Wikipedia

User:Bostonalumn/GrpE

< User:Bostonalumn

GrpE (Gro-P like protein E) is a bacterial nucleotide exchange factor that is important for regulation of protein folding machinery. It is a heat-inducible protein and during stress it prevents unfolded proteins from accumulating in the cytoplasm.[1][2] Accumulation of unfolded proteins in the cytoplasm can lead to cell death.[3]

GrpE Protein
Annotated GrpE structure at 2.8A
Crystal structure of GrpE homodimer interacting with ATPase binding site of DnaK, resolved at 2.8 angstrom.
Identifiers
SymbolGrpE
PfamPF01025
InterProIPR000740
PROSITEPS01071
SCOP21dkg / SCOPe / SUPFAM
CDDcd00446
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

Discovery

edit

GrpE is a nucleotide exchange factor that was first discovered by researchers in 1977 as a protein necessary to propagate bacteriophage λ in Escherichia coli.[4] Bacteriophage λ is a virus that infects bacteria by highjacking the bacteria's own replication machinery.[5] GrpE assists phage λ replication through its role as a nucleotide exchange factor and significantly accelerating the exchange of nucleotides. By using a mutant screen, researchers knocked out certain genes in E. coli and then tested whether the bacteria was able to replicate, GrpE was found to be crucial to propagation. Since this time GrpE has been identified in all bacteria and in archea where DnaK and DnaJ are present.[6]

The crystal structure of GrpE was determined in 1997 at 2.8 angstrom and identified GrpE as a homodimer that binds DnaK, a heat-shock protein involved in de novo protein folding.[7] GrpeE's structure determination was important because it demonstrated the interaction of nucleotide exchange factors at the nucleotide binding domain of DnaK.[8]

Structure

edit

Functional domains

edit

The GrpE homodimer has three distinct domains:

  • N-terminal disordered regions — 33 amino acids can compete for binding to the substrate binding cleft of DnaK. Amino acids 34-39 have not been visualized because they are either too disordered or too unstructured to be crystallized.
  • α-helices — four α-helices, two short and two long, are stalk-like and parallel to each other. These helices come together to form a helical bundle however, there is no superhelical twisting due to the heptad-hendecad (7-11-7-11) spacing of hydrophobic residues in these helices. Portions of this helical bundle are able to bind to Domain IIB of DnaK. These helices also act as thermosensors.
  • C-terminal β-sheets — one β-sheet from each protein stick out from the helices like arms. The β-sheets are compact, the one proximal to DnaK interacts with its ATP binding cleft directly by inserting itself into the cleft and causing a conformational shift in Domain IIB causing the release of ADP. The distal β-sheet does not interact with DnaK.[1][2]

Binding induces a conformational change

edit

Binding of GrpE's proximal β-sheet to Domain IIB of DnaK causes a 14° outward rotation of the nucleotide binding cleft, disrupting the binding of three side chains to the adenine and ribose rings of the nucleotide. This conformational change shifts DnaK from a closed to an "open" conformation and allows the release of ADP from the binding cleft.[9]

Function

edit

Bacteriophage λ Replication

edit

The discovery of GrpE demonstrated its critical role in phage λ replication. Mutations of GrpE, so that it is no longer functional, prevents phage λ replication in vivo and greatly decreases replication in vitro. In vitro overexpression of DnaK can recover phage λ replication without GrpE. GrpE's pivotal role in phage λ replication is at the origin of replication, after assembly of DnaB and other replication factors, GrpE facilitates bidirectional DNA unwinding through interaction with DnaK.[10]

Nucleotide Exchange Factor

edit
 
Co-chaperone DnaJ brings in unfolded protein to substrate binding site of DnaK and hydrolyzes ADP. GrpE then interacts with the nucleotide binding cleft of DnaK to induce a conformational change and ADP release, the substrate is also released.[11][12]

Nucleotide exchange factors are proteins that catalyze the release of adenosine diphosphate (ADP) to facilitate binding of adenosine triphosphate (ATP). ATP has three phosphate groups and the removal of one of the phosphate groups releases energy which is used to fuel a reaction. This removal of a phosphate group reduces ATP to ADP. GrpE is a nucleotide exchange factor that causes the release of bound ADP from DnaK, a heat shock protein important in de novo protein folding. DnaK, in its "open" conformation, binds ATP with low affinity and has a fast exchange rate for unfolded proteins. Once DnaJ, a co-chaperone, brings an unfolded protein to DnaK ATP is hydrolyzed to ADP to facilitate folding of the protein. At this point, the DnaJ•DnaK•ADP complex is in a stable conformation and requires GrpE to bind DnaK, change its conformation, and release ADP from the N-terminal ATPase domain of DnaK. Once ADP is released from the cycle is able to continue. [13][14]

