Solvent tolerance in Gram-negative bacteria

Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain for degrading aromatic compounds

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.

Overcoming barriers to medium-chain fatty alcohol production

Medium-chain fatty alcohols (mcFaOHs) are aliphatic primary alcohols containing six to twelve carbons that are widely used in materials, pharmaceuticals, and cosmetics. Microbial biosynthesis has been touted as a route to less-abundant chain-length molecules and as a sustainable alternative to current petrochemical processes. Several metabolic engineering strategies for producing mcFaOHs have been demonstrated in the literature, yet processes continue to suffer from poor selectivity and mcFaOH toxicity, leading to reduced titers, rates, and yields of the desired compounds. This opinion examines the current state of microbial mcFaOH biosynthesis, summarizing engineering efforts to tailor selectivity and improve product tolerance by implementing engineering strategies that circumvent or overcome mcFaOH toxicity.

The Azotobacter vinelandii AlgU regulon during vegetative growth and encysting conditions: A proteomic approach

In the Pseduomonadacea family, the extracytoplasmic function sigma factor AlgU is crucial to withstand adverse conditions. Azotobacter vinelandii, a closed relative of Pseudomonas aeruginosa, has been a model for cellular differentiation in Gram-negative bacteria since it forms desiccation-resistant cysts. Previous work demonstrated the essential role of AlgU to withstand oxidative stress and on A. vinelandii differentiation, particularly for the positive control of alginate production. In this study, the AlgU regulon was dissected by a proteomic approach under vegetative growing conditions and upon encystment induction. Our results revealed several molecular targets that explained the requirement of this sigma factor during oxidative stress and extended its role in alginate production. Furthermore, we demonstrate that AlgU was necessary to produce alkyl resorcinols, a type of aromatic lipids that conform the cell membrane of the differentiated cell. AlgU was also found to positively regulate stress resistance proteins such as OsmC, LEA-1, or proteins involved in trehalose synthesis. A position-specific scoring-matrix (PSSM) was generated based on the consensus sequence recognized by AlgU in P. aeruginosa, which allowed the identification of direct AlgU targets in the A. vinelandii genome. This work further expands our knowledge about the function of the ECF sigma factor AlgU in A. vinelandii and contributes to explains its key regulatory role under adverse conditions.

Underpinning the ecological response of mixed chlorinated volatile organic compounds (CVOCs) associated with contaminated and bioremediated groundwaters: A potential nexus of microbial community structure and function for strategizing efficient bioremediation

Understanding the structure, dynamics, and functionality of microbial communities is essential for developing sustainable and effective bioremediation strategies, particularly for sites contaminated with mixed chlorinated volatile organic compounds (CVOCs), which can make the biodegradation process more complex and challenging. In this study, 16S rRNA amplicon sequencing revealed a significant change in microbial distribution in response to CVOCs contamination. The loss of sensitive taxa such as Proteobacteria and Acidobacteriota was observed, while CVOCs-resistant taxa such as Campilobacterota were found significantly enriched in contaminated sites. Additionally, varying abundances of crucial enzymes involved in the sequential biodegradation of CVOCs were expressed depending on the contamination level. Association analysis revealed that specific genera such as Sulfurospirillum, Azospira, Trichlorobacter, Acidiphilium, and Magnetospririllum could relatively survive under higher levels of CVOC contamination, whereas pH, ORP and temperature had a negative influence in their abundance and distribution. However, Dechloromonas, Thiobacillus, Pseudarcicella, Hydrogenophaga, and Sulfuritalea showed a negative relationship with CVOC contamination, highlighting their sensitivity towards CVOC contamination. These findings provide valuable insights into the relationship among ecological responses, the groundwater bacterial community, and their functionality in response to mixed CVOC contamination, offering a fundamental basis for developing effective and sustainable bioremediation strategies for CVOC-contaminated groundwater systems.

Viability and transcriptional responses of multidrug resistant E. coli to chromium stress

The viability of multidrug resistant (MDR) bacteria in environment is critical for the spread of antimicrobial resistance. In this study, two Escherichia coli strains, MDR LM13 and susceptible ATCC25922, were used to elucidate differences in their viability and transcriptional responses to hexavalent chromium (Cr(VI)) stress. The results show that the viability of LM13 was notably higher than that of ATCC25922 under 2-20 mg/L Cr(VI) exposure with bacteriostatic rates of 3.1%-57%, respectively, for LM13 and 0.9%-93.1%, respectively, for ATCC25922. The levels of reactive oxygen species and superoxide dismutase in ATCC25922 were much higher than those in LM13 under Cr(VI) exposure. Additionally, 514 and 765 differentially expressed genes were identified from the transcriptomes of the two strains (log₂|FC| > 1, p < 0.05). Among them, 134 up-regulated genes were enriched in LM13 in response to external pressure, but only 48 genes were annotated in ATCC25922. Furthermore, the expression levels of antibiotic resistance genes, insertion sequences, DNA and RNA methyltransferases, and toxin-antitoxin systems were generally higher in LM13 than in ATCC25922. This work shows that MDR LM13 has a stronger viability under Cr(VI) stress, and therefore may promote the dissemination of MDR bacteria in environment.

Minicell-forming Escherichia coli mutant with increased chemical production capacity and tolerance to toxic compounds

Minicell, a small spherical form of bacterium produced by abnormal fission, possesses cytoplasmic constituents similar to those of the parental cell, except for genomic DNA. E. coli strains were engineered to produce minicells and value-added chemicals. Minicell-forming mutants showed enhanced tolerance to toxic chemicals and a higher intracellular NADH/NAD⁺ ratio than the wild-type. When toxic chemicals such as isobutanol, isobutyraldehyde, and isobutyl acetate were produced in this mutant, the titers increased by 67 %, 175 %, and 214 %, respectively. In addition, morphological changes and membrane dispersion mechanisms in minicell-forming mutants improved lycopene production by 259 %. This increase in production capacity was more pronounced when biomass hydrolysate was used as the substrate. Isobutanol and lycopene production also increased by 92 % and 295 %, respectively, on using the substrate in the mutant. It suggests that minicell-forming mutants are an excellent platform for biochemical production.

Antimicrobial Preservatives for Protein and Peptide Formulations: An Overview

Biological drugs intended for multi-dose application require the presence of antimicrobial preservatives to avoid microbial growth. As the presence of certain preservatives has been reported to increase protein and peptide particle formation, it is essential to choose a preservative compatible with the active pharmaceutical ingredient in addition to its preservation function. Thus, this review describes the current status of the use of antimicrobial preservatives in biologic formulations considering (i) appropriate preservatives for protein and peptide formulations, (ii) their physico-chemical properties, (iii) their in-/compatibilities with other excipients or packaging material, and (iv) their interactions with the biological compound. Further, (v) we present an overview of licensed protein and peptide formulations.

Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas-Rahnella Co-Culture

Pseudomonas fluorescens GM16 associates with Populus, a model plant in biofuel production. Populus releases abundant phenolic glycosides such as salicin, but P. fluorescens GM16 cannot utilize salicin, whereas Pseudomonas strains are known to utilize compounds similar to the aglycone moiety of salicin-salicyl alcohol. We propose that the association of Pseudomonas to Populus is mediated by another organism (such as Rahnella aquatilis OV744) that degrades the glucosyl group of salicin. In this study, we demonstrate that in the Rahnella-Pseudomonas salicin co-culture model, Rahnella grows by degrading salicin to glucose 6-phosphate and salicyl alcohol which is secreted out and is subsequently utilized by P. fluorescens GM16 for its growth. Using various quantitative approaches, we elucidate the individual pathways for salicin and salicyl alcohol metabolism present in Rahnella and Pseudomonas, respectively. Furthermore, we were able to establish that the salicyl alcohol cross-feeding interaction between the two strains on salicin medium is carried out through the combination of their respective individual pathways. The research presents one of the potential advantages of salicyl alcohol release by strains such as Rahnella, and how phenolic glycosides could be involved in attracting multiple types of bacteria into the Populus microbiome.

Antibacterial Effects of ZnO Nanodisks: Shape Effect of the Nanostructure on the Lethality in Escherichia coli

The role of the shape of the nanostructure on the antibacterial effects of ZnO nanodisks has been investigated by detailed mass spectrometry-based proteomics along with other spectroscopic and microscopic studies on E. coli. The primary interaction study of the E. coli cells in the presence of ZnO nanodisks showed rigorous cell surface damage disrupting the cell wall/membrane components detected by microscopic and ATR-FTIR studies. Protein profiling of whole-cell extracts in the presence and absence of ZnO nanodisks identified several proteins that are upregulated and downregulated under the stress of the nanodisks. This suggests that the bacterial response to the primary stress leads to a secondary impact of ZnO nanodisk toxicity via regulation of the expression of specific proteins. Results showed that the ZnO nanodisks lead to the over-expression of peptidyl-dipeptidase Dcp, Transketolase-1, etc., which are important to maintaining the osmotic balance in the cell. The abrupt change in osmotic pressure leads to mechanical injury to the membrane, and nutritional starvation conditions, which is revealed from the expression of the key proteins involved in membrane-protein assembly, maintaining membrane integrity, cell division processes, etc. Thus, indicating a deleterious effect of ZnO nanodisk on the protective layer of E. coli. ZnO nanodisks seem to primarily affect the protective membrane layer, inducing cell death via the development of osmotic shock conditions, as one of the possible reasons for cell death. These results unravel a unique behavior of the disk-shaped ZnO nanostructure in executing lethality in E. coli, which has not been reported for other known shapes or morphologies of ZnO nanoforms.

High-Yield, Magnetic Harvesting of Extracellular Outer-Membrane Vesicles from Escherichia coli

Extracellular outer-membrane vesicles (OMVs) are attractive for use as drug nanocarriers, because of their high biocompatibility and ability to enter cells. However, widespread use is hampered by low yields. Here, a high-yield method for magnetic harvesting of OMVs from Escherichia coli is described. To this end, E. coli are grown in the presence of magnetic iron-oxide nanoparticles (MNPs). Uptake of MNPs by E. coli is low and does not increase secretion of OMVs. Uptake of MNPs can be enhanced through PEGylation of MNPs. E. coli growth in the presence of PEGylated MNPs increases bacterial MNP-uptake and OMV-secretion, accompanied by upregulation of genes involved in OMV-secretion. OMVs containing MNPs can be magnetically harvested at 60-fold higher yields than achieved by ultracentrifugation. Functionally, magnetically-harvested OMVs and OMVs harvested by ultracentrifugation are both taken-up in similar numbers by bacteria. Uniquely, in an applied magnetic field, magnetically-harvested OMVs with MNPs accumulate over the entire depth of an infectious biofilm. OMVs harvested by ultracentrifugation without MNPs only accumulate near the biofilm surface. In conclusion, PEGylation of MNPs is essential for their uptake in E. coli and yields magnetic OMVs allowing high-yield magnetic-harvesting. Moreover, magnetic OMVs can be magnetically targeted to a cargo delivery site in the human body.

Listeria monocytogenes is a solvent tolerant organism secreting a solvent stable lipase: potential biotechnological applications

Purpose

The emerging biobased economy will require robust, adaptable, organisms for the production and processing of biomaterials as well as for bioremediation. Recently, the search for solvent tolerant organisms and solvent tolerant enzymes has intensified. Resilient organisms secreting solvent stable lipases are of particular interest for biotechnological applications.

Methods

Screening of soil samples for lipase-producing organisms was carried out on Rhodamine B plates. The most productive lipase-producing organisms were further screened for their resistance to solvents commonly used in biotechnological applications.

Results

In the course of screening, one of the isolated organisms that exhibited extracellular lipase activity, was identified as the human pathogen Listeria monocytogenes through 16S rRNA sequencing. Further exploration revealed that this organism was resistant to solvents ranging from log P − 0.81 to 4.0. Moreover, in the presence of these solvents, L. monocytogenes secreted an extracellular, solvent tolerant, lipase activity. This lipase retained approximately 80% activity when incubated in 30% (v/v) methanol for 24 h.

Conclusion

These findings identify L. monocytogenes as a potentially useful organism for biotechnological applications. However, the fact that Listeria is a pathogen is problematic and it will require the use of non-pathogenic or attenuated Listeria strains for practical applications. Nonetheless, the ability to adapt to rapidly changing environmental conditions, to grow at low temperatures, to resist solvents and to secrete an extracellular solvent tolerant lipase are unique and highly useful characteristics. The potential application of L. monocytogenes in wastewater bioremediation and plastics degradation is discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10529-022-03284-5.

