trxB1 overexpression response to hydrogen peroxide stress in Lactobacillus plantarum WCFS1

Two independent chemostat cultivations were performed for both wild type and trxB1 over-expression strain, NZ7602. Three hybridization experiments, all with the same hybridization scheme (see overall design), were performed with samples obtained from these chemostats before and after treatment with hydrogen peroxide (30 minutes 2.5 mM peroxide). Two of these experiments used samples obtained from the same fermentation. In each experiment three arrays were used. Per array two cDNA labeled targets were hybridized on custom designed L. plantarum WCFS1 11K Agilent oligo microarrays (GEO Acc. Nr. GPL4318) using the Agilent 60-mer oligo microarray processing protocol version 4.1. These microarrays contained an average of 3 probes per gene. Dried slides were scanned in the Scan Array Express (PerkinElmer Life Sciences; Packard Bioscience) at 10 microns. Spot intensity data was quantified (average intensity) in ImaGene version 5.0 (BioDiscovery, Inc., El Segundo, CA). Signal intensities of all probes were corrected against background and normalized by fitting a plot of M (= 2log [cy5 intensity/cy3 intensity]) against A (= 0.5 • 2log [cy5 intensity • cy3 intensity]) using the lowess algorithm in BASE [32]. The fold change (FC) is defined as 2M. For the statistical analysis we used microarray analysis of variation (R/maanova) [33] In this maanova test we used three variables: fermentation, treatment, and genotype. We tested the model taking into consideration the interaction between genotype and treatment. Significantly regulated genes were defined as genes whose nominal adjusted pvalues were less than 10% and a FC>1.5. The maanova test resulted only in two sets of interesting data because the interaction effect did not reveal significant changes in transcript levels. One dataset representing the transcripts affected as a result of the overproduction of TR and another set representing the transcripts affected due to oxidative stress. These two datasets were denominated genotype and hydrogen peroxide datasets respectively

Effect of Amino Acid Availability on Vitamin B12 Production in Lactobacillus reuteri▿ †

Recent functional genomics and genome-scale modeling approaches indicated that B12 production in Lactobacillus reuteri could be improved by optimization of the medium. Here we show that a series of systematic single-amino-acid omissions could significantly modulate the production of B12 from nearly undetectable levels (with omission of isoleucine) to levels 20-fold higher than the levels previously reported (with omission of cysteine). Using cDNA microarray experiments, we analyzed the transcriptional response of L. reuteri to medium lacking cysteine. The results supported the observed high level of B12 production and provided new avenues for future improvement of production of vitamin B12

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1

BACKGROUND: Thioredoxin (TRX) is a powerful disulfide oxido-reductase that catalyzes a wide spectrum of redox reactions in the cell. The aim of this study is to elucidate the role of the TRX system in the oxidative stress response in Lactobacillus plantarum WCFS1. RESULTS: We have identified the trxB1-encoded thioredoxin reductase (TR) as a key enzyme in the oxidative stress response of Lactobacillus plantarum WCFS1. Overexpression of the trxB1 gene resulted in a 3-fold higher TR activity in comparison to the wild-type strain. Subsequently, higher TR activity was associated with an increased resistance towards oxidative stress. We further determined the global transcriptional response to hydrogen peroxide stress in the trxB1-overexpression and wild-type strains grown in continuous cultures. Hydrogen peroxide stress and overproduction of TR collectively resulted in the up-regulation of 267 genes. Additionally, gene expression profiling showed significant differential expression of 27 genes in the trxB1-overexpression strain. Over expression of trxB1 was found to activate genes associated with DNA repair and stress mechanisms as well as genes associated with the activity of biosynthetic pathways for purine and sulfur-containing amino acids. A total of 16 genes showed a response to both TR overproduction and hydrogen peroxide stress. These genes are involved in the purine metabolism, energy metabolism (gapB) as well as in stress-response (groEL, npr2), and manganese transport (mntH2). CONCLUSION: Based on our findings we propose that overproduction of the trxB1-encoded TR in L. plantarum improves tolerance towards oxidative stress. This response coincides with simultaneous induction of a group of 16 transcripts of genes. Within this group of genes, most are associated with oxidative stress response. The obtained crossover between datasets may explain the phenotype of the trxB1-overexpression strain, which appears to be prepared for encountering oxidative stress. This latter property can be used for engineering robustness towards oxidative stress in industrial strains of L. plantarum

Skeletal isomerisation of oleic acid over ferrierite : Influence of acid site number, accessibility and strength on activity and selectivity

Protonated ferrierite shows superior activity and selectivity in the liquid-phase isomerisation of linear unsaturated fatty acids to (mono-)branched-chain unsaturated fatty acids, (Mo)BUFA. This high selectivity is remarkable, as most of the interior surface of the zeolite is blocked already at the onset of reaction, limiting reaction to the pore mouth. A detailed study of the relationship between ferrierite acidity and performance is reported for five commercial catalysts; significant differences were found, independently of their bulk Si/AI ratios. Initial pore conversion correlates with Bronsted acidity in the 10-MR channels, as determined by adsorption/desorption of pyridine and FTIR. A low density of external acid sites reduces oligomerisation of fatty acids, while a high ratio of Bronsted to Lewis sites explains the observed high BUFA yield. The combination of FTIR with CO adsorption, and temperature-programmed desorption of NH3, confirms that the presence of strong but few Bronsted acid sites in the 10-MR channels increases selectivity to MoBUFA. (C) 2015 Elsevier Inc. All rights reserved

Skeletal isomerisation of oleic acid over ferrierite in the presence and absence of triphenylphosphine : Pore mouth catalysis and related deactivation mechanisms

