Distinct yet linked: chaperone networks in the eukaryotic cytosol
Genome Biology volume 7, Article number: 208 (2006)
The terms chaperone and heat-shock protein are frequently used as synonyms, but this is an oversimplification. Although one subset of chaperones is induced by heat stress, a distinct group fails to respond in the same manner. Recent work reveals that this latter group is linked to the translational apparatus and functions in co-translational processes.
A decade ago it was recognized that chaperone systems in bacteria form a lateral network of cooperating proteins . The idea of chaperones acting in parallel, with the capacity to replace each other, turned out to be a best-seller and is now generally accepted. Recent work by Albanese et al.  in the yeast Saccharomyces cerevisiae now modifies this concept and suggests the existence of distinct and independent chaperone networks in eukaryotes. One network consists of heat-inducible chaperones that can rescue or dispose of proteins in response to various environmental stresses. The other is thought to be required specifically during de novo protein folding.
A chaperone is not always a heat-shock protein as well
Some years ago Brown and co-workers  analyzed the transcriptional profiles of yeast in response to environmental changes, including a variety of stress conditions. Now, Albanese et al.  have performed clustering analysis of these datasets for chaperone-encoding genes, discovering that transcription of a defined group is co-regulated with the 138 yeast ribosomal protein genes. The authors termed this subgroup 'chaperones linked to protein synthesis' (CLIPS).
Ribosome biogenesis is strictly controlled, and ribosomal protein genes form one of the most prominent clusters in studies of the yeast transcriptome. One important characteristic of the ribosomal gene cluster is that heat stress leads to its downregulation . This means that CLIPS mRNA levels are changing in the opposite direction of the 'classic' heat shock factor-dependent chaperones . Prominent examples of chaperones co-regulated with the ribosomal protein genes are TRiC (chaperonin-containing T-complex), pre-foldin, NAC (nascent-polypeptide associated complex), RAC (ribosome-associated complex), and the Hsp70 homolog Ssb. Consistent with the lack of induction of CLIPS by heat stress, yeast strains lacking nonessential CLIPS are not specifically sensitive to elevated temperatures [4–7], although exceptions have been reported [8, 9].
CLIPS interact with polysomes and cope with specific stress conditions
In their comprehensive survey, Albanese et al.  used sucrose gradient fractionation to investigate which cytosolic chaperones have the propensity to interact with polysomes. When these results are combined with previous analyses it becomes clear that the extent of ribosome association is characteristic for each chaperone [4–6, 10–13]. For example, among the yeast homologs of Hsp70 classified as CLIPS , only a minor fraction of Ssa [2, 11] and Sse1 , about half of Ssb , and virtually all of Ssz1  is ribosome-associated. These differences suggest that some CLIPS are confined to co-translational processes, whereas others serve multiple functions in the cell.
Stimulated by the transcriptome data, the polysome association, and the lack of temperature sensitivity, Albanese et al.  tested the idea that CLIPS specifically mediate de novo protein folding. The question was tackled using the imino acid analog azetidine-2-carboxylic acid (AZC), which is incorporated into proteins competitively with proline and affects de novo folding. Indeed, yeast strains lacking CLIPS such as Ssb were hypersensitive to AZC. On the basis of these findings the authors propose a model in which CLIPS chaperone polypeptides during their synthesis but fail to handle misfolding of preexisting proteins induced by heat stress. Consistent with this model, Albanese et al.  find that toxic misfolded protein species cause growth defects in yeast strains lacking Ssb. To that end they used the so-called GroEL trap, which is an elegant molecular device that captures unfolded polypeptides but is unable to mediate folding . When GroEL trap was expressed in a yeast strain lacking Ssb, growth defects were attenuated, suggesting that simple capturing of misfolded polypeptides can suppress growth defects in the absence of Ssb.
In this context it is worth noting that AZC also affects the stability of proteins . The drug is known to selectively repress expression of ribosomal protein genes while heat shock factor-regulated genes are strongly induced . Furthermore, it has been reported that defects in the disposal of misfolded proteins result in hypersensitivity to this drug . More than a decade ago, Ssb was discovered as a multicopy suppressor of a yeast strain carrying a temperature-sensitive mutation in an essential proteasome subunit . One possible scenario would thus be that Ssb and other CLIPS are involved in the degradation of proteins that fail to fold correctly. Earlier observations by Frydman and co-workers  had indicated, however, that the degradation of the VHL tumor suppressor was independent of Ssb. From the new data one may now speculate that high cellular concentrations of Ssb reduce de novo misfolding, alleviating the pressure on the malfunctioning proteasome.
