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1.
J Bacteriol ; 206(7): e0013624, 2024 Jul 25.
Article in English | MEDLINE | ID: mdl-38975763

ABSTRACT

Although members of the genus Pseudomonas share specific morphological, metabolic, and genomic traits, the diversity of niches and lifestyles adopted by the family members is vast. One species of the group, Pseudomonas putida, thrives as a colonizer of plant roots and frequently inhabits soils polluted with various types of chemical waste. Owing to a combination of historical contingencies and inherent qualities, a particular strain, P. putida KT2440, emerged time ago as an archetype of an environmental microorganism amenable to recombinant DNA technologies, which was also capable of catabolizing chemical pollutants. Later, the same bacterium progressed as a reliable platform for programming traits and activities in various biotechnological applications. This article summarizes the stepwise upgrading of P. putida KT2440 from being a system for fundamental studies on the biodegradation of aromatic compounds (especially when harboring the TOL plasmid pWW0) to its adoption as a chassis of choice in metabolic engineering and synthetic biology. Although there are remaining uncertainties about the taxonomic classification of KT2440, advanced genome editing capabilities allow us to tailor its genetic makeup to meet specific needs. This makes its traditional categorization somewhat less important, while also increasing the strain's overall value for contemporary industrial and environmental uses.


Subject(s)
Biodegradation, Environmental , Pseudomonas putida , Soil Microbiology , Synthetic Biology , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Synthetic Biology/methods , Metabolic Engineering , Plasmids/genetics
2.
Microb Biotechnol ; 17(7): e14531, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39031514

ABSTRACT

Pseudomonas putida has become an increasingly important chassis for producing valuable bioproducts. This development is not least due to the ever-improving genetic toolbox, including gene and genome editing techniques. Here, we present a novel, one-plasmid design of a critical genetic tool, the pEMG/pSW system, guaranteeing one engineering cycle to be finalized in 3 days. The pEMG/pSW system proved in the last decade to be valuable for targeted genome engineering in Pseudomonas, as it enables the deletion of large regions of the genome, the integration of heterologous gene clusters or the targeted generation of point mutations. Here, to expedite genetic engineering, two alternative plasmids were constructed: (1) The sacB gene from Bacillus subtilis was integrated into the I-SceI expressing plasmid pSW-2 as a counterselection marker to accelerated plasmid curing; (2) double-strand break introducing gene I-sceI and sacB counterselection marker were integrated into the backbone of the original pEMG vector, named pEMG-RIS. The single plasmid of pEMG-RIS allows rapid genome editing despite the low transcriptional activity of a single copy of the I-SceI encoding gene. Here, the usability of the pEMG-RIS is shown in P. putida KT2440 by integrating an expression cassette including an msfGFP gene in 3 days. In addition, a large fragment of 12.1 kb was also integrated. In summary, we present an updated pEMG/pSW genome editing system that allows efficient and rapid genome editing in P. putida. All plasmids designed in this study will be available via the Addgene platform.


Subject(s)
Gene Editing , Plasmids , Pseudomonas putida , Recombination, Genetic , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Plasmids/genetics , Gene Editing/methods , Genetic Vectors/genetics , Bacillus subtilis/genetics
3.
ACS Synth Biol ; 13(7): 2060-2072, 2024 Jul 19.
Article in English | MEDLINE | ID: mdl-38968167

ABSTRACT

Genomic integration is commonly used to engineer stable production hosts. However, so far, for many microbial workhorses, only a few integration sites have been characterized, thereby restraining advanced strain engineering that requires multiple insertions. Here, we report on the identification of novel genomic integration sites, so-called landing pads, for Pseudomonas putida KT2440. We identified genomic regions with constant expression patterns under diverse experimental conditions by using RNA-Seq data. Homologous recombination constructs were designed to insert heterologous genes into intergenic sites in these regions, allowing condition-independent gene expression. Ten potential landing pads were characterized using four different msfGFP expression cassettes. An insulated probe sensor was used to study locus-dependent effects on recombinant gene expression, excluding genomic read-through of flanking promoters under changing cultivation conditions. While the reproducibility of expression in the landing pads was very high, the msfGFP signals varied strongly between the different landing pads, confirming a strong influence of the genomic context. To showcase that the identified landing pads are also suitable candidates for heterologous gene expression in other Pseudomonads, four equivalent landing pads were identified and characterized in Pseudomonas taiwanensis VLB120. This study shows that genomic "hot" and "cold" spots exist, causing strong promoter-independent variations in gene expression. This highlights that the genomic context is an additional parameter to consider when designing integrable genomic cassettes for tailored heterologous expression. The set of characterized genomic landing pads presented here further increases the genetic toolbox for deep metabolic engineering in Pseudomonads.


