Genome-scale conserved molecular principles of mRNA half-life regulation

Abstract

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

Comparison of Xrn1 and Rat1 5′→3′ exoribonucleases in budding yeast supports the unique role of Xrn1 in co-translational mRNA decay

“…Rat1 is smaller (116 kDa in yeast) and also functions in several nuclear RNAs decay pathways, including those linked to RNA pol II-coupled mRNA transcriptional termination (Kim et al, 2004). Both Xrn1 and Rat1 substrates are single-stranded unstructured 5'Phosphate end with lengths of at least four nucleotides (Nagarajan et al, 2013;Basu et al, 2021). Many of Xrn1 functions require only two-thirds of the molecule, which is homologous to Rat1.…”

“…SKI2 encodes a co-factor of the 3'-5' RNA exosome, which is essential for its cytoplasmic function . The enzymatic mechanism of Rat1 is assumed to be processive and similar to that of Xrn1 because it shares the active site and shows extensive conservation around it (Nagarajan et al, 2013;Basu et al, 2021). Rat1 is also a deNADing enzyme similar to Xrn1 (Sharma et al, 2022).…”