesticated Bacillus strains are extensively used as non-natural hosts for chemical production due to their high tolerance of toxic substrates or products. However, they are difficult to genomically modify due to their low transformation efficiencies. In this study, the Bacillus-E. coli shuttle vector pHY300PLK, which is widely used in gram-positive bacteria, was adopted for genome integration in organic solvent-tolerant Bacillus isolates. The Bacillus-replicative vector was used to deliver homologous recombinant DNA and propagate itself inside the host cell, increasing the likelihood of genome integration of the recombinant DNA. Then, the unintegrated vectors were cured by cell cultivation in antibiotic-free medium with facilitation of nickel ions. The developed protocol was successfully demonstrated and validated by the disruption of amyE gene in B. subtilis 168. With an improved clonal selection protocol, the probability of clonal selection of the amyE::cat genome-integrated mutants was increased up to 42.0 ± 10.2%. Genome integration in undomesticated, organic solvent tolerant Bacillus strains was also successfully demonstrated with amyE as well as proB gene creating the gene-disrupted mutants with the corresponding phenotype and genotype. Not only was this technique effectively applied to several strains of undomesticated B. subtilis, but it was also successfully applied to B. cereus. This study validates the possibility of the application of Bacillus-replicative vector as well as the developed protocol in a variety of genome modification of undomesticated Bacillus species.

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Recent advances in synthetic biochemistry have resulted in a wealth of novel hypothetical enzymatic reactions that are not matched to protein-encoding genes, deeming them “orphan.” A large number of known metabolic enzymes are also orphan, leaving important gaps in metabolic network maps. Proposing genes for the catalysis of orphan reactions is critical for applications ranging from biotechnology to medicine. In this work, the computational method BridgIT identified potential enzymes of orphan reactions and nearly all theoretically possible biochemical transformations, providing candidate genes to catalyze these reactions to the research community. The BridgIT online tool will allow researchers to fill the knowledge gaps in metabolic networks and will act as a starting point for designing novel enzymes to catalyze nonnatural transformations.

Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, limiting protein engineering applications. Associating orphan and novel reactions with known biochemistry and suggesting enzymes to catalyze them is a daunting problem. We propose the method BridgIT to identify candidate genes and catalyzing proteins for these reactions. This method introduces information about the enzyme binding pocket into reaction-similarity comparisons. BridgIT assesses the similarity of two reactions, one orphan and one well-characterized nonorphan reaction, using their substrate reactive sites, their surrounding structures, and the structures of the generated products to suggest enzymes that catalyze the most-similar nonorphan reactions as candidates for also catalyzing the orphan ones. We performed two large-scale validation studies to test BridgIT predictions against experimental biochemical evidence. For the 234 orphan reactions from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 2011 (a comprehensive enzymatic-reaction database) that became nonorphan in KEGG 2018, BridgIT predicted the exact or a highly related enzyme for 211 of them. Moreover, for 334 of 379 novel reactions in 2014 that were later cataloged in KEGG 2018, BridgIT predicted the exact or highly similar enzymes. BridgIT requires knowledge about only four connecting bonds around the atoms of the reactive sites to correctly annotate proteins for 93% of analyzed enzymatic reactions. Increasing to seven connecting bonds allowed for the accurate identification of a sequence for nearly all known enzymatic reactions.

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia toward sustainable production of the second generation of biofuels, with methyl ethyl ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent. However, as of today, a sustainable and economically viable production of MEK has not yet been achieved despite several attempts of introducing biosynthetic pathways in industrial microorganisms. We used BNICE.ch as a retrobiosynthesis tool to discover all novel pathways around MEK. Out of 1325 identified compounds connecting to MEK with one reaction step, we selected 3-oxopentanoate, but-3-en-2-one, but-1-en-2-olate, butylamine, and 2-hydroxy-2-methylbutanenitrile for further study. We reconstructed 3 679 610 novel biosynthetic pathways toward these 5 compounds. We then embedded these pathways into the genome-scale model of E. coli, and a set of 18 622 were found to be the most biologically feasible ones on the basis of thermodynamics and their yields. For each novel reaction in the viable pathways, we proposed the most similar KEGG reactions, with their gene and protein sequences, as candidates for either a direct experimental implementation or as a basis for enzyme engineering. Through pathway similarity analysis we classified the pathways and identified the enzymes and precursors that were indispensable for the production of the target molecules. These retrobiosynthesis studies demonstrate the potential of BNICE.ch for discovery, systematic evaluation, and analysis of novel pathways in synthetic biology and metabolic engineering studies.

