A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle.

A novel topology of regulatory networks abstracted from the budding yeast cell cycle is studied by constructing a simple nonlinear model. A ternary positive feedback loop with only positive regulations is constructed with elements that activates the subsequent element in a clockwise fashion. A ternary negative feedback loop with only negative regulations is constructed with the elements that inhibit the subsequent element in an anticlockwise fashion. Positive feedback loop exhibits bistability, whereas the negative feedback loop exhibits limit cycle oscillations. The novelty of the topology is that the corresponding elements in these two homogeneous feedback loops are linked by the binary positive feedback loops with only positive regulations. This results in the emergence of mixed feedback loops in the network that displays complex behaviour like the coexistence of multiple steady states, relaxation oscillations and chaos. Importantly, the arrangement of the feedback loops brings in the notion of checkpoint in the model. The model also exhibits domino-like behaviour, where the limit cycle oscillations take place in a stepwise fashion. As the aforementioned topology is abstracted from the budding yeast cell cycle, the events that govern the cell cycle are considered for the present study. In budding yeast, the sequential activation of the transcription factors, cyclins and their inhibitors form mixed feedback loops. The transcription factors that involve in the positive regulation in a clockwise orientation generates ternary positive feedback loop, while the cyclins and their inhibitors that involve in the negative regulation in an anticlockwise orientation generates ternary negative feedback loop. The mutual regulation between the corresponding elements in the transcription factors and the cyclins and their inhibitors generates binary positive feedback loops. The bifurcation diagram constructed for the whole system can be related to the different events of the cell cycle in terms of dynamical system theory. The checkpoint mechanism that plays an important role in different phases of the cell cycle are accounted for by silencing appropriate feedback loops in the model.

A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae.

Eukaryotic cells respond to DNA damage by arresting the cell cycle and modulating gene expression to ensure efficient DNA repair. We used global transcriptome analysis to investigate the role of ploidy and mating-type in inducing the response to damage in various Saccharomyces cerevisiae strains. We observed a response to DNA damage specific to haploid strains that seemed to be controlled by chromatin regulatory proteins. Consistent with these microarray data, we found that mating-type factors controlled the chromatin-dependent silencing of a reporter gene. Both these analyses demonstrate the existence of an irradiation-specific response in strains (haploid or diploid) with only one mating-type factor. This response depends on the activities of Hdf1 and Sir2. Overall, our results suggest the existence of a new regulation pathway dependent on mating-type factors, chromatin structure remodeling, Sir2 and Hdf1 and independent of Mec1 kinase.

Codon bias signatures, organization of microorganisms in codon space, and lifestyle.

New and simple numerical criteria based on a codon adaptation index are applied to the complete genomic sequences of 80 Eubacteria and 16 Archaea, to infer weak and strong genome tendencies toward content bias, translational bias, and strand bias. These criteria can be applied to all microbial genomes, even those for which little biological information is known, and a codon bias signature, that is the collection of strong biases displayed by a genome, can be automatically derived. A codon bias space, where genomes are identified by their preferred codons, is proposed as a novel formal framework to interpret genomic relationships. Principal component analysis confirms that although GC content has a dominant effect on codon bias space, thermophilic and mesophilic species can be identified and separated by codon preferences. Two more examples concerning lifestyle are studied with linear discriminant analysis: suitable separating functions characterized by sets of preferred codons are provided to discriminate: translationally biased (hyper)thermophiles from mesophiles, and organisms with different respiratory characteristics, aerobic, anaerobic, facultative aerobic and facultative anaerobic. These results suggest that codon bias space might reflect the geometry of a prokaryotic "physiology space." Evolutionary perspectives are noted, numerical criteria and distances among organisms are validated on known cases, and various results and predictions are discussed both on methodological and biological grounds.

Codon adaptation index as a measure of dominating codon bias.

UNLABELLED: We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a 'universal' measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a sole source of biological information, the algorithm provides a reference set of genes which is highly representative of the bias. This set can be used to compute the CAI of genes of prokaryotic and eukaryotic organisms, including those whose functional annotation is not yet available. An important application concerns the detection of a reference set characterizing translational bias which is known to correlate to expression levels; in this case, the algorithm becomes a key tool to predict gene expression levels, to guide regulatory circuit reconstruction, and to compare species. The algorithm detects also leading-lagging strands bias, GC-content bias, GC3 bias, and horizontal gene transfer. The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. AVAILABILITY: http://www.ihes.fr/~materials.

