A yeast expression vector and leucine selection in Escherichia coli to aid in the identification of novel genes.

The complete sequencing of the Saccharomyces cerevisiae genome provides a powerful tool for studying and elucidating essential cellular processes. To aid in the application of this resource to investigations into the molecular mechanisms of endoplasmic reticulum-associated protein degradation, a simple procedure was designed to generate a unique 2-microm LEU2-selectable yeast expression vector. Putative genes easily inserted into this vector are under control of the ADH1 promoter and transcription terminator sequences. Furthermore, a LEU2 selection in both yeast and Escherichia coli was used to allow the isolation of underrepresented plasmid from a pool of multiple vectors. Together, these advances in technology will be useful in the systematic analysis of novel yeast gene function.

Differential fates of invertase mutants in the yeast endoplasmic reticulum.

A number of proteins have been identified as substrates for endoplasmic reticulum (ER)-associated protein degradation (ERAD) and we describe here a new model substrate with which to study this process. Two secretion-defective forms of yeast invertase that accumulated in the ER to greatly different levels were examined: Suc2-538p levels were low, while Suc2-533p was present in high amounts. Because Suc2-533p and Suc2-538p mRNA levels were comparable, we examined whether Suc2-538p was targeted for degradation. Both mutant polypeptide levels were unaffected in a yeast strain deficient in vacuolar protease activity and, additionally, we showed that Suc2-538p was stabilized in ERAD-deficient strains, demonstrating that Suc2-538p was a substrate for ERAD.

The requirement for molecular chaperones during endoplasmic reticulum-associated protein degradation demonstrates that protein export and import are mechanistically distinct.

Polypeptide import into the yeast endoplasmic reticulum (ER) requires two hsp70s, Ssa1p in the cytosol and BiP (Kar2p) in the ER lumen. After import, aberrant polypeptides may be exported to the cytoplasm for degradation by the proteasome, and defects in the ER chaperone calnexin (Cne1p) compromise their degradation. Both import and export require BiP and the Sec61p translocation complex, suggesting that import and export may be mechanistically related. We now show that the cne1Delta and two kar2 mutant alleles exhibit a synthetic interaction and that the export and degradation of pro-alpha factor is defective in kar2 mutant microsomes. Pulse-chase analysis indicates that A1PiZ, another substrate for degradation, is stabilized in the kar2 strains at the restrictive temperature. Because two of the kar2 mutants examined are proficient for polypeptide import, the roles of BiP during ER protein export and import differ, indicating that these processes must be mechanistically distinct. To examine whether Ssa1p drives polypeptides from the ER and is also required for degradation, we assembled reactions using strains either containing a mutation in SSA1 or in which the level of Ssa1p could be regulated. We found that pro-alpha factor and A1PiZ were degraded normally, indicating further that import and export are distinct and that other cytosolic factors may pull polypeptides from the ER.

Selective protein degradation in the yeast exocytic pathway.

Protein degradation in the exocytic pathway was studied in Saccharomyces cerevisiae using human alpha-1-protease inhibitor (A1Pi) as a reporter molecule. Yeast cells transformed with A1Pi cDNA genes synthesized A1Pi that entered the secretion pathway and accumulated in the endoplasmic reticulum (ER). Cells expressing A1PiM (wild-type) accumulated about 10-fold more A1Pi than cells expressing A1PiZ (secretion defective variant). Analyses of A1Pi mRNA indicated that the low level of A1PiZ relative to A1PiM was not the result of differential gene transcription. Pulse-chase A1Pi radiolabeling showed that A1PiM and A1PiZ were degraded at different rates and suggested a rapid specific turnover of newly synthesized A1PiZ in the ER. Accumulated A1Pi was degraded at comparable rates in both wild-type cells and cells deficient in vacuolar protease activity, indicating that degradation of A1Pi did not occur in the vacuole. Studies to investigate the intracellular location of the degradative process, using temperature-sensitive secretion defective yeast strains, suggested the possibility that degradation occurs not only in the ER but at a second site accessed by vesicle transport. Together, these results demonstrate that a selective protein degradation process operates early in the yeast cell exocytic pathway.

Construction and expression of alpha 1-proteinase inhibitor mutants and the effects of these mutations on secretion of the variant inhibitors.