Optimisation of enzyme cascades for chiral amino alcohol synthesis in aid of host cell integration using a statistical experimental design approach

Chiral amino alcohols are compounds of pharmaceutical interest as they are building blocks of sphingolipids, antibiotics, and antiviral glycosidase inhibitors. Due to the challenges of chemical synthesis we recently developed two TK-TAm reaction cascades using natural and low cost feedstocks as substrates: a recycling cascade comprising of 2 enzymes and a sequential 3-step enzyme cascade yielding 30% and 1% conversion, respectively. In order to improve the conversion yield and aid the future host strain engineering for whole cell biocatalysis, we used a combination of microscale experiments and statistical experimental design. For this we implemented a full factorial design to optimise pH, temperature and buffer type, followed by the application of Response Surface Methodology for the optimisation of substrates and enzymes concentrations. Using purified enzymes we achieved 60% conversion for the recycling cascade and 3-fold improvement using the sequential pathway. Based on the results, limiting steps and individual requirements for host cell metabolic integration were identified expanding the understanding of the cascades without implementing extensive optimisation modelling. Therefore, the approach described here is well suited for optimising reaction conditions as well as defining the relative enzyme expression levels required for construction of microbial cell factories.

Increasing the Resistance of Living Cells against Oxidative Stress by Nonnatural Surfactants as Membrane Guards

The importation of construction principles or even constituents from biology into materials science is a prevailing concept. Vice versa, the cellular level modification of living systems with nonnatural components is much more difficult to achieve. It has been done for analytical purposes, for example, imaging, to learn something about intracellular processes. Cases describing the improvement of a biological function by the integration of a nonnatural (nano)constituent are extremely rare. Because biological membranes contain some kind of a surfactant, for example, phospholipids, our idea is to modify cells with a newly synthesized surfactant. However, this surfactant is intended to possess an additional functionality, which is the reduction of oxidative stress. We report the synthesis of a surfactant with Janus-type head group architecture, a fullerene C₆₀ modified by five alkyl chains on one side and an average of 20 oxygen species on the other hemisphere. It is demonstrated that the amphiphilic properties of the fullerenol surfactant are similar to that of lipids. Not only quenching of reactive oxygen species (superoxide, hydroxyl radicals, peroxynitrite, and hydrogen peroxide) was successful, but also the fullerenol surfactant exceeds benchmark antioxidant agents such as quercetin. The surfactant was then brought into contact with different cell types, and the viability even of delicate cells such as human liver cells (HepG2) and human dopaminergic neurons (LUHMES) has proven to be extraordinarily high. We could show further that the cells take up the fullerenol surfactant, and as a consequence, they are protected much better against oxidative stress.

Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds

Terpenoid flavor and fragrance compounds are of high interest to the aroma industry. Microbial production offers an alternative sustainable access to the desired terpenoids independent of natural sources. Genetically engineered microorganisms can be used to synthesize terpenoids from cheap and renewable resources. Due to its modular architecture, terpenoid biosynthesis is especially well suited for the microbial cell factory concept: a platform host engineered for a high flux toward the central C₅ prenyl diphosphate precursors enables the production of a broad range of target terpenoids just by varying the pathway modules converting the C₅ intermediates to the product of interest. In this review typical terpenoid flavor and fragrance compounds marketed or under development by biotech and aroma companies are given, and the specificities of the aroma market are discussed. The main part of this work focuses on key strategies and recent advances to engineer microbes to become efficient terpenoid producers.

Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production

In the wake of the uprising global energy crisis, microalgae have emerged as an alternate feedstock for biofuel production. In addition, microalgae bear immense potential as bio-cell factories in terms of producing key chemicals, recombinant proteins, enzymes, lipid, hydrogen and alcohol. Abstraction of such high-value products (algal biorefinery approach) facilitates to make microalgae-based renewable energy an economically viable option. Synthetic biology is an emerging field that harmoniously blends science and engineering to help design and construct novel biological systems, with an aim to achieve rationally formulated objectives. However, resources and tools used for such nuclear manipulation, construction of synthetic gene network and genome-scale reconstruction of microalgae are limited. Herein, we present recent developments in the upcoming field of microalgae employed as a model system for synthetic biology applications and highlight the importance of genome-scale reconstruction models and kinetic models, to maximize the metabolic output by understanding the intricacies of algal growth. This review also examines the role played by microalgae as biorefineries, microalgal culture conditions and various operating parameters that need to be optimized to yield biofuel that can be economically competitive with fossil fuels.

