Sub-MIC streptomycin and tetracycline enhanced Staphylococcus aureus Guangzhou-SAU749 biofilm formation, an in-depth study on transcriptomics

Staphylococcus aureus is a major human pathogen, a potential "Super-bug" and a typical biofilm forming bacteria. With usage of large amount of antibiotics, the residual antibiotics in clinical settings further complicate the colonization, pathogenesis and resistance of S. aureus. This study aimed at investigating the phenotypical and global gene expression changes on biofilm formation of a clinical S. aureus isolate treated under different types of antibiotics. Firstly, an isolate Guangzhou-SAU749 was selected from a large sale of previously identified S. aureus isolates, which exhibited weak biofilm formation in terms of biomass and viability. Secondly, 9 commonly prescribed antibiotics for S. aureus infections treatment, together with 10 concentrations ranging from 1/128 to 4 minimum inhibitory concentration (MIC) with 2-fold serial dilution, were used as different antibiotic stress conditions. Then, biofilm formation of S. aureus Guangzhou-SAU749 at different stages including 8 h, 16 h, 24 h, and 48 h, was tested by crystal violet and MTS assays. Thirdly, the whole genome of S. aureus Guangzhou-SAU749 was investigated by genome sequencing on PacBio platform. Fourthly, since enhancement of biofilm formation occurred when treated with 1/2 MIC tetracycline (TCY) and 1/4 MIC streptomycin (STR) since 5 h, the relevant biofilm samples were selected and subjected to RNA-seq and bioinformatics analysis. Last, expression of two component system (TCS) and biofilm associated genes in 4 h, 8 h, 16 h, 24 h, and 48 h sub-MIC TCY and STR treated biofilm samples were performed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Although most antibiotics lowered the biomass and cell viability of Guangzhou-SAU749 biofilm at concentrations higher than MIC, certain antibiotics including TCY and STR promoted biofilm formation at sub-MICs. Additionally, upon genome sequencing, RNA-seq and RT-qPCR on biofilm samples treated with sub-MIC of TCY and STR at key time points, genes lytR, arlR, hssR, tagA, clfB, atlA and cidA related to TCS and biofilm formation were identified to contribute to the enhanced biofilm formation, providing a theoretical basis for further controlling on S. aureus biofilm formation.

Inulin increases the EPS biosynthesis of Lactobacillus delbrueckii ssp. bulgaricus LDB-C1

OBJECTIVE

Its eps gene cluster, the antioxidant activity and monosaccharide composition of exopolysaccharides, the expression levels of related genes at different fermentations were analyzed for clarifying the exopolysaccharide biosynthesis mechanism of Lactobacillus delbrueckii subsp. bulgaricus LDB-C1.

RESULTS

The comparison analysis of eps gene clusters indicated that the gene clusters present diversity and strain specificity. The crude exopolysaccharides from LDB-C1 exhibited a good antioxidant activity. Compared with glucose, fructose, galactose, and fructooligosaccharide, inulin significantly improved the exopolysaccharide biosynthesis. The structures of EPSs were significantly different under different carbohydrate fermentation conditions. Inulin obviously increased the expressions of most EPS biosynthesis related genes at fermentation 4 h.

CONCLUSION

Inulin accelerated the beginning of the exopolysaccharide production in LDB-C1, and the enzymes promoted by inulin was beneficial for the accumulation of exopolysaccharide at the whole fermentation process.

Bacterial envelope stress responses: Essential adaptors and attractive targets

Millions of deaths a year across the globe are linked to antimicrobial resistant infections. The need to develop new treatments and repurpose of existing antibiotics grows more pressing as the growing antimicrobial resistance pandemic advances. In this review article, we propose that envelope stress responses, the signaling pathways bacteria use to recognize and adapt to damage to the most vulnerable outer compartments of the microbial cell, are attractive targets. Envelope stress responses (ESRs) support colonization and infection by responding to a plethora of toxic envelope stresses encountered throughout the body; they have been co-opted into virulence networks where they work like global positioning systems to coordinate adhesion, invasion, microbial warfare, and biofilm formation. We highlight progress in the development of therapeutic strategies that target ESR signaling proteins and adaptive networks and posit that further characterization of the molecular mechanisms governing these essential niche adaptation machineries will be important for sparking new therapeutic approaches aimed at short-circuiting bacterial adaptation.

