Induction of heat shock proteins DnaK, GroEL, and GroES by salt stress in Lactococcus lactis

Effects of osmotic stress on Listeria monocytogenes ATCC 7644: persistent cells and heat resistance

Persistent bacteria are a microbial subpopulation that, exposed to bactericidal treatment, is killed at a slower rate than the rest of the population they are part of. They can be triggered either following stress or stochastically without external signals. The hallmark of persistent bacteria is the biphasic killing curve, a sign that, within a microbial population, two subpopulations are inactivated at a different rate. Furthermore, when plated into a fresh medium and in the absence of stressors, persistent bacteria typically remain in the lag phase longer before resuming active replication. This study aims to evaluate in vitro whether the formation of persistent cells in a strain of Listeria monocytogenes can be triggered by exposure to osmotic stress and if this phenomenon can increase heat resistance in the bacterial population. In a first experiment, the lag time distribution of a L. monocytogenes strain grown in a 6% NaCl broth was evaluated using the software ScanLag. A stationary phase broth culture was inoculated on agar plates placed on an office scanner inside an incubator at 37°C. The plates were scanned every 20' for 4 days and the acquired images were automatically elaborated with the aid of MatLab software in order to evaluate the appearance times of every single colony. The experiment was also carried out on a control culture obtained by growing the strain in the broth without salt. In a second experiment, the same broth cultures, after proper dilutions to rebalance NaCl concentration, were subjected to a heat treatment at 51°C and the death curves obtained were parameterized using the GinaFit system. Results showed that the lag phase of 31.40% of the salt culture colonies was long enough to suppose the formation of persistent bacteria. Analyses of the thermal survival curves showed that the shoulder and tail model was the one that best represented the inactivation trend of the salt culture, unlike the control culture, whose trend was essentially linear. Results of the present study show how exposure to salt could induce the formation of persistent bacteria in a L. monocytogenes strain. The last raises concerns as persistent cells may not only be undetected with common analytical techniques but they even show a greater heat resistance.

Bacterial proteomics and its application for pathogenesis studies

Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which leads to preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic methods to study various macromolecules of bacteria, which are complementary methods and provide comprehensive information. Proteomic approaches are used to identify proteins and their cell applications. Furthermore, to study bacterial proteins, macromolecules are involved in the bacteria's structures and functions. These protein-based methods provide comprehensive information about the cells, such as the external structures, internal compositions, post-translational modifications, and mechanisms of particular actions such as biofilm formation, antibiotic resistance, and adaptation to the environment, which are helpful in promoting bacterial pathogenesis. These methods use various devices such as MALDI-TOF MS, LC-MS, and two-dimensional electrophoresis, which are valuable tools for studying different structural and functional proteins of the bacteria and their mechanisms of pathogenesis that causes rapid, easy, and accurate diagnosis of the infections.

Evaluation of non-thermal effect of microwave radiation and its mode of action in bacterial cell inactivation

A growing body of literature has recognized the non-thermal effect of pulsed microwave radiation (PMR) on bacterial systems. However, its mode of action in deactivating bacteria has not yet been extensively investigated. Nevertheless, it is highly important to advance the applications of PMR from simple to complex biological systems. In this study, we first optimized the conditions of the PMR device and we assessed the results by simulations, using ANSYS HFSS (High Frequency Structure Simulator) and a 3D particle-in-cell code for the electron behavior, to provide a better overview of the bacterial cell exposure to microwave radiation. To determine the sensitivity of PMR, Escherichia coli and Staphylococcus aureus cultures were exposed to PMR (pulse duration: 60 ns, peak frequency: 3.5 GHz) with power density of 17 kW/cm² at the free space of sample position, which would induce electric field of 8.0 kV/cm inside the PBS solution of falcon tube in this experiment at 25 °C. At various discharges (D) of microwaves, the colony forming unit curves were analyzed. The highest ratios of viable count reductions were observed when the doses were increased from 20D to 80D, which resulted in an approximate 6 log reduction in E. coli and 4 log reduction in S. aureus. Moreover, scanning electron microscopy also revealed surface damage in both bacterial strains after PMR exposure. The bacterial inactivation was attributed to the deactivation of oxidation-regulating genes and DNA damage.

Proteomic analysis of Lactobacillus casei in response to different pHs using two-dimensional electrophoresis and MALDI TOF mass spectroscopy

Background and Objectives:

Lactobacillus casei, an acid-resistant bacterium, has a protective role against the pathogens. So we aimed to determine the proteome of Lactobacillus casei ATCC39392 strain in response to different pHs of 5 and 7 using proteomic analysis.

Materials and Methods:

Supernatant and bacterial extraction of Lactobacillus casei ATCC39392 adapts at pHs 5 and 7 were isolated using sodium dodecyl sulfate–polyacrylamide gel and two-dimensional gel electrophoresis. The comparison of results showed that 7 protein spots were seen in pH 5 but not in pH 7. Afterward, they were excised and sent for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to be identified.

Results:

Seven different proteins (four secretory and three structural) with different roles in human body health were identified. Prescribed proteins include putative cell wall associated Hydrolase, Glycoside Hydrolase, beta-N-Acetyl hexosaminidase, Histidine Kinase, Chaperonin, metal dependent Hydrolase and Lysozyme.

