Role and mechanism of the Hsp70 molecular chaperone machines in bacterial pathogens

The Role of Heat Shock Protein 70 (HSP70) in the Pathogenesis of Ocular Diseases-Current Literature Review

Heat shock proteins (HSPs) have been attracting the attention of researchers for many years. HSPs are a family of ubiquitous, well-characterised proteins that are generally regarded as protective multifunctional molecules that are expressed in response to different types of cell stress. Their activity in many organs has been reported, including the heart, brain, and retina. By acting as chaperone proteins, HSPs help to refold denatured proteins. Moreover, HSPs elicit inhibitory activity in apoptotic pathways and inflammation. Heat shock proteins were originally classified into several subfamilies, including the HSP70 family. The aim of this paper is to systematise information from the available literature about the presence of HSP70 in the human eye and its role in the pathogenesis of ocular diseases. HSP70 has been identified in the cornea, lens, and retina of a normal eye. The increased expression and synthesis of HSP70 induced by cell stress has also been demonstrated in eyes with pathologies such as glaucoma, eye cancers, cataracts, scarring of the cornea, ocular toxpoplasmosis, PEX, AMD, RPE, and diabetic retinopathy. Most of the studies cited in this paper confirm the protective role of HSP70. However, little is known about these molecules in the human eye and their role in the pathogenesis of eye diseases. Therefore, understanding the role of HSP70 in the pathophysiology of injuries to the cornea, lens, and retina is essential for the development of new therapies aimed at limiting and/or reversing the processes that cause damage to the eye.

Bacterial heat shock protein: A new crosstalk between T lymphocyte and macrophage via JAK2/STAT1 pathway in bloodstream infection

Bloodstream infection (BSI) refers to the infection of blood by pathogens. Severe immune response to BSI can lead to sepsis, a systemic infection leading to multiple organ dysfunction, coupled with drug resistance, mortality, and limited clinical treatment options. This work aims to further investigate the new interplay between bacterial exocrine regulatory protein and host immune cells in the context of highly drug-resistant malignant BSI. Whether interfering with related regulatory signaling pathways can reverse the inflammatory disorder of immune cells. In-depth analysis of single-cell sequencing results in Septic patients for potential immunodeficiency factors. Analysis of key proteins enriched by host cells and key pathways using proteomics. Cell models and animal models validate the pathological effects of DnaK on T cells, MAITs, macrophages, and osteoclasts. The blood of patients was analyzed for the immunosuppression of T cells and MAITs. We identified that S. maltophilia-DnaK was enriched in immunodeficient T cells. The activation of the JAK2/STAT1 axis initiated the exhaustion of T cells. Septic patients with Gram-negative bacterial infections exhibited deficiencies in MAITs, which correspond to IFN-γ. Cellular and animal experiments confirmed that DnaK could facilitate MAIT depletion and M1 polarization of macrophages. Additionally, Fludarabine mitigated M1 polarization of blood, liver, and spleen in mice. Interestingly, DnaK also repressed osteoclastogenesis of macrophages stimulated by RANKL. S.maltophilia-DnaK prompts the activation of the JAK2/STAT1 axis in T cells and the M1 polarization of macrophages. Targeting the DnaK's crosstalk can be a potentially effective approach for treating the inflammatory disorder in the broad-spectrum drug-resistant BSI.

Peptide-based molecules for the disruption of bacterial Hsp70 chaperones

DnaK is a chaperone that aids in nascent protein folding and the maintenance of proteome stability across bacteria. Due to the importance of DnaK in cellular proteostasis, there have been efforts to generate molecules that modulate its function. In nature, both protein substrates and antimicrobial peptides interact with DnaK. However, many of these ligands interact with other cellular machinery as well. Recent work has sought to modify these peptide scaffolds to create DnaK-selective and species-specific probes. Others have reported protein domain mimics of interaction partners to disrupt cellular DnaK function and high-throughput screening approaches to discover clinically-relevant peptidomimetics that inhibit DnaK. The described work provides a foundation for the design of new assays and molecules to regulate DnaK activity.

DnaJ, a heat shock protein 40 family member, is essential for the survival and virulence of plant pathogenic Pseudomonas cichorii JBC1

Bacterial plant pathogens must cope with various environmental conditions and defenses from their hosts for colonization and infection. Heat shock proteins (HSPs) play critical roles in a variety of cellular processes, such as the maintenance of cellular homeostasis in response to environmental stress. However, the significance of HSP40 family protein DnaJ in virulence of plant pathogenic bacteria has not yet been explored. To elucidate the function of DnaJ in Pseudomonas cichorii JBC1 (PcJBC1) virulence, we generated dnaJ-deficient (JBC1ΔdnaJ) mutant using CRISPR-CAS9. The disease severity by JBC1ΔdnaJ was significantly reduced compared with wild-type (WT) and dnaJ-complemented (JBC1ΔdnaJ + pdnaJ) strain. The defect of DnaJ suppressed siderophore production, extracellular DNA (eDNA) release, biofilm formation, and swarming motility and made the strain sensitive to stresses such as heat and H2O2. The supplementation of eDNA recovered the amount of biofilm formation by JBC1ΔdnaJ. Our results indicate that DnaJ is a key player in the survival and colonization of bacterial plant pathogens on plant surfaces as well as bacterial responses to abiotic and biotic stresses, which are determinative to cause disease. These findings can broaden our understanding of plant and bacterial pathogen interactions.

Tobacco smoke exacerbates Filifactor alocis pathogenicity

AIM

Filifactor alocis has recently emerged as a periodontal pathobiont that appears to thrive in the oral cavity of smokers. We hypothesized that identification of smoke-responsive F. alocis genes would provide insight into adaptive strategies and that cigarette smoke would enhance F. alocis pathogenesis in vivo.

MATERIALS AND METHODS

F. alocis was grown in vitro and cigarette smoke extract-responsive genes determined by RNAseq. Mice were exposed, or not, to mainstream 1R6F research cigarette smoke and infected with F. alocis, or not, in an acute ligature model of periodontitis. Key clinical, infectious, and immune data were collected.

RESULTS

In culture, F. alocis growth was unaffected by smoke conditioning and only a small number of genes were specifically regulated by smoke exposure. Reduced murine mass, differences in F. alocis-cognizant antibody production, and altered immune profiles as well as altered alveolar bone loss were all attributable to smoke exposure and/or F. alocis infection in vivo.

CONCLUSIONS

F. alocis is well-adapted to tobacco-rich conditions and its pathogenesis is enhanced by tobacco smoke exposure. A smoke-exposed ligature model of periodontitis shows promise as a tool with which to further unravel mechanisms underlying tobacco-enhanced, bacteria-induced disease.

Loss of thermotolerance in antibiotic-resistant Acinetobacter baumannii

Bacterium Acinetobacter baumannii is a leading cause of nosocomial infections. The occurrence of antibiotic-resistant A. baumannii isolates outside hospitals suggests that monitoring of this pathogen in environmental samples is needed. Survival of pandrug-resistant A. baumannii was followed on selective plates with and without carbapenems in water and soil. After a few days of starvation, A. baumannii lost the ability to be cultivated at 44°C on plates supplemented with carbapenems. Once cultivated on plates without carbapenems and/or at 36°C, A. baumannii could grow again at 44°C in the presence of carbapenems. Comparative proteomic analysis revealed that impaired membrane integrity and reduced function of efflux pumps due to elevated temperature combined with antibiotic exposure were the main reasons for this phenomenon. Loss of thermotolerance in the presence of antibiotics points to the need for temperature adjustment in long-term monitoring of A. baumannii in environmental samples, to avoid the underestimation of viable bacteria.