Subject(s)
Pseudomonas putida , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Gene Expression Profiling/methods , Promoter Regions, Genetic/genetics , Genome, Bacterial/genetics , Homologous Recombination , Transcriptome/genetics
4.
Molecules ; 29(14)2024 Jul 11.
Article in English | MEDLINE | ID: mdl-39064867

ABSTRACT

Surfactants are amphiphilic molecules that are capable of mixing water and oil. Biosurfactants are eco-friendly, low-toxicity, and stable to a variety of environmental factors. Optimizing conditions for microorganisms to produce biosurfactants can lead to improved production suitable for scaling up. In this study, we compared heterologous expression levels of the luminescence system luxCDABE operon controlled by regulatable promoters araC-PBAD and its strong version araC-PBAD-SD in Escherichia coli K12, Pseudomonas aeruginosa PAO1, and P. putida KT2440. Real-time monitoring of luminescence levels in the three strains indicated that luxCDABE controlled by araC-PBAD-SD promoter with 0.2% arabinose supplementation in P. putida produced the highest level of luminescence. By using the araC-PBAD-SD promoter-controlled rhlAB expression in P. putida, we were able to produce mono-rhamnolipid at a level of 1.5 g L-1 when 0.02% arabinose was supplemented. With the same system to express olsB, lyso-ornithine lipid was produced at a level of 10 mg L-1 when 0.2% arabinose was supplemented. To our knowledge, this is the first report about optimizing conditions for lyso-ornithine lipid production at a level up to 10 mg L-1. Taken together, our results demonstrate that regulatable araC-PBAD-SD promoter in P. putida KT2440 is a useful system for heterologous production of biosurfactants.


Subject(s)
Glycolipids , Ornithine , Promoter Regions, Genetic , Pseudomonas putida , Surface-Active Agents , Glycolipids/biosynthesis , Glycolipids/metabolism , Pseudomonas putida/metabolism , Pseudomonas putida/genetics , Surface-Active Agents/metabolism , Ornithine/metabolism , Ornithine/analogs & derivatives , Pseudomonas aeruginosa/metabolism , Pseudomonas aeruginosa/genetics , Arabinose/metabolism , Gene Expression Regulation, Bacterial , Escherichia coli/metabolism , Escherichia coli/genetics , Operon , Lipids
5.
ISME J ; 18(1)2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38952008

ABSTRACT

Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.


Subject(s)
Rhizosphere , Solanum lycopersicum , Succinic Acid , Solanum lycopersicum/microbiology , Succinic Acid/metabolism , Microbial Interactions , Soil Microbiology , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Pseudomonas putida/growth & development
6.
Environ Sci Technol ; 58(25): 11041-11052, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38860668

ABSTRACT

Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO2 efflux.


Subject(s)
Carbon Dioxide , Carbon , Carbon Dioxide/metabolism , Carbon/metabolism , Metabolic Networks and Pathways , Pseudomonas putida/metabolism , Biomass
7.
Appl Microbiol Biotechnol ; 108(1): 369, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38861200

ABSTRACT

Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene terephthalate) (PET). Recently, the use of EG as a starting material for the production of bio-fuels or bio-chemicals is gaining attention as a sustainable process since EG can be derived from materials not competing with human food stocks including CO2, syngas, lignocellulolytic biomass, and PET waste. In order to design and construct microbial process for the conversion of EG to value-added chemicals, microbes capable of catabolizing EG such as Escherichia coli, Pseudomonas putida, Rhodococcus jostii, Ideonella sakaiensis, Paracoccus denitrificans, and Acetobacterium woodii are candidates of chassis for the construction of synthetic pathways. In this mini-review, we describe EG catabolic pathways and catabolic enzymes in these microbes, and further review recent advances in microbial conversion of EG to value-added chemicals by means of metabolic engineering. KEY POINTS: • Ethylene glycol is a potential next-generation feedstock for sustainable industry. • Microbial conversion of ethylene glycol to value-added chemicals is gaining attention. • Ethylene glycol-utilizing microbes are useful as chassis for synthetic pathways.