Conclusion:

Seven isolated proteins with anti-cancer and digestive impresses are proper subjects in therapy or drug delivery approaches especially oral drug usage for protection against stomach acidic area.

tepR encoding a bacterial enhancer-binding protein orchestrates the virulence and interspecies competition of Burkholderia glumae through qsmR and a type VI secretion system

The pathogenesis of the rice pathogenic bacterium Burkholderia glumae is under the tight regulation of the tofI/tofR quorum-sensing (QS) system. tepR, encoding a group I bacterial enhancer-binding protein, negatively regulates the production of toxoflavin, the phytotoxin acting as a major virulence factor in B. glumae. In this study, through a transcriptomic analysis, we identified the genes that were modulated by tepR and/or the tofI/tofR QS system. More than half of the differentially expressed genes, including the genes for the biosynthesis and transport of toxoflavin, were significantly more highly expressed in the ΔtepR mutant but less expressed in the ΔtofI-tofR (tofI/tofR QS-defective) mutant. In consonance with the transcriptome data, other virulence-related functions of B. glumae, extracellular protease activity and flagellum-dependent motility, were also negatively regulated by tepR, and this negative regulatory function of tepR was dependent on the IclR-type transcriptional regulator gene qsmR. Likewise, the ΔtepR mutant exhibited a higher level of heat tolerance in congruence with the higher transcription levels of heat shock protein genes in the mutant. Interestingly, tepR also exhibited its positive regulatory function on a previously uncharacterized type VI secretion system (denoted as BgT6SS-1). The survival of the both ΔtepR and ΔtssD (BgT6SS-1-defective) mutants was significantly compromised compared to the wild-type parent strain 336gr-1 in the presence of the natural rice-inhabiting bacterium, Pantoea sp. RSPAM1. Taken together, this study revealed pivotal regulatory roles of tepR in orchestrating multiple biological functions of B. glumae, including pathogenesis, heat tolerance, and bacterial interspecies competition.

Survival of Lactobacillus salivarius CECT 4063 and Stability of Antioxidant Compounds in Dried Apple Snacks as Affected by the Water Activity, the Addition of Trehalose and High Pressure Homogenization

Survival of probiotic microorganisms in dried foods is optimal for water activity (a_w) values between 0.1 and 0.3. Encapsulating and adding low-molecular weight additives can enhance probiotic viability in intermediate a_w food products, but the effectiveness of sub-lethal homogenization is still not proven. This study evaluates the effect of 10% (w/w) trehalose addition and/or 100 MPa homogenization on Lactobacillussalivarius CECT 4063 counts and antioxidant properties of apple slices dried to different water activity values (freeze-drying to a a_w of 0.25 and air-drying at 40 °C to a a_w of 0.35 and 0.45) during four-week storage. Optical and mechanical properties of dried samples were also analyzed. Freeze-drying had the least effect on the microbial counts and air drying at 40 °C to a a_w of 0.35 had the greatest effect. Antioxidant properties improved with drying, especially with convective drying. Decreases in both microbial and antioxidant content during storage were favored in samples with higher water activity values. Adding trehalose improved cell survival during storage in samples with a water activity of 0.35, but 100 MPa homogenization increased the loss of viability in all cases. Air-dried samples became more translucent and reddish, rather rubbery and less crispy than freeze-dried ones.

Gene regulation of the Lactobacillus vini in response to industrial stress in the fuel ethanol production

The industrial ethanol fermentation imposes several stresses to microorganisms. However, some bacterial species are well adapted and manage to endure these harmful conditions. Lactobacillus vini is one of the most found bacteria in these environments, indicating the existence of efficient tolerance mechanisms. In view of this premise, the present study aimed to describe the tolerance of L. vini to several stressing agents encounter in industrial environments and the genetic components of the stress response. In general, L. vini showed significant tolerance to stressors commonly found in fuel-ethanol fermentations, and only doses higher than normally reached in processes restrained its growth. The lag phase and the growth rate were the most responsive kinetic parameter affected. Gene expression analysis revealed that uspII gene positively responded to all conditions tested, a typical profile of a general stress response gene. In addition, the results also revealed aspects of regulatory modules of co-expressed genes responding to different stresses, and also the similarities of response mechanism with basis in common cellular damages. Altogether, these data contribute to uncover the factors that could favour L. vini in the industrial fermentation which could be shared with other well adapted species and reports the first stress response genes in this bacterium.

Molecular cloning, expression, and functional characterization of 70-kDa heat shock protein, DnaK, from Bacillus halodurans

In the present study, we report cloning, sequencing, and functional characterization dnaK gene of B. halodurans that is the central component in cellular network of molecular chaperones. The 3D structures of DnaK obtained by I-TASSER server showed that the overall structures of DnaK from B. halodurans and human HSP70 chaperone BiP are very similar with a homology of 88.8%. The purified recombinant DnaK consists of a His-tag at C-terminus and show a band on approximately 70-kDa region in SDS-PAGE. The resultant refolding assay revealed that the refolding rate was considerably improved by the addition of the novel DnaK chaperone for the refolding of heat-denatured carbonic anhydrase. Also, salt resistance experiments indicated that E. coli + DnaK survival had enhanced by 4.4-fold as compared with control cells in 0.4 M NaCl. The number of E. coli + DnaK colonies was 2.5-fold higher than control colonies in pH 9.5. We showed that DnaK refolding functions were decreased by increasing Cd²⁺ in nanomolar concentrations. Hg²⁺ had a biphasic effect on recombinant DnaK refolding function: inhibition at low and stimulation at high concentrations. It was concluded that the DnaK from B. halodurans can potentially be employed for improving functional properties of proteins in various applications.

Seawater salt-trapped Pseudomonas aeruginosa survives for years and gets primed for salinity tolerance

Background

In nature, microorganisms have to adapt to long-term stressful conditions often with growth limitations. However, little is known about the evolution of the adaptability of new bacteria to such environments. Pseudomonas aeruginosa, an opportunistic pathogen, after natural evaporation of seawater, was shown to be trapped in laboratory-grown halite crystals and to remain viable after entrapment for years. However, how this bacterium persists and survives in such hypersaline conditions is not understood.

Results

In this study, we aimed to understand the basis of survival, and to characterise the physiological changes required to develop salt tolerance using P. aeruginosa as a model. Several clones of P. aeruginosa were rescued after 14 years in naturally evaporated marine salt crystals. Incubation of samples in nutrient-rich broth allowed re-growth and subsequent plating yielded observable colonies. Whole genome sequencing of the P. aeruginosa isolates confirmed the recovery of the original strain. The re-grown strains, however, showed a new phenotype consisting of an enhanced growth in growing salt concentration compared to the ancestor strain. The intracellular accumulation of K⁺ was elicited by high concentration of Na⁺ in the external medium to maintain the homeostasis. Whole transcriptomic analysis by microarray indicated that 78 genes had differential expression between the parental strain and its derivative clones. Sixty-one transcripts were up-regulated, while 17 were down-regulated. Based on a collection of single-gene knockout mutants and gene ontology analysis, we suggest that the adaptive response in P. aeruginosa to hyper-salinity relies on multiple gene product interactions.