Direct Photosynthetic Production of Plastic Building Block Chemicals from CO2

Hydroxy acids have attracted attention as building block chemicals due to their roles as precursors for the production of various pharmaceuticals, vitamins, antibiotics, and flavor compounds as well as monomers for biodegradable plastic polyesters. The current approach to hydroxy acid production relies on nonrenewable fossil resources such as petroleum for raw materials, raising issues such as the rising costs of starting materials and environmental incompatibility. Recently, synthetic biology approaches based on the rational design and reconstruction of new biological systems were implemented to produce chemicals from a variety of renewable substrates. In addition to research using heterotrophic organic carbon-dependent Escherichia coli or yeasts, photosynthetic microorganisms such as cyanobacteria possessing the ability to absorb solar radiation and fix carbon dioxide (CO₂) as a sole carbon source have been engineered into a new type of microbial cell factory to directly produce hydroxy acids from CO₂. In this chapter, recent progress regarding the direct photosynthetic production of three important hydroxy acids-3-hydroxypropionate (3-HP), 3-hydroxybutyrate (3-HB), and 3-hydroxyvalerate (3-HV)-from CO₂ in cyanobacteria is summarized and discussed.

A review of computational tools for design and reconstruction of metabolic pathways

Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.

Designing a New Entry Point into Isoprenoid Metabolism by Exploiting Fructose-6-Phosphate Aldolase Side Reactivity of Escherichia coli

The 2C-methyl-d-erythritol-4-phosphate (MEP) pathway in Escherichia coli has been highlighted for its potential to provide access to myriad isoprenoid chemicals of industrial and therapeutic relevance and discover antibiotic targets to treat microbial human pathogens. Here, we describe a metabolic engineering strategy for the de novo construction of a biosynthetic pathway that produces 1-dexoxy-d-xylulose-5-phosphate (DXP), the precursor metabolite of the MEP pathway, from the simple and renewable starting materials d-arabinose and hydroxyacetone. Unlike most metabolic engineering efforts in which cell metabolism is reprogrammed with enzymes that are highly specific to their desired reaction, we highlight the promiscuous activity of the native E. coli fructose-6-phosphate aldolase as central to the metabolic rerouting of carbon to DXP. We use mass spectrometric isotopomer analysis of intracellular metabolites to show that the engineered pathway is able to support in vivo DXP biosynthesis in E. coli. The engineered DXP synthesis is further able to rescue cells that were chemically inhibited in their ability to produce DXP and to increase terpene titers in strains harboring the non-native lycopene pathway. In addition to providing an alternative metabolic pathway to produce isoprenoids, the results here highlight the potential role of pathway evolution to circumvent metabolic inhibitors in the development of microbial antibiotic resistance.

Synthetic metabolic bypass for a metabolic toggle switch enhances acetyl-CoA supply for isopropanol production by Escherichia coli

Almost all synthetic pathways for biofuel production are designed to require endogenous metabolites in glycolysis, such as phosphoenolpyruvate, pyruvate, and acetyl-CoA. However, such metabolites are also required for bacterial cell growth. To reduce the metabolic imbalance between cell growth and target chemical production, we previously constructed a metabolic toggle switch (MTS) as a conditional flux redirection tool controlling metabolic flux of TCA cycle toward isopropanol production. This approach succeeded to improve the isopropanol production titer and yield while ensuring sufficient cell growth. However, excess accumulation of pyruvate, the precursor for acetyl-CoA synthesis, was also observed. In this study, for efficient conversation of pyruvate to acetyl-CoA (pyruvate oxidation), we designed a synthetic metabolic bypass composed of poxB and acs with the MTS for acetyl-CoA supply from the excess pyruvate. When this designed bypass was expressed at the appropriate expression level associated with the conditional metabolic flux redirection, pyruvate accumulation was prevented, and the isopropanol production titer and yield were improved. Final isopropanol production titer of strain harboring MTS with the synthetic metabolic bypass improved 4.4-fold compared with strain without metabolic flux regulation, and it was 1.3-fold higher than that of strain harboring the conventional MTS alone. Additionally, glucose consumption was also improved 1.7-fold compared with strain without metabolic flux regulation. On the other hand, introduction of the synthetic metabolic bypass alone showed no improvement in isopropanol production and glucose consumption. These results showed that the improvement in bio-production process caused by synergy between the MTS and the synthetic metabolic bypass.

