Non-conventional hosts for the production of fuels and chemicals

Screening of broad-host expression promoters for shuttle expression vectors in non-conventional yeasts and bacteria

BACKGROUND

Non-conventional yeasts and bacteria gain significance in synthetic biology for their unique metabolic capabilities in converting low-cost renewable feedstocks into valuable products. Improving metabolic pathways and increasing bioproduct yields remain dependent on the strategically use of various promoters in these microbes. The development of broad-spectrum promoter libraries with varying strengths for different hosts is attractive for biosynthetic engineers.

RESULTS

In this study, five Yarrowia lipolytica constitutive promoters (yl.hp4d, yl.FBA1in, yl.TEF1, yl.TDH1, yl.EXP1) and five Kluyveromyces marxianus constitutive promoters (km.PDC1, km.FBA1, km.TEF1, km.TDH3, km.ENO1) were selected to construct promoter-reporter vectors, utilizing α-amylase and red fluorescent protein (RFP) as reporter genes. The promoters' strengths were systematically characterized across Y. lipolytica, K. marxianus, Pichia pastoris, Escherichia coli, and Corynebacterium glutamicum. We discovered that five K. marxianus promoters can all express genes in Y. lipolytica and that five Y. lipolytica promoters can all express genes in K. marxianus with variable expression strengths. Significantly, the yl.TEF1 and km.TEF1 yeast promoters exhibited their adaptability in P. pastoris, E. coli, and C. glutamicum. In yeast P. pastoris, the yl.TEF1 promoter exhibited substantial expression of both amylase and RFP. In bacteria E. coli and C. glutamicum, the eukaryotic km.TEF1 promoter demonstrated robust expression of RFP. Significantly, in E. coli, The RFP expression strength of the km.TEF1 promoter reached ∼20% of the T7 promoter.

CONCLUSION

Non-conventional yeast promoters with diverse and cross-domain applicability have great potential for developing innovative and dynamic regulated systems that can effectively manage carbon flux and enhance target bioproduct synthesis across diverse microbial hosts.

Industrial biotechnology goes thermophilic: Thermoanaerobes as promising hosts in the circular carbon economy

Transitioning away from fossil feedstocks is imperative to mitigate climate change, and necessitates the utilization of renewable, alternative carbon and energy sources to foster a circular carbon economy. In this context, lignocellulosic biomass and one-carbon compounds emerge as promising feedstocks that could be renewably upgraded by thermophilic anaerobes (thermoanaerobes) via gas fermentation or consolidated bioprocessing to value-added products. In this review, the potential of thermoanaerobes for cost-efficient, effective and sustainable bioproduction is discussed. Metabolic and bioprocess engineering approaches are reviewed to draw a comprehensive picture of current developments and future perspectives for the conversion of renewable feedstocks to chemicals and fuels of interest. Selected bioprocessing scenarios are outlined, offering practical insights into the applicability of thermoanaerobes at a large scale. Collectively, the potential advantages of thermoanaerobes regarding process economics could facilitate an easier transition towards sustainable bioprocesses with renewable feedstocks.

Promoter engineering enables precise metabolic regulation towards efficient β-elemene production in Ogataea polymorpha

Precisely controlling gene expression is beneficial for optimizing biosynthetic pathways for improving the production. However, promoters in nonconventional yeasts such as Ogataea polymorpha are always limited, which results in incompatible gene modulation. Here, we expanded the promoter library in O. polymorpha based on transcriptional data, among which 13 constitutive promoters had the strengths ranging from 0-55% of PGAP, the commonly used strong constitutive promoter, and 2 were growth phase-dependent promoters. Subsequently, 2 hybrid growth phase-dependent promoters were constructed and characterized, which had 2-fold higher activities. Finally, promoter engineering was applied to precisely regulate cellular metabolism for efficient production of β-elemene. The glyceraldehyde-3-phosphate dehydrogenase gene GAP was downregulated to drive more flux into pentose phosphate pathway (PPP) and then to enhance the supply of acetyl-CoA by using phosphoketolase-phosphotransacetylase (PK-PTA) pathway. Coupled with the phase-dependent expression of synthase module (ERG20∼LsLTC2 fusion), the highest titer of 5.24 g/L with a yield of 0.037 g/(g glucose) was achieved in strain YY150U under fed-batch fermentation in shake flasks. This work characterized and engineered a series of promoters, that can be used to fine-tune genes for constructing efficient yeast cell factories.

