Specific regions of the SulA protein recognized and degraded by the ATP-dependent ClpYQ (HslUV) protease in Escherichia coli

Chang, Chun-Yang; Weng, Yu‐Ting; Hwang, Lin-Yi; Hu, Huiting; Shih, Po-Shu; Kuan, Jung-En; Wu, Kefeng; Wu, Whei-Fen

doi:10.1016/j.micres.2018.12.003

Cited by 9 publications

(8 citation statements)

References 53 publications

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“…In bacteria, ATP‐dependent Lon proteases control directly the intracellular concentrations of many important proteins, for example modulating cell division and survival in response to metabolic, chemical, thermal and DNA damage stress [ 51 ]. A range of substrates and their interactions with Lon have been studied; however, many of the substrates are also degraded by other protease systems, for example Clp [ 52 , 53 ], significantly complicating analyses. A key challenge is thus to identify Lon‐specific substrates and their mechanism of recognition.…”

Section: Discussionmentioning

confidence: 99%

Cryo‐EM structure of the full‐length Lon protease from Thermus thermophilus

Coscia

Löwe

2021

FEBS Letters

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In bacteria, Lon is a large hexameric ATP‐dependent protease that targets misfolded and also folded substrates, some of which are involved in cell division and survival of cellular stress. The N‐terminal domain of Lon facilitates substrate recognition, but how the domains confer such activity has remained unclear. Here, we report the full‐length structure of Lon protease from Thermus thermophilus at 3.9 Å resolution in a substrate‐engaged state. The six N‐terminal domains are arranged in three pairs, stabilized by coiled‐coil segments and forming an additional channel for substrate sensing and entry into the AAA+ ring. Sequence conservation analysis and proteolysis assays confirm that this architecture is required for the degradation of both folded and unfolded substrates in bacteria.

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Section: Discussionmentioning

confidence: 99%

Cryo‐EM structure of the full‐length Lon protease from Thermus thermophilus

Coscia

Löwe

2021

FEBS Letters

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“…In G. icigianus , this possibility may be due to the activation of two enzymes, excinuclease ABC subunit UvrB, which is ATP-dependent (EP10_00715), and methylated-DNA-protein-cysteine methyltransferase (EP10_00085) ( Table 2 ), which is involved in the repair of DNA and its methylated fragments. Indeed, DNA methylation in bacteria is commonly associated with restriction-modification systems that act as key moderators of horizontal gene transfer [ 65 ]. DNA methylation plays an important role in bacterial biology: phenomena such as the DNA replication time, chromosome division into daughter cells, DNA repair, transposition time, and conjugal plasmid transfer are sensitive to the methylation states of specific DNA sites [ 66 , 67 , 68 ].…”

Section: Discussionmentioning

confidence: 99%

Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation

Bannikova

Khlebodarova

Vasilieva

et al. 2022

IJMS

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Studying the effects of terahertz (THz) radiation on the proteome of temperature-sensitive organisms is limited by a number of significant technical difficulties, one of which is maintaining an optimal temperature range to avoid thermal shock as much as possible. In the case of extremophilic species with an increased temperature tolerance, it is easier to isolate the effects of THz radiation directly. We studied the proteomic response to terahertz radiation of the thermophilic Geobacillus icigianus, persisting under wide temperature fluctuations with a 60 °C optimum. The experiments were performed with a terahertz free-electron laser (FEL) from the Siberian Center for Synchrotron and Terahertz Radiation, designed and employed by the Institute of Nuclear Physics of the SB of the RAS. A G. icigianus culture in LB medium was THz-irradiated for 15 min with 0.23 W/cm2 and 130 μm, using a specially designed cuvette. The life cycle of this bacterium proceeds under conditions of wide temperature and osmotic fluctuations, which makes its enzyme systems stress-resistant. The expression of several proteins was shown to change immediately after fifteen minutes of irradiation and after ten minutes of incubation at the end of exposure. The metabolic systems of electron transport, regulation of transcription and translation, cell growth and chemotaxis, synthesis of peptidoglycan, riboflavin, NADH, FAD and pyridoxal phosphate cofactors, Krebs cycle, ATP synthesis, chaperone and protease activity, and DNA repair, including methylated DNA, take part in the fast response to THz radiation. When the response developed after incubation, the systems of the cell’s anti-stress defense, chemotaxis, and, partially, cell growth were restored, but the respiration and energy metabolism, biosynthesis of riboflavin, cofactors, peptidoglycan, and translation system components remained affected and the amino acid metabolism system was involved.