The PAUSE software for analysis of translational control over protein targeting: application to E. nidulans membrane proteins.

The PAUSE software has been developed as a new tool to study translational control over protein targeting. This makes it possible to correlate the position of clusters of rare codons in a gene, predicted to cause a translational pause, with the position of hydrophobic stretches in the encoded protein, predicted to span a membrane or to act as a cleavable signal for targeting to the secretory pathway. Furthermore, this software gathers these correlations over whole sets of genes. The PAUSE software is described here, and its use is illustrated on a set of membrane proteins from the fungus Emericella nidulans. Preferential distances of about 45 codons and of about 70 codons between putative transmembrane domains and predicted translational pauses were observed. Given that approximately 30 residues are required to span the large ribosomal subunit, the predicted pauses would therefore occur when the hydrophobic domain starts protruding from the ribosome ('+45 pause'), or fully protrudes as a hairpin ('+70 pause'). Thus, these specific pauses might reflect a translational control over membrane protein targeting or early recognition ('+45 pause'), and over insertion or folding ('+70 pause').

Morphogenesis and dynamics of the yeast Golgi apparatus.

A kinetic and morphometric study was conducted with the electron microscope to clarify the biogenesis and structural diversity of the Golgi apparatus in the yeast Saccharomyces cerevisiae. Secretion was synchronized by inhibiting protein synthesis and/or by subjecting thermosensitive secretory mutants to double temperature shifts. Five membrane-bounded structures disappeared or reappeared in an orderly manner at approximately the rate of secretory protein flow. 1) The first detectable post-ER intermediates were very short-lived clusters of small vesicles that appeared next to the endoplasmic reticulum (ER). 2) Their constituent small vesicles were rapidly bridged by membrane tubules in a SEC18-dependent manner, giving short-lived tubular clusters of small vesicles, analogous to mammalian vesicular-tubular clusters. 3) Fine and 4) large nodular networks (coated with the Golgi protein Sec7), and 5) secretory granules. Upon relieving a secretory block, each structure successively reappeared, seemingly by transformation of the previous one. When no secretory cargo was to be transported, these structures were not renewed. They disappeared more than five times faster than some Golgi enzymes such as Och1p, implying that the latter are recycled and perhaps partially retained. Retention could arise from intra-compartmental flow of cargo/carrier, hinted at by the varying calibers within a single nodular network.

Sec7p directs the transitions required for yeast Golgi biogenesis.

Endoplasmic reticulum (ER)-to-Golgi traffic in yeast proceeds by the maturation of membrane compartments from post-ER vesicles to intermediate small vesicle tubular clusters (VTCs) to Golgi nodular membrane networks (Morin-Ganet et al., Traffic 2000; 1: 56-68). The balance between ER and Golgi compartments is maintained by COPII- and COPI-mediated anterograde and retrograde traffic, which are dependent on Sec7p and ARF function. The sec7-4 temperature-sensitive allele is a mutation in the highly conserved Sec7 domain (Sec7d) found in all ARF-guanine nucleotide exchange factor proteins. Post-ER trafficking is rapidly inactivated in sec7-4 mutant yeast at the restrictive temperature. This conditional defect prevented the normal production of VTCs and instead generated Golgi-like tubes emanating from the ER exit sites. These tubes progressively developed into stacked cisternae defining the landmark sec7 mutant phenotype. Consistent with the in vivo results, a Sec7d peptide inhibited ER-to-Golgi transport and displaced Sec7p from its membrane anchor in vitro. The similarities in the consequences of inactivating Sec7p or ARFs in vivo was revealed by genetic disruption of yeast ARFs or by addition of brefeldin A (BFA) to whole cells. These treatments, as in sec7-4 yeast, affected the morphology of membrane compartments in the ER-Golgi transition. Further evidence for Sec7p involvement in the transition for Golgi biogenesis was revealed by in vitro binding between distinct domains of Sec7p with ARFs, COPI and COPII coat proteins. These results suggest that Sec7p coordinates membrane transitions in Golgi biogenesis by directing and scaffolding the binding and disassembly of coat protein complexes to membranes, both at the VTC transition from ER exit sites to form Golgi elements and for later events in Golgi maturation.

