A Novel Biosynthetic Pathway for the Production of Acrylic Acid through β-Alanine Route in Escherichia coli

Exploring the gut microbiome: A potential biomarker for cancer diagnosis, prognosis, and therapy

The gut microbiome, a complex community of trillions of microorganisms in the intestines, is crucial in maintaining human health. Recent advancements in microbiome research have unveiled a compelling link between the gut microbiome and cancer development and progression. Alterations in the composition and function of the gut microbiome, known as dysbiosis, have been implicated in various types of cancer, including, esophageal, liver, colon, pancreatic, and gastrointestinal. However, the specific gut microbial strains associated with the development or progression of cancers in various tissues remain largely unclear. Here, we summarize current research findings on the gut microbiome of multiple cancers. This review aims to identify key gut microbial targets that closely influence cancer development based on current research findings. To accurately evaluate the effectiveness of the gut microbiome as a clinical tool for cancer, further research is needed to explore its potential as a biomarker and therapeutic strategy.

Effects of different orchard tree pruning residues on the yield and nutrient composition of Lentinus edodes

Introduction

As the scale of Lentinus edodes cultivation expands, challenges such as substrate shortages and rising production costs in mushroom cultivation have become increasingly prominent. Fruit tree pruning residue has the potential to serve as an alternative substrate, offering a sustainable solution. This study evaluates the feasibility of incorporating various types of fruit tree pruning residues into L. edodes cultivation.

Methods

Different ratios of Quercus sawdust (QS), Malus pumila pruning (MPP), Vitis vinifera pruning (VVP), Actinidia deliciosa pruning (ADP), Ziziphus jujuba pruning (ZJP), and Morus alba pruning (MAP) were tested as substrates. The effects on yield, amino acid profiles, and protein content of L. edodes fruiting bodies were analyzed. The control substrate comprised 80% QS, and the experimental groups incorporated varying ratios of fruit tree residues.

Results

Compared with the control, yields increased by 14.86% (QS-MPP), 8.1% (QS-VVP), 18.92% (QS-ZJP), and 22.97% (QS-MAP). The MAP group had 21.21% higher ash content, while the QS-MAP group exhibited the highest crude protein content (10.84% increase). The QS-MPP group showed the highest crude fiber content (1.72 g/100 g). Crude polysaccharide and fat contents in the ZJP group increased by 110.77% and 10.15%, respectively. Mineral content varied, with QS-MPP showing the highest calcium, potassium, manganese, and magnesium levels, and VVP exhibiting the highest iron and copper levels. Amino acid analysis revealed QS-MPP had the highest levels of threonine, valine, isoleucine, serine, cysteine, glycine, and histidine, while QS-VVP had the highest leucine, aspartate, glutamate, and arginine levels. The best formulation was determined as 40% QS, 40% MPP, 17% bran, 1% sucrose, 1% CaCO3, and 1% gypsum.

Discussion

These results highlight the potential of fruit tree pruning residues as a sustainable substrate for L. edodes cultivation, ensuring high yields and enhanced nutritional quality. This approach can contribute to cost-effective and environmentally friendly mushroomproduction.

Microbial production of an aromatic homopolyester

We report the development of a metabolically engineered bacterium for the fermentative production of polyesters containing aromatic side chains, serving as sustainable alternatives to petroleum-based plastics. A metabolic pathway was constructed in an Escherichia coli strain to produce poly[d-phenyllactate(PhLA)], followed by three strategies to enhance polymer production. First, polyhydroxyalkanoate (PHA) granule-associated proteins (phasins) were introduced to increase the polymer accumulation. Next, metabolic engineering was performed to redirect the metabolic flux toward PhLA. Furthermore, PHA synthase was engineered based on in silico simulation results to enhance the polymerization of PhLA. The final strain was capable of producing 12.3 g/l of poly(PhLA), marking it the first bio-based process for producing an aromatic homopolyester. Additional heterologous gene introductions led to the high level production of poly(3-hydroxybutyrate-co-11.7 mol% PhLA) copolymer (61.4 g/l). The strategies described here will be useful for the bio-based production of aromatic polyesters from renewable resources.