Kinetics

edit

The interaction between GrpE and the nucleotide binding cleft of DnaK is strong with a Kd between 1 nM, assessed during active conformation using transient kinetics, and a Kd of 30 nM, based on inactive conformation through surface plasmon resonance.[2] This low dissociation constant indicates that GrpE readily binds to DnaK.[15] Binding of GrpE to DnaK•ADP greatly reduces the affinity of ADP for DnaK by 200-fold and accelerates the rate of nucleotide release by 5000-fold. This process facilitates the de novo folding of unfolded protein by DnaK. [2][13]

Protein Folding

edit

DnaK functions to fold proteins in the cytoplasm, it does so by binding the substrate, and using energy in the form of ATP hydrolysis, folds it. After ATP hydroylsis the DnaK•ADP complex relies on GrpE to induce a conformational change and release the nucleotide so that the cycle can continue.[1][2] GrpE also has an important role in substrate release from DnaK. The disordered N-terminal region of GrpE competes for binding to DnaK's substrate binding cleft. Mutated GrpE, without its disordered N-terminal domain, is still able to bind to DnaK•ADP and induce a conformational change in the nucleotide binding cleft but the substrate will not be released.[8]

Thermosensor

edit

GrpE is a nucleotide exchange factor for DnaK, a heat shock protein, as a result GrpE is temperature sensitive and its activity is downregulated by temperature.[1] In biology, reversible unfolding of α-helices begins at 35°C with a midpoint Tm of 50°C, this unfolding affects the structural integrity of GrpE and prevents binding of GrpE to DnaK•ADP. This has an important physiological role to limit the substrate cycling and subsequent ATP expenditure during heat stress. The thermal regulation of DnaK slows protein folding and prevents unfolded proteins from accumulating in the cytoplasm at high temperatures.[2][13][14]

Regulation

edit

Transcription

edit

In the archeas' genome, the gene for GrpE is located upstream of the gene for DnaK which, is upstream of the gene for DnaJ. Out of these three proteins, only the promoter region of GrpE has a complete TATA binding box and upstream heat-responsive binding site. This suggests that, in Archea, these three genes are transcribed at the same time.[6]

In E. coli, GrpE's transcription is regulated by binding of the heat-shock specific subunit of RNA polymerase, σ32.[16] Under physiological conditions, σ32 is kept at low levels through inactivation by interacting with DnaK and DnaJ, then subsequent degradation by proteases. However, during heat shock these proteins are unable to interact with σ32 and target it for degradation. Therefore, during heat shock, σ32 binds to the promoter region of heat shock proteins and causes rapid induction of these genes. [17]

Other Biological Systems

edit

Eukaryote Homologues

edit

In Saccharomyces cerevisiae, the GrpE homologue, Mge1, is found in mitochondria.[18] Mge1 is a nucleotide exchange factor important for shuttling proteins across mitochondrial membranes and in protein folding, it interacts with a yeast homologue of DnaK. Mge1 has a similar role as a thermosensor.[18] Yeast have additional GrpE homologues including Sil1p and Fes1p.[19] In humans, mitochondrial organelles have GrpE-like 1 (GRPEL1) protein.[20]


In eukaryotic cells, there any many additional eukaryotic GrpE homologues.[19] Members of the BAG family specifically, BAG1 are the main nucleotide exchange factors for heat shock protein 70kDa (Hsp70), which is the eukaryotic equivalent of DnaK. Other nucleotide exchange factors that interact with heat-shock proteins in eukaryotes include, Sse1p, Sil1p, Hip, and HspBP1.[1][19] These eukaryotic nucleotide exchange factors are all heat-shock inducible meaning that they serve a similar function as GrpE, to protect the cell from unfolded protein aggregation. These nucleotide exchange factors always interact with subdomain IIB of the nucleotide binding cleft of their respective heat-shock proteins. The binding of the nucleotide exchange factor to a nucleotide binding cleft and the shift to an "open" conformation is conserved from prokaryotes to eukaryotes.[1][21]

