Small heat shock proteins, IbpA and IbpB, are involved in resistances to heat and superoxide stresses in Escherichia coli

Nitazoxanide inhibits pili assembly by targeting BamB to synergize with polymyxin B against drug-resistant Escherichia coli

Gram-negative bacteria rely on pili assembly for pathogenicity, with the chaperone-usher (CU) pathway regulating pilus biogenesis. Nitazoxanide (NTZ) inhibits CU pathway-mediated P pilus biogenesis by specifically interfering with the proper folding of the outer membrane protein (OMP) usher, primarily mediated by the β-barrel assembly machinery (BAM) complex. In this study, we identified the BAM complex components BamB and the BamA POTRA2 domain as key binding targets for NTZ. Molecular dynamics simulations and Bio-Layer Interferometry revealed that BamB residues S61 and R195 are critical for NTZ binding. NTZ activated the Cpx two-component system and induced inner membrane perturbations, which resulted from the accumulation of misfolded P pilus subunits. Upregulation of the ibpAB gene, which protects the bacteria against NTZ-induced oxidative stress, was also observed. Importantly, NTZ combined with polymyxin B enhanced the latter's antibacterial activity against both susceptible and MCR-positive E. coli strains. This enhancement was achieved through NTZ-induced increases in inner membrane permeability, oxidative stress, and inhibition of efflux pump activity and biofilm formation. This study provides new insights into the antimicrobial mechanism of NTZ and highlights its potential as an antibiotic adjuvant by targeting BamB to inhibit the CU pathway, restoring the efficacy of polymyxin B against multidrug-resistant bacteria.

hmuSTUV operon positively regulates the alginate gene cluster to mediate the pathogenicity of Pseudomonas donghuensis HYS

Pseudomonas donghuensis HYS is highly virulent to Caenorhabditis elegans, but with mechanistic details that are not fully understood. The hmuSTUV operon was reported to participate in the synthesis of heme in Pseudomonas. However, the exact role of the hmuSTUV operon in Pseudomonas virulence has not been elucidated. In this study, we report for the first time that the hmuSTUV operon in P. donghuensis HYS causes host virulence, and that hmuS was a key gene for the toxicity of this operon. Furthermore, RNA-seq data showed that hmuS deletion inhibited alginate gene expression, thereby inhibiting biofilm formation. The hmuSTUV operon and alginate gene cluster are conserved in Pseudomonas. By constructing mutant strains carrying GFP, we found that the hmuS deletion reduced colonisation of HYS to the host gut. Moreover, the expression of the alginate gene cluster was controlled by the construction of a L-arabinose-inducible promoter. hmuS positively regulated alginate gene cluster expression, mediating bacterial virulence against C. elegans. In addition, HYS originating from the East Lake of Wuhan City was more pathogenic to zebrafish than any other pathogenic Pseudomonas, through impairment of zebrafish neurodevelopment and locomotor ability, by colonizing to the zebrafish brain. In conclusion, the hmuSTUV operon positively regulated the alg gene cluster, thereby disabling bacterial biofilm formation and colonisation to mediate bacterial pathogenicity to the host. These novel findings revealed the critical interaction between the hmuSTUV operon and the alg gene cluster in the bacterial virulence of Pseudomonas, providing new insights into Pseudomonas pathogenicity.

Two new oligomers of E. coli small heat-shock protein IbpB identified under heat stress exhibit maximum holding chaperone activity

Escherichia coli small heat-shock protein IbpB (MW: 16 KDa) has holding chaperone activity and is present in cells at 30 °C as two large oligomers of MW 2.0-3.0 MDa and 600-700 KDa. We report here about the presence of two additional oligomers of MW around 400 and 130 KDa in cells under heat-stress at 50 °C. These two smaller oligomers possess the most chaperone activity, as observed from the extent of inhibition of inactivation and aggregation separately, of L-Lactate dehydrogenase in the presence of the individual oligomers at 52 and 60 °C, respectively. It is suggested here that the two larger oligomers act as poorly active storage forms, which under heat stress dissociate partially into smaller oligomers with high holdase activity.

A microaerobically induced small heat shock protein contributes to Rhizobium leguminosarum/Pisum sativum symbiosis and interacts with a wide range of bacteroid proteins

During the establishment of the symbiosis with legume plants, rhizobia are exposed to hostile physical and chemical microenvironments to which adaptations are required. Stress response proteins including small heat shock proteins (sHSPs) were previously shown to be differentially regulated in bacteroids induced by Rhizobium leguminosarum bv. viciae UPM791 in different hosts. In this work, we undertook a functional analysis of the host-dependent sHSP RLV_1399. A rlv_1399-deleted mutant strain was impaired in the symbiotic performance with peas but not with lentil plants. Expression of rlv_1399 gene was induced under microaerobic conditions in a FnrN-dependent manner consistent with the presence of an anaerobox in its regulatory region. Overexpression of this sHSP improves the viability of bacterial cultures following exposure to hydrogen peroxide and to cationic nodule-specific cysteine-rich (NCR) antimicrobial peptides. Co-purification experiments have identified proteins related to nitrogenase synthesis, stress response, carbon and nitrogen metabolism, and to other relevant cellular functions as potential substrates for RLV_1399 in pea bacteroids. These results, along with the presence of unusually high number of copies of shsp genes in rhizobial genomes, indicate that sHSPs might play a relevant role in the adaptation of the bacteria against stress conditions inside their host.IMPORTANCEThe identification and analysis of the mechanisms involved in host-dependent bacterial stress response is important to develop optimal Rhizobium/legume combinations to maximize nitrogen fixation for inoculant development and might have also applications to extend nitrogen fixation to other crops. The data presented in this work indicate that sHSP RLV_1399 is part of the bacterial stress response to face specific stress conditions offered by each legume host. The identification of a wide diversity of sHSP potential targets reveals the potential of this protein to protect essential bacteroid functions. The finding that nitrogenase is the most abundant RLV_1399 substrate suggests that this protein is required to obtain an optimal nitrogen-fixing symbiosis.

Relevance of genetic causes and environmental adaptation of Cronobacter spp. isolated from infant and follow-up formula production factories and retailed products in China: A 7-year period of continuous surveillance based on genome-wide analysis

The possible contamination routes, environmental adaptation, and genetic basis of Cronobacter spp. in infant and follow-up formula production factories and retailed products in mainland China have been determined by laboratory studies and whole-genome comparative analysis in a 7-year nationwide continuous surveillance spanning from 2012 to 2018. The 2-year continuous multicenter surveillance of the production process (conducted in 2013 and 2014) revealed that the source of Cronobacter spp. in the dry-blending process was the raw dry ingredients and manufacturing environment (particularly in the vibro sieve and vacuum cleaner), while in the combined process, the main contamination source was identified as the packing room. It is important to note that, according to the contamination control knowledge obtained from the production process surveillance, the contamination rate of retail powdered infant formula (PIF) and follow-up formula (FUF) products in China decreased significantly from 2016 onward, after improving the hygiene management practices in factories. The prevalence of Cronobacter spp. in retailed PIF and FUF in China in 2018 was dramatically reduced from 1.55 % (61/3925, in 2012) to an average as low as 0.17 % (13/7655 in 2018). Phenotype determination and genomic analysis were performed on a total of 90 Cronobacter spp. isolates obtained from the surveillance. Of the 90 isolates, only two showed resistance to either cefazolin or cefoxitin. The multilocus sequence typing results revealed that C. sakazakii sequence type 1 (ST1), ST37, and C. malonaticus ST7 were the dominant sequence types (STs) collected from the production factories, while C. sakazakii ST1, ST4, ST64, and ST8 were the main STs detected in the retailed PIF and FUF nationwide. One C. sakazakii ST4 isolate (1.1 %, 1/90) had strong biofilm-forming ability and 13 isolates (14.4 %, 13/90) had weak biofilm-forming ability. Genomic analysis revealed that Cronobacter spp. have a relatively stable core-genome and an increasing pan-genome size. Plasmid IncFIB (pCTU3) was prevalent in this genus and some contained 14 antibacterial biocide- and metal-resistance genes (BMRGs) including copper, silver, and arsenic resistant genes. Plasmid IncN_1 was predicted to contain 6 ARGs. This is the first time that a multi-drug resistance IncN_1 type plasmid has been reported in Cronobacter spp. Genomic variations with respect to BMRGs, virulence genes, antimicrobial resistance genes (ARGs), and genes involved in biofilm formation were observed among strains of this genus. There were apparent differences in copies of bcsG and flgJ between the biofilm-forming group and non-biofilm-forming group, indicating that these two genes play key roles in biofilm formation. The findings of this study have improved our understanding of the contamination characteristics and genetic basis of Cronobacter spp. in PIF and FUF and their production environment in China and provide important guidance to reduce contamination with this pathogen during the production of PIF and FUF.

