Expression and Function of Different Guanine-Plus-Cytosine Content 16S rRNA Genes in Haloarcula hispanica at Different Temperatures

Abstract

The halophilic archaeon Haloarcula hispanica harbors three ribosomal RNA (rRNA) operons (rrnA, rrnB, and rrnC) that contain the 16S rRNA genes rrsA, rrsB, and rrsC, respectively. Although rrsB and rrsC (rrsBC) have almost identical sequences, the rrsA and rrsBC sequences differ by 5.4%, and they differ by 2.5% with respect to guanine-plus-cytosine content (PGC). The strong correlation between the typical growth temperatures of archaea and PGC of their 16S rRNA genes suggests that H. hispanica may harbor different 16S rRNA genes having different PGC to maintain rapid growth in a wide range of temperatures. We therefore performed reverse transcription-coupled quantitative PCR to assess expression levels of rrsA (PGC, 58.9%) and rrsBC (PGC, 56.4–56.5%) at various temperatures. The expression ratio of rrsA to rrsBC increased with culture temperature. Mutants with complete deletions of one or two of the three rRNA operons were constructed and their growth rates at different temperatures compared to that of the wild-type. The growth characteristics of the rRNA operon single-mutant strains were indistinguishable from the wild-type. The rRNA operon double-mutant strains maintained the same temperature range as wild-type but displayed reduced growth rates. In particular, the double-mutant strains grew much slower than wild-type at low temperature related to minimum growth temperature of the wild-type. On the other hand, at physiologically high temperatures the wild-type and the double-mutant strain which harbors only rrnA with high-PGC rrsA grew significantly faster than the double-mutant strain which harbors only rrnC with low-PGC rrsC. These findings suggest the importance of 16S rRNAs transcribed from rrsA with high-PGC in maintaining rapid growth of this halophilic archaeon at raised growth temperatures.

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

“…Haloarcula strains have been isolated from solar salterns and salt lakes in deserts (Juez et al 1986 ; Oren et al 1990 ), where large day-night temperature variations are observed (Wieland et al 2005 ; Sima et al 2013 ; Andrade et al 2015 ; Naghoni et al 2017 ). These strains have two or three copies of rRNA operons ( rrnA , rrnB and rrnC ) in their genomes (Baliga et al 2004 ; Liu et al 2011 ; Ding et al 2014 ; Yun et al 2015 ; Sato et al 2017 ). Each rRNA operon contains a 5S rRNA gene, a 16S rRNA gene ( rrsA , rrsB or rrsC , respectively) and a 23S rRNA gene.…”

“…The 23S rRNA gene sequences show limited diversity (0.3–2%). For 16S rRNA gene sequences, rrsB and rrsC ( rrsBC ) show almost identical sequences, whereas rrsA shows different sequences (4–6%) from rrsBC (Mevarech et al 1989 ; Mylvaganam and Dennis 1992 ; Dennis 1999 ; Sato et al 2017 ). The different sequences of 16S rRNA genes were first reported in Haloarcula marismortui (Mevarech et al 1989 ).…”

“…Sato et al ( 2017 ) used Haloarcula hispanica to verify a hypothesis that high- P GC rrsA (58.9%) and low- P GC rrsBC (56.4–56.5%) are expressed at high and low temperatures, respectively. They also investigated the physiological advantage of harbouring high- and low- P GC 16S rRNA genes with respect to the growth of H. hispanica under various temperature conditions.…”

“…At the T max , i.e., 50 °C, the expression level of rrsA was significantly higher than those of rrsBC . Sato et al ( 2017 ) also constructed mutant strains with only one of three rRNA operons and cultivated the strains at various temperatures. The mutant strain harbouring only rrnA including high- P GC rrsA grew significantly slower than the wild-type strain at the T min 25 °C, but it grew as fast as the wild-type at 45 °C ( T opt ) and 50 °C ( T max ).…”

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes

“…GC contents could confound this correlation, because G:C base pairs are linked by three hydrogen interactions, while A:T and A:U base pairs by only two hydrogen bridges. Hence GC contents usually increases with temperature, as it confers higher stability to structures formed by nucleotide chains [188] , [189] , [190] . However, GC codon content does not correlate with body temperature for mitochondria of the above mentioned lepidosaurian species (r = − 0.0425, one-tailed P = 0.379).…”