Disruption of YHC8, a member of the TSR1 gene family, reveals its direct involvement in yeast protein translocation.

Genetic studies of Saccharomyces cerevisiae have identified many components acting to deliver specific proteins to their cellular locations. Genome analysis, however, has indicated that additional genes may also participate in such protein trafficking. The product of the yeast Yarrowia lipolytica TSR1 gene promotes the signal recognition particle-dependent translocation of secretory proteins through the endoplasmic reticulum. Here we describe the identification of a new gene family of proteins that is well conserved among different yeast species. The TSR1 genes encode polypeptides that share the same protein domain distribution and, like Tsr1p, may play an important role in the early steps of the signal recognition particle-dependent translocation pathway. We have identified five homologues of the TSR1 gene, four of them from the yeast Saccharomyces cerevisiae and the other from Hansenula polymorpha. We generated a null mutation in the S. cerevisiae YHC8 gene, the closest homologue to Y. lipolytica TSR1, and used different soluble (carboxypeptidase Y, alpha-factor, invertase) and membrane (dipeptidyl-aminopeptidase) secretory proteins to study its phenotype. A large accumulation of soluble protein precursors was detected in the mutant strain. Immunofluorescence experiments show that Yhc8p is localized in the endoplasmic reticulum. We propose that the YHC8 gene is a new and important component of the S. cerevisiae endoplasmic reticulum membrane and that it functions in protein translocation/insertion of secretory proteins through or into this compartment.

Expression, purification, and characterization of Sss1p, an essential component of the yeast Sec61p protein translocation complex.

Sss1p, a 8.9-kDa membrane protein, is an essential component of the protein translocation complex involved in the transport of secretory proteins across the Saccharomyces cerevisiae endoplasmic reticulum membrane. In order to determine the high resolution structure of Sss1p by NMR, we have undertaken its overexpression and purification. We first inserted the yeast SSS1 gene into the pGEX-2T plasmid expression vector. Sss1p was expressed as fusions with Schistosoma japonica glutathione S-transferase (GST-Sss1p) in MC1061 Escherichia coli cells. Maximum yield of GST-Sss1p was obtained from cells harvested 2 h after induction at 37 degreesC in Luria broth medium. GST-Sss1p was found associated predominantly with the membrane pool and was readily extracted with Triton X-100. Detergent-solubilized GST-Sss1p was isolated by adsorption on glutathione-agarose beads. Sss1p was released from its GST carrier by cleavage with thrombin and its recovery was maximized by addition of dodecyl maltoside. Desorbed Sss1p was loaded on a high-performance liquid chromatography hydroxyapatite column equilibrated in phosphate buffer supplemented with dodecyl maltoside and the fractions containing Sss1p were subsequently purified to homogeneity by reverse-phase chromatography on a C4 column. The entire purification protocol can be completed in 5-6 h and yields about 0.4 mg of Sss1p per gram of transformed cells. CD and preliminary 1H NMR experiments show that purified Sss1p solubilized in SDS micelles is very stable and adopts a helical secondary structure.

Expression of the yeast BFR2 gene is regulated at the transcriptional level and through degradation of its product.

The essential Saccharomyces cerevisiae gene BFR2 has been isolated as a high-copy suppressor of the growth defects induced by Brefeldin A, a drug that disrupts the Golgi apparatus and its protein influx. Furthermore, BFR2 has been found to display genetic interactions with four mutations affecting protein transport to the Golgi apparatus. Here we show that the level of BFR2 mRNA rapidly increased over fivefold in response to cold shock, and over threefold following nutrient replenishment by dilution of cells from exhausted to fresh minimal medium. During subsequent growth, the transcript level returned to its basal values, except for a transient drop toward the end of the exponential phase. The early burst of transcription was not caused by toxic compounds in the fresh medium, or by synchrony among cells that had simultaneously entered their first cell cycle. The BFR2 gene product (Bfr2p) was synthesized following the early burst of mRNA, and was no longer produced when the mRNA was back to basal level. Bfr2p was finally degraded after growth became limited, and reached undetectable levels in exhausted medium. Under steady-state conditions of lengthened exponential phase, the intracellular level of Bfr2p remained constant. This peculiar pattern of gene expression suggests that Bfr2p is essential for mass growth or cell proliferation, whereas it is either toxic or not required during nutrient-limited growth.

