Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress

The Description and Analysis of the Complete Genome of Dermacoccus barathri FBCC-B549 Strain

Dermacoccus barathri is the first reported pathogen within the Dermacoccus genus to cause a catheter-related bloodstream infection, which occurred in 2015. In this study, the complete genome assembly of Dermacoccus barathri was constructed, and the complete genome of Dermacoccus barathri FBCC-B549 consists of a single chromosome (3,137,745 bp) without plasmids. The constructed genome of D. barathri was compared with those of two closely related species within the Dermacoccus genus. D. barathri exhibited a pattern similar to Dermacoccus abyssi in terms of gene clusters and synteny analysis. Contrary to previous studies, biosynthetic gene cluster (BGC) analysis for predicting secondary metabolites revealed the presence of the LAP biosynthesis pathway in the complete genome of D. barathri, predicting the potential synthesis of the secondary metabolite plantazolicin. Furthermore, an analysis to investigate the potential pathogenicity of D. barathri did not reveal any antibiotic resistance genes; however, nine virulence factors were identified in the Virulence Factor Database (VFDB). According to these matching results in the VFDB, despite identifying a few factors involved in biofilm formation, further research is required to determine the actual impact of D. barathri on pathogenicity. The complete genome of D. barathri is expected to serve as a valuable resource for future studies on D. barathri, which currently lack sufficient genomic sequence information.

Transcriptomic signature of bacteria exposed to benzalkonium chloride

The COVID-19 pandemic has highlighted our reliance on biocides, the increasing prevalence of resistance to biocides is a risk to public health. Bacterial exposure to the biocide, benzalkonium chloride (BAC), resulted in a unique transcriptomic profile, characterised by both a short and long-term response. Differential gene expression was observed in four main areas: motility, membrane composition, proteostasis, and the stress response. A metabolism shift to protect the proteome and the stress response were prioritised suggesting these are main resistance mechanisms. Whereas "well-established" mechanisms, such as biofilm formation, were not found to be differentially expressed after exposure to BAC.

Global approaches for protein thiol redox state detection

Due to its nucleophilicity, the thiol group of cysteine is chemically very versatile. Hence, cysteine often has important functions in a protein, be it as the active site or, in extracellular proteins, as part of a structural disulfide. Within the cytosol, cysteines are typically reduced. But the nucleophilicity of its thiol group makes it also particularly prone to post-translational oxidative modifications. These modifications often lead to an alteration of the function of the affected protein and are reversible in vivo, e.g. by the thioredoxin and glutaredoxin system. The in vivo-reversible nature of these modifications and their genesis in the presence of localized high oxidant levels led to the paradigm of thiol-based redox regulation, the adaptation, and modulation of the cellular metabolism in response to oxidative stimuli by thiol oxidation in regulative proteins. Consequently, the proteomic study of these oxidative posttranslational modifications of cysteine plays an indispensable role in redox biology.

Transcription tuned by S-nitrosylation underlies a mechanism for Staphylococcus aureus to circumvent vancomycin killing

Treatment of Staphylococcus aureus infections is a constant challenge due to emerging resistance to vancomycin, a last-resort drug. S-nitrosylation, the covalent attachment of a nitric oxide (NO) group to a cysteine thiol, mediates redox-based signaling for eukaryotic cellular functions. However, its role in bacteria is largely unknown. Here, proteomic analysis revealed that S-nitrosylation is a prominent growth feature of vancomycin-intermediate S. aureus. Deletion of NO synthase (NOS) or removal of S-nitrosylation from the redox-sensitive regulator MgrA or WalR resulted in thinner cell walls and increased vancomycin susceptibility, which was due to attenuated promoter binding and released repression of genes involved in cell wall metabolism. These genes failed to respond to H₂O₂-induced oxidation, suggesting distinct transcriptional responses to alternative modifications of the cysteine residue. Furthermore, treatment with a NOS inhibitor significantly decreased vancomycin resistance in S. aureus. This study reveals that transcriptional regulation via S-nitrosylation underlies a mechanism for NO-mediated bacterial antibiotic resistance.

Efficient biosynthesis of (R)-mandelic acid from styrene oxide by an adaptive evolutionary Gluconobacter oxydans STA

BACKGROUND

(R)-mandelic acid (R-MA) is a highly valuable hydroxyl acid in the pharmaceutical industry. However, biosynthesis of optically pure R-MA remains significant challenges, including the lack of suitable catalysts and high toxicity to host strains. Adaptive laboratory evolution (ALE) was a promising and powerful strategy to obtain specially evolved strains.