Emerging nonmodel eukaryotes for biofuel production

Microbial synthesis of biofuels offers a promising solution to the global environmental and energy concerns. However, the main challenge of microbial cell factories is their high fermentation costs. Model hosts, such as Escherichia coli and Saccharomyces cerevisiae, are typically used for proof-of-concept studies of producing different types of biofuels, however, they have a limited potential for biofuel production at an industrially relevant scale due to the weak stability/robustness and narrow substrate scope. With the advancements of synthetic biology and metabolic engineering, nonmodel eukaryotes, with naturally favorable phenotypic and metabolic features, have been emerging as promising biofuel producers. Here, we introduce the emerging nonmodel eukaryotes for the biofuel production and discuss their specific advantages, especially those with the capacity of producing cellulosic ethanol, higher alcohols, and fatty acid-/terpene-derived biofuel molecules. We also propose the challenges and prospects for developing nonmodel eukaryotic as the ideal hosts for future biofuel production.

Investigating and Modeling the Factors That Affect Genetic Circuit Performance

Over the past 2 decades, synthetic biology has yielded ever more complex genetic circuits that are able to perform sophisticated functions in response to specific signals. Yet, genetic circuits are not immediately transferable to an outside-the-lab setting where their performance is highly compromised. We propose introducing a broader test step to the design-build-test-learn workflow to include factors that might contribute to unexpected genetic circuit performance. As a proof of concept, we have designed and evaluated a genetic circuit in various temperatures, inducer concentrations, nonsterilized soil exposure, and bacterial growth stages. We determined that the circuit's performance is dramatically altered when these factors differ from the optimal lab conditions. We observed significant changes in the time for signal detection as well as signal intensity when the genetic circuit was tested under nonoptimal lab conditions. As a learning effort, we then proceeded to generate model predictions in untested conditions, which is currently lacking in synthetic biology application design. Furthermore, broader test and learn steps uncovered a negative correlation between the time it takes for a gate to turn ON and the bacterial growth phases. As the synthetic biology discipline transitions from proof-of-concept genetic programs to appropriate and safe application implementations, more emphasis on test and learn steps (i.e., characterizing parts and circuits for a broad range of conditions) will provide missing insights on genetic circuit behavior outside the lab.

Mechanistic investigation of a D to N mutation in DAHP synthase that dictates carbon flux into the shikimate pathway in yeast

3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key enzyme in the shikimate pathway for the biosynthesis of aromatic compounds. _L-Phe and _L-Tyr bind to the two main DAHPS isoforms and inhibit their enzyme activities, respectively. Synthetic biologists aim to relieve such inhibitions in order to improve the productivity of aromatic compounds. In this work, we reported a point mutant of yeast DHAPS, Aro3^D154N, which retains the wild type enzyme activity but converts it highly inert to the inhibition by _L-Phe. The Aro3 crystal structure along with the molecular dynamics simulations analysis suggests that the D154N mutation distant from the inhibitor binding cavity may reduce the binding affinity of _L-Phe. Growth assays demonstrated that substitution of the conserved D154 with asparagine suffices to relieve the inhibition of _L-Phe on Aro3, _L-Tyr on Aro4, and the inhibitions on their corresponding homologues from diverse yeasts. The importance of our discovery is highlighted by the observation of 29.1% and 43.6% increase of yield for the production of tyrosol and salidroside respectively upon substituting ARO3 with ARO3^D154N. We anticipate that this allele would be used broadly to increase the yield of various aromatic products in metabolically diverse microorganisms.

Global metabolic rewiring of the nonconventional yeast Ogataea polymorpha for biosynthesis of the sesquiterpenoid β-elemene

Bioproduction of natural products via microbial cell factories is a promising alternative to traditional plant extraction. Recently, nonconventional microorganisms have emerged as attractive chassis hosts for biomanufacturing. One such microorganism, Ogataea polymorpha is an industrial yeast used for protein expression with numerous advantages, such as thermal-tolerance, a wide substrate spectrum and high-density fermentation. Here, we systematically rewired the cellular metabolism of O. polymorpha to achieve high-level production of the sesquiterpenoid β-elemene by optimizing the mevalonate pathway, enhancing the supply of NADPH and acetyl-CoA, and downregulating competitive pathways. The engineered strain produced 509 mg/L and 4.7 g/L of β-elemene under batch and fed-batch fermentation, respectively. Therefore, this study identified the potential industrial application of O. polymorpha as a good microbial platform for producing sesquiterpenoids.