Human alpha 1-proteinase inhibitor (A1Pi) deficiency, associated with the Z variant A1Pi gene, results from defective secretion of the inhibitor from the liver and appears to be a direct consequence of replacement of Glu342 with Lys. To investigate the effect of the amino acid occupying position 342 on secretion of A1Pi, we have used oligonucleotide-directed mutagenesis of A1Pi cDNA to randomly change the codon specifying this amino acid. Since replacement of Glu342 by Lys leads to a change in the predicted secondary structure for this protein, we also tested the possibility that defective secretion of A1PiZ is the result of this type of alteration. For this purpose, site-directed mutagenesis was used to produce sequences encoding A1Pi retaining Glu342 but predicted to have A1PiZ type secondary structure. The effects of 10 different amino acids occupying position 342 on the secretion of A1Pi were determined by pulse-chase experiments and by enzyme-linked immunosorbent assay of medium from transiently transfected COS cells. Results of these studies show that secretion of A1Pi is most efficient when position 342 is occupied by a negatively charged amino acid, efficient but somewhat less so when occupied by a neutral amino acid, and least efficient when a positively charged residue is present. The mutation designed to alter secondary structure had no effect on the secretion of A1Pi. As indicated by immunofluorescence microscopy and mobility of intracellular A1Pi on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, lowered secretion is accompanied by accumulation of A1Pi in the endoplasmic reticulum of the transfected cells. These results are compatible with the ideas that secretion of A1Pi is directly influenced by the amino acid occupying position 342, that a positively charged amino acid in this position is especially detrimental to secretion of this protein, and that the rate-limiting step in the secretion of the altered forms is transport from endoplasmic reticulum to Golgi.

Intracellular transport of rat serum albumin is altered by a genetically engineered deletion of the propeptide.

Many secreted proteins are synthesized with aminoterminal propeptides which are removed prior to secretion. There is increasing interest in the physiological roles of these propeptides, especially as mediators of intracellular protein trafficking. To investigate whether or not the propeptide of serum albumin offers an advantage in albumin secretion, we used oligonucleotide-directed mutagenesis to delete the 18 base pairs which encode the propeptide from a cDNA gene for rat serum albumin (RSA), inserted the deleted gene into COS cells, and studied the secretion of the gene product (RSA delta pro). Quantitative enzyme-linked immunosorbent assay analysis of medium from transfected cells showed that RSA delta pro was secreted at about 64% of the level of RSA. Furthermore, pulse-chase protein labeling studies demonstrated that the rate of secretion for RSA delta pro was greatly decreased relative to RSA. Immunofluorescent analyses of transfected cells showed accumulation of RSA delta pro in the endoplasmic reticulum, suggesting that transport through and/or exit from the ER was affected. The electrophoretic migration of secreted and intracellular forms of RSA and RSA delta pro indicated that they were the same molecular weight, and a specific amino-terminal binding assay, using nickel 63, confirmed the absence and proper cleavage of the prepeptide. These findings demonstrate that transport of RSA delta pro through the secretion pathway is inhibited and that the inhibition is due to the absence of the propeptide.

Molecular basis for defective secretion of the Z variant of human alpha-1-proteinase inhibitor: secretion of variants having altered potential for salt bridge formation between amino acids 290 and 342.

Human alpha-1-proteinase inhibitor (A1PI) deficiency, associated with the Z-variant A1PI (A1PI/Z) gene, results from defective secretion of the inhibitor from the liver. The A1PI/Z gene exhibits two point mutations which specify amino acid substitutions, Val-213 to Ala and Glu-342 to Lys. The functional importance of these substitutions in A1PI deficiency was investigated by studying the secretion of A1PI synthesized in COS cells transfected with A1PI genes altered by site-directed mutagenesis. This model system correctly duplicates the secretion defect seen in individuals homozygous for the A1PI/Z allele and shows that the substitution of Lys for Glu-342 alone causes defective secretion of A1PI. The substitution of Lys for Glu-342 eliminates the possibility for a salt bridge between residues 342 and 290, which may decrease the conformational stability of the molecule and thus account for the secretion defect. However, when we removed the potential to form a salt bridge from the wild-type inhibitor by changing Lys-290 to Glu (A1PI/SB-290Glu), secretion was not reduced to the 19% of normal level seen for A1PI/Z-342Lys; in fact, 75% of normal secretion was observed. When the potential for salt bridge formation was returned to A1PI/Z-342Lys by changing Lys-290 to Glu, only 46% of normal secretion was seen. These data indicate that the amino acid substitution at position 342, rather than the potential to form the 290-342 salt bridge, is the critical alteration leading to the defect in A1PI secretion.

An enrichment selection for mutants resulting from oligonucleotide-directed mutagenesis of double-stranded DNA.

We report here a simple and rapid procedure for enrichment and selection of mutants from oligonucleotide-directed mutagenesis on double-stranded plasmid DNA. Mutagenic oligonucleotides were designed to insert or delete a unique restriction site with silent codon changes. After mutagenesis, plasmid DNA from all resulting colonies was pooled, restricted with the appropriate endonuclease, and the resulting unique form of DNA (linear or circular) was isolated and used for transformation of competent E. coli. These procedures provided an enrichment of mutant plasmid from the 4% obtained by more conventional techniques to greater than 65%.