Genome-wide identification and low-salinity stress analysis of the Hsp70 gene family in swimming crab (Portunus trituberculatus)

No genome-wide identification and expression analysis have been performed on the heat shock protein 70 (Hsp70) gene family, which is essential to key cellular processes and responses to environmental change, in decapods. In the present study, we identified nine members of the Hsp70 gene family within the genome of swimming crab (Portunus trituberculatus) and provided insights into their response to long-term low-salinity stress. Results demonstrated that gene structure and motifs are conserved among members of this gene family in P. trituberculatus. Under low-salinity stress, the expression of this gene family in the gill of P. trituberculatus showed that hsc70l.2 was significantly upregulated, hyou1 was significantly downregulated. The hsc70l.4 was not expressed. Furthermore, selection test on duplicated genes showed a negative selection on hsc70l.1, hsc70l.2, hsc70l.3, and hsc70l.4, suggesting functional redundancy. This may be the first study that systematically identified and analyzed the Hsp70 gene family in decapods. These results can provide fundamental data for the biological research of P. trituberculatus and enhance understanding of the biological function of Hsp70 in crustaceans adapting to salinity changes.

Non-homologous End Joining-Mediated Insertional Mutagenesis Reveals a Novel Target for Enhancing Fatty Alcohols Production in Yarrowia lipolytica

Non-homologous end joining (NHEJ)-mediated integration is effective in generating random mutagenesis to identify beneficial gene targets in the whole genome, which can significantly promote the performance of the strains. Here, a novel target leading to higher protein synthesis was identified by NHEJ-mediated integration that seriously improved fatty alcohols biosynthesis in Yarrowia lipolytica. One batch of strains transformed with fatty acyl-CoA reductase gene (FAR) showed significant differences (up to 70.53-fold) in fatty alcohol production. Whole-genome sequencing of the high-yield strain demonstrated that a new target YALI0_A00913g ("A1 gene") was disrupted by NHEJ-mediated integration of partial carrier DNA, and reverse engineering of the A1 gene disruption (YlΔA1-FAR) recovered the fatty alcohol overproduction phenotype. Transcriptome analysis of YlΔA1-FAR strain revealed A1 disruption led to strengthened protein synthesis process that was confirmed by sfGFP gene expression, which may account for enhanced cell viability and improved biosynthesis of fatty alcohols. This study identified a novel target that facilitated synthesis capacity and provided new insights into unlocking biosynthetic potential for future genetic engineering in Y. lipolytica.

Stress response modulation: the key to survival of pathogenic and spoilage bacteria during poultry processing

The control of bacterial contaminants on meat is a key area of interest in the food industry. Bacteria are exposed to a variety of stresses during broiler processing which challenge bacterial structures and metabolic pathways causing death or sublethal injury. To counter these stresses, bacteria possess robust response systems that can induce shifts in the transcriptome and proteome to enable survival. Effective adaptive responses, such as biofilm formation, shock protein production and metabolic flexibility, require rapid induction and implementation at a cellular and community level to facilitate bacterial survival in adverse conditions. This review aims to provide an overview of the scientific literature pertaining to the regulation of complex adaptive processes used by bacteria to survive the processing environment, with particular focus on species that impact the quality and safety of poultry products like Campylobacter spp., Salmonella enterica and Pseudomonas spp.

JC-10 probe as a novel method for analyzing the mitochondrial membrane potential and cell stress in whole zebrafish embryos

BACKGROUND

A sensitive method to investigate cellular stress and cytotoxicity is based on measuring mitochondrial membrane potential. Recently, JC-10, was developed to measure mitochondrial membrane potential in vitro and used as an indicator for cytotoxicity. Yet, JC-10 has never been used in vivo (whole organism). In normal cells, JC-10 concentrates in the mitochondrial matrix, where it forms red fluorescent aggregates. However, in apoptotic/necrotic cells, JC-10 diffuses out of the mitochondria, changes to monomeric form, and stains cells in green. Here, we aimed to develop and optimize a JC-10 assay to measure cytotoxicity in zebrafish embryo. We also investigated the effectiveness of JC-10 assay by comparing it to common cytotoxicity assays.

METHODS

Zebrafish embryos were exposed to a toxic surfactant AEO-7 at no observed effect concentration (6.4 μg/L), and then cytotoxicity was measured using (i) JC-10 mitochondrial assay, (ii) acridine orange (AO), (iii) TUNEL assay, and (iv) measuring the level of Hsp70 by western blotting.

RESULTS

As compared to the negative control, embryos treated with NOEC of AEO-7 did not show significant cytotoxicity when assessed by AO, TUNEL or western blotting. However, when JC-10 was used under the same experimental conditions, a significant increase of green:red fluorescent ratio signal was detected in the AEO-7 treated embryos, indicating mitochondrial damage and cellular cytotoxicity. Noteworthy, the observed green: red ratio increase was dose dependent, suggesting specificity of the JC-10 assay.

CONCLUSION

JC-10 is a sensitive in vivo method, thus, can be used as surrogate assay to measure cytotoxicity in whole zebrafish embryos.

Can heat shock protein 70 (HSP70) serve as biomarkers in Antarctica for future ocean acidification, warming and salinity stress?

The Antarctic Peninsula is one of the fastest-warming places on Earth. Elevated sea water temperatures cause glacier and sea ice melting. When icebergs melt into the ocean, it “freshens” the saltwater around them, reducing its salinity. The oceans absorb excess anthropogenic carbon dioxide (CO2) causing decline in ocean pH, a process known as ocean acidification. Many marine organisms are specifically affected by ocean warming, freshening and acidification. Due to the sensitivity of Antarctica to global warming, using biomarkers is the best way for scientists to predict more accurately future climate change and provide useful information or ecological risk assessments. The 70-kilodalton (kDa) heat shock protein (HSP70) chaperones have been used as biomarkers of stress in temperate and tropical environments. The induction of the HSP70 genes (Hsp70) that alter intracellular proteins in living organisms is a signal triggered by environmental temperature changes. Induction of Hsp70 has been observed both in eukaryotes and in prokaryotes as response to environmental stressors including increased and decreased temperature, salinity, pH and the combined effects of changes in temperature, acidification and salinity stress. Generally, HSP70s play critical roles in numerous complex processes of metabolism; their synthesis can usually be increased or decreased during stressful conditions. However, there is a question as to whether HSP70s may serve as excellent biomarkers in the Antarctic considering the long residence time of Antarctic organisms in a cold polar environment which appears to have greatly modified the response of heat responding transcriptional systems. This review provides insight into the vital roles of HSP70 that make them ideal candidates as biomarkers for identifying resistance and resilience in response to abiotic stressors associated with climate change, which are the effects of ocean warming, freshening and acidification in Antarctic organisms.

