Effect of cinnamic acid on the growth and on plasma membrane H+–ATPase activity of Saccharomyces cerevisiae

Chemometric study on the biochemical marker of the manglicolous fungi to illustrate its potentiality as a bio indicator for heavy metal pollution in Indian Sundarbans

The study represents in vitro chemometric approach for assessing the heavy metal pollution in Indian Sundarbans. Physio-chemical and elemental characterisation of the sediment samples of Indian Sundarbans had shown high enrichments of toxic metal ions. It was characterised by elevated enrichment factors (2.16-10.12), geo-accumulation indices (0.03 -1.21), contamination factors (0.7-3.43) and pollution load indices (1.0-1.25) which showed progressive sediment quality deterioration and ecotoxicological risk due to metal ions contamination. The physio-chemical parameters of the sediments were replicated and computational chemometric modeling was utilized to assess fungal metabolic growth. All the fungi isolates had shown maximum metabolic activity in high temperature, alkaline pH, and high salinity. Further, the fungal metabolic activity was assessed in different gradient of heavy metal concentration. The significant deterioration of biochemical marker with increasing concentration of heavy metal indicates the status of the microbial health due to toxic metal pollution in the mangrove habitat.

Tolerance of Yarrowia lipolytica to inhibitors commonly found in lignocellulosic hydrolysates

BACKGROUND

Lignocellulosic material is a suitable renewable carbon and energy source for microbial cell factories, such as Yarrowia lipolytica. To be accessible for microorganisms, the constituent sugars need to be released in a hydrolysis step, which as a side effect leads to the formation of various inhibitory compounds. However, the effects of these inhibitory compounds on the growth of Y. lipolytica have not been thoroughly investigated.

RESULTS

Here we show the individual and combined effect of six inhibitors from three major inhibitor groups on the growth of Y. lipolytica. We engineered a xylose consuming strain by overexpressing the three native genes XR, XDH, and XK and found that the inhibitor tolerance of Y. lipolytica is similar in glucose and in xylose. Aromatic compounds could be tolerated at high concentrations, while furfural linearly increased the lag phase of the cultivation, and hydroxymethylfurfural only inhibited growth partially. The furfural induced increase in lag phase can be overcome by an increased volume of inoculum. Formic acid only affected growth at concentrations above 25 mM. In a synthetic hydrolysate, formic acid, furfural, and coniferyl aldehyde were identified as the major growth inhibitors.

CONCLUSION

We showed the individual and combined effect of inhibitors found in hydrolysate on the growth of Y. lipolytica. Our study improves understanding of the growth limiting inhibitors found in hydrolysate and enables a more targeted engineering approach to increase the inhibitor tolerance of Y. lipolytica. This will help to improve the usage of Y. lipolytica as a sustainable microbial cell factory.

Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution

Toxicity from the external presence or internal production of compounds can reduce the growth and viability of microbial cell factories and compromise productivity. Aromatic compounds are generally toxic for microorganisms, which makes their production in microbial hosts challenging. Here we use adaptive laboratory evolution to generate Saccharomyces cerevisiae mutants tolerant to two aromatic acids, coumaric acid and ferulic acid. The evolution experiments were performed at low pH (3.5) to reproduce conditions typical of industrial processes. Mutant strains tolerant to levels of aromatic acids near the solubility limit were then analyzed by whole genome sequencing, which revealed prevalent point mutations in a transcriptional activator (Aro80) that is responsible for regulating the use of aromatic amino acids as the nitrogen source. Among the genes regulated by Aro80, ESBP6 was found to be responsible for increasing tolerance to aromatic acids by exporting them out of the cell. Further examination of the native function of Esbp6 revealed that this transporter can excrete fusel acids (byproducts of aromatic amino acid catabolism) and this role is shared with at least one additional transporter native to S. cerevisiae (Pdr12). Besides conferring tolerance to aromatic acids, ESBP6 overexpression was also shown to significantly improve the secretion in coumaric acid production strains. Overall, we showed that regulating the activity of transporters is a major mechanism to improve tolerance to aromatic acids. These findings can be used to modulate the intracellular concentration of aromatic compounds to optimize the excretion of such products while keeping precursor molecules inside the cell.

