Bioinformatics Advance Access originally published online on February 8, 2005
Bioinformatics 2005 21(10):2558-2559; doi:10.1093/bioinformatics/bti313
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Protein function prediction using the Protein Link EXplorer (PLEX)
1Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology 1 University Station, A4800 Austin, TX 78712-1064, USA
2Department of Chemistry and Biochemistry, University of Texas at Austin 1 University Station, A4800 Austin, TX 78712-1064, USA
*To whom correspondence should be addressed.
 |
Abstract |
|---|
 TOP Abstract INTRODUCTIONIMPLEMENTATIONREFERENCES |
|---|
Summary: We introduce the Protein Link EXplorer (PLEX), a web-based environment that allows the construction of a phylogenetic profile for any given amino acid sequence, and its comparison with profiles of 
350 000 predicted genes from 89 genomes, as a means of interactively identifying functionally linked genes and predicting protein function. PLEX can be searched iteratively and also enables searches for chromosomal gene neighbors and Rosetta Stone linkages. PLEX search results are accompanied by quantitative estimates of linkage confidence, enabling users to take advantage of coinheritance, operon and gene fusion-based methods for inferring gene function and reconstructing cellular systems and pathways.
Availability: http://bioinformatics.icmb.utexas.edu/plex
Contact: marcotte{at}icmb.utexas.edu
|
INTRODUCTION |
|---|
|
TOPAbstractINTRODUCTIONIMPLEMENTATIONREFERENCES |
|---|
Functional annotation of completely sequenced genomes has proved to be a formidable task, and large fractions of genes are as yet uncharacterized. Even in well-studied genomes, such as that of Escherichia coli,
30% of the genes are annotated as being of unknown function. In the malarial parasite Plasmodium falciparum, 60% of the genes lack functional assignments (Gardner et al., 2002). To better understand the biology of these organisms, associating functions, even general functions, with the uncharacterized genes is of paramount importance. We have created the web-based Protein Link EXplorer (PLEX) system to allow interactive exploration of comparative genomics tools for inferring linkages between genes, specifically through the use of phylogenetic profile analysis (Pellegrini et al., 1999), Rosetta Stone links (Marcotte et al., 1999; Enright et al., 1999), and the inference of operons based upon the distance between adjacent genes (Salgado et al., 2000). While pre-calculated linkages from phylogenetic profiles are available in the STRING (von Mering et al., 2003) and Predictome (Mellor et al., 2002) databases, tools for the construction and search of user-input phylogenetic profiles are not widely accessible. Using PLEX, a phylogenetic profile can be constructed from any given amino acid sequence, or even specified manually to reflect desired phylogenetic distributions, then compared with pre-calculated profiles of 350 111 proteins from 89 bacterial, archaeal and eukaryotic genomes in the PLEX database. Information about Rosetta Stone protein links and chromosomal gene neighbors is provided, and iterative searches are feasible. We anticipate the system will be of use to any biologist hoping to gain insight into a particular cellular system or to suggest genes responsible for an observed phenotype. For first time users of the system, a short guided tour is available at http://bioinformatics.icmb.utexas.edu/plex/tour/
|
IMPLEMENTATION |
|---|
|
TOPAbstractINTRODUCTIONIMPLEMENTATIONREFERENCES |
|---|
The PLEX system is based upon a mySQL relational database, storing gene sequences, chromosomal positions, pre-computed phylogenetic profiles and Rosetta Stone linkages, accessible via PERL scripts from a web-based interface. PLEX first compares a user-entered amino acid sequence, using BLASTP under default settings, to