Subject(s)
Ethylene Glycol , Metabolic Engineering , Ethylene Glycol/metabolism , Metabolic Networks and Pathways , Bacteria/metabolism , Pseudomonas putida/metabolism , Biofuels , Escherichia coli/metabolism , Escherichia coli/genetics
8.
Metab Eng ; 84: 69-82, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38839037

ABSTRACT

Sunscreen has been used for thousands of years to protect skin from ultraviolet radiation. However, the use of modern commercial sunscreen containing oxybenzone, ZnO, and TiO2 has raised concerns due to their negative effects on human health and the environment. In this study, we aim to establish an efficient microbial platform for production of shinorine, a UV light absorbing compound with anti-aging properties. First, we methodically selected an appropriate host for shinorine production by analyzing central carbon flux distribution data from prior studies alongside predictions from genome-scale metabolic models (GEMs). We enhanced shinorine productivity through CRISPRi-mediated downregulation and utilized shotgun proteomics to pinpoint potential competing pathways. Simultaneously, we improved the shinorine biosynthetic pathway by refining its design, optimizing promoter usage, and altering the strength of ribosome binding sites. Finally, we conducted amino acid feeding experiments under various conditions to identify the key limiting factors in shinorine production. The study combines meta-analysis of 13C-metabolic flux analysis, GEMs, synthetic biology, CRISPRi-mediated gene downregulation, and omics analysis to improve shinorine production, demonstrating the potential of Pseudomonas putida KT2440 as platform for shinorine production.


Subject(s)
Metabolic Engineering , Pseudomonas putida , Sunscreening Agents , Pseudomonas putida/metabolism , Pseudomonas putida/genetics , Sunscreening Agents/metabolism
9.
Metab Eng ; 84: 145-157, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38936762

ABSTRACT

Biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However, aromatic compounds derived from lignin commonly contain methoxy groups, and O-demethylation of these substrates is often a rate-limiting reaction that influences catabolic efficiency. Several enzyme families catalyze aromatic O-demethylation, but they are rarely compared in vivo to determine an optimal biocatalytic strategy. Here, two pathways for aromatic O-demethylation were compared in Pseudomonas putida KT2440. The native Rieske non-heme iron monooxygenase (VanAB) and, separately, a heterologous tetrahydrofolate-dependent demethylase (LigM) were constitutively expressed in P. putida, and the strains were optimized via adaptive laboratory evolution (ALE) with vanillate as a model substrate. All evolved strains displayed improved growth phenotypes, with the evolved strains harboring the native VanAB pathway exhibiting growth rates ∼1.8x faster than those harboring the heterologous LigM pathway. Enzyme kinetics and transcriptomics studies investigated the contribution of selected mutations toward enhanced utilization of vanillate. The VanAB-overexpressing strains contained the most impactful mutations, including those in VanB, the reductase for vanillate O-demethylase, PP_3494, a global regulator of vanillate catabolism, and fghA, involved in formaldehyde detoxification. These three mutations were combined into a single strain, which exhibited approximately 5x faster vanillate consumption than the wild-type strain in the first 8 h of cultivation. Overall, this study illuminates the details of vanillate catabolism in the context of two distinct enzymatic mechanisms, yielding a platform strain for efficient O-demethylation of lignin-related aromatic compounds to value-added products.


