Are there any generalized molecular principles of thermal adaptation? Here, integrating the concepts of structural bioinformatics, sequence analysis, and classical knot theory, we develop a robust computational framework that seeks for mechanisms of thermal adaptation by comparing orthologous mesophilic‐thermophilic and mesophilic‐hyperthermophilic proteins of remarkable structural and topological similarities, and still leads us to context‐independent results. A comprehensive analysis of 4741 high‐resolution, non‐redundant X‐ray crystallographic structures collected from 11 hyperthermophilic, 32 thermophilic and 53 mesophilic prokaryotes unravels at least five “nearly universal” signatures of thermal adaptation, irrespective of the enormous sequence, structure, and functional diversity of the proteins compared. A careful investigation further extracts a set of amino acid changes that can potentially enhance protein thermal stability, and remarkably, these mutations are overrepresented in protein crystallization experiments, in disorder‐to‐order transitions and in engineered thermostable variants of existing mesophilic proteins. These results could be helpful to find a precise, global picture of thermal adaptation.

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Precise control of protein and messenger RNA (mRNA) degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. However, while molecular factors influencing protein degradation have been extensively explored on a genome scale, and in multiple organisms, such a comprehensive understanding remains missing for mRNAs. Here, we analyzed multiple genome-scale experimental yeast mRNA half-life data in light of experimentally derived mRNA secondary structures and protein binding data, along with high-resolution X-ray crystallographic structures of the RNase machines. Results unraveled a consistent genome-scale trend that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; the lengths of the 5 0 -terminal, 3 0 -terminal, and internal unstructured segments that affect mRNA half-life are compatible with molecular structures of the 5 0 exo-, 3 0 exo-, and endoribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments, and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side comparison of molecular principles underlying controlled protein and mRNA degradation in yeast unravels their remarkable mechanistic similarities and suggests how the intrinsic structural features of the two molecular species, at two different levels of the central dogma, regulate their half-lives on genome scale.

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1 Precise control of protein and mRNA degradation is essential for cellular metabolism and homeostasis. 2Controlled and specific degradation of both molecular species necessitates their engagements with the 3 respective degradation machineries; this engagement involves a disordered/unstructured segment of the 4 substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. Here, we 5 report that mRNAs comprising longer terminal and/or internal unstructured segments have significantly 6 shorter half-lives; the lengths of the 5′ terminal, 3′ terminal and internal unstructured segments that 7 affect mRNA half-life are compatible with molecular structures of the 5′ exo-3′ exoand endo-8 ribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, 9presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene 10 duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments 11and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side 12 comparison of molecular principles underlying controlled protein and mRNA degradation unravels their 13 remarkable mechanistic similarities, and suggests how the intrinsic structural features of the two 14 molecular species regulate their half-lives on genome-scale and during evolution. 15 Keywords 16 Messenger RNA, mRNA stability, mRNA degradation, Xrn1, Exosome, Rrp44, protein-RNA 17 interaction 18 19 20 21 22 23 24 25 26 27 28 29 30 31 P a g e | 3