Biosensor-assisted evolution for high-level production of 4-hydroxyphenylacetic acid in Escherichia coli

4-Hydroxyphenylacetic acid (4HPAA) is an important building block for synthesizing drugs, agrochemicals, and biochemicals, and requires sustainable production to meet increasing demand. Here, we use a 4HPAA biosensor to overcome the difficulty of conventional library screening in identification of preferred mutants. Strains with higher 4HPAA production and tolerance are successfully obtained by atmospheric and room temperature plasma (ARTP) mutagenesis coupled with adaptive laboratory evolution using this biosensor. Genome shuffling integrates preferred properties in the strain GS-2-4, which produces 25.42 g/L 4HPAA. Chromosomal mutations of the strain GS-2-4 are identified by whole genome sequencing. Through comprehensive analysis and experimental validation, important genes, pathways and regulations are revealed. The best gene combination in inverse engineering, acrD-aroG, increases 4HPAA production of strain GS-2-4 by 37% further. These results emphasize precursor supply and stress resistance are keys to efficient 4HPAA biosynthesis. Our work shows the power of biosensor-assisted screening of mutants from libraries. The methods developed here can be easily adapted to construct cell factories for the production of other aromatic chemicals. Our work also provides many valuable target genes to build cell factories for efficient 4HPAA production in the future.

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

Synthesis of aromatic amino acids from 2G lignocellulosic substrates

Pseudomonas putida is a highly solvent‐resistant microorganism and useful chassis for the production of value‐added compounds from lignocellulosic residues, in particular aromatic compounds that are made from phenylalanine. The use of these agricultural residues requires a two‐step treatment to release the components of the polysaccharides of cellulose and hemicellulose as monomeric sugars, the most abundant monomers being glucose and xylose. Pan‐genomic studies have shown that Pseudomonas putida metabolizes glucose through three convergent pathways to yield 6‐phosphogluconate and subsequently metabolizes it through the Entner–Doudoroff pathway, but the strains do not degrade xylose. The valorization of both sugars is critical from the point of view of economic viability of the process. For this reason, a P. putida strain was endowed with the ability to metabolize xylose via the xylose isomerase pathway, by incorporating heterologous catabolic genes that convert this C5 sugar into intermediates of the pentose phosphate cycle. In addition, the open reading frame T1E_2822, encoding glucose dehydrogenase, was knocked‐out to avoid the production of the dead‐end product xylonate. We generated a set of DOT‐T1E‐derived strains that metabolized glucose and xylose simultaneously in culture medium and that reached high cell density with generation times of around 100 min with glucose and around 300 min with xylose. The strains grew in 2G hydrolysates from diluted acid and steam explosion pretreated corn stover and sugarcane straw. During growth, the strains metabolized > 98% of glucose, > 96% xylose and > 85% acetic acid. In 2G hydrolysates P. putida 5PL, a DOT‐T1E derivative strain that carries up to five independent mutations to avoid phenylalanine metabolism, accumulated this amino acid in the medium. We constructed P. putida 5PLΔgcd (xylABE) that produced up to 250 mg l⁻¹ of phenylalanine when grown in 2G pretreated corn stover or sugarcane straw. These results support as a proof of concept the potential of P. putida as a chassis for 2G processes.

Challenges and opportunities in biological funneling of heterogeneous and toxic substrates beyond lignin

Significant developments in the understanding and manipulation of microbial metabolism have enabled the use of engineered biological systems toward a more sustainable energy and materials economy. While developments in metabolic engineering have primarily focused on the conversion of carbohydrates, substantial opportunities exist for using these same principles to extract value from more heterogeneous and toxic waste streams, such as those derived from lignin, biomass pyrolysis, or industrial waste. Funneling heterogeneous substrates from these streams toward valuable products, termed biological funneling, presents new challenges in balancing multiple catabolic pathways competing for shared cellular resources and engineering against perturbation from toxic substrates. Solutions to many of these challenges have been explored within the field of lignin valorization. This perspective aims to extend beyond lignin to highlight the challenges and discuss opportunities for use of biological systems to upgrade previously inaccessible waste streams.

Exposure to 1-Butanol Exemplifies the Response of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius to Solvent Stress

Sulfolobus acidocaldarius is a thermoacidophilic crenarchaeon with optimal growth at 80°C and pH 2 to 3. Due to its unique physiological properties, allowing life at environmental extremes, and the recent availability of genetic tools, this extremophile has received increasing interest for biotechnological applications. In order to elucidate the potential of tolerating process-related stress conditions, we investigated the response of S. acidocaldarius toward the industrially relevant organic solvent 1-butanol. In response to butanol exposure, biofilm formation of S. acidocaldarius was enhanced and occurred at up to 1.5% (vol/vol) 1-butanol, while planktonic growth was observed at up to 1% (vol/vol) 1-butanol. Confocal laser-scanning microscopy revealed that biofilm architecture changed with the formation of denser and higher tower-like structures. Concomitantly, changes in the extracellular polymeric substances with enhanced carbohydrate and protein content were determined in 1-butanol-exposed biofilms. Using scanning electron microscopy, three different cell morphotypes were observed in response to 1-butanol. Transcriptome and proteome analyses were performed comparing the response of planktonic and biofilm cells in the absence and presence of 1-butanol. In response to 1% (vol/vol) 1-butanol, transcript levels of genes encoding motility and cell envelope structures, as well as membrane proteins, were reduced. Cell division and/or vesicle formation were upregulated. Furthermore, changes in immune and defense systems, as well as metabolism and general stress responses, were observed. Our findings show that the extreme lifestyle of S. acidocaldarius coincided with a high tolerance to organic solvents. This study provides what may be the first insights into biofilm formation and membrane/cell stress caused by organic solvents in S. acidocaldarius IMPORTANCE Archaea are unique in terms of metabolic and cellular processes, as well as the adaptation to extreme environments. In the past few years, the development of genetic systems and biochemical, genetic, and polyomics studies has provided deep insights into the physiology of some archaeal model organisms. In this study, we used S. acidocaldarius, which is adapted to the two extremes of low pH and high temperature, to study its tolerance and robustness as well as its global cellular response toward organic solvents, as exemplified by 1-butanol. We were able to identify biofilm formation as a primary cellular response to 1-butanol. Furthermore, the triggered cell/membrane stress led to significant changes in culture heterogeneity accompanied by changes in central cellular processes, such as cell division and cellular defense systems, thus suggesting a global response for the protection at the population level.

Transporter proteins in Zymomonas mobilis contribute to the tolerance of lignocellulose-derived phenolic aldehyde inhibitors

Transporter proteins are of great importance for improving the tolerance of fermentation strains to lignocellulose-derived furans and phenolic inhibitors. Different from the documented transporter proteins responsible for the tolerance of furfural and 5-hydroxymethyl-furfural (HMF), transporters responsible for that of varied phenolic aldehyde inhibitors were less investigated and elucidated. Here, an interesting phenomenon was found that no phenolic alcohols were accumulated from phenolic aldehydes degradation in Zymomonas mobilis. A transcriptional profiling of transporter genes was established in Z. mobilis ZM4 under phenolic aldehydes stress using DNA microarray. Six transporter proteins were identified as the potential candidates responsible for the tolerance of phenolic aldehydes including ABC transporter (ZMO0799 and ZMO0800), MFS transporter (ZMO1288 and ZMO1856), and RND transporter (ZMO0282 and ZMO0798). Furthermore, the analysis showed that the key transporters were significantly correlated with oxidoreductases and transcriptional regulators. This work would provide several important transporter genes serving as synthetic biology tools for improving the robustness of biorefinery strains.

