Identification of a Common Subnuclear Localization Signal

Abstract

Proteins share peptidic sequences, such as a nuclear localization signal (NLS), which guide them to particular membranebound compartments. Similarities have also been observed within different classes of signals that target proteins to membrane-less subnuclear compartments. Common localization signals affect spatial and temporal subcellular organization and are thought to allow the coordinated response of different molecular networks to a given signaling cue. Here we identify a higher-order and predictive code, {[RR(I/L)X 3 r] (n, n>1) ؉[L(/N)(V/L)] (n,n>1) }, that establishes high-affinity interactions between a group of proteins and the nucleolus in response to a specific signal. This position-independent code is referred to as a nucleolar detention signal regulated by H ؉ (NoDS H؉ ) and the class of proteins includes the cIAP2 apoptotic regulator, VHL ubiquitylation factor, HSC70 heat shock protein and RNF8 transcription regulator. By identifying a common subnuclear targeting consensus sequence, our work reveals rules governing the dynamics of subnuclear organization and ascribes new modes of regulation to several proteins with diverse steady-state distributions and dynamic properties. INTRODUCTIONBiochemical processes occurring in the nucleus contribute to its compartmentalization, which facilitates the control of molecular networks (Chubb and Bickmore, 2003). Unlike the cytoplasm, compartmentalization in the nucleus does not rely on the concentration of molecules behind membranes to enhance biochemical reactions. Similar gene loci and regulatory proteins are concentrated within specific membraneless nuclear substructures such as speckles, PML bodies, Cajal bodies, and nucleoli (Misteli, 2001(Misteli, , 2004Chubb and Bickmore, 2003;Isogai and Tjian, 2003;Zimber et al., 2004).The temporal and spatial precision of intranuclear dynamics of nucleic acids and polypeptides is central to the proper control of the cell cycle, transcription, apoptosis, ubiquitylation, ribosomal biogenesis, and several other pathways (Shou et al., 1999;Visintin et al., 1999;Weber et al., 1999;Dundr et al., 2000Dundr et al., , 2004Barseguian et al., 2002;Wong et al., 2002;Isogai and Tjian, 2003;Leung et al., 2004;Zaidi et al., 2005). For example, silent gene loci at the nuclear periphery can move centripetally when activated to be repositioned away from repressive factors and closer to activators concentrated within particular subnuclear compartments (Kosak and Groudine, 2004;Misteli, 2004).Several molecules rely on common peptidic sequences to localize to a given membrane-bound compartment. This includes nuclear localization/export signals (NLS or NES, respectively;Conti and Izaurralde, 2001;Kutay and Guttinger, 2005; and cell membrane localization signals (Shikano et al., 2005). Identification of such sequences has been instrumental in the functional characterization of a very large number of proteins. Some similarities have also been observed within each class of subnuclear targeting signal. This has been the case for the nucleolus...

Principles of protein targeting to the nucleolus

“…The localization or exclusion of proteins from the nucleolus is subject to dramatic changes upon cellular stimuli, stress and complete reorganization during cell cycle progression. [23][24][25] In a previous study, we have shown that a reporter protein traverses nucleoli rapidly with less obstruction compared to nucleoplasmic regions rich in chromatin. 26 In that study, we described a structural feature of the nucleolus with channel like regions void of nucleic acids and proteins that facilitates a fast movement of non-nucleolar proteins through this compartment.…”

Management of rRNA Transcription Activity in a Human Genome

“…The plurifunctional nature of the nucleolus is evident in its response to physiological stimuli and stress conditions accompanied by nucleolar remodeling, and a decrease or interruption in rRNA synthesis [20,21] as well as the capture of numerous seemingly unrelated factors involved in a wide array of cellular functions [22][23][24][25].…”

Where no RNA polymerase has gone before

“…Hallmarks of nucleolar remodeling include a decrease or interruption in rRNA synthesis 8,9 as well as the capture of numerous seemingly unrelated factors involved in a wide array of cellular functions. [10][11][12][13] Though these phenomena have been observed for many years, they have only recently been mechanistically linked to the expression of novel species of noncoding RNA (ncRNA) originating from the ribosomal intergenic spacer (IGS). 13,14 In this Commentary, recent and unexpected advances in our understanding of the transcriptional activity and biological role of the IGS are discussed.…”

“…13,40 These proteins share a consensus amino acid sequence that targets them to the IGS for static detention in the nucleolus, the nucleolar detention signal (NoDS). 12,13 This discrete code is composed of an arginine motif (R-R-I/L-X 3 -r) along with several hydrophobic repeats (L-Φ/N-L/V; where Φ represents any hydrophobic residue). 12 Bioinformatic studies suggest that up to 9% of all proteins encode an NoDS and consequently could be regulated by the nucleolus.…”

“…12,13 This discrete code is composed of an arginine motif (R-R-I/L-X 3 -r) along with several hydrophobic repeats (L-Φ/N-L/V; where Φ represents any hydrophobic residue). 12 Bioinformatic studies suggest that up to 9% of all proteins encode an NoDS and consequently could be regulated by the nucleolus.…”