The impact of heat treatment on E. coli cell physiology in rich and minimal media considering oxidative secondary stress

AIMS

This study investigates the cell physiology of thermally injured bacterial cells, with a specific focus on oxidative stress and the repair mechanisms associated with oxidative secondary stress.

METHODS AND RESULTS

We explored the effect of heat treatment on the activity of two protective enzymes, levels of intracellular reactive oxygen species, and redox potential. The findings reveal that enzyme activity slightly increased after heat treatment, gradually returning to baseline levels during subculture. The response of Escherichia coli cells to heat treatment, as assessed by the level of superoxide radicals generated and redox potential, varied based on growth conditions, namely minimal and rich media. Notably, the viability of injured cells improved when antioxidants were added to agar media, even in the presence of metabolic inhibitors.

CONCLUSIONS

These results suggest a complex system involved in repairing damage in heat-treated cells, particularly in rich media. While repairing membrane damage is crucial for cell regrowth and the electron transport system plays a critical role in the recovery process of injured cells under both tested conditions.

IbpAB small heat shock proteins are not host factors for bacteriophage ϕX174 replication

Bacteriophage ϕX174 is a small icosahedral virus of the Microviridae with a rapid replication cycle. Previously, we found that in ϕX174 infections of Escherichia coli, the most highly upregulated host proteins are two small heat shock proteins, IbpA and IbpB, belonging to the HSP20 family, which is a universally conserved group of stress-induced molecular chaperones that prevent irreversible aggregation of proteins. Heat shock proteins were found to protect against ϕX174 lysis, but IbpA/B have not been studied. In this work, we disrupted the ibpA and ibpB genes and measured the effects on ϕX174 replication. We found that in contrast to other E. coli heat shock proteins, they are not necessary for ϕX174 replication; moreover, their absence has no discernible effect on ϕX174 fecundity. These results suggest IbpA/B upregulation is a response to ϕX174 protein expression but does not play a role in phage replication, and they are not Microviridae host factors.

The metabolic slowdown caused by the deletion of pspA accelerates protein aggregation during stationary phase facilitating antibiotic persistence

Entering a dormant state is a prevailing mechanism used by bacterial cells to transiently evade antibiotic attacks and become persisters. The dynamic progression of bacterial dormancy depths driven by protein aggregation has been found to be critical for antibiotic persistence in recent years. However, our current understanding of the endogenous genes that affects dormancy depth remains limited. Here, we discovered a novel role of phage shock protein A (pspA) gene in modulating bacterial dormancy depth. Deletion of pspA of Escherichia coli resulted in increased bacterial dormancy depths and prolonged lag times for resuscitation during the stationary phase. ∆pspA exhibited a higher persister ratio compared to the wild type when challenged with various antibiotics. Microscopic images revealed that ∆pspA showed accelerated formation of protein aggresomes, which were collections of endogenous protein aggregates. Time-lapse imaging established the positive correlation between protein aggregation and antibiotic persistence of ∆pspA at the single-cell level. To investigate the molecular mechanism underlying accelerated protein aggregation, we performed transcriptome profiling and found the increased abundance of chaperons and a general metabolic slowdown in the absence of pspA. Consistent with the transcriptomic results, the ∆pspA strain showed a decreased cellular ATP level, which could be rescued by glucose supplementation. Then, we verified that replenishment of cellular ATP levels by adding glucose could inhibit protein aggregation and reduce persister formation in ∆pspA. This study highlights the novel role of pspA in maintaining proteostasis, regulating dormancy depth, and affecting antibiotic persistence during stationary phase.

Effects of small heat shock proteins from thermotolerant bacteria on the stress resistance of Escherichia coli to temperature, pH, and hyperosmolarity

Small heat shock proteins (HSPs), such as HSP20, represent cellular thermal resistance mechanisms, to avoid protein aggregation at elevated temperatures. Recombinantly expressed HSP20s serve as a molecular tool for improving the tolerance of living cells to various physical and chemical stressors. Here, we aimed to heterologously express 18 HSP20s from 12 thermotolerant bacteria in Escherichia coli and evaluate their effects on various physical and chemical cellular stresses. Seventeen HSP20s were successfully expressed as soluble proteins. Recombinant E. coli cells were subjected to heat, cold, acidic, alkaline, and hyperosmolar stress to evaluate the effects of HSP20 proteins on stress resistance. Notably, the overexpression of 15 HSP20s enhanced the stress resistance of E. coli compared to that of the control strain. In particular, HSPs from Tepidimonas sediminis and Oceanithermus profundus improved the stress tolerance of E. coli under all tested conditions. In addition, E. coli harboring HSP20 from T. sediminis retained cell viability even after heat treatment at 52 °C for 5 days. To our knowledge, this is the first report of E. coli tolerance to prolonged (> 100 h) high-temperature stress. These findings indicate the potential of thermotolerant HSPs as molecular tools for improving stress tolerance in E. coli.

A review on oligomeric polydispersity and oligomers-dependent holding chaperone activity of the small heat-shock protein IbpB of Escherichia coli

Inclusion body-associated proteins IbpA and IbpB of MW 16 KDa are the two small heat-shock proteins (sHSPs) of Escherichia coli, and they have only holding, but not folding, chaperone activity. In vitro holdase activity of IbpB is more than that of IbpA, and in combination, they synergise. Both IbpA and IbpB monomers first form homodimers, which as building blocks subsequently oligomerize to make heavy oligomers with MW of MDa range; for IbpB, the MW range of heavy oligomers is 2.0-3.0 MDa, whereas for IbpA oligomers, the values in MDa are not so specified/reported. By temperature upshift, such large oligomers of IbpB, but not of IbpA, dissociate to make relatively small oligomeric assemblies of MW around 600-700KDa. The larger oligomers of IbpB are assumed to be inactive storage form, which on facing heat or oxidative stress dissociate into smaller oligomers of ATP-independent holding chaperone activity. These smaller oligomers bind with stress-induced partially denatured/unfolded and thereby going to be aggregated proteins, to give them protection against permanent damage and aggregation. On withdrawal of stress, IbpB transfers the bound substrate protein to the ATP-dependent bi-chaperone system DnaKJE-ClpB, having both holdase and foldase properties, to finally refold the protein. Of the two sHSPs IbpA and IbpB of E. coli, this review covers the recent advances in research on IbpB only.