Conclusions

The individual gene contributions build up the observed phenotype, but do not ease the identification of salinity-related metabolic pathways. The long-term inclusion of P. aeruginosa in salt crystals primes the bacteria, mediating a readjustment of the bacterial physiology to growth in higher salt concentrations. Our findings provide a starting point to understand how P. aeruginosa, a relevant environmental and pathogenic bacterium, survives to long-term salt stress.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1499-2) contains supplementary material, which is available to authorized users.

Quantitative Proteomic Analysis of the Response of Probiotic Putative Lactococcus lactis NCDO 2118 Strain to Different Oxygen Availability Under Temperature Variation

Lactococcus lactis is a gram positive facultative anaerobe widely used in the dairy industry and human health. L. lactis subsp. lactis NCDO 2118 is a strain that exhibits anti-inflammatory and immunomodulatory properties. In this study, we applied a label-free shotgun proteomic approach to characterize and quantify the NCDO 2118 proteome in response to variations of temperature and oxygen bioavailability, which constitute the environmental conditions found by this bacterium during its passage through the host gastro-intestinal tract and in other industrial processes. From this proteomic analysis, a total of 1,284 non-redundant proteins of NCDO 2118 were characterized, which correspond to approximately 54% of its predicted proteome. Comparative proteomic analysis identified 149 and 136 proteins in anaerobic (30°C and 37°C) and non-aerated (30°C and 37°C) conditions, respectively. Our label-free proteomic analysis quantified a total of 1,239 proteins amongst which 161 proteins were statistically differentially expressed. Main differences were observed in cellular metabolism, stress response, transcription and proteins associated to cell wall. In addition, we identified six strain-specific proteins of NCDO 2118. Altogether, the results obtained in our study will help to improve the understanding about the factors related to both physiology and adaptive processes of L. lactis NCDO 2118 under changing environmental conditions.

Comparative proteomic analysis of four biotechnological strains Lactococcus lactis through label-free quantitative proteomics

Lactococcus lactis is a bacteria with high biotechnological potential, where is frequently used in the amino acid production and production of fermented dairy products, as well as drug delivery systems and mucosal vaccine vector. The knowledge of a functional core proteome is important extremely for both fundamental understanding of cell functions and for synthetic biology applications. In this study, we characterized the L. lacits proteome from proteomic analysis of four biotechnological strains L. lactis: L. lactis subsp. lactis NCDO2118, L. lactis subsp. lactis IL1403, L. lactis subsp. cremoris NZ9000 and L. lactis subsp. cremoris MG1363. Our label-free quantitative proteomic analysis of the whole bacterial lysates from each strains resulted in the characterization of the L. lactis core proteome that was composed by 586 proteins, which might contribute to resistance of this bacterium to different stress conditions as well as involved in the probiotic characteristic of L. lactis. Kegg enrichment analysis shows that ribosome, metabolic pathways, pyruvate metabolism and microbial metabolism in diverse environments were the most enriched. According to our quantitative proteomic analysis, proteins related to translation process were the more abundant in the core proteome, which represent an important step in the synthetic biology. In addition, we identified a subset of conserved proteins that are exclusive of the L. lactis subsp. cremoris or L. lactis subsp. lactis, which some are related to metabolic pathway exclusive. Regarding specific proteome of NCDO2118, we detected 'strain-specific proteins'. Finally, proteogenomics analysis allows the identification of proteins, which were not previously annotated in IL1403 and MG1363. The results obtained in this study allowed to increase our knowledge about the biology of L. lactis, which contributes to the implementation of strategies that make it possible to increase the biotechnological potential of this bacterium.

Stress Response and Virulence Potential Modulating Effect of Peppermint Essential Oil in Campylobacter jejuni

Campylobacter jejuni is one of the most common food-borne bacteria that causes gastrointestinal symptoms. In the present study we have investigated the molecular basis of the anti-Campylobacter effect of peppermint essential oil (PEO), one of the oldest EO used to treat gastrointestinal diseases. Transcriptomic, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and proteomic, two-dimensional polyacryl amid gel electrophoresis (2D-PAGE) methods have revealed that, in the presence of a sublethal concentration of PEO, the expression of several virulence-associated genes was decreased (cheY 0.84x; flhB 0.79x; flgE 0.205x; cadF 0.08x; wlaB 0.89x; porA 0.25x; cbf2 4.3x) while impaired motility was revealed with a functional analysis. Scanning electron micrographs of the exposed cells showed that, unlike in the presence of other stresses, the originally curved C. jejuni cells straightened upon PEO exposure. Gaining insight into the molecular background of this stress response, we have revealed that in the presence of PEO C. jejuni dominantly exerts a general stress response that elevates the expression of general stress genes like dnaK, groEL, groES (10.41x, 3.63x, and 4.77x). The most important genes dps, sodB, and katA involved in oxidative stress responses showed however moderate transcriptional elevations (1,58x, 1,55x, and 1,85x).

Increased salinity improves the thermotolerance of mesophilic anammox consortia

While the application of anammox-based process for mesophilic sidestream treatment is at present the state of the art and mainstream treatment at ambient temperature is also in development, the feasibility of thermophilic anammox process is still unclear. This study investigated the effects of salinity on the thermotolerance of mesophilic anammox sludge. In batch activity tests, 45 °C seems to be the critical temperature for the tolerance of mesophilic anammox consortia without acclimatization or amendments. The optimal anammox activity at 40, 42.5, and 45 °C can be achieved with the amendment of salt at 5-8, 8-10, and ~12 g NaCl L^-1, respectively. However, this improvement effect was limited at 50 °C or when the shock duration was longer than 24 h even at 45 °C. In continuous-flow bioreactors, mesophilic anammox consortia could gradually adapt to 40-50 °C under a transition of 2.5 °C, and the performance was enhanced by an increase in salinity, which may be associated with the increase in extracellular polymeric substances. A nitrogen removal rate of 0.53 kgN m^-3 d^-1 was finally obtained at 50 °C. Overall, these interesting results facilitate further opportunities for thermophilic anammox process.

Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress

Prolonged heat stress is one of the harsh conditions Lactobacillus casei strains encounter as non-starter lactic acid bacteria in dairy product manufacture. To understand the physiological and molecular mechanisms through which Lb. casei GCRL163 adapts to persistent elevated temperature, label-free quantitative proteomics of cell-free extracts was used to characterize the global responses of the strain cultured anaerobically in bioreactors at 30 to 45°C, pH 6.5, together with GC-MS for fatty acid methyl ester analysis at different growth phases. At higher growth temperatures, repression of energy-consuming metabolic pathways, such as fatty acid, nucleotide and amino acid biosynthesis, was observed, while PTS- and ABC-type transporter systems associated with uptake of nitrogen and carbon sources were up-regulated. Alkaline shock protein Asp23_2 was only detected at 45°C, expressed at high abundance, and presumptive α-L-fucosidase only at 40 and 45°C, with highly increased abundance (log2-fold change of 7) at 45°C. We identified a novel SecB homolog as a protein export chaperone putatively involved in posttranslational translocation systems, which was down-regulated as growth temperature increased and where the modelled 3D-structure shared architectural similarities with the Escherichia coli SecB protein. Membrane lipid analyses revealed temporal changes in fatty acid composition, cyclization of oleic acid to cyclopropane and novel cyclopentenyl moieties, and reduced synthesis of vaccenic acid, at higher temperatures. An 18kDa α-crystallin domain, Hsp20 family heat shock protein was more highly up-regulated in response to heat stress compared to other molecular chaperones, suggesting this protein could be a useful biomarker of prolonged heat stress in Lb. casei GCRL163.

Bacterial inactivation by plasma treated water enhanced by reactive nitrogen species

There is a growing body of literature that recognizes the importance of plasma treated water (PTW) for inactivation of microorganism. However, very little attention has been paid to the role of reactive nitrogen species (RNS) in deactivation of bacteria. The aim of this study is to explore the role of RNS in bacterial killing, and to develop a plasma system with increased sterilization efficiency. To increase the concentration of reactive oxygen and nitrogen species (RONS) in solution, we have used vapor systems (DI water/HNO₃ at different wt%) combined with plasma using N₂ as working gas. The results show that the addition of the vapor system yields higher RONS contents. Furthermore, PTW produced by N₂ + 0.5 wt% HNO₃ vapor comprises a large amount of both RNS and ROS, while PTW created by N₂ + H₂O vapor consists of a large amount of ROS, but much less RNS. Interestingly, we observed more deactivation of E. Coli with PTW created by N₂ + 0.5 wt% HNO₃ vapor plasma as compared to PTW generated by the other plasma systems. This work provides new insight into the role of RNS along with ROS for deactivation of bacteria.

Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19

Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp. paracasei TMW 1.1434 (isogenic with F19) under 11 typical stress conditions, including among others oxidative, osmotic, pH, and pressure stress. We identified and quantified >1900 proteins in triplicate analyses, representing 65% of all genes encoded in the genome. The identified genes were thoroughly annotated in terms of subcellular localization prediction and biological functions, suggesting unbiased and comprehensive proteome coverage. In total, 427 proteins were significantly differentially expressed in at least one condition. Most notably, our analysis suggests that optimal preconditioning toward drying was predicted to be alkaline and high-pressure stress preconditioning. Taken together, we believe the presented strategy may serve as a prototypic example for the analysis and utility of employing quantitative-mass-spectrometry-based proteomics to study bacterial physiology.

Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs

Bacteria can deploy various mechanisms to combat environmental stresses. Many genes have previously been identified in Lactococcus lactis that are involved in sensing the stressors and those that are involved in regulating and mounting a defense against the stressful conditions. However, the expression of small regulatory RNAs (sRNAs) during industrially relevant stress conditions has not been assessed yet in L. lactis, while sRNAs have been shown to be involved in many stress responses in other bacteria. We have previously reported the presence of hundreds of putative regulatory RNAs in L. lactis, and have used high-throughput RNA sequencing (RNA-seq) in this study to assess their expression under six different stress conditions. The uniformly designed experimental set-up enabled a highly reliable comparison between the different stress responses and revealed that many sRNAs are differentially expressed under the conditions applied. The primary stress responses of L. lactis NCDO712 was benchmarked to earlier work and, for the first time, the differential expression was assessed of transfer RNAs (tRNAs) and the genes from the six recently sequenced plasmids of NCDO712. Although, we only applied stresses for 5 min, the majority of the well-known specific stress-induced genes are already differentially expressed. We find that most tRNAs decrease after all stresses applied, except for a small number, which are increased upon cold stress. Starvation was shown to induce the highest differential response, both in terms of number and expression level of genes. Our data pinpoints many novel stress-related uncharacterized genes and sRNAs, which calls for further assessment of their molecular and cellular function. These insights furthermore could impact the way parameters are designed for bacterial culture production and milk fermentation, as we find that very short stress conditions already greatly alter gene expression.

Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes

The human pathogen Listeria monocytogenes continues to pose a challenge in the food industry, where it is known to contaminate ready-to-eat foods and grow during refrigerated storage. Increased knowledge of the cold-stress response of this pathogen will enhance the ability to control it in the food-supply-chain. This study utilized strand-specific RNA sequencing and whole cell fatty acid (FA) profiling to characterize the bacterium's cold stress response. RNA and FAs were extracted from a cold-tolerant strain at five time points between early lag phase and late stationary-phase, both at 4°C and 20°C. Overall, more genes (1.3×) were suppressed than induced at 4°C. Late stationary-phase cells exhibited the greatest number (n = 1,431) and magnitude (>1,000-fold) of differentially expressed genes (>2-fold, p<0.05) in response to cold. A core set of 22 genes was upregulated at all growth phases, including nine genes required for branched-chain fatty acid (BCFA) synthesis, the osmolyte transporter genes opuCBCD, and the internalin A and D genes. Genes suppressed at 4°C were largely associated with cobalamin (B12) biosynthesis or the production/export of cell wall components. Antisense transcription accounted for up to 1.6% of total mapped reads with higher levels (2.5×) observed at 4°C than 20°C. The greatest number of upregulated antisense transcripts at 4°C occurred in early lag phase, however, at both temperatures, antisense expression levels were highest in late stationary-phase cells. Cold-induced FA membrane changes included a 15% increase in the proportion of BCFAs and a 15% transient increase in unsaturated FAs between lag and exponential phase. These increases probably reduced the membrane phase transition temperature until optimal levels of BCFAs could be produced. Collectively, this research provides new information regarding cold-induced membrane composition changes in L. monocytogenes, the growth-phase dependency of its cold-stress regulon, and the active roles of antisense transcripts in regulating its cold stress response.

High-throughput mass spectrometry analysis revealed a role for glucosamine in potentiating recovery following desiccation stress in Chironomus

Desiccation tolerance is an essential survival trait, especially in tropical aquatic organisms that are vulnerable to severe challenges posed by hydroperiodicity patterns in their habitats, characterized by dehydration-rehydration cycles. Here, we report a novel role for glucosamine as a desiccation stress-responsive metabolite in the underexplored tropical aquatic midge, Chironomus ramosus. Using high- throughput liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS) analysis, biochemical assays and gene expression studies, we confirmed that glucosamine was essential during the recovery phase in C. ramosus larvae. Additionally, we demonstrated that trehalose, a known stress-protectant was crucial during desiccation but did not offer any advantage to the larvae during recovery. Based on our findings, we emphasise on the collaborative interplay of glucosamine and trehalose in conferring overall resilience to desiccation stress and propose the involvement of the trehalose-chitin metabolic interface in insects as one of the stress-management strategies to potentiate recovery post desiccation through recruitment of glucosamine.

A partial proteome reference map of Tetragenococcus halophilus and comparative proteomic and physiological analysis under salt stress

Tetragenococcus halophilus, a moderately halophilic Gram-positive lactic acid bacteria, was widely existed in many food fermentation systems, where salt stress is an environmental condition commonly encountered.

MALDI-TOF Mass Spectrometry Enables a Comprehensive and Fast Analysis of Dynamics and Qualities of Stress Responses of Lactobacillus paracasei subsp. paracasei F19

Lactic acid bacteria (LAB) are widely used as starter cultures in the manufacture of foods. Upon preparation, these cultures undergo various stresses resulting in losses of survival and fitness. In order to find conditions for the subsequent identification of proteomic biomarkers and their exploitation for preconditioning of strains, we subjected Lactobacillus (Lb.) paracasei subsp. paracasei TMW 1.1434 (F19) to different stress qualities (osmotic stress, oxidative stress, temperature stress, pH stress and starvation stress). We analysed the dynamics of its stress responses based on the expression of stress proteins using MALDI-TOF mass spectrometry (MS), which has so far been used for species identification. Exploiting the methodology of accumulating protein expression profiles by MALDI-TOF MS followed by the statistical evaluation with cluster analysis and discriminant analysis of principle components (DAPC), it was possible to monitor the expression of low molecular weight stress proteins, identify a specific time point when the expression of stress proteins reached its maximum, and statistically differentiate types of adaptive responses into groups. Above the specific result for F19 and its stress response, these results demonstrate the discriminatory power of MALDI-TOF MS to characterize even dynamics of stress responses of bacteria and enable a knowledge-based focus on the laborious identification of biomarkers and stress proteins. To our knowledge, the implementation of MALDI-TOF MS protein profiling for the fast and comprehensive analysis of various stress responses is new to the field of bacterial stress responses. Consequently, we generally propose MALDI-TOF MS as an easy and quick method to characterize responses of microbes to different environmental conditions, to focus efforts of more elaborate approaches on time points and dynamics of stress responses.

Ribosomal dimerization factor YfiA is the major protein synthesized after abrupt glucose depletion in Lactococcus lactis

We analysed the response of the model bacterium Lactococcus lactis to abrupt depletion of glucose after several generations of exponential growth. Glucose depletion resulted in a drastic drop in the energy charge accompanied by an extremely low GTP level and an almost total arrest of protein synthesis. Strikingly, the cell prioritized the continued synthesis of a few proteins, of which the ribosomal dimerization factor YfiA was the most highly expressed. Transcriptome analysis showed no immediate decrease in total mRNA levels despite the lowered nucleotide pools and only marginally increased levels of the yfiA transcript. Severe up-regulation of genes in the FruR, CcpA, ArgR and AhrC regulons were consistent with a downshift in carbon and energy source. Based upon the results, we suggest that transcription proceeded long enough to record the transcriptome changes from activation of the FruR, CcpA, ArgR and AhrC regulons, while protein synthesis stopped due to an extremely low GTP concentration emerging a few minutes after glucose depletion. The yfiA deletion mutant exhibited a longer lag phase upon replenishment of glucose and a faster death rate after prolonged starvation supporting that YfiA-mediated ribosomal dimerization is important for keeping long-term starved cells viable and competent for growth initiation.

Stress Physiology of Lactic Acid Bacteria

Lactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g., Lactococcus lactis), probiotic (e.g., several Lactobacillus spp.), and pathogenic (e.g., Enterococcus and Streptococcus spp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the "stressome" of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.

