RNAs are widespread in all biological systems (except for DNA viruses) and are involved in multi-laterally adapted systems that control numerous cellular processes, the magnitudes of which are still being explored. Principally, there are two broad categories of RNAs, namely coding and non-coding (ncRNA)—this summary refers only to the latter.
ncRNA molecules, such as housekeeping RNAs (ribosomal, transfer, small nuclear, and small nucleolar RNAs) and the thousands of regulatory RNAs that are the subject of ongoing intense studies, can form structures ranging from primary to quaternary levels. These are as follows: primary structures of approximately 22 nucleotides, as in guided single stranded microRNAs (miRNA); double stranded miRNA interference segments exist as secondary shapes; tertiary level structures which are broadly composed of RNAs and protein complexes called ribonucleoproteins as in RNase P and RNase MRP (Mitochondrial RNA Processing) complexes; at the quaternary level, again in conjunction with proteins, various co-factors and metal ions (e.g., Zn), RNAs form huge ncRNA-nanomachines as in spliceosomes, the Varkud satellite (VS), RNA-induced silencing complex (RISC) and ribosomes. These structures are multifunctional and are broadly regulatory, being involved in gene regulation as well as interfering with and processing both small and large RNAs [54
]. Such processing actions are well orchestrated, even to the point of efficient shredding of any unwanted RNAs—for example “used” coding mRNA within the cell is degraded rapidly (via RISC centres) so as to prevent them from being translated further. Recent discoveries have also demonstrated that ncRNAs can act as riboswitches (e.g., glmS
ribozymes), whereby they regulate their own activity and perform genetic control by a metabolite binding mRNA [55
]. They can control the activities of some plasmids (e.g., R1 plasmid of E. coli
) via antisense RNA as in the hok/sok
]. It is suggested by Kotakis (also as outlined later) that ncRNA-directed transfer of genes can occur from “organellar” entities (e.g., chloroplasts) to the nuclei of eukaryotes [57
]. Furthermore, ncRNAs can act as shielding triggers against invading mobile genetic elements, thereby affording protection against incoming attacks by any “parasitic” nucleotide sequences found in the environment [58
]. ncRNAs, in addition to their ribozymatic activities and ability to carry genetic codes (e.g., influenza, an RNA virus), are significant in that the hallmark of their modular architectural structure implies that structural and possible functional similarities exist among them [54
]. A unique aspect of ncRNAs is that they are highly conserved and so it is thought that they are molecular relics which delineated a “hypothetical” entity called LUCA, which pre-dated the three domains of life, namely Archaea, Bacteria and Eukarya.
The conserved nature of ncRNAs allowed Jheeta (Chairman, NoR HGT and LUCA) to postulate that it is highly feasible that these ncRNA molecules could still have overall control of cellular activity and perhaps this is the reason why DNA replication still requires this ncRNA primer. This is particularly relevant as there are large numbers of newly discovered ncRNAs whose functions are still to be explained and validated.