Subject(s)
Pseudomonas putida , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Metabolic Engineering , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Demethylation , Directed Molecular Evolution
10.
Environ Microbiol ; 26(6): e16671, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38863081

ABSTRACT

The environmental bacterium, Pseudomonas putida, possesses a broad spectrum of metabolic pathways. This makes it highly promising for use in biotechnological production as a cell factory, as well as in bioremediation strategies to degrade various aromatic pollutants. For P. putida to flourish in its environment, it must withstand the continuous threats posed by bacteriophages. Interestingly, until now, only a handful of phages have been isolated for the commonly used laboratory strain, P. putida KT2440, and no phage defence mechanisms have been characterized. In this study, we present a new Collection of Environmental P. putida Phages from Estonia, or CEPEST. This collection comprises 67 double-stranded DNA phages, which belong to 22 phage species and 9 phage genera. Our findings reveal that most phages in the CEPEST collection are more infectious at lower temperatures, have a narrow host range, and require an intact lipopolysaccharide for P. putida infection. Furthermore, we show that cryptic prophages present in the P. putida chromosome provide strong protection against the infection of many phages. However, the chromosomal toxin-antitoxin systems do not play a role in the phage defence of P. putida. This research provides valuable insights into the interactions between P. putida and bacteriophages, which could have significant implications for biotechnological and environmental applications.


Subject(s)
Host Specificity , Pseudomonas putida , Pseudomonas putida/virology , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Prophages/genetics , Pseudomonas Phages/genetics , Pseudomonas Phages/isolation & purification , Estonia , Bacteriophages/genetics , Bacteriophages/isolation & purification
11.
Chemosphere ; 361: 142496, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38825245

ABSTRACT

The widespread and inevitable use of plastic has led to prospective ecological problems through Bisphenol A (BPA), a synthetic chemical in plastic manufacturing. The present study addresses a unique methodology for eliminating BPA using the assistance of Pseudomonas putida. In the present work, biomass was torrefied to generate biochar with highly porous networks that could accommodate the bacterial species for effective colonization and multiplication. The designed biochar-bacterial globules demonstrated the ability to effectively remove BPA (96.88%) at a concentration of up to 2 g/L. The biochar-bacterial globules could effectively adsorb BPA at a low concentration of 20 mg/L. The alteration in pH did not impact the globule's performance, providing additional support for the practical utilization of these globules in polluted water bodies. In addition, the biochar-bacterial globules exhibited superior effectiveness in degradation compared to the standard levels, particularly in saline conditions. The simplicity and effectiveness of the approach make it promising for real-world implementation in addressing ecological problems associated with BPA contamination.


Subject(s)
Benzhydryl Compounds , Biodegradation, Environmental , Charcoal , Phenols , Pseudomonas putida , Water Pollutants, Chemical , Benzhydryl Compounds/chemistry , Pseudomonas putida/metabolism , Charcoal/chemistry , Adsorption
12.
Sci Rep ; 14(1): 14480, 2024 06 24.
Article in English | MEDLINE | ID: mdl-38914637

ABSTRACT

Aloe barbadensis is a drought-tolerant perennial medicinal plant with both nutritional and cosmetic uses. Drought is one of the main abiotic stresses limiting plant growth and development. However, the use of drought-resistant plants combined with beneficial soil micro-organisms could improve the effectiveness of biological methods to mitigate drought damage. This research aims to evaluate the effects of Funneliformis mosseae (MF), plant growth-promoting rhizobacteria (PGPR) (including Pseudomonas putida and Pantoea agglomerans), and their co-inoculation on the macronutrient status, antioxidant enzyme activities, and other morphophysiological traits of A. barbadensis under four irrigation regimes [25%, 50%, 75% and 100% of water requirement (WR)]. Three harvests were conducted, revealing that inoculation enhanced the survival rate and shoot fresh weight (SFW) compared to the control plants. However, at 25% WR, the SFW was reduced by 43% more than the control. across all harvests, while the PGPR + MF treatment showed increases of more than 19%, 11%, and 17% compared to the control, MF, and PGPR treatments, respectively. The results also showed that A. barbadensis exhibited innate drought tolerance up to a 50% WR level by enhancing physiological defenses, such as antioxidant enzyme activity. Inoculation increased the macronutrient status of the plant at all levels of irrigation regimes especially under severe drought conditions. The highest levels of nitrogen (N) (16.24 mg g-1 DW) and phosphorus (P) (11.29 mg g-1 DW) were observed in the PGPR + MF treatment at 100% WR. The maximum relative water content under MF inoculation and 75% WR (98.24%) (98.24%) was reached. PGPR + MF treatment alleviated drought-induced osmotic stress, as indicated by reduced antioxidant enzyme activities and electrolyte leakage. However, P. putida and P. agglomerans strains alone or in combination with F. mosseae increased plant yield, macronutrient uptake and antioxidant enzyme activity. This study underscores the potential of these PGPR and MF strains as invaluable biological tools for the cultivation of A. barbadensis in regions with severe drought stress.