Optimisation of trans-cinnamic acid and hydrocinnamyl alcohol production with recombinant Saccharomyces cerevisiae and identification of cinnamyl methyl ketone as a by-product

Trans-cinnamic acid (tCA) and hydrocinnamyl alcohol (HcinOH) are valuable aromatic compounds with applications in the flavour, fragrance and cosmetic industry. They can be produced with recombinant yeasts from sugars via phenylalanine after expression of a phenylalanine ammonia lyase (PAL) and an aryl carboxylic acid reductase. Here, we show that in Saccharomyces cerevisiae a PAL enzyme from the bacterium Photorhabdus luminescens was superior to a previously used plant PAL enzyme for the production of tCA. Moreover, after expression of a UDP-glucose:cinnamate glucosyltransferase (FaGT2) from Fragaria x ananassa, tCA could be converted to cinnamoyl-D-glucose which is expected to be less toxic to the yeast cells. Production of tCA and HcinOH from glucose could be increased by eliminating feedback-regulated steps of aromatic amino acid biosynthesis and diminishing the decarboxylation step of the competing Ehrlich pathway. Finally, an unknown by-product resulting from further metabolisation of a carboligation product of cinnamaldehyde (cinALD) with activated acetaldehyde, mediated by pyruvate decarboxylases, could be identified as cinnamyl methyl ketone providing a new route for the biosynthesis of precursors, such as (2S,3R) 5-phenylpent-4-ene-2,3-diol, necessary for the chemical synthesis of specific biologically active drugs such as daunomycin.

Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to Brettanomyces bruxellensis contamination is currently a problem. This yeast causes a "horse sweat" flavor in wine, which is an undesired organoleptic attribute. To date, 6 B. bruxellensis annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of B. bruxellensis LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of B. bruxellensis LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of B. bruxellensis LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast B. bruxellensis.

Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance

A major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because the mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variations in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene overexpression in different Saccharomyces cerevisiae (yeast) strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six different S. cerevisiae strains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to identify common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene overexpression in three different strains, we revealed the breadth of the background-specific effects of gene fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms.

IMPORTANCE

Recent studies on natural variation within Saccharomyces cerevisiae have uncovered substantial phenotypic diversity. Here, we took advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated the physiological states of cells when exposed to this stress. We also explored the strain-specific effects of gene overexpression to further identify strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.

Phytochemical profiling as a solution to palliate disinfectant limitations

The indiscriminate use of biocides for general disinfection has contributed to the increased incidence of antimicrobial tolerant microorganisms. This study aims to assess the potential of seven phytochemicals (tyrosol, caffeic acid, ferulic acid, cinnamaldehyde, coumaric acid, cinnamic acid and eugenol) in the control of planktonic and sessile cells of Staphylococcus aureus and Escherichia coli. Cinnamaldehyde and eugenol showed antimicrobial properties, minimum inhibitory concentrations of 3-5 and 5-12 mM and minimum bactericidal concentrations of 10-12 and 10-14 mM against S. aureus and E. coli, respectively. Cinnamic acid was able to completely control adhered bacteria with effects comparable to peracetic acid and sodium hypochlorite and it was more effective than hydrogen peroxide (all at 10 mM). This phytochemical caused significant changes in bacterial membrane hydrophilicity. The observed effectiveness of phytochemicals makes them interesting alternatives and/or complementary products to commonly used biocidal products. Cinnamic acid is of particular interest for the control of sessile cells.

