Articles (30)


17 June 2024

Cytosine Deaminase-Assisted Mutator for Genome Evolution in Cupriavidus necator

Cupriavidus necator H16 has been intensively explored for its potential as a versatile microbial cell factory, especially for its CO2 fixation capability over the past few decades. However, rational metabolic engineering remains challenging in the construction of microbial cell factories with complex phenotypes due to the limited understanding of its metabolic regulatory network. To overcome this obstacle, laboratory adaptive evolution emerges as an alternative. In the present study, CAM (cytosine deaminase-assisted mutator) was established for the genome evolution of C. necator, addressing the issue of low mutation rates. By fusing cytosine deaminase with single-stranded binding proteins, CAM introduced genome-wide C-to-T mutations during DNA replication. This innovative approach could boost mutation rates, thereby expediting laboratory adaptive evolution. The applications of CAM were demonstrated in improving cell factory robustness and substrate utilization, with H2O2 resistance and ethylene glycol utilization as illustrative case studies. This genetic tool not only facilitates the development of efficient cell factories but also opens avenues for exploring the intricate phenotype-genotype relationships in C. necator.

Haojie Pan
Zhijiao Wang
Jiazhang Lian*


24 May 2024

Current Progress on Microbial l-malic Acid Production

As an important intermediate in the tricarboxylic acid (TCA) cycle, l-malic acid (l-MA) is also one of the 12 important platform bulk chemicals with high added value. Owing to its various applications in food, pharmaceuticals, cosmetics and industry, the global l-MA market size is growing year by year. Over the last few decades, increasing concerns regarding fossil fuels depletion and excessive CO2 emissions have led the global commitment to fostering a green economy and sustainable development. Alternatively, the sustainable microbial fermentation of l-MA has gradually attracted more and more attention. Here, this review summarizes the common l-MA biosynthesis pathways and compares the differences between different chassis microorganisms as well. Moreover, regulation strategies of genetic metabolic engineering and fermentation process to boost the l-MA production are summarized, and the research status of l-MA production from the cheaper substrates is also discussed. Finally, the direction of further exploration of industrialized l-MA biosynthesis is proposed, which provides a theoretical guidance on promoting technological innovation in industrial l-MA production.

Lu Mou
Min Qiu
Wankui Jiang
Wenming Zhang
Fengxue Xin
Yujia Jiang*
Min Jiang*


20 May 2024

Advancements in the Bio-degradation of Plastic Waste into Value-added Chemicals: A Recent Perspective

Plastics are an essential component of modern life, but the plastic waste has caused significant environmental pollution and economic losses. The effective solution to these problems is the biodegradation and high-value conversion of plastic waste. After biodegradation, plastic waste is broken into smaller molecules and eventually transformed into innocuous substances like water, carbon dioxide and biomass. High-value conversion enables plastic waste to be converted into products with higher economic value and environmental friendliness. Based on this, we summarize the biodegradation methods of bioplastics and analyze the shortage of these methods. Subsequently, we summarize the progress of converting the degradation products into value-added chemicals, comprehensively analyze the advantages and disadvantages of these bioconversion process, and propose some strategies to address these disadvantages. Finally, we analyze the significance of establishing a microbial-based conversion process that integrates the degradation and the conversion, and propose some potential strategies.

Mingda  Li
Zhenya  Chen*
Yi-Xin  Huo


13 May 2024

Expression of Redox Partner Fusions for Light Driven Cytochrome P450s in the Cyanobacterium Synechocystis sp. PCC. 6803

Cytochrome P450s (P450s) catalyze stereo- and regioselective monooxygenations in the biosynthesis of a wide range of valuable natural compounds. The turnover of P450s requires dedicated electron transfer, usually via a NADPH-dependent reductase. The need for an NADPH-dependent reductase can be circumvented if expressed in photosynthetic organisms by exploiting the photosynthetic reducing power. However, partitioning reducing equivalents towards the P450s needs further optimization. Using our model P450, SbCYP79A1, we have previously shown that by targeting this P450 to the thylakoid membrane, the P450 can obtain its reducing power directly from photosystem I via soluble ferredoxin. Furthermore, we demonstrated using transient expression that fusing a soluble electron carrier to this P450 improves electron partitioning towards the P450 in tobacco. In order to characterize these fusions in a stably transformed organism, we expressed three different redox partner fusions in the cyanobacterium Synechocystis sp. PCC. 6803. We show that biochemical trends observed in the tobacco system are recapitulated in stably transformed Synechocystis sp. PCC. 6803. Overall, the FMN binding domain fusion produces the most oxime per unit of enzyme with and without the presence of the endogenous competing electron sink FNR and NADP+. However, the overall yield of oxime is comparable to the other strains, due to poor steady state levels of the fusion protein. Synechocystis sp. PCC. strains expressing the P450-FMN fusion also display a chlorotic phenotype that can be rescued by switching the nitrogen source from nitrate to ammonia, implying impaired nitrate assimilation. Optimizing electron transport towards the P450 is indeed possible in vivo but also highlights interference with native metabolic processes.

