Genome sequencing of Pseudomonas aeruginosa strain M2 illuminates traits of an opportunistic pathogen of burn wounds

Pseudomonas aeruginosa is a Gram-negative nosocomial pathogen and one of the most prevalent organisms isolated from burn wounds worldwide. Pseudomonas aeruginosa strain M2 (O5 serotype, type B flagella) is utilized for examining the murine model associated with burns. Pseudomonas aeruginosa M2 is similar in lethality to common laboratory P. aeruginosa strains when infecting CD-1 mice. Conversely, we recently showed that, relative to these strains, P. aeruginosa M2-infected mice are more susceptible to sepsis and demonstrate a 6-log reduction in LD50 from subcutaneous infection at the infection site directly after 10% total body surface area burn. To better understand this striking phenotypic difference from other P. aeruginosa strains employed in burn models, we sequenced the P. aeruginosa M2 genome. A total of 4,136,641 read pairs were obtained, providing an average genome coverage of 97.5X; subsequent assembly yielded a draft genome with 187 contigs comprising 6,360,304 bp with a G + C content of 66.45%. Genome-based phylogeny estimation of 92 P. aeruginosa strains placed P. aeruginosa M2 with P. aeruginosa-12-4-4(59), a nonairway clinical strain isolated from the blood culture of a burn patient. Phylogenomic analyses identified genes shared between P. aeruginosa M2 and P. aeruginosa 14, another strain exhibiting increased lethality in thermal tissues, as well as P. aeruginosa M2 unique genes with diverse functions like degradation of toxic aromatic compounds, iron scavenging, swarming motility and biofilm formation, defense against invasive DNA, and host assault. Predicted lateral gene transfers illuminate proteins heretofore uncharacterized for roles in P. aeruginosa biology. Our work yields a rich resource for assessing P. aeruginosa genes required for increased lethality in burn tissue seroma.

The role of the Cer1 transposon in horizontal transfer of transgenerational memory

Animals face both external and internal dangers: pathogens threaten from the environment, and unstable genomic elements threaten from within. C. elegans protects itself from pathogens by "reading" bacterial small RNAs, using this information to both induce avoidance and transmit memories for four generations. Here, we found that memories can be transferred from either lysed animals or from conditioned media to naive animals via Cer1 retrotransposon-encoded virus-like particles. Moreover, Cer1 functions internally at the step of transmission of information from the germline to neurons and is required for learned avoidance. The presence of the Cer1 retrotransposon in wild C. elegans strains correlates with the ability to learn and inherit small-RNA-induced pathogen avoidance. Together, these results suggest that C. elegans has co-opted a potentially dangerous retrotransposon to instead protect itself and its progeny from a common pathogen through its inter-tissue signaling ability, hijacking this genomic element for its own adaptive immunity benefit.

Functional reprogramming of Candida glabrata epithelial adhesins: the role of conserved and variable structural motifs in ligand binding

For host-cell interaction, the human fungal pathogen Candida glabrata harbors a large family of more than 20 cell wall-attached epithelial adhesins (Epas). Epa family members are lectins with binding pockets containing several conserved and variable structural hot spots, which were implicated in mediating functional diversity. In this study, we have performed an elaborate structure-based mutational analysis of numerous Epa paralogs to generally determine the role of diverse structural hot spots in conferring host cell binding and ligand binding specificity. Our study reveals that several conserved structural motifs contribute to efficient host cell binding. Moreover, our directed motif exchange experiments reveal that the variable loop CBL2 is key for programming ligand binding specificity, albeit with limited predictability. In contrast, we find that the variable loop L1 affects host cell binding without significantly influencing the specificity of ligand binding. Our data strongly suggest that variation of numerous structural hot spots in the ligand binding pocket of Epa proteins is a main driver of their functional diversification and evolution.

A Receptor Tyrosine Kinase Plays Separate Roles in Sensory Integration and Associative Learning in C. elegans

Associative learning and sensory integration are two behavioral processes that involve the sensation and processing of stimuli followed by an altered behavioral response to these stimuli, with learning requiring memory formation and retrieval. We found that the cellular and molecular actions of scd-2 dissociate sensory integration and associative learning. This was discovered through investigation of a Caenorhabditis elegans mutation (lrn-2 (mm99)) affecting both processes. After mapping and sequencing, lrn-2 was found to be allelic to the gene, scd-2. scd-2-mediated associative learning and sensory integration operate in separate neurons as separate processes. We also find that memories can form from associations that are processed and stored independently from the integration of stimuli preceding an immediate behavioral decision.

