The relevance of enzyme specificity for coenzymes and the presence of 6-phosphogluconate dehydrogenase for polyhydroxyalkanoates production in the metabolism of Pseudomonas sp. LFM046

Dynamic and Static Regulation of Nicotinamide Adenine Dinucleotide Phosphate: Strategies, Challenges, and Future Directions in Metabolic Engineering

Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a crucial cofactor in metabolic networks. The efficient regeneration of NADPH is one of the limiting factors for productivity in biotransformation processes. To date, many metabolic engineering tools and static regulation strategies have been developed to regulate NADPH regeneration. However, traditional static regulation methods often lead to the NADPH/NADP+ imbalance, causing disruptions in cell growth and production. These methods also fail to provide real-time monitoring of intracellular NADP(H) or NADPH/NADP+ levels. In recent years, various biosensors have been developed for the detection, monitoring, and dynamic regulate of the intracellular NADP(H) levels or the NADPH/NADP+ balance. These NADPH-related biosensors are mainly used in the cofactor engineering of bacteria, yeast, and mammalian cells. This review analyzes and summarizes the NADPH metabolic regulation strategies from both static and dynamic perspectives, highlighting current challenges and potential solutions, and discusses future directions for the advanced regulation of the NADPH/NADP+ balance.

Constant fed-batch cultivation with glucose and propionate as co-substrate: A strategy to fine-tune polyhydroxyalkanoates monomeric composition in Pseudomonas spp

Pseudomonas sp. LFM693 is a 2-methylisocitrate lyase (prpB) disrupted mutant. This enzyme catalyzes a step in the 2-methylcitrate cycle, the only known and described pathway for propionate oxidation in this organism. The affected mutants can efficiently produce PHA containing even and odd-chain length hydroxyalkanoates (HAeven/odd) in the presence of propionate and glucose. In this study, a constant fed-batch configuration was utilized to control the composition of PHA and decrease the toxicity of propionate. The incorporation of HAodd into the copolymer was linear, ranging from 7 to approximately 30 %, and correlated directly with the propionate/glucose molar ratio in the feeding solution. This allowed for the molecular composition of the mclPHA to be fine-tuned with minimum process monitoring and control. The average PHA content was 52 % cell dry weight with a molar composition that favored 3-hydroxyalkanoates containing C8, C9, and C10. The conversion factor of propionate to HAodd varied between 0.36 and 0.53 mol·mol-1 (YHAodd/prop.), which are significantly lower than the theoretical maximum efficiency (1.0 mol·mol-1). These results along with the lack of 2-methylisocitrate as a byproduct provides further support for the evidence that the mutant prpB- is still capable of oxidizing propionate.

Oxidation of propionate in Pseudomonas sp. LFM046: Relevance to the synthesis of polyhydroxyalkanoates containing odd-chain length monomers and 2-methylisocitrate

Pseudomonas sp. LFM046 produces polyhydroxyalkanoates of medium-chain length. When carbohydrates are used, only monomers of even-length chains (3HAeven) are generated. Propionate, when used as a co-substrate, enabled the synthesis of odd-chain length monomers, albeit with poor yields (Y3HAodd/prop.) of approx. 10 %. A mini-Tn5 mutant (LFM693) was generated by interrupting the prpB gene, which encodes the 2-methylisocitrate lyase responsible for one step in propionate oxidation via 2-methylcitrate cycle. At low propionate concentrations of 0.1-0.3 g.L-1, LFM693 showed higher Y3HAodd/prop. In contrast, the propionyl incorporation into the polymer was less efficient at high propionate concentrations. The excretion of 2-methylisocitrate partially explained this reduced efficiency. However, mass balances and 13C isotopomer analysis revealed significant propionate oxidation in LFM693 of 21 % and 46 % for propionate concentrations of 0.5 and 1.0 g.L-1, respectively. Experiments using C1-labeled (13C) propionate revealed an alternative propionate oxidation pathway (α-oxidation, β-oxidation, or 3-methylmalate) whose genes are yet to be revealed.

An NADPH-auxotrophic Corynebacterium glutamicum recombinant strain and used it to construct L-leucine high-yielding strain

