SWM1, a developmentally regulated gene, is required for spore wall assembly in Saccharomyces cerevisiae

Isc10, an Inhibitor That Links the Anaphase-Promoting Complex to a Meiosis-Specific Mitogen-Activated Protein Kinase

Smk1 is a meiosis-specific mitogen-activated protein kinase (MAPK) in yeast that controls spore differentiation. It is activated by a MAPK binding protein, Ssp2, upon completion of the meiotic divisions. The activation of Smk1 by Ssp2 is positively regulated by a meiosis-specific coactivator of the anaphase promoting complex (APC/C) E3 ubiquitin ligase, Ama1. Here, we identify Isc10 as an inhibitor that links APC/C^Ama1 to Smk1 activation. Isc10 and Smk1 form an inhibited complex during meiosis I (MI). Ssp2 is produced later in the program, and it forms a ternary complex with Isc10 and Smk1 during MII that is poised for activation. Upon completion of MII, Isc10 is ubiquitylated and degraded in an AMA1-dependent manner, thereby triggering the activation of Smk1 by Ssp2. Mutations that caused Ssp2 to be produced before MII, or isc10Δ mutations, modestly reduced the efficiency of spore differentiation whereas spores were nearly absent in the double mutant. These findings define a pathway that couples spore differentiation to the G₀-like phase of the cell cycle.

Effect of co-culture with Tetragenococcus halophilus on the physiological characterization and transcription profiling of Zygosaccharomyces rouxii

Zygosaccharomyces rouxii and Tetragenococcus halophilus are widely existed and play vital roles during the manufacture of fermented foods such as soy sauce. The aim of this study was to elucidate the effect of T. halophilus CGMCC 3792 on the physiological characterizations and transcription profiling of Z. rouxii CGMCC 3791. Salt tolerance analysis revealed that co-culture with T. halophilus enhanced the salt tolerance of Z. rouxii during salt stress. Analysis of the volatile compounds revealed that co-culture reduced the level of 1-butanol, improved the level of octanoic acid which all were produced by T. halophilus and reduced the level of phenylethyl alcohol produced by Z. rouxii. The presence of Z. rouxii decreased the contents of 3,4-dimethylbenzaldehyde and acetic acid produced by T. halophilus. In addition, co-culture improved the content of benzyl alcohol significantly. Analysis of membrane fatty acid showed that co-culture improved the content of palmitic (C16:0) and stearic (C18:0) acids in cells of Z. rouxii, and reduced the contents of myristic (C14:0), palmitoleic acid (C16:1) and oleic acid (C18:1). In order to further explore the interactions between the two strains, RNA-seq technology was used to investigate the effect of co-culture with T. halophilus on the transcription profiling of Z. rouxii. By comparing cells incubated in co-culture group with cells incubated in single-culture group, a total of 967 genes were considered as differentially expressed genes (DEGs). Among the DEGs, 72 genes were up-regulated, while 895 genes were down-regulated. These DEGs took party in various activities in cells of Z. rouxii, and the result showed co-culture with T. halophilus had a positive effect on proteolysis, the attachment of a cell to another cell, extracellular protein accumulation, energy metabolism, and a negative effect on oxidative phosphorylation, small molecular substances metabolism, DNA replication and repair, and transcription in cells of Z. rouxii. Results presented in this study may contribute to further understand the interactions between Zygosaccharomyces rouxii and Tetragenococcus halophilus.

Sporulation in the budding yeast Saccharomyces cerevisiae

In response to nitrogen starvation in the presence of a poor carbon source, diploid cells of the yeast Saccharomyces cerevisiae undergo meiosis and package the haploid nuclei produced in meiosis into spores. The formation of spores requires an unusual cell division event in which daughter cells are formed within the cytoplasm of the mother cell. This process involves the de novo generation of two different cellular structures: novel membrane compartments within the cell cytoplasm that give rise to the spore plasma membrane and an extensive spore wall that protects the spore from environmental insults. This article summarizes what is known about the molecular mechanisms controlling spore assembly with particular attention to how constitutive cellular functions are modified to create novel behaviors during this developmental process. Key regulatory points on the sporulation pathway are also discussed as well as the possible role of sporulation in the natural ecology of S. cerevisiae.

