Finding nuclear localization signals

Abstract

A variety of nuclear localization signals (NLSs) are experimentally known although only one motif was available for database searches through PROSITE. We initially collected a set of 91 experimentally verified NLSs from the literature. Through iterated 'in silico mutagenesis' we then extended the set to 214 potential NLSs. This final set matched in 43% of all known nuclear proteins and in no known non-nuclear protein. We estimated that >17% of all eukaryotic proteins may be imported into the nucleus. Finally, we found an overlap between the NLS and DNA-binding region for 90% of the proteins for which both the NLS and DNA-binding regions were known. Thus, evolution seemed to have used part of the existing DNA-binding mechanism when compartmentalizing DNA-binding proteins into the nucleus. However, only 56 of our 214 NLS motifs overlapped with DNA-binding regions. These 56 NLSs enabled a de novo prediction of partial DNAbinding regions for ∼800 proteins in human, fly, worm and yeast.

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

“…In short, amino acid sequences for those proteins identified by MS were extracted from the SOL genomics protein database v. ITAG2.4 (Tomato Genome, 2012). This data set was subjected to predictnls (default settings) (Cokol et al ., 2000) and nlstradamus (two‐state model; posterior threshold 0.6) (Nguyen Ba et al ., 2009) to identify proteins with nuclear localization signals, and the Nucleolar Localization Sequence Detector ( nod ) (default settings) (Scott et al ., 2010, 2011) to identify proteins with nucleolar localization signals. Additionally, we used wolf psort (plant) (Horton et al ., 2007) and filtered all proteins marked as nuclear.…”

Protein Disulfide Isomerase-2 of Arabidopsis Mediates Protein Folding and Localizes to Both the Secretory Pathway and Nucleus, Where It Interacts with Maternal Effect Embryo Arrest Factor

“…genome.jp/). Nuclear localization signals were predicted using the algorithm of Cokol et al (2000) at (http://cubic.bioc.columbia. edu/services/predictNLS/) and signal peptides were identified with (http://www.cbs.dtu.dk/services/).…”

Expression of a Myelin Proteolipid Protein (Plp)-lacZ Transgene is Reduced in both the CNS and PNS of Plp jp Mice

“…Since the PLP/DM20 C-terminus portion is out of frame in the mutant, it is possible that a nuclear localization signal (NLS) might have inadvertently been created. However, neither Plp jp PLP nor wild-type PLP contains an NLS when analyzed with a program that searches for NLS (http://cubic.bioc.columbia.edu/predictNLS) [41,42]. Furthermore Anderson et al [40] demonstrated that expression of the Plp jp PLP protein in Schwann cells did not prevent expression of wild type PLP protein.…”