Biotechnology for a circular economy

The utilization of one-carbon assimilation pathways for bioproduction represents a promising direction towards a more sustainable bio-based economy. Here, the authors compare the thermodynamic efficiencies and energy demand of C1-assimilation pathways and discuss their implementation for energy, material, and food production.

Using one carbon (C1) molecules as primary feedstock for bioproduction holds great potential for a circular and carbon neutral economy. Here, the authors discuss the potential of merging knowledge gained from natural and synthetic C1-trophic organisms to expedite the development of efficient C1-based biomanufacturing.

There are several pathways for CO₂ fixation in photoautotrophic and chemoautotrophic microorganisms. Here, the authors provide experimental demonstration for the operation of the reductive glycine pathway in a natural microorganism, Desulfovibrio desulfuricans.

Methylotrophic metabolism enables growth on methanol, an alternative to sugar fermentation. Here the authors use adaptive laboratory evolution to uncover native methylotrophy capacity in Saccharomyces cerevisiae.

Microalgae used for CO₂ removal in an industrial exhaust gas stream usually has low CO₂ tolerance. Here, the authors increase CO₂ tolerance by expressing a single H + -pump and enable microalgal valorization of industrial flue gas.

Using one carbon compounds as feedstock is a promising approach in abating climate change. Here, the authors report the conversion of E. coli into a synthetic methylotroph that assimilates methanol via the ribulose monophosphate cycle and a set of distinctive mutations.

Concentrating CO₂ around Rubisco is critical to improve photosynthetic efficiency for biomass yield. Here, the authors report the self-assembly of metal-organic frameworks (MOFs) on the surface of green alga Chlorella pyrenoidosa to enhance the photosynthetic carbon fixation.

An attractive route for carbon-negative synthesis of biochemical products is the reverse β-oxidation pathway coupled to the Wood-Ljungdahl pathway. Here the authors use a high-throughput in vitro prototyping workflow to screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity.

Wang et al. improve the methanol tolerance for the synthetic methylotroph, Corynebacterium glutamicum. They generate 3 new strains by directed evolution and use biochemical, transcriptomic, and genetic approaches to characterize the pathways underlying the enhanced methanol metabolism. Their findings are important for biomanufacturing purposes.

Włodarczyk et al. discover that cyanobacterium Synechococcus sp. PCC 11901 accumulates three times more biomass than other cyanobacterial strains in the same conditions. An engineered version of this strain also produces as much free fatty acid as other commonly used heterotrophic microorganisms, suggesting its utility for the sustainable production of carbon-based molecules.

Engineering microbial cell factories for the production of useful plant natural products (PNPs) is a resource-conserving and environmentally-friendly synthesis route. Here, the authors review recent developments that enable engineering of hosts, pathways, and enzymes to make PNPs and PNP derivatives.

Yeasts, Saccharomyces cerevisiae and Pichia pastoris, are promising chassis for the production of nature products (NPs). Here, the author discusses establishing a comprehensive platform for sustainable production of NPs via system-associated optimization at genetics, temporal controllers, productivity screening, and scalability levels.

Biotechnology is emerging as a promising approach to increase resilience, flexibility, and efficiency of space missions. In this Perspective, the authors outline design-scenarios and provide a techno-economic analysis of their deployment.

Despite the advances in engineered living materials (ELMs), the diversity of ELMs especially those that are capable of autonomous self-fabrication and regeneration, is low. Here, the authors engineer a resilient ELM biocomposite using Bacillus subtilis and secreted EutM proteins as selfassembling scaffold building blocks.

Industrial sugarcane ethanol fermentations are accomplished by a microbial community dominated by S. cerevisiae and co-occurring bacteria. Here, the authors investigate how microbial community composition contributes to community function and reveal the role of acetaldehyde in improving yeast growth rate and ethanol production.

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.

Establishing methods to access the chemical space that lies beyond canonical terpenoid biosynthesis will increase the applications of isoprenoids. Here, the authors reconstruct the modular structure of terpene biosynthesis on 16-carbon backbones by engineered yeast and synthesize 28 different unique terpenes.

The top down cheminformatics method is usually used for the reconstitution of heterologous pathway to produce plant natural products. Here, the authors report a bottom up computational workflow for the identification of potential products and the enzymes required to make them in a noscapine pathway in yeast.