Expression, stability, and replacement of glucan-remodeling enzymes during developmental transitions in Saccharomyces cerevisiae

Sporulation is a developmental variation of the yeast life cycle whereby four spores are produced within a diploid cell, with proliferation resuming after germination. The GAS family of glycosylphosphatidylinositol-anchored glucan-remodeling enzymes exemplifies functional interplay between paralogous genes during the yeast life cycle. GAS1 and GAS5 are expressed in vegetative cells and repressed during sporulation while GAS2 and GAS4 exhibit a reciprocal pattern. GAS3 is weakly expressed in all the conditions and encodes an inactive protein. Although Gas1p functions in cell wall formation, we show that it persists during sporulation but is relocalized from the plasma membrane to the epiplasm in a process requiring End3p-mediated endocytosis and the Sps1 protein kinase of the p21-activated kinase family. Some Gas1p is also newly synthesized and localized to the spore membrane, but this fraction is dispensable for spore formation. By way of contrast, the Gas2-Gas4 proteins, which are essential for spore wall assembly, are rapidly degraded after spore formation. On germination, Gas1p is actively synthesized and concentrated in the growing part of the spore, which is essential for its elongation. Thus Gas1p is the primary glucan-remodeling enzyme required in vegetative growth and during reentry into the proliferative state. The dynamic interplay among Gas proteins is crucial to couple glucan remodeling with morphogenesis in developmental transitions.

Confining euchromatin/heterochromatin territory: jumonji crosses the line

Heterochromatin is typically highly condensed, gene-poor, and transcriptionally silent, whereas euchromatin is less condensed, gene-rich, and more accessible to transcription. Besides acting as a graveyard for selfish mobile DNA repeats, heterochromatin contributes to important biological functions, such as chromosome segregation during cell division. Multiple features of heterochromatin-including the presence or absence of specific histone modifications, DNA methylation, and small RNAs-have been implicated in distinguishing heterochromatin from euchromatin in various organisms. Cells malfunction if the genome fails to restrict repressive chromatin marks within heterochromatin domains. How euchromatin and heterochromatin territories are confined remains poorly understood. Recent studies from the fission yeast Schizosaccharomyces pombe, the flowering plant Arabidopsis thaliana, and the filamentous fungus Neurospora crassa have revealed a new role for Jumonji C (JmjC) domain-containing proteins in protecting euchromatin from heterochromatin marks.

The anaphase promoting complex targeting subunit Ama1 links meiotic exit to cytokinesis during sporulation in Saccharomyces cerevisiae

Ascospore formation in yeast is accomplished through a cell division in which daughter nuclei are engulfed by newly formed plasma membranes, termed prospore membranes. Closure of the prospore membrane must be coordinated with the end of meiosis II to ensure proper cell division. AMA1 encodes a meiosis-specific activator of the anaphase promoting complex (APC). The activity of APC(Ama1) is inhibited before meiosis II, but the substrates specifically targeted for degradation by Ama1 at the end of meiosis are unknown. We show here that ama1Delta mutants are defective in prospore membrane closure. Ssp1, a protein found at the leading edge of the prospore membrane, is stabilized in ama1Delta mutants. Inactivation of a conditional form of Ssp1 can partially rescue the sporulation defect of the ama1Delta mutant, indicating that an essential function of Ama1 is to lead to the removal of Ssp1. Depletion of Cdc15 causes a defect in meiotic exit. We find that prospore membrane closure is also defective in Cdc15 and that this defect can be overcome by expression of a form of Ama1 in which multiple consensus cyclin-dependent kinase phosphorylation sites have been mutated. These results demonstrate that APC(Ama1) functions to coordinate the exit from meiosis II with cytokinesis.