Functional overlap of distinct chaperone networks
On the basis of its interaction with polysomes, Albanese et al.  classify Ssa, the housekeeping Hsp70 in the yeast cytosol, as a CLIPS. In contrast to most CLIPS, however, SSA is regulated in a heat shock factor-dependent manner and is also involved in the rescue of proteins denatured after an up-shift in temperature [2, 19]. In folding, Ssa is thought to act predominantly posttranslationally, and may ensure that nascent polypeptides that have initiated folding on the ribosome complete the process after their release . Ssa's regulation and function thus overlaps with the CLIPS as well as with the heat shock factor-regulated chaperone network.
Is it possible to assign clear-cut functions to Ssb and Ssa, the major cytosolic Hsp70s in yeast? To date, only limited information is available. Ssa-dependent folding of a few proteins has been demonstrated in vivo. These Ssa substrates did not require Ssb for folding [20, 21]. Instead, Ssb was found to cooperate with the TRiC machinery, which is engaged in the folding of a specific set of substrates . Interestingly, Albanese et al.  find that Ssb is the most efficient binder of nascent polypeptides among the chaperones compared in this study. Whether this interaction is functionally confined to the delivery of folding-competent polypeptides to TRiC awaits further investigation.
Chaperone networks in yeast and higher eukaryotes
Most components of the yeast chaperone networks are present also in higher eukaryotes, suggesting that the mechanisms of protein biogenesis are conserved in eukaryotes. Some of the ribosome-associated chaperones have been discovered only recently. The Hsp40 homolog MPP11 [22, 23] and the Hsp70 homolog Hsp70L1  form a heterodimer functionally equivalent to yeast RAC [6, 23]. In yeast, both subunits of RAC are tightly connected to Ssb and the three chaperones form a functional triad [12, 24]. Ssb, the central player of the yeast CLIPS system , does not, however, seem to have an obvious counterpart in mammalian cells. This has led to the suggestion that mammalian Hsc70, a close homolog of yeast Ssa, serves a dual function and mediates processes that in yeast are divided between Ssa and Ssb . In agreement with this, Hsc70 cooperates with TRiC, a function that in yeast is performed by Ssb [13, 25]. Thus, compared with Ssa, Hsc70 even more intimately connects with cytosolic and ribosome-associated chaperone networks. The question of how interconnections are established and what distinguishes yeast and mammalian chaperone networks will certainly continue to be a central topic for researchers in the field.
Buchberger A, Schröder H, Hesterkamp T, Schönfeld HJ, Bukau B: Substrate shuttling between the DnaK and GroEL systems indicates a chaperone network promoting protein folding. J Mol Biol. 1996, 261: 328-333. 10.1006/jmbi.1996.0465.
Albanese V, Yam AY, Baughman J, Parnot C, Frydman J: Systems analyses reveal two chaperone networks with distinct functions in eukaryotic cells. Cell. 2006, 124: 75-88. 10.1016/j.cell.2005.11.039.
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000, 11: 4241-4257.
Nelson RJ, Ziegelhoffer T, Nicolet C, Werner-Washburne M, Craig EA: The translation machinery and 70 kd heat shock protein cooperate in protein synthesis. Cell. 1992, 71: 97-105. 10.1016/0092-8674(92)90269-I.
Yan W, Schilke B, Pfund C, Walter W, Kim S, Craig EA: Zuotin, a ribosome-associated DnaJ molecular chaperone. EMBO J. 1998, 17: 4809-4817. 10.1093/emboj/17.16.4809.
Gautschi M, Lilie H, Fünfschilling U, Mun A, Ross S, Lithgow T, Rücknagel P, Rospert S: RAC, a stable ribosome-associated complex in yeast formed by the DnaK-DnaJ homologs Ssz1p and zuotin. Proc Natl Acad Sci USA. 2001, 98: 3762-3767. 10.1073/pnas.071057198.
Geissler S, Siegers K, Schiebel E: A novel protein complex promoting formation of functional alpha- and gamma-tubulin. EMBO J. 1998, 17: 952-966. 10.1093/emboj/17.4.952.
Werner-Washburne M, Stone DE, Craig EA: Complex interactions among members of an essential subfamily of hsp70 genes in Saccharomyces cerevisiae. Mol Cell Biol. 1987, 7: 2568-2577.
Grallath S, Schwarz JP, Bottcher UM, Bracher A, Hartl FU, Siegers K: L25 functions as a conserved ribosomal docking site shared by nascent chain-associated complex and signal-recognition particle. EMBO Rep. 2006, 7: 78-84. 10.1038/sj.embor.7400551.
