biostudies-literatureNiwa TMinistry of Education, Culture, Sports, Science and Technology3772https://www.ebi.ac.uk/biostudies/studies/S-EPMC9228906biostudies-literatureUnknown27(12)The <i>Escherichia coli</i> chaperonin GroEL/ES (GroE) is one of the most extensively studied molecular chaperones. So far, ~80 proteins in <i>E. coli</i> are identified as GroE substrates that obligately require GroE for folding in vivo. In GroE-depleted cells, these substrates, when overexpressed, tend to form aggregates, whereas the GroE substrates expressed at low or endogenous levels are degraded, probably due to misfolded states. However, the protease(s) involved in the degradation process has not been identified. We conducted a mass-spectrometry-based proteomics approach to investigate the effects of three ATP-dependent proteases, Lon, ClpXP, and HslUV, on the <i>E. coli</i> proteomes under GroE-depleted conditions. A label-free quantitative proteomic method revealed that Lon proteaMolecules (Basel, Switzerland)Shotgun Proteomics Revealed Preferential Degradation of Misfolded In Vivo Obligate GroE Substrates by Lon Protease in <i>Escherichia coli</i>.PMC9228906JP26116002, JP18H03984, JP20H05925, 17K15073Niwa TTaguchi HChadani YfalseShotgun Proteomics Revealed Preferential Degradation of Misfolded In Vivo Obligate GroE Substrates by Lon Protease in <i>Escherichia coli</i>.The <i>Escherichia coli</i> chaperonin GroEL/ES (GroE) is one of the most extensively studied molecular chaperones. So far, ~80 proteins in <i>E. coli</i> are identified as GroE substrates that obligately require GroE for folding in vivo. In GroE-depleted cells, these substrates, when overexpressed, tend to form aggregates, whereas the GroE substrates expressed at low or endogenous levels are degraded, probably due to misfolded states. However, the protease(s) involved in the degradation process has not been identified. We conducted a mass-spectrometry-based proteomics approach to investigate the effects of three ATP-dependent proteases, Lon, ClpXP, and HslUV, on the <i>E. coli</i> proteomes under GroE-depleted conditions. A label-free quantitative proteomic method revealed that Lon protea2022-01-01T00:00:00Z2022 Jun2025-04-04T11:28:46.36Z2025-04-04T11:28:46.36ZS-EPMC92289063574489410.3390/molecules27123772