Two component system CpxR/A regulates the prodigiosin biosynthesis by negative control in Serratia marcescens FS14

Prodigiosin is a tripyrrole red secondary metabolite synthesized by many microorganisms, including Serratia marcescens. In this study, we found that the deletion of the gene of sensor kinase CpxA dramatically decreased the prodigiosin production, while the deletion of the gene of the response regulator CpxR or both genes of CpxRA has no effect on prodigiosin production, the kinase function of CpxA is not essential for its regulation on prodigiosin production while the phosphorylation site of CpxR is required. We further demonstrated that the CpxA regulates the prodigiosin biosynthesis at the transcriptional level and the phosphatase activity of CpxA plays vital roles in the regulation of prodigiosin biosynthesis. Finally, we proposed that CpxR/A regulates the prodigiosin biosynthesis by negative control and the phosphorylation level of CpxR may determine the positive or negative control of the genes it regulated.

A review on the origin of multidrug-resistant Salmonella and perspective of tailored phoP gene towards avirulence

Salmonellosis continues to remain a health problem as the causative organism Salmonella spp. developed resistance to many of the antibiotics. As per World Health Organization (WHO), it is estimated that enteric fever, accounts for almost 16 million cases annually and over 600,000 deaths worldwide. Recent data revealed that the multi-drug resistance (MDR) rate of enteric fever was as high as 70% in Asian countries, as compared with the overall reported incidence of 50%. Emergence of MDR typhoid fever demands the use of newer antibiotics which also not offer promising effect in recent days. Effective antimicrobial therapy is required to control morbidity and prevent death from typhoid fever. The studies on PhoP/Q regulation revealed it as a best-characterized transcriptional regulation; a two-component system required for Salmonella pathogenesis which controls the expression of more than 40 genes. The PhoP DNA binding proteins possess positively charged amino acids such as arginine, lysine and histidine which present in the DNA binding site. Prevention of PhoP binding in phoP box may ultimately prevent the expression of many regulatory mechanism which plays vital role in Salmonella virulence. Deepness study of PhoP protein and various mutation swots may offer effectual controlling of MDR Salmonella.

The response regulator ArcA enhances biofilm formation in the vpsT manner under the anaerobic condition in Vibrio cholerae

Vibrio cholerae, the agent of severe diarrheal disease cholera, is known to form biofilm to persist in the environmental and the host^,s intestines. The bacteria execute a complex regulatory pathway producing virulence factors that allow colonization and cause disease in response to environmental signals in the intestine, including low oxygen-limited condition. VpsR and VpsT are primary regulators of the biofilm formation-regulatory network. In this study, we determined that anaerobic induction enhanced biofilm formation via the two component system, ArcB/A, which functions as a positive regulator of toxT expression. The biofilm formation has reduced approximately 2.4-fold in the ΔarcA mutant compared to the wild type in anaerobic condition. Chip-qPCR and EMSA assays confirmed that ArcA can bind directly to the vpsT promoter and then activates the expression of biofilm formation related genes, vpsA-K and vpsL-Q. Meanwhile, the ΔarcA mutant decreased the ability of colonization in intestine with CI (competition index) of 0.27 compared to wild type strain. These results suggest that ArcA links the expression of virulence and biofilm synthesis genes during anaerobic condition, and contributes to understand the complex relationship between biofilm formation and the intestinal signals during infection.

bulgaricus

Lactobacillus delbrueckii subsp. bulgaricus is currently one of the most valuable lactic acid bacteria (LAB) and widely used in global dairy industry. The acid tolerance and adaptation ability of LAB is the key point of their survival and proliferation during fermentation process and in gastrointestinal tract of human body. Two component system (TCS) is one of the most important mechanisms to allow bacteria to sense and respond to changes of environmental conditions. TCS typically consists of a histidine protein kinase (HPK) and a corresponding response regulator (RR). Our previous study indicated a TCS (JN675228/JN675229) was involved in acid adaptation in L. bulgaricus. To reveal the role of JN675228 (HPK1)/JN675229 (RR1) in acid adaptation, the target genes of JN675228 (HPK1)/JN675229 (RR1) were identified by means of a proteomic approach complemented with transcription data in the present study. The results indicated that HPK1/RR1 regulated the acid adaptation ability of bacteria by means of many pathways, including the proton pump related protein, classical stress shock proteins, carbohydrate metabolism, nucleotide biosynthesis, DNA repair, transcription and translation, peptide transport and degradation, and cell wall biosynthesis, etc. To our knowledge, this is the first report with the effect of acid adaptation-related TCS HPK1/RR1 on its target genes. This study will offer experimental basis for clarifying the acid adaptation regulation mechanism of L. bulgaricus, and provide a theoretical basis for this bacterium in industry application.

