Nucleoid clumping is dispensable for the Dps-dependent hydrogen peroxide resistance in Staphylococcus aureus

Complementary Roles of Two DNA Protection Proteins from Deinococcus geothermalis

The roles of two interrelated DNA protection protein in starved cells (Dps)-putative Dps Dgeo_0257 and Dgeo_0281-as orthologous proteins to DrDps1 for DNA binding, protection, and metal ion sensing were characterised in a Deinococcus geothermalis strain. Dgeo_0257 exhibited high DNA-binding affinity and formed a multimeric structure but lacked the conserved amino acid sequence for ferroxidase activity. In contrast, the Dgeo_0281 (DgDps1) protein was abundant in the early exponential phase, had a lower DNA-binding activity than Dgeo_0257, and was mainly observed in its monomeric or dimeric forms. Electrophoretic mobility shift assays demonstrated that both purified proteins bound nonspecifically to DNA, and their binding ability was affected by certain metal ions. For example, in the presence of ferrous and ferric ions, neither Dgeo_0257 nor Dgeo_0281 could readily bind to DNA. In contrast, both proteins exhibited more stable DNA binding in the presence of zinc and manganese ions. Mutants in which the dps gene was disrupted exhibited higher sensitivity to oxidative stress than the wild-type strain. Furthermore, the expression levels of each gene showed an opposite correlation under H₂O₂ treatment conditions. Collectively, these findings indicate that the putative Dps Dgeo_0257 and DgDps1 from D. geothermalis are involved in DNA binding and protection in complementary interplay ways compared to known Dps.

The Conformation of the N-Terminal Tails of Deinococcus grandis Dps Is Modulated by the Ionic Strength

DNA-binding proteins from starved cells (Dps) are homododecameric nanocages, with N- and C-terminal tail extensions of variable length and amino acid composition. They accumulate iron in the form of a ferrihydrite mineral core and are capable of binding to and compacting DNA, forming low- and high-order condensates. This dual activity is designed to protect DNA from oxidative stress, resulting from Fenton chemistry or radiation exposure. In most Dps proteins, the DNA-binding properties stem from the N-terminal tail extensions. We explored the structural characteristics of a Dps from Deinococcus grandis that exhibits an atypically long N-terminal tail composed of 52 residues and probed the impact of the ionic strength on protein conformation using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism and small-angle X-ray scattering. A novel high-spin ferrous iron-binding site was identified in the N-terminal tails, using Mössbauer spectroscopy. Our data reveals that the N-terminal tails are structurally dynamic and alter between compact and extended conformations, depending on the ionic strength of the buffer. This prompts the search for other physiologically relevant modulators of tail conformation and hints that the DNA-binding properties of Dps proteins may be affected by external factors.

Dps Is a Universally Conserved Dual-Action DNA-Binding and Ferritin Protein

The DNA-binding protein from starved cells, Dps, is a universally conserved prokaryotic ferritin that, in many species, also binds DNA. Dps homologs have been identified in the vast majority of bacterial species and several archaea. Dps also may play a role in the global regulation of gene expression, likely through chromatin reorganization. Dps has been shown to use both its ferritin and DNA-binding functions to respond to a variety of environmental pressures, including oxidative stress. One mechanism that allows Dps to achieve this is through a global nucleoid restructuring event during stationary phase, resulting in a compact, hexacrystalline nucleoprotein complex called the biocrystal that occludes damaging agents from DNA. Due to its small size, hollow spherical structure, and high stability, Dps is being developed for applications in biotechnology.