RESULTS

Herein, we report a new cell factory of the Gluconobacter oxydans to biocatalytic styrene oxide into R-MA by utilizing the G. oxydans endogenous efficiently incomplete oxidization and the epoxide hydrolase (SpEH) heterologous expressed in G. oxydans. With a new screened strong endogenous promoter P12780, the production of R-MA was improved to 10.26 g/L compared to 7.36 g/L of using Plac. As R-MA showed great inhibition for the reaction and toxicity to cell growth, adaptive laboratory evolution (ALE) strategy was introduced to improve the cellular R-MA tolerance. The adapted strain that can tolerate 6 g/L R-MA was isolated (named G. oxydans STA), while the wild-type strain cannot grow under this stress. The conversion rate was increased from 0.366 g/L/h of wild type to 0.703 g/L/h by the recombinant STA, and the final R-MA titer reached 14.06 g/L. Whole-genome sequencing revealed multiple gene-mutations in STA, in combination with transcriptome analysis under R-MA stress condition, we identified five critical genes that were associated with R-MA tolerance, among which AcrA overexpression could further improve R-MA titer to 15.70 g/L, the highest titer reported from bulk styrene oxide substrate.

CONCLUSIONS

The microbial engineering with systematic combination of static regulation, ALE, and transcriptome analysis strategy provides valuable solutions for high-efficient chemical biosynthesis, and our evolved G. oxydans would be better to serve as a chassis cell for hydroxyl acid production.

Construction of an experimental study and addition of adapter sequences using HiDi DNA polymerase for improving DNA normalization methods relevant to novel gene discovery

Microorganisms in the environment can be distinguished into dominant and rare microbial species based on their genes. It is difficult to obtain genetic information derived from rare microbial species (rare genes) because of the differences in relative abundance. DNA normalization is an approach that is used to obtain genetic information derived from rare microbial species from an environmental sample. This method involves the addition of adapter sequences for the amplification, denaturation, and reassociation of the DNA fragments and single-stranded DNA (ssDNA)/double-stranded DNA (dsDNA) separation. In this method, the amount of a high-copy-number of DNA fragments and a low-copy-number of DNA fragments can be equalized. Improvements in this technique are expected to provide novel genetic information or genes in rare microbial species. However, few model experimental systems have been reported to validate the DNA normalization techniques. This study is aimed to improve the DNA normalization technique used to obtain genetic information of rare genes from rare microbial species. An experimental study was constructed with two antibiotic resistance genes, whose copy numbers differed up to a million-fold. Both genes were mixed and the mixture of DNA fragments, of high- and low-copy-number, containing these genes was normalized by separating ssDNA/dsDNA fragments using hydroxyapatite. Normalized DNA fragments were introduced into Escherichia coli and DNA normalization was evaluated by counting colonies. Moreover, we improved the method to amplify a low-copy-number of DNA fragments by the addition of adapter sequences to DNA fragments using HiDi DNA polymerase to increase the efficiency of DNA normalization. This normalization method was achieved with a 100,000-fold difference. These methods allowed for quantitative evaluation of the DNA normalization efficiency. The experimental data and methods obtained in this study are expected to improve the DNA normalization efficiency to obtain novel genetic information or genes.

Redox proteome analysis of auranofin exposed ovarian cancer cells (A2780)

The effects of Auranofin (AF) on protein expression and protein oxidation in A2780 cancer cells were investigated through a strategy based on simultaneous expression proteomics and redox proteomics determinations. Bioinformatics analysis of the proteomics data supports the view that the most critical cellular changes elicited by AF treatment consist of thioredoxin reductase inhibition, alteration of the cell redox state, impairment of the mitochondrial functions, metabolic changes associated with conversion to a glycolytic phenotype, induction of ER stress. The occurrence of the above cellular changes was extensively validated by performing direct biochemical assays. Our data are consistent with the concept that AF produces its effects through a multitarget mechanism that mainly affects the redox metabolism and the mitochondrial functions and results into severe ER stress. Results are discussed in the context of the current mechanistic knowledge existing on AF.

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Redox proteomics allows to underline cell adaptation mechanisms in response to Auranofin treatment in ovarian cancer cells.

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BRCA1 is one of the major candidates of the ovarian cancer cell adaptation to Auranofin treatment.

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Auranofin alters the oxidative phosphorylation and mitochondrial protein import machinery.

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TRAP1 C501 modulates Auranofin toxicity.

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Auranofin induces severe stress of the endoplasmic reticulum.