SERS-based microdroplet platform for high-throughput screening of Escherichia coli strains for the efficient biosynthesis of D-phenyllactic acid

D-Phenyllactic acid (D-PLA) is a potent antimicrobial typically synthesized through chemical methods. However, due to the complexity and large pollution of these reactions, a simpler and more eco-friendly approach was needed. In this study, a strain for D-PLA biosynthesis was constructed, but the efficiency was restricted by the activity of D-lactate dehydrogenase (DLDH). To address this issue, a DLDH mutant library was constructed and the Surface-Enhanced Raman Spectroscopy (SERS) was employed for the precise quantification of D-PLA at the single-cell level. The TB24 mutant exhibited a significant improvement in D-PLA productivity and a 23.03-fold increase in enzymatic activity, which was attributed to the enhanced hydrogen bonding and increased hydrophobicity within the substrate-binding pocket. By implementing multi-level optimization strategies, including the co-expression of glycerol dehydrogenase (GlyDH) with DLDH, chassis cell replacement, and RBS engineering, a significant increase in D-PLA yields was achieved, reaching 128.4 g/L. This study underscores the effectiveness of SERS-based microdroplet high-throughput screening (HTS) in identifying superior mutant enzymes and offers a strategy for large-scale D-PLA biotransformation.

Sustainable production and degradation of plastics using microbes

Plastics are indispensable in everyday life and industry, but the environmental impact of plastic waste on ecosystems and human health is a huge concern. Microbial biotechnology offers sustainable routes to plastic production and waste management. Bacteria and fungi can produce plastics, as well as their constituent monomers, from renewable biomass, such as crops, agricultural residues, wood and organic waste. Bacteria and fungi can also degrade plastics. We review state-of-the-art microbial technologies for sustainable production and degradation of bio-based plastics and highlight the potential contributions of microorganisms to a circular economy for plastics.

Designing artificial pathways for improving chemical production

Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.

Microbial production of odd-chain fatty acids

Odd-chain fatty acids (OcFAs) and their derivatives have attracted much attention due to their beneficial physiological effects and their potential to be alternatives to advanced fuels. However, cells naturally produce even-chain fatty acids (EcFAs) with negligible OcFAs. In the process of biosynthesis of fatty acids (FAs), the acetyl-CoA serves as the starter unit for EcFAs, and propionyl-CoA works as the starter unit for OcFAs. The lack of sufficient propionyl-CoA, the precursor, is usually regarded as the main restriction for large-scale bioproduction of OcFAs. In recent years, synthetic biology strategies have been used to modify several microorganisms to produce more propionyl-CoA that would enable an efficient biosynthesis of OcFAs. This review discusses several reported and potential metabolic pathways for propionyl-CoA biosynthesis, followed by advances in engineering several cell factories for OcFAs production. Finally, trends and challenges of synthetic biology driven OcFAs production are discussed.

Repurposing of waste PET by microbial biotransformation to functionalized materials for additive manufacturing

Plastic waste is an outstanding environmental thread. Poly(ethylene terephthalate) (PET) is one of the most abundantly produced single-use plastics worldwide, but its recycling rates are low. In parallel, additive manufacturing is a rapidly evolving technology with wide-ranging applications. Thus, there is a need for a broad spectrum of polymers to meet the demands of this growing industry and address post-use waste materials. This perspective article highlights the potential of designing microbial cell factories to upcycle PET into functionalized chemical building blocks for additive manufacturing. We present the leveraging of PET hydrolyzing enzymes and rewiring the bacterial C2 and aromatic catabolic pathways to obtain high-value chemicals and polymers. Since PET mechanical recycling back to original materials is cost-prohibitive, the biochemical technology is a viable alternative to upcycle PET into novel 3D printing materials, such as replacements for acrylonitrile butadiene styrene. The presented hybrid chemo-bio approaches potentially enable the manufacturing of environmentally friendly degradable or higher-value high-performance polymers and composites and their reuse for a circular economy.

ONE-SENTENCE SUMMARY

Biotransformation of waste PET to high-value platform chemicals for additive manufacturing.

Linking Pedobacter lusitanus NL19 volatile exometabolome with growth medium composition: what can we learn using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry?