Expression, Rapid Purification and Functional Analysis of DnaK from Rhodococcus ruber

BACKGROUND

Heat shock proteins (HSPs) represent a group of important proteins which are produced by all kinds of organisms especially under stressful conditions. DnaK, an Hsp70 homolog in prokaryotes, has indispensable roles when microbes was confronted with stress conditions. However, few data on DnaK from Rhodococcus sp. were available in the literature. In a previous study, we reported that toluene and phenol stress gave rise to a 29.87-fold and 3.93-fold increase for the expression of DnaK from R. ruber SD3, respectively. Thus, we deduced DnaK was in correlation with the organic solvent tolerance of R. ruber SD3.

OBJECTIVE

To elucidate the role of DnaK in the organic solvent tolerance of R. ruber SD3, expression, purification and functional analysis of Dnak from R. ruber SD3 were performed in the present paper.

METHODS

In this article, DnaK from R. ruber SD3 was heterologously expressed in E. coli BL21(DE3) and purified by affinity chromatography. Functional analysis of DnaK was performed using determination of kinetics, docking, assay of chaperone activity and microbial growth.

RESULTS

The recombinant DnaK was rapidly purified by affinity chromatography with the purification fold of 1.9 and the recovery rate of 57.9%. Km, Vmax and Kcat for Dnak from R. ruber SD3 were 80.8 μM, 58.1 nmol/min and 374.3 S-1, respectively. The recombinant protein formed trimer in vitro, with the calculated molecular weight of 214 kDa. According to In-silico analysis, DnaK interacted with other molecular chaperones and some important proteins in the metabolism. The specific activity of catalase in the presence of recombinant DnaK was 1.85 times or 2.00 times that in the presence of BSA or Tris-HCl buffer after exposure to 54 °C for 1h. E. coli transformant with pET28-dnak showed higher growth than E. coli transformant with pET28 at 43°C and in the presence of phenol, respectively.

CONCLUSION

The biochemical properties and the interaction analysis of DnaK from R. ruber SD3 deepened our understanding of DnaK function. DnaK played an important role in microbial growth when R. ruber was subjected to various stress such as heating and organic solvent.

Adaptive laboratory evolution of Pseudomonas putida and Corynebacterium glutamicum to enhance anthranilate tolerance

Microbial bioproduction of the aromatic acid anthranilate (ortho-aminobenzoate) has the potential to replace its current, environmentally demanding production process. The host organism employed for such a process needs to fulfil certain demands to achieve industrially relevant product levels. As anthranilate is toxic for microorganisms, the use of particularly robust production hosts can overcome issues from product inhibition. The microorganisms Corynebacterium glutamicum and Pseudomonas putida are known for high tolerance towards a variety of chemicals and could serve as promising platform strains. In this study, the resistance of both wild-type strains towards anthranilate was assessed. To further enhance their native tolerance, adaptive laboratory evolution (ALE) was applied. Sequential batch fermentation processes were developed, adapted to the cultivation demands for C. glutamicum and P. putida, to enable long-term cultivation in the presence of anthranilate. Isolation and analysis of single mutants revealed phenotypes with improved growth behaviour in the presence of anthranilate for both strains. The characterization and improvement of both potential hosts provide an important basis for further process optimization and will aid the establishment of an industrially competitive method for microbial synthesis of anthranilate.

Phenotypic and Genomic Analysis of Clostridium beijerinckii NRRL B-598 Mutants With Increased Butanol Tolerance

N-Butanol, a valuable solvent and potential fuel extender, can be produced via acetone-butanol-ethanol (ABE) fermentation. One of the main drawbacks of ABE fermentation is the high toxicity of butanol to producing cells, leading to cell membrane disruption, low culture viability and, consequently, low produced concentrations of butanol. The goal of this study was to obtain mutant strains of Clostridium beijerinckii NRRL B-598 with improved butanol tolerance using random chemical mutagenesis, describe changes in their phenotypes compared to the wild-type strain and reveal changes in the genome that explain improved tolerance or other phenotypic changes. Nine mutant strains with stable improved features were obtained by three different approaches and, for two of them, ethidium bromide (EB), a known substrate of efflux pumps, was used for either selection or as a mutagenic agent. It is the first utilization of this approach for the development of butanol-tolerant mutants of solventogenic clostridia, for which generally there is a lack of knowledge about butanol efflux or efflux mechanisms and their regulation. Mutant strains exhibited increase in butanol tolerance from 36% up to 127% and the greatest improvement was achieved for the strains for which EB was used as a mutagenic agent. Additionally, increased tolerance to other substrates of efflux pumps, EB and ethanol, was observed in all mutants and higher antibiotic tolerance in some of the strains. The complete genomes of mutant strains were sequenced and revealed that improved butanol tolerance can be attributed to mutations in genes encoding typical stress responses (chemotaxis, autolysis or changes in cell membrane structure), but, also, to mutations in genes X276_07980 and X276_24400, encoding efflux pump regulators. The latter observation confirms the importance of efflux in butanol stress response of the strain and offers new targets for rational strain engineering.

How to outwit nature: Omics insight into butanol tolerance

The energy crisis, depletion of oil reserves, and global climate changes are pressing problems of developed societies. One possibility to counteract that is microbial production of butanol, a promising new fuel and alternative to many petrochemical reagents. However, the high butanol toxicity to all known microbial species is the main obstacle to its industrial implementation. The present state of the art review aims to expound the recent advances in modern omics approaches to resolving this insurmountable to date problem of low butanol tolerance. Genomics, transcriptomics, and proteomics show that butanol tolerance is a complex phenomenon affecting multiple genes and their expression. Efflux pumps, stress and multidrug response, membrane transport, and redox-related genes are indicated as being most important during butanol challenge, in addition to fine-tuning of global regulators of transcription (Spo0A, GntR), which may further improve tolerance. Lipidomics shows that the alterations in membrane composition (saturated lipids and plasmalogen increase) are very much species-specific and butanol-related. Glycomics discloses the pleiotropic effect of CcpA, the role of alternative sugar transport, and the production of exopolysaccharides as alternative routes to overcoming butanol stress. Unfortunately, the strain that simultaneously syntheses and tolerates butanol in concentrations that allow its commercialization has not yet been discovered or produced. Omics insight will allow the purposeful increase of butanol tolerance in natural and engineered producers and the effective heterologous expression of synthetic butanol pathways in strains hereditary butanol-resistant up to 3.2 - 4.9% (w/v). Future breakthrough can be achieved by a detailed study of the membrane proteome, of which 21% are proteins with unknown functions.