Role of endoplasmic reticulum-derived vesicles in the formation of Golgi elements in sec23 and sec18 Saccharomyces Cerevisiae mutants.

BACKGROUND: In the yeast Saccharomyces cerevisiae, the Golgi apparatus consists of individual networks of membranous tubules interspersed throughout the cytoplasm. When sec23 and sec18 mutants are shifted from the permissive (20 degrees C) to the restrictive (37 degrees C) temperature, the secretory pathway is blocked between endoplasmic reticulum (ER) and Golgi elements. When examined with an electron microscope, sec23 displays an excess of ER membranes, whereas sec18 accumulates small vesicles. The present investigation describes the kinetics of the ultrastructural modifications of the Golgi and vesicular elements when sec23 and sec18 mutants are shifted for 10 min to restrictive temperature and then returned to permissive temperature for various time intervals. METHODS: S. cerevisiae sec23 and sec18 mutants from exponentially growing cultures at 20 degrees C were maintained for 10 min at the restrictive temperature of 37 degrees C and returned to the permissive temperature of 20 degrees C for different time intervals. Following fixation in glutaraldehyde and postfixation in potassium ferrocyanide reduce osmium, 80- to 200-nm-thick sections were prepared from Epon-embedded yeast cells. Using the thicker sections, stereopairs of electron microscopy photographs were prepared and used to visualize the three-dimensional configuration of the organelles. To follow the modifications of cell organelles, cell sections were selected at random in thinner sections and cell organelles were scored. RESULTS: At permissive temperature (20 degrees C), the Golgi apparatus consisted of individual networks of tubules dispersed in the cytoplasm, as in the wild type strain. When both mutants were shifted for 10 min at the restrictive temperature (37 degrees C), the main structural feature was the disappearance of all Golgi networks. In sec23 mutant cells, there was an increase in number of tubular, nonnodular networks corresponding to terminal portions of the endoplasmic reticulum; in sec18 cells, small 20- to 50-nm tubules and vesicles accumulated in the cytoplasm. Within minutes after the return of sec23 cells to permissive temperature (20 degrees C), small vesicles and tubules started to accumulate to reach a number similar or greater than that noted in sec18 cells observed under the same conditions. At later time intervals and in both mutants, the small tubules and vesicles decreased in number. This decrease was concomitant with the reappearance of fine nodular networks, followed later on by the reconstruction of networks of larger caliber and the formation of secretion granules. CONCLUSIONS: It is concluded that a block of the secretory pathway upstream of the Golgi compartment leads to the disappearance of Golgi networks. The small vesicles and tubules that accumulate during the block in sec18 cells and within minutes after the shift at 20 degrees C in sec23 cells appear to fuse together to form new Golgi networks. Thus, the small vesicles would not fuse with a preexisting Golgi apparatus but would rather fuse together to produce new Golgi networks. Such networks appear as transitory structures continuously undergoing renewal.

Over-expression of the yeast BFR2 gene partially suppresses the growth defects induced by Brefeldin A and by four ER-to-Golgi mutations.

The fungal metabolite Brefeldin A (BFA) disrupts the Golgi apparatus and its incoming protein flux. We developed a genetic approach to identify yeast proteins involved in the protein transport step that BFA blocks. The BFR2 gene (YDR299W) was thus isolated as a high-copy suppressor of the growth defects induced by BFA in a sensitive strain of Saccharomyces cerevisiae. Although BFR2 over-expression did not cause a secretory block or slow-down, it partially suppressed the growth defect of four mutants blocked at the step of budding or docking of small vesicles en route to the Golgi (sec13-1, sec16-2, sec23-1, ypt1-1). The essential BFR2 gene was predicted to encode an extremely hydrophilic product containing two short regions with potential coiled-coils, one of which corresponds to a cluster of acidic residues.

The Srp40 protein plays a dose-sensitive role in preribosome assembly or transport and depends on its carboxy-terminal domain for proper localization to the yeast nucleoskeleton.

