Way For Bacteria Research Articles

The two-component system expression patterns and immune regulatory mechanism of Vibrio parahaemolyticus with different genotypes at the early stage of infection in THP-1 cells.

Vibrio parahaemolyticus must endure various challenging circumstances while being swallowed by phagocytes of the innate immune system. Moreover, bacteria should recognize and react to environmental signals quickly in host cells. Two-component system (TCS) is an important way for bacteria to perceive external environmental signals and transmit them to the interior to trigger the associated regulatory mechanism. However, the regulatory function of V. parahaemolyticus TCS in innate immune cells is unclear. Here, the expression patterns of TCS in V. parahaemolyticus-infected THP-1 cell-derived macrophages at the early stage were studied for the first time. Based on protein-protein interaction network analysis, we mined and analyzed seven critical TCS genes with excellent research value in the V. parahaemolyticus regulating macrophages, as shown below. VP1503, VP1502, VPA0021, and VPA0182 could regulate the ATP-binding-cassette (ABC) transport system. VP1735, uvrY, and peuR might interact with thermostable hemolysin proteins, DNA cleavage-related proteins, and TonB-dependent siderophore enterobactin receptor, respectively, which may assist V. parahaemolyticus in infected macrophages. Subsequently, the potential immune escape pathways of V. parahaemolyticus regulating macrophages were explored by RNA-seq. The results showed that V. parahaemolyticus might infect macrophages by controlling apoptosis, actin cytoskeleton, and cytokines. In addition, we found that the TCS (peuS/R) could enhance the toxicity of V. parahaemolyticus to macrophages and might contribute to the activation of macrophage apoptosis. IMPORTANCE This study could offer crucial new insights into the pathogenicity of V. parahaemolyticus without tdh and trh genes. In addition, we also provided a novel direction of inquiry into the pathogenic mechanism of V. parahaemolyticus and suggested several TCS key genes that may assist V. parahaemolyticus in innate immune regulation and interaction.

Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa.

A common way for bacteria to cooperate is via the secretion of beneficial public goods (proteases, siderophores, biosurfactants) that can be shared amongst individuals in a group. Bacteria often simultaneously deploy multiple public goods with complementary functions. This raises the question whether natural selection could favour division of labour where subpopulations or species specialize in the production of a single public good, whilst sharing the complementary goods at the group level. Here we use an experimental system, where we mix engineered specialists of the bacterium Pseudomonas aeruginosa that can each only produce one of the two siderophores, pyochelin or pyoverdine and explore the conditions under which specialization can lead to division of labour. When growing pyochelin and pyoverdine specialists at different mixing ratios under different levels of iron limitation, we found that specialists could only successfully complement each other in environments with moderate iron limitation and grow as good as the generalist wildtype but not better. Under more stringent iron limitation, the dynamics in specialist communities was characterized by mutual cheating and with higher proportions of pyochelin producers greatly compromising group productivity. Nonetheless, specialist communities remained stable through negative frequency‐dependent selection. Our work shows that specialization in a bacterial community can be spurred by cheating and does not necessarily result in beneficial division of labour. We propose that natural selection might favour fine‐tuned regulatory mechanisms in generalists over division of labour because the former enables generalists to remain flexible and adequately adjust public good investments in fluctuating environments.

Carbon source type can affect tetracycline removal by Pseudomonas sp. TC952 through regulation of extracellular polymeric substances composition and production

The objective of this work is to elucidate the mechanism of tetracycline (TC) removal by Pseudomonas sp. TC952. The TC removal characteristics of strain TC952 under various environmental conditions were studied. Results showed that the bio-removal efficiency was significantly affected by initial TC and peptone concentration, pH values, divalent metal ion (Zn2+) and carbon source, and the strain TC952 efficiently removed approximately 72.8% of TC within 6 days with 10 g/L peptone. The best conditions for strain TC952 to remove TC are as follows: initial TC concentration is 50 mg/L, solution initial pH is 7, Zn2+ concentration is 0.1 μg/L, carbon source is peptone. And through intra- and extracellular fractions assay and extracellular polymeric substances (EPS) component analysis, TC removal by strain TC952 was mainly attributed to the adsorption by bacterial EPS and bacterial cell. Furthermore, different carbon source affected the EPS production content and component of strain TC952, so EPS produced under peptone and serine conditions could bio-adsorb TC and formed a buffer area outside the cells, thus reducing or preventing TC from entering the bacteria cells. All the results obtained showed that secretion of EPS and adsorption of TC by EPS and bacterial cell wall may be a common way for bacteria to reduce TC in the environment, which brought novel insights for better management of TC contamination by functional bacteria and for understanding the natural removal process of antibiotics by microorganisms in the environment.

