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Identification and Characterization of Cryptic Extremophile Traits by Experimental Evolution

ABSTRACT: Extremely thermoacidophilic Crenarchaeota belonging to the family Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. However, the pH extremes of these habitats often exceed the acid tolerance of type species and strains. Here, experimental evolution was used to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains are named super acid resistant crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance while genome and transcriptome resequencing provided insights into the underlying mechanisms responsible for evolved thermoacidophily. Transcriptomics of the evolved strains indicates that their unique phenotype may be due to an increased rate of membrane turnover under strong acid conditions.

ORGANISM(S): Saccharolobus solfataricus

PROVIDER: GSE76423 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA307257

REPOSITORIES: GEO

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Project description:Listeria monocytogenes is a gram-positive, food-borne pathogen responsible for invasive infections with high overall mortality. Early host defenses encountered by L. monocytogenes following ingestion include low pH of the stomach and bile present in the small intestinal lumen. We hypothesized that “epidemic” strains are better able to withstand exposure to low pH and bile encountered in the gastrointestinal tract as compared to most “environmental” strains. Furthermore, we hypothesized that epidemic and environmental strains would have distinct transcriptional programs upon exposure to these conditions. Our treatments included 1 hr exposure to acid (pH 5.5 and 3.5) and bile (0.3%) stress. Strains were pre-exposed to pH 5.5 (1 hr) before being treated with pH 3.5. We used a collection of 12 previously characterized epidemic and environmental strains and each strainXtreatment combination included 3 biological replicates for each microarray experiment. All microarray experiments were two color competitive hybridizations that paired experimental conditions with the same strain at neutral pH for acid stress and pH 5.5 for bile stress. Transcriptomes of environmental strains exposed to acid and bile stress showed remarkably greater number of genes with differences of ≥2-fold expression levels as compared to epidemic strains (5 and 7, respectively). Environmental strains were characterized by up-regulation of several stress related genes and down-regulation of several cell envelope biosynthesis and virulence related genes, suggesting that complex regulatory networks orchestrate the cellular changes in the environmental strains to overcome stressful environments. The transcriptome of epidemic strains, in contrast, showed muted responses to these stress conditions implying their pre-adaptability to acid and bile stress encountered during natural infection that may enable epidemic strains to survive and become “primed” for subsequent colonization and infection in the lower gastrointestinal tract. Keywords: stress response, comparative transcriptomics, acid-adaptation, differential virulence, acid-stress response, bile-stress response

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Identification and Characterization of Cryptic Extremophile Traits by Experimental Evolution

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