NESbase version 1.0: a database of nuclear export signals

T. la Cour (2003). Nucleic Acids Res DOI: 10.1093/nar/gkg101 Citations: 228

Leucine-rich nuclear export signals were scattered through the literature and annotated in no protein database. This work curated 80 experimentally determined signals from over 200 articles into NESbase. Only 36% match the accepted NES consensus motif.

Parts used

NES

Key findings

  • A leucine-rich nuclear export signal consists of four to five hydrophobic residues within a region of about 10 amino acids. Those residues are predominantly leucine but may also be isoleucine, valine, methionine or phenylalanine. A mutational study of the protein kinase A inhibitor (PKI) signal shows that leucines at the carboxy-terminal end of the signal matter more for function than those at the amino-terminal end.
  • The widely used consensus motif L-x(2,3)-[LIVFM]-x(2,3)-L-x-[LI] describes only a minority of real nuclear export signals: just 36% of the experimentally validated leucine-rich signals aligned for the NESbase sequence logo match it. Pattern matching against this consensus is therefore insufficient to identify export signals.
  • Acidic residues are a recurring feature of leucine-rich nuclear export signals alongside the hydrophobic core. In a sequence logo built from 58 signals that were shown to be necessary or sufficient for export and whose pathway was experimentally verified, aligned over a 25-residue window, glutamic acid and aspartic acid are prominent after the hydrophobic residues. In the nuclear export signal region of p53 aligned across 17 species and the paralog p73, acidic residues are conserved both between species and between the two paralogs, though their positions are not generally conserved across unrelated signals.
  • Nuclear export signals are absent from the general protein sequence databases: they are not annotated in SWISS-PROT, PIR or PROSITE, so NESbase 1.0 was assembled entirely from published literature, screening over 200 articles to yield 75 entries covering 80 experimentally determined signals.
  • An export signal and an import signal rarely coexist in the same annotated protein. Cross-referencing NESbase entries against the NLSdb database of nuclear localization signals finds only 7 entries that also carry an experimentally verified localization signal and 13 that carry a potential one, so the overlap between curated export and import signals is small.
  • CRM1, also called exportin1 or Xpo1, is the export receptor for leucine-rich nuclear export signals, and the fungicide leptomycin B inhibits that pathway by binding CRM1 directly. Crm1p of Saccharomyces cerevisiae is the exception in being leptomycin B insensitive, and a single amino acid substitution makes it sensitive. CRM1 is not the only receptor that recognizes a leucine-rich signal: calreticulin exports PKI in a signal-dependent but leptomycin B insensitive manner.

Abstract

Protein export from the nucleus is often mediated by a Leucine-rich Nuclear Export Signal (NES). NESbase is a database of experimentally validated Leucine-rich NESs curated from literature. These signals are not annotated in databases such as SWISS-PROT, PIR or PROSITE. Each NESbase entry contains information of whether NES was shown to be necessary and/or sufficient for export, and whether the export was shown to be mediated by the export receptor CRM1. The compiled information was used to make a sequence logo of the Leucine-rich NESs, displaying the conservation of amino acids within a window of 25 residues. Surprisingly, only 36% of the sequences used for the logo fit the widely accepted NES consensus L-x(2,3)-[LIVFM]-x(2,3)-L-x-[LI]. The database is available online at http://www.cbs.dtu.dk/databases/NESbase/.