Characterization and function analysis of Hsp60 and Hsp10 under different acute stresses in black tiger shrimp, Penaeus monodon

Heat shock proteins (Hsps) are a class of highly conserved proteins produced in virtually all living organisms from bacteria to humans. Hsp60 and Hsp10, the most important mitochondrial chaperones, participate in environmental stress responses. In this study, the full-length complementary DNAs (cDNAs) of Hsp60 (PmHsp60) and Hsp10 (PmHsp10) were cloned from Penaeus monodon. Sequence analysis showed that PmHsp60 and PmHsp10 encoded polypeptides of 578 and 102 amino acids, respectively. The expression profiles of PmHsp60 and PmHsp10 were detected in the gills and hepatopancreas of the shrimps under pH challenge, osmotic stress, and heavy metal exposure, and results suggested that PmHsp60 and PmHsp10 were involved in the responses to these stimuli. ATPase and chaperone activity assay indicated that PmHsp60 could slow down protein denaturation and that Hsp60/Hsp10 may be combined to produce a chaperone complex with effective chaperone and ATPase activities. Overall, this study provides useful information to help further understand the functional mechanisms of the environmental stress responses of Hsp60 and Hsp10 in shrimp.

Adaptation of Lactococcus lactis to high growth temperature leads to a dramatic increase in acidification rate

Lactococcus lactis is essential for most cheese making, and this mesophilic bacterium has its growth optimum around 30 °C. We have, through adaptive evolution, isolated a mutant TM29 that grows well up to 39 °C, and continuous growth at 40 °C is possible if pre-incubated at a slightly lower temperature. At the maximal permissive temperature for the wild-type, 38 °C, TM29 grows 33% faster and has a 12% higher specific lactate production rate than its parent MG1363, which results in fast lactate accumulation. Genome sequencing was used to reveal the mutations accumulated, most of which were shown to affect thermal tolerance. Of the mutations with more pronounced effects, two affected expression of single proteins (chaperone; riboflavin transporter), two had pleiotropic effects (RNA polymerase) which changed the gene expression profile, and one resulted in a change in the coding sequence of CDP-diglyceride synthase. A large deletion containing 10 genes was also found to affect thermal tolerance significantly. With this study we demonstrate a simple approach to obtain non-GMO derivatives of the important L. lactis that possess properties desirable by the industry, e.g. thermal robustness and increased rate of acidification. The mutations we have identified provide a genetic basis for further investigation of thermal tolerance.

Transcriptional Analyses of Mandarins Seriously Infected by 'Candidatus Liberibacter asiaticus'

A range of leaf symptoms, including blotchy mottle, yellowing, and small, upright leaves with a variety of chlorotic patterns resembling those induced by zinc deficiencies, are associated with huanglongbing (HLB, yellow shoot disease), a worldwide destructive citrus disease. HLB is presumably caused by the phloem-limited fastidious prokaryotic α-proteobacterium ‘Candidatus Liberibacter spp.’ Previous studies focused on the proteome and transcriptome analyses of citrus 5 to 35 weeks after ‘Ca. L. spp.’ inoculation. In this study, gene expression profiles were analyzed from mandarin Citrus reticulate Blanco cv. jiaogan leaves after a 2 year infection with ‘Ca. L. asiaticus’. The Affymetrix microarray analysis explored 2,017 differentially expressed genes. Of the 1,364 genes had known functions, 938 (46.5%) were up-regulated. Genes related to photosynthesis, carbohydrate metabolic, and structure were mostly down-regulated, with rates of 92.7%, 61.0%, and 80.2%, respectively. Genes associated with oxidation-reduction and transport were mostly up-regulated with the rates of 75.0% and 64.6%, respectively. Our data analyses implied that the infection of ‘Ca. L. asiaticus’ could alter hormone crosstalk, inducing the jasmine acid pathway and depressing the ethylene and salicylic acid pathways in the citrus host. This study provides an enhanced insight into the host response of citrus to ‘Ca. L. asiaticus’ infection at a two-years infection stage.

A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World

Here we present the first report on the taxonomic diversity of the microbial communities of the saline desert of the Great Rann of Kutch, Gujarat, India, using a metagenomic approach. Seven samples, differing in salinity levels and covering different seasons, were analysed to investigate the dynamics of microbial communities in relation to salinity and season. Metagenomic data generated using whole metagenome sequencing revealed that despite its very high salinity (4.11-30.79 %), the saline desert's microbiota had a rich microbial diversity that included all major phyla. Notably, 67 archaeal genera, representing more than 60 % of all known archaeal genera, were present in this ecosystem. A strong positive correlation (0.85) was observed between the presence of the extremely halophilic bacterium Salinibacter and salinity level. Taxonomic and functional comparisons of the saline desert metagenome with those of other publicly available metagenomes (i.e. sea, hypersaline lagoon, solar saltern, brine, hot desert) was carried out. The microbial community of the Kutch was found to be unique yet more similar to the sea biomes followed by hypersaline lagoon.

Transcriptomic and proteomic analysis of Oenococcus oeni PSU-1 response to ethanol shock

The correct development of malolactic fermentation depends on the capacity of Oenococcus oeni to survive under harsh wine conditions. The presence of ethanol is one of the most stressful factors affecting O. oeni performance. In this study, the effect of ethanol addition (12% vol/vol) on O. oeni PSU-1 has been evaluated using a transcriptomic and proteomic approach. Transcriptomic analysis revealed that the main functional categories of the genes affected by ethanol were metabolite transport and cell wall and membrane biogenesis. It was also observed that some genes were over-expressed in response to ethanol stress (for example, the heat shock protein Hsp20 and a dipeptidase). Proteomic analysis showed that several proteins are affected by the presence of ethanol. Functions related to protein synthesis and stability are the main target of ethanol damage. In some cases the decrease in protein concentration could be due to the relocation of cytosolic proteins in the membrane, as a protective mechanism. The omic approach used to study the response of O. oeni to ethanol highlights the importance of the cell membrane in the global stress response and opens the door to future studies on this issue.

