Temperature-dependent expression of different guanine-plus-cytosine content 16S rRNA genes in Haloarcula strains of the class Halobacteria

Haloarcula strains, which are halophilic archaea, harbour two to three copies of 16S rRNA genes (rrsA, rrsB and rrsC) in their genomes. While rrsB and rrsC (rrsBC) show almost identical sequences, rrsA shows 4–6% sequence difference and 1–3% guanine-plus-cytosine content (P(GC)) difference compared to rrsBC. Based on the strong correlation between the P(GC) of 16S rRNA genes and the growth temperatures of the prokaryotes, we hypothesised that high-P(GC)rrsA and low-P(GC)rrsBC are expressed at high and low temperatures, respectively. To verify the hypothesis, we performed sequence analyses and expression surveys of each 16S rRNA gene in eight Haloarcula strains. The secondary structure prediction of the 16S rRNA via computer simulation showed that the structural stability of 16S rRNAs transcribed from rrsA was higher than that of 16S rRNAs transcribed from rrsBC. We measured expression levels of rrsA and rrsBC under various temperature conditions by reverse-transcriptase quantitative PCR. The expression ratio of high-P(GC)rrsA to low-P(GC)rrsBC increased with cultivation temperatures in seven of eight Haloarcula strains. Our results suggest that the transcription of high-P(GC)rrsA and low-P(GC)rrsBC may be regulated in response to environmental temperature, and that 16S rRNAs transcribed from high-P(GC)rrsA function under high temperature conditions close to the maximum growth temperature. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10482-018-1144-3) contains supplementary material, which is available to authorized users.