The formation and nature of coke (precursor) species has been studied during the skeletal isomerisation of oleic acid catalysed by protonated ferrierite, in the presence and absence of a triphenylphosphine promoter. UV-Vis and FT-IR spectroscopic analyses of the spent catalyst materials, complemented by NMR and mass spectrometry of the coke deposits extracted after HF dissolution, provide new insights into the deactivation mechanisms. Initial high catalyst activity and selectivity are quickly lost, despite conservation of the framework integrity, as a result of severe deactivation. Pore blockage is detected very early in the reaction, and only the pore mouth is actively employed. Additionally, polyenylic carbocations formed by hydrogen transfer reactions poison the active sites; they are considered to be the precursors to traces of condensed aromatics detected in the spent catalyst. Dodecyl benzene is the major "coke" constituent, and its precursor probably also competes for the active sites

Thioredoxin reductase enzyme activity measurements showed as nmolDTNB reduced per min per mg protein

<p><b>Copyright information:</b></p><p>Taken from "Thioredoxin reductase is a key factor in the oxidative stress response of WCFS1"</p><p>http://www.microbialcellfactories.com/content/6/1/29</p><p>Microbial Cell Factories 2007;6():29-29.</p><p>Published online 28 Aug 2007</p><p>PMCID:PMC2174512.</p><p></p> The strain NZ7601 was grown (black bars) aerobically and (gray bars) anaerobically at 37°C and was induced with 0 or 50 ng/ml nisinZ. After 5 hours of induction cell free extracts were prepared and TR activity was measured. The data shown above is the result of three independent experiments

Weblogo representation of conserved promotor regions in peroxide affected genes found using bioinformatics tools A) Regulatory motif -and B) uncharacterized regulatory motif

<p><b>Copyright information:</b></p><p>Taken from "Thioredoxin reductase is a key factor in the oxidative stress response of WCFS1"</p><p>http://www.microbialcellfactories.com/content/6/1/29</p><p>Microbial Cell Factories 2007;6():29-29.</p><p>Published online 28 Aug 2007</p><p>PMCID:PMC2174512.</p><p></p

Large Ferrierite Crystals as Models for Catalyst Deactivation during Skeletal Isomerisation of Oleic Acid : Evidence for Pore Mouth Catalysis

Large zeolite crystals of ferrierite have been used to study the deactivation, at the single particle level, of the alkyl isomerisation catalysis of oleic acid and elaidic acid by a combination of visible micro-spectroscopy and fluorescence microscopy (both polarised wide-field and confocal modes). The large crystals did show the desired activity, albeit only traces of the isomerisation product were obtained and low conversions were achieved compared to commercial ferrierite powders. This limited activity is in line with their lower external non-basal surface area, supporting the hypothesis of pore mouth catalysis. Further evidence for the latter comes from visible micro-spectroscopy, which shows that the accumulation of aromatic species is limited to the crystal edges, while fluorescence microscopy strongly suggests the presence of polyenylic carbocations. Light polarisation associated with the spatial resolution of fluorescence microscopy reveals that these carbonaceous deposits are aligned only in the larger 10-MR channels of ferrierite at all crystal edges. The reaction is hence further limited to these specific pore mouths

Large Ferrierite Crystals as Models for Catalyst Deactivation during Skeletal Isomerisation of Oleic Acid: Evidence for Pore Mouth Catalysis

Large zeolite crystals of ferrierite have been used to study the deactivation, at the single particle level, of the alkyl isomerisation catalysis of oleic acid and elaidic acid by a combination of visible micro-spectroscopy and fluorescence microscopy (both polarised wide-field and confocal modes). The large crystals did show the desired activity, albeit only traces of the isomerisation product were obtained and low conversions were achieved compared to commercial ferrierite powders. This limited activity is in line with their lower external non-basal surface area, supporting the hypothesis of pore mouth catalysis. Further evidence for the latter comes from visible micro-spectroscopy, which shows that the accumulation of aromatic species is limited to the crystal edges, while fluorescence microscopy strongly suggests the presence of polyenylic carbocations. Light polarisation associated with the spatial resolution of fluorescence microscopy reveals that these carbonaceous deposits are aligned only in the larger 10-MR channels of ferrierite at all crystal edges. The reaction is hence further limited to these specific pore mouths

Scale dependence of effective geochemical rates in weathering mine waste rock

International audienceHydrogeochemical models for the prediction of drainage quality from full-scale mine waste-rock piles are often parameterized using data from small-scale laboratory or field experiments of short duration. Yet, many model parameters and processes (e.g., sulfide-oxidation rates) vary strongly with the spatiotemporal dimensions of the experiment: the “upscaling” of prediction models remains a critical challenge for mine-waste management worldwide. Here, we investigate scale dependence in laboratory and field experiments that spanned orders-of-magnitude in size (i.e. 2 kg to 100,000 kg) at the Antamina mine in Peru. Normalized drainage mass loading rates systematically decreased with increasing scale, irrespective of waste-rock type. A process-based reactive-transport model was used to simulate observed rates and reproduce the geochemical composition of drainage across scales. Long-term trends in drainage quality could be quantitatively reproduced when the model was parameterized with mostly scale- and experiment-specific measured bulk properties or literature values, leaving geochemical rate coefficients the sole calibrated model parameters. Analysis of these fitted parameters revealed that the scale dependence of geochemical rates was largely explained by reactive mineral surface area. This work demonstrates that practical drainage quality predictions for full-scale waste-rock piles can be established from readily available bulk parameters determined at multiple scales