Plant Homologues

edit

In plants, GrpE homologues, CGE1 and CGE2, are found in chloroplasts. CGE1 has two splice isoforms that differ in 6 amino acids in the N-terminal, with isoform CGE1b being 6 nucleotides longer than CGE1a. This N-terminal domain is important in substrate release through competitive binding to the heat-shock protein. All of these plant nucleotide exchange factors interact directly with the cpHsc70, the plant homologue of DnaK. They are heat-inducible however, at 43°C, they are not as effective as GrpE at protecting the cell from unfolded protein accumulation.[22][23][24]

Role in Disease

edit

Bacterial Pathogenesis

edit

GrpE has an important role in bacteria's infection of host species.[25][26][27] Enterococci are bacteria that are commonly found in the guts of humans and other animals, they are pH, temperature, and salt insensitive.[28] These bacteria are antibiotic resistant and are dangerous when they produce an infectious biofilm.[29][28] Enterococcal biofilm is prevalent in hospital and surgical settings, it is responsible for 25% of catheter-related infections[28], is found in 50% of root-filled teeth with apical periodontitis[29], and can be isolated from other wounds.[28] GrpE is found in the genome of Enterococcus faecilis and Enterococcus faecium and is critical for enterococcal biofilm attachment to polystyrene tubes,[27] a plastic polymer commonly used in hospital settings.[30]

Group A Streptococcus pyogenes is a bacteria that can lead to common infections, including strep throat and impetigo, but is also responsible for life-threatening infections.[31][26] During infection, GrpE helps streptococcus bacteria adhere to pharyngeal epithelial cells.[26] GrpE in Streptococcus binds to endogenous proline-rich proteins in saliva, allowing adhesion of the bacteria to the host.[26]

