Ribosome-tethered molecular chaperones: the first line of defense against protein misfolding?

The Hsp70 Ssz1 modulates the function of the ribosome-associated J-protein Zuo1

J-proteins are obligate partners of Hsp70s, forming a ubiquitous class of molecular chaperone machinery. The ribosome-associated Hsp70 of yeast Ssb binds nascent polypeptides as they exit the ribosome. Here we report that the ribosome-associated J-protein Zuo1 is the partner of Ssb. However, Zuo1 efficiently stimulates the ATPase activity of Ssb only when in complex with another Hsp70, Ssz1. Ssz1 binds ATP, but none of the 11 different amino acid substitutions in the ATP-binding cleft affected Ssz1 function in vivo, suggesting that neither nucleotide binding nor hydrolysis is required. We propose that Ssz1's predominant function in the cell is to facilitate Zuo1's ability to function as a J-protein partner of Ssb on the ribosome, serving as an example of an Hsp70 family member that has evolved to carry out functions distinct from that of a chaperone.

Activation and expression of proteins during synchronous germination of aerial spores of Streptomyces granaticolor

Synchronously germinating aerial spores of Streptomyces granaticolor were used to study protein activation and expression during the transition from dormant to metabolically active vegetative forms. The first phase of protein activation is associated with the solubility of proteins. Three major chaperones, DnaK, Trigger factor, and GroEL, were identified in spores. Enhancement in rate of protein synthesis during germination was accompanied by the association of TF and DnaK with ribosomes. During germination, the chaperones TF, GroEL, and DnaK undergo reversible phosphorylation. GroEL was phosphorylated on both Ser and Thr, whereas phosphorylation of DnaK and TF was detected on Thr only. A proteomic approach was used to gain more information on protein expression during germination on two types of media differing in the ability of cells to produce antibiotic granaticin. To obtain an overview of the metabolic activity of germinating spores, glycolytic enzymes, enzymes of citric acid cycle, metabolism of amino acids and nucleic acids, and components of the protein synthesis system were identified and analyzed using the proteomic database. The results were deposited on the SWICZ proteomic server and are accessible on http://proteom.biomed.cas.cz.

Human Mpp11 J protein: ribosome-tethered molecular chaperones are ubiquitous

The existence of specialized molecular chaperones that interact directly with ribosomes is well established in microorganisms. Such proteins bind polypeptides exiting the ribosomal tunnel and provide a physical link between translation and protein folding. We report that ribosome-associated molecular chaperones have been maintained throughout eukaryotic evolution, as illustrated by Mpp11, the human ortholog of the yeast ribosome-associated J protein Zuo. When expressed in yeast, Mpp11 partially substituted for Zuo by partnering with the multipurpose Hsp70 Ssa, the homolog of mammalian Hsc70. We propose that in metazoans, ribosome-associated Mpp11 recruits the multifunctional soluble Hsc70 to nascent polypeptide chains as they exit the ribosome.

High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome

Proteomic studies have addressed the composition of plant chloroplast ribosomes and 70S ribosomes from the unicellular organism Chlamydomonas reinhardtii But comprehensive characterization of cytoplasmic 80S ribosomes from higher plants has been lacking. We have used two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) to analyse the cytoplasmic 80S ribosomes from the model flowering plant Arabidopsis thaliana. Of the 80 ribosomal protein families predicted to comprise the cytoplasmic 80S ribosome, we have confirmed the presence of 61; specifically, 27 (84%) of the small 40S subunit and 34 (71%) of the large 60S subunit. Nearly half (45%) of the ribosomal proteins identified are represented by two or more distinct spots in the 2-DE gel indicating that these proteins are either post-translationally modified or present as different isoforms. Consistently, MS-based protein identification revealed that at least one-third (34%) of the identified ribosomal protein families showed expression of two or more family members. In addition, we have identified a number of non-ribosomal proteins that co-migrate with the plant 80S ribosomes during gradient centrifugation suggesting their possible association with the 80S ribosomes. Among them, RACK1 has recently been proposed to be a ribosome-associated protein that promotes efficient translation in yeast. The study, thus provides the basis for further investigation into the function of the other identified non-ribosomal proteins as well as the biological meaning of the various ribosomal protein isoforms.