Enhancing n-Butanol Tolerance of Escherichia coli by Overexpressing of Stress-Responsive Molecular Chaperones

Microbial tolerance to organic solvents is critical for efficient production of biofuels. In this study, n-butanol tolerance of Escherichia coli JM109 was improved by overexpressing of genes encoding stress-responsive small RNA-regulator, RNA chaperone, and molecular chaperone. Gene rpoS, coding for sigma S subunit of RNA polymerase, was the most efficient in improving n-butanol tolerance of E. coli. The highest OD₆₀₀ and the specific growth rate of JM109/pQE80L-rpoS reached 1.692 and 0.144 h^-1 respectively at 1.0% (v/v) n-butanol. Double and triple expression of molecular chaperones rpoS, secB, and groS were conducted and optimized. Recombinant strains JM109/pQE80L-secB-rpoS and JM109/pQE80L-groS-secB-rpoS exhibited the highest n-butanol tolerance, with specific growth rates of 0.164 and 0.165 h^-1, respectively. Membrane integrity, potentials, and cell morphology analyses demonstrated the high viability of JM109/pQE80L-groS-secB-rpoS. This study provides guidance on employing various molecular chaperones for enhancing the tolerance of E. coli against n-butanol.

Changes in Vibrio natriegens Growth Under Simulated Microgravity

The growth rate of bacteria increases under simulated microgravity (SMG) with low-shear force. The next-generation microbial chassis Vibrio natriegens (V. natriegens) is a fast-growing Gram-negative, non-pathogenic bacterium with a generation time of less than 10 min. Screening of a V. natriegens strain with faster growth rate was attempted by 2-week continuous long-term culturing under SMG. However, the rapid growth rate of this strain made it difficult to obtain the desired mutant strain with even more rapid growth. Thus, a mutant with slower growth rate emerged. Multi-omics integration analysis was conducted to explore why this mutant grew more slowly, which might inform us about the molecular mechanisms of rapid growth of V. natriegens instead. The transcriptome data revealed that whereas genes related to mechanical signal transduction and flagellin biogenesis were up-regulated, those involved in adaptive responses, anaerobic and nitrogen metabolism, chromosome segregation and cell vitality were down-regulated. Moreover, genome-wide chromosome conformation capture (Hi-C) results of the slower growth mutant and wide type indicated that SMG-induced great changes of genome 3D organization were highly correlated with differentially expressed genes (DEGs). Meanwhile, whole genome re-sequencing found a significant number of structure variations (SVs) were enriched in regions with lower interaction frequency and down-regulated genes in the slower growth mutant compared with wild type (WT), which might represent a prophage region. Additionally, there was also a decreased interaction frequency in regions associated with well-orchestrated chromosomes replication. These results suggested that SMG might regulate local gene expression by sensing stress changes through conformation changes in the genome region of genes involved in flagellin, adaptability and chromosome segregation, thus followed by alteration of some physiological characteristics and affecting the growth rate and metabolic capacity.

Role of efflux in enhancing butanol tolerance of bacteria

N-butanol, a valued solvent and potential fuel extender, could possibly be produced by fermentation using either native producers, i.e. solventogenic Clostridia, or engineered platform organisms such as Escherichia coli or Pseudomonas species, if the main process obstacle, a low final butanol concentration, could be overcome. A low final concentration of butanol is the result of its high toxicity to production cells. Nevertheless, bacteria have developed several mechanisms to cope with this toxicity and one of them is active butanol efflux. This review presents information about a few well characterized butanol efflux pumps from Gram-negative bacteria (P. putida and E. coli) and summarizes knowledge about putative butanol efflux systems in Gram-positive bacteria.

Monitoring, assessment, and prediction of microbial shifts in coupled catalysis and biodegradation of 1,4-dioxane and co-contaminants

Microbial community dynamics were characterized following combined catalysis and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Although a few specific bacterial taxa are capable of removing 1,4-dioxane and individual CVOCs, many microorganisms are inhibited when these contaminants are present in mixtures. Chemical catalysis by tungstated zirconia (WO_x/ZrO₂) and hydrogen peroxide (H₂O₂) as a non-selective treatment was designed to achieve nearly 20% 1,4-dioxane and over 60% trichloroethene and 50% dichloroethene removals. Post-catalysis, bioaugmentation with 1,4-dioxane metabolizing bacterial strain,Pseudonocardia dioxanivorans CB1190, removed the remaining 1,4-dioxane. The evolution of the microbial community under different conditions was time-dependent but relatively independent of the concentrations of contaminants. The compositions of microbiomes tended to be similar regardless of complex contaminant mixtures during the biodegradation phase, indicating a r-K strategy transition attributed to the shock experienced during catalysis and the subsequent incubation. The originally dominant genera Pseudomonas and Ralstonia were sensitive to catalytic oxidation, and were overwhelmed by Sphingomonas, Rhodococcus, and other catalyst-tolerant microbes, but microbes capable of biodegradation of organics thrived during the incubation. Methane metabolism, chloroalkane-, and chloroalkene degradation pathways appeared to be responsible for CVOC degradation, based on the identifications of haloacetate dehalogenases, 2-haloacid dehalogenases, and cytochrome P450 family. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase that were in line with shifting predominant genera, confirming the deterministic processes guiding the microbial assembly. Collectively, this study demonstrated that catalysis followed by bioaugmentation is an effective treatment for 1,4-dioxane in the presence of high CVOC concentrations, and it enhanced our understanding of microbial ecological impacts resulting from abiotic-biological treatment trains. These results will be valuable for predicting treatment synergies that lead to cost savings and improve remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.

Engineering transport systems for microbial production

The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.

Design and engineering of whole-cell biocatalytic cascades for the valorization of fatty acids

This review presents the key factors to construct a productive whole-cell biocatalytic cascade exemplified for the biotransformation of renewable fatty acids.