Adhesion Properties of Lactobacillus plantarum Dad-13 and Lactobacillus plantarum Mut-7 on Sprague Dawley Rat Intestine

Adhesion capacity is considered one of the selection criteria for probiotic strains. The purpose of this study was to determine the adhesion properties of two candidate probiotics, Lactobacillus plantarum Dad-13 and Lactobacillus plantarum Mut-7. The evaluation included the hydrophobicity of the cell surface using microbial adhesion to hydrocarbons (MATH), autoaggregation, and the adhesion of L. plantarum Dad-13 and L. plantarum Mut-7 to the intestinal mucosa of Sprague Dawley rat, followed by genomic analysis of the two L. plantarum strains. L. plantarum Dad-13 and L. plantarum Mut-7 showed a high surface hydrophobicity (78.9% and 83.5%) and medium autoaggregation ability (40.9% and 57.5%, respectively). The exposure of both isolates to the surface of the rat intestine increased the total number of lactic acid bacteria on the colon compartment, from 2.9 log CFU/cm2 to 4.4 log CFU/cm2 in L. plantarum Dad-13 treatment and to 3.86 log CFU/cm2 in L. plantarum Mut-7 treatment. The results indicate the ability of two L. plantarum to attach to the surface of the rat intestine. The number of indigenous E. coli in the colon also decreased when the compartment was exposed to L. plantarum Dad-13 and Mut-7, from 2.9 log CFU/cm2 to 1 log CFU/cm2. Genomic analysis revealed that both strains have genes related to adhesion properties that could play an important role in increasing the adherence of probiotics to the intestinal mucosa such as gene encoding fibronectin-binding protein, chaperonin heat shock protein 33 (Hsp33), and genes related to the capsule and cell wall biosynthesis. Based on these findings, we believe that L. plantarum Dad-13 and L. plantarum Mut-7 have adhesion properties to the intestinal mucosa in the rat intestine model system. The present research will be essential to elucidate the molecular mechanism associated with adhesion in our two probiotic strains.

The Hsp70-Chaperone Machines in Bacteria

The ATP-dependent Hsp70s are evolutionary conserved molecular chaperones that constitute central hubs of the cellular protein quality surveillance network. None of the other main chaperone families (Tig, GroELS, HtpG, IbpA/B, ClpB) have been assigned with a comparable range of functions. Through a multitude of functions Hsp70s are involved in many cellular control circuits for maintaining protein homeostasis and have been recognized as key factors for cell survival. Three mechanistic properties of Hsp70s are the basis for their high versatility. First, Hsp70s bind to short degenerate sequence motifs within their client proteins. Second, Hsp70 chaperones switch in a nucleotide-controlled manner between a state of low affinity for client proteins and a state of high affinity for clients. Third, Hsp70s are targeted to their clients by a large number of cochaperones of the J-domain protein (JDP) family and the lifetime of the Hsp70-client complex is regulated by nucleotide exchange factors (NEF). In this review I will discuss advances in the understanding of the molecular mechanism of the Hsp70 chaperone machinery focusing mostly on the bacterial Hsp70 DnaK and will compare the two other prokaryotic Hsp70s HscA and HscC with DnaK.

Physiological Functions of Heat Shock Proteins

Heat shock proteins (HSPs) are molecular chaperones involved in a variety of life activities. HSPs function in the refolding of misfolded proteins, thereby contributing to the maintenance of cellular homeostasis. Heat shock factor (HSF) is activated in response to environmental stresses and binds to heat shock elements (HSEs), promoting HSP translation and thus the production of high levels of HSPs to prevent damage to the organism. Here, we summarize the role of molecular chaperones as anti-heat stress molecules and their involvement in immune responses and the modulation of apoptosis. In addition, we review the potential application of HSPs to cancer therapy, general medicine, and the treatment of heart disease.

The DnaK/DnaJ Chaperone System Enables RNA Polymerase-DksA Complex Formation in Salmonella Experiencing Oxidative Stress

Our previous biochemical approaches showed that the oxidoreductase activity of the DnaJ protein facilitates the interaction of oxidized DksA with RNA polymerase. Investigations herein demonstrate that under biologically relevant conditions the DnaJ- and DksA-codependent activation of the stringent response in Salmonella undergoing oxidative stress involves the DnaK chaperone. Oxidation of DksA cysteine residues stimulates redox-based and holdase interactions with zinc-binding and C-terminal domains of DnaJ. Genetic and biochemical evidence indicates that His³³ in the HPD motif in the J domain of DnaJ facilitates interactions of unfolded DksA with DnaK. A mutation in His³³ in the J domain prevents the presentation of unfolded DksA to DnaK without limiting the oxidoreductase activity mapped to DnaJ's zinc-2 site. Thr¹⁹⁹ in the ATPase catalytic site of DnaK is required for the formation of the DksA/RNA polymerase complex. The DnaK/DnaJ/DksA complex enables the formation of an enzymatically active RNA polymerase holoenzyme that stimulates transcription of branched-chain amino acid and histidine metabolic genes in Salmonella exposed to reactive oxygen species. The DnaK/DnaJ chaperone protects Salmonella against the cytotoxicity associated with reactive oxygen species generated by the phagocyte NADPH oxidase in the innate host response. The antioxidant defenses associated with DnaK/DnaJ can in part be ascribed to the elicitation of the DksA-dependent stringent response and the protection this chaperone system provides against protein carbonylation in Salmonella undergoing oxidative stress.IMPORTANCE DksA was discovered 30 years ago in a screen for suppressors that reversed the thermosensitivity of Escherichia coli mutant strains deficient in DnaK/DnaJ, raising the possibility that this chaperone system may control DksA function. Since its serendipitous discovery, DksA has emerged as a key activator of the transcriptional program called the stringent response in Gram-negative bacteria experiencing diverse adverse conditions, including nutritional starvation or oxidative stress. DksA activates the stringent response through the allosteric control this regulatory protein exerts on the kinetics of RNA polymerase promoter open complexes. Recent investigations have shown that DksA overexpression protects dnaKJ mutant bacteria against heat shock indirectly via the ancestral chaperone polyphosphate, casting doubt on a possible complexation of DnaK, DnaJ, and DksA. Nonetheless, research presented herein demonstrates that the cochaperones DnaK and DnaJ enable DksA/RNA polymerase complex formation in response to oxidative stress.

High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica

The microalga Nannochloropsis oceanica is considered a promising platform for the sustainable production of high-value lipids and biofuel feedstocks. However, current lipid yields of N. oceanica are too low for economic feasibility. Gaining fundamental insights into the lipid metabolism of N. oceanica could open up various possibilities for the optimization of this species through genetic engineering. Therefore, the aim of this study was to discover novel genes associated with an elevated neutral lipid content. We constructed an insertional mutagenesis library of N. oceanica, selected high lipid mutants by five rounds of fluorescence-activated cell sorting, and identified disrupted genes using a novel implementation of a rapid genotyping procedure. One particularly promising mutant (HLM23) was disrupted in a putative APETALA2-like transcription factor gene. HLM23 showed a 40%-increased neutral lipid content, increased photosynthetic performance, and no growth impairment. Furthermore, transcriptome analysis revealed an upregulation of genes related to plastidial fatty acid biosynthesis, glycolysis and the Calvin-Benson-Bassham cycle in HLM23. Insights gained in this work can be used in future genetic engineering strategies for increased lipid productivity of Nannochloropsis.

Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing

Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacterium that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used for this species. In this study, we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses, and transport were underrepresented. The majority of Pf-5 essential genes were part of the P. protegens core genome. Comparison of the essential gene set of Pf-5 with those of two plant-associated pseudomonads, P. simiae and P. syringae, and the well-studied opportunistic human pathogen P. aeruginosa PA14 showed that the four species share a large number of essential genes, but each species also had uniquely essential genes. Comparison of the Pf-5 in silico-predicted and in vitro-determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles may improve our understanding of the biological processes important for bacterial survival and growth.IMPORTANCE Essential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analyses of all genes of a bacterial species and rapid determination of essential gene sets. We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of three other pseudomonads highlights how gene essentiality varies between closely related species.

Comparative transcriptomic study of Escherichia coli O157:H7 in response to ohmic heating and conventional heating

In this study, the high-throughput Illumina HiSeq 2000 mRNA sequencing technique was used to investigate the transcriptome response of Escherichia coli O157:H7 exposed to ohmic heating (OH) and water bath heating (WB). Compared to untreated samples, a total of 293, 516, and 498 genes showed differential expression after HVOH (high voltage short time ohmic heating), LVOH (low voltage long time ohmic heating), and WB, respectively. Therefore, LVOH had the potential to cause comparable effects on the transcriptome of E. coli O157:H7 as compared to WB, but not HVOH. These results indicated that additional non-thermal effects were not reflected on transcriptome of E. coli O157:H7 using both HVOH and LVOH, in particular the HVOH. Most of differentially expressed genes involved in information storage and processing, and cellular processes and signaling showed up-regulation whereas most of genes related to the metabolism were down-regulated after HVOH, LVOH, and WB. In addition, more attention needs to be paid to the up-regulation of a large number of virulence genes, which might increase the ability of surviving E. coli O157:H7 to infect host cells after HVOH, LVOH, and WB. This transcriptomic study on the response of E. coli O157:H7 to OH protomes the understanding of inactivation mechanism of OH on the molecular level and opens the door to future studies for OH.

Interaction analyses based on growth parameters of GWAS between Escherichia coli and Staphylococcus aureus

To accurately explore the interaction mechanism between Escherichia coli and Staphylococcus aureus, we designed an ecological experiment to monoculture and co-culture E. coli and S. aureus. We co-cultured 45 strains of E. coli and S. aureus, as well as each species individually to measure growth over 36 h. We implemented a genome wide association study (GWAS) based on growth parameters (λ, R, A and s) to identify significant single nucleotide polymorphisms (SNPs) of the bacteria. Three commonly used growth regression equations, Logistic, Gompertz, and Richards, were used to fit the bacteria growth data of each strain. Then each equation's Akaike's information criterion (AIC) value was calculated as a commonly used information criterion. We used the optimal growth equation to estimate the four parameters above for strains in co-culture. By plotting the estimates for each parameter across two strains, we can visualize how growth parameters respond ecologically to environment stimuli. We verified that different genotypes of bacteria had different growth trajectories, although they were the same species. We reported 85 and 52 significant SNPs that were associated with interaction in E. coli and S. aureus, respectively. Many significant genes might play key roles in interaction, such as yjjW, dnaK, aceE, tatD, ftsA, rclR, ftsK, fepA in E. coli, and scdA, trpD, sdrD, SAOUHSC_01219 in S. aureus. Our study illustrated that there were multiple genes working together to affect bacterial interaction, and laid a solid foundation for the later study of more complex inter-bacterial interaction mechanisms.

Review on Stress Tolerance in Campylobacter jejuni

Campylobacter spp. are the leading global cause of bacterial colon infections in humans. Enteropathogens are subjected to several stress conditions in the host colon, food complexes, and the environment. Species of the genus Campylobacter, in collective interactions with certain enteropathogens, can manage and survive such stress conditions. The stress-adaptation mechanisms of Campylobacter spp. diverge from other enteropathogenic bacteria, such as Escherichia coli, Salmonella enterica serovar Typhi, S. enterica ser. Paratyphi, S. enterica ser. Typhimurium, and species of the genera Klebsiella and Shigella. This review summarizes the different mechanisms of various stress-adaptive factors on the basis of species diversity in Campylobacter, including their response to various stress conditions that enhance their ability to survive on different types of food and in adverse environmental conditions. Understanding how these stress adaptation mechanisms in Campylobacter, and other enteric bacteria, are used to overcome various challenging environments facilitates the fight against resistance mechanisms in Campylobacter spp., and aids the development of novel therapeutics to control Campylobacter in both veterinary and human populations.

First report on the characterization of pathogenic Rahnella aquatilis KCL-5 from crucian carp: Revealed by genomic and proteomic analyses

Rahnella aquatilis is an important pathogen of several aquatic organisms and is found widely distributed in the freshwater, soil, fish and human clinical samples. Our previously published study reported a novel pathogenic R. aquatilis strain KCL-5 to crucian carp (Carassius auratus). To further investigate the characteristics and pathogenesis caused by R. aquatilis, we here report on the pathological changes, bacterial genomic and proteomic analyses of strain KCL-5. Significantly pathological changes in liver, intestine, spleen and gills were observed in infected fish. The genome consists of one circular chromosome 5,062,299 bp with 52.02% GC content and two plasmids (506,827 bp, 52.16%; 173,433 bp, 50.00%) and predicted 5,653 genes, 77 tRNAs and 22 rRNAs. Some virulence factors were characterized, including outer membrane protein, haemolysin, RTX toxin, chemotaxis and T3SS secretion system. Antimicrobial resistance genes such as EmrAB-TolC, MexABC-OpmB and RosAB efflux pump were found in strain KCL-5. KEGG analysis showed that mainly functional modules were ABC transporters, biosynthesis of amino acids, two-component system, quorum sensing, flagellum assembly and chemotaxis, in which most of them were identified by using 2-DE/MS analyses. To our knowledge, this was first report on the molecular characteristics of R. aquatilis by multi-omics approaches, which will provide insights into the pathogenic mechanism of R. aquatilis infection in fish.

Altered proteome of a Burkholderia pseudomallei mutant defective in short-chain dehydrogenase affects cell adhesion, biofilm formation and heat stress tolerance

Burkholderia pseudomallei is a Gram-negative bacillus that causes melioidosis and is recognized as an important public health problem in southeast Asia and northeast Australia. The treatment of B. pseudomallei infection is hampered by resistance to a wide range of antimicrobial agents and no vaccine is currently available. At present, the underlying mechanisms of B. pseudomallei pathogenesis are poorly understood. In our previous study, we reported that a B. pseudomallei short-chain dehydrogenase (SDO; BPSS2242) mutant constructed by deletion mutagenesis showed reduced B. pseudomallei invasion and initial intracellular survival. This indicated that SDO is associated with the pathogenesis of melioidosis. In the present study, the role of B. pseudomallei SDO was further investigated using the SDO deletion mutant by a proteomic approach. The protein profiles of the SDO mutant and wild-type K96243 were investigated through gel-based proteomic analysis. Quantitative intensity analysis of three individual cultures of the B. pseudomallei SDO mutant revealed significant down-regulation of five protein spots compared with the wild-type. Q-TOF MS/MS identified the protein spots as a glutamate/aspartate ABC transporter, prolyl-tRNA synthetase, Hsp70 family protein, quinone oxidoreductase and a putative carboxypeptidase. Functional assays were performed to investigate the role of these differentially expressed proteins in adhesion to host cells, biofilm induction and survival under heat stress conditions. The SDO deletion mutant showed a decreased ability to adhere to host cells. Moreover, biofilm formation and the survival rate of bacteria under heat stress conditions were also reduced in the mutant strain. Our findings provide insight into the role of SDO in the survival and pathogenesis of B. pseudomallei at the molecular level, which may be applied to the prevention and control of B. pseudomallei infection.