A novel ruthenium-silver based antimicrobial potentiates aminoglycoside activity against Pseudomonas aeruginosa

The rapid dissemination of antibiotic resistance combined with the decline in the discovery of novel antibiotics represents a major challenge for infectious disease control that can only be mitigated by investments in novel treatment strategies. Alternative antimicrobials, including silver, have regained interest due to their diverse mechanisms of inhibiting microbial growth. One such example is AGXX, a broad-spectrum antimicrobial that produces highly cytotoxic reactive oxygen species (ROS) to inflict extensive macromolecular damage. Due to the connections identified between ROS production and antibiotic lethality, we hypothesized that AGXX could potentially increase the activity of conventional antibiotics. Using the gram-negative pathogen Pseudomonas aeruginosa, we screened possible synergistic effects of AGXX on several antibiotic classes. We found that the combination of AGXX and aminoglycosides tested at sublethal concentrations led to a rapid exponential decrease in bacterial survival and restored the sensitivity of a kanamycin-resistant strain. ROS production contributes significantly to the bactericidal effects of AGXX/aminoglycoside treatments, which is dependent on oxygen availability and can be reduced by the addition of ROS scavengers. Additionally, P. aeruginosa strains deficient in ROS detoxifying/repair genes were more susceptible to AGXX/aminoglycoside treatment. We further demonstrate that this synergistic interaction was associated with a significant increase in outer and inner membrane permeability, resulting in increased antibiotic influx. Our study also revealed that AGXX/aminoglycoside-mediated killing requires an active proton motive force across the bacterial membrane. Overall, our findings provide an understanding of cellular targets that could be inhibited to increase the activity of conventional antimicrobials. IMPORTANCE The emergence of drug-resistant bacteria coupled with the decline in antibiotic development highlights the need for novel alternatives. Thus, new strategies aimed at repurposing conventional antibiotics have gained significant interest. The necessity of these interventions is evident especially in gram-negative pathogens as they are particularly difficult to treat due to their outer membrane. This study highlights the effectiveness of the antimicrobial AGXX in potentiating aminoglycoside activities against P. aeruginosa. The combination of AGXX and aminoglycosides not only reduces bacterial survival rapidly but also significantly re-sensitizes aminoglycoside-resistant P. aeruginosa strains. In combination with gentamicin, AGXX induces increased endogenous oxidative stress, membrane damage, and iron-sulfur cluster disruption. These findings emphasize AGXX's potential as a route of antibiotic adjuvant development and shed light on potential targets to enhance aminoglycoside activity.

The Functionality of IbpA from Acholeplasma laidlawii Is Governed by Dynamic Rearrangement of Its Globular-Fibrillar Quaternary Structure

Small heat shock proteins (sHSPs) represent a first line of stress defense in many bacteria. The primary function of these molecular chaperones involves preventing irreversible protein denaturation and aggregation. In Escherichia coli, fibrillar EcIbpA binds unfolded proteins and keeps them in a folding-competent state. Further, its structural homologue EcIbpB induces the transition of EcIbpA to globules, thereby facilitating the substrate transfer to the HSP70-HSP100 system for refolding. The phytopathogenic Acholeplasma laidlawii possesses only a single sHSP, AlIbpA. Here, we demonstrate non-trivial features of the function and regulation of the chaperone-like activity of AlIbpA according to its interaction with other components of the mycoplasma multi-chaperone network. Our results show that the efficiency of the A. laidlawii multi-chaperone system is driven with the ability of AlIbpA to form both globular and fibrillar structures, thus combining functions of both IbpA and IbpB when transferring the substrate proteins to the HSP70-HSP100 system. In contrast to EcIbpA and EcIbpB, AlIbpA appears as an sHSP, in which the competition between the N- and C-terminal domains regulates the shift of the protein quaternary structure between a fibrillar and globular form, thus representing a molecular mechanism of its functional regulation. While the C-terminus of AlIbpA is responsible for fibrils formation and substrate capture, the N-terminus seems to have a similar function to EcIbpB through facilitating further substrate protein disaggregation using HSP70. Moreover, our results indicate that prior to the final disaggregation process, AlIbpA can directly transfer the substrate to HSP100, thereby representing an alternative mechanism in the HSP interaction network.

Black Phosphorus/MnO2 Nanocomposite Disrupting Bacterial Thermotolerance for Efficient Mild-Temperature Photothermal Therapy

The emergence of multi-drug resistant (MDR) pathogens is a major public health concern, posing a substantial global economic burden. Photothermal therapy (PTT) at mild temperature presents a promising alternative to traditional antibiotics due to its biological safety and ability to circumvent drug resistance. However, the efficacy of mild PTT is limited by bacterial thermotolerance. Herein, a nanocomposite, BP@Mn-NC, comprising black phosphorus nanosheets and a manganese-based nanozyme (Mn-NZ) is developed, which possesses both photothermal and catalytic properties. Mn-NZ imparts glucose oxidase- and peroxidase-like properties to BP@Mn-NC, generating reactive oxygen species (ROS) that induce lipid peroxidation and malondialdehyde accumulation across the bacterial cell membrane. This process disrupts unprotected respiratory chain complexes exposed on the bacterial cell membrane, leading to a reduction in the intracellular adenosine triphosphate (ATP) content. Consequently, mild PTT mediated by BP@Mn-NC effectively eliminates MDR infections by specifically impairing bacterial thermotolerance because of the dependence of bacterial heat shock proteins (HSPs) on ATP molecules for their proper functioning. This study paves the way for the development of a novel photothermal strategy to eradicate MDR pathogens, which targets bacterial HSPs through ROS-mediated inhibition of bacterial respiratory chain activity.

The Novel Silver-Containing Antimicrobial Potentiates Aminoglycoside Activity Against Pseudomonas aeruginosa

The rapid dissemination of antibiotic resistance combined with the decline in the discovery of novel antibiotics represents a major challenge for infectious disease control that can only be mitigated by investments into novel treatment strategies. Alternative antimicrobials, including silver, have regained interest due to their diverse mechanisms of inhibiting microbial growth. One such example is AGXX®, a broad-spectrum silver containing antimicrobial that produces highly cytotoxic reactive oxygen species (ROS) to inflict extensive macromolecular damage. Due to connections identified between ROS production and antibiotic lethality, we hypothesized that AGXX® could potentially increase the activity of conventional antibiotics. Using the gram-negative pathogen Pseudomonas aeruginosa, we screened possible synergistic effects of AGXX® on several antibiotic classes. We found that the combination of AGXX® and aminoglycosides tested at sublethal concentrations led to a rapid exponential decrease in bacterial survival and restored sensitivity of a kanamycin-resistant strain. ROS production contributes significantly to the bactericidal effects of AGXX®/aminoglycoside treatments, which is dependent on oxygen availability and can be reduced by the addition of ROS scavengers. Additionally, P. aeruginosa strains deficient in ROS detoxifying/repair genes were more susceptible to AGXX®/aminoglycoside treatment. We further demonstrate that this synergistic interaction was associated with significant increase in outer and inner membrane permeability, resulting in increased antibiotic influx. Our study also revealed that AGXX®/aminoglycoside-mediated killing requires an active proton motive force across the bacterial membrane. Overall, our findings provide an understanding of cellular targets that could be inhibited to increase the activity of conventional antimicrobials.

Evaluation of distinct modes of oxidative secondary injury generated in heat-treated cells of Escherichia coli with solid/liquid and complex/semi-synthetic media sets

AIMS

To characterize and evaluate oxidative secondary injury generated in heat-treated Escherichia coli cells during recovery cultivation either on agar or in a broth of a semi-synthetic enriched M9 (EM9) medium and a complex Luria broth (LB) medium with different types of antioxidants.

