Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex

Abstract

A functional association is uncovered between the ribosome-associated trigger factor (TF) chaperone and the ClpXP degradation complex. Bioinformatic analyses demonstrate conservation of the close proximity of tig, the gene coding for TF, and genes coding for ClpXP, suggesting a functional interaction. The effect of TF on ClpXP-dependent degradation varies based on the nature of substrate. While degradation of some substrates are slowed down or are unaffected by TF, surprisingly, TF increases the degradation rate of a third class of substrates. These include λ phage replication protein λO, master regulator of stationary phase RpoS, and SsrA-tagged proteins. Globally, TF acts to enhance the degradation of about 2% of newly synthesized proteins. TF is found to interact through multiple sites with ClpX in a highly dynamic fashion to promote protein degradation. This chaperone–protease cooperation constitutes a unique and likely ancestral aspect of cellular protein homeostasis in which TF acts as an adaptor for ClpXP.

Bacterial Hsp90 Facilitates the Degradation of Aggregation-Prone Hsp70–Hsp40 Substrates

“…Thus, the data suggest that bacterial Hsp90 is involved in the sorting of aggregation-prone proteins toward native refolding by the Hsp70/Hsp40 system, or in case of Hsp70/Hsp40 failure, toward more degradation, for example through the HslUV protease. Such interplay between chaperones and proteases has been observed in E. coli, where trigger factor (TF) specifically cooperates with the ClpXP protease to promote the degradation of specific proteins, which represent a significant portion (about 2%) of newly synthesized proteins (Rizzolo et al, 2021). Accordingly, it has been demonstrated that in the α-proteobacterium Caulobacter crescentus, DnaK depletion is suppressed by HslUV, by attenuating the activity of the σ 32 factor (Schramm et al, 2017).…”

A uniform benchmark for testing ssrA-derived degrons in the Escherichia coli ClpXP pathway

“…Degradation observed in the ΔsspB strain was similar to that observed for WT and ΔclpX strains, corroborating the redundancy of the ClpX pathway or the SspB itself. Recently, it was shown that the E. coli ribosome-associated trigger factor (TF), a chaperonin which is highly abundant in the cell and acts early during the folding process, enhances degradation in vitro and in vivo of various ClpXP complex substrates including ssrA-taged proteins (Rizzolo et al , 2021). The role of TF as an additional adaptor could contribute to the lack of an effect of sspB deletion on our tested eGFP-degrons.…”

Reprogramming of the Caseinolytic Protease by ADEP Antibiotics: Molecular Mechanism, Cellular Consequences, Therapeutic Potential

“…Besides, elaborate feedback loops exist, in which either adaptors are themselves recognized as Clp protease substrates or Clp-ATPases, in a ClpP-independent chaperone function, protect substrates from Clp protease degradation ( Kirstein et al, 2009b ). Recently, it was also detected that the ribosome-associated trigger factor chaperone Tig modulates substrate degradation rates of ClpXP ( Rizzolo et al, 2021 ).…”

“…In Leptospira , trigger factor (TF) is chromosomally colocalized with ClpP and ClpX, and the same applies to E. coli and many other organisms. This observation led two research teams to test a potential functional connection ( Choudhury et al, 2021 ; Rizzolo et al, 2021 ). The addition of TF to Leptospira ClpXP stimulated casein degradation by the protease ( Choudhury et al, 2021 ).…”

“…The addition of TF to Leptospira ClpXP stimulated casein degradation by the protease ( Choudhury et al, 2021 ). In the E. coli study, proteolytic activation of ClpXP by Tig was demonstrated for a broader range of protein substrates in vitro , and from pulse-chase experiments in E. coli cells it was estimated that about 2% of newly synthesized proteins are degraded in a TF-dependent manner ( Rizzolo et al, 2021 ). Peptide array mapping, mutagenesis and NMR analyses jointly support an interaction model which involves all three domains of TF and the AAA+ plus zinc-binding-domain of ClpX, establishing TF as a new adapter for ClpX ( Rizzolo et al, 2021 ).…”