Subject(s)
Aloe , Mycorrhizae , Aloe/metabolism , Aloe/microbiology , Mycorrhizae/physiology , Droughts , Pseudomonas putida/metabolism , Antioxidants/metabolism , Plant Roots/microbiology , Plant Roots/growth & development , Water/metabolism , Stress, Physiological , Soil Microbiology , Pantoea , Dehydration , Fungi
13.
PLoS One ; 19(6): e0303210, 2024.
Article in English | MEDLINE | ID: mdl-38843174

ABSTRACT

Cellular metabolic activity can be detected by tetrazolium-based colorimetric assays, which rely on dehydrogenase enzymes from living cells to reduce tetrazolium compounds into colored formazan products. Although these methods have been used in different fields of microbiology, their application to the detection of bacteria with plastic-degrading activity has not been well documented. Here, we report a microplate-adapted method for the detection of bacteria metabolically active on the commercial polyester polyurethane (PU) Impranil®DLN using the tetrazolium salt 2,3-bis [2-methyloxy-4-nitro-5-sulfophenyl]-2H-tetrazolium-5-carboxanilide (XTT). Bacterial cells that are active on PU reduce XTT to a water-soluble orange dye, which can be quantitatively measured using a microplate reader. We used the Pseudomonas putida KT2440 strain as a study model. Its metabolic activity on Impranil detected by our novel method was further verified by Fourier-transform infrared spectroscopy (FTIR) analyses. Measurements of the absorbance of reduced XTT at 470 nm in microplate wells were not affected by the colloidal properties of Impranil or cell density. In summary, we provide here an easy and high-throughput method for screening bacteria active on PU that can be adapted to other plastic substrates.


Subject(s)
Polyurethanes , Pseudomonas putida , Tetrazolium Salts , Polyurethanes/chemistry , Pseudomonas putida/metabolism , Tetrazolium Salts/chemistry , Spectroscopy, Fourier Transform Infrared/methods , Water/chemistry , Colorimetry/methods
14.
Nat Commun ; 15(1): 5299, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38906854

ABSTRACT

Adenosine-5'-triphosphate (ATP), the primary energy currency in cellular processes, drives metabolic activities and biosynthesis. Despite its importance, understanding intracellular ATP dynamics' impact on bioproduction and exploiting it for enhanced bioproduction remains largely unexplored. Here, we harness an ATP biosensor to dissect ATP dynamics across different growth phases and carbon sources in multiple microbial strains. We find transient ATP accumulations during the transition from exponential to stationary growth phases in various conditions, coinciding with fatty acid (FA) and polyhydroxyalkanoate (PHA) production in Escherichia coli and Pseudomonas putida, respectively. We identify carbon sources (acetate for E. coli, oleate for P. putida) that elevate steady-state ATP levels and boost FA and PHA production. Moreover, we employ ATP dynamics as a diagnostic tool to assess metabolic burden, revealing bottlenecks that limit limonene bioproduction. Our results not only elucidate the relationship between ATP dynamics and bioproduction but also showcase its value in enhancing bioproduction in various microbial species.


