Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species

Abstract

BackgroundThe environment has been playing an instrumental role in shaping and maintaining the morphological, physiological and biochemical diversities of prokaryotes. It has been debatable whether the whole-genome Guanine-Cytosine (GC) content levels of prokaryotic organisms are correlated with their optimal growth temperatures. Since the GC content is variable within a genome, we here focus on the correlation between the genic GC content levels and the temperature range conditions of prokaryotic organisms.ResultsThe GC content levels in the coding regions of four genes were consistently identified as correlated with the temperature range condition when the association analysis was applied to (i) the 722 mesophilic and 93 thermophilic/hyperthermophilic organisms regardless of their phylogeny, oxygen requirement, salinity, or habitat conditions, and (ii) partial lists of organisms when organisms with certain phylogeny, oxygen requirement, salinity or habitat conditions were excluded. These four genes are K01251 (adenosylhomocysteinase), K03724 (DNA repair and recombination proteins), K07588 (LAO/AO transport system kinase), and K09122 (hypothetical protein).To further validate the identified correlation relationships, we examined to what extent the temperature range condition of an organism can be predicted based on the GC content levels in the coding regions of the selected genes. The 84.52% accuracy for the complete genomes, the 84.09% accuracy for the in-progress genomes, and 82.70% accuracy for the metagenomes, especially when being compared to the 50% accuracy rendered by random guessing, suggested that the temperature range condition of a prokaryotic organism can generally be predicted based on the GC content levels of the selected genomic regions.ConclusionsThe results rendered by various statistical tests and prediction tests indicated that the GC content levels of the coding/non-coding regions of certain genes are highly likely to be correlated with the temperature range conditions of prokaryotic organisms. Therefore, it is promising to carry out “reverse ecology” and to complete the ecological characterizations of prokaryotic organisms, i.e., to infer their temperature range conditions based on the GC content levels of certain genomic regions.

Phenotypic divergence of thermotolerance: Molecular basis and cold adaptive evolution related to intrinsic DNA flexibility of glacier‐inhabitingCryobacteriumstrains

“…By analysing most bacterial families, Musto et al (2004Musto et al ( , 2006 proposed a correlation between the optimal growth temperature (T OPT ) and the genome GC content in prokaryotes. This proposal was supported by the result of Zheng and Wu (2010). However, this finding is controversial.…”

Rapid Bioinformatic Identification of Thermostabilizing Mutations

“…However, as the number of sequenced genomes and characterized species increases, the sensitivity of these methods will also increase. Additionally, if modeling of growth temperature is used (30,58,59), many more OGTs can be approximated. Increasing the OGT and sequence data will improve the statistical power of both methods and allow investigators to study exclusively eukaryotic genes, for which few thermophilic orthologs are available (Fig.…”

The Family Bradyrhizobiaceae

“…In contrast, the DNA GC content among all of the genera ranges from 59 % to 71 %, and the genus Afipia has the highest variation in this parameter (7.5 %). All of the species studied from the genera belonging to the family Bradyrhizobiaceae can be considered C+G-rich bacteria, which may relate to their mesophilic characteristics (Zheng and Wu 2010).…”