Distinctive transcriptome alterations of prefrontal pyramidal neurons in schizophrenia and schizoaffective disorder.

Schizophrenia is associated with alterations in working memory that reflect dysfunction of dorsolateral prefrontal cortex (DLPFC) circuitry. Working memory depends on the activity of excitatory pyramidal cells in DLPFC layer 3 and, to a lesser extent, in layer 5. Although many studies have profiled gene expression in DLPFC gray matter in schizophrenia, little is known about cell-type-specific transcript expression in these two populations of pyramidal cells. We hypothesized that interrogating gene expression, specifically in DLPFC layer 3 or 5 pyramidal cells, would reveal new and/or more robust schizophrenia-associated differences that would provide new insights into the nature of pyramidal cell dysfunction in the illness. We also sought to determine the impact of other variables, such as a diagnosis of schizoaffective disorder or medication use at the time of death, on the patterns of gene expression in pyramidal neurons. Individual pyramidal cells in DLPFC layers 3 or 5 were captured by laser microdissection from 36 subjects with schizophrenia or schizoaffective disorder and matched normal comparison subjects. The mRNA from cell collections was subjected to transcriptome profiling by microarray followed by quantitative PCR validation. Expression of genes involved in mitochondrial (MT) or ubiquitin-proteasome system (UPS) functions were markedly downregulated in the patient group (P-values for MT-related and UPS-related pathways were <10(-7) and <10(-5), respectively). MT-related gene alterations were more prominent in layer 3 pyramidal cells, whereas UPS-related gene alterations were more prominent in layer 5 pyramidal cells. Many of these alterations were not present, or found to a lesser degree, in samples of DLPFC gray matter from the same subjects, suggesting that they are pyramidal cell specific. Furthermore, these findings principally reflected alterations in the schizophrenia subjects were not present or present to a lesser degree in the schizoaffective disorder subjects (diagnosis of schizoaffective disorder was the most significant covariate, P<10(-6)) and were not attributable to factors frequently comorbid with schizophrenia. In summary, our findings reveal expression deficits in MT- and UPS-related genes specific to layer 3 and/or layer 5 pyramidal cells in the DLPFC of schizophrenia subjects. These cell type-specific transcriptome signatures are not characteristic of schizoaffective disorder, providing a potential molecular-cellular basis of differences in clinical phenotypes.

Human BIN3 complements the F-actin localization defects caused by loss of Hob3p, the fission yeast homolog of Rvs161p.

The BAR adaptor proteins encoded by the RVS167 and RVS161 genes from Saccharomyces cerevisiae form a complex that regulates actin, endocytosis, and viability following starvation or osmotic stress. In this study, we identified a human homolog of RVS161, termed BIN3 (bridging integrator-3), and a Schizosaccharomyces pombe homolog of RVS161, termed hob3+ (homolog of Bin3). In human tissues, the BIN3 gene was expressed ubiquitously except for brain. S. pombe cells lacking Hob3p were often multinucleate and characterized by increased amounts of calcofluor-stained material and mislocalized F-actin. For example, while wild-type cells localized F-actin to cell ends during interphase, hob3Delta mutants had F-actin patches distributed randomly around the cell. In addition, medial F-actin rings were rarely found in hob3Delta mutants. Notably, in contrast to S. cerevisiae rvs161Delta mutants, hob3Delta mutants showed no measurable defects in endocytosis or response to osmotic stress, yet hob3+ complemented the osmosensitivity of a rvs161Delta mutant. BIN3 failed to rescue the osmosensitivity of rvs161Delta, but the actin localization defects of hob3Delta mutants were completely rescued by BIN3 and partially rescued by RVS161. These findings suggest that hob3+ and BIN3 regulate F-actin localization, like RVS161, but that other roles for this gene have diverged somewhat during evolution.

Loss of Rhb1, a Rheb-related GTPase in fission yeast, causes growth arrest with a terminal phenotype similar to that caused by nitrogen starvation.

