Abstract 1553: Delineating the role of multiple copies of RNA binding domains in human nucleolin and its homologs using a computational approach

Abstract

Abstract All eukaryotes have nucleoli, the sub-nuclear compartments where ribosomes synthesis occur. Nucleolin (NCL), an abundant RNA binding phosphoprotein,constitutes 5-10% of total nucleolar proteins. This multifunctional protein plays defined role/s in many critical cellular processes e.g. chromatin remodeling, ribosome biogenesis, transcriptional and translational regulation of various non-coding as well as coding RNAs. NCL binds to its target RNAs via two or multiple RNA binding domains (RBDs) to control gene expression during normal cell cycle as well as during cellular response to stress. A variety of tumors express elevated levels of NCL where NCL plays a direct role/s in increasing expressions of genes involved in cell survival, angiogenesis and metastasis. A comparison of NCL in various organisms shows that it is highly conserved, especially in its RNA binding domains that can vary in number (2 to 4 consecutive domains). Interestingly, the individual NCL-RBDs are more conserved across different species rather than within the same protein. RBDs are known to interact in pairs with RNA via RNA recognition motifs called RNP motifs, and complementary nucleic acid motifs or elements in RNA allow interaction with NCL. Vertebrate NCL proteins contains four RBDs, however most studies have focused only on the role/s of RDB 1,2; none probing the possible functional redundancy of the additional RBDs nor identifying any target-specificity for the RBD 3,4 in human NCL and other homologs. Earlier data from our lab suggested RBD 3,4 can bind RNA in a structurally analogous manner to RBD1,2 albeit with altered affinity. Here, we continue this research by investigating various homologs of human NCL to better understand the conserved mechanism of its interaction with RNA and whether the additional RBDs, are in fact, redundant in function. To test this hypothesis, RBDs from various homologs were modeled using template based methods and analyzed by a combination of sequence and structure analysis tools. We show that there are key residue differences in individual RBDs from various homologs that potentially manifest as differences in binding affinities. This study reveals new insights into NCL RBD function and describes the evolution of RBD function with respect to nucleic acid binding. Citation Format: Kamrun Begum, Ruchama Chaya Steinberg, Anjana Saxena, Shaneen Singh. Delineating the role of multiple copies of RNA binding domains in human nucleolin and its homologs using a computational approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1553. doi:10.1158/1538-7445.AM2017-1553