A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation

Nicolaou, Sergios A.; Gaida, Stefan M.; Papoutsakis, Eleftherios T.

doi:10.1016/j.ymben.2010.03.004

Cited by 485 publications

(381 citation statements)

References 321 publications

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“…Microorganisms have been modified to address other challenges in biofuel production, including biofuel toxicity, which has been summarized in several reviews (Boyarskiy and Tullman-Ercek 2015;Dunlop et al 2011;Jones et al 2015;Mukhopadhyay 2015;Nicolaou et al 2010;Ramos et al 2002). (Bokinsky et al 2011).…”

Section: Engineering Il Tolerance In Bacteriamentioning

confidence: 99%

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

Simmons

Singer

et al. 2016

Appl Microbiol Biotechnol

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Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs not only inhibit enzyme activities, but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes.While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.

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Section: Engineering Il Tolerance In Bacteriamentioning

confidence: 99%

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

Simmons

Singer

et al. 2016

Appl Microbiol Biotechnol

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“…Some of the mechanisms leading to increased tolerance in these solvent‐tolerant strains have been identified and described, and efflux pumps (Kieboom & de Bont, 2001; Mosqueda & Ramos, 2000; Ramos, Duque, Godoy, & Segura, 1998) as well as changes in the membrane composition (Heipieper & De Bont, 1994), have been shown to be important for tolerance in these strains. Some of the changes that can occur in the membrane, when bacteria are exposed to hydrophobic solvents, include vesicle formation, alteration of phospholipid composition, and reduced permeability of the cell membrane (Heipieper & De Bont, 1994; Nicolaou, Gaida, & Papoutsakis, 2010; Ramos et al, 2002). The mechanisms behind tolerance in the model strain P. putida KT2440 has also been studied for different compounds (Benndorf, Thiersch, Loffhagen, Kunath, & Harms, 2006; Domínguez‐Cuevas, González‐Pastor, Marqués, Ramos, & de Lorenzo, 2006; Fernandez, Conde et al, 2012; Fernandez, Niqui‐Arroyo, Conde, Ramos, & Duque, 2012; Roca, Rodríguez‐Herva, Duque, & Ramos, 2008; Santos, Benndorf, & Sá‐Correia, 2004).…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide identification of tolerance mechanisms toward p‐coumaric acid in Pseudomonas putida

Calero

Jensen

Bojanovič

et al. 2017

Biotech & Bioengineering

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The soil bacterium Pseudomonas putida KT2440 has gained increasing biotechnological interest due to its ability to tolerate different types of stress. Here, the tolerance of P. putida KT2440 toward eleven toxic chemical compounds was investigated. P. putida was found to be significantly more tolerant toward three of the eleven compounds when compared to Escherichia coli. Increased tolerance was for example found toward p‐coumaric acid, an interesting precursor for polymerization with a significant industrial relevance. The tolerance mechanism was therefore investigated using the genome‐wide approach, Tn‐seq. Libraries containing a large number of miniTn5‐Km transposon insertion mutants were grown in the presence and absence of p‐coumaric acid, and the enrichment or depletion of mutants was quantified by high‐throughput sequencing. Several genes, including the ABC transporter Ttg2ABC and the cytochrome c maturation system (ccm), were identified to play an important role in the tolerance toward p‐coumaric acid of this bacterium. Most of the identified genes were involved in membrane stability, suggesting that tolerance toward p‐coumaric acid is related to transport and membrane integrity.

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“…The main challenge to this "one pot" strategy is process inhibition of laboratory microorganisms by secondary products of polysaccharide catabolism and fermentation, as well as by residual ionic liquid from the pretreatment step (18). For instance, many ionic liquids are highly toxic to microorganisms as a result of the increase in osmotic pressure, potential effects on membrane fluidity and structure, and inhibition of enzymatic activity (11,13,(19)(20)(21)(22); however, the specific mechanisms of toxicity are currently not well-understood, making this an area of intense interest in the field.…”

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confidence: 99%

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium,Enterobacter lignolyticus

Khudyakov

D’haeseleer

Borglin

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.osmotic stress | osmolytes | membrane lipids | differential gene expression | whole genome metabolic reconstruction

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A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation

Cited by 485 publications

References 321 publications

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

Genome‐wide identification of tolerance mechanisms toward p‐coumaric acid in Pseudomonas putida

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium,Enterobacter lignolyticus

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