Abstract
Functional but silent peroxisomal targeting signals have been found in non- peroxisomal proteins. This discovery has important implications for sequence-based signal prediction and for evolution.
Highlights
Can sequence segments coding for subcellular targeting or for posttranslational modifications occur in proteins that are not substrates in either of these processes? considerable effort has been invested in achieving low false-positive prediction rates, even accurate sequence-analysis tools for the recognition of these motifs generate a small but noticeable number of protein hits that lack the appropriate biological context but cannot be rationalized as false positives
Considerable effort has been invested in achieving low false-positive prediction rates, our experience with tools for recognizing glycosyl phosphatidylinositol (GPI) lipid [2,3] and myristoyl [4,5,6] anchor attachment sites and for predicting potential targets for peroxisomal targeting signal 1 (PTS1)-dependent translocation to peroxisomes [7] shows that a small but noticeable number of proteins without appropriate biological context are systematically hit by these tools
We were not able to rationalize these results as false predictions as the proteins' carboxyl termini did not deviate from the generalized PTS1 sequence pattern [13]
Summary
Can sequence segments coding for subcellular targeting or for posttranslational modifications occur in proteins that are not substrates in either of these processes? considerable effort has been invested in achieving low false-positive prediction rates, even accurate sequence-analysis tools for the recognition of these motifs generate a small but noticeable number of protein hits that lack the appropriate biological context but cannot be rationalized as false positives. Considerable effort has been invested in achieving low false-positive prediction rates, our experience with tools for recognizing glycosyl phosphatidylinositol (GPI) lipid [2,3] and myristoyl [4,5,6] anchor attachment sites and for predicting potential targets for PTS1-dependent translocation to peroxisomes [7] shows that a small but noticeable number of proteins without appropriate biological context (for example with contradictory subcellular localization or in taxa without the modifying enzyme or receptor) are systematically hit by these tools. All three of the sequence-analysis tools mentioned above check query sequences for a recognition pattern that is explicitly described in terms of its physical properties and it is possible to check the concordance between pattern descriptions and query sequence individually This visual inspection is frequently unable to rationalize the findings as false-positive predictions, as all known components of the pattern appear to be present. We discuss the evolutionary perspective of functional localization signals in unrelated proteins as well as the consequences for experimental localization determination and function prediction from sequence
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