Coutilization of glucose and acetate for the production of pyruvate by engineered Escherichia coli

Alternate routes to acetate tolerance lead to varied isoprenol production from mixed carbon sources in Pseudomonas putida

Lignocellulose is a renewable resource for the production of a diverse array of platform chemicals, including the biofuel isoprenol. Although this carbon stream provides a rich source of sugars, other organic compounds, such as acetate, can be used by microbial hosts. Here, we examined the growth and isoprenol production in a Pseudomonas putida strain pre-tolerized ("PT") background where its native isoprenol catabolism pathway is deleted, using glucose and acetate as carbon sources. We found that PT displays impaired growth in minimal medium containing acetate and often fails to grow in glucose-acetate medium. Using a mutant recovery-based approach, we generated tolerized strains that overcame these limitations, achieving fast growth and isoprenol production in the mixed carbon feed. Changes in the glucose and acetate assimilation routes, including an upregulation in PP_0154 (SpcC, succinyl-CoA:acetate CoA-transferase) and differential expression of the gluconate assimilation pathways, were key for higher isoprenol titers in the tolerized strains, whereas a different set of mechanisms were likely enabling tolerance phenotypes in media containing acetate. Among these, a coproporphyrinogen-III oxidase (HemN) was upregulated across all tolerized strains and in one isolate required for acetate tolerance. Utilizing a defined glucose and acetate mixture ratio reflective of lignocellulosic feedstocks for isoprenol production in P. putida allowed us to obtain insights into the dynamics and challenges unique to dual carbon source utilization that are obscured when studied separately. Together, this enabled the development of a P. putida bioconversion chassis able to use a more complex carbon stream to produce isoprenol.IMPORTANCEAcetate is a relatively abundant component of many lignocellulosic carbon streams and has the potential to be used together with sugars, especially in microbes with versatile catabolism such as P. putida. However, the use of mixed carbon streams necessitates additional optimization. Furthermore, the use of P. putida for the production of the biofuel target, isoprenol, requires the use of engineered strains that have additional growth and production constraints when cultivated in acetate and glucose mixtures. In this study, we generate acetate-tolerant P. putida strains that overcome these challenges and examine their ability to produce isoprenol. We show that acetate tolerance and isoprenol production, although independent phenotypes, can both be optimized in a given P. putida strain. Using proteomics and whole genome sequencing, we examine the molecular basis of both phenotypes and show that tolerance to acetate can occur via alternate routes and result in different impacts on isoprenol production.

Newly isolated halotolerant Gordonia terrae S-LD serves as a microbial cell factory for the bioconversion of used soybean oil into polyhydroxybutyrate

Polyhydroxybutyrate (PHB) is a class of biodegradable polymers generally used by prokaryotes as carbon sources and for energy storage. This study explored the feasibility of repurposing used soybean oil (USO) as a cost-effective carbon substrate for the production of PHB by the strain Gordonia terrae S-LD, marking the first report on PHB biosynthesis by this rare actinomycete species. This strain can grow under a broad range of temperatures (25-40 ℃), initial pH values (4-10), and salt concentrations (0-7%). The findings indicate that this strain can synthesize PHB at a level of 2.63 ± 0.6 g/L in a waste-containing medium containing 3% NaCl within a 3 L triangular flask, accounting for 66.97% of the cell dry weight. Furthermore, 1H NMR, 13C NMR, and GC-MS results confirmed that the polymer was PHB. The thermal properties of PHB, including its melting (Tm) and crystallization (Tc) temperatures of 176.34 °C and 56.12 °C respectively, were determined via differential scanning calorimetry analysis. The produced PHB was characterized by a weight-average molecular weight (Mw) of 5.43 × 105 g/mol, a number-average molecular weight (Mn) of 4.00 × 105 g/mol, and a polydispersity index (PDI) of 1.36. In addition, the whole genome was sequenced, and the PHB biosynthetic pathway and quantitative expression of key genes were delineated in the novel isolated strain. In conclusion, this research introduces the first instance of polyhydroxyalkanoate (PHA) production by Gordonia terrae using used soybean oil as the exclusive carbon source, which will enrich strain resources for future PHB biosynthesis.

