Immobilization of Proteins in the Nucleolus by Ribosomal Intergenic Spacer Noncoding RNA

Abstract

Cellular pathways are established and maintained by stochastic interactions of highly mobile molecules. The nucleolus plays a central role in the regulation of these molecular networks by capturing and immobilizing proteins. Here, we report a function for noncoding RNA (ncRNA) in the regulation of protein dynamics of key cellular factors, including VHL, Hsp70 and MDM2/PML. Stimuli-specific loci of the nucleolar intergenic spacer produce ncRNA capable of capturing and immobilizing proteins that encode a discrete peptidic code referred to as the nucleolar detention sequence (NoDS). Disruption of the NoDS/intergenic RNA interaction enables proteins to evade nucleolar sequestration and retain their dynamic profiles. Mislocalization of intergenic ncRNA triggers protein immobilization outside of the nucleolus, demonstrating that these ncRNA species can operate independently from the nucleolar architecture. We propose a model whereby protein immobilization by ncRNA is a posttranslational regulatory mechanism.

Principles of protein targeting to the nucleolus

“…In this study, the deletion of arginine motifs in the NoDS of Hsp70 prevents nucleolar accumulation as well as the precipitation of a peptide NoDS failed without arginines in the motif. 60 Sequence alignment of the NoLS for the human La protein with several other nucleolar localization domains of human proteins revealed a (R/K) (R/K) £ (R/K) motif appearing frequently as single or multiple copies and similar motifs had been known before. 61,62 The importance of arginines has also been shown for a number of RNA binding proteins with arginine rich motifs.…”

Firefly luciferase mutants as sensors of proteome stress

“…Key stress-related proteins like Hsc70/Hsp70 immediately translocate to the nucleolus during heat stress or acidosis (Audas et al, 2012;Banski et al, 2010;Welch and Feramisco, 1984).…”

Management of rRNA Transcription Activity in a Human Genome

“…Four stimuli-specific loci producing their own RNAs are currently denoted in the rIGS. They were termed IGS27RNA, IGS22RNA, IGS16RNA, and IGS pRNA [26][27][28]. Functional studies of these molecules have revealed new mechanisms for the regulation of rRNA expression, as well as a novel posttranslation regulatory pathway termed the nucleolar detention pathway.…”

“…Functional studies of these molecules have revealed new mechanisms for the regulation of rRNA expression, as well as a novel posttranslation regulatory pathway termed the nucleolar detention pathway. All proteins captured by rIGSlncRNAs contain the nucleolar detention signal (NoDS),i.e., a position-independent consensus sequence, which consists of at least one arginine motif (RRI/L) and a minimum of two hydrophobic triplets (LhL/v, where h represents a hydrophobic residue) [26]. These molecules have diverse functions in ubiquitination, proteasomal degradation, protein folding, and DNA replication and methylation, indicating that the NoDS may control important aspects of cellular life [27].…”

“…JN872552-JN872556, and JN872557-JN872559, respectively) [26]. All GenBank accession numbers for IGS27RNA and for IGS22RNA are represented by practically identical sequences.…”