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

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. ClpXP is the main ATP-dependent proteolytic complex in bacteria, is essential for maintaining cellular protein homeostasis and is also critical for bacterial pathogenesis. Here, the authors establish a functional link between ClpXP and trigger actor, a chaperone involved in the early stages of protein folding.

[1]  K. Zeth,et al.  Insight into the RssB-Mediated Recognition and Delivery of σs to the AAA+ Protease, ClpXP , 2020, Biomolecules.

[2]  T. Baker,et al.  Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate , 2019, bioRxiv.

[3]  C. Kalodimos,et al.  Oligomerization of a molecular chaperone modulates its activity , 2018, eLife.

[4]  David Balchin,et al.  In vivo aspects of protein folding and quality control , 2016, Science.

[5]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[6]  Robert H. Vass,et al.  A Phosphosignaling Adaptor Primes the AAA+ Protease ClpXP to Drive Cell Cycle-Regulated Proteolysis. , 2015, Molecular cell.

[7]  W. Houry,et al.  Substrate Interaction Networks of the Escherichia coli Chaperones: Trigger Factor, DnaK and GroEL. , 2015, Advances in experimental medicine and biology.

[8]  W. Houry,et al.  Dynamics of the ClpP serine protease: A model for self-compartmentalized proteases , 2014, Critical reviews in biochemistry and molecular biology.

[9]  C. Kalodimos,et al.  Structural Basis for Protein Antiaggregation Activity of the Trigger Factor Chaperone , 2014, Science.

[10]  Ji-Hyun Kim,et al.  Heat shock protein (Hsp) 70 is an activator of the Hsp104 motor , 2013, Proceedings of the National Academy of Sciences.

[11]  W. Houry,et al.  Role of the N-terminal domain of the chaperone ClpX in the recognition and degradation of lambda phage protein O. , 2012, The journal of physical chemistry. B.

[12]  K. Hughes,et al.  YdiV: a dual function protein that targets FlhDC for ClpXP‐dependent degradation by promoting release of DNA‐bound FlhDC complex , 2012, Molecular microbiology.

[13]  S. Wodak,et al.  Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease. , 2011, Chemistry & biology.

[14]  W. Hendrickson,et al.  Promiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone , 2009, Cell.

[15]  J. Hudak,et al.  Utilization of synthetic peptides to evaluate the importance of substrate interaction at the proteolytic site of Escherichia coli Lon protease. , 2009, Biochimica et biophysica acta.

[16]  J. Kirstein,et al.  Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases , 2009, Nature Reviews Microbiology.

[17]  P. Schmieder,et al.  Large‐scale purification of ribosome‐nascent chain complexes for biochemical and structural studies , 2009, FEBS letters.

[18]  A. Emili,et al.  Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli. , 2009, Methods in molecular biology.

[19]  Claudio Altafini,et al.  Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms , 2008, PloS one.

[20]  Guillaume Thibault,et al.  The AAA+ superfamily of functionally diverse proteins , 2008, Genome Biology.

[21]  W. Houry,et al.  ClpP: A distinctive family of cylindrical energy‐dependent serine proteases , 2007, FEBS letters.

[22]  T. Baker,et al.  Altered Tethering of the SspB Adaptor to the ClpXP Protease Causes Changes in Substrate Delivery* , 2007, Journal of Biological Chemistry.

[23]  H. Song,et al.  Structural basis of SspB-tail recognition by the zinc binding domain of ClpX. , 2007, Journal of molecular biology.

[24]  F. Hartl,et al.  Real-time observation of trigger factor function on translating ribosomes , 2006, Nature.

[25]  Michael K. Coleman,et al.  Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. , 2006, Journal of proteome research.

[26]  W. Houry,et al.  Large nucleotide‐dependent movement of the N‐terminal domain of the ClpX chaperone , 2006, The EMBO journal.

[27]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.

[28]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[29]  Tania A. Baker,et al.  Asymmetric Interactions of ATP with the AAA+ ClpX6 Unfoldase: Allosteric Control of a Protein Machine , 2005, Cell.

[30]  T. Baker,et al.  Versatile modes of peptide recognition by the AAA+ adaptor protein SspB , 2005, Nature Structural &Molecular Biology.

[31]  N. Ban,et al.  Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins , 2004, Nature.

[32]  H. Patzelt,et al.  Trigger Factor Peptidyl-prolyl cis/trans Isomerase Activity Is Not Essential for the Folding of Cytosolic Proteins in Escherichia coli* , 2004, Journal of Biological Chemistry.

[33]  Robert T Sauer,et al.  Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study. , 2004, Molecular cell.

[34]  W. Houry,et al.  Solution Structure of the Dimeric Zinc Binding Domain of the Chaperone ClpX* , 2003, Journal of Biological Chemistry.

[35]  W. Houry,et al.  The N-terminal Zinc Binding Domain of ClpX Is a Dimerization Domain That Modulates the Chaperone Function* , 2003, Journal of Biological Chemistry.