The Rheb GTPase is most similar in primary sequence to the Ras, Rap, R-Ras, and Ral GTPases, which regulate cell growth and differentiation in many cell types. A likely fission yeast homologue of mammalian Rheb, which we designated Rhb1, was identified by genome sequencing. Our investigation of rhb1 showed that rhb1(-) cells arrested cell growth and division with a terminal phenotype similar to that of nitrogen-starved cells. In particular, cells depleted of Rhb1 arrested as small, round cells with 1N DNA content, arrested more quickly in low-nitrogen medium, and induced expression of fnx1 and mei2 mRNA, two mRNAs that were normally induced by nitrogen starvation. Since mammalian Rheb binds and may regulate Raf-1, a Ras effector, we tested for functional overlap between Ras1 and Rhb1 in fission yeast. This analysis showed that Ras1 overexpression did not suppress rhb1(-) mutant phenotypes, Rhb1 overexpression did not suppress ras1(-) mutant phenotypes, and ras1(-) rhb1(-) double mutants had phenotypes equal to the sum of the corresponding single-mutant phenotypes. Hence, there is no evidence for overlapping functions between Ras1 and Rhb1. On the basis of this study, we hypothesize that Rhb1 negatively regulates entry into stationary phase when extracellular nitrogen levels are adequate for growth. If this hypothesis is correct, then Rhb1 and Ras1 regulate alternative responses to limiting nutrients.

Byr4 localizes to spindle-pole bodies in a cell cycle-regulated manner to control Cdc7 localization and septation in fission yeast.

Cytokinesis and septation in the fission yeast Schizosaccharomyces pombe are studied as a model for mammalian cell division. In fission yeast, septation is positively regulated by Spg1, a Ras family GTPase that localizes to spindle-pole bodies (SPBs) throughout the cell cycle. As cells enter mitosis, Spg1 accumulates in an active, GTP-bound form and binds the Cdc7 protein kinase to cause Cdc7 translocation to SPBs. Cdc7 disappears from one SPB in mid-anaphase and from the second SPB in late mitosis. Byr4 plus Cdc16 negatively regulate septation by forming a two-component GTPase-activating protein for Spg1. These results led us to hypothesize that Byr4 localization to SPBs regulated the nucleotide state of Spg1, due to its ability to form Spg1GAP activity with Cdc16 and thus the binding of Cdc7 to Spg1 at SPBs. To test this hypothesis, Byr4 localization was determined using indirect immunofluorescence. This analysis revealed that Byr4 was localized to SPBs that did not contain Cdc7. In byr4(-) mutants, Cdc7 localized to interphase SPBs and only symmetrically localized to mitotic SPBs. In contrast, Byr4 overexpression prevented Spg1 and Cdc7 localization to SPBs. These results suggest that Byr4 localization to SPBs maintains Spg1 in an inactive form, presumably by stimulating Spg1 GTPase activity with Cdc16, and that loss of Byr4 from mitotic SPBs increases the active fraction of Spg1 and thereby increases Spg1-Cdc7 binding. Byr4 localization to SPBs was decreased in spg1, cdc16, sid4, and cdc11 mutants as well as in several mutants that affect medial F-actin structures, suggesting that multiple pathways regulate Byr4 localization to SPBs.

Regions of Byr4, a regulator of septation in fission yeast, that bind Spg1 or Cdc16 and form a two-component GTPase-activating protein with Cdc16.