METHODS AND RESULTS

E. coli cells grown in the EM9 and LB broth were heated at 50^o C in a buffer (pH7.0). Heated cells were recovered on the same kind of agar medium as that used for growth, with or without different antioxidants. Although these antioxidants mostly protected the cells from oxidative secondary injury on the recovery media, sodium thiosulfate and sodium pyruvate were most protective on EM9 and LB agars, respectively. Determination of viability using the most probable number and growth delay analysis methods showed significant reductions in the protective effects of antioxidants in the EM9 and LB media.

CONCLUSION

Oxidative secondary injury generated in heated E. coli cells was found to be qualitatively and quantitatively diverse under cellular and environmental conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results suggest that different modes of oxidation should be considered in viability determination and injured cell enumeration of heat-treated cells.

Noninvasive assessment of gut function using transcriptional recording sentinel cells

Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome-scale records. Microbial sentinels that traverse the gastrointestinal tract capture a wide range of genes and pathways that describe interactions with the host, including quantitative shifts in the molecular environment that result from alterations in the host diet, induced inflammation, and microbiome complexity. We demonstrate multiplexed recording using barcoded CRISPR arrays, enabling the reconstruction of transcriptional histories of isogenic bacterial strains in vivo. Record-seq therefore provides a scalable, noninvasive platform for interrogating intestinal and microbial physiology throughout the length of the intestine without manipulations to host physiology and can determine how single microbial genetic differences alter the way in which the microbe adapts to the host intestinal environment.

Cellular Effects of 2',3'-Cyclic Nucleotide Monophosphates in Gram-Negative Bacteria

Organismal adaptations to environmental stimuli are governed by intracellular signaling molecules such as nucleotide second messengers. Recent studies have identified functional roles for the noncanonical 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) in both eukaryotes and prokaryotes. In Escherichia coli, 2',3'-cNMPs are produced by RNase I-catalyzed RNA degradation, and these cyclic nucleotides modulate biofilm formation through unknown mechanisms. The present work dissects cellular processes in E. coli and Salmonella enterica serovar Typhimurium that are modulated by 2',3'-cNMPs through the development of cell-permeable 2',3'-cNMP analogs and a 2',3'-cyclic nucleotide phosphodiesterase. Utilization of these chemical and enzymatic tools, in conjunction with phenotypic and transcriptomic investigations, identified pathways regulated by 2',3'-cNMPs, including flagellar motility and biofilm formation, and by oligoribonucleotides with 3'-terminal 2',3'-cyclic phosphates, including responses to cellular stress. Furthermore, interrogation of metabolomic and organismal databases has identified 2',3'-cNMPs in numerous organisms and homologs of the E. coli metabolic proteins that are involved in key eukaryotic pathways. Thus, the present work provides key insights into the roles of these understudied facets of nucleotide metabolism and signaling in prokaryotic physiology and suggest broad roles for 2',3'-cNMPs among bacteria and eukaryotes. IMPORTANCE Bacteria adapt to environmental challenges by producing intracellular signaling molecules that control downstream pathways and alter cellular processes for survival. Nucleotide second messengers serve to transduce extracellular signals and regulate a wide array of intracellular pathways. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified as contributing to the regulation of cellular pathways in eukaryotes and prokaryotes. In this study, we define previously unknown cell processes that are affected by fluctuating 2',3'-cNMP levels or RNA oligomers with 2',3'-cyclic phosphate termini in E. coli and Salmonella Typhimurium, providing a framework for studying novel signaling networks in prokaryotes. Furthermore, we utilize metabolomics databases to identify additional prokaryotic and eukaryotic species that generate 2',3'-cNMPs as a resource for future studies.

Comparative proteomic profiling reveals specific adaption of Vibrio anguillarum to oxidative stress, iron deprivation and humoral components of innate immunity

The gram-negative bacterium Vibrio (Listonella) anguillarum (VA) is the causative agent of vibriosis, a terminal hemorrhagic septicemia affecting the aquacultural industry across the globe. In the current study we used label-free quantitative proteomics to investigate how VA adapts to conditions that mimic defined aspects of vibriosis-related stress such as exposure to oxidative stress (H₂O₂), exposure to humoral factors of innate immunity through incubation with Atlantic salmon serum, and iron deprivation upon supplementation of 2,2'-dipyridyl (DIP) to the growth medium. We also investigated how regulation of virulence factors may be governed by the VA growth phase and availability of nutrients. All experimental conditions explored revealed stress-specific proteomic adaption of VA and only nine proteins were found to be commonly regulated in all conditions. A general observation made for all stress-related conditions was regulation of multiple metabolic pathways. Notably, iron deprivation and exposure to Atlantic salmon serum evoked upregulation of iron acquisition mechanisms. The findings made in the present study represent a source of potential virulence determinants that can be of use in the search for means to understand vibriosis. SIGNIFICANCE: Vibriosis in fish and shellfish caused by V. anguillarum (VA) is responsible for large economic losses in the aquaculture sector across the globe. However, not much is known about the defense mechanism of this pathogen to percept and adapt to the imposed stresses during infection. Analyzing the response of VA to multiple host-related physiochemical stresses, the quantitative proteomic analysis of the present study indicates modulation of several virulence determinants and key defense networks of this pathogen. Our findings provide a theoretical basis to enhance our understanding of VA pathogenesis and can be employed to improve current intervention strategies to control vibriosis in aquaculture.

Detection Time Distribution of Microcolonies Formed by Individual Heat-Injured Cells of Escherichia coli

The microcolony formation at 30℃ on an enriched minimal salts agar plates by individual Escherichia coli cells heated at 50℃ was monitored with a time-lapse shadow image analysis system, MicroBio μ3D^TM AutoScanner. While the time course of microcolony count detected every half an hour for the unheated cells seemingly demonstrated a normal distribution, that for the heated cell population demonstrated totally the growth delay probably resulting from cell injury and also interestingly distributed in its rather deformed pattern with a tailing. Those patterns of the cumulative counts of appearing microcolonies during the post-heating cultivation period were expressed in three different mathematical models. This approach may be proposed as a rapid cultivation method predictable for enumeration of viable and repairable injured cells in practical use.

Understanding the role of hydrophobic patches in protein disaggregation

Protein folding is a very complex process and, so far, the mechanism of folding still intrigues the research community. Despite a large conformational space available (O(10⁴⁷) for a 100 amino acid residue), most proteins fold into their native state within a very short time. While small proteins fold relatively fast (a few microseconds) large globular proteins may take as long as several milliseconds to fold. During the folding process, the protein synthesized in the ribosome is exposed to the crowded environment of the cell and is easily prone to misfolding and aggregation due to interactions with other proteins or biomacromolecules present within the cell. These large proteins, therefore, rely on chaperones for their folding and repair. Chaperones are known to have hydrophobic patchy domains that play a crucial role in shielding the protein against misfolding and disaggregation of aggregated proteins. In the current article, Monte Carlo simulations carried out in the framework of the hydrophobic-polar (H-P) lattice model indicate that hydrophobic patchy domains drastically reduce the inter-protein interactions and are efficient in disaggregating proteins. The effectiveness of the disaggregation depends on the size and distribution of these patches on the surface and also on the strength of the interaction between the protein and the surface. Further, our results indicate that when the patch is complementary to the exposed hydrophobic patch of the protein, protein disaggregation is accompanied by stabilization of the protein even relative to its bulk behavior due to favorable protein-surface interactions. We believe that these findings shed light on the role of the class of chaperones known as heat shock proteins (Hsps) on protein disaggregation and refolding.