Cdc15 is required for spore morphogenesis independently of Cdc14 in Saccharomyces cerevisiae

In Saccharomyces cerevisiae exit from mitosis requires the Cdc14 phosphatase to reverse CDK-mediated phosphorylation. Cdc14 is released from the nucleolus by the Cdc14 early anaphase release (FEAR) and mitotic exit network (MEN) pathways. In meiosis, the FEAR pathway is essential for exit from anaphase I. The MEN component Cdc15 is required for the formation of mature spores. To analyze the role of Cdc15 during sporulation, a conditional mutant in which CDC15 expression was controlled by the CLB2 promoter was used. Cdc15-depleted cells proceeded normally through the meiotic divisions but were unable to properly disassemble meiosis II spindles. The morphology of the prospore membrane was aberrant and failed to capture the nuclear lobes. Cdc15 was not required for Cdc14 release from the nucleoli, but it was essential to maintain Cdc14 released and for its nucleo-cytoplasmic transport. However, cells carrying a CDC14 allele with defects in nuclear export (Cdc14-DeltaNES) were able to disassemble the spindle and to complete spore formation, suggesting that the Cdc14 nuclear export defect was not the cause of the phenotypes observed in cdc15 mutants.

Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1

Epigenetically silent transposons and repeats constitute a substantial proportion of eukaryotic genomes, but their impact on cellular gene function remains largely unexplored. In Arabidopsis, transposons are silenced by DNA methylation, and this methylation is often abolished by mutations in a chromatin-remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1). The ddm1 mutation induces various types of developmental abnormalities through de-repression of transposons and repeats. Here, we report a novel mechanism for a ddm1-induced syndrome, called bonsai (bns). We identified the gene responsible for the bns phenotypes by genetic linkage analysis and subsequent transcriptional analysis. The bns phenotypes are due to silencing of a putative Anaphase-Promoting Complex (APC) 13 gene. The BNS gene silencing was associated with DNA hypermethylation, which is in contrast to the ddm1-induced hypomethylation in the other genomic regions. This paradoxical BNS hypermethylation was reproducibly induced during self-pollination of the ddm1 mutant, and it was mediated by a long interspersed nuclear element (LINE) retrotransposon flanking the BNS gene. We discuss possible molecular mechanisms and the evolutionary implications of transposon-mediated epigenetic changes in the BNS locus.

Ascospore formation in the yeast Saccharomyces cerevisiae

Sporulation of the baker's yeast Saccharomyces cerevisiae is a response to nutrient depletion that allows a single diploid cell to give rise to four stress-resistant haploid spores. The formation of these spores requires a coordinated reorganization of cellular architecture. The construction of the spores can be broadly divided into two phases. The first is the generation of new membrane compartments within the cell cytoplasm that ultimately give rise to the spore plasma membranes. Proper assembly and growth of these membranes require modification of aspects of the constitutive secretory pathway and cytoskeleton by sporulation-specific functions. In the second phase, each immature spore becomes surrounded by a multilaminar spore wall that provides resistance to environmental stresses. This review focuses on our current understanding of the cellular rearrangements and the genes required in each of these phases to give rise to a wild-type spore.

Morphogenetic pathway of spore wall assembly in Saccharomyces cerevisiae

The Saccharomyces cerevisiae spore is protected from environmental damage by a multilaminar extracellular matrix, the spore wall, which is assembled de novo during spore formation. A set of mutants defective in spore wall assembly were identified in a screen for mutations causing sensitivity of spores to ether vapor. The spore wall defects in 10 of these mutants have been characterized in a variety of cytological and biochemical assays. Many of the individual mutants are defective in the assembly of specific layers within the spore wall, leading to arrests at discrete stages of assembly. The localization of several of these gene products has been determined and distinguishes between proteins that likely are involved directly in spore wall assembly and probable regulatory proteins. The results demonstrate that spore wall construction involves a series of dependent steps and provide the outline of a morphogenetic pathway for assembly of a complex extracellular structure.