The J-protein family: modulating protein assembly, disassembly and translocation

DnaJ is a molecular chaperone and the prototypical member of the J-protein family. J proteins are defined by the presence of a J domain that can regulate the activity of 70-kDa heat-shock proteins. Sequence analysis on the genome of Saccharomyces cerevisiae has revealed 22 proteins that establish four distinguishing structural features of the J domain: predicted helicity in segments I-IV, precisely placed interhelical contact residues, a lysine-rich surface on helix II and placement of the diagnostic sequence HPD between the predicted helices II and III. We suggest that this definition of the J-protein family could be used for other genome-wide studies. In addition, three J-like proteins were identified in yeast that contain regions closely resembling a J domain, but in which the HPD motif is non-conservatively replaced. We suggest that J-like proteins might function to regulate the activity of bona fide J proteins during protein translocation, assembly and disassembly.

The ribosome-bound chaperones RAC and Ssb1/2p are required for accurate translation in Saccharomyces cerevisiae

The chaperone homologs RAC (ribosome-associated complex) and Ssb1/2p are anchored to ribosomes; Ssb1/2p directly interacts with nascent polypeptides. The absence of RAC or Ssb1/2p results in a similar set of phenotypes, including hypersensitivity against the aminoglycoside paromomycin, which binds to the small ribosomal subunit and compromises the fidelity of translation. In order to understand this phenomenon we measured the frequency of translation termination and misincorporation in vivo and in vitro with a novel reporter system. Translational fidelity was impaired in the absence of functional RAC or Ssb1/2p, and the effect was further enhanced by paromomycin. The mutant strains suffered primarily from a defect in translation termination, while misincorporation was compromised to a lesser extent. Consistently, a low level of soluble translation termination factor Sup35p enhanced growth defects in the mutant strains. Based on the combined data we conclude that RAC and Ssb1/2p are crucial in maintaining translational fidelity beyond their postulated role as chaperones for nascent polypeptides.

The in vivo tyrosine phosphorylation level of yeast immunophilin Fpr3 is influenced by the LMW-PTP Ltp1

Tyr-phosphorylation in Saccharomyces cerevisiae is essential in controlling the activity of MAP kinase regulating mating, pseudohyphal growth, and cell wall biosynthesis. Yeast serves as a model system for studying the biological function of many protein kinases and PTPs. Two LMW-PTP from yeast have been cloned, namely, Ltp1 from S. cerevisiae and Stp1 from Schizosaccharomyces pombe. The sequences of both enzymes are relatively similar to those of the mammalian LMW-PTP. Recently we showed that the yeast immunophilin Fpr3 interacts with Stp1 and its dephosphorylated state induces a growth defective phenotype. Here we show the phosphatase activity of Ltp1 on Fpr3 and we demonstrated that Tyr 184 is the residue phosphorylated on in vivo Fpr3. We also described the marked activation of Ltp1 by adenine in S. cerevisiae proteome and determined in vivo the influence of tyrosine phosphorylation on Fpr3 localization.

Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome

Signal recognition particle (SRP) and trigger factor (TF) both bind to ribosomal protein L23 at the peptide exit area on the 50S subunit of the E. coli ribosome. In this study, we have developed a spin-down assay and used it to estimate KD values and the corresponding enthalpies for the binding of radio-labelled SRP and TF to naked ribosomes and to ribosomes carrying a tetrapeptidyl-tRNA in the P site. At 20 degrees C, the KD value for TF binding is 2 microM and for SRP it is 170 nM for naked as well as for translating ribosomes. At 4 degrees C, the KD values for TF and SRP binding are 1.1 microM and 90 nM, respectively. Competition binding experiments reveal that SRP and TF bind simultaneously to the ribosome with little affinity interference, showing that the factors have separate binding sites on L23. This makes an alternating binding mode for TF and SRP less plausible.

The Reg1-interacting proteins, Bmh1, Bmh2, Ssb1, and Ssb2, have roles in maintaining glucose repression in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, a type 1 protein phosphatase complex composed of the Glc7 catalytic subunit and the Reg1 regulatory subunit represses expression of many glucose-regulated genes. Here we show that the Reg1-interacting proteins Bmh1, Bmh2, Ssb1, and Ssb2 have roles in glucose repression. Deleting both BMH genes causes partially constitutive ADH2 expression without significantly increasing the level of Adr1 protein, the major activator of ADH2 expression. Adr1 and Bcy1, the regulatory subunit of cAMP-dependent protein kinase, are both required for this effect indicating that constitutive expression in Deltabmh1Deltabmh2 cells uses the same activation pathway that operates in Deltareg1 cells. Deletion of both BMH genes and REG1 causes a synergistic relief from repression, suggesting that Bmh proteins also act independently of Reg1 during glucose repression. A two-hybrid interaction with the Bmh proteins was mapped to amino acids 187-232, a region of Reg1 that is conserved in different classes of fungi. Deleting this region partially releases SUC2 from glucose repression. This indicates a role for the Reg1-Bmh interaction in glucose repression and also suggests a broad role for Bmh proteins in this process. An in vivo Reg1-Bmh interaction was confirmed by copurification of Bmh proteins with HA(3)-TAP-tagged Reg1. The nonconventional heat shock proteins Ssb1 and Ssb2 are also copurified with HA(3)-TAP-tagged Reg1. Deletion of both SSB genes modestly decreases repression of ADH2 expression in the presence of glucose, suggesting that Ssb proteins, perhaps through their interaction with Reg1, play a minor role in glucose repression.