Advances in Studies on Horizontal Gene Transfer Promoting the Evolution of Resistance Genes of Periodontal Pathogens

Horizontal gene transfer (HGT) plays an important role in bacterial evolution. HGT is an important way for bacteria to rapidly obtain genetic improvement. HGT promotes the transmission of biological characteristics such as virulence, antibiotic resistance and allometabolism in microorganisms. The bacteria in the mouth are abundant and abundant. Bacterial virulence gene (Virulence genes, VGs) and antibiotic resistance genes (Antibiotic resistance genes, ARGs) besides through vertical transmission by parental, also can through HGT in oral symbiotic species or genus within the transmission. HGT promotes the spread of virulence genes and resistance genes, becomes an important driving force for the adaptive evolution of oral microorganisms, increases the difficulty of the treatment of oral bacterial infectious diseases (periodontal disease, periradicular lesions, Periimplantitis, etc.), and brings serious harm to human oral health and even general health. With modern microbiology, genetics, molecular biology, the macro development of disciplines, such as genomics, electron microscope and laser confocal microscope, nucleic acid hybridization (especially the 16 sRNA gene sequencing) and other modern analysis technology has been widely applied in periodontal pathogens resistance genes, through the study of HGT way spread and made some progress. This paper will analyze and summarize the literature on the spread of resistance genes of common periodontal pathogens through HGT method in recent years, in order to provide reference for the follow-up study of resistance of periodontal pathogens, as well as for the solution of resistance of periodontal pathogens and the treatment of periodontal diseases.

CRISPR-Cas: Removing Boundaries of the Nature

The CRISPR-Cas 9 system, which is known as a natural way of bacteria to defend against phage infection and plasmid transfer, has been re-purposed as a RNA-guided DNA targeting strategy for genome editing. Together with the advances gained in DNA sequencing technology, this platform opened a new era in molecular biology since its recognition was specified by 20-nt single-guide RNA which made technique easier, efficient and simple for application in any organism. Thus, many studies have discussed and performed the applications of CRISPR-Cas systems on different organisms for genome editing. Moreover, targeted gene regulations, epigenetic modulation, chromatin imaging and manipulation could also be applied with this system. Besides all its potential promising aspects, this tool might have some side effects like off-target mutations. In addition, unexpected results have also been reported after some gene editing applications. Thus, this review provides a brief history of gene editing tools together with the overview of the latest applications, regulations and ethical/structural aspects of the CRISPR Cas system.

Bacterial siderophores in community and host interactions.

Iron is an essential trace element for most organisms. A common way for bacteria to acquire this nutrient is through the secretion of siderophores, which are secondary metabolites that scavenge iron from environmental stocks and deliver it to cells via specific receptors. While there has been tremendous interest in understanding the molecular basis of siderophore synthesis, uptake and regulation, questions about the ecological and evolutionary consequences of siderophore secretion have only recently received increasing attention. In this Review, we outline how eco-evolutionary questions can complement the mechanistic perspective and help to obtain a more integrated view of siderophores. In particular, we explain how secreted diffusible siderophores can affect other community members, leading to cooperative, exploitative and competitive interactions between individuals. These social interactions in turn can spur co-evolutionary arms races between strains and species, lead to ecological dependencies between them and potentially contribute to the formation of stable communities. In brief, this Review shows that siderophores are much more than just iron carriers: they are important mediators of interactions between members of microbial assemblies and the eukaryotic hosts they inhabit.

CRISPR: No Sign of Slowing Down

CRISPR: No Sign of Slowing Down

Environmental changes bridge evolutionary valleys

Molecular Evolution Molecular evolution of individual protein molecules can be described in a “landscape” of possible amino acid sequences containing peaks and valleys. Peaks characterize the beneficial nature of particular sequences for the success of organismal reproduction. Steinberg and Ostermeier designed a way for bacteria evolving under lab conditions to cross valleys in this landscape to achieve superior fitness outcomes. Sci. Adv. 10.1126.sciadv.1500921 (2016).

Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria.