In vivo characterization of the nonessential budding yeast anaphase-promoting complex/cyclosome components Swm1p, Mnd2p and Apc9p

We have examined the in vivo requirement of two recently identified nonessential components of the budding yeast anaphase-promoting complex, Swm1p and Mnd2p, as well as that of the previously identified subunit Apc9p. swm1Delta mutants exhibit synthetic lethality or conditional synthetic lethality with other APC/C subunits and regulators, whereas mnd2Delta mutants are less sensitive to perturbation of the APC/C. swm1Delta mutants, but not mnd2Delta mutants, exhibit defects in APC/C substrate turnover, both during the mitotic cell cycle and in alpha-factor-arrested cells. In contrast, apc9Delta mutants exhibit only minor defects in substrate degradation in alpha-factor-arrested cells. In cycling cells, degradation of Clb2p, but not Pds1p or Clb5p, is delayed in apc9Delta. Our findings suggest that Swm1p is required for full catalytic activity of the APC/C, whereas the requirement of Mnd2p for APC/C function appears to be negligible under standard laboratory conditions. Furthermore, the role of Apc9p in APC/C-dependent ubiquitination may be limited to the proteolysis of a select number of substrates.

Swm1/Apc13 is an evolutionarily conserved subunit of the anaphase-promoting complex stabilizing the association of Cdc16 and Cdc27

The anaphase-promoting complex (APC/C) is a large ubiquitin-protein ligase which controls progression through anaphase by triggering the degradation of cell cycle regulators such as securin and B-type cyclins. The APC/C is an unusually complex ligase containing at least 10 different, evolutionarily conserved components. In contrast to APC/C's role in cell cycle regulation little is known about the functions of individual subunits and how they might interact with each other. Here, we have analyzed Swm1/Apc13, a small subunit recently identified in the budding yeast complex. Database searches revealed proteins related to Swm1/Apc13 in various organisms including humans. Both the human and the fission yeast homologues are associated with APC/C subunits, and they complement the phenotype of an SWM1 deletion mutant of budding yeast. Swm1/Apc13 promotes the stable association with the APC/C of the essential subunits Cdc16 and Cdc27. Accordingly, Swm1/Apc13 is required for ubiquitin ligase activity in vitro and for the timely execution of APC/C-dependent cell cycle events in vivo.

Swm1p subunit of the APC/cyclosome is required for activation of the daughter-specific gene expression program mediated by Ace2p during growth at high temperature in Saccharomyces cerevisiae

SWM1 was originally identified for its role in the late steps of the sporulation process, being required for spore wall assembly. This protein, recently identified as one of the core subunits of the anaphase-promoting complex (APC) is also required to complete cell separation in vegetative cells during growth at high temperature. Mutants lacking SWM1 show a thermosensitive growth defect that is suppressed by osmotic support in the culture medium. At the restrictive temperature, swm1 mutants are unable to complete separation, forming chains of cells that remain associated and, with prolonged incubation times, the stability of the cell wall is compromised, resulting in cell lysis. This separation defect is due to a reduction in expression of CTS1 (the gene encoding chitinase) and a group of genes involved in cell separation (such as ENG1,SCW11, DSE1 and DSE2). Interestingly, these genes are specifically regulated by the transcription factor Ace2p, suggesting that Swm1p is required for normal expression of Ace2p-dependent genes during growth at high temperatures. Although no defect in Ace2p localization can be observed at 28 degrees C, this transcription factor is unable to enter the nucleus of the daughter cell during growth at 38 degrees C. Under these growth conditions, swm1 cells undergo a delay in exit from mitosis, as determined by analysis of Clb2p degradation and Cdc28p-Clb2p kinase assays, and this could be the reason for the cytoplasmic localization of Ace2p.