Heat Shock Protein DnaJ in Pseudomonas aeruginosa Affects Biofilm Formation via Pyocyanin Production

Heat shock proteins (HSPs) play important biological roles, and they are implicated in bacterial response to environmental stresses and in pathogenesis of infection. The role of HSPs in P. aeruginosa, however, remains to be fully elucidated. Here, we report the unique role of HSP DnaJ in biofilm formation and pathogenicity in P. aeruginosa. A dnaJ mutant produced hardly any pyocyanin and formed significantly less biofilms, which contributed to decreased pathogenicity as demonstrated by reduced mortality rate in a Drosophila melanogaster infection model. The reduced pyocyanin production in the dnaJ mutant was a result of the decreased transcription of phenazine synthesis operons including phzA1, phzA2, phzS, and phzM. The reduction of biofilm formation and initial adhesion in the dnaJ mutant could be reversed by exogenously added pyocyanin or extracellular DNA (eDNA). Consistent with such observations, absence of dnaJ significantly reduced the release of eDNA in P. aeruginosa and addition of exogenous pyocyanin could restore eDNA release. These results indicate dnaJ mutation caused reduced pyocyanin production, which in turn caused the decreased eDNA, resulting in decreased biofilm formation. DnaJ is required for pyocyanin production and full virulence in P. aeruginosa; it affects biofilm formation and initial adhesion via pyocyanin, inducing eDNA release.

Functional characterization and subcellular distribution of two recombinant cytosolic HSP70 isoforms from Entamoeba histolytica under normal and stress conditions

Amoebiasis is a human intestinal disease caused by the parasite Entamoeba histolytica. It has been previously demonstrated that E. histolytica heat shock protein 70 (EhHSP70) plays an important role in amoebic pathogenicity by protecting the parasite from the dangerous effects of oxidative and nitrosative stresses. Despite its relevance, this protein has not yet been characterized. In this study, the EhHSP70 genes were cloned, and the two recombinant EhHSP70 proteins were expressed, purifying and biochemically characterized. Additionally, after being subjected to some host stressors, the intracellular distribution of the proteins in the parasite was documented. Two amoebic HSP70 isoforms, EhHSP70-A and EhHSP70-B, with 637 and 656 amino acids, respectively, were identified. Kinetic parameters of ATP hydrolysis showed low rates, which were in accordance with those of the HSP70 family members. Circular dichroism analysis showed differences in their secondary structures but similarities in their thermal stability. Immunocytochemistry in trophozoites detected EhHSP70 in the nuclei and cytoplasm as well as a slight overexpression when the parasites were subjected to oxidants and heat. The structural differences of amoebic HSP70s with their human counterparts may be used to design specific inhibitors to treat human amoebiasis.

Evidences of differential endoproteolytic processing on the surfaces of Mycoplasma hyopneumoniae and Mycoplasma flocculare

Mycoplasma hyopneumoniae and Mycoplasma flocculare are genetic similar bacteria that colonize the swine respiratory tract. However, while M. hyopneumoniae is a pathogen that causes porcine enzootic pneumonia, M. flocculare is a commensal. Adhesion to the respiratory epithelium is mediated by surface-displayed adhesins, and at least some M. hyopneumoniae adhesins are post-translational proteolytically processed, producing differential proteoforms with differential adhesion properties. Based on LC-MS/MS data, we assessed differential proteolytic processing among orthologs of the five most abundant adhesins (p97 and p216) or adhesion-related surface proteins (DnaK, p46, and ABC transporter xylose-binding lipoprotein) from M. hyopneumoniae strains 7448 (pathogenic) and J (non-pathogenic), and M. flocculare. Both surface and cytoplasmic non-tryptic cleavage events were mapped and compared, and antigenicity predictions were performed for the resulting proteoforms. It was demonstrated that not only bona fide adhesins, but also adhesion-related proteins undergo proteolytical processing. Moreover, most of the detected cleavage events were differential among M. hyopneumoniae strains and M. flocculare, and also between cell surface and cytoplasm. Overall, our data provided evidences of a complex scenario of multiple antigenic proteoforms of adhesion-related proteins, that is differential among M. hyopneumoniae strains and M. flocculare, altering the surface architecture and likely contributing to virulence and pathogenicity.

Exosomes released by breast cancer cells under mild hyperthermic stress possess immunogenic potential and modulate polarization in vitro in macrophages

Macrophages play a dual role in tumor initiation and progression, with both tumor-promoting and tumor-suppressive effects; hence, it is essential to understand the distinct responses of macrophages to tumor progression and therapy. Mild hyperthermia has gained importance as a therapeutic regimen against cancer due to its immunogenic nature, efficacy, and potential synergy with other therapies, yet the response of macrophages to molecular signals from hyperthermic cancer cells has not yet been clearly defined. Due to limited response rate of breast cancer to conventional therapeutics the development, and understanding of alternative therapies like hyperthermia is pertinent. In order to determine conditions corresponding to mild thermal dose, cytotoxicity of different hyperthermic temperatures and treatment durations were tested in normal murine macrophages and breast cancer cell lines. Examination of exosome release in hyperthermia-treated cancer cells revealed enhanced efflux and a larger size of exosomes released under hyperthermic stress. Exposure of naïve murine macrophages to exosomes released from 4T1 and EMT-6 cells posthyperthermia treatment, led to an increased expression of specific macrophage activation markers. Further, exosomes released by hyperthermia-treated cancer cells had increased content of heat shock protein 70 (Hsp70). Together, these results suggest a potential immunogenic role for exosomes released from cancer cells treated with mild hyperthermia.