Lawrence  Sutardja
Silas Busck  Mellor
Nadia Dodge
Annemarie  Matthes
Meike  Burow
Agnieszka  ZygadloNielsen
Poul Erik  Jensen*


08 April 2024

Tolerance in Solventogenic Clostridia for Enhanced Butanol Production: Genetic Mechanisms and Recent Strain Engineering Advances

Biobutanol is a promising candidate for replacing fossil fuels due to its superior properties compared to ethanol. Solventogenic clostridia can naturally produce biobutanol among other valuable chemicals. Lignocellulosic material stands out as a promising source for biobutanol production, avoiding competition with food production and making use of residues from both agroindustry and forestry activities. However, Clostridium strains are subject to different chemical stressors, including oxygen, self-product inhibition, inhibitors generated during biomass pretreatment and hydrolysis, and others. Recent advances in genetic engineering tools have enabled the metabolic engineering of Clostridium strains to increase their robustness and tolerance to these stressors. This review provides a summary of the various types of inhibitors, the genetic mechanisms related to tolerance, and recent strain engineering efforts for tolerance enhancement. In addition, we offer a valuable perspective on the future research directions in this area.

Pablo  Jiménez-Bonilla
Shangjun  Wang
Tyler  Whitfield
David  Blersch
Yifen  Wang
Luz-Estela  Gonzalez-de-Bashan
Wei  Luo
Yi  Wang*


25 March 2024

Proteomic Analysis of Pleurotus ostreatus Grown on Glucose and Xylose Mixtures in Submerged Fermentation Provides Insights into Differentiated Mycelial Composition

Pleurotus ostreatus, an edible white-rot fungus of great commercial and nutritional value, grows by metabolizing mainly glucose and xylose, the two major sugars in lignocellulosic biomass. In this study, a comparative proteomic analysis of P. ostreatus grown in submerged fermentation on a medium with glucose, xylose and mixtures of them as carbon sources was conducted. In the same conditions, the metabolic response of the fungus was evaluated in the production of the main nutritional components of the fungus such as proteins, lipids, and intracellular and extracellular polysaccharides. The proteomic analysis revealed that glucose and xylose upregulate different clusters of proteins. Glucose mainly up-regulates macromolecule metabolic processes, translation and glycolysis whereas xylose up-regulates, small molecule metabolic processes and tricarboxylic acid cycle (TCA). The mixtures show mostly similarities with the proteome response to glucose, although there are differential responses depending on xylose concentration. The carbon source type found to affect the basic macromolecule metabolic processes, with amino acids biosynthesis to differentiate mostly. An analysis of the upregulated proteins through the STRING database revealed that xylose upregulates mostly proteins related to amino acid biosynthesis. Leucine, Valine and Isoleucine biosynthesis pathways were found to be the most triggered pathway. All the branched-chain amino acids (BCAAs)-related enzymes intensities were gradually increased when xylose concentration was increased in the growth medium. BCAAs play an important role in the human diet so the enhancement of BCAAs biosynthesis pathway for P. ostreatus could convert it to a very remarkable protein substitute in human diet. These findings provide new insights into the proteomic and metabolic response of the fungus to the major sugars of lignocellulosic biomass, which are not well understood until now. 

Georgios Bakratsas
Martina  Samiotaki
Petros Katapodis*
Haralambos  Stamatis


22 March 2024

Modulation of the MEP Pathway for Overproduction of 13-R-manoyl Oxide in Cyanobacteria

The cyanobacterium Synechocystis sp. PCC 6803 has gained scientific interest for its potential to use solar energy and atmospheric CO2 for the production of high-value chemicals like pharmaceuticals, flavors, and fragrances. Forskolin is a diterpenoid found in the root cork of the plant Plectranthus barbatus and its biosynthetic pathway is initiated by two terpene synthases that convert geranylgeranyl diphosphate (GGDP) into the precursor 13-R-manoyl oxide (13-R-MO). Using the cyanobacterium Synechocystis sp. PCC 6803 as host, we expressed the two terpene synthases resulting in the synthesis of 0.83 mg/L 13-R-MO. Three different geranylgeranyl diphosphate synthases (GGDPSs) were selected for screening; a prokaryotic (Synechococcus sp. JA-3-3Ab (Sj)), a yeast (Saccharomyces cerevisiae (Sc)), and a plant (P. barbatus (Pb)) derived GGDPS. Strains containing the prokaryotic Sj- or the yeast ScGGDPS consistently yielded more 13-R-MO than the base strain. By overexpression of 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) positioned at the entry of the 2-C-methyl-d-erythritol 4-phosphate pathway (MEP) together with the prokaryotic SjGGDPS, the 13-R-MO titer was increased 11-fold to reach 9.7 mg/L by boosting the synthesis of GGDP, the direct substrate for the diterpenoid synthases. We further show that application of a n-dodecane overlay to remove 13-R-MO from the culture medium provided a 2–3 fold increase of the 13-R-MO in a separate cultivation system.