Comparative transcriptome assembly and genome-guided profiling for Brettanomyces bruxellensis LAMAP2480 during p-coumaric acid stress

Brettanomyces bruxellensis has been described as the main contaminant yeast in wine production, due to its ability to convert the hydroxycinnamic acids naturally present in the grape phenolic derivatives, into volatile phenols. Currently, there are no studies in B. bruxellensis which explains the resistance mechanisms to hydroxycinnamic acids, and in particular to p-coumaric acid which is directly involved in alterations to wine. In this work, we performed a transcriptome analysis of B. bruxellensis LAMAP248rown in the presence and absence of p-coumaric acid during lag phase. Because of reported genetic variability among B. bruxellensis strains, to complement de novo assembly of the transcripts, we used the high-quality genome of B. bruxellensis AWRI1499, as well as the draft genomes of strains CBS2499 and0 g LAMAP2480. The results from the transcriptome analysis allowed us to propose a model in which the entrance of p-coumaric acid to the cell generates a generalized stress condition, in which the expression of proton pump and efflux of toxic compounds are induced. In addition, these mechanisms could be involved in the outflux of nitrogen compounds, such as amino acids, decreasing the overall concentration and triggering the expression of nitrogen metabolism genes.

Growth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain

Introduction

Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. Because intracellular levels of key metabolites are growth-rate dependent, slow growth can significantly affect biomass-specific productivity. Using an engineered Saccharomyces cerevisiae strain expressing a heterologous pathway for resveratrol production as a model energy-requiring product, the impact of specific growth rate on yeast physiology and productivity was investigated in aerobic, glucose-limited chemostat cultures.

Results

Stoichiometric analysis revealed that de novo resveratrol production from glucose requires 13 moles of ATP per mole of produced resveratrol. The biomass-specific production rate of resveratrol showed a strong positive correlation with the specific growth rate. At low growth rates a substantial fraction of the carbon source was invested in cellular maintenance-energy requirements (e.g. 27 % at 0.03 h⁻¹). This distribution of resources was unaffected by resveratrol production. Formation of the by-products coumaric, phloretic and cinnamic acid had no detectable effect on maintenance energy requirement and yeast physiology in chemostat. Expression of the heterologous pathway led to marked differences in transcript levels in the resveratrol-producing strain, including increased expression levels of genes involved in pathways for precursor supply (e.g. ARO7 and ARO9 involved in phenylalanine biosynthesis). The observed strong differential expression of many glucose-responsive genes in the resveratrol producer as compared to a congenic reference strain could be explained from higher residual glucose concentrations and higher relative growth rates in cultures of the resveratrol producer.

Conclusions

De novo resveratrol production by engineered S. cerevisiae is an energy demanding process. Resveratrol production by an engineered strain exhibited a strong correlation with specific growth rate. Since industrial production in fed-batch reactors typically involves low specific growth rates, this study emphasizes the need for uncoupling growth and product formation via energy-requiring pathways.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0321-6) contains supplementary material, which is available to authorized users.

Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris

Lignocellulosic biomass hydrolysates hold great potential as a feedstock for microbial biofuel production, due to their high concentration of fermentable sugars. Present at lower concentrations are a suite of aromatic compounds that can inhibit fermentation by biofuel-producing microbes. We have developed a microbial-mediated strategy for removing these aromatic compounds, using the purple nonsulfur bacterium Rhodopseudomonas palustris. When grown photoheterotrophically in an anaerobic environment, R. palustris removes most of the aromatics from ammonia fiber expansion (AFEX) treated corn stover hydrolysate (ACSH), while leaving the sugars mostly intact. We show that R. palustris can metabolize a host of aromatic substrates in ACSH that have either been previously described as unable to support growth, such as methoxylated aromatics, and those that have not yet been tested, such as aromatic amides. Removing the aromatics from ACSH with R. palustris, allowed growth of a second microbe that could not grow in the untreated ACSH. By using defined mutants, we show that most of these aromatic compounds are metabolized by the benzoyl-CoA pathway. We also show that loss of enzymes in the benzoyl-CoA pathway prevents total degradation of the aromatics in the hydrolysate, and instead allows for biological transformation of this suite of aromatics into selected aromatic compounds potentially recoverable as an additional bioproduct.