Enhancing D-pantothenate production in Escherichia coli through multiplex combinatorial strategies

D-pantothenate, universally acknowledged as vitamin B5, has garnered considerable interest owing to its crucial functionality in the feed, pharmaceutical, and cosmeceutical sectors. Development of microbial strains for D-pantothenate hyperproducer has emerged as a prominent research direction in recent years. Herein, we converted an engineered Escherichia coli with low yield to a plasmid-free hyperproducer of D-pantothenate using multiplex combinatorial strategies. First, an initial strain was obtained through prolonging the cell lifespan. To promote the accumulation of D-pantothenic acid, the supply of cofactors was adaptively enhanced. Additionally, the heterologous gene panE from Pseudomonas aeruginosa, which encodes ketopantoate reductase (EC 1.1.1.169) catalyzing the synthesis of d-pantoate from α-ketopantoate, was screened and integrated into the chromosome. Subsequently, a strategy of acetate recycling and NOG pathway reconstruction were introduced and successfully to improve the D-pantothenate titer to 5.48 g/L. Additionally, we screened the regulatory factors and optimized its second codon to further increase the DPA yield of the engineered strains to 6.02 g/L in shake flask. The final engineered strain DS6 could efficiently produce 72.40 g/L D-pantothenate, which is 3.18-fold higher than the original strain. This study proposed a novel multiplex combination strategy for developing microbial cell factory of D-pantothenate, which was beneficial for the advancement of efficient D-pantothenate production.

Metabolic analyses of Yarrowia lipolytica for biopolymer production reveals roadblocks and strategies for microbial utilizing volatile fatty acids as sustainable feedstocks

This study quantifies metabolic features of engineered Yarrowia lipolytica strains for converting volatile fatty acids (VFAs) into poly-3-hydroxybutyrate (PHB) via 13C-metabolic flux analysis and RNA-Seq. Yarrowia lipolytica is unable to grow with C4 ∼ C6 VFAs due to substrate toxicity, while propionate (C3) metabolism leads to slow growth and minimal PHB production due to enzymatic limitations in substrate assimilation pathways. Acetate is a viable but challenging VFA feedstock. Comparing to glucose, acetate catabolism results in low ATP/ADP ratios, high enzyme usage, substantial CO2 release (>50 % of input carbon), and limited NADPH. Several strategies may overcome these roadblocks: 1) glucose-VFA co-catabolism improves energy charge, alleviates metabolic imbalances, reduces flux rigidity, and lowers the enzyme expression burden; 2) overexpressing acetyl-CoA synthetase and nitrogen limitation increase acetate uptake and PHB synthesis during glucose-acetate co-utilization; and 3) repression of oxidase facilitates fluxes towards PHB synthesis. The results provide insights into efficient utilization of acetate as feedstock.

Poly-3-hydroxybutyrate production from acetate by recombinant Pseudomonas stutzeri with blocked L-leucine catabolism and enhanced growth in acetate

Acetate is a low-cost feedstock for the production of different bio-chemicals. Electrochemical reduction of CO2 into acetate and subsequent acetate fermentation is a promising method for transforming CO2 into value-added chemicals. However, the significant inhibitory effect of acetate on microbial growth remains a barrier for acetate-based biorefinery. In this study, the deletion of genes involved in L-leucine degradation was found to be beneficial for the growth of Pseudomonas stutzeri A1501 in acetate. P. stutzeri (Δpst_3217), in which the hydroxymethylglutaryl-CoA lyase catalyzing β-hydroxy-β-methylglutaryl-CoA into acetyl-CoA and acetoacetate was deleted, grew faster than other mutants and exhibited increased tolerance to acetate. Then, the genes phbCAB from Ralstonia eutropha H16 for poly-3-hydroxybutyrate (PHB) biosynthesis were overexpressed in P. stutzeri (∆pst_3217) and the recombinant strain P. stutzeri (∆pst_3217-phbCAB) can accumulate 0.11 g L-1 PHB from commercial acetate. Importantly, P. stutzeri (∆pst_3217-phbCAB) can also use CO2-derived acetate to produce PHB and the accumulated PHB accounted for 5.42% (w/w) of dried cell weight of P. stutzeri (∆pst_3217-phbCAB).

RETRACTED: Ascertaining the Influence of Lacto-Fermentation on Changes in Bovine Colostrum Amino and Fatty Acid Profiles

The aim of this study was to collect samples of bovine colostrum (BCOL) from different sources (agricultural companies A, B, C, D and E) in Lithuania and to ascertain the influence of lacto-fermentation with Lactiplantibacillus plantarum strain 135 and Lacticaseibacillus paracasei strain 244 on the changes in bovine colostrum amino (AA), biogenic amine (BA), and fatty acid (FA) profiles. It was established that the source of the bovine colostrum, the used LAB, and their interaction had significant effects (p < 0.05) on AA contents; lactic acid bacteria (LAB) used for fermentation was a significant factor for aspartic acid, threonine, glycine, alanine, methionine, phenylalanine, lysine, histidine, and tyrosine; and these factor's interaction is significant on most of the detected AA concentrations. Total BA content showed significant correlations with glutamic acid, serine, aspartic acid, valine, methionine, phenylalanine, histidine, and gamma amino-butyric acid content in bovine colostrum. Despite the differences in individual FA contents in bovine colostrum, significant differences were not found in total saturated (SFA), monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids. Finally, the utilization of bovine colostrum proved to be challenging because of the variability on its composition. These results suggest that processing bovine colostrum into value-added formulations for human consumption requires the adjustment of its composition since the primary production stage. Consequently, animal rearing should be considered in the employed bovine colostrum processing technologies.