The yeast SRP40 gene product (Srp40p) is a highly serine-rich protein organized in three distinct domains. The roles of these domains in localizing Srp40p were determined. By indirect immunofluorescence microscopy, Srp40p localizes to punctate, sometimes fibrillar, subnuclear structures that might include the nucleolus. Its amino-terminal and medial domains are similar. They each start with a short basic stretch containing a nuclear localization signal, followed by a long acidic stretch with 76% serines; such acidic stretches are thought to mediate binding to ribosomal proteins in the nucleolus. Either domain is sufficient to determine nuclear localization of Srp40p. The Srp40p carboxy-terminal domain shows significant homology to the cognate domain of Nopp140, a mammalian nucleolar phosphoprotein of 140 kD. The carboxy-terminal domain alone, or fused to a reporter protein, displays a punctate localization outside the nucleus. Srp40p and Nopp140 share a highly homologous 39-residue motif within their similar carboxy-terminal domains. Inside or outside the nucleus, this motif is important to prevent Srp40p diffusion or degradation. These observations suggest that the punctate immunoreactive structure is nucleoskeletal and might result from Srp40p self-assembly. SRP40 genetically interacts with four mutants affected in stable RNA synthesis and one mutant blocked in protein translocation to the endoplasmic reticulum. Growth defects, but no translocation or rRNA transcription/maturation phenotypes, were observed upon SRP40 inactivation or strong overexpression. Together, these data point to a dispensable, dosage-sensitive, role of Srp40p in preribosome assembly or transport.

NMR conformational study of the cytoplasmic domain of the canine Sec61 gamma protein from the protein translocation pore of the endoplasmic reticulum membrane.

Conformational studies of the synthesized N-terminal cytoplasmic domain of the canine Sec61 gamma protein, an essential protein from the translocation pore of secretory proteins across the endoplasmic reticulum membrane, were performed using two-dimensional proton NMR spectroscopy. This canine domain is one of the smallest domains within the homologous protein family and may thus constitute the minimal functional structure. The peptide was solubilized in pure aqueous solution or in the presence of dodecylphosphocholine micelles mimicking a membrane-solution interface. In pure aqueous solution, the peptide is remarkably unfolded. Forming a stable complex with dodecylphosphocholine micelles, it acquires a well-defined alpha-helix-loop-alpha-helix secondary structure, with the helix, highly amphipathic, lying at the micelle surface. The loop comprising four residues is delimited by two flanking helix-capping structures, highly conserved in the whole homologous protein family. No tertiary structure, which could have been revealed by interhelix NOE contacts, was observed. From these experimental results and using general arguments based on sequence information and knowledge of peptide-membrane interactions, a structure of the entire Sec61 gamma protein in membrane bilayers is proposed.

Modifications of the Golgi apparatus in Saccharomyces cerevisiae lacking microtubules.

BACKGROUND: Disassembly of cytoplasmic microtubules by nocodazole in cultured mammalian cells leads to the disruption of the continuous ribbonlike Golgi apparatus and dispersal of the Golgi elements from their normal juxtanuclear location, close to the microtubule-organizing center (MTOC), toward the cell periphery. Clearing of the drug induces reassembly of the microtubules from the MTOC and reorganization of the Golgi elements into a continuous ribbonlike juxtanuclear structure. In the yeast Saccharomyces cerevisiae, the Golgi apparatus does not form a continuous structure as in mammalian cells but instead constitutes independent units dispersed throughout the cytoplasm. It is the purpose of this article to investigate the role of microtubules in the structure and distribution of the Golgi elements in S. cerevisiae by studying the ultrastructure of cell organelles either in mutant cells deficient in beta-tubulin or in wild-type cells treated with the microtubule-depolymerizing drug nocodazole. METHODS: Two S. cerevisiae yeast strains were used in this study: a control wild-type strain, CUY226 (ade2-101, his3-delta 200, leu2-delta 1, lys2-801, ura3-52 Mat alpha), and a mutant strain, CUY66 (tub2-401, ade2-101, ura3-52, Mat alpha). Nocodazole was added to the wild-type cells cultivated at 30 degrees C, and cells were fixed 5 min, 20 min, and 60 min, respectively, after adding the drug to the culture. Both strains were fixed and examined 5 min, 20 min, and 60 min after shifting the cultures from the permissive temperature of 30 degrees C to the restrictive temperature of 14 degrees C. Cells were fixed in 2% glutaraldehyde, treated for 15 min in 1% sodium metaperiodate, postfixed in reduced osmium, and embedded in Epon. To visualize the three-dimensional configuration of cell organelles, stereopairs were prepared from sections stained with lead citrate and tilted at +/- 15 degrees from the 0 degree position of the goniometric stage of the electron microscope. RESULTS: In mutant cells shifted to restrictive temperature and wild-type cells treated with nocodazole, the main ultrastructural modification was a fragmentation of networks of membranous tubules, which probably correspond to the yeast Golgi apparatus. Secretion granules were still present in growing buds, and they were dispersed in the cytoplasm, which contained in addition numerous small vesicles in the 30-60-nm diameter range. CONCLUSIONS: In normal cells, small vesicles may originate from the endoplasmic reticulum and fuse together to give rise to Golgi networks (Rambourg et al. 1994. Anat. Rec., 240:32-41). If this hypothesis is correct, the observations reported might indicate that intact microtubules orient the flow of small vesicles and favour their fusion into Golgi networks.