IbpB-bound substrate release in living cells as revealed by unnatural amino acid-mediated photo-crosslinking

Small heat shock proteins (sHSPs) are known to bind non‐native substrates and prevent irreversible aggregation in an ATP‐independent manner. However, the dynamic interaction between sHSPs and their substrates in vivo is less studied. Here, by utilizing a genetically incorporated crosslinker, we characterized the interaction between sHSP IbpB and its endogenous substrates in living cells. Through photo‐crosslinking analysis of five Bpa variants of IbpB, we found that the substrate binding of IbpB in living cells is reversible upon short‐time exposure at 50 °C. Our data provide in vivo evidence that IbpB engages in dynamic substrate release under nonstress conditions and suggest that photo‐crosslinking may be a suitable method for investigating dynamic interaction between molecular chaperones and their substrates in living cells.

Strategies to Dissect Host-Microbial Immune Interactions That Determine Mucosal Homeostasis vs. Intestinal Inflammation in Gnotobiotic Mice

When identifying the key immunologic-microbial interactions leading to either mucosal homeostasis in normal hosts or intestinal inflammatory responses in genetically susceptible individuals, it is important to not only identify microbial community correlations but to also define the functional pathways involved. Gnotobiotic rodents are a very effective tool for this purpose as they provide a highly controlled environment in which to identify the function of complex intestinal microbiota, their individual components, and metabolic products. Herein we review specific strategies using gnotobiotic mice to functionally evaluate the role of various intestinal microbiota in host responses. These studies include basic comparisons between host responses in germ-free (GF), specific-pathogen-free or conventionally raised wild-type mice or those with underlying genetic susceptibilities to intestinal inflammation. We also discuss what can be learned from studies in which GF mice are colonized with single wild-type or genetically-modified microbial isolates to examine the functions of individual bacteria and their targeted bacterial genes, or colonized by multiple defined isolates to determine interactions between members of defined consortia. Additionally, we discuss studies to identify functions of complex microbial communities from healthy or diseased human or murine hosts via fecal transplant into GF mice. Finally, we conclude by suggesting ways to improve studies of immune-microbial interactions using gnotobiotic mice.

Heat and Pressure Resistance in Escherichia coli Relates to Protein Folding and Aggregation

The locus of heat resistance (LHR) confers extreme heat resistance in Escherichia coli. This study explored the role of the LHR in heat and pressure resistance of E. coli, as well as its relationship with protein folding and aggregation in vivo. The role of LHR was investigated in E. coli MG1655 and the pressure resistant E. coli LMM1010 expressing an ibpA-yfp fusion protein to visualize inclusion bodies by fluorescence microscopy. The expression of proteins by the LHR was determined by proteomic analysis; inclusion bodies of untreated and treated cells were also analyzed by proteomics, and by fluorescent microscopy. In total, 11 proteins of LHR were expressed: sHSP20, ClpK_GI, sHSP, YdfX1 and YdfX2, HdeD, KefB, Trx, PsiE, DegP, and a hypothetical protein. The proteomic analysis of inclusion bodies revealed a differential abundance of proteins related to oxidative stress in strains carrying the LHR. The LHR reduced the presence of inclusion bodies after heat or pressure treatment, indicating that proteins expressed by the LHR prevent protein aggregation, or disaggregate proteins. This phenotype of the LHR was also conferred by expression of a fragment containing only sHSP20, ClpK_GI, and sHSP. The LHR and the fragment encoding only sHSP20, ClpK_GI, and sHSP also enhanced pressure resistance in E. coli MG1655 but had no effect on pressure resistance of E. coli LMM1010. In conclusion, the LHR confers pressure resistance to some strains of E. coli, and reduces protein aggregation. Pressure and heat resistance are also dependent on additional LHR-encoded functions.

Sub-minimum inhibitory concentration ceftazidime inhibits Escherichia coli biofilm formation by influencing the levels of the ibpA gene and extracellular indole

Escherichia coli is a common pathogen of bacterial biofilm infections. Sub-minimum inhibitory concentration ceftazidime (sub-MIC CAZ) could inhibit the biofilm formation of E. coli. Deletion of the ibpAB genes could increase the extracellular indole concentration of E. coli and then inhibit biofilm formation. Therefore, we speculated that sub-MIC CAZ might inhibit biofilm formation via ibpAB. In this study, the results showed that sub-MIC CAZ could significantly inhibit biofilm formation, swimming motility and the expression of the ibpA gene, while it could increase the expression of tnaA gene and extracellular indole concentration. Knockout of the ibpA gene resulted in a decrease in biofilm formation and swimming motility and an increase in the indole concentration. When treated with sub-MIC CAZ, the tnaA gene expression, indole concentration, biofilm formation and swimming motility of MG1655 ΔibpA were similar to those of the control group. The results indicated that sub-MIC CAZ might inhibit the biofilm formation of E. coli by increasing the extracellular indole concentration and downregulating the ibpA gene.

The Salmonella Specific, σE-Regulated, STM1250 and AgsA, Function With the sHsps IbpA and IbpB, to Counter Oxidative Stress and Survive Macrophage Killing

The host presents an array of environments which induce bacterial stress including changes in pH, antimicrobial compounds and reactive oxygen species. The bacterial envelope sits at the interface between the intracellular and extracellular environment and its maintenance is essential for Salmonella cell viability under a range of conditions, including during infection. In this study, we aimed to understand the contribution of the σ^H- and σ^E-regulated small heat shock proteins IbpA, IbpB, and AgsA and the putative σ^E-regulated stress response protein STM1250 to the Salmonella envelope stress response. Due to shared sequence identity, regulatory overlap, and the specificity of STM1250 and AgsA to Salmonella sp., we hypothesized that functional overlap exists between these four stress response proteins, which might afford a selective advantage during Salmonella exposure to stress. We present here new roles for three small heat shock proteins and a putative stress response protein in Salmonella that are not limited to heat shock. We have shown that, compared to WT, a quadruple mutant is significantly more sensitive to hydrogen peroxide, has a lower minimum bactericidal concentration to the cationic antimicrobial peptide polymyxin B, and is attenuated in macrophages.

Construction and characterization of broad-host-range reporter plasmid suitable for on-line analysis of bacterial host responses related to recombinant protein production

BACKGROUND

Bacteria are widely used as hosts for recombinant protein production due to their rapid growth, simple media requirement and ability to produce high yields of correctly folded proteins. Overproduction of recombinant proteins may impose metabolic burden to host cells, triggering various stress responses, and the ability of the cells to cope with such stresses is an important factor affecting both cell growth and product yield.

RESULTS

Here, we present a versatile plasmid-based reporter system for efficient analysis of metabolic responses associated with availability of cellular resources utilized for recombinant protein production and host capacity to synthesize correctly folded proteins. The reporter plasmid is based on the broad-host range RK2 minimal replicon and harbors the strong and inducible XylS/Pm regulator/promoter system, the ppGpp-regulated ribosomal protein promoter PrpsJ, and the σ32-dependent synthetic tandem promoter Pibpfxs, each controlling expression of one distinguishable fluorescent protein. We characterized the responsiveness of all three reporters in Escherichia coli by quantitative fluorescence measurements in cell cultures cultivated under different growth and stress conditions. We also validated the broad-host range application potential of the reporter plasmid by using Pseudomonas putida and Azotobacter vinelandii as hosts.

CONCLUSIONS

The plasmid-based reporter system can be used for analysis of the total inducible recombinant protein production, the translational capacity measured as transcription level of ribosomal protein genes and the heat shock-like response revealing aberrant protein folding in all studied Gram-negative bacterial strains.