Lawrence Chuk  Sutardja
Nadia  Dodge
Sandra Lambert  Walby
Nicholas Jeffrey  Butler
Thiyagarajan  Gnanasekaran
Birger Lindberg  Møller
Poul Erik  Jensen*


21 February 2024

One-pot Multi-enzyme Cascade Synthesis of Bifunctional Compounds from Vegetable Oils

Green and efficient biocatalytic technology has become a complementary or alternative means of organic synthesis. Chemicals with two functional groups, such as α,ω-dicarboxylic acids, ω-amino fatty acids and ω-hydroxy fatty acids, are widely used in the synthesis of polymers such as polyesters and polyamides. In recent years, the production of biodegradable materials using renewable and abundant vegetable oils as green raw materials has attracted increasing attention, receiving an additional impetus from synthetic biology. This paper presents the recent research progress in the production of bifunctional chemicals with medium chain lengths of C8–C12 using multi-enzyme cascades. Recent studies have developed multilevel optimization strategies to improve the efficiency, economics, and sustainability of multi-enzyme cascades. Cofactor regeneration strategies were developed to avoid large additions of expensive coenzymes. Protein engineering strategies were applied to improve enzyme stability and catalytic performance. In addition, blocking the β-oxidation pathway, improving the efficiency of substrate transport across membranes and increasing cellular robustness are effective optimization strategies for whole-cell catalytic systems. In addition, we discuss the development prospects of producing high value-added fine chemicals from vegetable oils using one-pot multi-enzyme reaction systems.

Xiaoxia Gao
Ran Lu
Yueyue Zhou
Lu Lin*
Xiao-Jun Ji*


13 February 2024

Development and Perspective of Production of Terpenoids in Yeast

Terpenoids are a large class of secondary metabolites known for their remarkable diverse biological activities, making them widely utilized in the pharmaceutical, food, cosmetic, biofuel and agricultural fields. However, the current production of terpenoids heavily relies on plant extraction and chemical synthesis, which brings about concerns regarding infield, environmental and ecological issues. With the advancements in metabolic engineering and emerging synthetic biology tools, it is now possible to sustainably produce these high value-added terpenoids using microbial chassis. Among them, yeast has emerged as a promising candidate for the heterologous biosynthesis of terpenoids due to its inherent advantages, including robustness, safety, and the availability of sufficient precursor. This review focuses on the diverse strategies employed to enable terpenoids production in yeasts. These strategies encompass metabolic engineering approaches to optimize the mevalonate pathway, protein engineering techniques to improve terpenoid biosynthesis, the applications of organelles compartmentalization, high throughput screening and global approaches for the development of efficient cell factories. Furthermore, this review discusses the future prospects and challenges associated with yeast-based terpenoid production, while also emphasizing guidelines for future studies in this field.

Yaying Xia
Congna Li
Ruidi Cao
Lu Qin
Shuobo Shi*


06 February 2024

Bio-Based Production of Uroporphyrin in Escherichia coli

Uroporphyrin (UP) is a porphyrin compound with medical applications and a key precursor for heme biosynthesis. However, there is no biosynthetic strategy for UP production. In this study, we present a novel bioprocess for enhanced production of UP in engineered Escherichia coli. We first implemented the Shemin/C4 pathway heterologously in an E. coli strain with an enlarged intracellular pool of succinyl-CoA. Using a plasmid with the trc promoter regulating the expression of a synthesized gene operon, the effects of key pathway genes, including hemA, hemB, hemC, and hemD, on UP biosynthesis were characterized. By cultivating the resulting engineered E. coli strains in a batch bioreactor with 30 g/L glycerol under aerobic conditions, up to 901.9 mg/L UP was produced. Most of the synthesized UP was extracellularly secreted with a high purity more than 80 wt%, facilitating its downstream purification. The study paves the way for large-scale bio-based production of UP using synthetic biology and metabolic engineering strategies.

Bahareh  Arab
Adam W.  Westbrook
Murray  Moo-Young
Yilan  Liu
C. Perry  Chou*