Effect of a post-hatch lipopolysaccharide challenge in Turkey poults and ducklings after a primary embryonic heat stress

The effect of embryonic thermal manipulation on the post-hatch immune response to a lipopolysaccharide (LPS) challenge was studied in Pekin ducklings and turkey poults. Commercial duck and turkey eggs were distributed among four treatments: SS-Control (37.5 °C from embryonic day [ED] 1 to 25); SS-LPS (37.5 °C from ED1 to 25 + LPS at D0 [hatch]); HH-LPS (38 °C from ED1 to 25 + LPS at D0; SH-LPS (37.5 °C from ED1 to 10 and 38 °C from ED 11 to 25 + LPS at D0). At ED16 and ED24, the egg shell temperature of the duck and turkey eggs in the HH and SH treatments were higher (P ≤ 0.01) than the SS treatment. Ducklings and poults in the HH treatment had the lowest yolk free body weight at hatch (P ≤ 0.05). At 24, 48, and 72 h post-LPS injection, ducklings and poults in the HH-LPS treatment had significantly reduced BW compared with the SS-Con treatments (P ≤ 0.05). Ducklings and poults in the SH-LPS and HH-LPS treatments had increased plasma heat shock protein 70 (HSP70) and lower splenic HSP70 mRNA amounts than the SS-LPS treatments at 24, and 48 h post-challenge (P ≤ 0.05). At 48 and 72 h, macrophage nitric oxide (NO) production in ducklings and poults in the SH-LPS and HH-LPS treatments was lower than in the SS-LPS treatments (P ≤ 0.05). Ducklings and poults in the SH-LPS treatment had increased thymocyte proliferation compared to the SS-LPS treatment at 24, 48 and 72 h (P ≤ 0.05). At 24 h, ducklings in the SH-LPS treatment had increased splenic IL-10 and reduced IFNγ and IL-6 mRNA abundance. However, both ducklings and poults in the HH-LPS treatment had increased IFNγ, and IL-10 mRNA abundance compared to the SS-LPS treatment (P ≤ 0.05). At 48 h, SH-LPS ducklings and poults had lower splenic IL-10 mRNA abundance (P ≤ 0.05) while the HH-LPS treatment resulted in comparable splenic IL-10 mRNA compared to the SS-LPS treatment (P ≥ 0.05). Ducklings and poults in the SH-LPS treatment had increased thymic and splenic CD8⁺/CD4⁺ ratios at 24 h versus the SS-LPS treatment (P ≤ 0.05). In conclusion, embryonic thermal manipulation from ED11-25 increased extracellular HSP70 release, thymocyte proliferation and IL-10 but decreased splenic HSP70 and IFNγ mRNA amounts at 24 h post-LPS injection. This suggests that mild heat stress during the later stages of incubation could potentially prime the embryonic immune system thereby enhances the immune response as earlier than 24 h to eliminate the inflammatory response without affecting the growth performance by increase the extracellular release of HSP70 in both ducklings and poults. Continuous exposure to the small increase in temperature from ED 1-25 (HH) caused an imbalance between pro (IFNγ)- and anti-inflammatory cytokines(IL-10) which affects hatchling responses to an inflammatory challenge and increased mortality. The amount of extracellular HSP70 could potentially play an important role in modulating the immune response against inflammatory challenges.

Expression of DnaK and HtrA genes under high temperatures and their impact on thermotolerance of a Salmonella serotype isolated from tahini product

Background

Salmonella is considered to be the second largest source of infection in food-borne diseases. It is also considered one of the most important dangers particularly in the meat and dairy industry. Therefore, the main objective of our study was to determine the relationship between thermotolerance of a Salmonella serotype and the expression of DnaK and HtrA genes.

Results

In this study, expression of the two genes DnaK and HtrA was compared under four different temperatures 37 °C, 42 °C, 50 °C, and 55 °C in two serotypes of Salmonella enterica subsp. enterica. One of them was isolated from tahini product and identified as Salmonella enterica subsp. enterica serovar choleraesuis. This identified serotype was found to be more thermotolerant than the second serotype (Salmonella enterica subsp. enterica serovar typhimurium (ATCC 13311)), which was used as reference. This conclusion was based on D and Z values, which were used to compare thermoresistance ability of the two serotypes under four different temperatures 60 °C, 65 °C, 70 °C, and 75 °C. In addition, the results of qRT-PCR showed that after 43 °C (induction temperature), the relative expression (fold change) of DnaK and HtrA genes increased up to 5 and 47, respectively, comparing to their expression at 37 °C.

Conclusions

Thermotolerance of the identified S. choleraesuis serotype showed significantly high expression levels of DnaK and HtrA genes.

Transcriptome Profiling Analysis of Bovine Vaginal Epithelial Cell Response to an Isolated Lactobacillus Strain

Bovine bacterial vaginitis causes infertility, abortion, and postpartum uterine diseases, causing serious economic loss to the dairy industry. The large-scale use of antibiotics destroys normal genital tract flora and hinders the defense mechanisms of the host. Recent research suggests that lactobacilli present in the vaginal microflora of healthy cows constitute the primary microbiological barrier to infection by genital pathogens, exerting a protective role on the reproductive tract via specific adherence to the epithelium and the production of inhibitory substances. Our research identified the mechanisms for Lactobacillus adhesion and pathogenic inhibition, providing valuable information for the development of new probiotics and the discovery of novel therapeutic targets for the prevention of infections in dairy cows.

Lactobacillus strain SQ0048 isolated from bovine vagina has been shown to exhibit specific adherence to the epithelium and to produce inhibitory substances; however, the underlying mechanisms remain unclear. We cultured and identified primary bovine vaginal epithelial cells treated with SQ0048 to investigate the pathways involved in host cell responses using transcriptome sequencing (RNA-seq). Transcription profiling showed 296 significantly altered differentially expressed genes (DEGs), of which 170 were upregulated and 126 downregulated. Gene Ontology (GO) enrichment analysis of the DEGs revealed significant enrichment of 424 GO terms throughout the differentiation process (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were successfully annotated as members of 171 pathways, with 23 significantly enriched KEGG pathways (P < 0.05). A relatively high number of genes were enriched for the endoplasmic reticulum protein processing and interleukin-17 (IL-17) signaling pathways and for antigen processing and presentation. DEGs were verified by quantitative reverse transcription-PCR (RT-qPCR) and determination of which were most enriched for endoplasmic reticulum protein processing pathways, the activation of which might be a major factor underlying Lactobacillus adhesion to cells and pathogenic inhibition.

IMPORTANCE Bovine bacterial vaginitis causes infertility, abortion, and postpartum uterine diseases, causing serious economic loss to the dairy industry. The large-scale use of antibiotics destroys normal genital tract flora and hinders the defense mechanisms of the host. Recent research suggests that lactobacilli present in the vaginal microflora of healthy cows constitute the primary microbiological barrier to infection by genital pathogens, exerting a protective role on the reproductive tract via specific adherence to the epithelium and the production of inhibitory substances. Our research identified the mechanisms for Lactobacillus adhesion and pathogenic inhibition, providing valuable information for the development of new probiotics and the discovery of novel therapeutic targets for the prevention of infections in dairy cows.

The ER Lumenal Hsp70 Protein FpLhs1 Is Important for Conidiation and Plant Infection in Fusarium pseudograminearum

Heat shock protein 70s (Hsp70s) are a class of molecular chaperones that are highly conserved and ubiquitous in organisms ranging from microorganisms to plants and humans. Hsp70s play key roles in cellular development and protecting living organisms from environmental stresses such as heat, drought, salinity, acidity, and cold. However, their functions in pathogenic fungi are largely unknown. Here, a total of 14 FpHsp70 genes were identified in Fusarium pseudograminearum, including 3 in the mitochondria, 7 in the cytoplasm, 2 in the endoplasmic reticulum (ER), 1 in the nucleus, and 1 in the plastid. However, the exon–intron boundaries and protein motifs of the FpHsp70 have no consistency in the same subfamily. Expression analysis revealed that most FpHsp70 genes were up-regulated during infection, implying that FpHsp70 genes may play important roles in F. pseudograminearum pathogenicity. Furthermore, knockout of an ER lumenal Hsp70 homolog FpLhs1 gene reduced growth, conidiation, and pathogenicity in F. pseudograminearum. These mutants also showed a defect in secretion of some proteins. Together, FpHsp70s might play essential roles in F. pseudograminearum and FpLhs1 is likely to act on the development and virulence by regulating protein secretion.