Advances in mining and expressing microbial biosynthetic gene clusters

Natural products (NPs) especially the secondary metabolites originated from microbes exhibit great importance in biomedical, industrial and agricultural applications. However, mining biosynthetic gene clusters (BGCs) to produce novel NPs has been hindered owing that a large population of environmental microbes are unculturable. In the past decade, strategies to explore BGCs directly from (meta)genomes have been established along with the fast development of high-throughput sequencing technologies and the powerful bioinformatics data-processing tools, which greatly expedited the exploitations of novel BGCs from unculturable microbes including the extremophilic microbes. In this review, we firstly summarized the popular bioinformatics tools and databases available to mine novel BGCs from (meta)genomes based on either pure cultures or pristine environmental samples. Noticeably, approaches rooted from machine learning and deep learning with focuses on the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs) were dramatically increased in recent years. Moreover, synthetic biology techniques to express the novel BGCs in culturable native microbes or heterologous hosts were introduced. This working pipeline including the discovery and biosynthesis of novel NPs will greatly advance the exploitations of the abundant but unexplored microbial BGCs.

Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues

Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.

Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications

A variety of yeast species have been considered ideal hosts for metabolic engineering to produce value-added chemicals, including the model organism Saccharomyces cerevisiae, as well as non-conventional yeasts including Yarrowia lipolytica, Kluyveromyces marxianus, and Pichia pastoris. However, the metabolic capacity of these microbes is not simply dictated or implied by genus or species alone. Within the same species, yeast strains can display distinct variations in their phenotypes and metabolism, which affect the performance of introduced pathways and the production of interesting compounds. Moreover, it is unclear how this metabolic potential corresponds to function upon rewiring these organisms. These reports thus point out a new consideration for successful metabolic engineering, specifically: what are the best strains to utilize and how does one achieve effective metabolic engineering? Understanding such questions will accelerate the host selection and optimization process for generating yeast cell factories. In this review, we survey recent advances in studying yeast strain variations and utilizing non-type strains in pathway production and metabolic engineering applications. Additionally, we highlight the importance of employing portable methods for metabolic rewiring to best access this metabolic diversity. Finally, we conclude by highlighting the importance of considering strain diversity in metabolic engineering applications.

Design of stable and self-regulated microbial consortia for chemical synthesis

Microbial coculture engineering has emerged as a promising strategy for biomanufacturing. Stability and self-regulation pose a significant challenge for the generation of intrinsically robust cocultures for large-scale applications. Here, we introduce the use of multi-metabolite cross-feeding (MMCF) to establish a close correlation between the strains and the design rules for selecting the appropriate metabolic branches. This leads to an intrinicially stable two-strain coculture where the population composition and the product titer are insensitive to the initial inoculation ratios. With an intermediate-responsive biosensor, the population of the microbial coculture is autonomously balanced to minimize intermediate accumulation. This static-dynamic strategy is extendable to three-strain cocultures, as demonstrated with de novo biosynthesis of silybin/isosilybin. This strategy is generally applicable, paving the way to the industrial application of microbial cocultures.

Stability and tunability are two desirable properties of microbial consortia-based bioproduction. Here, the authors integrate a caffeate-responsive biosensor into two and three strains coculture system to achieve autonomous regulation of strain ratios for coniferol and silybin/isosiltbin production, respectively.

Glucose/Xylose Co-Fermenting Saccharomyces cerevisiae Increases the Production of Acetyl-CoA Derived n-Butanol From Lignocellulosic Biomass

Efficient xylose catabolism in engineered Saccharomyces cerevisiae enables more economical lignocellulosic biorefinery with improved production yields per unit of biomass. Yet, the product profile of glucose/xylose co-fermenting S. cerevisiae is mainly limited to bioethanol and a few other chemicals. Here, we introduced an n-butanol-biosynthesis pathway into a glucose/xylose co-fermenting S. cerevisiae strain (XUSEA) to evaluate its potential on the production of acetyl-CoA derived products. Higher n-butanol production of glucose/xylose co-fermenting strain was explained by the transcriptomic landscape, which revealed strongly increased acetyl-CoA and NADPH pools when compared to a glucose fermenting wild-type strain. The acetate supplementation expected to support acetyl-CoA pool further increased n-butanol production, which was also validated during the fermentation of lignocellulosic hydrolysates containing acetate. Our findings imply the feasibility of lignocellulosic biorefinery for producing fuels and chemicals derived from a key intermediate of acetyl-CoA through glucose/xylose co-fermentation.

Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli

Previously, Escherichia coli was engineered to produce isobutyl acetate (IBA). Titers greater than the toxicity threshold (3 g/L) were achieved by using layer-assisted production. To avoid this costly and complex method, adaptive laboratory evolution (ALE) was applied to E. coli for improved IBA tolerance. Over 37 rounds of selective pressure, 22 IBA-tolerant mutants were isolated. Remarkably, these mutants not only tolerate high IBA concentrations, they also produce higher IBA titers. Using whole-genome sequencing followed by CRISPR/Cas9 mediated genome editing, the mutations (SNPs in metH, rho and deletion of arcA) that confer improved tolerance and higher titers were elucidated. The improved IBA titers in the evolved mutants were a result of an increased supply of acetyl-CoA and altered transcriptional machinery. Without the use of phase separation, a strain capable of 3.2-fold greater IBA production than the parent strain was constructed by combing select beneficial mutations. These results highlight the impact improved tolerance has on the production capability of a biosynthetic system.

Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number

Background

Synechocystis sp. PCC 6803 provides a well-established reference point to cyanobacterial metabolic engineering as part of basic photosynthesis research, as well as in the development of next-generation biotechnological production systems. This study focused on expanding the current knowledge on genomic integration of expression constructs in Synechocystis, targeting a range of novel sites in the chromosome and in the native plasmids, together with established loci used in literature. The key objective was to obtain quantitative information on site-specific expression in reference to replicon copy numbers, which has been speculated but never compared side by side in this host.

Results

An optimized sYFP2 expression cassette was successfully integrated in two novel sites in Synechocystis chromosome (slr0944; sll0058) and in all four endogenous megaplasmids (pSYSM/slr5037-slr5038; pSYSX/slr6037; pSYSA/slr7023; pSYSG/slr8030) that have not been previously evaluated for the purpose. Fluorescent analysis of the segregated strains revealed that the expression levels between the megaplasmids and chromosomal constructs were very similar, and reinforced the view that highest expression in Synechocystis can be obtained using RSF1010-derived replicative vectors or the native small plasmid pCA2.4 evaluated in comparison. Parallel replicon copy number analysis by RT-qPCR showed that the expression from the alternative loci is largely determined by the gene dosage in Synechocystis, thereby confirming the dependence formerly proposed based on literature.

Conclusions

This study brings together nine different integrative loci in the genome of Synechocystis to demonstrate quantitative differences between target sites in the chromosome, the native plasmids, and a RSF1010-based replicative expression vector. To date, this is the most comprehensive comparison of alternative integrative sites in Synechocystis, and provides the first direct reference between expression efficiency and replicon gene dosage in the context. In the light of existing literature, the findings support the view that the small native plasmids can be notably more difficult to target than the chromosome or the megaplasmids, and that the RSF1010-derived vectors may be surprisingly well maintained under non-selective culture conditions in this cyanobacterial host. Altogether, the work broadens our views on genomic integration and the rational use of different integrative loci versus replicative plasmids, when aiming at expressing heterologous genes in Synechocystis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01622-2.

Critical parameters and procedures for anaerobic cultivation of yeasts in bioreactors and anaerobic chambers

All known facultatively fermentative yeasts require molecular oxygen for growth. Only in a small number of yeast species, these requirements can be circumvented by supplementation of known anaerobic growth factors such as nicotinate, sterols and unsaturated fatty acids. Biosynthetic oxygen requirements of yeasts are typically small and, unless extensive precautions are taken to minimize inadvertent entry of trace amounts of oxygen, easily go unnoticed in small-scale laboratory cultivation systems. This paper discusses critical points in the design of anaerobic yeast cultivation experiments in anaerobic chambers and laboratory bioreactors. Serial transfer or continuous cultivation to dilute growth factors present in anaerobically pre-grown inocula, systematic inclusion of control strains and minimizing the impact of oxygen diffusion through tubing are identified as key elements in experimental design. Basic protocols are presented for anaerobic-chamber and bioreactor experiments.

Recent advances in the microbial production of isopentanol (3-Methyl-1-butanol)

As the effects of climate change become increasingly severe, metabolic engineers and synthetic biologists are looking towards greener sources for transportation fuels. The design and optimization of microorganisms to produce gasoline, diesel, and jet fuel compounds from renewable feedstocks can significantly reduce dependence on fossil fuels and thereby produce fewer emissions. Over the past two decades, a tremendous amount of research has contributed to the development of microbial strains to produce advanced fuel compounds, including branched-chain higher alcohols (BCHAs) such as isopentanol (3-methyl-1-butanol; 3M1B) and isobutanol (2-methyl-1-propanol). In this review, we provide an overview of recent advances in the development of microbial strains for the production of isopentanol in both conventional and non-conventional hosts. We also highlight metabolic engineering strategies that may be employed to enhance product titers, reduce end-product toxicity, and broaden the substrate range to non-sugar carbon sources. Finally, we offer glimpses into some promising future directions in the development of isopentanol producing microbial strains.