Comparative transcriptomic analysis reveals novel genes and regulatory mechanisms of Tetragenococcus halophilus in response to salt stress

Tetragenococcus halophilus, a moderately halophilic Gram-positive bacterium, was isolated from Chinese style soy sauce. This species is a valuable resource for investigating salt tolerance mechanisms and improving salinity resistance in microorganisms. RNA-seq was used to sequence T. halophilus samples treated with 0 M (T1), 1 M (T2), and 3.5 M NaCl (T3). Comparative transcriptomic analyses of the different treatments were performed using gene ontology and Kyoto encyclopedia of genes and genome. The comparison of T1 and T2 by RNA-seq revealed that genes involved in transcription, translation, membrane system, and division were highly up-regulated under optimum salt condition. The comparison of T2 and T3 showed that genes related to heat shock proteins or the ATP-binding cassette transport systems were significantly up-regulated under maximum-salt condition. In addition, a considerable proportion of the significantly differently expressed genes identified in this study are novel. These data provide a crucial resource that may determine specific responses to salt stress in T. halophilus.

Quantifying variability on thermal resistance of Listeria monocytogenes

Knowledge of the impact of strain variability and growth history on thermal resistance is needed to provide a realistic prediction and an adequate design of thermal treatments. In the present study, apart from quantifying strain variability on thermal resistance of Listeria monocytogenes, also biological variability and experimental variability were determined to prioritize their importance. Experimental variability was defined as the repeatability of parallel experimental replicates and biological variability was defined as the reproducibility of biologically independent reproductions. Furthermore, the effect of growth history was quantified. The thermal inactivation curves of 20 L. monocytogenes strains were fitted using the modified Weibull model, resulting in total 360 D-value estimates. The D-value ranged from 9 to 30 min at 55 °C; from 0.6 to 4 min at 60 °C; and from 0.08 to 0.6 min at 65 °C. The estimated z-values of all strains ranged from 4.4 to 5.7 °C. The strain variability was ten times higher than the experimental variability and four times higher than the biological variability. Furthermore, the effect of growth history on thermal resistance variability was not significantly different from that of strain variability and was mainly determined by the growth phase.

Transcriptomic and functional analysis of NaCl-induced stress in Enterococcus faecalis

The robust physiology of Enterococcus faecalis facilitates tolerance to various stresses. We here report the transcriptional response of E. faecalis V583 to growth in the presence of 6.5% NaCl. Among the early responses observed was an immediate down-regulation of mscL, accompanied by an up-regulation of genes predicted to be involved in uptake of extracellular potassium and glycine betaine. The high NaCl concentration also induced expression of chaperons and cell envelope related traits, such as the enterococcal polysaccharide antigen (epa) locus. Functional genetic analysis revealed reduced salt stress resistance in both epaB and epaE mutants. The reduced salt resistance phenotype associated with the epaB mutant was restored by complementation, hence demonstrating a role of Epa in the physiological robustness of E. faecalis. Furthermore, we demonstrate that Epa confers increased resistance towards multiple cell envelope stress-inducing factors. Accordingly, these findings delineate a potential link between the robust nature of E. faecalis and its ability to perform as a human pathogen, and provide a new perspective on the mechanisms by which Epa contributes to virulence. Notably, the high NaCl concentration also resulted in strict repression of the gelE-sprE operon and impaired gelatinase activity. We demonstrate that NaCl antagonize the GBAP-pheromone dependent induction in a concentration dependent manner.

Glycine betaine-mediated potentiation of HSP gene expression involves calcium signaling pathways in tobacco exposed to NaCl stress

Glycine betaine (GB) can enhance heat tolerance and the accumulation of heat-shock protein (HSP) in plants, but the effects of GB on HSP accumulation during salt stress were not previously known. To investigate the mechanism of how GB influences the expression of HSP, wild-type tobacco (Nicotiana tabacum) seedlings pretreated with exogenous GB and BADH-transgenic tobacco plants that accumulated GB in vivo were studied during NaCl stress. A transient Ca(2+) efflux was observed in the epidermal cells of the elongation zone of tobacco roots after NaCl treatment for 1-2 min. After 24 h of NaCl treatment, an influx of Ca(2+) was observed; a low concentration of GB significantly increased NaCl-induced Ca(2+) influx. GB increased the intracellular free calcium ion concentration and enhanced the expression of the calmodulin (CaM) and heat-shock transcription factor (HSF) genes resulting in potentiated levels of HSPs. Pharmacological experiments confirmed that Ca(2+) and CaM increased HSFs and HSPs gene expression, which coincided with increased the levels of HSP70 accumulation. These results suggest a mechanism by which GB acted as a cofactor in the NaCl induction of a Ca(2+) -permeable current. A possible regulatory model of Ca(2+) -CaM in the signal transduction pathway for induction of transcription and translation of the active HSPs is described.

Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress

In this study we tested 39 Lactococcus lactis strains isolated from diverse habitats for their robustness under heat and oxidative stress, demonstrating high diversity in survival (up to 4 log units). Strains with an L. lactis subsp. lactis phenotype generally displayed more-robust phenotypes than strains with an L. lactis subsp. cremoris phenotype, whereas the habitat from which the strains had been isolated did not appear to influence stress survival. Comparison of the stress survival phenotypes with already available comparative genomic data sets revealed that the absence or presence of specific genes, including genes encoding a GntR family transcriptional regulator, a manganese ABC transporter permease, a cellobiose phosphotransferase system (PTS) component, the FtsY protein, and hypothetical proteins, was associated with heat or oxidative stress survival. Finally, 14 selected strains also displayed diversity in survival after spray drying, ranging from 20% survival for the most robust strains, which appears acceptable for industrial application, to 0.1% survival for the least-tolerant strains. The high and low levels of survival upon spray drying correlated clearly with the combined robustness under heat and oxidative stress. These results demonstrate the relevance of screening culture collections for robustness under heat and oxidative stress on top of the typical screening for acidifying and flavor-forming properties.