In the fission yeast Schizosaccharomyces pombe, septation and constriction of the actomyosin ring for cell division are positively regulated by the Spg1 GTPase, a member of the Ras superfamily. Spg1 is negatively regulated by Byr4 and Cdc16, which together form a two-component GTPase-activating protein for the Spg1 GTPase. To better understand how Byr4 regulates septation, Byr4 mutants were tested for in vitro functions. This analysis revealed that Byr4 contained one Cdc16-binding site and four Spg1-binding sites (SBS), designated SBS1-SBS4. Although mutants with a single SBS bound Spg1 and inhibited GTP dissociation, the equilibrium binding affinity of these mutants was 28-280-fold weaker than Byr4. Because some Byr4 mutants with multiple SBSs bound Spg1 tighter than the corresponding mutants with a single SBS, multiple SBSs probably interact to cause the high affinity binding of Byr4 to Spg1. A region of Byr4 that bound Spg1, SBS4, and the region that bound Cdc16, Cdc16-binding site, was necessary and sufficient to form Cdc16-dependent Spg1GAP activity that was similar to that of wild-type Byr4 with Cdc16.

Functional analysis of domains in the Byr2 kinase.

The activation of mitogen-activated protein (MAP) kinase cascades by the Ras GTPase is an evolutionarily conserved signal transduction mechanism. To better understand the interaction between Ras and its target kinase, we study the yeast Schizosaccharomyces pombe where the Ras1 GTPase activates the Byr2 kinase. The Byr2 kinase contains an N-terminal regulatory region and a C-terminal kinase region. The regulatory region can be divided into a sterile-alpha motif (SAM) that binds Ste4, a Ras1-binding domain (RBD) that binds activated Ras1, and a catalytic binding domain (CBD) that interacts with the Byr2 kinase domain. To analyze the importance of functional domains of the Byr2 kinase, a biological assay was used that exploited the ability of Byr2 to partially bypass the need for Ras1 in sporulation. Analysis of mutants using this assay showed that SAM and RBD were very important for Ras1-stimulated sporulation. Three activating mutations were identified within the N-terminal lobe of the Byr2 kinase domain that partially bypassed the need for Ras1 for sporulation. These activating mutations may identify a region of the Byr2 kinase domain that interacts with the CBD since mutations in the CBD which disrupt binding to the kinase domain also increase Byr2 function.

Byr4 and Cdc16 form a two-component GTPase-activating protein for the Spg1 GTPase that controls septation in fission yeast.

BACKGROUND: Spatial and temporal control of cytokinesis ensures the accurate transmission of genetic material and the correct development of multicellular organisms. An excellent model system in which to study cytokinesis is Schizosaccharomyces pombe because there are similarities between cytokinesis in S. pombe and mammals and because genes involved in S. pombe cytokinesis have been characterized. In particular, formation of the septum is positively regulated by the Spg1 GTPase and its effector, the Cdc7 kinase. Septation is negatively regulated by Cdc16, a protein similar to GTPase-activating proteins (GAPs) for Ypt GTPases, and by Byr4, a protein of unknown biochemical function. This study investigates the relationship between Byr4, Cdc16, and Spg1. RESULTS: Genetic interactions were observed between byr4, cdc16, and spg1 mutants. Byr4 bound to Cdc16 and Spg1 in yeast two-hybrid assays and in coprecipitations in vitro and in yeast. Byr4 inhibited the dissociation and hydrolysis of GTP bound to Spg1, but when Byr4 and Cdc16 were combined together they displayed Spg1GAP activity in vitro; Cdc16 alone had no detectable GAP activity. The binding of Byr4 to Spg1 and the Byr4-Cdc16 Spg1GAP activity were specific because Byr4 and Cdc16 did not bind to or affect the GTPase activities of the seven known S pombe Ypt family GTPase. CONCLUSIONS: Byr4 and Cdc16 form a two-component GAP for the Spg1 GTPase. Byr4 and Cdc16 appear to negatively regulate septation in S. pombe by modulating the nucleotide state of Spg1 possibly in a spatially or temporally controlled manner.

ras1 and pat1 alleles interact to quantitatively and qualitatively alter conjugation in fission yeast.