The "+70 pause": hypothesis of a translational control of membrane protein assembly.

Sequences of 66 genes encoding bacterial or yeast membrane proteins have been examined for the respective positioning of putative transmembrane domains and translational pauses. The latter were operationally defined as clusters of at least 17 non-preferred codons along the mRNA. The putative transmembrane domains were defined as stretches of at least 17 hydrophobic amino acids in the encoded protein. For yeast non-mitochondrial membrane proteins, it was observed that clusters of non-preferred codons occur more frequently about 56 to 75 codons after a hydrophobic stretch in the encoded protein. About 40 amino acid residues are required to span the large ribosomal subunit. Such clusters were thus predicted to cause a severe slow-down in peptide elongation, just when the hydrophobic stretch fully protrudes from the ribosome. This transient slow-down of the ribosome pace has consequently been named the "+70 pause". This pause was not observed for mitochondrial or bacterial membrane proteins, which are thought to insert post-translationally in their respective membranes. Because insertion of yeast proteins in the endoplasmic reticulum membrane is generally cotranslational instead, it is possible that the "+70 pause" reflects the coupling of translation, targeting, insertion and folding in this case. The pause may, for instance, give time for productive interaction of the newly synthesized hydrophobic domain with the proper targeting/insertion machineries. Thus, it would favor entrance of the stalled protein domain into the proper pathway.

Transformations of membrane-bound organelles in sec 14 mutants of the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica.

BACKGROUND: In early descriptions of ultrastructural alterations of secretory (sec) mutants of the yeast Saccharomyces cerevisiae, two mutants, sec7 and sec14, were shown to produce cell structures, the so-called Berkeley bodies thought at first to correspond to Golgi structures. In sec7 mutants grown at restrictive temperature, secretion granules soon dis-appeared, whereas networks of Golgi tubules increased in size and transformed into stacks of seven to eight flattened elements. At these time intervals, structures resembling Berkeley bodies appeared to be extensions of the endoplasmic reticulum (Rambourg et al., 1993). It is the purpose of the present study to examine by electron microscopy S. cerevisiae sec14 mutants and to compare the modifications along their secretory pathway with those occurring in a homologous mutant of Yarrowia lipolytica. METHODS: S. cerevisiae sec 14 mutant cells coming from exponentially growing cultures were examined either at 24 degrees C or after shifting at 37 degrees C for 0, 2, 5, 10, 15, 20, 30, 45, 60, 90, and 120 min. Y. lipolytica mutant cells were first cultured in YNB in 5000 medium and then transferred for 0, 6, 8, 12, 20, and 24 hr, in a phosphate-buffered YPD medium, which allows wild cells to differentiate from yeast to mycelian form. In both cases, cells were fixed in 2% glutaraldehyde, treated for 15 min in 1% sodium metaperiodate, post-fixed in reduced osmium, and embedded in Epon. To visualize the three-dimensional configuration of cell organelles, stereopairs were prepared from section stained with lead citrate and tilted at +/- 15 degrees from the 0 degree position of the goniometric stage of the electron microscope. RESULTS: In S. cerevisiae mutant cells shifted for 2 min at the restrictive temperature, faintly stained networks of thin anastomosed tubules were located at close proximity and often continuous with faintly stained ER cisternae. More intensely stained tubular networks with nodular dilations having the size of secretion granules were dispersed throughout the cytoplasm. Later on, the faintly stained ER elements and related tubular networks decreased in number, whereas the intensely stained nodular tubular networks increased in frequency. The incidence of secretion granules also increased and were distributed at random throughout the cytoplasm. Widemeshed, intensely stained fenestrated spheres were often encountered and increased in number, in parallel to the increase in the number of nodular tubular networks. At late time intervals, the fenestrated spheres decreased in number as they seemingly transformed into spherical bodies identical to vacuoles. In contrast to what occurred in S. cerevisiae sec14 mutant, the main ultrastructural modification observed in Y. lipolytica transferred to the YPD medium was the formation of deep plasma membrane invaginations. CONCLUSIONS: It appears that two functionally homologous PI/PC transfer proteins (Sec14psc and Sec14pyl) control distinct physiological processes in the two sec14 mutants examined. Such differences are perhaps related to the regulatory role of these proteins in different target organelles, i.e., the Golgi apparatus in S. cerevisiae or the plasma membrane in Y. lipolytica.