Rational Engineering of Phenylalanine Accumulation in Pseudomonas taiwanensis to Enable High-Yield Production of Trans-Cinnamate

Microbial biocatalysis represents a promising alternative for the production of a variety of aromatic chemicals, where microorganisms are engineered to convert a renewable feedstock under mild production conditions into a valuable chemical building block. This study describes the rational engineering of the solvent-tolerant bacterium Pseudomonas taiwanensis VLB120 toward accumulation of L-phenylalanine and its conversion into the chemical building block t-cinnamate. We recently reported rational engineering of Pseudomonas toward L-tyrosine accumulation by the insertion of genetic modifications that allow both enhanced flux and prevent aromatics degradation. Building on this knowledge, three genes encoding for enzymes involved in the degradation of L-phenylalanine were deleted to allow accumulation of 2.6 mM of L-phenylalanine from 20 mM glucose. The amino acid was subsequently converted into the aromatic model compound t-cinnamate by the expression of a phenylalanine ammonia-lyase (PAL) from Arabidopsis thaliana. The engineered strains produced t-cinnamate with yields of 23 and 39% Cmol Cmol⁻¹ from glucose and glycerol, respectively. Yields were improved up to 48% Cmol Cmol⁻¹ from glycerol when two enzymes involved in the shikimate pathway were additionally overexpressed, however with negative impact on strain performance and reproducibility. Production titers were increased in fed-batch fermentations, in which 33.5 mM t-cinnamate were produced solely from glycerol, in a mineral medium without additional complex supplements. The aspect of product toxicity was targeted by the utilization of a streamlined, genome-reduced strain, which improves upon the already high tolerance of P. taiwanensis VLB120 toward t-cinnamate.

Targeting 16S rDNA for Stable Recombinant Gene Expression in Pseudomonas

Ribosomal RNA (rRNA) operons have recently been identified as promising sites for chromosomal integration of genetic elements in Pseudomonas putida, a bacterium that has gained considerable popularity as a microbial cell factory. We have developed a tool for targeted integration of recombinant genes into the rRNA operons of various Pseudomonas strains, where the native context of the rRNA clusters enables effective transcription of heterologous genes. However, a sufficient translation of foreign mRNA  transcriptionally fused to rRNA required optimization of RNA secondary structures, which was achieved utilizing synthetic ribozymes and a bicistronic design. The generated tool further enabled the characterization of the six rRNA promoter units of P. putida S12 under different growth conditions. The presence of multiple, almost identical rRNA operons in Pseudomonas also allowed the integration of multiple copies of heterologous genetic elements. The integration of two expression cassettes and the resulting disruption of rRNA units only moderately affects growth rates, and the constructs were highly stable over more than 160 generations.

Adaptive Responses of Shewanella decolorationis to Toxic Organic Extracellular Electron Acceptor Azo Dyes in Anaerobic Respiration

Bacterial anaerobic respiration using an extracellular electron acceptor plays a predominant role in global biogeochemical cycles. However, the mechanisms of bacterial adaptation to the toxic organic pollutant as the extracellular electron acceptor during anaerobic respiration are not clear, which limits our ability to optimize the strategies for the bioremediation of a contaminated environment. Here, we report the physiological characteristics and the global gene expression of an ecologically successful bacterium, Shewanella decolorationis S12, when using a typical toxic organic pollutant, amaranth, as the extracellular electron acceptor. Our results revealed that filamentous shift (the cells stretched to fiber-like shapes as long as 18 μm) occurred under amaranth stress. Persistent stress led to a higher filamentous cell rate and decolorization ability in subcultural cells compared to parental strains. In addition, the expression of genes involved in cell division, the chemotaxis system, energy conservation, damage repair, and material transport in filamentous cells was significantly stimulated. The detailed roles of some genes with significantly elevated expressions in filamentous cells, such as the outer membrane porin genes ompA and ompW, the cytochrome c genes arpC and arpD, the global regulatory factor gene rpoS, and the methyl-accepting chemotaxis proteins genes SHD_2793 and SHD_0015, were identified by site-directed mutagenesis. Finally, a conceptual model was proposed to help deepen our insights into both the bacterial survival strategy when toxic organics were present and the mechanisms by which these toxic organics were biodegraded as the extracellular electron acceptors.IMPORTANCE Keeping toxic organic pollutants (TOPs) in tolerable levels is a huge challenge for bacteria in extremely unfavorable environments since TOPs could serve as energy substitutes but also as survival stresses when they are beyond some thresholds. This study focused on the underlying adaptive mechanisms of ecologically successful bacterium Shewanella decolorationis S12 when exposed to amaranth, a typical toxic organic pollutant, as the extracellular electron acceptor. Our results suggest that filamentous shift is a flexible and valid way to solve the dilemma between the energy resource and toxic stress. Filamentous cells regulate gene expression to enhance their degradation and detoxification capabilities, resulting in a strong viability. These novel adaptive responses to TOPs are believed to be an evolutionary achievement to succeed in harsh habitats and thus have great potential to be applied to environment engineering or synthetic biology if we could picture every unknown node in this pathway.

Enhancing butanol tolerance of Escherichia coli reveals hydrophobic interaction of multi-tasking chaperone SecB

BACKGROUND

Escherichia coli has been proved to be one promising platform chassis for the production of various natural products, such as biofuels. Product toxicity is one of the main bottlenecks for achieving maximum production of biofuels. Host strain engineering is an effective approach to alleviate solvent toxicity issue in fermentation.

RESULTS

Thirty chaperones were overexpressed in E. coli JM109, and SecB recombinant strain was identified with the highest n-butanol tolerance. The tolerance (T) of E. coli overexpressing SecB, calculated by growth difference in the presence and absence of solvents, was determined to be 9.13% at 1.2% (v/v) butanol, which was 3.2-fold of the control strain. Random mutagenesis of SecB was implemented and homologously overexpressed in E. coli, and mutant SecB_T10A was identified from 2800 variants rendering E. coli the highest butanol tolerance. Saturation mutagenesis on T10 site revealed that hydrophobic residues were required for high butanol tolerance of E. coli. Compared with wild-type (WT) SecB, the T of SecB_T10A strain was further increased from 9.14 to 14.4% at 1.2% butanol, which was 5.3-fold of control strain. Remarkably, E. coli engineered with SecB_T10A could tolerate as high as 1.8% butanol (~ 14.58 g/L). The binding affinity of SecB_T10A toward model substrate unfolded maltose binding protein (preMBP) was 11.9-fold of that of WT SecB as determined by isothermal titration calorimetry. Residue T10 locates at the entrance of hydrophobic substrate binding groove of SecB, and might play an important role in recognition and binding of cargo proteins.

CONCLUSIONS

SecB chaperone was identified by chaperone mining to be effective in enhancing butanol tolerance of E. coli. Maximum butanol tolerance of E. coli could reach 1.6% and 1.8% butanol by engineering single gene of SecB or SecB_T10A. Hydrophobic interaction is vital for enhanced binding affinity between SecB and cargo proteins, and therefore improved butanol tolerance.