Production of C2-C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies

C2-C4 diols classically derived from fossil resource are very important bulk chemicals which have been used in a wide range of areas, including solvents, fuels, polymers, cosmetics, and pharmaceuticals. Production of C2-C4 diols from renewable resources has received significant interest in consideration of the reducing fossil resource and the increasing environmental issues. While bioproduction of certain diols like 1,3-propanediol has been commercialized in recent years, biosynthesis of many other important C2-C4 diol isomers is highly challenging due to the lack of natural synthesis pathways. Recent advances in synthetic biology have enabled the de novo design of completely new pathways to non-natural molecules from renewable feedstocks. In this study, we review recent advances in bioproduction of C2-C4 diols, focusing on new metabolic pathways and metabolic engineering strategies being developed. We also discuss the challenges and future trends toward the development of economically competitive processes for bio-based diol production.

Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals

Background

Economically viable biobased production of bulk chemicals and biofuels typically requires high product titers. During microbial bioconversion this often leads to product toxicity, and tolerance is therefore a critical element in the engineering of production strains.

Results

Here, a systems biology approach was employed to understand the chemical stress response of Escherichia coli, including a genome-wide screen for mutants with increased fitness during chemical stress. Twelve chemicals with significant production potential were selected, consisting of organic solvent-like chemicals (butanol, hydroxy-γ-butyrolactone, 1,4-butanediol, furfural), organic acids (acetate, itaconic acid, levulinic acid, succinic acid), amino acids (serine, threonine) and membrane-intercalating chemicals (decanoic acid, geraniol). The transcriptional response towards these chemicals revealed large overlaps of transcription changes within and between chemical groups, with functions such as energy metabolism, stress response, membrane modification, transporters and iron metabolism being affected. Regulon enrichment analysis identified key regulators likely mediating the transcriptional response, including CRP, RpoS, OmpR, ArcA, Fur and GadX. These regulators, the genes within their regulons and the above mentioned cellular functions therefore constitute potential targets for increasing E. coli chemical tolerance. Fitness determination of genome-wide transposon mutants (Tn-seq) subjected to the same chemical stress identified 294 enriched and 336 depleted mutants and experimental validation revealed up to 60 % increase in mutant growth rates. Mutants enriched in several conditions contained, among others, insertions in genes of the Mar-Sox-Rob regulon as well as transcription and translation related gene functions.

Conclusions

The combination of the transcriptional response and mutant screening provides general targets that can increase tolerance towards not only single, but multiple chemicals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0577-5) contains supplementary material, which is available to authorized users.

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.

Enhanced production of nargenicin A1 and creation of a novel derivative using a synthetic biology platform

Nargenicin A1, an antibacterial produced by Nocardia sp. CS682 (KCTC 11297BP), demonstrates effective activity against various Gram-positive bacteria. Hence, we attempted to enhance nargenicin A1 production by utilizing the cumulative effect of synthetic biology, metabolic engineering and statistical media optimization strategies. To facilitate the modular assembly of multiple genes for genetic engineering in Nocardia sp. CS682, we constructed a set of multi-monocistronic vectors, pNV18L1 and pNV18L2 containing hybrid promoter (derived from ermE* and promoter region of neo ^r ), ribosome binding sites (RBS), and restriction sites for cloning, so that each cloned gene was under its own promoter and RBS. The multi-monocistronic vector, pNV18L2 containing transcriptional terminator showed better efficiency in reporter gene assay. Thus, multiple genes involved in the biogenesis of pyrrole moiety (ngnN2, ngnN3, ngnN4, and ngnN5 from Nocardia sp. CS682), glucose utilization (glf and glk from Zymomonas mobilis), and malonyl-CoA synthesis (accA2 and accBE from Streptomyces coelicolor A3 (2)), were cloned in pNV18L2. Further statistical optimization of specific precursors (proline and glucose) and their feeding time led to ~84.9 mg/L nargenicin from Nocardia sp. GAP, which is ~24-fold higher than Nocardia sp. CS682 (without feeding). Furthermore, pikC from Streptomyces venezuelae was expressed to generate Nocardia sp. PikC. Nargenicin A1 acid was characterized as novel derivative of nargenicin A1 produced from Nocardia sp. PikC by mass spectrometry (MS) and nuclear magnetic resonance (NMR) analyses. We also performed comparative analysis of the anticancer and antibacterial activities of nargenicin A1 and nargenicin A1 acid, which showed a reduction in antibacterial potential for nargenicin A1 acid. Thus, the development of an efficient synthetic biological platform provided new avenues for enhancing or structurally diversifying nargenicin A1 by means of pathway designing and engineering.

