A positive correlation between GC content and growth temperature in prokaryotes

Abstract

Background GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. Results With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation. Conclusions This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C

“…Then, we randomly drew 155 bacteria from the 681 bacteria 1000 times. In > 95% rounds of resampling, the positive correlations became statistically non-significant ( p > 0.05) ( Hu et al, 2022 ). The results suggest that the effective sample size in phylogenetically related data is much smaller than the census number of the analyzed lineages.…”

Senecavirus A Enhances Its Adaptive Evolution via Synonymous Codon Bias Evolution

“…In the long neck-chain formed by RNA secondary structures, the GC base pair acquires three hydrogen bonds, which contribute to the structural stability of RNA secondary structures [ 50 , 51 ]. Studies have shown that the genome temperature optima and radiation resistance positively correlate with GC content owing to improved RNA structural stability [ 52 , 53 ]. Another benefit of increased GC content is that it promotes mRNA stability.…”

Molecular Characterization and Phylogenetic Analysis of Pseudomonas aeruginosa Obtained from Wound Infection

“…Previous studies on based on other microorganisms indicate that there is a direct relation between the molecular composition of nucleotides (primarily GC content) and growth temperatures (Topt)of microbes (Rudi, 2009;Hu et al, 2022). Moreover, it has been previously established the structural RNAs are more sensitive to temperature variation in comparison to genomic DNA (Hu et al, 2022). Therefore, the molecular composition (GC and AT content) in Pseudomonas species was analyzed to evaluate the role of GC content with respect to the survival of the bacterium.…”