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Large-scale identification of protein–protein interaction of Escherichia coli K-12

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Arifuzzaman, Mohammad, Maeda, Maki, Itoh, Aya, Nishikata, Kensaku, Takita, Chiharu, Saito, Rintaro, Ara, Takeshi, Nakahigashi, Kenji, Huang, Hsuan-Cheng, Hirai, Aki, Tsuzuki, Kohei, Nakamura, Seira, Altaf-Ul-Amin, Mohammad, Oshima, Taku, Baba, Tomoya, Yamamoto, Natsuko, Kawamura, Tomoyo, Ioka-Nakamichi, Tomoko, Kitagawa, Masanari, Tomita, Masaru, Kanaya, Shigehiko, Wada, Chieko, Mori, Hirotada·2006·Genome Research

DOI 10.1101/gr.4527806PMC PMC1457052

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Abstract

Protein–protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular activities, targeted-drug design, and whole cell engineering. A large-scale comprehensive pull-down assay was performed using a His-tagged Escherichia coli ORF clone library. Of 4339 bait proteins tested, partners were found for 2667, including 779 of unknown function. Proteins copurifying with hexahistidine-tagged baits on a Ni 2+-NTA column were identified by MALDI-TOF MS (matrix-assisted laser desorption ionization time of flight mass spectrometry). An extended analysis of these interacting networks by bioinformatics and experimentation should provide new insights and novel strategies for E. coli systems biology.

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Authors: Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.-C., Hirai, A., Tsuzuki, K., Nakamura, S., Altaf-Ul-Amin, M., Oshima, T., Baba, T., Yamamoto, N., Kawamura, T., Ioka-Nakamichi, T., Kitagawa, M., Tomita, M., Kanaya, S., Wada, C., & Mori, H.
Affiliations: Japan Bioindustry Association (JP)
Japan Science and Technology Agency (JP)
Institute for Advanced Biosciences, Keio University (JP)
Nara Institute of Science and Technology (JP)
National Yang Ming University (TW)
Kyoto University (JP)
ORCID: Arifuzzaman, Mohammad
Maeda, Maki
Saito, Rintaro
Ara, Takeshi
Huang, Hsuan-Cheng
Oshima, Taku
Baba, Tomoya
Kitagawa, Masanari
Tomita, Masaru
Kanaya, Shigehiko
Wada, Chieko
Mori, Hirotada
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2006-04-10
Volume: 16
Issue: 5
Pages: 686-691
ISSN: 1088-9051 (ISSN-L)
DOI: 10.1101/gr.4527806
PMC: PMC1457052
OpenAlex: W2137012036
Cited by: 403
References: 44
Citations by year: 2026: 4 · 2025: 7 · 2024: 12 · 2023: 9 · 2022: 11 · 2021: 3 · 2020: 16 · 2019: 15 · 2018: 12 · 2017: 12 · 2016: 16 · 2015: 23 · 2014: 22 · 2013: 21 · 2012: 36
Type: posted content
Language: en
Open access: bronze
doi.org
Locations: Genome Research (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed (publishedVersion)
Funders: Core Research for Evolutional Science and Technology
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords: protein-protein interaction, Escherichia coli K-12, pull-down assay, protein-protein interaction network, interactome networks, protein function, systems biology, drug target identification
MeSH terms: Histidine, Models, Biological, Gene Library, Open Reading Frames, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Proteome, Escherichia coli Proteins, Proteomics, Escherichia coli K12

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Large-scale identification of protein–protein interaction of Escherichia coli K-12

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