Corynebacterium glutamicum is a major workhorse in industrial biomanufacturing of amino acids. Here, the authors employ CRISPR-assisted rational flux-tuning and CRISPRi screening of a L-proline exporter to covert a wild-type C. glutamicum to a hyperproducer of L-proline.

Chondroitin sulfate (CS) is a type of sulfated glycosaminoglycan that is manufactured by extraction from animal tissues for the treatment of osteoarthritis and in drug delivery applications. Here, the authors report the development of single microbial cell factories capable of compete, one-step biosynthesis of animal-free CS production in E. coli.

Using CRISPR/Cas9 technology and Golden Gate Assembly, a toolkit including 147 plasmids and 137 promoters enables chromosomal integration of markerless DNA and easy assembly of new gRNAs, effectively proven in a novel Y. lipolytica production strain.

Arabinose-inducible artificial transcription factors were developed using CRISPR/dCas9 and plant-derived transcription factors for orthogonal gene expression in Salmonella and E. coli.

While tricarboxylic acid cycle (TCA cycle) is required for heterotrophic microbes, it reduces carbon yield of industrial products due to the release of excess CO2. Here, the authors construct an E. coli strain without a functional TCA cycle and demonstrate its feasibility as a chassis strain for production of four separate compounds.

Lignin conversion to higher value products is essential to the economic viability of lignocellulosic biorefineries. Here, the authors demonstrate the bioconversion of alkali pretreated lignin to itaconic acid by dynamic two stage fermentation using a signal-amplified nitrogen-limitation biosensor.

The crucial first step in the biodegradation of polyethylene plastic is oxidation of the polymer. This has traditionally required abiotic pre-treatment, but now Bertocchini and colleagues report two wax worm enzymes capable of catalyzing this oxidation and subsequent degradation at room temperature.

Cellulosic hydrolysates contain substantial amounts of acetate, which is toxic to fermenting microorganisms. Here, the authors engineer Baker’s yeast to co-consume xylose and acetate for triacetic acid lactone production from a hemicellulose hydrolysate of switchgrass.

Muconic acid is a platform chemical with wide industrial applicability. Here, the authors report efficient muconate production from glucose and xylose by engineered Pseudomonas putida strain using adaptive laboratory evolution, metabolic modeling, and rational strain engineering strategies.

The degradation of PET using PETase enzymes has great potential but can face problems with incomplete degradation. Here, the authors identified two BHETases from the environment and engineered them to improve their hydrolysis efficiency for applications in dual-enzyme PET recycling and tandem chemical-enzymatic PET upcycling systems.

Microbial degradation of polyvinyl chloride (PVC) has previously been reported, but little is known about the degrading strains and enzymes. Here, Zhe et al. isolate a PVC-degrading bacterium from the gut of insect larvae and shed light on the PVC degradation pathway using a multi-omic approach.

Polyehylene terephthalate (PET) biodegradation is greatly improved when recombinant IsPETase is expressed in Pichia pastoris and the enzyme’s partial removal of N-terminal glycosylation, retaining high thermostability.

Marine ecosystems are dominated by microbial communities. Inspired by the photoelectric conversion feature of the marine ecosystems, the authors design a four-species microbial community to mimic primary producer, primary degrader, and ultimate consumers, and show its ability to convert light into electricity for over one month.

Growth limitation caused by mutual shading and the high harvest cost hamper algal biofuel production. Here, the authors overcome these two problems by designing a semi-continuous algal cultivation system and an aggregation-based sedimentation strategy to achieve high levels production of biomass and limonene.

The low extracellular electron transfer activity hampers the application of cyanobacteria in biophotovoltaics. Here, the authors report an order-of-magnitude enhancement in photocurrent generation of the cyanobacterium by deprivation of the outer cell membrane.

Product toxicity is one of the factors that hinder biofuel production. Here, the authors engineer the actin cytoskeleton to increase cell growth and production of n-butanol and medium-chain fatty acids in Saccharomyces cerevisiae.

Kato et al. describe the isolation of a mutant Chlamydomonas sp. KOR1 that accumulates lipid even during diurnal cycles and has extensive mutations in the ISA1 gene encoding a starch debranching enzyme (DBE). They further demonstrate that disruption of DBE can improve biofuel production under light/dark conditions, through accelerated carbohydrate repartitioning into lipid and carotenoid.

Synechococcus elongatus PCC 7942 was modified to import and use monosaccharides, which allows it to grow on lignocellulosic lysate and produce 2,3-butanediol.