References

edit
  1. ^ a b c d e f Bracher, Andreas; Verghese, Jacob (2015-04-07). "The nucleotide exchange factors of Hsp70 molecular chaperones". Frontiers in Molecular Biosciences. 2. doi:10.3389/fmolb.2015.00010. ISSN 2296-889X. PMC 4753570. PMID 26913285.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  2. ^ a b c d e f Harrison, Celia (July 2003). "GrpE, a nucleotide exchange factor for DnaK". Cell Stress Chaperones. 8(3): 218–224 – via Pubmed.
  3. ^ Richter, Klaus; Haslbeck, Martin; Buchner, Johannes (2010-10). "The Heat Shock Response: Life on the Verge of Death". Molecular Cell. 40 (2): 253–266. doi:10.1016/j.molcel.2010.10.006. {{cite journal}}: Check date values in: |date= (help)
  4. ^ Saito, Haruo; Uchida, Hisao (1977-06-15). "Initiation of the DNA replication of bacteriophage lambda in Escherichia coli K12". Journal of Molecular Biology. 113 (1): 1–25. doi:10.1016/0022-2836(77)90038-9. ISSN 0022-2836.
  5. ^ Griffiths, Anthony JF; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. (2000). "Lambda phage: a complex of operons". An Introduction to Genetic Analysis. 7th edition.
  6. ^ a b Hickey, Anthony J.; de Macario, Everly Conway; Macario, Alberto J. L. (2002-1). "Transcription in the Archaea: Basal Factors, Regulation, and Stress Gene Expression". Critical Reviews in Biochemistry and Molecular Biology. 37 (4): 199–258. doi:10.1080/10409230290771500. ISSN 1040-9238. {{cite journal}}: Check date values in: |date= (help)
  7. ^ Harrison, Celia J.; Hayer-Hartl, Manajit; Liberto, Maurizio Di; Hartl, F.-Ulrich; Kuriyan, John (1997-04-18). "Crystal Structure of the Nucleotide Exchange Factor GrpE Bound to the ATPase Domain of the Molecular Chaperone DnaK". Science. 276 (5311): 431–435. doi:10.1126/science.276.5311.431. ISSN 0036-8075. PMID 9103205.
  8. ^ a b Brodsky, Jeffrey L.; Bracher, Andreas (2013). Nucleotide Exchange Factors for Hsp70 Molecular Chaperones. Landes Bioscience.
  9. ^ The networking of chaperones by co-chaperones : control of cellular protein homeostasis. Blatch, Gregory L.,, Edkins, Adrienne Lesley,. Cham. ISBN 9783319117317. OCLC 898028354.{{cite book}}: CS1 maint: extra punctuation (link) CS1 maint: others (link)
  10. ^ Wyman, C.; Vasilikiotis, C.; Ang, D.; Georgopoulos, C.; Echols, H. (1993-11-25). "Function of the GrpE heat shock protein in bidirectional unwinding and replication from the origin of phage lambda". The Journal of Biological Chemistry. 268 (33): 25192–25196. ISSN 0021-9258. PMID 8227083.
  11. ^ Calloni, Giulia; Chen, Taotao; Schermann, Sonya M.; Chang, Hung-chun; Genevaux, Pierre; Agostini, Federico; Tartaglia, Gian Gaetano; Hayer-Hartl, Manajit; Hartl, F. Ulrich (2012-03). "DnaK Functions as a Central Hub in the E. coli Chaperone Network". Cell Reports. 1 (3): 251–264. doi:10.1016/j.celrep.2011.12.007. {{cite journal}}: Check date values in: |date= (help); no-break space character in |first3= at position 6 (help); no-break space character in |first7= at position 5 (help); no-break space character in |first9= at position 3 (help)
  12. ^ Prokaryotic systems biology. Krogan, Nevan J.,, Babu, Mohan,. Cham. ISBN 978-3-319-23603-2. OCLC 930781755.{{cite book}}: CS1 maint: extra punctuation (link) CS1 maint: others (link)
  13. ^ a b c Bhandari, Vaibhav; Houry, Walid A. (2015), Krogan, PhD, Nevan J.; Babu, PhD, Mohan (eds.), "Substrate Interaction Networks of the Escherichia coli Chaperones: Trigger Factor, DnaK and GroEL", Prokaryotic Systems Biology, vol. 883, Springer International Publishing, pp. 271–294, doi:10.1007/978-3-319-23603-2_15, ISBN 9783319236025, retrieved 2019-11-18
  14. ^ a b Winter, Jeannette; Jakob, Ursula (2004-1). "Beyond Transcription—New Mechanisms for the Regulation of Molecular Chaperones". Critical Reviews in Biochemistry and Molecular Biology. 39 (5–6): 297–317. doi:10.1080/10409230490900658. ISSN 1040-9238. {{cite journal}}: Check date values in: |date= (help)
  15. ^ Bisswanger, Hans. (2008). Enzyme kinetics : principles and methods (2nd rev. and updated ed ed.). Weinheim: Wiley-VCH. ISBN 978-3-527-31957-2. OCLC 225406378. {{cite book}}: |edition= has extra text (help)
  16. ^ Arsène, F.; Tomoyasu, T.; Bukau, B. (2000-04-10). "The heat shock response of Escherichia coli". International Journal of Food Microbiology. 55 (1–3): 3–9. doi:10.1016/s0168-1605(00)00206-3. ISSN 0168-1605. PMID 10791710.