Mnd2 and Swm1 are core subunits of the Saccharomyces cerevisiae anaphase-promoting complex

The anaphase-promoting complex (APC) is a multisubunit E3 ubiquitin ligase that regulates the metaphase-anaphase transition and exit from mitosis in eukaryotic cells. Eleven subunits have been previously identified in APC from budding yeast. We have identified two additional subunits, Mnd2 and Swm1, by mass spectrometry. Both Mnd2 and Swm1 were found specifically associated with a highly purified preparation of APC from haploid yeast whole cell extract. Moreover, the APC co-purified with epitope-tagged Mnd2 and Swm1. Both proteins were present in APC preparations from haploid cells arrested in G(1), S, and M phases and from meiotic diploid cells, indicating that they are constitutive components of the complex throughout the yeast cell cycle. Mnd2 interacted strongly with Cdc23, Apc5, and Apc1 when coexpressed in an in vitro transcription/translation reaction. Swm1 also interacted with Cdc23 and Apc5 in this system. Previous studies described meiotic defects for mutations in MND2 and SWM1. Here, we show that mnd2delta and swm1delta haploid strains exhibit slow growth and accumulation of G(2)/M cells comparable with that seen in apc9delta or apc10Delta strains and consistent with an APC defect. Taken together, these results demonstrate that Swm1 and Mnd2 are functional components of the yeast APC.

Doc1 mediates the activity of the anaphase-promoting complex by contributing to substrate recognition

The anaphase-promoting complex (APC) is a multisubunit E3 ubiquitin ligase that targets specific cell cycle-related proteins for degradation, regulating progression from metaphase to anaphase and exit from mitosis. The APC is regulated by binding of the coactivator proteins Cdc20p and Cdh1p, and by phosphorylation. We have developed a purification strategy that allowed us to purify the budding yeast APC to near homogeneity and identify two novel APC-associated proteins, Swm1p and Mnd2p. Using an in vitro ubiquitylation system and a native gel binding assay, we have characterized the properties of wild-type and mutant APC. We show that both the D and KEN boxes contribute to substrate recognition and that coactivator is required for substrate binding. APC lacking Apc9p or Doc1p/Apc10 have impaired E3 ligase activities. However, whereas Apc9p is required for structural stability and the incorporation of Cdc27p into the APC complex, Doc1p/Apc10 plays a specific role in substrate recognition by APC-coactivator complexes. These results imply that Doc1p/Apc10 may play a role to regulate the binding of specific substrates, similar to that of the coactivators.

Proteomics analysis identifies new components of the fission and budding yeast anaphase-promoting complexes

The anaphase-promoting complex (APC) is a conserved multisubunit ubiquitin ligase required for the degradation of key cell cycle regulators. Components of the APC have been identified through genetic screens in both Schizosaccharomyces pombe and Saccharomyces cerevisiae as well as through biochemical purification coupled with mass spectrometric protein identification. With these approaches, 11 subunits of the core S. cerevisiae APC have been identified. Here, we have applied a tandem affinity purification approach coupled with direct analysis of the purified complexes by mass spectrometry (DALPC) to reveal additional subunits of both the S. pombe and S. cerevisiae APCs. Our data increase the total number of identified APC subunits to 13 in both yeasts and indicate that previous approaches were biased against the identification of small subunits. These results underscore the power of direct analysis of protein complexes by mass spectrometry and set the foundation for further functional and structural studies of the APC.

Control of chitin synthesis through Shc1p, a functional homologue of Chs4p specifically induced during sporulation

The Saccharomyces cerevisiae SHC1 gene encodes a protein with a high homology to Chs4p, a positive regulator of chitin synthase III (CSIII) during vegetative growth. SHC1 is not expressed during vegetative growth but is strongly induced during sporulation as a mid-late gene. shc1/shc1 mutants do not show any defect in the total rate of sporulation and meiosis occurs normally. However, shc1/shc1 ascospores be-come highly permeable to DAPI, much more sensitive to glusulase treatment, and have very low levels of chitosan in their cell walls. All these observations indicate that Shc1p is required for proper maturation of the ascospore through its participation in the synthesis of the chitosan layer. Lack of SHC1 during sporulation can be partially compensated by over-expression of the CHS4 gene. During vegetative growth, SHC1 has no apparent function but, when ectopically overexpressed, it can substitute Chs4p as an activator of the CSIII activity; however, Shc1p fails to localize it properly, as Chs4p does. In conclusion, S. cerevisiae contains two functionally redundant genes in the control of CSIII activity: CHS4, whose function is restricted to vegetative growth because Chs4p is rapidly degraded during sporulation, and SHC1, whose function in cell wall ascospore assembly is transcriptionally restricted to the sporulation process.