A sensitive synthetic reporter for visualizing cytokinin signaling output in rice

BACKGROUND

Cytokinins play many essential roles in plant growth and development, mainly through signal transduction pathways. Although the cytokinin signaling pathway in rice has been clarified, no synthetic reporter for cytokinin signaling output has been reported for rice. The sensitive synthetic reporter two-component signaling sensor (TCSn) is used in the model plant Arabidopsis; however, whether the reporter reflects the cytokinin signaling output pattern in rice remains unclear.

RESULTS

Early-cytokinin-responsive type-A OsRR-binding element (A/G)GAT(C/T) was more clustered in the 15 type-A OsRRs than in the 13 control genes. Quantitative polymerase chain reaction analysis showed that the relative expression of seven type-A OsRRs in roots and shoots was significantly induced by exogenous cytokinin application, and that of seven OsRRs, mainly in roots, was inhibited by exogenous auxin application. We constructed a transgenic rice plant harboring a beta-glucuronidase (GUS) driven by the synthetic promoter TCSn. TCSn::GUS was expressed in the meristem of germinated rice seed and rice seedlings. Furthermore, TCSn::GUS expression in rice seedlings was induced specifically by exogenous cytokinin application and decreased by exogenous auxin application. Moreover, no obvious reduction in GUS levels was observed after three generations of selfing of transgenic plants, indicating that TCSn::GUS is not subject to transgene silencing.

CONCLUSIONS

We report here a robust and sensitive synthetic sensor for monitoring the transcriptional output of the cytokinin signaling network in rice.

Multiscale approach to the activation and phosphotransfer mechanism of CpxA histidine kinase reveals a tight coupling between conformational and chemical steps

Sensor histidine kinases (SHKs) are an integral component of the molecular machinery that permits bacteria to adapt to widely changing environmental conditions. CpxA, an extensively studied SHK, is a multidomain homodimeric protein with each subunit consisting of a periplasmic sensor domain, a transmembrane domain, a signal-transducing HAMP domain, a dimerization and histidine phospho-acceptor sub-domain (DHp) and a catalytic and ATP-binding subdomain (CA). The key activation event involves the rearrangement of the HAMP-DHp helical core and translation of the CA towards the acceptor histidine, which presumably results in an autokinase-competent complex. In the present work we integrate coarse-grained, all-atom, and hybrid QM-MM computer simulations to probe the large-scale conformational reorganization that takes place from the inactive to the autokinase-competent state (conformational step), and evaluate its relation to the autokinase reaction itself (chemical step). Our results highlight a tight coupling between conformational and chemical steps, underscoring the advantage of CA walking along the DHp core, to favor a reactive tautomeric state of the phospho-acceptor histidine. The results not only represent an example of multiscale modelling, but also show how protein dynamics can promote catalysis.

Functional analysis of BAS2108-2109 two component system: Evidence for protease regulation in Bacillus anthracis

BACKGROUND

Bacillus anthracis (BA) is a major bioterrorism concern which has evolved complex regulatory mechanisms for its virulence factors. Secreted proteases play an imperative role in the pathogenesis of BA, however their regulation remains elusive. Two component systems (TCS) are often employed by bacteria to sense and adapt to the environmental perturbations. In several pathogens, TCS are commonly associated with the regulation of virulence factors including proteases. The genome of BA encodes 41 TCS pairs, however, the role of any TCS in regulation of its proteases is not known.

PRINCIPAL FINDINGS

The study established BAS2108-2109 as a prototypical TCS where BAS2108 functions as a histidine kinase and BAS2109 as the response regulator. The expression of BAS2109 was found to be elevated under host simulated conditions and in pellicle forming cells. Electrophoretic mobility shift assay (EMSA) and lacZ reporter assay revealed positive autoregulation of the BAS2108-2109 operon by BAS2109. Collective analysis of ANS assay and EMSA demonstrated Lys167, Thr179 and Thr182 residues are crucial for the DNA binding activity of BAS2109. EMSA analysis further highlighted BAS2109 as the transcriptional regulator for different genes of BA, particularly proteases. Upregulation of proteases in BA overexpressing BAS2109 further strengthen its role in protease regulation.