In all studied organisms, a substantial portion of the transcriptome consists of non-coding RNAs that frequently execute regulatory functions. Here, we have compared the primary transcriptomes of the cyanobacteria Synechocystis sp. PCC 6714 and PCC 6803 under 10 different conditions. These strains share 2854 protein-coding genes and a 16S rRNA identity of 99.4%, indicating their close relatedness. Conserved major transcriptional start sites (TSSs) give rise to non-coding transcripts within the sigB gene, from the 5′UTRs of cmpA and isiA, and 168 loci in antisense orientation. Distinct differences include single nucleotide polymorphisms rendering promoters inactive in one of the strains, e.g., for cmpR and for the asRNA PsbA2R. Based on the genome-wide mapped location, regulation and classification of TSSs, non-coding transcripts were identified as the most dynamic component of the transcriptome. We identified a class of mRNAs that originate by read-through from an sRNA that accumulates as a discrete and abundant transcript while also serving as the 5′UTR. Such an sRNA/mRNA structure, which we name ‘actuaton’, represents another way for bacteria to remodel their transcriptional network. Our findings support the hypothesis that variations in the non-coding transcriptome constitute a major evolutionary element of inter-strain divergence and capability for physiological adaptation.

Study of Bacterial Adhesion on Different Glycopolymer Surfaces by Quartz Crystal Microbalance with Dissipation

Protein-carbohydrate interactions are involved in a wide variety of cellular recognition processes including cell growth regulation, differentiation and adhesion, the immune response, and viral or bacterial infections. A common way for bacteria to achieve adhesion is through their fimbriae which possess cellular lectins that can bind to complementary carbohydrates on the surface of the host tissues. In this work, we synthesized glycopolymers using reversible addition-fragmentation chain transfer (RAFT) polymerization which were subsequently immobilized on a sensor surface for studies of bacterial adhesion by quartz crystal microbalance with dissipation (QCM-D). Ricinus communis Agglutinin (RCA120), a galactose specific lectin, was first studied by QCM-D to determine the specific lectin interactions to the different glycopolymers-treated surfaces. Subsequently, Pseudomonas aeruginosa PAO1 (a Gram-negative bacterium with galactose-specific binding C-type lectin (PA-IL)) and Escherichia coli K-12 (a Gram-negative bacterium with mannose-specific binding lectin) were then used as model bacteria to study bacterial adhesion mechanisms on different polymer-treated sensor surfaces by the coupled resonance theory. Our results showed that lectin-carbohydrate interactions play significant roles in comparison to the nonspecific interactions, such as electrostatic interactions. A significantly higher amount of P. aeruginosa PAO1 could adhere on the glycopolymer surface with strong contact point stiffness as compared to E. coli K-12 on the same surface. Furthermore, in comparison to E. coli K-12, the adhesion of P. aeruginosa PAO1 to the glycopolymers was found to be highly dependent on the presence of calcium ions due to the specific C-type lectin interactions of PA-IL, and also the enhanced bacterial adhesion is attributed to the stiffer glycopolymer surface in higher ionic strength condition.

Type II secretion: the substrates that won't go away

Type II secretion systems (T2SSs) generally release their substrates into the culture medium. A few T2SS substrates remain anchored to or bound at the surface of the bacteria after secretion. Since they handle already folded proteins, T2SSs are the best way for bacteria to target, at their surface, proteins containing a cofactor, proteins that have to be folded in the cytoplasm or in the periplasm, or multimeric proteins. However, how a T2SS deals with membrane-anchored proteins is not yet understood. While this type of protein has until now been overlooked, new proteomic approaches will facilitate its identification.

Molecular Basis for the Maintenance of Envelope Integrity in Selenomonas ruminantium: Cadaverine Biosynthesis and Covalent Modification into the Peptidoglycan Play a Major Role

Polyamine is a small organic polycation composed of a hydrocarbon backbone with multiple amino groups which ubiquitously exists in all living organisms from bacteria to higher animals. The critical step of polyamine biosynthesis generally includes the amino acid-decarboxylating reaction to produce the primary diamines, such as a synthesis of putrescine (NH(3)(+)·(CH(2))(4)·NH(3)(+)) from ornithine, and cadaverine (NH(3)(+)·(CH(2))(5)·NH(3)(+)) from lysine, which are catalyzed by pyridoxal-5'-phosphate (PLP; vitamin B(6))-dependent decarboxylases. Synthesized polyamines are implicated in a wide variety of cytoplasmic reactions such as DNA replication and protein synthesis, and are essential for proper growth of the organisms. However, in Selenomonas ruminantium, a strictly anaerobic Gram-negative bacterium dominant in sheep rumen, cadaverine displays its function in a quite distinctive scheme compared to the general bacteria reported. It serves as an essential constituent of the peptidoglycan for the maintenance of envelope integrity through an interaction with the periplasm-exposed SLH domain of Mep45, the outer membrane protein of this bacterium. Furthermore, cytoplasmic biosynthesis of cadaverine occurs totally in a eukaryotic-like manner rather than in a conventional way of bacteria. Lysine/ornithine decarboxylase (LDC/ODC), a PLP-dependent enzyme responsible for cadaverine synthesis in this bacterium, displays significant homology to the eukaryotic ODC but not to the general bacterial LDC nor ODC, and its activity is tightly regulated by antizyme-mediated proteolysis, a regulatory process generally found in eukaryotes. These findings represent the biological diversity of this bacterium beyond the preexisting knowledge related to the polyamine-physiology, cell envelope-architecture, and the regulatory system for the enzyme. In this review we will describe (i) the cadaverine-containing peptidoglycan of S. ruminantium: its chemical structure, biosynthesis, and biological function, and (ii) cellular biosynthesis of cadaverine by LDC/ODC and its antizyme-mediated regulation. In addition, we will briefly refer to (iii) the phylogenetic position and characteristics of S. ruminantium and its unique cadaverine-physiology.