To identify novel components of ras1+ signalling in Schizosaccharomyces pombe, extragenic suppressors of the mating defect of ras1 effector mutants were isolated. A novel allele of pat1, pat1-e1, was isolated that increases the mating of ras1-D43E mutants to near wild-type levels but does not suppress the mating defect of ras1-I41M, ras1-Y37F, or ras1-Y45I mutants. This allele-specific suppression is not a characteristic of all pat1 alleles since pat1-3 and pat1-114 partially and equally suppress ras1-D43E and ras1-I41M mutants. Analysis of mating cultures showed that ras1-D43E and pat1-e1 interact to qualitatively alter the mating response. While pat1-e1 ras1-D43E cells were delayed in agglutination, cell-cycle delay, and mat1-Pm transcription, they induce mat1-Mc at the same time and mate more rapidly than other mating cultures. These results suggest that pheromone signalling, but not nutritional signalling, is delayed in pat1-e1 ras1-D43E cells. We hypothesize that this delay causes an elevated pheromone response and thus suppression of the mating defect of the ras1-D43E mutant by pat1-e1.

The Byr2 kinase translocates to the plasma membrane in a Ras1-dependent manner.

The activation of mitogen-activated protein kinase cascades by the Ras GTPase is an evolutionarily conserved signal transduction mechanism. To better understand the interaction between Ras and its target kinase, we study the yeast Schizosaccharomyces pombe where the Ras1 GTPase activates the Byr2 kinase. Cell fractionation and immunofluorescence showed that Ras1 was localized to the plasma membrane and that Byr2 was in the cytoplasm. When Ras1 was overexpressed, Byr2 was translocated to the plasma membrane. Byr2 translocation was dependent on binding to Ras1 since Ras1-V12, an activated mutant of Ras1, caused more Byr2 translocation than Ras1, since Ras1-D38E, an effector domain mutant, did not cause Byr2 translocation, and since the Ras1-binding domain of Byr2 was necessary and sufficient to cause Byr2 translocation. The Byr2 protein was usually not uniform around the plasma membrane, but was frequently enriched at the cell ends and at the region of septal deposition. This uneven membrane localization depended upon regions of the Byr2 regulatory domain, in addition to those required for Ras1 binding, suggesting that these Byr2 domains participate in protein-protein interactions.

A novel suppressor of ras1 in fission yeast, byr4, is a dosage-dependent inhibitor of cytokinesis.

A novel gene, designated byr4, was identified in Schizosaccharomyces pombe that affects the mitotic cell cycle and shows genetic interactions with the ras1 signaling pathways. Null alleles of byr4 cause cell cycle arrest in late mitosis and permit multiple rounds of septation. The multiple septa typically divide two nuclei, but the nuclei frequently do not stain equally with 4',6-diamidino-2-phenylindole (DAPI), suggesting that byr4 is required for proper karyokinesis. Overexpression of byr4 inhibits cytokinesis, but cell cycle progression continues leading to multinucleate cells. When byr4 is overexpressed, the early steps in the cytokinesis pathway, including formation of the medial F-actin ring, occur normally; however, the later steps in the pathway, including contraction of the F-actin ring, septation, and rearrangement of the medial F-actin following mitosis, rarely occur, byr4 shows two genetic interactions with ras1. The inhibition of cytokinesis by byr4 overexpression was exacerbated by null alleles of ras1 and scd1, suggesting a link between pathways needed for cell polarity and cytokinesis. Overexpression of byr4 also partially bypasses the need for ras1 for sporulation. The electrophoretic mobility of the byr4 protein varied in response to mutants that perturb cytokinesis and karyokinesis, suggesting interactions between byr4 and these gene products. A more rapidly migrating byr4 protein was found in cells with mutations in cdc16, which undergo repeated septation, and in cdc15, which fail to form a medial F-actin ring in mitosis. A slower migrating byr4 protein was found in cells with a mutation in the beta-tubulin gene, which arrests cells at the metaphase-anaphase transition.