SIGNIFICANCE

This is the first report to identify a TCS pair for its role in the regulation of proteases of BA. Importance of proteases in the pathogenesis of BA is well documented, therefore, studying the regulatory networks governing their expression will help in identification of new drug targets.

An integrated network analysis identifies how ArcAB enables metabolic oscillations in the nitric oxide detoxification network of Escherichia coli

The virulences of many pathogens depend on their abilities to detoxify the immune antimicrobial nitric oxide (NO•). The functions of bacterial NO• detoxification machinery depend on oxygen (O₂ ), with O₂ inhibiting some enzymes, whereas others use it as a substrate. Previously, Escherichia coli NO• detoxification was found to be highly attenuated under microaerobic conditions and metabolic oscillations were observed. The oscillations in [NO•] and [O₂ ] were found to result from the inhibitory action of NO• on aerobic respiration, the catalytic inactivation of NO• by Hmp (an NO• dioxygenase), and an imbalanced competition for O₂ between Hmp and cytochrome terminal oxidase activity. Here the authors investigated the role of the ArcAB two component system (TCS) in microaerobic NO• detoxification. The authors observed that wild-type, ΔarcA, and ΔarcB had comparable initial NO• clearance times; however, the mutant cultures failed to exhibit [NO•] and [O₂ ] oscillations. Using an approach that employed experimentation and computational modeling, the authors found that the loss of oscillations in ΔarcA was due to insufficient induction of cytochrome bd-I expression. Collectively, these results establish ArcAB as a TCS that influences NO• detoxification in E. coli within the physiologically-relevant microaerobic regime.

AdeR protein regulates adeABC expression by binding to a direct-repeat motif in the intercistronic spacer

Overexpression of the efflux pump AdeABC is associated with tigecycline resistance of multi-drug resistant Acinetobacter baumannii (MDRAB). A two-component regulatory system, sensor AdeS and regulator AdeR proteins regulate the pump. However, the detailed mechanism of the AdeR protein to enhance the expression of adeABC operon is not well defined. We illustrated the biological characteristics of AdeR proteins by comparing a mutant AdeR protein of a tigecycline resistant MDRAB to the wild AdeR protein. By analyzing a series of deletion constructs, a minimal gene cassette of the intercistronic spacer DNA fragment specifically bound with the adeR protein and resulted in band shifting in electrophoresis mobility shifting assays (EMSA). A conserve direct repeat motif was observed in the intercistronic spacer DNA. We demonstrated the AdeR protein was a direct-repeat-binding protein. Two common residue mutations on the AdeR proteins of tigecycline resistant MDRAB isolates could reduce their binding affinity with the intercistronic spacer. The free intercistronic spacer may then more efficiently support the read-through of the adeABC operon during the co-transcriptional translation in tigecycline resistant MDRAB isolates.

Rv1027c-Rv1028c encode functional KdpDE two--component system in Mycobacterium tuberculosis

In Mycobacteriumtuberculosis Rv1027c-Rv1028c genes are predicted to encode KdpDE two component system, which is highly conserved across all bacterial species. Here, we show that the system is functionally active and KdpD sensor kinase undergoes autophosphorylation and transfers phosphoryl group to KdpE, response regulator protein. We identified His(642) and Asp(52) as conserved phosphorylation sites in KdpD and KdpE respectively and by SPR analysis confirmed the physical interaction between them. KdpD was purified with prebound divalent ions and their importance in phosphorylation was established using protein refolding and ion chelation approaches. Genetically a single transcript encoded both KdpD and KdpE proteins. Overall, we report that M. tuberculosis KdpDE system operates like a canonical two component system.

Analysis of DevR regulated genes in Mycobacterium tuberculosis

The DevRS two component system of Mycobacterium tuberculosis is responsible for its dormancy in host and becomes operative under hypoxic condition. It is experimentally known that phosphorylated DevR controls the expression of several downstream genes in a complex manner. In the present work we propose a theoretical model to show role of binding sites in DevR mediated gene expression. Individual and collective role of binding sites in regulating DevR mediated gene expression has been shown via modeling. Objective of the present work is twofold. First, to describe qualitatively the temporal dynamics of wild type genes and their known mutants. Based on these results we propose that DevR controlled gene expression follows a specific pattern which is efficient in describing other DevR mediated gene expression. Second, to analyze behavior of the system from information theoretical point of view. Using the tools of information theory we have calculated molecular efficiency of the system and have shown that it is close to the maximum limit of isothermal efficiency.