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Bioinformatics Advance Access first published online on November 15, 2007
This version published online on November 16, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm513
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Low folding propensity and high translation efficiency distinguish in vivo substrates of GroEL from other E. coli proteins

Orly Noivirt-Brik 1, Ron Unger 2 and Amnon Horovitz 1,*

1Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel
2The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel

*To whom correspondence should be addressed. Prof. Amnon Horovitz, E-mail: Amnon.Horovitz{at}weizmann.ac.il


  Abstract

Motivation: Theoretical considerations have indicated that the amount of chaperonin GroEL in Escherichia coli cells is sufficient to fold only about 2-5% of newly synthesized proteins under normal physiological conditions, thereby suggesting that only a subset of E. coli proteins fold in vivo in a GroEL-dependent manner. Recently, members of this subset were identified in two independent studies that resulted in two partially overlapping lists of GroEL-interacting proteins. The objective of the work described here was to identify sequence-based features of GroEL-interacting proteins that distinguish them from other E. coli proteins and that may account for their dependence on the chaperonin system.

Results: Our analysis shows that GroEL-interacting proteins have, on average, low folding propensities and high translation efficiencies. These two properties in combination can increase the risk of aggregation of these proteins and, thus, cause their folding to be chaperonin-dependent. Strikingly, we find that these properties are absent in proteins homologous to the E. coli GroEL-interacting proteins in Ureaplasma urealyticum, an organism that lacks a chaperonin system, thereby confirming our conclusions.

Contact: Amnon.Horovitz{at}weizmann.ac.il

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Thomas Lengauer

Received on July 10, 2007; revised on August 28, 2007; accepted on October 8, 2007

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