Oxidative stress at high temperatures in Lactococcus lactis due to an insufficient supply of Riboflavin

Lactococcus lactis MG1363 was found to be unable to grow at temperatures above 37°C in a defined medium without riboflavin, and the cause was identified to be dissolved oxygen introduced during preparation of the medium. At 30°C, growth was unaffected by dissolved oxygen and oxygen was consumed quickly. Raising the temperature to 37°C resulted in severe growth inhibition and only slow removal of dissolved oxygen. Under these conditions, an abnormally low intracellular ratio of [ATP] to [ADP] (1.4) was found (normally around 5), which indicates that the cells are energy limited. By adding riboflavin to the medium, it was possible to improve growth and oxygen consumption at 37°C, and this also normalized the [ATP]-to-[ADP] ratio. A codon-optimized redox-sensitive green fluorescent protein (GFP) was introduced into L. lactis and revealed a more oxidized cytoplasm at 37°C than at 30°C. These results indicate that L. lactis suffers from heat-induced oxidative stress at increased temperatures. A decrease in intracellular flavin adenine dinucleotide (FAD), which is derived from riboflavin, was observed with increasing growth temperature, but the presence of riboflavin made the decrease smaller. The drop was accompanied by a decrease in NADH oxidase and pyruvate dehydrogenase activities, both of which depend on FAD as a cofactor. By overexpressing the riboflavin transporter, it was possible to improve FAD biosynthesis, which resulted in increased NADH oxidase and pyruvate dehydrogenase activities and improved fitness at high temperatures in the presence of oxygen.

Response of heat-shock protein (HSP) genes to temperature and salinity stress in the antarctic psychrotrophic bacterium Psychrobacter sp. G

Temperature and salinity fluctuations are two of the most important factors affecting the growth of polar bacteria. In an attempt to better understand the function of heat-shock proteins (HSPs) in the adaptive mechanisms of the Antarctic psychrotrophic bacterium Psychrobacter sp. G to such conditions, genes Hsp845, Hsp2538, Hsp2666, and Hsp2667 were cloned on the basis of the draft genome. The expression characteristics of these HSP genes under different stress conditions were analyzed by the qRT-PCR method. Expression of Hsp845 and Hsp2667 was inhibited significantly by low temperature (0 and 10 °C, respectively). There was no difference of expression when Hsp2538 and Hsp2666 were exposed to 0 °C but the expression of Hsp2666 was inhibited when exposed to 10 °C. Expression of Hsp2538 and Hsp2667 was not sensitive but expression of Hsp845 and Hsp2666 was increased at low salinity (0 and 15, respectively). Expression of the four HSP genes was enhanced at high salinity (90 and 120) and at high temperature independent of salinity. By contrast, low temperature had no significant effect independent of salinity.

Proteomics analysis of the Flp regulon in Lactococcus lactis subsp. cremoris

Lactococcus lactis subsp. cremoris MG1363 genome sequence was completed and encodes two flp genes flpA and flpB. Research carried out has suggested that the flpB proteins are transcriptional regulators that respond to the environmental oxygen level. A variety of flp deletion mutant strains with single and double mutation were created. Wild-type (MG1363) and its flp(-) derivatives were compared by 2DE to identify changes in protein intensity under different aerobic/anaerobic growth conditions. In total, 416 ± 20 and 444 ± 32 protein spots were quantified from anaerobic and aerobic cells, respectively, on pH 4-7 gels. Forty-five protein spots that changed were excised from 2DE gel, digested with trypsin and identified from their MALDI-TOF MS Peptide Mass Fingerprint. A variety of proteins were affected by the flp mutations and oxygen level. Some proteins were controlled by FlpA and FlpB independently and some required both FlpA and B for regulation. The identified proteins that are regulated by the Flp proteins can be grouped by biochemical function. These groups are oxidative stress, electron transfer, sugars, cell wall, ABC transporters, arginine metabolism, and pyrimidine biosynthesis pathway.

Development of a Stress-Inducible Controlled Expression (SICE) system in Lactococcus lactis for the production and delivery of therapeutic molecules at mucosal surfaces

In recent years, recombinant lactic acid bacteria (LAB) have been successfully used as safe mucosal delivery vectors. Herein, we report on the development of a Stress-Inducible Controlled Expression (SICE) system in L. lactis for the production and delivery of proteins of health interest (both therapeutic and vaccine related) at mucosal surfaces. This system is episomal in nature and is composed of a vector carrying an expression cassette under the transcriptional control of a stress-inducible promoter. The functionality of the SICE system was validated in vivo using two different routes of administration: oral and intranasal, and in two different murine models of human pathologies: (i) a model of therapy against inflammatory bowel diseases (IBD) and (ii) a model of vaccination against human papillomavirus type-16 (HPV-16).

Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates

Burkholderia sp. C3, an efficient polycyclic aromatic hydrocarbon degrader, can utilize nine of the ten N-methylcarbamate insecticides including carbaryl as a sole source of carbon. Rapid hydrolysis of carbaryl in C3 is followed by slow catabolism of the resulting 1-naphthol. This study focused on metabolomes and proteomes in C3 cells utilizing carbaryl in comparison to those using glucose or nutrient broth. Sixty of the 867 detected proteins were involved in primary metabolism, adaptive sensing and regulation, transport, stress response, and detoxification. Among the 41 proteins expressed in response to carbaryl were formate dehydrogenase, aldehyde-alcohol dehydrogenase and ethanolamine utilization protein involved in one carbon metabolism. Acetate kinase and phasin were 2 of the 19 proteins that were not detected in carbaryl-supported C3 cells, but detected in glucose-supported C3 cells. Down-production of phasin and polyhydroxyalkanoates in carbaryl-supported C3 cells suggests insufficient carbon sources and lower levels of primary metabolites to maintain an ordinary level of metabolism. Differential metabolomes (~196 identified polar metabolites) showed up-production of metabolites in pentose phosphate pathways and metabolisms of cysteine, cystine and some other amino acids, disaccharides and nicotinate, in contract to down-production of most of the other amino acids and hexoses. The proteomic and metabolomic analyses showed that carbaryl-supported C3 cells experienced strong toxic effects, oxidative stresses, DNA/RNA damages and carbon nutrient deficiency.