Bacterial immobilization and remineralization of N at different growth rates and N concentrations

An experiment was designed to resolve two largely unaddressed questions about the turnover of N in soils. One is the influence of microbial growth rate on mobilization and remineralization of cellular N. The other is to what extent heterotrophic immobilization of NO 3 - is controlled by the soil concentration of NH 4 + . Bacteria were extracted from a deciduous forest soil and inoculated into an aqueous medium. Various N pool dilution/enrichment experiments were carried out to: (1) calculate the gross N immobilization and remineralization rates; (2) investigate their dependence on NH 4 + and NO 3 - concentrations; (3) establish the microbial preference for NH 4 + and NO 3 - depending on the NH 4 + / NO 3 - concentration ratio. Remineralization of microbial N occurred mainly at high growth rates and NH 4 + concentrations. There was a positive correlation between NH 4 + immobilization and remineralization rates, and intracellular recycling of N seemed to be an efficient way for bacteria to withstand low inorganic N concentrations. Thus, extensive remineralization of microbial N is likely to occur only when environmental conditions promote high growth rates. The results support previous observations of high NO 3 - immobilization rates, especially at low NH 4 + concentrations, but NO 3 - was also immobilized at high NH 4 concentrations. The latter can be understood if part of the microbial community has a preference for NO 3 - over NH 4 + .

Is biofilm a cause of silent chronic inflammation in haemodialysis patients? A fascinating working hypothesis

Knowledge of biofilm formation and its biological rolein chronic subclinical inflammation has largely evolvedover the past years [1–5]. The development of a biofilmis a very effective way for bacteria to survive facinghostile conditions and to resist biocides and antimicro-bial substances. The initial event in biofilm formationis the adhesion of microbes to surfaces. The surfaceproperties of medical devices are usually modified bya conditioning film of organic material. The effect ofsingle blood proteins or of whole blood itself dependson bacterial strains. Fibrinogen and fibronectin bothenhance Staphylococcus aureus binding and inhibitStaphylococcus epidermidis or Gram-negative bacteriaadherence, while whole blood promotes Pseudomonasaeruginosa biofilm formation [6].Biofilm is not a static simple matrix made ofhomogeneous slime embedding bacteria. This sessilemulticellular community is a dynamic complex systemmade of exopolysaccharide matrix embedding livingmicroorganisms with a phenotype modified fromplanktonic (free-floating) bacteria. Biofilm is a livingmaterial that evolves according to local microenviron-mental conditions (hydrodynamic and biochemicalconditions, thickness, shear stress and possiblyothers). Biofilm has a spatial heterogeneity (channels,towers) that seems to be linked to the type of bacteriaand may differ in relation to oxygen limitation, pH,nutrient access and growth rates.However, despite these important acquisitions, therole of biofilm in haemodialysis patients is undefined.At present, we are unable to define the extent and theincidence of biofilm formation in the haemodialysispopulation. No method exists to detect biofilm in vivoand to ascertain its eradication. In principle, bacteriaare often shown to form biofilm using ‘extreme’ andunrealistic experimental conditions. Detection of bio-film is usually performed by surface ultrastructuralanalysis alone or in combination with methods tostain the bacterial nuclear DNA using membrane-permeable or impermeable fluorochromes (to detectdead or live bacteria, respectively). In this editorial,we will describe several potential sites of bacterialcontamination and possibly of biofilm formation inhaemodialyis patients, such as the vascular access(arterio-venous fistula and graft or venous catheters)and the hydraulic circuit of the water treatment andof haemodialysis monitors.

How Does Influenza Virus Pave the Way for Bacteria?

How Does Influenza Virus Pave the Way for Bacteria?