A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC)

Shiga toxin (Stx) released by Shiga toxin producing Escherichia coli (STEC) causes life-threatening illness. Its production and release require induction of Stx-encoding prophage resident within the STEC genome. We identified two different STEC strains, PA2 and PA8, bearing Stx-encoding prophage whose sequences primarily differ by the position of an IS629 insertion element, yet differ in their abilities to kill eukaryotic cells and whose prophages differ in their spontaneous induction frequencies. The IS629 element in ϕPA2, disrupts an ORF predicted to encode a DNA adenine methyltransferase, whereas in ϕPA8, this element lies in an intergenic region. Introducing a plasmid expressing the methyltransferase gene product into ϕPA2 bearing-strains increases both the prophage spontaneous induction frequency and virulence to those exhibited by ϕPA8 bearing-strains. However, a plasmid bearing mutations predicted to disrupt the putative active site of the methyltransferase does not complement either of these defects. When complexed with a second protein, the methyltransferase holoenzyme preferentially uses 16S rRNA as a substrate. The second subunit is responsible for directing the preferential methylation of rRNA. Together these findings reveal a previously unrecognized role for rRNA methylation in regulating induction of Stx-encoding prophage.

Homeostasis of cellular amino acids in Acanthamoeba castellanii exposed to different media under amoeba-bacteria coculture conditions

BACKGROUND

Acanthamoeba castellanii is a free-living protist that feeds on diverse bacteria. A. castellanii has frequently been utilized in studies on microbial interactions. Grazing bacteria also exhibit diverse effects on the physiological characteristics of amoebae, such as their growth, encystation, and cytotoxicity. Since the composition of amoebae amino acids is closely related to cellular activities, it can indicate the overall responses of A. castellanii to various stimuli.

METHOD

A. castellanii was exposed to different culture conditions in low-nutrient medium with heat-killed DH5α to clarify their effects. A targeted metabolomic technique was utilized to evaluate the concentration of cellular amino acids. The amino acid composition and pathways were analyzed by two web-based tools: MetaboAnalyst and Pathview. Then, long-term exposure to A. castellanii was investigated through in silico and in vitro methods to elucidate the homeostasis of amino acids and the growth of A. castellanii.

RESULTS

Under short-term exposure, all kinds of amino acids were enriched in all exposed groups. In contrast to the presence of heat-killed bacteria, the medium exhibited obvious effects on the amino acid composition of A. castellanii. After long-term exposure, the amino acid composition was more similar to that of the control group. A. castellanii may achieve amino acid homeostasis through pathways related to alanine, aspartate, citrulline, and serine.

DISCUSSION

Under short-term exposure, compared to the presence of bacteria, the type of medium exerted a more powerful effect on the amino acid composition of the amoeba. Previous studies focused on the interaction of the amoeba and bacteria with effective secretion systems and effectors. This may have caused the effects of low-nutrient environments to be overlooked.

CONCLUSION

When A. castellanii was stimulated in the coculture system through various methods, such as the presence of bacteria and a low-nutrient environment, it accumulated intracellular amino acids within a short period. However, different stimulations correspond to different amino acid compositions. After long-term exposure, A. castellanii achieved an amino acid equilibrium by downregulating the biosynthesis of several amino acids.

O-Polysaccharides of LPS Modulate E. coli Uptake by Acanthamoeba castellanii

Protozoan grazing is a major cause of bacterial mortality and controls bacterial population size and composition in the natural environment. To enhance their survival, bacteria evolved many defense strategies to avoid grazing by protists. Cell wall modification is one of the defense strategies that helps bacteria escape from recognition and/or internalization by its predators. Lipopolysaccharide (LPS) is the major component of Gram-negative bacterial cell wall. LPS is divided into three regions: lipid A, oligosaccharide core and O-specific polysaccharide. O-polysaccharide as the outermost region of E. coli LPS provides protection against predation by Acanthamoeba castellanii; however, the characteristics of O-polysaccharide contribute to this protection remain unknown. Here, we investigate how length, structure and composition of LPS affect E. coli recognition and internalization by A. castellanii. We found that length of O-antigen does not play a significant role in regulating bacterial recognition by A. castellanii. However, the composition and structure of O-polysaccharide play important roles in providing resistance to A. castellanii predation.

