HDV Ribozyme Encode Ribopepzyme

Ribozyme, discovered by Cech in 1981, is a kind of single-strand RNA molecule who serves to cleave RNA substrate via specific base pairing. Thus, the proposal RNA could have the enzyme catalytic activity appeared. Human hepatitis delta virus (HDV) is a satellite virus of human hepatitis B virus. The genome of HDV is a single-stranded circular RNA molecule (1680 nucleotides) that is thought to replicate by a rolling circle mechanism. During replication both genomic and antigenomic strands of HDV RNA undergo a self-cleavage reaction (ribozyme). The HDV ribozyme motif belongs to a group of small ribozymes, such as hammerhead, hairpin and Neurospora VS ribozymes. This ribozyme just have only one specific cleavage site which locates between 688nt/689nt in genome RNA and 903nt/904nt in antigenome RNA. If we distinguish the ribozyme nucleotide sequence further, it could be separated into two parts, one is the substrate, and the other is the enzyme. Both of them construct the trans acting mode.Since the emergence of natural ribozymes,'RNA World'is supported by most of biologists. These findings lent increased credibility to the hypothesis of an RNA world, where RNA served both as the genetic material and the principal cellular enzyme, probably assisted in the latter role by metal ions, amino acids and other small molecule cofactors. The RNA world hypothesis posits that as cellular metabolism became more sophisticated, increasing demandson biocatalysts provided the impetus for the transition to protein enzymes. Descendants from this proposed RNA-dominated era inhabit today's world in the form of naturally occurring ribozymes present in organisms ranging from bacteria to humans. If this is true, part of the catalytic function of modern protein enzymes should inherit from catalytic RNA molecules.Via the analysis of nucleotide sequences of natural HDV ribozyme and of the smallest trans-acting genomic HDV ribozyme (tMTS-U), we found that a basic peptide always exists if we translate those nucleotide sequences into amino acid sequence. However, the basic peptide is the essential element which could ensure to form peptide-RNA complex. After the chemical synthesis of three basic peptides and identifying the reaction between peptides and RNA, surprisingly, those peptides have the cleaving RNA substrate activity as ribozymes do. For this reason, we name them'ribopepzyme'. Three peptides are RPZHDV(+),RPZHDV(-),RPZSHDV, respectively. The activity of ribopepzyme is lower than RNase and similar to ribozyme. It could be affected by pH and results have tremendous differences when pH ranges from 4-9. The pH profile shows a shell shape.Especially, divalent cations suppress ribopepzyme activity strongly which is different from ribozyme completely. Besides, the flexibility and specificity of ribopepzyme enhance in a certain extent. It means to say, ribopepzyme could cleave kinds of RNA substrates. UV spectrum and CD spectrum were considered to determine the process of peptide and RNA interaction. When forming the peptide-RNA complex, therewould be a series of conformation transition, the major transition is from random coil toα-helix conformation. This result just is in good agreement with our prediction. Together those above and some bioinformation part, we believe that the catalytic mechanism should be the general acid-base mechanism. Arginine would play an important role that is involved in positioning and polarizing the phosphate of the scissile phosphodiester bond and/or stabilization of the transition state. If arginine serves as proton donor, serine would be the best candidate to be proton acceptor.The emergence of ribopepzme indicates that the catalytic function could transfer in the biology world. Although the activity is lower than RNase, the constitution and structure are simper than RNase. It just shows the character of ancient molecule. In other words, ribopepzyme would be the ancestor of modern RNase. If we regard this process as a kind of evolution, from ribozyme to ribopepzyme displays a direct evolution wandering between different molecular species. For the diversity of ribozyme sequence and function, it could be cited as a strategy for developing versatile catalytic peptides. More and more novel function molecules could emerge by this way.