Three-dimensional structure of tubular networks, presumably Golgi in nature, in various yeast strains: a comparative study.

BACKGROUND: In the yeast Saccharomyces cerevisiae, the Golgi apparatus consists of discrete units distributed throughout the cytoplasm. When such units are examined in three dimensions, in relatively thick sections prepared for the electron microscope, they usually appear as small tubular networks with a stained material accumulating in dilations located at the junctions of membranous tubules. To see whether such tubular networks are observed in other yeast species, the three-dimensional structure of organelles in eight additional yeast strains, endowed with diverse biological properties, are examined. METHODS: Yeast strains were grown at 24 degrees C in YPD medium (2% Bactopeptone, 1% Bactoyeast extract, and 2% glucose). Cells that were examined by electron microscopy came from exponentially growing cultures grown in a shaking water bath and maintained at a OD 600 (optical density at 600 nm) of 0.5. Cells were fixed in a fixative containing 2% glutaraldehyde in 0.1 M cacodylate buffer pH 7.4 and 0.8 M sorbitol. They were then treated for 15 min in 1% sodium metaperiodate and postfixed for 1 hr in potassium ferrocyanide-osmic acid. They were preembedded in agarose prior to dehydration and finally embedded in Epon. In these conditions, the preservation of cell organelles was improved and the cytoplasmic retraction from the cell wall was minimized. Photographs of sections tilted at +/- 15 degrees from the 0 degrees position of the goniometric stage were used to prepare stereopairs from which the three-dimensional configuration of the organelles was visualized. RESULTS: In all yeast strains, tubular networks appeared as separate elements or units disperse throughout the cytoplasm. Each unit consisted of anastomosed membranous tubules. In some strains such as Saccharomyces cerevisiae, Zygosaccharomyces rouxii, or Saccharomyces pombe, such units appeared mainly as polygonal networks of intensely stained membranous tubules. Along these networks, distensions filled with stained material were similar in size to nearby secretory granules, suggesting that the latter formed by fragmentation of the tubular networks. In Hansenula polymorpha, Pichia pastoris, and Debaryomyces hansenii, networks of anastomosed tubules were closely superposed to each other and formed parallel arrays reminiscent of the stacks of Golgi saccules seen in mammalian cells. However, in contrast to what is usually found in the latter, the layers making up the parallel arrays in yeasts, were clearly continuous to each other. In other strains, i.e., Kluyveromyces lactis, Candida albicans, and Candida parapsilosis, the situation was intermediate and their cytoplasm contained only arrays of small size with two or at most three superposed layers of membranous tubules. Small vesicles in the 30-50 nm range were rarely encountered in most yeast strains. CONCLUSIONS: It is therefore concluded that tubular networks, presumably Golgi in nature, are present in all yeasts examined so far. Yet, in some strains, these tubular networks may be arranged in parallel arrays or stacks.