Subject(s)
Adenosine Triphosphate , Biosensing Techniques , Escherichia coli , Fatty Acids , Polyhydroxyalkanoates , Pseudomonas putida , Adenosine Triphosphate/metabolism , Biosensing Techniques/methods , Escherichia coli/metabolism , Escherichia coli/genetics , Pseudomonas putida/metabolism , Pseudomonas putida/genetics , Fatty Acids/metabolism , Polyhydroxyalkanoates/metabolism , Polyhydroxyalkanoates/biosynthesis , Energy Metabolism , Carbon/metabolism , Oleic Acid/metabolism
15.
Microb Biotechnol ; 17(6): e14514, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38923400

ABSTRACT

Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss of PDH affects metabolism in Pseudomonas putida. PDH inactivation resulted in a strain unable to utilize compounds whose assimilation converges at pyruvate, including sugars and several amino acids, whereas compounds that generate acetyl-CoA supported growth. PDH inactivation also resulted in the loss of carbon catabolite repression (CCR), which inhibits the assimilation of non-preferred compounds in the presence of other preferred compounds. Pseudomonas putida can degrade many aromatic compounds, most of which produce acetyl-CoA, making it useful for biotransformation and bioremediation. However, the genes involved in these metabolic pathways are often inhibited by CCR when glucose or amino acids are also present. Our results demonstrate that the PDH-null strain can efficiently degrade aromatic compounds even in the presence of other preferred substrates, which the wild-type strain does inefficiently, or not at all. As the loss of PDH limits the assimilation of many sugars and amino acids and relieves the CCR, the PDH-null strain could be useful in biotransformation or bioremediation processes that require growth with mixtures of preferred substrates and aromatic compounds.


Subject(s)
Catabolite Repression , Pseudomonas putida , Pyruvate Dehydrogenase Complex , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Pseudomonas putida/enzymology , Pyruvate Dehydrogenase Complex/metabolism , Pyruvate Dehydrogenase Complex/genetics , Hydrocarbons, Aromatic/metabolism , Biodegradation, Environmental , Acetyl Coenzyme A/metabolism , Pyruvic Acid/metabolism , Gene Deletion , Metabolic Networks and Pathways/genetics
16.
ACS Synth Biol ; 13(7): 2246-2252, 2024 Jul 19.
Article in English | MEDLINE | ID: mdl-38875315

ABSTRACT

Transcription factor (TF)-based biosensors are useful synthetic biology tools for applications in a variety of areas of biotechnology. A major challenge of biosensor circuits is the limited repertoire of identified and well-characterized TFs for applications of interest, in addition to the challenge of optimizing selected biosensors. In this work, we implement the IclR family repressor TF TtgV from Pseudomonas putida DOT-T1E as an indole-derivative biosensor in Escherichia coli. We optimize the genetic circuit utilizing different components, providing insights into biosensor design and expanding on previous studies investigating this TF. We discover novel physiologically relevant ligands of TtgV, such as skatole. The broad specificity of TtgV makes it a useful target for directed evolution and protein engineering toward desired specificity. TtgV, as an indole-derivative biosensor, is a promising genetic component for the detection of compounds with biological activities relevant to health and the gut microbiome.


Subject(s)
Biosensing Techniques , Escherichia coli , Indoles , Pseudomonas putida , Transcription Factors , Biosensing Techniques/methods , Indoles/metabolism , Indoles/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Synthetic Biology/methods , Protein Engineering/methods
17.
J Phys Chem B ; 128(27): 6529-6541, 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38935925

ABSTRACT

Antimicrobial resistance in bacteria often arises from their ability to actively identify and expel toxic compounds. The bacterium strain Pseudomonas putida DOT-T1E utilizes its TtgABC efflux pump to confer robust resistance against antibiotics, flavonoids, and organic solvents. This resistance mechanism is intricately regulated at the transcriptional level by the TtgR protein. Through molecular dynamics and alchemical free energy simulations, we systematically examine the binding of seven flavonoids and their derivatives with the TtgR transcriptional regulator. Our simulations reveal distinct binding geometries and free energies for the flavonoids in the active site of the protein, which are driven by a range of noncovalent forces encompassing van der Waals, electrostatic, and hydrogen bonding interactions. The interplay of molecular structures, substituent patterns, and intermolecular interactions effectively stabilizes the bound flavonoids, confining their movements within the TtgR binding pocket. These findings yield valuable insights into the molecular determinants that govern ligand recognition in TtgR and shed light on the mechanism of antimicrobial resistance in P. putida DOT-T1E.