DafA Cycles Between the DnaK Chaperone System and Translational Machinery

DafA is encoded by the dnaK operon of Thermus thermophilus and mediates the formation of a highly stable complex between the chaperone DnaK and its co-chaperone DnaJ under normal growth conditions. DafA(Tth) contains 87 amino acid residues and is the only member of the DnaK(Tth) chaperone system for which no corresponding protein has yet been identified in other organisms and whose particular function has remained elusive. Here, we show directly that the DnaK(Tth)-DnaJ(Tth)-DafA(Tth) complex cannot represent the active chaperone species since DafA(Tth) inhibits renaturation of firefly luciferase by suppressing substrate association. Since DafA(Tth) must be released before the substrate proteins can bind we hypothesized that free DafA(Tth) might have regulatory functions connected to the heat shock response. Here, we present evidence that supports this hypothesis. We identified the 70S ribosome as binding target of free DafA(Tth). Our results show that the association of DafA(Tth) and 70S ribosomes does not require the participation of DnaK(Tth) or DnaJ(Tth). On the contrary, the assembly of DnaK(Tth)-DnaJ(Tth)-DafA(Tth) and ribosome-DafA(Tth) complexes seems to be competitive. These findings strongly suggest the involvement of DafA(Tth) in regulatory processes occurring at a translational level, which could represent a new mechanism of heat shock response as an adaptation to elevated temperature.

Trigger Factor from Thermus thermophilus Is a Zn2+-dependent Chaperone

The ribosome-associated chaperone trigger factor (TF) of Escherichia coli interacts with a variety of newly synthesized polypeptides to assist their correct folding. Here, we report that the TF of thermophilic eubacterium, Thermus thermophilus, arrested spontaneous folding of green fluorescent protein by forming a 1:1 binary complex. The complex was isolable by gel-filtration but was shown to be dynamic because green fluorescent protein was released by alpha-casein in large excess. Unexpectedly, EDTA completely abolished the folding-arrest activity of TF, and analysis revealed that the TF from our preparation contained approximately 0.5 mol Zn2+/mol TF. The folding-arrest activity of TF that was saturated with Zn2+ (approximately 1 mol/mol TF) was twice as efficient as that of untreated TF. Thus, chaperone activity of thermophilic TF is Zn2+-dependent.

Translational coupling to an upstream gene promotes folding of the mycobacterial plasmid pAL5000 replication protein RepB and thereby its origin binding activity

In the mycobacterial plasmid pAL5000 replication region, the replication genes repA and repB are organized in an operon. Earlier, a RepB-dependent origin binding activity was detected in Escherichia coli cells expressing the repA-repB operon. This activity was maximal when expression of the two genes was coupled (A. Basu, M. Chawla-Sarkar, S. Chakrabarti, and S. K. Das Gupta, J. Bacteriol. 184:2204-2214, 2002). In this study we have shown that translational coupling makes a significant difference in the structure and function of RepB. When repB expression was coupled to repA, the polypeptide folded into an active structure (referred to as RepB*), which possessed higher helical content than RepB expressed independently. RepB* could also be distinguished from the less active RepB on the basis of sensitivity to OmpT, an outer membrane protease of E. coli: RepB* was sensitive to the protease, whereas RepB was resistant. Similar conformational differences between RepB* and RepB could be observed when repA was replaced with an unrelated gene, malE (encoding maltose binding protein). These results show that translational coupling of repB to an upstream gene is necessary for better folding and origin binding activity. It is speculated that in coupled systems where translation machinery is passed on from the upstream to the downstream open reading frame, cotranslational folding of the polypeptide expressed from the downstream open reading frame is enhanced due to increased folding competence of translationally primed ribosomes.