Transcriptomic Analysis of the Brucella melitensis Rev.1 Vaccine Strain in an Acidic Environment: Insights Into Virulence Attenuation

The live attenuated Brucella melitensis Rev.1 (Elberg-originated) vaccine strain is widely used to control the zoonotic infection brucellosis in small ruminants, but the molecular mechanisms underlying the attenuation of this strain have not been fully characterized. Following their uptake by the host cell, Brucella replicate inside a membrane-bound compartment—the Brucella-containing vacuole—whose acidification is essential for the survival of the pathogen. Therefore, identifying the genes that contribute to the survival of Brucella in acidic environments will greatly assist our understanding of its molecular pathogenic mechanisms and of the attenuated virulence of the Rev.1 strain. Here, we conducted a comprehensive comparative transcriptome analysis of the Rev.1 vaccine strain against the virulent reference strain 16M in cultures grown under either normal or acidic conditions. We found 403 genes that respond differently to acidic conditions in the two strains (FDR < 0.05, fold change ≥ 2). These genes are involved in crucial cellular processes, including metabolic, biosynthetic, and transport processes. Among the highly enriched genes that were downregulated in Rev.1 under acidic conditions were acetyl-CoA synthetase, aldehyde dehydrogenase, cell division proteins, a cold-shock protein, GroEL, and VirB3. The downregulation of these genes may explain the attenuated virulence of Rev.1 and provide new insights into the virulence mechanisms of Brucella.

YocM a small heat shock protein can protect Bacillus subtilis cells during salt stress

Small heat shock proteins (sHsp) occur in all domains of life. By interacting with misfolded or aggregated proteins these chaperones fulfill a protective role in cellular protein homeostasis. Here, we demonstrate that the sHsp YocM of the Gram-positive model organism Bacillus subtilis is part of the cellular protein quality control system with a specific role in salt stress response. In the absence of YocM the survival of salt shocked cells is impaired, and increased levels of YocM protect B. subtilis exposed to heat or salt. We observed a salt and heat stress-induced localization of YocM to intracellular protein aggregates. Interestingly, purified YocM appears to accelerate protein aggregation of different model substrates in vitro. In addition, the combined presence of YocM and chemical chaperones, which accumulate in salt stressed cells, can facilitate in vitro a synergistic protective effect on protein misfolding. Therefore, the beneficial role of YocM during salt stress could be related to a mutual functional relationship with chemical chaperones and adds a new possible functional aspect to sHsp chaperone activities.

The oligomeric plasticity of Hsp20 of Sulfolobus acidocaldarius protects environment-induced protein aggregation and membrane destabilization

Small heat shock proteins (sHsps) are a ubiquitous family of molecular chaperones that rescue misfolded proteins from irreversible aggregation during cellular stress. Many such sHsps exist as large polydisperse species in solution, and a rapid dynamic subunit exchange between oligomeric and dissociated forms modulates their function under a variety of stress conditions. Here, we investigated the structural and functional properties of Hsp20 from thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. To provide a framework for investigating the structure-function relationship of Hsp20 and understanding its dynamic nature, we employed several biophysical and biochemical techniques. Our data suggested the existence of a ~24-mer of Hsp20 at room temperature (25 °C) and a higher oligomeric form at higher temperature (50 °C-70 °C) and lower pH (3.0-5.0). To our surprise, we identified a dimeric form of protein as the functional conformation in the presence of aggregating substrate proteins. The hydrophobic microenvironment mainly regulates the oligomeric plasticity of Hsp20, and it plays a key role in the protection of stress-induced protein aggregation. In Sulfolobus sp., Hsp20, despite being a non-secreted protein, has been reported to be present in secretory vesicles and it is still unclear whether it stabilizes substrate proteins or membrane lipids within the secreted vesicles. To address such an issue, we tested the ability of Hsp20 to interact with membrane lipids along with its ability to modulate membrane fluidity. Our data revealed that Hsp20 interacts with membrane lipids via a hydrophobic interaction and it lowers the propensity of in vitro phase transition of bacterial and archaeal lipids.

Transcriptomic approach and membrane fatty acid analysis to study the response mechanisms of Escherichia coli to thyme essential oil, carvacrol, 2-(E)-hexanal and citral exposure

AIMS

The application of essential oils (EOs) and their components as food preservatives is promising but requires a deeper understanding of their mechanisms of action. This study aims to evaluate the effects of thyme EO, carvacrol, citral and 2-(E)-hexenal, on whole-genome gene expression (the transcriptome), as well as the fatty acid (FA) composition of the cell membranes of Escherichia coli K12.

METHODS AND RESULTS

Therefore, we studied the response against 1 h of exposure to sublethal concentrations of natural antimicrobials, of exponentially growing E. coli K12, using DNA microarray technology and a gas chromatographic method. The results show that treatment with a sublethal concentration of the antimicrobials strongly affects global gene expression in E. coli for all antimicrobials used. Major changes in the expression of genes involved in metabolic pathways as well as in FA biosynthesis and protection against oxidative stress were evidenced. Moreover, the sublethal treatments resulted in increased levels of unsaturated and cyclic FAs as well as an increase in the chain length compared to the controls.

CONCLUSIONS

The down-regulation of genes involved in aerobic metabolism indicates a shift from respiration to fermentative growth. Moreover, the results obtained suggest that the cytoplasmic membrane of E. coli is the major cellular target of EOs and their components. In addition, the key role of membrane unsaturated FAs in the response mechanisms of E. coli to natural antimicrobials has been confirmed in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

The transcriptomic data obtained signify a further step to understand the mechanisms of action of natural antimicrobials also when sublethal concentrations and short-term exposure. In addition, this research goes in deep correlating the transcriptomic modification with the changes in E. coli FA composition of cell membrane identified as the main target of the natural antimicrobials.

Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia coli cells

Protein misfolding and aggregation are typically perceived as inevitable and detrimental processes tied to a stress- or age-associated decline in cellular proteostasis. A careful reassessment of this paradigm in the E. coli model bacterium revealed that the emergence of intracellular protein aggregates (PAs) was not related to cellular aging but closely linked to sublethal proteotoxic stresses such as exposure to heat, peroxide, and the antibiotic streptomycin. After removal of the proteotoxic stress and resumption of cellular proliferation, the polarly deposited PA was subjected to limited disaggregation and therefore became asymmetrically inherited for a large number of generations. Many generations after the original PA-inducing stress, the cells inheriting this ancestral PA displayed a significantly increased heat resistance compared to their isogenic, PA-free siblings. This PA-mediated inheritance of heat resistance could be reproduced with a conditionally expressed, intracellular PA consisting of an inert, aggregation-prone mutant protein, validating the role of PAs in increasing resistance and indicating that the resistance-conferring mechanism does not depend on the origin of the PA. Moreover, PAs were found to confer robustness to other proteotoxic stresses, as imposed by reactive oxygen species or streptomycin exposure, suggesting a broad protective effect. Our findings therefore reveal the potential of intracellular PAs to serve as long-term epigenetically inheritable and functional memory elements, physically referring to a previous cellular insult that occurred many generations ago and meanwhile improving robustness to a subsequent proteotoxic stress. The latter is presumably accomplished through the PA-mediated asymmetric inheritance of protein quality control components leading to their specific enrichment in PA-bearing cells.