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“…SulA functions as a cell division inhibitor by interacting with and inhibiting the activity of FtsZ, a critical GTPase essential for septum formation [35,36]. The tertiary structure of SulA comprises four α helices and five β sheets [37,38]. FtsZ individually binds to each monomer of the SulA dimer in a crystal structure [37] and has been shown to protect SulA from degradation by ClpYQ protease [34,39].…”

Section: Introductionmentioning

confidence: 99%

“…FtsZ individually binds to each monomer of the SulA dimer in a crystal structure [37] and has been shown to protect SulA from degradation by ClpYQ protease [34,39]. A recently identified degron site of SulA, GFIMRP 147th , near the C-terminal was shown to be necessary for the recognition and binding of ClpYQ protease in degradation [38]. However, as of now, there is no reported crystal structure for the ClpY(6x)-substrate complex, and the mechanism underlying the recognition and discrimination of the degron site in natural substrates by the degrader for degradation remains unknown.…”

Section: Introductionmentioning

confidence: 99%

A Transient π–π or Cation–π Interaction between Degron and Degrader Dual Residues: A Key Step for the Substrate Recognition and Discrimination in the Processive Degradation of SulA by ClpYQ (HslUV) Protease in Escherichia coli

Lin,

Tsai,

Chou

et al. 2023

IJMS

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The Escherichia coli ATP-dependent ClpYQ protease constitutes ClpY ATPase/unfoldase and ClpQ peptidase. The Tyr91st residue within the central pore-I site of ClpY-hexamer is important for unfolding and translocating substrates into the catalytic site of ClpQ. We have identified the degron site (GFIMRP147th) of SulA, a cell-division inhibitor recognized by ClpYQ and that the Phe143rd residue in degron site is necessary for SulA native folded structure. However, the functional association of this degron site with the ClpYQ degrader is unknown. Here, we investigated the molecular insights into substrate recognition and discrimination by the ClpYQ protease. We found that the point mutants ClpYY91FQ, ClpYY91HQ, and ClpYY91WQ, carrying a ring structure at the 91st residue of ClpY, efficiently degraded their natural substrates, evidenced by the suppressed bacterial methyl-methane-sulfonate (MMS) sensitivity, the reduced β-galactosidase activity of cpsB::lacZ, and the lowest amounts of MBP-SulA in both in vivo and in vitro degradation analyses. Alternatively, mimicking the wild-type SulA, SulAF143H, SulAF143K and SulAF143W, harboring a ring structure or a cation side-group in 143rd residue of SulA, were efficiently degraded by ClpYQ in the bacterial cells, also revealing shorter half-lives at 41 °C and higher binding affinities towards ClpY in pull-down assays. Finally, ClpYY91FQ and ClpYY91HQ, were capable of effectively degrading SulAF143H and SulAF143K, highlighting a correspondingly functional interaction between the SulA 143rd and ClpY 91st residues. According to the interchangeable substituted amino acids, our results uniquely indicate that a transient π–π or cation−π interaction between the SulA 143rd and ClpY 91st residues could be aptly gripped between the degron site of substrates and the pore site of proteases (degraders) for substrate recognition and discrimination of the processive degradation.

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Specific regions of the SulA protein recognized and degraded by the ATP-dependent ClpYQ (HslUV) protease in Escherichia coli

Cited by 9 publications

References 53 publications

Cryo‐EM structure of the full‐length Lon protease from Thermus thermophilus

Cryo‐EM structure of the full‐length Lon protease from Thermus thermophilus

Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation

A Transient π–π or Cation–π Interaction between Degron and Degrader Dual Residues: A Key Step for the Substrate Recognition and Discrimination in the Processive Degradation of SulA by ClpYQ (HslUV) Protease in Escherichia coli

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