Proteomic Analysis of Horseweed (Conyza canadensis) Subjected to Caprylic Acid Stress

Caprylic acid (CAP) is anticipated to be a potential biocontrol herbicide in the control of weeds, however the molecular mechanism of how CAP affects weeds is poorly understood. Here, the physiological and biochemical (protein-level) changes in horseweed (Conyza canadensis L.) are studied under CAP treatment, with infrared gas analyzer and label-free quantitative proteomics methods. In total, 112 differentially-accumulated proteins (DAPs) (>1.5 fold change, p < 0.05) are present between treated horseweed and control samples, with 46 up-regulated and 66 down-regulated proteins. These DAPs are involved in 28 biochemical pathways, including photosynthesis pathways. In particular, six photosynthesis proteins show significant abundance changes in the CAP-treated horseweed. The qRT-PCR results confirm three of the six genes involved in photosynthesis. Moreover, by measuring photosynthesis characteristics, CAP was shown to decrease photosynthetic rate, stomatal conductance, intercellular CO₂ concentration, and the transpiration rate of horseweed. These results suggest that photosystem I is one of the main biological processes involved in the response of horseweed to CAP.

Transcriptomics of Haemophilus (Glässerella) parasuis serovar 5 subjected to culture conditions partially mimetic to natural infection for the search of new vaccine antigens

Background

Haemophilus (Glässerella) parasuis is the etiological agent of Glässer’s disease in pigs. Control of this disorder has been traditionally based on bacterins. The search for alternative vaccines has focused mainly on the study of outer membrane proteins. This study investigates the transcriptome of H. (G.) parasuis serovar 5 subjected to in vitro conditions mimicking to those existing during an infection (high temperature and iron-restriction), with the aim of detecting the overexpression of genes coding proteins exposed on bacterial surface, which could represent good targets as vaccine candidates.

Results

The transcriptomic approach identified 13 upregulated genes coding surface proteins: TbpA, TbpB, HxuA, HxuB, HxuC, FhuA, FimD, TolC, an autotransporter, a protein with immunoglobulin folding domains, another large protein with a tetratricopeptide repeat and two small proteins that did not contain any known domains. Of these, the first six genes coded proteins being related to iron extraction.

Conclusion

Six of the proteins have already been tested as vaccine antigens in murine and/or porcine infection models and showed protection against H. (G.) parasuis. However, the remaining seven have not yet been tested and, consequently, they could become useful as putative antigens in the prevention of Glässer’s disease. Anyway, the expression of this seven novel vaccine candidates should be shown in other serovars different from serovar 5.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1647-1) contains supplementary material, which is available to authorized users.

Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF

The robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome serves as an important genetic scaffold for evolution of this bacterium in the modern health care setting and also provides interesting vaccine and drug targets. We used an innovative pooling/sequencing strategy to map a large collection of arrayed transposon insertions in E. faecalis OG1RF and generated an arrayed library of defined mutants covering approximately 70% of the OG1RF genome. Then, we performed high-throughput transposon sequencing experiments using this library to determine core genomic determinants of bile resistance in OG1RF. This collection is a valuable resource for comprehensive, functional enterococcal genomics using both traditional and high-throughput approaches and enables immediate recovery of mutants of interest.

Enterococcus faecalis is a common commensal bacterium in animal gastrointestinal (GI) tracts and a leading cause of opportunistic infections of humans in the modern health care setting. E. faecalis OG1RF is a plasmid-free strain that contains few mobile elements yet retains the robust survival characteristics, intrinsic antibiotic resistance, and virulence traits characteristic of most E. faecalis genotypes. To facilitate interrogation of the core enterococcal genetic determinants for competitive fitness in the GI tract, biofilm formation, intrinsic antimicrobial resistance, and survival in the environment, we generated an arrayed, sequence-defined set of chromosomal transposon insertions in OG1RF. We used an orthogonal pooling strategy in conjunction with Illumina sequencing to identify a set of mutants with unique, single Himar-based transposon insertions. The mutants contained insertions in 1,926 of 2,651 (72.6%) annotated open reading frames and in the majority of hypothetical protein-encoding genes and intergenic regions greater than 100 bp in length, which could encode small RNAs. As proof of principle of the usefulness of this arrayed transposon library, we created a minimal input pool containing 6,829 mutants chosen for maximal genomic coverage and used an approach that we term SMarT (sequence-defined marinertechnology) transposon sequencing (TnSeq) to identify numerous genetic determinants of bile resistance in E. faecalis OG1RF. These included several genes previously associated with bile acid resistance as well as new loci. Our arrayed library allows functional screening of a large percentage of the genome with a relatively small number of mutants, reducing potential effects of bottlenecking, and enables immediate recovery of mutants following competitions.

IMPORTANCE The robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome serves as an important genetic scaffold for evolution of this bacterium in the modern health care setting and also provides interesting vaccine and drug targets. We used an innovative pooling/sequencing strategy to map a large collection of arrayed transposon insertions in E. faecalis OG1RF and generated an arrayed library of defined mutants covering approximately 70% of the OG1RF genome. Then, we performed high-throughput transposon sequencing experiments using this library to determine core genomic determinants of bile resistance in OG1RF. This collection is a valuable resource for comprehensive, functional enterococcal genomics using both traditional and high-throughput approaches and enables immediate recovery of mutants of interest.

Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129

Propionibacterium freudenreichii is a beneficial Gram-positive bacterium, traditionally used as a cheese-ripening starter, and currently considered as an emerging probiotic. As an example, the P. freudenreichii CIRM-BIA 129 strain recently revealed promising immunomodulatory properties. Its consumption accordingly exerts healing effects in different animal models of colitis, suggesting a potent role in the context of inflammatory bowel diseases. This anti-inflammatory effect depends on surface layer proteins (SLPs). SLPs may be involved in key functions in probiotics, such as persistence within the gut, adhesion to host cells and mucus, or immunomodulation. Several SLPs coexist in P. freudenreichii CIRM-BIA 129 and mediate immunomodulation and adhesion. A mutant P. freudenreichii CIRM-BIA 129ΔslpB (CB129ΔslpB) strain was shown to exhibit decreased adhesion to intestinal epithelial cells. In the present study, we thoroughly analyzed the impact of this mutation on cellular properties. Firstly, we investigated alterations of surface properties in CB129ΔslpB. Surface extractable proteins, surface charges (ζ-potential) and surface hydrophobicity were affected by the mutation. Whole-cell proteomics, using high definition mass spectrometry, identified 1,288 quantifiable proteins in the wild-type strain, i.e., 53% of the theoretical proteome predicted according to P. freudenreichii CIRM-BIA 129 genome sequence. In the mutant strain, we detected 1,252 proteins, including 1,227 proteins in common with the wild-type strain. Comparative quantitative analysis revealed 97 proteins with significant differences between wild-type and mutant strains. These proteins are involved in various cellular process like signaling, metabolism, and DNA repair and replication. Finally, in silico analysis predicted that slpB gene is not part of an operon, thus not affecting the downstream genes after gene knockout. This study, in accordance with the various roles attributed in the literature to SLPs, revealed a pleiotropic effect of a single slpB mutation, in the probiotic P. freudenreichii. This suggests that SlpB may be at a central node of cellular processes and confirms that both nature and amount of SLPs, which are highly variable within the P. freudenreichii species, determine the probiotic abilities of strains.