Subject(s)
Bacterial Proteins , Flavonoids , Pseudomonas putida , Thermodynamics , Adsorption , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Binding Sites , Flavonoids/chemistry , Flavonoids/metabolism , Molecular Dynamics Simulation , Protein Binding , Pseudomonas putida/metabolism , Transcription Factors/metabolism , Transcription Factors/chemistry
18.
Genome Biol Evol ; 16(6)2024 06 04.
Article in English | MEDLINE | ID: mdl-38849986

ABSTRACT

Many nonsporulating bacterial species survive prolonged resource exhaustion, by entering a state termed long-term stationary phase. Here, we performed long-term stationary phase evolutionary experiments on the bacterium Pseudomonas putida, followed by whole-genome sequencing of evolved clones. We show that P. putida is able to persist and adapt genetically under long-term stationary phase. We observed an accumulation of mutations within the evolving P. putida populations. Within each population, independently evolving lineages are established early on and persist throughout the 4-month-long experiment. Mutations accumulate in a highly convergent manner, with similar loci being mutated across independently evolving populations. Across populations, mutators emerge, that due to mutations within mismatch repair genes developed a much higher rate of mutation than other clones with which they coexisted within their respective populations. While these general dynamics of the adaptive process are quite similar to those we previously observed in the model bacterium Escherichia coli, the specific loci that are involved in adaptation only partially overlap between P. putida and E. coli.


Subject(s)
Adaptation, Physiological , Pseudomonas putida , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Adaptation, Physiological/genetics , Mutation , Genome, Bacterial , Evolution, Molecular
19.
Mol Cell Proteomics ; 23(5): 100765, 2024 May.
Article in English | MEDLINE | ID: mdl-38608840

ABSTRACT

Pseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example, low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins are incompletely understood but genetic disruption of their function causes PHA-related phenotypes. To improve our understanding of these proteins, we investigated the PHA pathways of P.putida KT2440 using three types of experiments. First, we profiled cells grown in nitrogen-limited and nitrogen-excess media using global expression proteomics, identifying sets of proteins found to coordinately increase or decrease within clustered pathways. Next, we analyzed the protein composition of isolated carbonosomes, identifying two new putative components. We carried out physical interaction screens focused on PHA-related proteins, generating a protein-protein network comprising 434 connected proteins. Finally, we confirmed that the outer membrane protein OprL (the Pal component of the Pal-Tol system) localizes to the carbonosome and shows a PHA-related phenotype and therefore is a novel phasin. The combined datasets represent a valuable overview of the protein components of the PHA system in P.putida highlighting the complex nature of regulatory interactions responsive to nutrient stress.


Subject(s)
Lipoproteins , Polyhydroxyalkanoates , Proteomics , Pseudomonas putida , Polyhydroxyalkanoates/metabolism , Pseudomonas putida/metabolism , Pseudomonas putida/genetics , Proteomics/methods , Lipoproteins/metabolism , Bacterial Outer Membrane Proteins/metabolism , Bacterial Outer Membrane Proteins/genetics , Bacterial Proteins/metabolism , Nitrogen/metabolism , Plant Lectins
20.
Microb Biotechnol ; 17(3): e14423, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38528784

ABSTRACT

Medium-chain-length α,ω-diols (mcl-diols) play an important role in polymer production, traditionally depending on energy-intensive chemical processes. Microbial cell factories offer an alternative, but conventional strains like Escherichia coli and Saccharomyces cerevisiae face challenges in mcl-diol production due to the toxicity of intermediates such as alcohols and acids. Metabolic engineering and synthetic biology enable the engineering of non-model strains for such purposes with P. putida emerging as a promising microbial platform. This study reviews the advancement in diol production using P. putida and proposes a four-module approach for the sustainable production of diols. Despite progress, challenges persist, and this study discusses current obstacles and future opportunities for leveraging P. putida as a microbial cell factory for mcl-diol production. Furthermore, this study highlights the potential of using P. putida as an efficient chassis for diol synthesis.


Subject(s)
Polyhydroxyalkanoates , Pseudomonas putida , Pseudomonas putida/genetics , Pseudomonas putida/metabolism , Polyhydroxyalkanoates/metabolism , Metabolic Engineering , Escherichia coli/genetics , Escherichia coli/metabolism , Synthetic Biology
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