Transcription Factor SrsR (YgfI) Is a Novel Regulator for the Stress-Response Genes in Stationary Phase in Escherichia coli K-12

Understanding the functional information of all genes and the biological mechanism based on the comprehensive genome regulation mechanism is an important task in life science. YgfI is an uncharacterized LysR family transcription factor in Escherichia coli. To identify the function of YgfI, the genomic SELEX (gSELEX) screening was performed for YgfI regulation targets on the E. coli genome. In addition, regulatory and phenotypic analyses were performed. A total of 10 loci on the E. coli genome were identified as the regulatory targets of YgfI with the YgfI binding activity. These predicted YgfI target genes were involved in biofilm formation, hydrogen peroxide resistance, and antibiotic resistance, many of which were expressed in the stationary phase. The TCAGATTTTGC sequence was identified as an YgfI box in in vitro gel shift assay and DNase-I footprinting assays. RT-qPCR analysis in vivo revealed that the expression of YgfI increased in the stationary phase. Physiological analyses suggested the participation of YgfI in biofilm formation and an increase in the tolerability against hydrogen peroxide. In summary, we propose to rename ygfI as srsR (a stress-response regulator in stationary phase).

Pseudomonas aeruginosa Initiates a Rapid and Specific Transcriptional Response during Surface Attachment

Chronic biofilm infections by Pseudomonas aeruginosa are a major contributor to the morbidity and mortality of patients. The formation of multicellular bacterial aggregates, called biofilms, is associated with increased resistance to antimicrobials and immune clearance and the persistence of infections. Biofilm formation is dependent on bacterial cell attachment to surfaces, and therefore, attachment plays a key role in chronic infections. We hypothesized that bacteria sense various surfaces and initiate a rapid, specific response to increase adhesion and establish biofilms. RNA sequencing (RNA-Seq) analysis identified transcriptional changes of adherent cells during initial attachment, identifying the bacterial response to an abiotic surface over a 1-h period. Subsequent screens investigating the most highly regulated genes in surface attachment identified 4 genes, pfpI, phnA, leuD, and moaE, all of which have roles in both metabolism and biofilm formation. In addition, the transcriptional responses to several different medically relevant abiotic surfaces were compared after initial attachment. Surprisingly, there was a specific transcriptional response to each surface, with very few genes being regulated in response to surfaces in general. We identified a set of 20 genes that were differentially expressed across all three surfaces, many of which have metabolic functions, including molybdopterin cofactor biosynthesis and nitrogen metabolism. This study has advanced the understanding of the kinetics and specificity of bacterial transcriptional responses to surfaces and suggests that metabolic cues are important signals during the transition from a planktonic to a biofilm lifestyle.

IMPORTANCE Bacterial biofilms are a significant concern in many aspects of life, including chronic infections of airways, wounds, and indwelling medical devices; biofouling of industrial surfaces relevant for food production and marine surfaces; and nosocomial infections. The effects of understanding surface adhesion could impact many areas of life. This study utilized emerging technology in a novel approach to address a key step in bacterial biofilm development. These findings have elucidated both conserved and surface-specific responses to several disease-relevant abiotic surfaces. Future work will expand on this report to identify mechanisms of biofilm initiation with the aim of identifying bacterial factors that could be targeted to prevent biofilms.

Defenses of multidrug resistant pathogens against reactive nitrogen species produced in infected hosts

Bacterial pathogens have sophisticated systems that allow them to survive in hosts in which innate immunity is the frontline of defense. One of the substances produced by infected hosts is nitric oxide (NO) that together with its derived species leads to the so-called nitrosative stress, which has antimicrobial properties. In this review, we summarize the current knowledge on targets and protective systems that bacteria have to survive host-generated nitrosative stress. We focus on bacterial pathogens that pose serious health concerns due to the growing increase in resistance to currently available antimicrobials. We describe the role of nitrosative stress as a weapon for pathogen eradication, the detoxification enzymes, protein/DNA repair systems and metabolic strategies that contribute to limiting NO damage and ultimately allow survival of the pathogen in the host. Additionally, this systematization highlights the lack of available data for some of the most important human pathogens, a gap that urgently needs to be addressed.

Gut biofilms: Bacteroides as model symbionts to study biofilm formation by intestinal anaerobes

Bacterial biofilms are communities of adhering bacteria that express distinct properties compared to their free-living counterparts, including increased antibiotic tolerance and original metabolic capabilities. Despite the potential impact of the biofilm lifestyle on the stability and function of the dense community of micro-organisms constituting the mammalian gut microbiota, the overwhelming majority of studies performed on biofilm formation by gut bacteria focused either on minor and often aerobic members of the community or on pathogenic bacteria. In this review, we discuss the reported evidence for biofilm-like structures formed by gut bacteria, the importance of considering the anaerobic nature of gut biofilms and we present the most recent advances on biofilm formation by Bacteroides, one of the most abundant genera of the human gut microbiota. Bacteroides species can be found attached to food particles and colonizing the mucus layer and we propose that Bacteroides symbionts are relevant models to probe the physiology of gut microbiota biofilms.