Phenolic characterization and antimicrobial activity of folk medicinal plant extracts for their applications in olive production

Phytophthora spp is important in plant pathology due to the importance of the diseases it causes. In olive trees, severe damages are caused by the disease known as "dry branch" occasioned by Phytophthora nicotianae, P. citrophthora and P. palmivora. Much effort has been made to find efficient methods of control, with a low negative impact on environment. In this regard, treatment with plant extracts is a valid strategy. The aims of the present study are (i) to determine the polyphenol composition of extracts of Thymus vulgaris, Origanum vulgare, Matricaria recutita, and Larrea divaricata by CZE, (ii) correlate the analytical composition of these extracts with the inhibition on the mycelial growth, and (iii) determine the individual antimicrobial activity of the most active ingredients. A simple methodology was developed for the determination of catechin, naringenin, cinnamic acid, syringic acid, chlorogenic acid, apigenin, vanillic acid, luteolin, quercetin, and caffeic acid in plant extracts by CZE. The extraction of phenolic compounds in extract was performed by a miniaturized solid phase extraction using a home-made minicolumn packed with suitable filtering material (C18 , 50 mg). The optimized analyses conditions were: 30 mM boric acid buffer, pH 9.50; capillary, 57 cm full length, 50 cm effective length, 75 μm id, hydrodynamic injection 30 mbar, 2 s; 25 kV; 25°C, detection by UV absorbance at 290 nm. Sample results suggest that phenolic composition seems to have a great influence on inhibition of pathogens. The highest inhibitions of mycelial growth were observed for cinnamic acid and naringenin.

Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors

Lignocellulosic hydrolysate (LCH) inhibitors are a large class of bioactive molecules that arise from pretreatment, hydrolysis, and fermentation of plant biomass. These diverse compounds reduce lignocellulosic biofuel yields by inhibiting cellular processes and diverting energy into cellular responses. LCH inhibitors present one of the most significant challenges to efficient biofuel production by microbes. Development of new strains that lessen the effects of LCH inhibitors is an economically favorable strategy relative to expensive detoxification methods that also can reduce sugar content in deconstructed biomass. Systems biology analyses and metabolic modeling combined with directed evolution and synthetic biology are successful strategies for biocatalyst development, and methods that leverage state-of-the-art tools are needed to overcome inhibitors more completely. This perspective considers the energetic costs of LCH inhibitors and technologies that can be used to overcome their drain on conversion efficiency. We suggest academic and commercial research groups could benefit by sharing data on LCH inhibitors and implementing "translational biofuel research."

Modeling the Efficacy of Triplet Antimicrobial Combinations: Yeast Suppression by Lauric Arginate, Cinnamic Acid, and Sodium Benzoate or Potassium Sorbate as a Case Study

The growth of four spoilage yeasts, Saccharomyces cerevisiae, Zygosaccharomyces bailii, Brettanomyces bruxellensis, and Brettanomyces naardenensis, was inhibited with three-agent (triplet) combinations of lauric arginate, cinnamic acid, and sodium benzoate or potassium sorbate. The inhibition efficacy was determined by monitoring the optical density of yeast cultures grown in microtiter plates for 7 days. The relationship between the optical density and the sodium benzoate and potassium sorbate concentrations followed a single-term exponential decay model. The critical effective concentration was defined as the concentration at which the optical density was 0.05, which became an efficacy criterion for the mixtures. Critical concentrations of sodium benzoate or potassium sorbate as a function of the lauric arginate and cinnamic acid concentrations were then fitted with an empirical model that mapped three-agent combinations of equal efficacy. The contours of this function are presented in tabulated form and as two- and three-dimensional plots. Triplet combinations were highly effective against all four spoilage yeasts at three practical pH levels, especially at pH 3.0. The triplet combinations were particularly effective for inhibiting growth of Z. bailii, and combinations containing potassium sorbate had synergistic activities. The equal efficacy concentration model also allowed tabulation of the cost of the various combinations of agents and identification of those most economically feasible.

