Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding

Eri Uemura, Tatsuya Niwa, Shintaro Minami, Kazuhiro Takemoto, Satoshi Fukuchi, Kodai Machida, Hiroaki Imataka, Takuya Ueda, Motonori Ota, Hideki Taguchi

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Abstract

A subset of the proteome is prone to aggregate formation, which is prevented by chaperones in the cell. To investigate whether the basic principle underlying the aggregation process is common in prokaryotes and eukaryotes, we conducted a large-scale aggregation analysis of ~500 cytosolic budding yeast proteins using a chaperone-free reconstituted translation system, and compared the obtained data with that of ~3,000 Escherichia coli proteins reported previously. Although the physicochemical properties affecting the aggregation propensity were generally similar in yeast and E. coli proteins, the susceptibility of aggregation in yeast proteins were positively correlated with the presence of intrinsically disordered regions (IDRs). Notably, the aggregation propensity was not significantly changed by a removal of IDRs in model IDR-containing proteins, suggesting that the properties of ordered regions in these proteins are the dominant factors for aggregate formation. We also found that the proteins with longer IDRs were disfavored by E. coli chaperonin GroEL/ES, whereas both bacterial and yeast Hsp70/40 chaperones have a strong aggregation-prevention effect even for proteins possessing IDRs. These results imply that a key determinant to discriminate the eukaryotic proteomes from the prokaryotic proteomes in terms of protein folding would be the attachment of IDRs.

Original languageEnglish
Article number678
JournalScientific reports
Volume8
Issue number1
DOIs
Publication statusPublished - 2018 Dec 1
Externally publishedYes

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Protein Folding
Proteome
Fungal Proteins
Escherichia coli Proteins
Yeasts
Intrinsically Disordered Proteins
Chaperonins
Proteins
Saccharomycetales
Eukaryota
Escherichia coli

ASJC Scopus subject areas

  • General

Cite this

Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. / Uemura, Eri; Niwa, Tatsuya; Minami, Shintaro; Takemoto, Kazuhiro; Fukuchi, Satoshi; Machida, Kodai; Imataka, Hiroaki; Ueda, Takuya; Ota, Motonori; Taguchi, Hideki.

In: Scientific reports, Vol. 8, No. 1, 678, 01.12.2018.

Research output: Contribution to journalArticle

Uemura, E, Niwa, T, Minami, S, Takemoto, K, Fukuchi, S, Machida, K, Imataka, H, Ueda, T, Ota, M & Taguchi, H 2018, 'Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding', Scientific reports, vol. 8, no. 1, 678. https://doi.org/10.1038/s41598-017-18977-5
Uemura, Eri ; Niwa, Tatsuya ; Minami, Shintaro ; Takemoto, Kazuhiro ; Fukuchi, Satoshi ; Machida, Kodai ; Imataka, Hiroaki ; Ueda, Takuya ; Ota, Motonori ; Taguchi, Hideki. / Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. In: Scientific reports. 2018 ; Vol. 8, No. 1.
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