Products of ribosomal protein (RP) genes have been found to play extra-ribosomal roles that range from DNA repair to RNA splicing. Their association with congenital disorders or cancers has also been widely documented. However, the relatively large number of different RPs, each with perhaps unique biological roles, has compounded the comprehensive elucidation of the physiological functions of each RPs. Experimental functional studies on the many and variegated RPs are labour intensive, time-consuming and costly. Moreover, experimental studies unguided by theoretically insights entail inaccurate results. Therefore, knowledge on the actual roles of these proteins remains largely undefined. A valid alternative is the use of bioinformatics resources to computationally predict functional roles of these biomolecules. Findings from such in silico studies of the RPS3 are reported herein. We reveal an array of possible extra-ribosomal functions that includes regulation of transcription (including via NF-κB-mediated, POK-induced and DNA-dependent), regulation of p53 activities and its stabilisation, inflammatory immune response, modulation of nNOS activities, and anti-oxidative capabilities. Our findings provide computational prediction of de novo extra-ribosomal functions of RPS3. These results will enhance the theoretical basis for designing future experimental studies on elucidating its definitive physiological roles.
Extra-ribosomal functions of ribosomal proteins have been widely accepted albeit an incomplete understanding of these roles. Standard experimental studies have limited usefulness in defining the complete biological significance of ribosomal proteins. An alternative strategy is via in silico analysis. Here, we sought a sequence-to-structure-to-function approach to computationally predict the extra-ribosomal functions of a subset of ribosomal proteins of the small ribosome subunit, namely RPS12, RPS19, RPS20 and RPS24. Three-dimensional structure constructed from amino acid sequence was precisely matched with structural neighbours to extrapolate possible functions. Our analysis reveals new logical roles for these ribosomal proteins, of which represent important information for planning experimental and further in silico studies to elucidate their physiological roles.
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