Effect of α-Cyclodextrin–Cinnamic Acid Inclusion Complexes on Populations of Escherichia coli O157:H7 and Salmonella enterica in Fruit Juices

Cinnamic acid (CA), a naturally occurring organic acid found in fruits and spices, has antimicrobial activity against spoilage and pathogenic bacteria, but low aqueous solubility limits its use. The purpose of this study was to determine the effectiveness of solubility-enhancing α-cyclodextrin–CA inclusion complexes against Escherichia coli O157:H7 and Salmonella enterica serovars suspended in apple cider or orange juice at two different incubation temperatures (4 and 26°C). Two concentrations (400 and 1,000 mg/liter) of α-cyclodextrin-CA inclusion complex were aseptically added to apple cider inoculated with E. coli O157:H7 (7 log CFU/ml) and orange juice inoculated with a cocktail of six Salmonella enterica serovars (7 log CFU/ml). Samples were extracted at 0 min, at 2 min, and at 24-h intervals for 7 days, serially diluted in 0.1% peptone, spread plated in duplicate onto tryptic soy agar, and incubated at 35°C for 24 h. Populations of E. coli O157:H7 in apple cider were significantly reduced (P ≤ 0.05) during the 7-day sampling period in all solutions regardless of temperature. Compared with the controls, populations were significantly reduced by the addition of 400 and 1,000 mg/liter inclusion complex, but reductions were not significantly different (P ≥ 0.05) between the two treatment groups (400 and 1,000 mg/liter). Salmonella was significantly reduced in all solutions regardless of temperature. There were significant differences between the control and each inclusion complex concentration at 4 and 26°C. Coupled with additional processing steps, α-cyclodextrin–CA inclusion complexes may provide an alternative to traditional heat processes.

Brettanomyces bruxellensis evolution and volatile phenols production in red wines during storage in bottles

AIMS

The presence of Brettanomyces bruxellensis is an important issue during winemaking because of its volatile phenols production capacities. The aim of this study is to provide information on the ability of residual B. bruxellensis populations to multiply and spoil finished wines during storage in bottles.

METHODS AND RESULTS

Several finished wines were studied. Brettanomyces bruxellensis populations were monitored during two and a half months, and volatile phenols as well as chemical parameters regularly determined. Variable growth and volatile phenols synthesis capacities were evidenced, in particularly when cells are in a noncultivable state. In addition, the volatile phenol production was clearly shown to be a two-step procedure that could strongly be correlated to the physiological state of the yeast population.

CONCLUSIONS

This study underlines the importance of minimizing B. bruxellensis populations at the end of wine ageing to reduce volatile phenols production risk once the wine in bottle. Moreover, the physiological state of the yeast seems to have an important impact on ethyl-phenols production, hence demonstrating the importance of taking into account this parameter when analysing wine spoilage risks.

SIGNIFICANCE AND IMPACT OF THE STUDY

Little data exist about the survival of B. bruxellensis once the wine in bottle. This study provides information on the alteration risks encountered during wine storage in bottle and reveals the importance of carrying on further studies to increase the knowledge on B. bruxellensis physiology.

Characterization of phenolic compounds in some Indian mango cultivars

Mangoes (Mangifera indica) are rich in phenolic acids as detected by high-performance liquid chromatography. The phenolics have prominent medicinal properties. Among six important commercial mango cultivars (Deshi, Langra, Chausa, Mallika, Dashahari and Amrapali) tannic acid was maximal in Mallika, while gallic acid was maximal in Chausa and all other varieties. Caffeic acid was maximal in Langra followed by Chausa and Amrapali. Many of the pharmacological properties attributed to mango might be due to the presence of phenolic acids in fairly significant amounts.

Chemotaxonomic variability in Zizyphus mouritiana varieties and its pharmacological properties in relation to human health

Twenty varieties of ber (Zizyphus mouritiana), namely umaran, katha, bilayati, kaithli, ZG-3, gola, safeda rohtak, takadi, tikari, banarasi karaka, seo, sonaur-2, sonaur-3, ilaichi, mundia murahra, pathan, kakrola gola, seb, golden yellow and chhuhara, were investigated for the presence of phenolic acids in stem bark, leaves and fruits using high performance liquid chromatograph. Results indicated the presence of tannic (retention time (Rt.) 2.76 min), gallic (Rt. 2.86 min), caffeic (Rt. 3.12 min), vanillic (Rt. 3.26 min), ferulic (Rt. 3.42 min), chlorogenic (Rt. 4.16 min) and cinnamic acids (Rt. 4.45 min) in varying amounts in different parts in of these varieties. In fruits of seven varieties, namely, kaithly, sonaur-2, sonaur-3, mundia murahra, pathan, golden yellow and chhuhara, oxalic acid (Rt. 3.00 min) was also detected. Pharmacological properties of phenolic acids of fruits in relation to human health and the possible implications of different phenolic acids in chemotaxonomy of different varieties of ber are discussed.