The Oligosaccharide Region of LPS Governs Predation of E. coli by the Bacterivorous Protist, Acanthamoeba castellanii

Protozoan predation is a major cause of bacterial mortality. The first step of predation for phagocytic amoebae is the recognition of their prey. Lipopolysaccharide (LPS) is a major component of Gram-negative bacteria and is only present on the outer leaflet of the outer membrane lipid bilayer. LPS consists of three distinct regions: lipid A, an oligosaccharide core, and O-polysaccharide. Previous research in our lab determined that the oligosaccharide (OS) region of LPS mediates the recognition and internalization of Escherichia coli by Acanthamoeba castellanii. The oligosaccharide region is conceptually divided into the inner core and outer core. The LPS of any given E. coli strain contains only one of five different OS structures: K-12 and R1 to R4. All OSs contain the same inner core sugars but different outer core sugars. Here, we show that the Kdo2 moiety of the inner core is necessary and sufficient for E. coli recognition and internalization by A. castellanii. We also show that the precise composition of the variable outer core OS region modulates the efficiency with which A. castellanii consumes bacteria. The latter finding indicates that outer core OS composition plays a role in bacterial defense against phagocytic predators. IMPORTANCE Rather than being transmitted from host to host, most opportunistic bacterial pathogens reside in the environment for significant amounts of time. Protist predation is a major cause of bacterial mortality. To enhance their survival in the environment, bacteria have evolved various defense strategies such as filamentation, increased motility, biofilm formation, toxin release, and modification of cell wall structure; strategies which also enhance their virulence to humans. This work shows that the major component of the bacterial cell wall, LPS, also known as bacterial endotoxin, is a "dual use" factor, regulating amoeba predation of bacteria in addition to its well-known role as a human virulence factor. Both these functions are governed by the same parts of LPS. Thus, the structure and composition of this "dual use" factor likely evolved as a response to constant voracious protist grazing pressure in the environment, rather than during short-term infections of human and animals.

Environmental Free-Living Amoebae Can Predate on Diverse Antibiotic-Resistant Human Pathogens

Here, we sought to test the resistance of human pathogens to unaltered environmental free-living amoebae. Amoebae are ubiquitous eukaryotic microorganisms and important predators of bacteria. Environmental amoebae have also been proposed to serve as both potential reservoirs and training grounds for human pathogens. However, studies addressing their relationships with human pathogens often rely on a few domesticated amoebae that have been selected to feed on rich medium, thereby possibly overestimating the resistance of pathogens to these predatory phagocytes. From an open-air composting site, we recovered over 100 diverse amoebae that were able to feed on Acinetobacter baumannii and Klebsiella pneumoniae. In a standardized and quantitative assay for predation, the isolated amoebae showed a broad predation spectrum, killing clinical isolates of A. baumannii, K. pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Interestingly, A. baumannii, which was previously reported to resist predation by laboratory strains of Acanthamoeba, was efficiently consumed by closely related environmental amoebae. The isolated amoebae were capable of feeding on highly virulent carbapenem-resistant or methicillin-resistant clinical isolates. In conclusion, the natural environment is a rich source of amoebae with broad-spectrum bactericidal activities, including against antibiotic-resistant isolates.

IMPORTANCE Free-living amoebae have been proposed to play an important role in hosting and disseminating various human pathogens. The resistance of human pathogens to predation by amoebae is often derived from in vitro experiments using model amoebae. Here, we sought to isolate environmental amoebae and to test their predation on diverse human pathogens, with results that challenge conclusions based on model amoebae. We found that the natural environment is a rich source of diverse amoebae with broad-spectrum predatory activities against human pathogens, including highly virulent and antibiotic-resistant clinical isolates.

Amoebae as Targets for Toxins or Effectors Secreted by Mammalian Pathogens

Numerous microorganisms, pathogenic for mammals, come from the environment where they encounter predators such as free-living amoebae (FLA). The selective pressure due to this interaction could have generated virulence traits that are deleterious for amoebae and represents a weapon against mammals. Toxins are one of these powerful tools that are essential for bacteria or fungi to survive. Which amoebae are used as a model to study the effects of toxins? What amoeba functions have been reported to be disrupted by toxins and bacterial secreted factors? Do bacteria and fungi effectors affect eukaryotic cells similarly? Here, we review some studies allowing to answer these questions, highlighting the necessity to extend investigations of microbial pathogenicity, from mammals to the environmental reservoir that are amoebae.