A Gip1p-Glc7p phosphatase complex regulates septin organization and spore wall formation

Sporulation of Saccharomyces cerevisiae is a developmental process in which a single cell is converted into four haploid spores. GIP1, encoding a developmentally regulated protein phosphatase 1 interacting protein, is required for spore formation. Here we show that GIP1 and the protein phosphatase 1 encoded by GLC7 play essential roles in spore development. The gip1Delta mutant undergoes meiosis and prospore membrane formation normally, but is specifically defective in spore wall synthesis. We demonstrate that in wild-type cells, distinct layers of the spore wall are deposited in a specific temporal order, and that gip1Delta cells display a discrete arrest at the onset of spore wall deposition. Localization studies revealed that Gip1p and Glc7p colocalize with the septins in structures underlying the growing prospore membranes. Interestingly, in the gip1Delta mutant, not only is Glc7p localization altered, but septins are also delocalized. Similar phenotypes were observed in a glc7-136 mutant, which expresses a Glc7p defective in interacting with Gip1p. These results indicate that a Gip1p-Glc7p phosphatase complex is required for proper septin organization and initiation of spore wall formation during sporulation.

Interaction of Knr4 protein, a protein involved in cell wall synthesis, with tyrosine tRNA synthetase encoded by TYS1 in Saccharomyces cerevisiae

The Knr4 protein, known to be involved in the regulation of cell wall assembly in Saccharomyces cerevisiae, strongly interacts with the tyrosine tRNA synthetase protein encoded by TYS1 as demonstrated by the genetic two-hybrid system and a biochemical pull-down experiment using GST--Tys1p fusion. Data reported here raise the possibility that this physical interaction between these proteins is required for dityrosine formation during the sporulation process. In addition, it is shown that the efficiency of spores formation was drastically reduced in diploid cells homozygous for the disruption of KNR4 or for a temperature-sensitive mutation of TYS1, although this effect could be independent of their protein interaction. Altogether, these data provide novel functions of Knr4p and Tys1p to those that were known before.

Mps1p regulates meiotic spindle pole body duplication in addition to having novel roles during sporulation

Sporulation in yeast requires that a modified form of chromosome segregation be coupled to the development of a specialized cell type, a process akin to gametogenesis. Mps1p is a dual-specificity protein kinase essential for spindle pole body (SPB) duplication and required for the spindle assembly checkpoint in mitotically dividing cells. Four conditional mutant alleles of MPS1 disrupt sporulation, producing two distinct phenotypic classes. Class I alleles of mps1 prevent SPB duplication at the restrictive temperature without affecting premeiotic DNA synthesis and recombination. Class II MPS1 alleles progress through both meiotic divisions in 30-50% of the population, but the asci are incapable of forming mature spores. Although mutations in many other genes block spore wall formation, the cells produce viable haploid progeny, whereas mps1 class II spores are unable to germinate. We have used fluorescently marked chromosomes to demonstrate that mps1 mutant cells have a dramatically increased frequency of chromosome missegregation, suggesting that loss of viability is due to a defect in spindle function. Overall, our cytological data suggest that MPS1 is required for meiotic SPB duplication, chromosome segregation, and spore wall formation.

Transcriptional regulation of meiosis in yeast

The genes required for meiosis and sporulation in yeast are expressed at specific points in a highly regulated temporal pathway. Recent experiments using DNA microarrays to examine gene expression during meiosis and the identification of many regulatory factors have provided important advances in our understanding of how genes are regulated at the different stages of meiosis.