Cinnamic acid inhibits growth but stimulates production of pathogenesis factors by in vitro cultures of Fusarium oxysporum f.sp. niveum

Long-term monoculture of watermelon leads to frequent occurrence of watermelon fusarium wilt caused by Fusarium oxysporum f.sp. niveum (FON). Some allelochemicals contained in watermelon root exudates and decaying residues are possibly responsible for promoting the wilt disease. The purpose of this study was to evaluate the allelopathic effect of artificially applied cinnamic acid on FON. Results demonstrated that hyphal growth of FON was strongly inhibited by cinnamic acid. At the highest concentration of cinnamic acid, the biomass in liquid culture was decreased by 63.3%, while colony diameter, conidial germination on plates, and conidial production in liquid culture were completely inhibited. However, mycotoxin production and activity of phytopathogenic enzymes were greatly stimulated. Mycotoxin yield, pectinase activity, proteinase activity, cellulase activity, and amylase activity were increased by 490, 590, 760, 2006, and 27.0%, respectively. It was concluded that cinnamic acid dramatically stimulated mycotoxin production and activities of hydrolytic enzymes by FON but inhibited growth and germination of FON. The findings presented here indicate that cinnamic acid is involved in promoting watermelon fusarium wilt.

The proteome and transcriptome analysis of Bacillus subtilis in response to salicylic acid

Phenolic acids that are present in plant-soil ecosystems can be considered as toxins which induce specific stress responses in microorganisms. In this paper, we have analyzed the global response of the soil bacterium Bacillus subtilis to salicylic acid using proteomics and transcriptomics. The results demonstrate that salicylic acid caused predominantly the induction of the SigmaB-dependent general stress response in B. subtilis which is not related to the acidic conditions. Treatment of B. subtilis with growth-inhibitory concentrations of 4 mM salicylic acid caused protein damage in B. subtilis as reflected by the induction of the CtsR and Spx regulons. Both phenolic acid decarboxylases (pads) of B. subtilis padC and bsdBCD (yclBCD) were induced by 4 mM salicylic acid that were previously shown to be involved in decarboxylation and detoxification of different phenolic acids. Deletion of the putative LysR-type regulator encoded by the divergently transcribed bsdA (yclA) gene upstream of the bsdBCD operon revealed that BsdA is the transcriptional activator of bsdBCD expression in response to salicylic acid. Phenotype analysis of bsdA and padC single and double mutants demonstrated that both pads confer resistance to salicylic acid in B. subtilis.

Cloning, deletion, and characterization of PadR, the transcriptional repressor of the phenolic acid decarboxylase-encoding padA gene of Lactobacillus plantarum

Lactobacillus plantarum displays a substrate-inducible padA gene encoding a phenolic acid decarboxylase enzyme (PadA) that is considered a specific chemical stress response to the inducing substrate. The putative regulator of padA was located in the padA locus based on its 52% identity with PadR, the padA gene transcriptional regulator of Pediococcus pentosaceus (L. Barthelmebs, B. Lecomte, C. Diviès, and J.-F. Cavin, J. Bacteriol. 182:6724-6731, 2000). Deletion of the L. plantarum padR gene clearly demonstrates that the protein it encodes is the transcriptional repressor of divergently oriented padA. The padR gene is cotranscribed with a downstream open reading frame (ORF1), the product of which may belong to a group of universal stress proteins (Usp). The padR deletion mutant overexpressed padA constitutively, and the padA promoter appears to be tightly regulated in this bacterium. Gel mobility shift assays using the padA gene promoter region and purified PadR expressed in Escherichia coli indicated that operator DNA binding by PadR was not eliminated by addition of p-coumarate. Gel mobility shift assays using partially purified extracts of native PadR protein from both phenolic acid-induced and noninduced L. plantarum cells demonstrate that inactivation of PadR by phenolic acids requires the integrity of L. plantarum and mediation by a specific protein absent in E. coli.