[36]  D. Schneider,et al.  Sequential recognition of two distinct sites in σS by the proteolytic targeting factor RssB and ClpX , 2003, The EMBO journal.

[37]  B. Bukau,et al.  Targeted delivery of an ssrA-tagged substrate by the adaptor protein SspB to its cognate AAA+ protein ClpX. , 2003, Molecular cell.

[38]  T. Baker,et al.  Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. , 2003, Molecular cell.

[39]  Holger Patzelt,et al.  Trigger Factor and DnaK possess overlapping substrate pools and binding specificities , 2003, Molecular microbiology.

[40]  T. Baker,et al.  Characterization of a specificity factor for an AAA+ ATPase: assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer. , 2002, Chemistry & biology.

[41]  J. Schneider-Mergener,et al.  Binding specificity of Escherichia coli trigger factor , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[42]  A. Joachimiak,et al.  Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase. , 2001, Structure.

[43]  S. Gottesman,et al.  The RssB response regulator directly targets sigma(S) for degradation by ClpXP. , 2001, Genes & development.

[44]  T. Baker,et al.  Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase , 2001, Nature Structural Biology.

[45]  T. Baker,et al.  A specificity-enhancing factor for the ClpXP degradation machine. , 2000, Science.

[46]  R. Sauer,et al.  The SsrA–SmpB system for protein tagging, directed degradation and ribosome rescue , 2000, Nature Structural Biology.

[47]  B. Bukau,et al.  Trigger factor and DnaK cooperate in folding of newly synthesized proteins , 1999, Nature.

[48]  R. Sauer,et al.  SmpB, a unique RNA‐binding protein essential for the peptide‐tagging activity of SsrA (tmRNA) , 1999, The EMBO journal.

[49]  F. Hartl,et al.  Polypeptide Flux through Bacterial Hsp70 DnaK Cooperates with Trigger Factor in Chaperoning Nascent Chains , 1999, Cell.

[50]  R. Hengge-aronis,et al.  Regulation of RpoS proteolysis in Escherichia coli: the response regulator RssB is a recognition factor that interacts with the turnover element in RpoS. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[51]  C. Georgopoulos,et al.  Recognition, Targeting, and Hydrolysis of the λ O Replication Protein by the ClpP/ClpX Protease* , 1999, Journal of Biological Chemistry.

[52]  T. E. Shrader,et al.  Species variation in ATP-dependent protein degradation: protease profiles differ between mycobacteria and protease functions differ between Mycobacterium smegmatis and Escherichia coli. , 1999, Gene.

[53]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[54]  E V Koonin,et al.  AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. , 1999, Genome research.

[55]  C. Georgopoulos,et al.  Recognition, targeting, and hydrolysis of the lambda O replication protein by the ClpP/ClpX protease. , 1999, The Journal of biological chemistry.

[56]  S. Gottesman,et al.  Regulation of Proteolysis of the Stationary-Phase Sigma Factor RpoS , 1998, Journal of bacteriology.

[57]  V. Ramakrishnan,et al.  The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids. , 1997, Structure.

[58]  A. Goldberg,et al.  Trigger factor is induced upon cold shock and enhances viability of Escherichia coli at low temperatures. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[59]  R. Sauer,et al.  Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA , 1996, Science.

[60]  T. Schweder,et al.  Regulation of Escherichia coli starvation sigma factor (sigma s) by ClpXP protease , 1996, Journal of bacteriology.

[61]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[62]  J. Wall,et al.  Scanning transmission electron microscopy and small-angle scattering provide evidence that native Escherichia coli ClpP is a tetradecamer with an axial pore. , 1995, Biochemistry.

[63]  Erik Remaut,et al.  Tight Transcriptional Control Mechanism Ensures Stable High-Level Expression from T7 Promoter-Based Expression Plasmids , 1995, Bio/Technology.

[64]  A. Toussaint,et al.  A new component of bacteriophage Mu replicative transposition machinery: the Escherichia coli ClpX protein , 1994, Molecular microbiology.

[65]  S. Gottesman,et al.  ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities. , 1993, The Journal of biological chemistry.

[66]  P. Kiley,et al.  The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. , 1993, Genes & development.

[67]  A. Ishihama,et al.  Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[68]  T. Baker,et al.  Division of labor among monomers within the Mu transposase tetramer , 1993, Cell.

[69]  Akira Ishihama,et al.  Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[70]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[71]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[72]  S. Lecker,et al.  ProOmpA is stabilized for membrane translocation by either purified E. coli trigger factor or canine signal recognition particle , 1988, Cell.

[73]  J. G. Nørby [11] Coupled assay of Na+,K+-ATPase activity , 1988 .

[74]  J. G. Nørby Coupled assay of Na+,K+-ATPase activity. , 1988, Methods in enzymology.

[75]  A. Roberts,et al.  Purification and properties of a type beta transforming growth factor from bovine kidney. , 1983, Biochemistry.