Pablo I. Nikel

Adaptive laboratory evolution rewires Pseudomonas putida for resource-efficient acetate assimilation

This study improves acetate tolerance in Pseudomonas putida through adaptive laboratory evolution and identifies gacA and fabB as key targets for efficient acetate assimilation.

Automated mini-bioreactors reveal the temporal dynamics and multi-omics responses of CRISPRi knockdowns in Pseudomonas putida

The paper uses automated mini-bioreactors to study the temporal dynamics and multi-omics responses of CRISPRi knockdowns in Pseudomonas putida, identifying a critical time window for phenotypic impact.

Improving acetate metabolism of Pseudomonas putida KT2440 by evolutionary and rational engineering

This paper improves acetate metabolism in P. putida KT2440 through rational and evolutionary engineering, enhancing growth rate and HAA production.

Computational pipeline reveals nature's untapped reservoir of halogenating enzymes

The paper develops a computational pipeline and database to annotate halogenating enzymes in genomic and metagenomic data, revealing underexplored clusters and improving predictions of microbial halogenated natural products.

A rapid HPLC-based method to determine NAD(P)(H) and NMN redox cofactor concentrations and ratios in microbes

This paper introduces a rapid HPLC-based method to measure NAD(P)(H) and NMN redox cofactor concentrations and ratios in microbes, validated against a classical assay and applied to engineered E. coli and Pseudomonas putida.

Seven mutations unlock strict synthetic methylotrophy in engineered Pseudomonas putida

The paper engineers Pseudomonas putida to strictly metabolize methanol through seven mutations, enabling growth on methanol as the sole carbon source.

Multiparameter optimization extends the lifetime of cell-free protein synthesis in a high-throughput format

This study optimizes DNA template design, reaction composition, and lysate genotype to extend CFPS reaction lifetime in a high-throughput format, achieving >14 h productivity and high deGFP yield.

A microbial growth-coupled platform for in vivo interrogation of Rubisco oxygenase activity

This paper develops a microbial platform to study Rubisco oxygenase activity in vivo by linking it to bacterial growth, enabling genetic screening and evolution of enzyme variants.

Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes

This study investigates how Pseudomonas putida uses two transhydrogenases to maintain redox balance across different metabolic conditions, revealing their essential roles in growth and stress tolerance.

Growth-coupled microbial biosynthesis of the animal pigment xanthommatin

This paper introduces a growth-coupled biosynthesis strategy (GrowBio) for producing xanthommatin, demonstrating its effectiveness in microbial production through engineered Pseudomonas putida.

Adaptive evolution of Pseudomonas putida in the presence of fluoride exposes moonlighting transporter functions

This study identifies a new fluoride tolerance mechanism in Pseudomonas putida independent of the CrcB efflux system, revealing moonlighting functions of transporters.

Mechanism-Guided Engineering of Fluorinase Unlocks EfficientNucleophilic Biofluorination

This paper enhances fluorinase catalytic efficiency by engineering mutants and optimizing reaction conditions, achieving a 60-fold increase in turnover rate.

Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation

This study engineers synthetic serine cycles in Pseudomonas putida to improve methanol assimilation, revealing novel metabolic topologies for C1 compound utilization.

Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system

This study optimizes a genome editing system for Cupriavidus necator H16, achieving high editing efficiency using an improved SIBR-Cas system.

Co-Substrate Free Valorisation of Lignin Monomers by Assimilation of C1 and C2 By-Products

This study shows how by-products from lignin conversion can be used by Pseudomonas putida to eliminate the need for additional carbon sources, improving lignin valorisation efficiency.

Genetic dissection of cyclic di-GMP signaling in Pseudomonas aeruginosa via diguanylate cyclase disruption

This study disrupts all 32 GGDEF domain-containing proteins in P. aeruginosa to analyze c-di-GMP signaling, revealing residual c-di-GMP levels and the importance of functional overlap in bacterial signaling.

CIFR (Clone-Integrate-Flip-out-Repeat): a toolset for iterative genome and pathway engineering of Gram-negative bacteria

CIFR enables iterative genome engineering in Gram-negative bacteria by allowing stable DNA insertions without antibiotic resistance cassettes.

Leveraging engineered Pseudomonas putida minicells for bioconversion of organic acids into short-chain methyl ketones

This paper demonstrates the use of engineered Pseudomonas putida minicells to convert organic acids into short-chain methyl ketones through pathway optimization and whole-cell biocatalysis.

Disentangling the regulatory response of Agrobacterium tumefaciens CHLDO to glyphosate for engineering whole-cell phosphonate biosensors

The paper develops whole-cell phosphonate biosensors using Agrobacterium tumefaciens CHLDO to detect glyphosate in environmental samples.

Expanding the biotechnological scope of metabolic sensors through computation-aided designs

This paper presents a computational workflow for designing and testing E. coli metabolic sensors that detect glyoxylate and glycolate across a wide concentration range, with applications in bioengineering and environmental monitoring.

Long-term evolution reveals the role of the circadian cycle in the environmental adaptation of cyanobacteria

The paper uses experimental evolution to show that circadian clock mutations in cyanobacteria enhance growth under continuous light by altering transcriptomic and metabolic responses.

The pAblo·pCasso self-curing vector toolset for unconstrained cytidine and adenine base-editing in Pseudomonas species

The paper develops a CRISPR-based base-editing toolkit for precise single-nucleotide modifications in Gram-negative bacteria, enabling gene inactivation and reversion with plasmid-free strain engineering.

High-yield enzymatic synthesis of mono- and trifluorinated alanine enantiomers

This study develops an enzymatic method to produce fluorinated alanine enantiomers with high yield and enantiomeric excess.

Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida

This study uses D-fluxomics to reveal the dynamic and hierarchical metabolism of glucose in Pseudomonas putida through the periplasmic gluconate shunt.

Integrated rational and evolutionary engineering of genome-reduced Pseudomonas putida strains empowers synthetic formate assimilation

The paper engineers genome-reduced Pseudomonas putida strains to assimilate formate as a carbon source using a modular approach and adaptive evolution, achieving faster growth and two distinct catabolic pathways.

A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes

This paper engineers a synthetic C2 auxotrophy in Pseudomonas putida to enable alternative sugar catabolism via the phosphoketolase shunt, improving growth through metabolic rewiring.

A non-conventional archaeal fluorinase identified by in silico mining catalyzes the fastest natural nucleophilic fluorination

The paper identifies a novel archaeal fluorinase with the highest reported fluorination rate and demonstrates its application in enhancing fluoronucleotide production in bacterial hosts.

Parameterization of regulatory nodes for engineering broad host range heterologous gene expression

The paper parameterizes five bacterial gene expression systems using a standardized vector format to compare their performance across different inducers.

Spatiotemporal manipulation of the mismatch repair system of Pseudomonas putida accelerates phenotype emergence

The paper develops inducible mutator devices in Pseudomonas putida to transiently inhibit the MMR system, increasing mutation rates and enabling rapid evolution of desired phenotypes.

Cofactor specificity of glucose-6-phosphate dehydrogenase isozymes in Pseudomonas putida reveals a general principle underlying glycolytic strategies in bacteria

The paper analyzes G6PDH isozymes in Pseudomonas putida to show how cofactor specificity and gene duplication contribute to redox balance and metabolic strategies in bacteria.