Photosensitizer Nanodot Eliciting Immunogenicity for Photo-Immunologic Therapy of Postoperative Methicillin-Resistant Staphylococcus aureus Infection and Secondary Recurrence

The treatment of postoperative infection caused by multidrug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA), has become an intractable clinical challenge owing to its low therapeutic efficacy and high risk of recurrence. Apart from imperfect antibacterial therapies, induction of insufficient immunogenicity, required for the successful clearance of a pathogen, may also contribute to the problem. Herein, an ultra-micro photosensitizer, AgB nanodots, using photothermal therapy, photodynamic therapy, and Ag⁺ ion sterilization, are utilized to efficiently clear invading MRSA both in vitro and in vivo. AgB nanodots are also found to upregulate host immunogenicity in a murine model and establish immunological memory by promoting the upregulated expression of danger signals that are commonly induced by stress-related responses, including sudden temperature spikes or excess reactive oxygen production. These stimulations boost the antibacterial effects of macrophages, dendritic cells, T cells, or even memory B cells, which is usually defined as infection-related immunogenic cell death. Hence, the proposed AgB nanodot strategy may offer a novel platform for the effective treatment of postoperative infection while providing a systematic immunotherapeutic strategy to combat persistent infections, thereby markedly reducing the incidence of recurrence following recovery from primary infections.

Stress Resistance and Pathogenicity of Nonthermal-Plasma-Induced Viable-but-Nonculturable Staphylococcus aureus through Energy Suppression, Oxidative Stress Defense, and Immune-Escape Mechanisms

The occurrence of viable-but-nonculturable (VBNC) bacteria poses a potential risk to food safety due to failure in conventional colony detection. In this study, induction of VBNC Staphylococcus aureus was conducted by exposure to an atmospheric-pressure air dielectric barrier discharge-nonthermal-plasma (DBD-NTP) treatment with an applied energy of 8.1 kJ. The stress resistance profiles and pathogenicity of VBNC S. aureus were further evaluated. We found that VBNC S. aureus showed levels of tolerance of heat, acid, and osmosis challenges comparable to those shown by culturable S. aureus, while VBNC S. aureus exhibited enhanced resistance to oxidative and antibiotic stress, relating to the mechanisms of cellular energy depletion, antioxidant response initiation, and multidrug efflux pump upregulation. Regarding pathogenicity, NTP-induced VBNC S. aureus retained the capacity to infect the HeLa host cells. Compared with the culturable counterparts, VBNC S. aureus caused reduced immune responses (Toll-like receptor [TLR], nucleotide-binding oligomerization domain [NOD]) in HeLa cells, which was attributed to suppression of biosynthesis of the recognized surface ligands (e.g., peptidoglycan). Additionally, the proteomic analysis revealed that upregulation of several virulence factors (ClfB, SdrD, SCIN, SasH, etc.) could ensure that VBNC S. aureus would adhere to and internalize into host cells and avoid the host attack. The camouflaged mechanisms described above led to VBNC S. aureus causing less damage to the host cells, and their activity might result in longer intracellular persistence, posing potential risks during NTP processing.IMPORTANCE The consumer demand for freshness and nutrition has accelerated the development of mild decontamination technologies. The incomplete killing of nonthermal (NT) treatments might induce pathogens to enter into a viable-but-nonculturable (VBNC) status as a survival strategy. The use of nonthermal plasma (NTP) as a novel food decontamination technology received increased attention in food industry during recent decades. Our previous work confirmed that the foodborne pathogen S. aureus was induced into VBNC status in response to NTP exposure. This work further revealed the development of stress resistance and virulence retention of NTP-induced VBNC S. aureus through the mechanisms of energy suppression, oxidative stress defense, and immune escape. The data provide fundamental knowledge of the potential risks posed by NTP-induced VBNC S. aureus, which require further parameter optimization of the NTP process or combination with other techniques to avoid the occurrence of VBNC bacteria.

What Happens in the Staphylococcal Nucleoid under Oxidative Stress?

The evolutionary success of Staphylococcus aureus as an opportunistic human pathogen is largely attributed to its prominent abilities to cope with a variety of stresses and host bactericidal factors. Reactive oxygen species are important weapons in the host arsenal that inactivate phagocytosed pathogens, but S. aureus can survive in phagosomes and escape from phagocytic cells to establish infections. Molecular genetic analyses combined with atomic force microscopy have revealed that the MrgA protein (part of the Dps family of proteins) is induced specifically in response to oxidative stress and converts the nucleoid from the fibrous to the clogged state. This review collates a series of evidences on the staphylococcal nucleoid dynamics under oxidative stress, which is functionally and physically distinct from compacted Escherichia coli nucleoid under stationary phase. In addition, potential new roles of nucleoid clogging in the staphylococcal life cycle will be proposed.

Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates

Background

Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061^T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis.

Results

The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061^T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results.

Conclusions

It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.

Formation of Staphylococcus aureus Biofilm in the Presence of Sublethal Concentrations of Disinfectants Studied via a Transcriptomic Analysis Using Transcriptome Sequencing (RNA-seq)

Staphylococcus aureus is a common biofilm-forming pathogen. Low doses of disinfectants have previously been reported to promote biofilm formation and to increase virulence. The aim of this study was to use transcriptome sequencing (RNA-seq) analysis to investigate global transcriptional changes in S. aureus in response to sublethal concentrations of the commonly used food industry disinfectants ethanol (EtOH) and chloramine T (ChT) and their combination (EtOH_ChT) in order to better understand the effects of these agents on biofilm formation. Treatment with EtOH and EtOH_ChT resulted in more significantly altered expression profiles than treatment with ChT. Our results revealed that EtOH and EtOH_ChT treatments enhanced the expression of genes responsible for regulation of gene expression (sigB), cell surface factors (clfAB), adhesins (sdrDE), and capsular polysaccharides (cap8EFGL), resulting in more intact biofilm. In addition, in this study we were able to identify the pathways involved in the adaptation of S. aureus to the stress of ChT treatment. Further, EtOH suppressed the effect of ChT on gene expression when these agents were used together at sublethal concentrations. These data show that in the presence of sublethal concentrations of tested disinfectants, S. aureus cells trigger protective mechanisms and try to cope with them.IMPORTANCE So far, the effect of disinfectants is not satisfactorily explained. The presented data will allow a better understanding of the mode of disinfectant action with regard to biofilm formation and the ability of bacteria to survive the treatment. Such an understanding could contribute to the effort to eliminate possible sources of bacteria, making disinfectant application as efficient as possible. Biofilm formation plays significant role in the spread and pathogenesis of bacterial species.

Identification of nucleoid associated proteins (NAPs) under oxidative stress in Staphylococcus aureus

Background

Bacterial nucleoid consists of genome DNA, RNA, and hundreds of nucleoid-associated proteins (NAPs). Escherichia coli nucleoid is compacted towards the stationary phase, replacing most log-phase NAPs with the major stationary-phase nucleoid protein, Dps. In contrast, Staphylococcus aureus nucleoid sustains the fiber structures throughout the growth. Instead, the Dps homologue, MrgA, expresses under oxidative stress conditions to clump the nucleoid, but the composition of the clumped nucleoid was elusive.

Results

The staphylococcal nucleoid under oxidative stress was isolated by sucrose gradient centrifugation, and the proteins were analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). We identified 299 proteins in the nucleoid under oxidative stress, including 113 csNAPs (contaminant-subtracted NAPs). Comparison with the previously identified csNAPs in log- and stationary phase indicated that one fifth of the csNAPs under oxidative stress were the constitutive nucleoid components; importantly, several factors including HU, SarA, FabZ, and ribosomes were sustained under oxidative stress. Some factors (e.g. SA1663 and SA0092/SA0093) with unknown functions were included in the csNAPs list specifically under oxidative stress condition.

Conclusion

Nucleoid constitutively holds Hu, SarA, FabG, and ribosomal proteins even under the oxidative stress, reflecting the active functions of the clumped nucleoid, unlikely to the dormant E. coli nucleoid compacted in the stationary phase or starvation.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1114-3) contains supplementary material, which is available to authorized users.

Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage

The study of the bacterial cell cycle at the single cell level can not only give insights on the fitness of the bacterial population but also reveal heterogeneous behavior. Typically, the DNA replication, the cell division, and the nucleoid conformation are appropriate representatives of the bacterial cell cycle. Because bacteria rapidly adapt their growth rate to environmental changes, the measure of cell cycle parameters gives valuable insights for the study of bacterial stress response or host-pathogen interactions. Here we describe methods to first introduce fluorescent fusion proteins and fluorescent tag within the chromosome of pathogenic bacteria to study these cell cycle steps; then to follow them within macrophages using a confocal spinning disk microscope.