Rapid interactome profiling by massive sequencing

Di Niro, Roberto; Sulic, Ana-Marija; Mignone, Flavio; D'Angelo, Sara; Bordoni, Roberta; Iacono, Michele; Marzari, Roberto; Gaiotto, Tiziano; Lavric, Miha; Bradbury, Andrew R.  M.; Biancone, Luigi; Zevin-Sonkin, Dina; De Bellis, Gianluca; Santoro, Claudio; Sblattero, Daniele

doi:10.1093/nar/gkq052

Rapid interactome profiling by massive sequencing

Journal Article · Tue Feb 09 00:00:00 EST 2010 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkq052· OSTI ID:1625469

Di Niro, Roberto ^[1]; Sulic, Ana-Marija ^[2]; Mignone, Flavio ^[3]; D'Angelo, Sara ^[4]; Bordoni, Roberta ^[5]; Iacono, Michele ^[5]; Marzari, Roberto ^[2]; Gaiotto, Tiziano ^[2]; Lavric, Miha ^[2]; Bradbury, Andrew R. M. ^[6]; Biancone, Luigi ^[7]; Zevin-Sonkin, Dina ^[8]; De Bellis, Gianluca ^[5]; Santoro, Claudio ^[4]; Sblattero, Daniele ^[4]

Univ. of Trieste (Italy). Dept. of Life Science; DOE/OSTI
Univ. of Trieste (Italy). Dept. of Life Science
Univ. of Milan (Italy). School of Pharmacy. Dept. of Structural Chemistry and Inorganic Stereochemistry
University of Eastern Piedmont Novara (Italy). IRCAD. Dept. of Medical Sciences
National Research Council (ITB CNR), Milan (Italy). Inst. of Biomedical Technologies
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Univ. of Turin (Italy). CERMS
QBI Enterprises Inc/Quark Pharmaceuticals Inc, Ness Ziona (Israel)

We have developed a high-throughput protein expression and interaction analysis platform that combines cDNA phage display library selection and massive gene sequencing using the 454 platform. A phage display library of open reading frame (ORF) fragments was created from mRNA derived from different tissues. This was used to study the interaction network of the enzyme transglutaminase 2 (TG2), a multifunctional enzyme involved in the regulation of cell growth, differentiation and apoptosis, associated with many different pathologies. After two rounds of panning with TG2 we assayed the frequency of ORFs within the selected phage population using 454 sequencing. Ranking and analysis of more than 120 000 sequences allowed us to identify several potential interactors, which were subsequently confirmed in functional assays. Within the identified clones, three had been previously described as interacting proteins (fibronectin, SMOC1 and GSTO2), while all the others were new. When compared with standard systems, such as microtiter enzyme-linked immunosorbant assay, the method described here is dramatically faster and yields far more information about the interaction under study, allowing better characterization of complex systems. For example, in the case of fibronectin, it was possible to identify the specific domains involved in the interaction.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1625469

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 9 Vol. 38; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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