Microbial metabolomics allows understanding and to comprehensively analyse metabolites, and their related cellular and metabolic processes, that are produced and released to the extracellular environment under specific conditions. In that regard, the main objective of this research is to understand the impact of culture media changes in the metabolic profile of Pedobacter lusitanus NL19 (NL19) and Pedobacter himalayensis MTCC 6384 (MTCC6384) and respective influence on the production of biotechnologically relevant compounds. Solid-phase microextraction combined with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry with time-of-flight analyser (GC × GC-ToFMS) was applied to comprehensively study the metabolites produced by NL19 and MTCC6384 both in tryptic soy broth 100% (TSB100) and tryptic soy broth with 25% casein peptone (PC25). A total of 320 metabolites were putatively identified, which belong to different chemical families: alcohols, aldehydes, esters, ethers, hydrocarbons, ketones, nitrogen compounds, sulphur compounds, monoterpenes, and sesquiterpenes. Metabolites that were statistically different from the control (sterile medium) were selected allowing for the construction of the metabolic profile of both strains. A set of 80 metabolites was tentatively associated to the metabolic pathways such as the metabolism of fatty acids, branched-chain aminoacids, phenylalanine, methionine, aromatic compounds, and monoterpene and sesquiterpene biosynthesis. This study allowed to better understand how slight changes of the culture media and thus the composition of nutrients impair the metabolic profile of bacteria, which may be further explored for metabolomics pipeline construction or biotechnological applications.

Improving 3-hydroxypropionic acid production in E. coli by in silico prediction of new metabolic targets

3-Hydroxypropionic acid (3-HP) production from renewable feedstocks is of great interest in efforts to develop greener processes for obtaining this chemical platform. Here we report an engineered E. coli strain for 3-HP production through the β-alanine pathway. To obtain a new strain capable of producing 3-HP, the pathway was established by overexpressing the enzymes pyruvate aminotransferase, 3-hydroxyacid dehydrogenase, and L-aspartate-1-decarboxylase. Further increase of the 3-HP titer was achieved using evolutionary optimizations of a genome-scale metabolic model of E. coli containing the adopted pathway. From these optimizations, three non-intuitive targets for in vivo assessment were identified: L-alanine aminotransferase and alanine racemase overexpression, and L-valine transaminase knock-out. The implementation of these targets in the production strain resulted in a 40% increase in 3-HP titer. The strain was further engineered to overexpress phosphoenolpyruvate carboxylase, reaching 0.79 ± 0.02 g/L of 3-HP when grown using glucose. Surprisingly, this strain produced 63% more of the desired product when grown using a mixture of glucose and xylose (1:1, C-mol), and gene expression analysis showed that the cellular adjustment to consume xylose had a positive impact on 3-HP accumulation. Fed-batch culture with xylose feeding led to a final titer of 29.1 g/L. These results reinforce the value of computational methods in strain engineering, enabling the design of more efficient strategies to be assessed. Moreover, higher production of 3-HP under a sugar mixture condition points towards the development of bioprocesses based on renewable resources, such as hemicellulose hydrolysates.

Prospects for carbon-negative biomanufacturing

Biomanufacturing has the potential to reduce demand for petrochemicals and mitigate climate change. Recent studies have also suggested that some of these products can be net carbon negative, effectively removing CO₂ from the atmosphere and locking it up in products. This review explores the magnitude of carbon removal achievable through biomanufacturing and discusses the likely fate of carbon in a range of target molecules. Solvents, cleaning agents, or food and pharmaceutical additives will likely re-release their carbon as CO₂ at the end of their functional lives, while carbon incorporated into non-compostable polymers can result in long-term sequestration. Future research can maximize its impact by focusing on reducing emissions, achieving performance advantages, and enabling a more circular carbon economy.

Process development, techno-economic analysis and life-cycle assessment for laccase catalyzed synthesis of lignin hydrogel

In this study, an effort has been undertaken to study process design, techno-economic analysis, and life-cycle assessment (LCA) of lignin hydrogel (LH) which has potential applications in environmental remediation. Minimum selling price (MSP) of LHs has been estimated to be 2,141 US$/ton and it lies within the range of market price (1,420-2,280 US$/ton) for commercial coagulants. Further, sensitivity analysis has been conducted and it was observed that "% efficiency of lignin hydrogel production" and "lignin price" were the most influential parameters. Uncertainty analysis has also been conducted to study the influence of volatility in the market price of lignin and total capital investment on MSP of LH. From LCA study, it was estimated that the proposed process will emit 2.8 kg CO2 eq. and 1.1 kg Oil eq./kg lignin hydrogel. The developed process can be utilized for lignin upgradation in biorefineries to develop economically feasible and sustainable processes.

