Thermophilic Bacteria Strictly Obey Szybalski's Transcription Direction Rule and Politely Purine-Load RNAs with Both Adenine and Guanine

Abstract

When transcription is to the right of the promoter, the "top," mRNA-synonymous strand of DNA tends to be purine-rich. When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich. This transcription-direction rule suggests that there has been an evolutionary selection pressure for the purine-loading of RNAs. The politeness hypothesis states that purine-loading prevents distracting RNA-RNA interactions and excessive formation of double-stranded RNA, which might trigger various intracellular alarms. Because RNA-RNA interactions have a distinct entropy-driven component, the pressure for the evolution of purine-loading might be greater in organisms living at high temperatures. In support of this, we find that Chargaff differences (a measure of purine-loading) are greater in thermophiles than in nonthermophiles and extend to both purine bases. In thermophiles the pressure to purine-load affects codon choice, indicating that some features of their amino acid composition (e.g., high levels of glutamic acid) might reflect purine-loading pressure (i.e., constraints on mRNA) rather than direct constraints on protein structure and function.

Codon usage between genomes is constrained by genome-wide mutational processes

“…The results of ref. 24 demonstrate that selection related to elevated growth temperature plays a role in establishing codon bias in thermophilic organisms, which may be related to the tendency for thermophilic organisms to systematically load RNA sequences with purines (25). However, our results emphasize the importance of mutational (not related to protein expression) forces in determining global trends in codon bias.…”

“…In addition, global forces differentiate the codon bias of genes between different organisms: species-specific codon bias is strongly correlated with overall genome percentage GC content (22,23), genes from organisms with similar phylogeny or with similar tRNA content have similar codon bias (22), and an organism's optimal growth temperature influences the codon bias of its genes (24). Most of these global forces are thought to be mutational, acting on all DNA sequences, although it has also been argued that growth temperature exerts a selective force on mRNA structure (25) and codon bias (24). Although both selection and mutation are clearly important for establishing codon bias, the relative importance of selection and mutation has been difficult to define in general.…”

Natural and artificial RNAs occupy the same restricted region of sequence space

“…However, the probability that a compatible sequence, once generated, will fold into the motif correctly is highest in sequences that are biased toward A, perhaps because of the unique contribution of A to base stacking (Gutell et al 2000). The combination of these two factors explains the overall compositional bias in the region in which randomly generated sequences are most likely to be functional, and suggests that the biases stem from rules of RNA selfassembly (Schultes et al 1999) rather than selection (Lao and Forsdyke 2000). Note that part of the contribution to self-assembly is that the sequences contain regions compatible with stems, which we count under the ''sequence requirements'' rather than the ''folding requirements'' in this study.…”

“…Many functional RNA molecules show a preference for purines (Elson and Chargaff 1955;Lao and Forsdyke 2000), and there is far more variation along the GC axis (i.e., the axis where the compositions of G and C are the same, as well as of A and U) than along the two other orthogonal axes of composition (Schultes et al 1997(Schultes et al , 1999Smit et al 2006). These patterns are replicated in both ribosomal RNA subunits from all three domains of life, although these key features may be due to selforganization of RNA during secondary structure assembly rather than due to selection for specific compositions (Smit et al 2006).…”

Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

“…As noted by other authors (e.g. Lao and Forsdyke 2000, Lambros et al 2003, and Paz et al 2004, the coding regions of many thermophilic genomes are purineloaded and possess codon biases that reflect that loading. Our method of using a "virtual coding strand" eliminated the variable of gene orientation.…”