Characterization of an unusual cold shock protein from Staphylococcus aureus

Potential and mechanism for bioremediation of papermaking black liquor by a psychrotrophic lignin-degrading bacterium, Arthrobacter sp. C2

To meet the challenge of bioremediation of black liquor in pulp and paper mills at low temperatures, a psychrotrophic lignin-degrading bacterium was employed in black liquor treatment for the first time. In this study, Arthrobacter sp. C2 exhibited excellent cold adaptability and lignin degradation ability, with a lignin degradation rate of 65.5% and a mineralization rate of 43.9% for 3 g/L lignin at 15 °C. Bioinformatics analysis and multiple experiments confirmed that cold shock protein 1 (Csp1) was the dominant cold regulator of strain C2, and dye-decolorizing peroxidase (DyP) played a crucial role in lignin degradation. Moreover, structural equation modeling (SEM), mRNA monitoring, and phenotypic variation analysis demonstrated that Csp1 not only mediated cold adaptation but also modulated DyP activity by controlling dyp gene expression, thus driving lignin depolymerization for strain C2 at low temperatures. Furthermore, 96.4% of color, 64.2% of chemical oxygen demand (COD), and 100% of nitrate nitrogen (NO₃^--N) were removed from papermaking black liquor by strain C2 within 15 days at 15 °C. This study provides insights into the association between the cold regulator and catalytic enzyme of psychrotrophic bacteria and offers a feasible alternative strategy for the bioremediation of papermaking black liquor in cold regions.

Overlapping and Distinct Functions of the Paralogous PagR Regulators of Bacillus anthracis

The Bacillus anthracis pagA gene, encoding the protective antigen component of anthrax toxin, is part of a bicistronic operon on pXO1 that codes for its own repressor, PagR1. In addition to the pagAR1 operon, PagR1 regulates sap and eag, two chromosome genes encoding components of the surface layer, a mounting structure for surface proteins involved in virulence. Genomic studies have revealed a PagR1 paralog, PagR2, encoded by a gene on pXO2. The amino acid sequences of the paralogues are 71% identical and show similarity to the ArsR family of transcription regulators. We determined that the expression of either rPagR1 or rPagR2 in a ΔpagR1 pXO1⁺/pXO2^- (PagR1-PagR2) background repressed the expression of pagA, sap, eag, and a newly discovered target, atxA, encoding virulence activator AtxA. Despite the redundancy in PagR1 and PagR2 function, we determined that purified rPagR1 bound DNA corresponding to the control regions of all four target genes and existed as a dimer in cell lysates, whereas rPagR2 exhibited weak binding to the DNA of the pagA and atxA promoters, did not bind sap or eag promoter DNA, and did not appear as a dimer in cell lysates. A single amino acid change in PagR2, S81Y, designed to match the native Y81 of PagR1, allowed for DNA-binding to the sap and eag promoters. Moreover, the S81Y mutation allowed for the detection of PagR2 homomultimers in coaffinity purification experiments. Our results expand our knowledge of the roles of the paralogues in B. anthracis gene expression and provide a potential mechanistic basis for differences in the functions of these repressors. IMPORTANCE The protective antigen component of the anthrax toxin is essential for the delivery of the enzymatic components of the toxin into host target cells. The toxin genes and other virulence genes of B. anthracis are regulated by multiple trans-acting regulators that respond to a variety of host-related signals. PagR1, one such trans-acting regulator, connects the regulation of plasmid-encoded and chromosome-encoded virulence genes by controlling both protective antigen and surface layer protein expression. Whether PagR2, a paralog of PagR1, also functions as a trans-acting regulator was unknown. This work advances our knowledge of the complex model of virulence regulation in B. anthracis and furthers our understanding of the intriguing evolution of this pathogen.

Rapid detection of airborne protein from Mycobacterium tuberculosis using a biosensor detection system

The developed biosensor detection system can complete the detection of air samples by collecting exhaled breath condensate, greatly reducing the time to diagnose tuberculosis.

In Silico Structural and Functional Analysis of Cold Shock Proteins in Pseudomonas fluorescens PF08 from Marine Fish

ABSTRACT

Pseudomonas fluorescens is a specific spoilage microorganism of refrigerated marine fish, and is highly adapted to low temperature. Cold shock proteins (CSPs) play an important role in cold adaptation of bacteria. In this study, CSP genes were identified from the genome of P. fluorescens PF08 by search of the conserved domain of CSPs with HMMER software, and the CSP physicochemical properties, structures, and functions were analyzed through bioinformatics. Five typical CSPs were identified in the P. fluorescens PF08 genome (PfCSPs). All five PfCSPs are small hydrophilic acidic proteins with a molecular mass of ca. 7.4 kDa. They are located in the cytoplasm and are nonsecretory and nontransmembrane proteins. Multiple sequence alignment analysis indicated that the CSPs are highly conserved between species, especially in DNA-binding sites and RNA-binding motifs that can bind to single-stranded DNA and RNA. The five PfCSPs clustered with CspD from Escherichia coli and Salmonella Typhimurium, which suggests a close homology and high functional similarity among the five PfCSPs and CspD. The secondary and tertiary structures of the PfCSPs are in accordance with the characteristics of the CSP family, and ligand binding sites with higher likelihood were found in PfCSPs. The five PfCSPs were predicted to interact with some of the same proteins that are involved in virulence, stress responses (including to low temperature), cell growth, ribosome assembly, and RNA degradation. The results provide further elucidation of the function of CSPs in adaptation to low temperatures by P. fluorescens.

