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Mol Cell Proteomics. 2018 May;17(5):961-973. doi: 10.1074/mcp.RA117.000474. Epub 2018 Feb 1.

Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori.

Author information

1
From the ‡Dept. of Computer Science.
2
§Center for Computational Science.
3
¶Dept. of Biology.
4
‖Sylvester Comprehensive Cancer Center, Univ. of Miami, Miami, FL 33156.
5
**German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany.
6
‡‡Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VI 23284.
7
§§German Cancer Research Center, 69120 Heidelberg, Germany.
8
¶¶Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Institute of Science and Technology. Barcelona, Catalonia, Spain.
9
‖‖Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
10
Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research Leipzig, 04318 Leipzig, Germany.
11
Institute of Bioanalysis, University of Applied Sciences and Arts of Coburg, Friedrich-Streib-Str. 2, 96450 Coburg, Germany.
12
Fraunhofer Institute for Cell Therapy and Immunology, Department of Therapy Validation, 04103 Leipzig, Germany.

Abstract

Helicobacter pylori is a common pathogen that is estimated to infect half of the human population, causing several diseases such as duodenal ulcer. Despite one of the first pathogens to be sequenced, its proteome remains poorly characterized as about one-third of its proteins have no functional annotation. Here, we integrate and analyze known protein interactions with proteomic and genomic data from different sources. We find that proteins with similar abundances tend to interact. Such an observation is accompanied by a trend of interactions to appear between proteins of similar functions, although some show marked cross-talk to others. Protein function prediction with protein interactions is significantly improved when interactions from other bacteria are included in our network, allowing us to obtain putative functions of more than 300 poorly or previously uncharacterized proteins. Proteins that are critical for the topological controllability of the underlying network are significantly enriched with genes that are up-regulated in the spiral compared with the coccoid form of H. pylori Determining their evolutionary conservation, we present evidence that 80 protein complexes are identical in composition with their counterparts in Escherichia coli, while 85 are partially conserved and 120 complexes are completely absent. Furthermore, we determine network clusters that coincide with related functions, gene essentiality, genetic context, cellular localization, and gene expression in different cellular states.

PMID:
29414760
PMCID:
PMC5930399
[Available on 2019-05-01]
DOI:
10.1074/mcp.RA117.000474

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