George R, Beddoe T, Landl K, Lithgow T: The yeast nascent polypeptide-associated complex initiates protein targeting to mitochondria in vivo. Proc Natl Acad Sci USA. 1998, 95: 2296-2301. 10.1073/pnas.95.5.2296.
Horton LE, James P, Craig EA, Hensold JO: The yeast hsp70 homologue Ssa is required for translation and interacts with Sis1 and Pab1 on translating ribosomes. J Biol Chem. 2001, 276: 14426-14433.
Gautschi M, Mun A, Ross S, Rospert S: A functional chaperone triad on the yeast ribosome. Proc Natl Acad Sci USA. 2002, 99: 4209-4214. 10.1073/pnas.062048599.
Siegers K, Bolter B, Schwarz JP, Bottcher UM, Guha S, Hartl FU: TRiC/CCT cooperates with different upstream chaperones in the folding of distinct protein classes. EMBO J. 2003, 22: 5230-5240. 10.1093/emboj/cdg483.
Fenton WA, Kashi Y, Furtak K, Horwich AL: Residues in chaperonin GroEL required for polypeptide binding and release. Nature. 1994, 371: 614-619. 10.1038/371614a0.
Trotter EW, Kao CM, Berenfeld L, Botstein D, Petsko GA, Gray JV: Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae. J Biol Chem. 2002, 277: 44817-44825. 10.1074/jbc.M204686200.
Hoshikawa C, Shichiri M, Nakamori S, Takagi H: A nonconserved Ala401 in the yeast Rsp5 ubiquitin ligase is involved in degradation of Gap1 permease and stress-induced abnormal proteins. Proc Natl Acad Sci USA. 2003, 100: 11505-11510. 10.1073/pnas.1933153100.
Ohba M: A 70-kDa heat shock cognate protein suppresses the defects caused by a proteasome mutation in Saccharomyces cerevisiae. FEBS Lett. 1994, 351: 263-266. 10.1016/0014-5793(94)00873-6.
McClellan AJ, Scott MD, Frydman J: Folding and quality control of the VHL tumor suppressor proceed through distinct chaperone pathways. Cell. 2005, 121: 739-748. 10.1016/j.cell.2005.03.024.
Haslbeck M, Miess A, Stromer T, Walter S, Buchner J: Disassembling protein aggregates in the yeast cytosol. The cooperation of Hsp26 with Ssa1 and Hsp104. J Biol Chem. 2005, 280: 23861-23868. 10.1074/jbc.M502697200.
Kim S, Schilke B, Craig EA, Horwich AL: Folding in vivo of a newly translated yeast cytosolic enzyme is mediated by the SSA class of cytosolic yeast Hsp70 proteins. Proc Natl Acad Sci USA. 1998, 95: 12860-12865. 10.1073/pnas.95.22.12860.
Crombie T, Boyle JP, Coggins JR, Brown AJ: The folding of the bifunctional TRP3 protein in yeast is influenced by a translational pause which lies in a region of structural divergence with Escherichia coli indoleglycerol-phosphate synthase. Eur J Biochem. 1994, 226: 657-664. 10.1111/j.1432-1033.1994.tb20093.x.
Hundley HA, Walter W, Bairstow S, Craig EA: Human Mpp11 J protein: ribosome-tethered molecular chaperones are ubiquitous. Science. 2005, 308: 1032-1034. 10.1126/science.1109247.
Otto H, Conz C, Maier P, Wölfle T, Suzuki CK, Jenö P, Rücknagel P, Stahl J, Rospert S: The chaperones MPP11 and Hsp70L1 form the mammalian ribosome-associated complex. Proc Natl Acad Sci USA. 2005, 102: 10064-10069. 10.1073/pnas.0504400102.
Huang P, Gautschi M, Walter W, Rospert S, Craig EA: The Hsp70 Ssz1 modulates the function of the ribosome-associated J-protein Zuo1. Nat Struct Mol Biol. 2005, 12: 497-504. 10.1038/nsmb942.
Feldman DE, Thulasiraman V, Ferreyra RG, Frydman J: Formation of the VHL-elongin BC tumor suppressor complex is mediated by the chaperonin TRiC. Mol Cell. 1999, 4: 1051-1061. 10.1016/S1097-2765(00)80233-6.
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Rospert, S., Chacinska, A. Distinct yet linked: chaperone networks in the eukaryotic cytosol. Genome Biol 7, 208 (2006). https://doi.org/10.1186/gb-2006-7-3-208
- Heat Stress
- Yeast Strain
- Ribosomal Protein Gene
- Nascent Polypeptide
- Hsp70 Homolog