The NADPH-regeneration enzymes in Corynebacterium glutamicum were inactivated to construct an NADPH-auxotrophic C. glutamicum strain by gene knockout and gene replacement. The resultant NADPH-auxotrophic C. glutamicum XL-1 ΔZMI_Cg::I_Sm (i.e., strain Leu-1) grew well in the basic medium only with gluconate as carbon source. Replacement of the native glyceraldehyde 3-phosphate dehydrogenase (NAD-GapDH_Cg) by NADP-GapDH_Ca from Clostridium acetobutylicum is an effective strategy for producing L-leucine in NADPH-prototrophic strain XL-1 and NADPH-auxotrophic strain Leu-1, whereas the L-leucine yield did not differ significantly between these strains (14.1 ± 1.8 g/L vs 16.2 ± 1.1 g/L). Enhancing the carbon flux in biosynthetic pathway by recombinant expression plasmid pEC-ABNCE promoted L-leucine production, but the shortage NADPH supply limited the L-leucine yield. The mutated promoters of zwf and icd_Cg were introduced into C. glutamicum with NADP-GapDH_Ca and pEC-ABNCE increased L-leucine yield (54.3 ± 2.9 g/L) and improved cell growth (OD₅₆₂ = 83.4 ± 7.5) in fed-batch fermentation because the resultant strain C. glutamicum XL-1 ΔMI_Cg::I_Sm G_Cg::G_Ca P_zwf-D1 P_icd-D2/pEC-ABNCE (i.e., strain Leu-9) exhibited the proper intracellular NADPH and NADH level. This is the first report of constructing an L-leucine high-yielding strain that reasonably supplies NADPH by optimizing the biosynthetic pathway of NADPH from an NADPH-auxotrophic strain.

Combination of biochar and AMF promotes phosphorus utilization by stimulating rhizosphere microbial co-occurrence networks and lipid metabolites of Phragmites

Agricultural biochar and arbuscular mycorrhizal fungi were used to promote the growth of Phragmites in the structural damaged and nutritional imbalanced littoral zone soils. Wheat straw biochar played a significant role in improving soil porosity and supplementing available phosphorus to 79.20 ± 3.20 mg/kg, compared with CK at 17.50 ± 0.88 mg/kg. The addition of Diversispora versiformis improved the plant net photosynthetic rate reaching up to 25.66 ± 0.65 μmol·m^-2·s^-1, which was 36.60 % higher than CK. The combination of biochar and fungi contributed to the whole plant dry weight biomass of 32.30 % and 234.00 % higher than the single biochar or AMF amendment groups, respectively. Meanwhile, the analysis of microbial co-occurrence networks showed the most relevant networks node species were mainly Talaromyces, Chaetomiacea and Gemmatimonadetes etc. Root lipid metabolite of Glycerophospholines further proved that phosphorus utilization was also enhanced endogenously in the rhizosphere soil. These results indicate that the combination of biochar and arbuscular mycorrhizal fungi play synergic role in enhancing phosphorus utilization endogenously and exogenously.

The combined effect of Diversispora versiformis and sodium bentonite contributes on the colonization of Phragmites in cadmium-contaminated soil

To promote the colonization of Phragmites in Cd polluted, nutrient deprived and structural damaged soil, the combined remediation using chemical and microbial modifiers were carried out in potting experiments. The co-application of Diversispora versiformis and sodium bentonite significantly improved the soil structure and phosphorus utilization of the plant, while decreasing the content of cadmium bound by diethylenetriaminepentaacetic acid by 77.72%. As a result, the Phragmites height, tillers, and photosynthetic capacity were increased by 71.60%, 38.37%, and 17.54%, respectively. Further analysis suggested the co-application increased the abundance of phosphorus-releasing microbial communities like Pseudomonassp. and Gemmatimonadetes. Results of rhizosphere metabolites also proved that the signal molecule of lysophosphatidylcholine regulated the phosphorus fixation and utilization by the plant. This work finds composite modifiers are effective in the colonization of Phragmites in Cd contaminated soil by decreasing the bioavailable Cd, increasing the abundance of functional microbial communities and regulating the phosphorus fixation.

Glucose metabolism in Pseudomonas aeruginosa is cyclic when producing Polyhydroxyalkanoates and Rhamnolipids

Pseudomonas aeruginosa is an important chassis for production of polyhydroxyalkanoates (PHA) and rhamnolipids (RHL). Advances in the understanding of the biosynthesis metabolism of these biocompounds are crucial for increasing yield. ¹³C-Metabolic Flux Ratio Analysis (¹³C-MFA) is a technique to estimate in vivo metabolic fluxes ratios. PHA and RHL are essentially non-growth associated products of biotechnological interest and both contain hydroxyalkanoates (HAs), whose labeling patterns could be accessed by GC-MS. In this study, to reveal the relative contributions of the Entner-Doudoroff (ED) pathway and the non-oxidative Pentose Phosphate (PP) pathway to PHA and RHL production, ¹³C-MFA was performed in Pseudomonas aeruginosa LFM634 when supplied with labeled glucose. This bacterial strain lacks both functional EMP and the oxidative PP branch. Labeling patterns in HAs were measured. Experiments with [U-¹³C] glucose indicated a low flux though PP pathway. An optimal design of labeling experiment showed that [6-¹³C] glucose would be the best substrate to enable an estimation of the ED flux with high accuracy. Results of experiments performed with this isotope indicated that about two-thirds of glyceraldehyde 3-phosphate is recycled through a cyclic ED architecture, suggesting that P. aeruginosa utilizes that cycle to regulate the NADPH/Acetyl-CoA ratio for PHA and RHL biosynthesis.