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.

In silico methods for linking genes and secondary metabolites: The way forward

In silico methods for linking genomic space to chemical space have played a crucial role in genomics driven discovery of new natural products as well as biosynthesis of altered natural products by engineering of biosynthetic pathways. Here we give an overview of available computational tools and then briefly describe a novel computational framework, namely retro-biosynthetic enumeration of biosynthetic reactions, which can add to the repertoire of computational tools available for connecting natural products to their biosynthetic gene clusters. Most of the currently available bioinformatics tools for analysis of secondary metabolite biosynthetic gene clusters utilize the “Genes to Metabolites” approach. In contrast to the “Genes to Metabolites” approach, the “Metabolites to Genes” or retro-biosynthetic approach would involve enumerating the various biochemical transformations or enzymatic reactions which would generate the given chemical moiety starting from a set of precursor molecules and identifying enzymatic domains which can potentially catalyze the enumerated biochemical transformations. In this article, we first give a brief overview of the presently available in silico tools and approaches for analysis of secondary metabolite biosynthetic pathways. We also discuss our preliminary work on development of algorithms for retro-biosynthetic enumeration of biochemical transformations to formulate a novel computational method for identifying genes associated with biosynthesis of a given polyketide or nonribosomal peptide.

Accessing Nature's diversity through metabolic engineering and synthetic biology

In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents.

Synthetic Ecology of Microbes: Mathematical Models and Applications

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

Metabolic engineering of Escherichia coli for the production of 1,3-diaminopropane, a three carbon diamine

Bio-based production of chemicals from renewable resources is becoming increasingly important for sustainable chemical industry. In this study, Escherichia coli was metabolically engineered to produce 1,3-diaminopropane (1,3-DAP), a monomer for engineering plastics. Comparing heterologous C₄ and C₅ pathways for 1,3-DAP production by genome-scale in silico flux analysis revealed that the C₄ pathway employing Acinetobacter baumannii dat and ddc genes, encoding 2-ketoglutarate 4-aminotransferase and L-2,4-diaminobutanoate decarboxylase, respectively, was the more efficient pathway. In a strain that has feedback resistant aspartokinases, the ppc and aspC genes were overexpressed to increase flux towards 1,3-DAP synthesis. Also, studies on 128 synthetic small RNAs applied in gene knock-down revealed that knocking out pfkA increases 1,3-DAP production. Overexpression of ppc and aspC genes in the pfkA deleted strain resulted in production titers of 1.39 and 1.35 g l⁻¹ of 1,3-DAP, respectively. Fed-batch fermentation of the final engineered E. coli strain allowed production of 13 g l⁻¹ of 1,3-DAP in a glucose minimal medium.