Production of biopolymer precursors beta-alanine and L-lactic acid from CO2 with metabolically versatile Rhodococcus opacus DSM 43205

Hydrogen oxidizing autotrophic bacteria are promising hosts for conversion of CO₂ into chemicals. In this work, we engineered the metabolically versatile lithoautotrophic bacterium R. opacus strain DSM 43205 for synthesis of polymer precursors. Aspartate decarboxylase (panD) or lactate dehydrogenase (ldh) were expressed for beta-alanine or L-lactic acid production, respectively. The heterotrophic cultivations on glucose produced 25 mg L⁻¹ beta-alanine and 742 mg L⁻¹ L-lactic acid, while autotrophic cultivations with CO₂, H₂, and O₂ resulted in the production of 1.8 mg L⁻¹ beta-alanine and 146 mg L⁻¹ L-lactic acid. Beta-alanine was also produced at 345 μg L⁻¹ from CO₂ in electrobioreactors, where H₂ and O₂ were provided by water electrolysis. This work demonstrates that R. opacus DSM 43205 can be engineered to produce chemicals from CO₂ and provides a base for its further metabolic engineering.

Synthetic spatial patterning in bacteria: advances based on novel diffusible signals

Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.

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.

Escherichia coli as a platform microbial host for systems metabolic engineering

Bio-based production of industrially important chemicals and materials from non-edible and renewable biomass has become increasingly important to resolve the urgent worldwide issues including climate change. Also, bio-based production, instead of chemical synthesis, of food ingredients and natural products has gained ever increasing interest for health benefits. Systems metabolic engineering allows more efficient development of microbial cell factories capable of sustainable, green, and human-friendly production of diverse chemicals and materials. Escherichia coli is unarguably the most widely employed host strain for the bio-based production of chemicals and materials. In the present paper, we review the tools and strategies employed for systems metabolic engineering of E. coli. Next, representative examples and strategies for the production of chemicals including biofuels, bulk and specialty chemicals, and natural products are discussed, followed by discussion on materials including polyhydroxyalkanoates (PHAs), proteins, and nanomaterials. Lastly, future perspectives and challenges remaining for systems metabolic engineering of E. coli are discussed.

Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant

The C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene when glucose is used as a renewable carbon source via biological processes. In this study, we construct an artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway together with tailored ferulic acid decarboxylase mutations. The rational design of the substrate-binding site of the enzyme by computational simulations improves ccMA decarboxylation and thus 1,3-butadiene production. We find that changing dissolved oxygen (DO) levels and controlling the pH are important factors for 1,3-butadiene production. Using DO-stat fed-batch fermentation, we produce 2.13 ± 0.17 g L-1 1,3-butadiene. The results indicate that we can produce unnatural/nonbiological compounds from glucose as a renewable carbon source via a rational enzyme design strategy.

A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli

Acrylic acid is a value-added chemical used in industry to produce diapers, coatings, paints, and adhesives, among many others. Due to its economic importance, there is currently a need for new and sustainable ways to synthesise it. Recently, the focus has been laid in the use of Escherichia coli to express the full bio-based pathway using 3-hydroxypropionate as an intermediary through three distinct pathways (glycerol, malonyl-CoA, and β-alanine). Hence, the goals of this work were to use COPASI software to assess which of the three pathways has a higher potential for industrial-scale production, from either glucose or glycerol, and identify potential targets to improve the biosynthetic pathways yields. When compared to the available literature, the models developed during this work successfully predict the production of 3-hydroxypropionate, using glycerol as carbon source in the glycerol pathway, and using glucose as a carbon source in the malonyl-CoA and β-alanine pathways. Finally, this work allowed to identify four potential over-expression targets (glycerol-3-phosphate dehydrogenase (G3pD), acetyl-CoA carboxylase (AccC), aspartate aminotransferase (AspAT), and aspartate carboxylase (AspC)) that should, theoretically, result in higher AA yields.

Microbial engineering for the production of C2-C6 organic acids

Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C₂-C₆ organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.

Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly

Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.