HIGHLIGHTS

Selected Metabolites Profiling of Staphylococcus aureus Following Exposure to Low Temperature and Elevated Sodium Chloride

Staphylococcus aureus is one of the main foodborne pathogens that can cause food poisoning. Due to this reason, one of the essential aspects of food safety focuses on bacterial adaptation and proliferation under preservative conditions. This study was aimed to determine the metabolic changes that can occur following the exposure of S. aureus to either low temperature conditions or elevated concentrations of sodium chloride (NaCl). The results revealed that most of the metabolites measured were reduced in cold-stressed cells, when compared to reference controls. The major reduction was observed in nucleotides and organic acids, whereas mannitol was significantly increased in response to low temperature. However, when S. aureus was exposed to elevated NaCl, a significant increase was observed in the metabolite levels, particularly purine and pyrimidine bases along with organic acids. The majority of carbohydrates remained constant in the cells grown under ideal conditions and those exposed to elevated NaCl concentrations. Partial least square discriminate analysis (PLS-DA) of the metabolomic data indicated that both, prolonged cold stress and osmotic stress conditions, generated cells with different metabolic profiles, in comparison to the reference controls. These results provide evidence that, when bacterial cells exposed to low temperatures or high concentrations of NaCl, experience in situ homeostatic alterations to adapt to new environmental conditions. These data supported the hypothesis that changes in metabolic homeostasis were critical to the adaptive processes required for survival under alterations in the environmental conditions.

Adaptive Metabolism in Staphylococci: Survival and Persistence in Environmental and Clinical Settings

Staphylococci are highly successful at colonizing a variety of dynamic environments, both nonpathogenic and those of clinical importance, and comprise the list of pathogens of global public health significance. Their remarkable survival and persistence can be attributed to a host of strategies, one of which is metabolic versatility—their ability to rapidly alter their metabolism in the presence of transient or long-term bacteriostatic and bactericidal conditions and facilitate cellular homeostasis. These attributes contribute to their widespread dissemination and challenging eradication particularly from clinical settings. The study of microbial behaviour at the metabolite level provides insight into mechanisms of survival and persistence under defined environmental and clinical conditions. This paper reviews the range of metabolic modulations that facilitate staphylococcal acclimatization and persistence in varying terrestrial and host conditions, and their public health ramifications in these settings.

Identification and characterization of an operon, msaABCR, that controls virulence and biofilm development in Staphylococcus aureus

Background

Community-acquired, methicillin-resistant Staphylococcus aureus strains often cause localized infections in immunocompromised hosts, but some strains show enhanced virulence leading to severe infections even among healthy individuals with no predisposing risk factors. The genetic basis for this enhanced virulence has yet to be determined. S. aureus possesses a wide variety of virulence factors, the expression of which is carefully coordinated by a variety of regulators. Several virulence regulators have been well characterized, but others have yet to be thoroughly investigated. Previously, we identified the msa gene as a regulator of several virulence genes, biofilm development, and antibiotic resistance. We also found evidence of the involvement of upstream genes in msa function.

Results

To investigate the mechanism of regulation of the msa gene (renamed msaC), we examined the upstream genes whose expression was affected by its deletion. We showed that msaC is part of a newly defined four-gene operon (msaABCR), in which msaC is a non-protein-coding RNA that is essential for the function of the operon. Furthermore, we found that an antisense RNA (msaR) is complementary to the 5′ end of the msaB gene and is expressed in a growth phase-dependent manner suggesting that it is involved in regulation of the operon.

Conclusion

These findings allow us to define a new operon that regulates fundamental phenotypes in S. aureus such as biofilm development and virulence. Characterization of the msaABCR operon will allow us to investigate the mechanism of function of this operon and the role of the individual genes in regulation and interaction with its targets. This study identifies a new element in the complex regulatory circuits in S. aureus, and our findings may be therapeutically relevant.

RNA-Seq-based analysis of cold shock response in Thermoanaerobacter tengcongensis, a bacterium harboring a single cold shock protein encoding gene

BACKGROUND

Although cold shock responses and the roles of cold shock proteins in microorganisms containing multiple cold shock protein genes have been well characterized, related studies on bacteria possessing a single cold shock protein gene have not been reported. Thermoanaerobacter tengcongensis MB4, a thermophile harboring only one known cold shock protein gene (TtescpC), can survive from 50° to 80 °C, but has poor natural competence under cold shock at 50 °C. We therefore examined cold shock responses and their effect on natural competence in this bacterium.

RESULTS

The transcriptomes of T. tengcongensis before and after cold shock were analyzed by RNA-seq and over 1200 differentially expressed genes were successfully identified. These genes were involved in a wide range of biological processes, including modulation of DNA replication, recombination, and repair; energy metabolism; production of cold shock protein; synthesis of branched amino acids and branched-chain fatty acids; and sporulation. RNA-seq analysis also suggested that T. tengcongensis initiates cell wall and membrane remodeling processes, flagellar assembly, and sporulation in response to low temperature. Expression profiles of TtecspC and failed attempts to produce a TtecspC knockout strain confirmed the essential role of TteCspC in the cold shock response, and also suggested a role of this protein in survival at optimum growth temperature. Repression of genes encoding ComEA and ComEC and low energy metabolism levels in cold-shocked cells are the likely basis of poor natural competence at low temperature.

CONCLUSION

Our study demonstrated changes in global gene expression under cold shock and identified several candidate genes related to cold shock in T. tengcongensis. At the same time, the relationship between cold shock response and poor natural competence at low temperature was preliminarily elucidated. These findings provide a foundation for future studies on genetic and molecular mechanisms associated with cold shock and acclimation at low temperature.