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Chapter 4 : How Nucleic Acids Cope with High Temperature
Category: Applied and Industrial Microbiology; Environmental Microbiology
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This chapter discusses the question of coping up of the nucleic acids with high temperature at the polynucleotide level—RNA, DNA, and their ribonucleoprotein derivatives (RNP/DNP). When nucleic acids are heated in aqueous solution, two types of phenomena take place: denaturation of their architecture and chemical degradation of their building blocks. In vivo, the half-lives of both RNA and DNA of thermophilic organisms are usually longer than that estimated in vitro, attesting to cellular strategies protecting the nucleic acids against the deleterious effects of heat. Despite the susceptibility of certain modified bases and of the ribonucleotide chain to thermal degradation, most naturally occurring tRNAs (especially those from hyperthermophilic organisms) appear fairly resistant to heat denaturation. Despite the intrinsic potentiality of nucleic acids to degrade at elevated temperatures, many hyperthermophiles can survive at very high temperatures approaching or even surpassing the boiling point of water. The majority of stable cellular RNAs, such as tRNA and rRNA molecules, contain a variety of modified nucleosides. Stabilizing strategies of RNAs and DNAs may be classified into three major categories: (i) those which are intrinsic to the chemical structures of the nucleic acids; (ii) those which are dependent on extrinsic interactions with other biomolecules; and (iii) those which are dependent on a battery of enzymes for detecting and repairing the DNA damage or to constantly renew functional RNA molecules. Genetic approach using mutant strains mutated in one or more biomolecules supposedly involved directly or indirectly in stabilization of nucleic acids should be more systematically used.
Strategies for thermostabilization of nucleic acids. In boxes are mentioned the various factors that allow a thermophilic organism to protect their nucleic acids against the deleterious effect of heat. A clear distinction between the giant extended macromolecule DNA and the more compact smaller RNA molecules has to be made. For details, see text.
Phylogenetic distribution of modified nucleosides in RNA from the three domains of life. Abbreviations of modified nucleosides are the conventional ones. For details, including the chemical structures, see in Limbach et al. (1995) . Lines point out which ones among the hypermodified nucleosides in Archaea correspond to non-ribose methylated counterparts in Eukarya or Bacteria.
Schematic representation of tertiary interactions in tRNA structure. Numbers indicate conventional tRNA positions. Abbreviations of modified nucleosides are those of Fig. 2 ; see also in Sprinzl and Vassilenko (2005) . Each nucleotide involved in stacking or base pairing with another nucleotide is represented by a rectangle. The rectangles representing nucleotides of the D-loop are in gray, while those representing nucleotides in the T-loop as well as nucleotides U8 and C48 located in between two stems are in white. Other parts of the tRNA molecule are represented by lines. Inside the dotted circle are elements that contributed to the 3D interaction, allowing an L-shaped spatial conformation to be formed from the 2D cloverleaf structure (see also Fig. 4 ). A wire representation of the 3D conformation is also indicated on the right side.
Main factors allowing tRNA molecules to function at high temperatures. On the left part are conventional schematic representations of 2D and 3D structures of tRNA. The remarkable features that are characteristic of a tRNA from a hyperthermophilic organism are indicated on the right side. In the boxes in the central part are indicated the various factors that allow a thermophilic organism to protect their nucleic acids against the deleterious effect of heat. For details, see text. Numbers indicate conventional tRNA positions; letters correspond to bases A, C, G, and U; R for purine, Y for pyrimidine, and N for any base.