A unique global metabolic trait of Pseudomonas bharatica CSV86T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids

Metabolic engineering of Pseudomonas bharatica CSV86T to degrade Carbaryl (1-naphthyl-N-methylcarbamate) via the salicylate-catechol route

Pseudomonas bharatica CSV86T displays the unique property of preferential utilization of aromatic compounds over simple carbon sources like glucose and glycerol and their co-metabolism with organic acids. Well-characterized growth conditions, aromatic compound metabolic pathways and their regulation, genome sequence, and advantageous eco-physiological traits (indole acetic acid production, alginate production, fusaric acid resistance, organic sulfur utilization, and siderophore production) make it an ideal host for metabolic engineering. Strain CSV86T was engineered for Carbaryl (1-naphthyl-N-methylcarbamate) degradation via salicylate-catechol route by expression of a Carbaryl hydrolase (CH) and a 1-naphthol 2-hydroxylase (1NH). Additionally, the engineered strain exhibited faster growth on Carbaryl upon expression of the McbT protein (encoded by the mcbT gene, a part of Carbaryl degradation upper operon of Pseudomonas sp. C5pp). Bioinformatic analyses predict McbT to be an outer membrane protein, and Carbaryl-dependent expression suggests its probable role in Carbaryl uptake. Enzyme activity and protein analyses suggested periplasmic localization of CH (carrying transmembrane domain plus signal peptide sequence at the N-terminus) and 1NH, enabling compartmentalization of the pathway. Enzyme activity, whole-cell oxygen uptake, spent media analyses, and qPCR results suggest that the engineered strain preferentially utilizes Carbaryl over glucose. The plasmid-encoded degradation property was stable for 75-90 generations even in the absence of selection pressure (kanamycin or Carbaryl). These results indicate the utility of P. bharatica CSV86T as a potential host for engineering various aromatic compound degradation pathways.IMPORTANCEThe current study describes engineering of Carbaryl metabolic pathway in Pseudomonas bharatica CSV86T. Carbaryl, a naphthalene-derived carbamate pesticide, is known to act as an endocrine disruptor, mutagen, cytotoxin, and carcinogen. Removal of xenobiotics from the environment using bioremediation faces challenges, such as slow degradation rates, instability of the degradation phenotype, and presence of simple carbon sources in the environment. The engineered CSV86-MEC2 overcomes these disadvantages as Carbaryl was degraded preferentially over glucose. Furthermore, the plasmid-borne degradation phenotype is stable, and presence of glucose and organic acids does not repress Carbaryl metabolism in the strain. The study suggests the role of outer membrane protein McbT in Carbaryl transport. This work highlights the suitability of P. bharatica CSV86T as an ideal host for engineering aromatic pollutant degradation pathways.

Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals

Organic pollutants are an increasing threat for wildlife and humans. Managing their removal is however complicated by the difficulties in predicting degradation rates. In this work, we demonstrate that the complexity of the pollutant profile, the set of co-existing contaminants, is a major driver of biodegradation in wastewater. We built representative assemblages out of one to five common pharmaceuticals (caffeine, atenolol, paracetamol, ibuprofen, and enalapril) selected along a gradient of biodegradability. We followed their individual removal by wastewater microbial communities. The presence of multichemical background pollution was essential for the removal of recalcitrant molecules such as ibuprofen. High-order interactions between multiple pollutants drove removal efficiency. We explain these interactions by shifts in the microbiome, with degradable molecules such as paracetamol enriching species and pathways involved in the removal of several organic pollutants. We conclude that pollutants should be treated as part of a complex system, with emerging pollutants potentially showing cascading effects and offering leverage to promote bioremediation.

Halopseudomonas species: Cultivation and molecular genetic tools

The Halopseudomonas species, formerly classified as Pseudomonas pertucinogena lineage, form a unique phylogenetic branch within the Pseudomonads. Most strains have recently been isolated from challenging habitats including oil- or metal-polluted sites, deep sea, and intertidal zones, suggesting innate resilience to physical and chemical stresses. Despite their comparably small genomes, these bacteria synthesise several biomolecules with biotechnological potential and a role in the degradation of anthropogenic pollutants has been suggested for some Halopseudomonads. Until now, these bacteria are not readily amenable to existing cultivation and cloning methods. We addressed these limitations by selecting four Halopseudomonas strains of particular interest, namely H. aestusnigri, H. bauzanensis, H. litoralis, and H. oceani to establish microbiological and molecular genetic methods. We found that C4 -C10 dicarboxylic acids serve as viable carbon sources in both complex and mineral salt cultivation media. We also developed plasmid DNA transfer protocols and assessed vectors with different origins of replication and promoters inducible with isopropyl-β-d-thiogalactopyranoside, l-arabinose, and salicylate. Furthermore, we have demonstrated the simultaneous genomic integration of expression cassettes into one and two attTn7 integration sites. Our results provide a valuable toolbox for constructing robust chassis strains and highlight the biotechnological potential of Halopseudomonas strains.