Effect of Sequential Acclimation to Various Carbon Sources on the Proteome of Acetobacter senegalensis LMG 23690T and Its Tolerance to Downstream Process Stresses

Acetic acid bacteria are very vulnerable to environmental changes; hence, they should get acclimated to different kinds of stresses when they undergo downstream processing. In the present study, Acetobacter senegalensis LMG 23690^T, a thermo-tolerant strain, was acclimated sequentially to different carbon sources including glucose (condition Glc), a mixture of glucose and ethanol (condition EtOH) and a mixture of glucose and acetic acid (condition GlcAA). Then, the effects of acclimation on the cell proteome profiles and some phenotypic characteristics such as growth in culture medium containing ethanol, and tolerance to freeze-drying process were evaluated. Based on the obtained results, despite the cells acclimated to Glc or EtOH conditions, 86% of acclimated cells to GlcAA condition were culturable and resumed growth with a short lag phase in a culture medium containing ethanol and acetic acid. Interestingly, if A. senegalensis LMG 23690^T had been acclimated to condition GlcAA, 92% of cells exhibited active cellular dehydrogenases, and 59% of cells were culturable after freeze-drying process. Proteome profiles comparison by 2D-DiGE and MS analysis, revealed distinct physiological status between cells exposed to different acclimation treatments, possibly explaining the resulting diversity in phenotypic characteristics. Results of proteome analysis by 2D-DiGE also showed similarities between the differentially expressed proteins of acclimated cells to EtOH condition and the proteome of acclimated cells to GlcAA condition. Most of the differentially regulated proteins are involved in metabolism, folding, sorting, and degradation processes. In conclusion, acclimation under appropriate sub-lethal conditions can be used as a method to improve cell phenotypic characteristics such as viability, growth under certain conditions, and tolerance to downstream processes.

The effect of organic solvents on selected microorganisms and model liposome membrane

The effect of methanol, ethanol, acetone, N,N-dimethylformamide (DMF), dimethyl sulfoxide and Nujol on the growth of Escherichia coli DH5α, Bacillus subtilis and Saccharomyces cerevisiae D273 was investigated. All of the tested cultures appeared susceptible to the organic media they were treated with, which evinced in apparent hindering of cell development. The observed diverse solvent tolerance, except from their different biochemical activity, may also be related to the changes in cell membrane fluidity induced by the solvent species. Parallel electron paramagnetic resonance investigations using egg yolk lecithin model liposomes revealed that the fluidity of the phospholipid system in cell membranes may either be considerably decreased (Nujol, DMF, ethanol) or increased (acetone), thus rendering difficult the intracellular nutrient supply. Hence, even the chemically neutral Nujol produced a distinct cell-growth inhibitory effect. These results are fairly consistent with the outcome of the survival tests, particularly for the bacteria strains.

A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol

Clostridium thermocellum is a good candidate organism for producing cellulosic biofuels due to its native ability to ferment cellulose, however its maximum biofuel titer is limited by tolerance. Wild type C. thermocellum is inhibited by 5 g/L n-butanol. Using growth adaptation in a chemostat, we increased n-butanol tolerance to 15 g/L. We discovered that several tolerant strains had acquired a D494G mutation in the adhE gene. Re-introducing this mutation recapitulated the n-butanol tolerance phenotype. In addition, it increased tolerance to several other primary alcohols including isobutanol and ethanol. To confirm that adhE is the cause of inhibition by primary alcohols, we showed that deleting adhE also increases tolerance to several primary alcohols.

Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants

Microbial community dynamics were characterized following combined oxidation and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Bioremediation is generally inhibited by co-contaminate CVOCs; with only a few specific bacterial taxa reported to metabolize or cometabolize 1,4-dioxane being unaffected. Chemical oxidation by hydrogen peroxide (H₂O₂) as a non-selective treatment demonstrated 50-80% 1,4-dioxane removal regardless of the initial CVOC concentrations. Post-oxidation bioaugmentation with 1,4-dioxane metabolizer Pseudonocardia dioxanivorans CB1190 removed the remaining 1,4-dioxane. The intrinsic microbial population, biodiversity, richness, and biomarker gene abundances decreased immediately after the brief oxidation phase, but recovery of cultivable microbiomes and a more diverse community were observed during the subsequent 9-week biodegradation phase. Results generated from the Illumina Miseq sequencing and bioinformatics analyses established that generally oxidative stress tolerant genus Ralstonia was abundant after the oxidation step, and Cupriavidus, Pseudolabrys, Afipia, and Sphingomonas were identified as dominant genera after aerobic incubation. Multidimensional analysis elucidated the separation of microbial populations as a function of time under all conditions, suggesting that temporal succession is a determining factor that is independent of 1,4-dioxane and CVOCs mixtures. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase, in line with the shifts of predominant genera and various developing directions during different steps of the treatment train. Collectively, this study demonstrated that chemical oxidation followed by bioaugmentation is effective for treating 1,4-dioxane, even in the presence of high levels of CVOC mixtures and residual peroxide, a disinfectant, and enhanced our understanding of microbial ecological impacts of the treatment train. These results will be valuable for predicting treatment synergies that lead to cost savings and improved remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.

Co-contaminant effects on 1,4-dioxane biodegradation in packed soil column flow-through systems

Biodegradation of 1,4-dioxane was examined in packed quartz and soil column flow-through systems. The inhibitory effects of co-contaminants, specifically trichloroethene (TCE), 1,1-dichloroethene (1,1-DCE), and copper (Cu²⁺) ions, were investigated in the columns either with or without bioaugmentation with a 1,4-dioxane degrading bacterium Pseudonocardia dioxanivorans CB1190. Results indicate that CB1190 cells readily grew and colonized in the columns, leading to significant degradation of 1,4-dioxane under oxic conditions. Degradation of 1,4-dioxane was also observed in the native soil (without bioaugmentation), which had been previously subjected to enhanced reductive dechlorination treatment for co-contaminants TCE and 1,1-DCE. Bioaugmentation of the soil with CB1190 resulted in nearly complete degradation at influent concentrations of 3-10 mg L^-1 1,4-dioxane and a residence reaction time of 40-80 h, but the presence of co-contaminants, 1,1-DCE and Cu²⁺ ions (up to 10 mg L^-1), partially inhibited 1,4-dioxane degradation in the untreated and bioaugmented soil columns. However, the inhibitory effects were much less severe in the column flow-through systems than those previously observed in planktonic cultures, which showed near complete inhibition at the same co-contaminant concentrations. These observations demonstrate a low susceptibility of soil microbes to the toxicity of 1,1-DCE and Cu²⁺ in packed soil flow-through systems, and thus have important implications for predicting biodegradation potential and developing sustainable, cost-effective technologies for in situ remediation of 1,4-dioxane contaminated soils and groundwater.