350 000 predicted genes from 89 genomes to construct a phylogenetic profile, which is then compared versus those in the database to identify genes with a similar phylogenetic distribution from a user-specified genome. Similarity is evaluated by identifying the phylogenetic profiles with maximal mutual information to the query profile (calculated as in Date and Marcotte, 2003). Genes recovered in the search can be chosen as queries for new searches, in this manner exploring the space of co-inherited genes. Additional functional linkages are provided in the form of Rosetta Stone linkages that are identified and ranked via a statistical measure of confidence based upon the hypergeometric distribution (Verjovsky Marcotte and Marcotte, 2002). Gene neighbors are included when neighboring genes on the chromosome are closer than a specified number of nucleotides [typically 40 nt, suggested by log-likelihood analysis of operon boundaries (Salgado et al., 2000)]. Figure 1 illustrates the use of PLEX with two examples from the Mycobacterium tuberculosis genome—the reconstruction of all subunits of the urease enzyme, and reconstruction of the isoprenoid biosynthesis pathway, including several potential new components, linked by PLEX to the main pathway. Starting from the amino acid sequence of the urease subunit UreA (red circle, Fig. 1A), a comparison with profiles of all genes in the M.tuberculosis genome revealed functional links with subunits UreB, UreC and UreG of the urease enzyme. Analysis of gene neighbors revealed the linkage between the UreB and UreA proteins. Rosetta Stone linkages were found between the A, B and C subunits, the composite genes (AB, AC, BC) occurring in eight different organisms. UreD and UreF were identified as operon partners by selecting UreB, UreC and UreG as queries; the distinct phylogenetic distributions of UreD and UreF are immediately evident in the figure (drawn at bottom). A similar analysis led to the reconstruction of the M.tuberculosis isoprenoid biosynthesis pathway (Fig. 1), starting from the sequence of the IspG protein. Along with the known components (labeled by the steps they catalyze), four additional proteins are implicated in the isoprenoid biosynthesis pathway: Rv3583 (a putative transcription factor), Rv2869c (a zinc metalloprotease), Rv1012 and IdsB (a putative polyprenyl synthetase).
|
Specifying constraints on the phylogenetic profiles provides another route to finding genes associated with a pathway (Huynen et al., 1998). For example, from a profile corresponding appropriately with flagellated and non-flagellated bacteria, PLEX returns genes involved in flagellar structure and biosynthesis. These genes can be chosen as queries for the determination of operon and Rosetta Stone linkages. In this manner, phenotypes can be associated directly with candidate genes and systems.
|
Acknowledgments |
|---|
The authors acknowledge funding from the Welch Foundation (F-1515), Packard Foundation, NSF, NIH (GM067779-01) and Beckman/MURI.
Received on September 29, 2004; revised on February 6, 2005; accepted on February 7, 2005
|
REFERENCES |
|---|
|
TOPAbstractINTRODUCTIONIMPLEMENTATIONREFERENCES |
|---|
Date, S.V. and Marcotte, E.M. (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol., 21, 1055–1062[CrossRef][Web of Science][Medline].
Enright, A.J., et al. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86–90[CrossRef][Medline].
Gardner, M.J., et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419, 498–511[CrossRef][Medline].
Huynen, M., et al. (1998) Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett., 426, 1–5[CrossRef][Web of Science][Medline].
Marcotte, E.M., et al. (1999) Detecting protein function and protein–protein interactions from genome sequences. Science, 285, 751–753
Mellor, J.C., et al. (2002) Predictome: a database of putative functional links between proteins. Nucleic Acids Res., 30, 306–309
Pellegrini, M., et al. (1999) Assigning protein functions by comparative analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285–4288
Salgado, H., et al. (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc. Natl Acad. Sci. USA, 97, 6652–6657
von Mering, C., et al. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res, 31, 258–261
Verjovsky Marcotte, C.J. and Marcotte, E.M. (2002) Predicting functional linkages from gene fusions with confidence. Appl. Bioinform., 1, 37–44.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. R Kensche, V. van Noort, B. E Dutilh, and M. A Huynen Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution J R Soc Interface, February 6, 2008; 5(19): 151 - 170. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. F. Waas, V. de Crecy-Lagard, and P. Schimmel Discovery of a Gene Family Critical to Wyosine Base Formation in a Subset of Phenylalanine-specific Transfer RNAs J. Biol. Chem., November 11, 2005; 280(45): 37616 - 37622. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||