Bio-synthesis of food additives and colorants-a growing trend in future food

Food additives and colorants are extensively used in the food industry to improve food quality and safety during processing, storage and packing. Sourcing of these molecules is predominately through three means: extraction from natural sources, chemical synthesis, and bio-production, with the first two being the most utilized. However, growing demands for sustainability, safety and "natural" products have renewed interest in using bio-based production methods. Likewise, the move to more cultured foods and meat alternatives requires the production of new additives and colorants. The production of bio-based food additives and colorants is an interdisciplinary research endeavor and represents a growing trend in future food. To highlight the potential of microbial hosts for food additive and colorant production, we focus on current advances for example molecules based on their utilization stage and bio-production yield as follows: (I) approved and industrially produced with high titers; (II) approved and produced with decent titers (in the g/L range), but requiring further engineering to reduce production costs; (III) approved and produced with very early stage titers (in the mg/L range); and (IV) new/potential candidates that have not been approved but can be sourced through microbes. Promising approaches, as well as current challenges and future directions will also be thoroughly discussed for the bioproduction of these food additives and colorants.

Snails as Taxis for a Large Yeast Biodiversity

Yeasts are unicellular fungi that harbour a large biodiversity of thousands of species, of which particularly ascomycetous yeasts are instrumental to human food and beverage production. There is already a large body of evidence showing that insects play an important role for yeast ecology, for their dispersal to new habitats and for breeding and overwintering opportunities. Here, we sought to investigate a potential role of the terrestrial snails Cepaea hortensis and C. nemoralis, which in Europe are often found in association with human settlements and gardens, in yeast ecology. Surprisingly, even in a relatively limited culture-dependent sampling size of over 150 isolates, we found a variety of yeast genera, including species frequently isolated from grape must such as Hanseniaspora, Metschnikowia, Meyerozyma and Pichia in snail excrements. We typed the isolates using standard ITS-PCR-sequencing, sequenced the genomes of three non-conventional yeasts H. uvarum, Meyerozyma guilliermondii and P. kudriavzevii and characterized the fermentation performance of these three strains in grape must highlighting their potential to contribute to novel beverage fermentations. Aggravatingly, however, we also retrieved several human fungal pathogen isolates from snail excrements belonging to the Candida clade, namely Ca. glabrata and Ca. lusitaniae. Overall, our results indicate that diverse yeasts can utilise snails as taxis for dispersal. This courier service may be largely non-selective and thus depend on the diet available to the snails.

De novo resveratrol production through modular engineering of an Escherichia coli-Saccharomyces cerevisiae co-culture

BACKGROUND

Resveratrol is a plant secondary metabolite with diverse, potential health-promoting benefits. Due to its nutraceutical merit, bioproduction of resveratrol via microbial engineering has gained increasing attention and provides an alternative to unsustainable chemical synthesis and straight extraction from plants. However, many studies on microbial resveratrol production were implemented with the addition of water-insoluble phenylalanine or tyrosine-based precursors to the medium, limiting in the sustainable development of bioproduction.

RESULTS

Here we present a novel coculture platform where two distinct metabolic background species were modularly engineered for the combined total and de novo biosynthesis of resveratrol. In this scenario, the upstream Escherichia coli module is capable of excreting p-coumaric acid into the surrounding culture media through constitutive overexpression of codon-optimized tyrosine ammonia lyase from Trichosporon cutaneum (TAL), feedback-inhibition-resistant 3-deoxy-d-arabinoheptulosonate-7-phosphate synthase (aroGfbr) and chorismate mutase/prephenate dehydrogenase (tyrAfbr) in a transcriptional regulator tyrR knockout strain. Next, to enhance the precursor malonyl-CoA supply, an inactivation-resistant version of acetyl-CoA carboxylase (ACC1S659A,S1157A) was introduced into the downstream Saccharomyces cerevisiae module constitutively expressing codon-optimized 4-coumarate-CoA ligase from Arabidopsis thaliana (4CL) and resveratrol synthase from Vitis vinifera (STS), and thus further improve the conversion of p-coumaric acid-to-resveratrol. Upon optimization of the initial inoculation ratio of two populations, fermentation temperature, and culture time, this co-culture system yielded 28.5 mg/L resveratrol from glucose in flasks. In further optimization by increasing initial net cells density at a test tube scale, a final resveratrol titer of 36 mg/L was achieved.

CONCLUSIONS

This is first study that demonstrates the use of a synthetic E. coli-S. cerevisiae consortium for de novo resveratrol biosynthesis, which highlights its potential for production of other p-coumaric-acid or resveratrol derived biochemicals.