Metabolic and Evolutionary Insights in the Transformation of Diphenylamine by a Pseudomonas putida Strain Unravelled by Genomic, Proteomic, and Transcription Analysis

Diphenylamine (DPA) is a common soil and water contaminant. A Pseudomonas putida strain, recently isolated from a wastewater disposal site, was efficient in degrading DPA. Thorough knowledge of the metabolic capacity, genetic stability and physiology of bacteria during biodegradation of pollutants is essential for their future industrial exploitation. We employed genomic, proteomic, transcription analyses and plasmid curing to (i) identify the genetic network of P. putida driving the microbial transformation of DPA and explore its evolution and origin and (ii) investigate the physiological response of bacterial cells during degradation of DPA. Genomic analysis identified (i) two operons encoding a biphenyl (bph) and an aniline (tdn) dioxygenase, both flanked by transposases and (ii) two operons and several scattered genes encoding the ortho-cleavage of catechol. Proteomics identified 11 putative catabolic proteins, all but BphA1 up-regulated in DPA- and aniline-growing cells, and showed that the bacterium mobilized cellular mechanisms to cope with oxidative stress, probably induced by DPA and its derivatives. Transcription analysis verified the role of the selected genes/operons in the metabolic pathway: DPA was initially transformed to aniline and catechol by a biphenyl dioxygenase (DPA-dioxygenase); aniline was then transformed to catechol which was further metabolized via the ortho-cleavage pathway. Plasmid curing of P. putida resulted in loss of the DPA and aniline dioxygenase genes and the corresponding degradation capacities. Overall our findings provide novel insights into the evolution of the DPA degradation pathway and suggests that the degradation capacity of P. putida was acquired through recruitment of the bph and tdn operons via horizontal gene transfer.

Flavonoid-derived anisotropic silver nanoparticles inhibit growth and change the expression of virulence genes in Escherichia coli SM10

We hereby present a novel greener and ecofriendly synthesis of anisotropic silver nanoparticles (AgNPs) using water soluble quercetin diphosphate (QDP). QDP was employed as a reducing, capping and stabilizing agent at room temperature without any extraneous reagents. The purpose of this study was to determine the effects of modified quercetin pentaphosphate silver nanoparticles (QPP-AgNPs) and quercetin diphosphate derived silver nanoparticles (QDP-AgNPs) on microbial growth and expressions of virulence-related genes in Escherichia coli SM10. The gene expression analysis was carried out for 12 genes which are related to virulence and stress in E. coli SM10, namely: RpoD, RpoS, ibpB, clpB, uspA, fliC, fimH, fimF, kdpE, artJ, hyaA, and gyrA. Results showed that QDP-AgNPs reduced the swarming motility by 98% which correlated with the reduction in the expression of FliC flagellar gene. A simultaneous increase in the expression of the fimbrial genes FimH and FimF that are related to motility was recorded. In contrast, treatment of the microbes with QPP-AgNPs resulted in 90% of the swarming motility at different patterns compared to QDP-AgNPs treatment for the gene expressions of motility elements. The study revealed that QDP-AgNPs up-regulated the stress related RpoD and ibpB expressions, while QPP-AgNPs up-regulated the stress related RpoS and uspA gene expressions. However, both QDP-AgNPs and QPP-AgNPs up-regulated kpdE, artJ and gry at different levels. QDP-AgNPs were also tested for their antibacterial and antifungal activities, which showed μmolar cidal activity. The growth kinetics of both Gram (−) and Gram (+) bacteria were strongly altered by QDP-AgNPs activity. Energy dispersive absorption spectroscopy (EDS) studies revealed that silver ions and/or the nanoparticles themselves transferred into bacterial cells. To the best of our knowledge, this is the first report of studying the genetic and kinetic response of bacteria to modified quercetin phosphate mediated silver nanoparticles and we hereby report that the molecules used to synthesize AgNPs bring about a strong effect on AgNPs manipulatory activity on the tested 12-genes.

We hereby present a novel greener and ecofriendly synthesis of anisotropic silver nanoparticles (AgNPs) using water soluble quercetin diphosphate (QDP). QDP was employed as a reducing, capping and stabilizing agent at room temperature without any extraneous reagents.

Metal nanoparticles: understanding the mechanisms behind antibacterial activity

As the field of nanomedicine emerges, there is a lag in research surrounding the topic of nanoparticle (NP) toxicity, particularly concerned with mechanisms of action. The continuous emergence of bacterial resistance has challenged the research community to develop novel antibiotic agents. Metal NPs are among the most promising of these because show strong antibacterial activity. This review summarizes and discusses proposed mechanisms of antibacterial action of different metal NPs. These mechanisms of bacterial killing include the production of reactive oxygen species, cation release, biomolecule damages, ATP depletion, and membrane interaction. Finally, a comprehensive analysis of the effects of NPs on the regulation of genes and proteins (transcriptomic and proteomic) profiles is discussed.

Elucidation of the molecular mechanism of heat shock proteins and its correlation with K722Q mutations in Lon protease

Cells withstand the effects of temperature change with the help of small heat shock proteins IbpA and IbpB. The IbpAB protein complex interacts with Lon protease in their free form and gets degraded at physiological temperature when there is no temperature stress. However, the proteolytic degradation of IbpAB is diminished when Lon is mutated. The mutation K722Q in Lon brings about some structural changes so that the proteolytic interactions between the heat shock proteins with that of the mutated Lon protease are lost. However, the detailed molecular aspects of the interactions are not yet fully understood. In the present, we made an attempt to analyze the biochemical aspects of the interactions between the small heat shock proteins IbpAB with wild type and mutant Lon protease. We for the first time deciphered the molecular details of the mechanism of interaction of small heat shock proteins with Lon protease bearing K722Q mutation i.e. the interaction pattern of heat shock proteins with mutant Lon protease at physiological temperature in absence of proteolytic machinery. Our study may therefore be useful to elucidate the mechanistic details of the correlation with IbpA, IbpB and Lon protease.

Proteome analysis reveals differential expression of proteins involved in triacylglycerol accumulation by Rhodococcus jostii RHA1 after addition of methyl viologen

Rhodococcus jostii RHA1 is able to degrade toxic compounds and accumulate high amounts of triacylglycerols (TAG) upon nitrogen starvation. These NADPH-dependent processes are essential for the adaptation of rhodococci to fluctuating environmental conditions. In this study, we used an MS-based, label-free and quantitative proteomic approach to better understand the integral response of R. jostii RHA1 to the presence of methyl viologen (MV) in relation to the synthesis and accumulation of TAG. The addition of MV promoted a decrease of TAG accumulation in comparison to cells cultivated under nitrogen-limiting conditions in the absence of this pro-oxidant. Proteomic analyses revealed that the abundance of key proteins of fatty acid biosynthesis, the Kennedy pathway, glyceroneogenesis and methylmalonyl-CoA pathway, among others, decreased in the presence of MV. In contrast, some proteins involved in lipolysis and β-oxidation of fatty acids were upregulated. Some metabolic pathways linked to the synthesis of NADPH remained activated during oxidative stress as well as under nitrogen starvation conditions. Additionally, exposure to MV resulted in the activation of complete antioxidant machinery comprising superoxide dismutases, catalases, mycothiol biosynthesis, mycothione reductase and alkyl hydroperoxide reductases, among others. Our study suggests that oxidative stress response affects TAG accumulation under nitrogen-limiting conditions through programmed molecular mechanisms when both stresses occur simultaneously.

Some Like It Hot: Heat Resistance of Escherichia coli in Food

Heat treatment and cooking are common interventions for reducing the numbers of vegetative cells and eliminating pathogenic microorganisms in food. Current cooking method requires the internal temperature of beef patties to reach 71°C. However, some pathogenic Escherichia coli such as the beef isolate E. coli AW 1.7 are extremely heat resistant, questioning its inactivation by current heat interventions in beef processing. To optimize the conditions of heat treatment for effective decontaminations of pathogenic E. coli strains, sufficient estimations, and explanations are necessary on mechanisms of heat resistance of target strains. The heat resistance of E. coli depends on the variability of strains and properties of food formulations including salt and water activity. Heat induces alterations of E. coli cells including membrane, cytoplasm, ribosome and DNA, particularly on proteins including protein misfolding and aggregations. Resistant systems of E. coli act against these alterations, mainly through gene regulations of heat response including EvgA, heat shock proteins, σE and σS, to re-fold of misfolded proteins, and achieve antagonism to heat stress. Heat resistance can also be increased by expression of key proteins of membrane and stabilization of membrane fluidity. In addition to the contributions of the outer membrane porin NmpC and overcome of osmotic stress from compatible solutes, the new identified genomic island locus of heat resistant performs a critical role to these highly heat resistant strains. This review aims to provide an overview of current knowledge on heat resistance of E. coli, to better understand its related mechanisms and explore more effective applications of heat interventions in food industry.

