Abstract
Cold environments dominate Earth’s biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a model organism for cold-adaptation, at both 4 °C and 15 °C, by integrating genomic and phenomic (high-throughput phenotyping) data and comparing the obtained results to the taxonomically related Antarctic bacterium Pseudoalteromonas sp. TB41 (PspTB41). Although the genome size of PspTB41 is considerably larger than PhTAC125, the higher number of genes did not reflect any higher metabolic versatility at 4 °C as compared to PhTAC125. Remarkably, protein S-thiolation regulated by glutathione and glutathionylspermidine appeared to be a new possible mechanism for cold adaptation in PhTAC125. More in general, this study represents an example of how ‘multi-omic’ information might potentially contribute in filling the gap between genotypic and phenotypic features related to cold-adaptation mechanisms in bacteria.
Highlights
Cold environments dominate Earth’s biosphere, hosting complex microbial communities with the ability to thrive at low temperatures
We have carried out a genome-scale comparison of two taxonomically related Antarctic P. haloplanktis strains, and linked the data to their high-throughput phenotypic characterization conducted under 4 °C and 15 °C by means of the Phenotype Microarray technology, revealing great differences for adaptation of bacteria to cold
The COG functional analysis performed on the genome of the two strains revealed at least three main differences: (i) the first one is related to the COG X category (‘No functional class found’), where PhTAC125 or Pseudoalteromonas sp. TB41 (PspTB41) share about 15% of orthologous genes, accounting for about 45% of the genes specific for the two strains (Fig. 1). (ii) The COG category L (‘Replication, recombination, repair’) was enriched in the PspTB41 genome
Summary
Cold environments dominate Earth’s biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. Little is known about the phenotypic features of PhTAC125 expressed at low temperatures (and at the whole cellular level) despite the importance of linking genome functionality and source environmental niche. This is even more important if we consider that a large fraction of the genes from genomic sequencing analysis have no ascribed function and even genes with ascribed functions are primarily based on DNA sequence homology, with little or no direct support of experimental data[33]
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