  17. ^ Tomoyasu, T.; Ogura, T.; Tatsuta, T.; Bukau, B. (1998-11). "Levels of DnaK and DnaJ provide tight control of heat shock gene expression and protein repair in Escherichia coli". Molecular Microbiology. 30 (3): 567–581. doi:10.1046/j.1365-2958.1998.01090.x. ISSN 0950-382X. PMID 9822822. {{cite journal}}: Check date values in: |date= (help)
  18. ^ a b Moro, Fernando; Muga, Arturo (2006-05). "Thermal Adaptation of the Yeast Mitochondrial Hsp70 System is Regulated by the Reversible Unfolding of its Nucleotide Exchange Factor". Journal of Molecular Biology. 358 (5): 1367–1377. doi:10.1016/j.jmb.2006.03.027. {{cite journal}}: Check date values in: |date= (help)
  19. ^ a b c The networking of chaperones by co-chaperones : control of cellular protein homeostasis. Blatch, Gregory L.,, Edkins, Adrienne Lesley,. Cham. ISBN 978-3-319-11731-7. OCLC 898028354.{{cite book}}: CS1 maint: extra punctuation (link) CS1 maint: others (link)
  20. ^ MacKenzie, James A.; Payne, R. Mark (2007-05). "Mitochondrial protein import and human health and disease". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 1772 (5): 509–523. doi:10.1016/j.bbadis.2006.12.002. PMC 2702852. PMID 17300922. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  21. ^ Dekker, Peter J.T.; Pfanner, Nikolaus (1997-07). "Role of mitochondrial GrpE and phosphate in the ATPase cycle of matrix Hsp70". Journal of Molecular Biology. 270 (3): 321–327. doi:10.1006/jmbi.1997.1131. {{cite journal}}: Check date values in: |date= (help)
  22. ^ de Luna-Valdez, L.A.; Villaseñor-Salmerón, C.I.; Cordoba, E.; Vera-Estrella, R.; León-Mejía, P.; Guevara-García, A.A. (2019-06). "Functional analysis of the Chloroplast GrpE (CGE) proteins from Arabidopsis thaliana". Plant Physiology and Biochemistry. 139: 293–306. doi:10.1016/j.plaphy.2019.03.027. {{cite journal}}: Check date values in: |date= (help)
  23. ^ Schroda, Michael; Vallon, Olivier; Whitelegge, Julian P.; Beck, Christoph F.; Wollman, Francis-André (2001-12). "The Chloroplastic GrpE Homolog of Chlamydomonas: Two Isoforms Generated by Differential Splicing". The Plant Cell. 13 (12): 2823–2839. doi:10.1105/tpc.010202. ISSN 1040-4651. {{cite journal}}: Check date values in: |date= (help)
  24. ^ Willmund, Felix; Mühlhaus, Timo; Wojciechowska, Maria; Schroda, Michael (2007-04-13). "The NH 2 -terminal Domain of the Chloroplast GrpE Homolog CGE1 Is Required for Dimerization and Cochaperone Function in Vivo". Journal of Biological Chemistry. 282 (15): 11317–11328. doi:10.1074/jbc.M608854200. ISSN 0021-9258.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  25. ^ Vanghele, MO; Ganea, EL (2010). "The role of bacterial molecular chaperones in pathogen survival within the host" (PDF). Rom J Biochem. 47.87: 100.
  26. ^ a b c d Brouwer, Stephan; Barnett, Timothy C.; Rivera-Hernandez, Tania; Rohde, Manfred; Walker, Mark J. (2016-11). "Streptococcus pyogenes adhesion and colonization". FEBS Letters. 590 (21): 3739–3757. doi:10.1002/1873-3468.12254. {{cite journal}}: Check date values in: |date= (help)
  27. ^ a b Paganelli, Fernanda L.; Willems, Rob J.; Leavis, Helen L. (2012-01). "Optimizing future treatment of enterococcal infections: attacking the biofilm?". Trends in Microbiology. 20 (1): 40–49. doi:10.1016/j.tim.2011.11.001. {{cite journal}}: Check date values in: |date= (help)
  28. ^ a b c d Ch'ng, Jun-Hong; Chong, Kelvin K. L.; Lam, Ling Ning; Wong, Jun Jie; Kline, Kimberly A. (01 2019). "Biofilm-associated infection by enterococci". Nature Reviews. Microbiology. 17 (2): 82–94. doi:10.1038/s41579-018-0107-z. ISSN 1740-1534. PMID 30337708. {{cite journal}}: Check date values in: |date= (help)
  29. ^ a b Gilmore, Michael S.; Clewell, Don B.; Ike, Yasuyoshi; Shankar, Nathan, eds. (2014). Enterococci: From Commensals to Leading Causes of Drug Resistant Infection. Boston: Massachusetts Eye and Ear Infirmary. PMID 24649510.
  30. ^ "What is Polystyrene? | Uses, Benefits, and Safety Facts". ChemicalSafetyFacts.org. 2014-05-01. Retrieved 2019-12-11.
  31. ^ Mandell, Douglas, and Bennett's principles and practice of infectious diseases. Bennett, John E. (John Eugene), 1933-, Dolin, Raphael,, Blaser, Martin J., (Ninth edition ed.). Philadelphia, PA. ISBN 978-0-323-55027-7. OCLC 1118693541. {{cite book}}: |edition= has extra text (help)CS1 maint: extra punctuation (link) CS1 maint: others (link)
Retrieved from "https://en.wikipedia.org/w/index.php?title=User:Bostonalumn/GrpE&oldid=930746809"