Role of yqiC in the Pathogenicity of Salmonella and Innate Immune Responses of Human Intestinal Epithelium

The yqiC gene of Salmonella enterica serovar Typhimurium (S. Typhimurium) regulates bacterial growth at different temperatures and mice survival after infection. However, the role of yqiC in bacterial colonization and host immunity remains unknown. We infected human LS174T, Caco-2, HeLa, and THP-1 cells with S. Typhimurium wild-type SL1344, its yqiC mutant, and its complemented strain. Bacterial colonization and internalization in the four cell lines significantly reduced on yqiC depletion. Post-infection production of interleukin-8 and human β-defensin-3 in LS174T cells significantly reduced because of yqiC deleted in S. Typhimurium. The phenotype of yqiC mutant exhibited few and short flagella, fimbriae on the cell surface, enhanced biofilm formation, upregulated type-1 fimbriae expression, and reduced bacterial motility. Type-1 fimbriae, flagella, SPI-1, and SPI-2 gene expression was quantified using real-time PCR. The data show that deletion of yqiC upregulated fimA and fimZ expression and downregulated flhD, fliZ, invA, and sseB expression. Furthermore, thin-layer chromatography and high-performance liquid chromatography revealed the absence of menaquinone in the yqiC mutant, thus validating the importance of yqiC in the bacterial electron transport chain. Therefore, YqiC can negatively regulate FimZ for type-1 fimbriae expression and manipulate the functions of its downstream virulence factors including flagella, SPI-1, and SPI-2 effectors.

Involvement of small heat shock proteins, trehalose, and lipids in the thermal stress management in Schizosaccharomyces pombe

Changes in the levels of three structurally and functionally different important thermoprotectant molecules, namely small heat shock proteins (sHsps), trehalose, and lipids, have been investigated upon heat shock in Schizosaccharomyces pombe. Both α-crystallin-type sHsps (Hsp15.8 and Hsp16) were induced after prolonged high-temperature treatment but with different kinetic profiles. The shsp null mutants display a weak, but significant, heat sensitivity indicating their importance in the thermal stress management. The heat induction of sHsps is different in wild type and in highly heat-sensitive trehalose-deficient (tps1Δ) cells; however, trehalose level did not show significant alteration in shsp mutants. The altered timing of trehalose accumulation and induction of sHsps suggest that the disaccharide might provide protection at the early stage of the heat stress while elevated amount of sHsps are required at the later phase. The cellular lipid compositions of two different temperature-adapted wild-type S. pombe cells are also altered according to the rule of homeoviscous adaptation, indicating their crucial role in adapting to the environmental temperature changes. Both Hsp15.8 and Hsp16 are able to bind to different lipids isolated from S. pombe, whose interaction might provide a powerful protection against heat-induced damages of the membranes. Our data suggest that all the three investigated thermoprotectant macromolecules play a pivotal role during the thermal stress management in the fission yeast.

Small heat-shock proteins, IbpAB, protect non-pathogenic Escherichia coli from killing by macrophage-derived reactive oxygen species

Many intracellular bacterial pathogens possess virulence factors that prevent detection and killing by macrophages. However, similar virulence factors in non-pathogenic bacteria are less well-characterized and may contribute to the pathogenesis of chronic inflammatory conditions such as Crohn’s disease. We hypothesize that the small heat shock proteins IbpAB, which have previously been shown to reduce oxidative damage to proteins in vitro and be upregulated in luminal non-pathogenic Escherichia strain NC101 during experimental colitis in vivo, protect commensal E. coli from killing by macrophage-derived reactive oxygen species (ROS). Using real-time PCR, we measured ibpAB expression in commensal E. coli NC101 within wild-type (wt) and ROS-deficient (gp91phox^-/-) macrophages and in NC101 treated with the ROS generator paraquat. We also quantified survival of NC101 and isogenic mutants in wt and gp91phox^-/- macrophages using gentamicin protection assays. Similar assays were performed using a pathogenic E. coli strain O157:H7. We show that non-pathogenic E. coli NC101inside macrophages upregulate ibpAB within 2 hrs of phagocytosis in a ROS-dependent manner and that ibpAB protect E. coli from killing by macrophage-derived ROS. Moreover, we demonstrate that ROS-induced ibpAB expression is mediated by the small E. coli regulatory RNA, oxyS. IbpAB are not upregulated in pathogenic E. coli O157:H7 and do not affect its survival within macrophages. Together, these findings indicate that ibpAB may be novel virulence factors for certain non-pathogenic E. coli strains.

A novel mechanism for small heat shock proteins to function as molecular chaperones

Small heat shock proteins (sHSPs) are molecular chaperones ubiquitously present in all forms of life, but their function mechanisms remain controversial. Here we show by cryo-electron microscopy and single particle 3D reconstruction that, at the low temperatures (4-25°C), CeHSP17 (a sHSP from Caenorhabditis elegans) exists as a 24-subunit spherical oligomer with tetrahedral symmetry. Our studies demonstrate that CeHSP17 forms large sheet-like super-molecular assemblies (SMAs) at the high temperatures (45-60°C), and such SMAs are apparently the form that exhibits chaperone-like activity. Our findings suggest a novel molecular mechanism for sHSPs to function as molecular chaperones.

Heat shock proteins IbpA and IbpB are required for NlpI-participated cell division in Escherichia coli

Lipoprotein NlpI of Escherichia coli is involved in the cell division, virulence, and bacterial interaction with eukaryotic host cells. To elucidate the functional mechanism of NlpI, we examined how NlpI affects cell division and found that induction of NlpI inhibits nucleoid division and halts cell growth. Consistent with these results, the cell division protein FtsZ failed to localize at the septum but diffused in the cytosol. Elevation of NlpI expression enhanced the transcription and the outer membrane localization of the heat shock protein IbpA and IbpB. Deletion of either ibpA or ibpB abolished the effects of NlpI induction, which could be restored by complementation. The C-terminus of NlpI is critical for the enhancement in IbpA and IbpB production, and the N-terminus of NlpI is required for the outer membrane localization of NlpI, IbpA, and IbpB. Furthermore, NlpI physically interacts with IbpB. These results indicate that over-expression of NlpI can interrupt the nucleoids division and the assembly of FtsZ at the septum, mediated by IbpA/IbpB, suggesting a role of the NlpI/IbpA/IbpB complex in the cell division.

Antimicrobial photodynamic inactivation in nanomedicine: small light strides against bad bugs

The relentless advance of drug-resistance among pathogenic microbes, mandates a search for alternative approaches that will not cause resistance. Photodynamic inactivation (PDI) involves the combination of nontoxic dyes with harmless visible light to produce reactive oxygen species that can selectively kill microbial cells. PDI can be broad-spectrum in nature and can also destroy microbial cells in biofilms. Many different kinds of nanoparticles have been studied to potentiate antimicrobial PDI by improving photosensitizer solubility, photochemistry, photophysics and targeting. This review will cover photocatalytic disinfection with titania nanoparticles, carbon nanomaterials (fullerenes, carbon nanotubes and graphene), liposomes and polymeric nanoparticles. Natural polymers (chitosan and cellulose), gold and silver plasmonic nanoparticles, mesoporous silica, magnetic and upconverting nanoparticles have all been used for PDI.