The contribution of proteomics to the unveiling of the survival strategies used by <i><scp>P</scp>seudomonas putida</i> in changing and hostile environments

Moreno, Renata; Rojo, Fernando

doi:10.1002/pmic.201200503

Cited by 18 publications

(9 citation statements)

References 92 publications

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“…This organism has been extensively studied for its ability to thrive in many environments, and thus detailed physiological information is available. 54,55 For example, it is known that the P. putida KT2440 genome harbors enzymes belonging to the catechol and protocatechuate branches of the β-ketoadipate pathway, and it has been engineered to convert lignin-derived compounds into molecules of interest. 12,14,19,56 The data presented in this work demonstrate that high initial concentrations of p-coumaric acid can be tolerated by P. putida and consumed with a rate that is on par with other carbon sources.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion

Rodríguez

Salvachúa

Katahira

et al. 2017

ACS Sustainable Chem. Eng.

125

114

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Lignin valorization offers significant potential to enhance the economic viability of lignocellulosic biorefineries. However, because of its heterogeneous and recalcitrant nature, conversion of lignin to value-added coproducts remains a considerable technical challenge. In this study, we employ base-catalyzed depolymerization (BCD) using a process-relevant solid lignin stream produced via deacetylation, mechanical refining, and enzymatic hydrolysis to enable biological lignin conversion. BCD was conducted with the solid lignin substrate over a range of temperatures at two NaOH concentrations, and the results demonstrate that the lignin can be partially extracted and saponified at temperatures as low as 60 °C. At 120 °C and 2% NaOH, the high extent of lignin solubility was accompanied by a considerable decrease in the lignin average molecular weight and the release of lignin-derived monomers including hydroxycinnamic acids. BCD liquors were tested for microbial growth using seven aromatic-catabolizing bacteria and two yeasts. Three organisms (Pseudomonas putida KT2440, Rhodotorula mucilaginosa, and Corynebacterium glutamicum) tolerate high BCD liquor concentrations (up to 90% v/v) and rapidly consume the main lignin-derived monomers, resulting in lignin conversion of up to 15%. Furthermore, as a proof of concept, muconic acid production from a representative lignin BCD liquor was demonstrated with an engineered P. putida KT2440 strain. These results highlight the potential for a mild lignin depolymerization process to enhance the microbial conversion of solid lignin-rich biorefinery streams.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion

Rodríguez

Salvachúa

Katahira

et al. 2017

ACS Sustainable Chem. Eng.

125

114

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“…A deeper understanding of adaptation processes and resistance mechanisms in P. putida KT2440 will help to optimize the biotechnological potential of this bacterium in the fields of agriculture, bioremediation, and biocatalysis and in the production of bioplastics (58). Further investigations will focus on the precise contribution of TtgABC in stress adaptation and the characterization of the ECF-10 signaling network, e.g., by identification of its activation mechanism and environmental stimuli and analysis of binding motifs and DNA interaction.…”

Section: Discussionmentioning

confidence: 99%

Knockout of Extracytoplasmic Function Sigma Factor ECF-10 Affects Stress Resistance and Biofilm Formation in Pseudomonas putida KT2440

Tettmann

Dötsch

Armant

et al. 2014

Appl Environ Microbiol

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Pseudomonas putida is a Gram-negative soil bacterium which is well-known for its versatile lifestyle, controlled by a large repertoire of transcriptional regulators. Besides one-and two-component regulatory systems, the genome of P. putida reveals 19 extracytoplasmic function (ECF) sigma factors involved in the adaptation to changing environmental conditions. In this study, we demonstrate that knockout of extracytoplasmic function sigma factor ECF-10, encoded by open reading frame PP4553, resulted in 2-to 4-fold increased antibiotic resistance to quinolone, ␤-lactam, sulfonamide, and chloramphenicol antibiotics. In addition, the ECF-10 mutant exhibited enhanced formation of biofilms after 24 h of incubation. Transcriptome analysis using Illumina sequencing technology resulted in the detection of 12 genes differentially expressed (>2-fold) in the ECF-10 knockout mutant strain compared to their levels of expression in wild-type cells. Among the upregulated genes were ttgA, ttgB, and ttgC, which code for the major multidrug efflux pump TtgABC in P. putida KT2440. Investigation of an ECF-10 and ttgA double-knockout strain and a ttgABC-overexpressing strain demonstrated the involvement of efflux pump TtgABC in the stress resistance and biofilm formation phenotypes of the ECF-10 mutant strain, indicating a new role for this efflux pump beyond simple antibiotic resistance in P. putida KT2440.

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“…aeruginosa infections ( Hauser et al., 2011 , Sadikot et al., 2012 ). Pseudomonas putida is a common soil bacterium and has been widely utilized for bioremediation and high-value chemical production ( Moreno and Rojo, 2013 , Nikel et al., 2016 ). Great efforts of metabolic engineering have been made to boost the capacity of P .…”

Section: Introductionmentioning

confidence: 99%

CRISPR/Cas9-based Genome Editing in Pseudomonas aeruginosa and Cytidine Deaminase-Mediated Base Editing in Pseudomonas Species

et al. 2018

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SummaryPseudomonas species are a large class of gram-negative bacteria that exhibit significant biomedical, ecological, and industrial importance. Despite the extensive research and wide applications, genetic manipulation in Pseudomonas species, in particular in the major human pathogen Pseudomonas aeruginosa, remains a laborious endeavor. Here we report the development of a genome editing method pCasPA/pACRISPR by harnessing the CRISPR/Cas9 and the phage λ-Red recombination systems. The method allows for efficient and scarless genetic manipulation in P. aeruginosa. By engineering the fusion of the cytidine deaminase APOBEC1 and the Cas9 nickase, we further develop a base editing system pnCasPA-BEC, which enables highly efficient gene inactivation and point mutations in a variety of Pseudomonas species, such as P. aeruginosa, Pseudomonas putida, Pseudomonas fluorescens, and Pseudomonas syringae. Application of the two genome editing methods will dramatically accelerate a wide variety of investigations, such as bacterial physiology study, drug target exploration, and metabolic engineering.

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The contribution of proteomics to the unveiling of the survival strategies used by Pseudomonas putida in changing and hostile environments

Cited by 18 publications

References 92 publications

Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion

Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion

Knockout of Extracytoplasmic Function Sigma Factor ECF-10 Affects Stress Resistance and Biofilm Formation in Pseudomonas putida KT2440

CRISPR/Cas9-based Genome Editing in Pseudomonas aeruginosa and Cytidine Deaminase-Mediated Base Editing in Pseudomonas Species

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