Development of efficient modules for recombinant protein expression and periplasmic localiszation in Pseudomonas bharatica CSV86T

Escherichia coli has been widely employed as a host for heterologous protein expression. However, due to certain limitations, alternative hosts like Pseudomonas, Lactococcus and Bacillus are being explored. Pseudomonas bharatica CSV86^T, a novel soil isolate, preferentially degrades wide range of aromatics over simple carbon sources like glucose and glycerol. Strain also possesses advantageous eco-physiological traits, making it an ideal host for engineering xenobiotic degradation pathways, which necessitates the development of heterologous expression systems. Based on the efficient growth, short lag-phase and rapid metabolism of naphthalene, Pnah and Psal promoters (regulated by NahR) were selected for expression. Pnah was found to be strong and leaky as compared to Psal, using 1-naphthol 2-hydroxylase (1NH, ∼66 kDa) as reporter gene in strain CSV86^T. The Carbaryl hydrolase (CH, ∼72kDa) from Pseudomonas sp. C5pp was expressed under Pnah in strain CSV86^T and could successfully be translocated to the periplasm due to the presence of the Tmd + Sp sequence. The recombinant CH was purified from the periplasmic fraction and the kinetic characteristics were found to be similar to the native protein from strain C5pp. These results potentiate the suitability of P. bharatica CSV86^T as a desirable host, while Pnah and the Tmd + Sp can be employed for overexpression and periplasmic localisation, respectively. Such tools find application in heterologous protein expression and metabolic engineering applications.

Low-temperature phenol-degrading microbial agent: construction and mechanism

In this study, three cold-tolerant phenol-degrading strains, Pseudomonas veronii Ju-A1 (Ju-A1), Leifsonia naganoensis Ju-A4 (Ju-A4), and Rhodococcus qingshengii Ju-A6 (Ju-A6), were isolated. All three strains can produce cis, cis-muconic acid by ortho-cleavage of catechol at 12 ℃. Response surface methodology (RSM) was used to optimize the proportional composition of low-temperature phenol-degrading microbiota. Degradation of phenol below 160 mg L^-1 by low-temperature phenol-degrading microbiota followed first-order degradation kinetics. When the phenol concentration was greater than 200 mg L^-1, the overall degradation trend was in accordance with the modified Gompertz model. The experiments showed that the microbial agent (three strains of low-temperature phenol-degrading bacteria were fermented separately and constructed in the optimal ratio) could completely degrade 200 mg L^-1 phenol within 36 h. The above construction method is more advantageous in bio-enhanced treatment of actual wastewater. Through the construction of microbial agents to enhance the degradation effect of phenol, it provides a feasible scheme for the biodegradation of phenol wastewater at low temperature and shows good application potential.

Glucose-6-Phosphate Dehydrogenase, ZwfA, a Dual Cofactor-Specific Isozyme Is Predominantly Involved in the Glucose Metabolism of Pseudomonas bharatica CSV86T

Glucose-6-phosphate dehydrogenase (Zwf) is an important enzyme in glucose metabolism via the Entner-Doudoroff pathway and the first enzyme in the oxidative pentose-phosphate pathway. It generates NAD(P)H during the conversion of glucose-6-phosphate (G6P) to 6-phosphogluconolactone, thus aiding in anabolic processes, energy yield, and oxidative stress responses. Pseudomonas bharatica CSV86T preferentially utilized aromatic compounds over glucose and exhibited a significantly lower growth rate on glucose (0.24 h-1) with a prolonged lag phase (~10 h). In strain CSV86T, glucose was metabolized via the intracellular phosphorylative route only because it lacked an oxidative (gluconate and 2-ketogluconate) route. The genome harbored three genes zwfA, zwfB, and zwfC encoding three Zwf isozymes. The present study aimed to understand gene arrangement, gene expression profiling, and molecular and kinetic properties of the purified enzymes to unveil their physiological significance in the strain CSV86T. The zwfA was found to be a part of the zwfA-pgl-eda operon, which was proximal to other glucose transport and metabolic clusters. The zwfB was found to be arranged as a gnd-zwfB operon, while zwfC was present independently. Among the three, zwfA was transcribed maximally, and the purified ZwfA displayed the highest catalytic efficiency, cooperativity with respect to G6P, and dual cofactor specificity. Isozymes ZwfB and ZwfC were NADP+-preferring and NADP+-specific, respectively. Among other functionally characterized Zwfs, ZwfA from strain CSV86T displayed poor catalytic efficiency and the further absence of oxidative routes of glucose metabolism reflected its lower growth rate on glucose compared to P. putida KT2440 and could be probable reasons for the unique carbon source utilization hierarchy. IMPORTANCE Pseudomonas bharatica CSV86T metabolizes glucose exclusively via the intracellular phosphorylative Entner-Doudoroff pathway leading the entire glucose flux through Zwf as the strain lacks oxidative routes. This may lead to limiting the concentration of downstream metabolic intermediates. The strain CSV86T possesses three isoforms of glucose-6-phosphate dehydrogenase, ZwfA, ZwfB, and ZwfC. The expression profile and kinetic properties of purified enzymes will help to understand glucose metabolism. Isozyme ZwfA dominated in terms of expression and displayed cooperativity with dual cofactor specificity. ZwfB preferred NADP+, and ZwfC was NADP+ specific, which may aid in redox cofactor balance. Such beneficial metabolic flexibility facilitated the regulation of metabolic pathways giving survival/fitness advantages in dynamic environments. Additionally, multiple genes allowed the distribution of function among these isoforms where the primary function was allocated to one of the isoforms.