Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere

Abstract

Results from previous experiments indicated that the Gram-negative α-proteobacterium Serratia liquefaciens strain ATCC 27592 was capable of growth under low temperature (0 °C), low pressure (0.7 kPa), and anoxic, CO₂-dominated atmosphere-conditions intended to simulate the near-subsurface environment of Mars. To probe the response of its transcriptome to this extreme environment, S. liquefaciens ATCC 27592 was cultivated under 4 different environmental simulations: 0 °C, 0.7 kPa, CO₂ atmosphere (Condition A); 0 °C, ~101.3 kPa, CO₂ atmosphere (Condition B); 0 °C, ~101.3 kPa, ambient N₂/O₂ atmosphere (Condition C); and 30 °C, ~101.3 kPa, N₂/O₂ atmosphere (Condition D; ambient laboratory conditions). RNA-seq was performed on ribosomal RNA-depleted total RNA isolated from triplicate cultures grown under Conditions A-D and the datasets generated were subjected to transcriptome analyses. The data from Conditions A, B, or C were compared to laboratory Condition D. Significantly differentially expressed transcripts were identified belonging to a number of KEGG pathway categories. Up-regulated genes under all Conditions A, B, and C included those encoding transporters (ABC and PTS transporters); genes involved in translation (ribosomes and their biogenesis, biosynthesis of both tRNAs and aminoacyl-tRNAs); DNA repair and recombination; and non-coding RNAs. Genes down-regulated under all Conditions A, B, and C included: transporters (mostly ABC transporters); flagellar and motility proteins; genes involved in phenylalanine metabolism; transcription factors; and two-component systems. The results are discussed in the context of Mars astrobiology and planetary protection.

Figure 1

Bioinformatics work flow. Total RNA was isolated, and libraries were constructed and sequenced. Raw reads were filtered for quality and sequence contaminants and aligned to the reference genome of S. liquefaciens strain ATCC 27592 to calculate differential expression levels.

Figure 2

Venn diagram depicting the number of differentially up-regulated genes (left) and down-regulated genes (right) identified from Conditions A, B, and C compared to Condition D. Numbers in overlapping regions denote genes shared between the different comparisons and numbers in non-overlapping regions denote genes unique to each comparison. See Table 1 for description of the conditions.

Figure 3

PCA plot of the data. Depicted are triplicate samples from Condition (A) (red) (B) (blue), (C) (green), and (D) (black). See Table 1 for description of the conditions.

Figure 4

Up-regulated genes sorted by KEGG orthology. The number of genes of a particular KEGG pathway are depicted as a fraction of the total number of genes classified in that pathway in the genome of S. liquefaciens. See Table 1 for description of the conditions.

Figure 5

Down-regulated genes sorted by KEGG orthology. The number of genes of a particular KEGG pathway are depicted as a fraction of the total number of genes classified in that pathway in the genome of S. liquefaciens. See Table 1 for description of the conditions.