Proteome data improves protein function prediction in the interactome of Helicobacter pylori

Stefan Wuchty, Stefan A. Müller, J. Harry Caufield, Roman Häuser, Patrick Aloy, Stefan Kalkhof, Peter Uetz

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)961-973
Number of pages13
JournalMolecular and Cellular Proteomics
Volume17
Issue number5
DOIs
StatePublished - May 1 2018

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Proteome
Helicobacter pylori
Proteins
Pathogens
Genes
Information Storage and Retrieval
Duodenal Ulcer
Controllability
Gene expression
Proteomics
Escherichia coli
Conservation
Bacteria
Observation
Gene Expression
Chemical analysis

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Molecular Biology

Cite this

Proteome data improves protein function prediction in the interactome of Helicobacter pylori. / Wuchty, Stefan; Müller, Stefan A.; Caufield, J. Harry; Häuser, Roman; Aloy, Patrick; Kalkhof, Stefan; Uetz, Peter.

In: Molecular and Cellular Proteomics, Vol. 17, No. 5, 01.05.2018, p. 961-973.

Research output: Contribution to journalArticle

Wuchty, Stefan ; Müller, Stefan A. ; Caufield, J. Harry ; Häuser, Roman ; Aloy, Patrick ; Kalkhof, Stefan ; Uetz, Peter. / Proteome data improves protein function prediction in the interactome of Helicobacter pylori. In: Molecular and Cellular Proteomics. 2018 ; Vol. 17, No. 5. pp. 961-973.
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