Effects of limonene, n-decane and n-decanol on growth and membrane fatty acid composition of the microalga Botryococcus braunii

Botryococcus braunii is a promising microalga for the production of biofuels and other chemicals because of its high content of internal lipids and external hydrocarbons. However, due to the very thick cell wall of B. braunii, traditional chemical/physical downstream processing very often is not as effective as expected and requires high amounts of energy. In this cases, the application of two-phase aqueous-organic solvent systems could be an alternative to cultivate microalgae allowing for a simultaneous extraction of the valuable compounds without significant negative effects on cell growth. Two-phase systems have been applied before, however, there are no studies so far on the mechanisms used by microalgae to survive in contact with solvents present as a second-phase. In this study, the effects of the solvents limonene, n-decane and n-decanol on growth of the microalga B. braunii as well as the adaptive cell response in terms of their phospholipid fatty acid contents were analized. A concentration-dependent negative effect of all three solvents on cell growth was observed. Effects were accompanied by changes of the membrane fatty acid composition of the alga as manifested by a decrease of the unsaturation . In addition, an association was found between the solvent hydrophobicity (given as log octanol–water partition coefficient (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {P}_{O-W}$$\end{document}PO-W) values) and their toxic effects, whereby n-decanol and n-decane emerged as the most and least toxic solvent respectively. Among the tested solvents, the latter promises to be the most suitable for a two-phase extraction system.

An RND transporter in the monoterpene metabolism of Castellaniella defragrans

The betaproteobacterium Castellaniella defragrans 65Phen grows on monoterpenes at concentrations toxic to many bacteria. Tolerance mechanisms include modifications of the membrane fatty acid composition and the mineralization of monoterpenes. In this study, we characterized an efflux transporter associated to the monoterpene metabolism. The inner-membrane transporter AmeD (apolar monoterpene efflux) affiliated to the HAE3 (hydrophobe/amphiphile efflux) family within the Resistance-Nodulation-Division (RND) superfamily. RND pumps of the HAE3 family are known for transporting substrates into the periplasm. AmeD is co-expressed with the outer membrane protein AmeA and the periplasmic proteins AmeB and AmeC, suggesting an export channel into the environment similar to HAE1-type RND exporters. Proteins AmeABCD are encoded within a genetic island involved in the metabolism of acyclic and cyclic monoterpenes. The deletion of ameABCD translated into a decrease in tolerance to monoterpenes in liquid cultures. The addition of acetate as cosubstrate in limonene-containing cultures partially alleviated monoterpene toxicity in the deletion mutant. Accumulation of Nile Red in cells of C. defragrans required dissipation of the proton motive force with carbonyl cyanide m-chlorophenylhydrazone (CCCP). Cells lacking AmeABCD accumulated more Nile Red, suggesting an export function of the proteins. Our observations suggest that the tetrapartite RND transporter AmeABCD acts as an exporter during monoterpene detoxification in C. defragrans.

What makes A. guillouiae SFC 500-1A able to co-metabolize phenol and Cr(VI)? A proteomic approach

Acinetobacter guillouiae SFC 500-1A is an environmental bacterium able to efficiently co-remediate phenol and Cr(VI). To further understand the molecular mechanisms triggered in this strain during the bioremediation process, variations in the proteomic profile after treatment with phenol and phenol plus Cr(VI) were evaluated. The proteomic analysis revealed the induction of the β-ketoadipate pathway for phenol oxidation and the assimilation of degradation products through TCA cycle and glyoxylate shunt. Phenol exposure increased the abundance of proteins associated to energetic processes and ATP synthesis, but it also triggered cellular stress. The lipid bilayer was suggested as a target of phenol toxicity, and changing fatty acids composition seemed to be the bacterial response to protect the membrane integrity. The involvement of two flavoproteins in Cr(VI) reduction to Cr(III) was also proposed. The results suggested the important role of chaperones, antioxidant response and SOS-induced proteins in the ability of the strain to mitigate the damage generated by phenol and Cr(VI). This research contributes to elucidate the mechanisms involved in A. guillouiae SFC 500-1A tolerance and co-remediation of phenol and Cr(VI). Such information may result useful not only to improve its bioremediation efficiency but also to identify putative markers of resistance in environmental bacteria.

Identification of ethanol tolerant outer membrane proteome reveals OmpC-dependent mechanism in a manner of EnvZ/OmpR regulation in Escherichia coli

Ethanol is an efficient disinfectant, but long-term and wide usage of ethanol leads to microbial tolerance. Bacteria with the tolerance are widely identified. However, mechanisms of the tolerance are not elucidated. To explore the mechanisms of outer membrane (OM) proteins underlying ethanol tolerance in bacteria, functional proteomic methodologies were utilized to characterize OM proteins of E. coli suddenly exposed to 3.125% ethanol. Of eleven proteins altered significantly, seven were OM proteins, in which LamB, FadL and OmpC were up-regulated, and OmpT, OmpF, Tsx and OmpA were down-regulated. The alterations were validated using Western blot. Then, functional characterization of the altered abundance of OM proteins was investigated in gene-deleted and gene-complemented mutants cultured in 1.56-6.25% ethanol. Higher inhibiting rate was detected in ΔompC than ΔlamB and ΔompA, but no difference was found between Δtsx, ΔompF, ΔfadL or ΔompT and control. Furthermore, EnvZ/OmpR two-component signal transduction system, which regulates OmpC and OmpF expression, was determined to participate in the tolerance. Finally, our results show that absence of envZ, ompR or ompC and ompA led to elevated and reduced intracellular ethanol, respectively. These findings indicate EnvZ-dependent phosphotransfer signaling pathway of the OmpR-mediated expression of OmpC plays a crucial role in ethanol tolerance.

BIOLOGICAL SIGNIFICANCE

Ethanol tolerance is an adaptation strategy of bacteria. In the present study, we used the proteomic approaches involving 2-DE and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) to determined outer membrane (OM) protein changes in E. coli K-12 after 2 h of 1/2 MIC of ethanol exposure. Under ethanol stress, seven differential OM proteins were found, which were validated by Western blot. Functions of these seven OM proteins were compared using their genetically modified strains. Furthermore, the role of EnvZ/OmpR two-component signal transduction system was identified in ethanol tolerance of E. coli. Finally, Loss of ompC, envZ or ompR increases intracellular ethanol, while absence of ompA reduces reversal effect. This is the first report of OM proteomics in E. coli exposed to ethanol. Our findings reveal an unknown OmpC-dependent mechanism of ethanol tolerance in a manner of EnvZ/OmpR regulation.