Label-free quantitative proteomics reveals the potential mechanisms of insoluble dietary fiber from okara in improving hepatic lipid metabolism of high-fat diet-induced mice

The high purity insoluble dietary fiber (IDF) from okara is a natural component with a potentially positive effect on a high-fat diet (HFD)-induced hepatic metabolic disorders, although its regulatory mechanism remains unclear. This study aims to elucidate the potential pathways and key proteins of IDF for the amelioration of hepatic lipid metabolism in mice fed with HFD. Here, we used label-free quantitative proteomics technology to quantity and identify differentially expressed proteins in the liver that are associated with IDF treatment. The differentially expressed proteins were assessed by GO annotation and KEGG pathways. Western blot and qRT-PCR analyses were conducted to validate the potential targets regulated by IDF. In total, 73 differentially expressed proteins were identified, of which 27 were up-regulated (FC > 1.5) and 46 were down-regulated (FC < 0.667). GO analysis suggested that differentially expressed proteins were mainly located in the cell and organelles, regulated biological processes, and were associated with enzyme activity and molecular binding. The KEGG pathway enrichment analysis further demonstrated glycolysis/gluconeogenesis, pyruvate metabolism, TCA cycle, arginine biosynthesis, alanine, aspartate and glutamate metabolism, and retinol metabolism were affected. The combination of proteomics, Western blot, and qRT-PCR suggested that ACS, ACLY, GOT1, GLS2, NAGS, CYP4A10, CYP3A25, and CYP2A5 in these pathways might be key proteins for IDF intervention. Taken together, our findings elucidate new mechanisms involved in how IDF affects hepatic metabolism, provide important information for the functional food industries, and improve the added value of okara. SIGNIFICANCE: Okara is evidenced as a high-quality by-product with several nutritional components, especially dietary fiber (50-60%) labeled as "The Seventh Nutrient". Previous studies have shown that IDF has a positive potential effect on a high-fat diet (HFD)-induced hepatic metabolic disorders, but its molecular mechanism remains unclear. To elucidate the therapeutic mechanism of IDF at the protein level, a label-free quantitative proteomic analysis was used to identify the dynamic changes of the liver proteome between HIDF and HFD groups in this study. These results provide a new perspective for exploring the therapeutic mechanism of IDF at the protein level and enlightenment for promoting the comprehensive utilization of okara.

High production of poly(3-hydroxybutyrate) in Escherichia coli using crude glycerol

Poly(3-hydroxybutyrate) (PHB) is a prominent bio-plastic and recognized as the potential replacement of petroleum-derived plastics. To make PHB cost-effective, the production scheme based on crude glycerol was developed using Escherichia coli. The heterogeneous synthesis pathway of PHB was introduced into the E. coli strain capable of efficiently utilizing glycerol. The central metabolism that links to the synthesis of acetyl-CoA and NADPH was further reprogrammed to improve the PHB production. Key genes were targeted for manipulation, involving those in glycolysis, the pentose phosphate pathway, and the tricarboxylic cycle. As a result, the engineered strain gained a 22-fold increase in the PHB titer. Finally, the fed-batch fermentation was conducted with the producer strain to give the PHB titer, content, and productivity reaching 36.3±3.0 g/L, 66.5±2.8%, and 1.2±0.1 g/L/h, respectively. The PHB yield on crude glycerol accounts for 0.3 g/g. The result indicates that the technology platform as developed is promising for the production of bio-plastics.

Metabolic engineering using acetate as a promising building block for the production of bio-based chemicals

The production of biofuels and biochemicals derived from microbial fermentation has received a lot of attention and interest in light of concerns about the depletion of fossil fuel resources and climatic degeneration. However, the economic viability of feedstocks for biological conversion remains a barrier, urging researchers to develop renewable and sustainable low-cost carbon sources for future bioindustries. Owing to the numerous advantages, acetate has been regarded as a promising feedstock targeting the production of acetyl-CoA-derived chemicals. This review aims to highlight the potential of acetate as a building block in industrial biotechnology for the production of bio-based chemicals with metabolic engineering. Different alternative approaches and routes comprised of lignocellulosic biomass, waste streams, and C1 gas for acetate generation are briefly described and evaluated. Then, a thorough explanation of the metabolic pathway for biotechnological acetate conversion, cellular transport, and toxin tolerance is described. Particularly, current developments in metabolic engineering of the manufacture of biochemicals from acetate are summarized in detail, with various microbial cell factories and strategies proposed to improve acetate assimilation and enhance product formation. Challenges and future development for acetate generation and assimilation as well as chemicals production from acetate is eventually shown. This review provides an overview of the current status of acetate utilization and proves the great potential of acetate with metabolic engineering in industrial biotechnology.