Adhesion of Campylobacter jejuni Is Increased in Association with Foodborne Bacteria

The aim of this study was to evaluate Campylobacter jejuni NTCT 11168 adhesion to abiotic and biotic surfaces when grown in co-culture with Escherichia coli ATCC 11229 and/or Listeria monocytogenes 4b. Adhesion of C. jejuni to polystyrene and to Caco-2 cells and Acanthamoeba castellanii was lower for at least 3 log CFU/mL compared to E. coli and L. monocytogenes. Electron micrographs of ultrathin sections revealed interactions of C. jejuni with host cells. In co-culture with E. coli and L. monocytogenes, adhesion of C. jejuni to all tested surfaces was significantly increased for more than 1 log CFU/mL. There was 10% higher aggregation for C. jejuni than for other pathogens, and high co-aggregation of co-cultures of C. jejuni with E. coli and L. monocytogenes. These data show that C. jejuni in co-cultures with E. coli and L. monocytogenes present significantly higher risk than C. jejuni as mono-cultures, which need to be taken into account in risk evaluation. C. jejuni adhesion is a prerequisite for their colonization, biofilm formation, and further contamination of the environment. C. jejuni survival under adverse conditions as a factor in their pathogenicity and depends on their adhesion to different surfaces, not only as individual strains, but also in co-cultures with other bacteria like E. coli and L. monocytogenes.

The dialogue between protozoa and bacteria in a microfluidic device

In nature, protozoa play a major role in controlling bacterial populations. This paper proposes a microfluidic device for the study of protozoa behaviors change due to their chemotactic response in the presence of bacterial cells. A three-channel microfluidic device was designed using a nitrocellulose membrane into which channels were cut using a laser cutter. The membrane was sandwiched between two glass slides; a Euglena suspension was then allowed to flow through the central channel. The two side channels were filled with either, 0.1% peptone as a negative control, or a Listeria suspension respectively. The membrane design prevented direct interaction but allowed Euglena cells to detect Listeria cells as secretions diffused through the nitrocellulose membrane. A significant number of Euglena cells migrated toward the chambers near the bacterial cells, indicating a positive chemotactic response of Euglena toward chemical cues released from Listeria cells. Filtrates collected from Listeria suspension with a series of molecular weight cutoffs (3k, 10k and 100k) were examined in Euglena chemotaxis tests. Euglena cells were attracted to all filtrates collected from the membrane filtration with different molecular weight cutoffs, suggesting small molecules from Listeria might be the chemical cues to attract protozoa. Headspace volatile organic compounds (VOC) released from Listeria were collected, spiked to 0.1% peptone and tested as the chemotactic effectors. It was discovered that the Euglena cells responded quickly to Listeria VOCs including decanal, 3,5- dimethylbenzaldehyde, ethyl acetate, indicating bacterial VOCs were used by Euglena to track the location of bacteria.

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

Bacterial pathogens and commensals are surrounded by diverse surface polysaccharides which include capsules and lipopolysaccharides. These carbohydrates play a vital role in bacterial ecology and interactions with the environment. Here, we review recent rapid advancements in this field, which have improved our understanding of the roles, structures, and genetics of bacterial polysaccharide antigens. Genetic loci encoding the biosynthesis of these antigens may have evolved as bacterial diversity-generating machines, driven by selection from a variety of forces, including host immunity, bacteriophages, and cell-cell interactions. We argue that the high adaptive potential of polysaccharide antigens should be taken into account in the design of polysaccharide-targeting medical interventions like conjugate vaccines and phage-based therapies.

A Mutation in the Mesorhizobium loti oatB Gene Alters the Physicochemical Properties of the Bacterial Cell Wall and Reduces Survival inside Acanthamoeba castellanii

In our previous report, we had shown that the free-living amoeba Acanthamoeba castellanii influenced the abundance, competiveness, and virulence of Mesorhizobium loti NZP2213, the microsymbiont of agriculturally important plants of the genus Lotus. The molecular basis of this phenomenon; however, had not been explored. In the present study, we demonstrated that oatB, the O-acetyltransferase encoding gene located in the lipopolysaccharide (LPS) synthesis cluster of M. loti, was responsible for maintaining the protective capacity of the bacterial cell envelope, necessary for the bacteria to fight environmental stress and survive inside amoeba cells. Using co-culture assays combined with fluorescence and electron microscopy, we showed that an oatB mutant, unlike the parental strain, was efficiently destroyed after rapid internalization by amoebae. Sensitivity and permeability studies of the oatB mutant, together with topography and nanomechanical investigations with the use of atomic force microscopy (AFM), indicated that the incomplete substitution of lipid A-core moieties with O-polysaccharide (O-PS) residues rendered the mutant more sensitive to hydrophobic compounds. Likewise, the truncated LPS moieties, rather than the lack of O-acetyl groups, made the oatB mutant susceptible to the bactericidal mechanisms (nitrosative stress and the action of lytic enzymes) of A. castellanii.