Effects of brefeldin A on the three-dimensional structure of the Golgi apparatus in a sensitive strain of Saccharomyces cerevisiae.

BACKGROUND: Brefeldin A (BFA), when added to the medium of cultured mammalian cells, induces a reversible block of secretion and disrupts the Golgi apparatus whereas Golgi enzyme markers appear to redistribute into the endoplasmic reticulum (ER). It has been shown in addition that in mammalian cells, BFA would prevent the assembly of coatomer proteins (COP) onto membranes by inhibiting the GTP-dependent interaction of the ADP-ribosylation factor (ARF) with such membranes. The purpose of the present study is to analyze, by stereoelectron microscopy, the structural modifications of Golgi elements and of the ER-Golgi relationship in a BFA-sensitive yeast mutant, S. cerevisiae erg6. METHODS: S. cerevisiae erg6 cells were placed in a medium containing 100 micrograms/ml BFA dissolved in 1% alcohol and collected after exposures of 0.5, 1.5, 5, 10, 15, 20, 30, and 70 min to the drug. Yeasts placed in a BFA-free medium but containing 1% alcohol served as controls. After fixation in 2% glutaraldehyde, the cells were postfixed in reduced osmium and embedded in Epon. Then 0.08-0.2 microns thick sections stained with lead citrate were examined with the electron microscope. Photographs of the thicker sections, tilted at +/- 15 degrees from the 0 degree position of the goniometric stage, were used to prepare stereopairs from which the three-dimensional configuration of the organelles was visualized. Since BFA is known to prevent the interaction of ARF with membranes, the phenotype of the arf1 mutant deficient in this protein was also examined for comparative purposes. RESULTS: In control cells, as in wild-type strains, two types of Golgi elements were observed: small networks of fine tubules seen close and occasionally connected to ER cisternae and coarser tubular networks showing nodular distensions having a size comparable to that of secretion granules. The latter networks were considered as trans-Golgi elements and the former as cis-Golgi elements. Several networks of both types were distributed throughout the cytoplasm. At short time intervals (0.5-5 min) of BFA treatment, the trans-Golgi elements disappeared from the cytoplasm, while the ER-connected cis-Golgi elements developed and formed large spheroidal masses frequently showing concentrically arranged fine tubular networks. Such spheroidal, cage-like structures later disappeared, and after 30 min Golgi elements were no longer identifiable, while ER cisternae assumed pleomorphic configurations as the cells showed signs of degeneration. S. cerevisiae arf1 mutants presented a phenotype similar to that of BFA-treated S. cerevisiae erg6. CONCLUSIONS: It is therefore concluded that soon after exposure to BFA there is, in this sensitive yeast mutant, a transitory hypertrophy of the ER-connected cis-Golgi network presumably resulting from a block at the exit end of this compartment. At longer time intervals (i.e., after 30 min) the Golgi elements are no longer formed, and the cells present signs of cell degeneration.

SSS1 encodes a stabilizing component of the Sec61 subcomplex of the yeast protein translocation apparatus.

The yeast SSS1 gene has been isolated as an extragenic high copy suppressor of sec61, a mutant displaying defects in protein translocation into the endoplasmic reticulum (ER). We found that SSS1 is an essential gene required for transfer of secretory precursors through the ER membrane. Here we demonstrate that the SSS1 product (Sss1p) is firmly bound to the ER membrane and exposes its amino-terminal half on the cytosolic side. Only detergent, or an alkali treatment, is effective at extracting Sss1p from the membrane. Coimmunoprecipitation experiments revealed that Sss1p and Sec61p participate in the same multisubunit complex. Cross-linking followed by immunoprecipitation specifically yielded an additional polypeptide of molecular mass 73 kDa. Moreover, Sss1p and Sec61p show mutually stabilizing interactions: Sss1p is destabilized in a sec61 mutant context, and mutated Sec61p is stabilized by Sss1p overproduction. These observations account for the isolation of SSS1 as a dosage-dependent suppressor of sec61. Since the polytopic integral membrane protein Sec61p is adjacent to translocating precursors and to ribosomes, and given the comparable translocation deficiencies of sss1 or sec61 mutants, we propose that Sss1p belongs to the "Sec61 subcomplex" that constitutes the pore of the membrane-bound translocation apparatus.