Building biological foundries for next-generation synthetic biology

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

Changing trends in biotechnology of secondary metabolism in medicinal and aromatic plants

Medicinal and aromatic plants are known to produce secondary metabolites that find uses as flavoring agents, fragrances, insecticides, dyes and drugs. Biotechnology offers several choices through which secondary metabolism in medicinal plants can be altered in innovative ways, to overproduce phytochemicals of interest, to reduce the content of toxic compounds or even to produce novel chemicals. Detailed investigation of chromatin organization and microRNAs affecting biosynthesis of secondary metabolites as well as exploring cryptic biosynthetic clusters and synthetic biology options, may provide additional ways to harness this resource. Plant secondary metabolites are a fascinating class of phytochemicals exhibiting immense chemical diversity. Considerable enigma regarding their natural biological functions and the vast array of pharmacological activities, amongst other uses, make secondary metabolites interesting and important candidates for research. Here, we present an update on changing trends in the biotechnological approaches that are used to understand and exploit the secondary metabolism in medicinal and aromatic plants. Bioprocessing in the form of suspension culture, organ culture or transformed hairy roots has been successful in scaling up secondary metabolite production in many cases. Pathway elucidation and metabolic engineering have been useful to get enhanced yield of the metabolite of interest; or, for producing novel metabolites. Heterologous expression of putative plant secondary metabolite biosynthesis genes in a microbe is useful to validate their functions, and in some cases, also, to produce plant metabolites in microbes. Endophytes, the microbes that normally colonize plant tissues, may also produce the phytochemicals produced by the host plant. The review also provides perspectives on future research in the field.

Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol

Increasingly complex metabolic pathways have been engineered by modifying natural pathways and establishing de novo pathways with enzymes from a variety of organisms. Here we apply retro-biosynthetic screening to a modular pathway design to identify a redox neutral, theoretically high yielding route to a branched C6 alcohol. Enzymes capable of converting natural E. coli metabolites into 4-methyl-pentanol (4MP) via coenzyme A (CoA)-dependent chemistry were taken from nine different organisms to form a ten-step de novo pathway. Selectivity for 4MP is enhanced through the use of key enzymes acting on acyl-CoA intermediates, a carboxylic acid reductase from Nocardia iowensis and an alcohol dehydrogenase from Leifsonia sp. strain S749. One implementation of the full pathway from glucose demonstrates selective carbon chain extension and acid reduction with 4MP constituting 81% (90±7 mg l(-1)) of the observed alcohol products. The highest observed 4MP titre is 192±23 mg l(-1). These results demonstrate the ability of modular pathway screening to facilitate de novo pathway engineering.

Fermentation of oxidized hexose derivatives by Clostridium acetobutylicum

Background

Clostridium acetobutylicum fermentations are promising for production of commodity chemicals from heterogeneous biomass due to the wide range of substrates the organism can metabolize. Much work has been done to elucidate the pathways for utilization of aldoses, but little is known about metabolism of more oxidized substrates. Two oxidized hexose derivatives, gluconate and galacturonate, are present in low cost feedstocks, and their metabolism will contribute to overall metabolic output of these substrates.

Results

A complete metabolic network for glucose, gluconate, and galacturonate utilization was generated using online databases, previous studies, genomic context, and experimental data. Gluconate appears to be metabolized via the Entner-Doudoroff pathway, and is likely dehydrated to 2-keto-3-deoxy-gluconate before phosphorylation to 2-keto-3-deoxy-6-P-gluconate. Galacturonate appears to be processed via the Ashwell pathway, converging on a common metabolite for gluconate and galacturonate metabolism, 2-keto-3-deoxygluconate. As expected, increasingly oxidized substrates resulted in increasingly oxidized products with galacturonate fermentations being nearly homoacetic. Calculations of expected ATP and reducing equivalent yields and experimental data suggested galacturonate fermentations were reductant limited. Galacturonate fermentation was incomplete, which was not due solely to product inhibition or the inability to utilize low concentrations of galacturonate. Removal of H₂ and CO₂ by agitation resulted in faster growth, higher cell densities, formation of relatively more oxidized products, and higher product yields for cultures grown on glucose or gluconate. In contrast, cells grown on galacturonate showed reduced growth rates upon agitation, which was likely due to loss in reductant in the form of H₂. The growth advantage seen on agitated glucose or gluconate cultures could not be solely attributed to improved ATP economics, thereby indicating other factors are also important.

Conclusions

The metabolic network presented in this work should facilitate similar reconstructions in other organisms, and provides a further understanding of the pathways involved in metabolism of oxidized feedstocks and carbohydrate mixtures. The nearly homoacetic fermentation during growth on galacturonate indicates further optimization of this and related organisms could provide a route to an effective biologically derived acetic acid production platform. Furthermore, the pathways could be targeted to decrease production of undesirable products during fermentations of heterogeneous biomass.