Differential expression of the major catalase, KatA in the two wild type Pseudomonas aeruginosa strains, PAO1 and PA14

KatA is the major catalase required for hydrogen peroxide (H₂O₂) resistance and acute virulence in Pseudomonas aeruginosa PA14, whose transcription is governed by its dual promoters (katAp1 and katAp2). Here, we observed that KatA was not required for acute virulence in another wild type P. aeruginosa strain, PAO1, but that PAO1 exhibited higher KatA expression than PA14 did. This was in a good agreement with the observation that PAO1 was more resistant than PA14 to H₂O₂ as well as to the antibiotic peptide, polymyxin B (PMB), supposed to involve reactive oxygen species (ROS) for its antibacterial activity. The higher KatA expression in PAO1 than in PA14 was attributed to both katAp1 and katAp2 transcripts, as assessed by S1 nuclease mapping. In addition, it was confirmed that the PMB resistance is attributed to both katAp1 and katAp2 in a complementary manner in PA14 and PAO1, by exploiting the promoter mutants for each -10 box (p1m, p2m, and p1p2m). These results provide an evidence that the two widely used P. aeruginosa strains display different virulence mechanisms associated with OxyR and Anr, which need to be further characterized for better understanding of the critical virulence pathways that may differ in various P. aeruginosa strains.

High frequency of double crossover recombination facilitates genome engineering in Pseudomonas aeruginosa PA14 and clone C strains

Pseudomonas aeruginosa is a key opportunistic human pathogen. An established procedure to replace a target gene is two-step allelic exchange, i.e. selection of single crossover at homologous sequences and subsequent counter selection to induce double crossover for excision of the suicide vector. In this study, we found that certain strains of P. aeruginosa display a high rate of instant double crossover upon introduction of a suicide vector containing an antibiotic resistance cassette flanked by adjacent sequences for gene replacement, making the counter selection step to achieve the second crossover superfluous. Assessment of a limited panel of target genes commonly showed negligible double crossover with a frequency <20 % in the genetic reference strain PAO1, whereas a high double crossover frequency of >70 % was observed for PA14 and clone C strains. Consequently, for certain P. aeruginosa strains replacement of an ORF by a antibiotic resistance cassette can be shortened by directly selecting for double crossover recombination.

Epidemiology of Pseudomonas aeruginosa in agricultural areas. J Med Microbiol 2018;67:1191-1201. [PMID: 30067169 DOI: 10.1099/jmm.0.000758]

A prevailing opinion is that the strains of Pseudomonas aeruginosa that infects both plants and humans are two separate species. This study strongly disputes that notion until the modern molecular technology proves otherwise. This paper examines a spectrum of strains occurring in nature, their habitats, dissemination, their relationship to clinical strains, and the environmental conditions that favor their colonization of plants. The isolates were obtained from clinical specimens, plants, soil, and water. The identity of these strains was confirmed using pyocin typing and biochemical assays. The data reveal that agricultural soils, potted ornamental plants, hoses, fountains, and faucets frequently harbored P. aeruginosa. However, it was not commonly found in semi-arid areas, suggesting that moisture and high humidity is necessary for colonization and survival. Though found in soil, P. aeruginosa was seldom isolated on edible plant parts. The pathogenicity of various strains on plants was tested by inoculating vegetables, lettuce slices (Lactuca sativa L. "Great Lakes"), celery stalks (Apium graveolens L. var. Dulce], potato tuber slices (Solanum tuberosum L. "Whiterose"), tomato (Lycopersicon esculentum L. Mill), cucumber (Cucumis sativus L.), rutabaga (Brassica campestris L.), and carrot (Daucus carota L. var sativa). There was considerable variation in the strains' ability to cause rot, but no difference was observed between clinical isolates and others from agricultural fields, water, and soil. Two of the clinical isolates from burn patients, P. aeruginosa PA13 and PA14, exhibited the greatest virulence in causing rot in all the plants that were tested, especially on cucumber, lettuce, potato, and tomato. The study discusses how closely the epidemiology of P. aeruginosa relates to many plant pathogens, and the ability of human isolates to colonize plants and food material under favorable conditions. The biochemical and phenotypic similarity among strains from the clinical and agricultural material is strongly indicative that they are the same species and that plants and soil are natural reservoirs for P. aeruginosa.