Temperature dependent selection in microbial genomes: An examination of intergenic regions and GC composition

Background/Question/Methods

It has long been argued that increased temperature may result in altered patterns of Guanine-Cytosine (GC) composition in microbial genomes due to the higher thermal stability of the GC base pairing.  However the manifestation of this selective pressure remains elusive.  It has been shown that no correlation exists between genome wide GC content and optimal growth temperature.  However, contemporary DNA sequencing technologies make it possible to address such questions more robustly.  Specifically, it is possible to expand the investigation of temperature and GC composition across thousands of genomes and to specific genomic features such as intergenic regions: the noncoding stretches between genes.  Intergenic regions are theoretically free of other selective pressures acting on sequence conservation and hence should show the most dramatic response to selection from higher temperatures.  Using the Integrated Microbial Genomes online database, I examine the distribution of intergenic GC content and compare across all available genomes of bacteria and archaea.  Additionally, I calculate the average length of intergenic DNA sequences containing no Guanines or Cytosines.  I examine the relationship of these factors as compared between mesophiles and thermophiles, categories which are used as proxies for optimal growth temperature due to the incomplete metadata associated with some genomes.

Results/Conclusions

Among both bacteria and archaea, thermophiles show no statistically significant difference from mesophiles in mean or variance of intergenic GC content.  The same pattern is observed when considering the average as well as the maximum tolerated length of intergenic DNA sequences containing no Guanines or Cytosines.  While a higher percent GC content has been hypothesized to stabilize DNA under high temperatures, these results indicate that temperature is not a factor in the evolution of GC composition in microbial genomes.  Due to a lack of other selective pressures (e.g. sequence conservation) as compared to the rest of the genome, intergenic regions would be expected to be the most heavily affected by a universal genomic selective pressure such as temperature.  The lack of such an effect contradicts previous genomic theory as well as some previous results utilizing smaller samples of data.  This implies the existence of other adaptations within thermophiles to stabilize their genomes, such as altered ionic concentrations or DNA supercoiling.