Beyond proteostasis: Roles of type I chaperonins in bacterial pathogenesis

Nearly all bacterial species express two or more chaperonin genes. Recent data indicate that type I chaperonins may be key players in bacterial infections. This is partly due to the well-known contribution of chaperonins in cellular proteostasis, the latter being compromised during bacterial host infection. In addition to their protein-folding activity, it has been revealed that certain chaperonins also exhibit moonlighting functions that can contribute in different ways to bacterial pathogenicity. Examples range from inducing adhesion molecules in Chlamydophila pneumoniae to supporting intracellular survival in Mycobacterium tuberculosis and Leishmania donovani, to inducing cytokines in Helicobacter pylori to promoting antimicrobial resistance in Escherichia coli, amongst others. This article provides a thorough reviews of our current understanding of the different mechanisms involving type I chaperonins during bacteria-host interactions, and suggests new areas to be explored and the potential of finding new targets for fighting bacterial infections.

Chaperonomics in leptospirosis

INTRODUCTION

Knowledge of the function of molecular chaperones is required for a better understanding of cellular proteostasis. Nevertheless, such information is currently dispersed as most of previous studies investigated chaperones on a single-angle basis. Recently, a new subdiscipline of chaperonology, namely 'chaperonomics' (defined as 'systematic analysis of chaperone genes, transcripts, proteins, or their interaction networks using omics technologies'), has been emerging to better understand biological, physiological, and pathological roles of chaperones. Areas covered: This review provides broad overviews of bacterial chaperones, heat shock proteins (HSPs), and leptospirosis, and then focuses on recent progress of chaperonomics applied to define roles of HSPs in various pathogenic and saprophytic leptospiral species and serovars. Expert commentary: Comprehensive analysis of leptospiral chaperones/HSPs using a chaperonomics approach holds great promise for better understanding of functional roles of chaperones/HSPs in bacterial survival and disease pathogenesis. Moreover, this new approach may also lead to further development of chaperones/HSPs-based diagnostics and/or vaccine discovery for leptospirosis.

Molecular mechanism for the influence of gender dimorphism on alcoholic liver injury in mice

It is known that women develop alcoholic liver injury more rapidly and have a lower alcohol toxic threshold than men. However, the detailed molecular mechanisms remain unclear. The precise mechanism responsible for the sex difference needs to be determined. Female and male mice were given ethanol by intragastric infusion every day for 4 weeks. The pathological changes were detected by hematoxylin-eosin, Sirius red, oil red O, periodic acid-Schiff, and Hochest33258 staining in the liver of female and male mice. The related gene and protein expression of hepatocytes stress, proliferation and apoptosis, glycogen synthesis, lipid metabolism, and hepatic fibrosis were also systematically analyzed in the female and male mice. Livers from ethanol-treated female mice had more serious hepatocyte necrosis, liver fibrosis ( P < 0.01), substantial micro/macrovesicular steatosis ( p < 0.01), glycogen consumption ( p < 0.05), and hepatocytes apoptosis ( p < 0.05) than ethanol-treated male mice. The expression of heat shock protein 27 (HSP27), HSP70, proliferating cell nuclear antigen, B-cell lymphoma/leukemia-2 (Bcl-2), and phosphorylated signal transducer and activators of transcription 3 (p-STAT3) was higher in ethanol-treated male mice than ethanol-treated female mice ( P < 0.05 or P < 0.01). But, the expression of Bax (Bcl-2-associated X protein), Caspase 3, CYP2E1 (cytochrome P4502E1), and transforming growth factor βl had the contrary results. Our study suggested that ethanol treatment induced more expression of HSP27 and HSP70, faster hepatocyte proliferation, higher level of glycogen, and interleukin-6 signaling pathway activation, but less hepatocyte apoptosis and CYP2E1 expression in male mice than female mice, which could be helpful to understand the molecular mechanism for the influence of sex difference on alcoholic liver injury.

Comparative genomic analysis of Myroides odoratimimus isolates

Myroides odoratimimus is an important nosocomial pathogen. Management of M. odoratimimus infection is difficult owing to the multidrug resistance and the unknown pathogenesis mechanisms. Based on our previous genomic sequencing data of M. odoratimimus PR63039 (isolated from a patient with the urinary tract infection), in this study, we further performed comparative genomic analysis for 10 selected Myroides strains. Our results showed that these Myroides genome contexts were very similar and phylogenetically related. Various prophages were identified in the four clinical isolate genomes, which possibly contributed to the genome evolution among the Myroides strains. CRISPR elements were only detected in the two clinical (PR63039 and CCUG10230) isolates and two environmental (CCUG12700 and H1bi) strains. With more stringent cutoff parameters in CARD analysis, the four clinical M. odoratimimus contained roughly equal antibiotic resistance genes, indicating their similar antibiotic resistance profiles. The three clinical (CCUG10230, CCUG12901, CIP101113) and three environmental (CCUG12700, L41, H1bi) M. odoratimimus strains were speculated to carry the indistinguishable virulent factors (VFs), which may involve in the similar pathogenesis mechanism. Moreover, some VFs might confer to the high capacity of dissemination, attacking tissue cells and induction of autoimmune complications. Our results facilitate the research of antibiotic resistance and the development of therapeutic regimens for the M. odoratimimus infections.

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass

Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored.

Coping with High Temperature: A Unique Regulation in A. tumefaciens

Elevation of temperature is a frequent and considerable stress for mesophilic bacteria. Therefore, several molecular mechanisms have evolved to cope with high temperature. We have been studying the response of Agrobacterium tumefaciens to temperature stress, focusing on two aspects: the heat-shock response and the temperature-dependent regulation of methionine biosynthesis. The results indicate that the molecular mechanisms involved in A. tumefaciens control of growth at high temperature are unique and we are still missing important information essential for understanding how these bacteria cope with temperature stress.

Molecular Mechanism of J-Domain-Triggered ATP Hydrolysis by Hsp70 Chaperones

Efficient targeting of Hsp70 chaperones to substrate proteins depends on J-domain cochaperones, which in synergism with substrates trigger ATP hydrolysis in Hsp70s and concomitant substrate trapping. We present the crystal structure of the J-domain of Escherichia coli DnaJ in complex with the E. coli Hsp70 DnaK. The J-domain interacts not only with DnaK's nucleotide-binding domain (NBD) but also with its substrate-binding domain (SBD) and packs against the highly conserved interdomain linker. Mutational replacement of contacts between J-domain and SBD strongly reduces the ability of substrates to stimulate ATP hydrolysis in the presence of DnaJ and compromises viability at heat shock temperatures. Our data demonstrate that the J-domain and the substrate do not deliver completely independent signals for ATP hydrolysis, but the J-domain, in addition to its direct influence on Hsp70s catalytic center, makes Hsp70 more responsive for the hydrolysis-inducing signal of the substrate, resulting in efficient substrate trapping.