Genome-wide transcriptional changes during the lag phase of Saccharomyces cerevisiae

The set of physiological and metabolic changes occurring immediately after inoculation and during the lag phase is thought to be of vital importance for optimal offset of fermentation. The transcriptional changes taking place during the lag phase after inoculation of a late-respiratory-phase yeast culture into fresh, minimal medium were investigated by use of Yeast GeneFilters. In response to the nutritional up-shift, 240 open reading frames were at least five-fold induced and 122 were at least five-fold repressed. These genes were hierarchically clustered according to their lag-phase expression patterns. The majority of the induced genes were most highly induced early in the lag phase, whereas strong repression generally occurred later. Clustering of the genes showed that many genes with similar roles had similar expression patterns. Repressed genes, however, did not cluster as tightly according to function as induced genes. Genes involved in RNA and protein synthesis and processing showed a peak in expression early in the lag phase, except most ribosomal protein genes, which were induced early and whose expression was sustained. Genes involved in chromatin/chromosome structure showed late induction. The correlation between function and expression pattern for these genes indicates regulation by similar mechanisms. Much of the transcriptional response observed appeared to be due to the presence of glucose in the new medium.

Inducible metabolism of phenolic acids in Pediococcus pentosaceus is encoded by an autoregulated operon which involves a new class of negative transcriptional regulator

Pediococcus pentosaceus displays a substrate-inducible phenolic acid decarboxylase (PAD) activity on p-coumaric acid. Based on DNA sequence homologies between the three PADs previously cloned, a DNA probe of the Lactobacillus plantarum pdc gene was used to screen a P. pentosaceus genomic library in order to clone the corresponding gene of this bacteria. One clone detected with this probe displayed a low PAD activity. Subcloning of this plasmid insertion allowed us to determine the part of the insert which contains a 534-bp open reading frame (ORF) coding for a 178-amino-acid protein presenting 81.5% of identity with L. plantarum PDC enzyme. This ORF was identified as the padA gene. A second ORF was located just downstream of the padA gene and displayed 37% identity with the product of the Bacillus subtilis yfiO gene. Subcloning, transcriptional analysis, and expression studies with Escherichia coli of these two genes under the padA gene promoter, demonstrated that the genes are organized in an autoregulated bicistronic operonic structure and that the gene located upstream of the padA gene encodes the transcriptional repressor of the padA gene. Transcription of this pad operon in P. pentosaceus is acid phenol dependent.

Knockout of the p-coumarate decarboxylase gene from Lactobacillus plantarum reveals the existence of two other inducible enzymatic activities involved in phenolic acid metabolism

Lactobacillus plantarum NC8 contains a pdc gene coding for p-coumaric acid decarboxylase activity (PDC). A food grade mutant, designated LPD1, in which the chromosomal pdc gene was replaced with the deleted pdc gene copy, was obtained by a two-step homologous recombination process using an unstable replicative vector. The LPD1 mutant strain remained able to weakly metabolize p-coumaric and ferulic acids into vinyl derivatives or into substituted phenyl propionic acids. We have shown that L. plantarum has a second acid phenol decarboxylase enzyme, better induced with ferulic acid than with p-coumaric acid, which also displays inducible acid phenol reductase activity that is mostly active when glucose is added. Those two enzymatic activities are in competition for p-coumaric and ferulic acid degradation, and the ratio of the corresponding derivatives depends on induction conditions. Moreover, PDC appeared to decarboxylate ferulic acid in vitro with a specific activity of about 10 nmol. min(-1). mg(-1) in the presence of ammonium sulfate. Finally, PDC activity was shown to confer a selective advantage on LPNC8 grown in acidic media supplemented with p-coumaric acid, compared to the LPD1 mutant devoid of PDC activity.