Characterization of a guanine nucleotide dissociation stimulator for a ras-related GTPase.

ras-related GTPases participate in signaling for a variety of cellular processes. The GTPases cycle between a GTP-bound active state and a GDP-bound inactive state. This cycling is partially controlled by guanine nucleotide dissociation stimulators (GDS, also known as exchange factors). We report on the molecular cloning of cDNAs encoding a new mammalian GDS protein, using sequences derived from the yeast ras GDS proteins as probes. The encoded protein stimulates the dissociation of guanine nucleotides from the ras-related ralA and ralB GTPases at a rate at least 30-fold faster than the intrinsic nucleotide dissociation rate. This new GDS, ralGDS, is at least 20-fold more active on the ralA and ralB GTPases than on any other GTPase tested, including other members of the ras family (H-ras, N-ras, K-ras, R-ras, rap1a and rap2), members of the rho family (rhoA, rhoB and CDC42-Hs) and members of the rab family (rab3a and ypt1). While the ralGDS protein is phosphorylated on serine residues, we find no evidence that phosphorylation affects the activity of insect cell-expressed ralGDS towards the ralA or ralB GTPase. The 3600 nucleotide ralGDS mRNA and the 115 kDa protein were found in all tissues and cell lines examined.

Association between GTPase activators for Rho and Ras families.

The ras-related low-molecular-mass GTPases participate in signal transduction involving a variety of cellular functions, including cell-cycle progression, cellular differentiation, cytoskeletal organization, protein transport and secretion. The cycling of these proteins between GTP-bound and GDP-bound states is partially controlled by GTPase activating proteins (GAPs) which stimulate the intrinsic GTP-hydrolysing activity of specific GTPases. The ras GTPase-activating protein (Ras-GAP) forms a complex with a second protein, p190 (M(r) 190,000), in growth-factor stimulated and tyrosine-kinase transformed cells. At its carboxy-terminal end, p190 contains a region that is conserved in the breakpoint cluster region, n-chimaerin, and Rho-GAP. Each of these three proteins exhibits GAP activity for at least one member of the rho family of small GTPases. We have tested recombinant p190 protein for GAP activity on GTPases of the ras, rho and rab families, and show here that p190 can function as a GAP specifically for members of the rho family. Consequently, the formation of a complex between Ras-GAP and p190 in growth-factor stimulated cells may allow the coupling of signalling pathways that involve ras and rho GTPases.

The sequence and transcript heterogeneity of the yeast gene ALG1, an essential mannosyltransferase involved in N-glycosylation.

The yeast gene ALG1 encodes a mannosyltransferase which participates in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation by catalyzing the formation of dolichol pyrophosphate (Dol-PP)-GlcNAc2Man from GDP-Man and Dol-PP-Glc-NAc2. The DNA region including the ALG1 gene was sequenced and found to contain an open reading frame of 1347 bases. The predicted ALG1 protein contained 449 amino acids (51.9 kDa) with a hydrophobic region near the amino terminus, suggesting it was an integral membrane protein, and four potential sites for N-glycosylation. Disruption of the ALG1 open reading frame by insertion of the URA3 gene showed that the ALG1 gene was essential for viability. Northern analysis and transcript protection showed that the ALG1 gene was transcribed into two classes of messages which differed by about 100 bases at their 5' end and shared a common 3' end. In actively growing cells the short transcript predominated, but as growth slowed the long transcript was more prevalent. The short transcript was predicted to encode the ALG1 protein while the long transcript was predicted to encode a 74-amino acid protein of unknown function. Disruption of the 74-amino acid reading frame, which ended 42 bases upstream of the potential start codon for the ALG1 protein, showed it was not essential for viability.

A 13-amino acid peptide in three yeast glycosyltransferases may be involved in dolichol recognition.

A 13-amino acid peptide was identified in three glycosyltransferases of the yeast endoplasmic reticulum. These enzymes, the products of the ALG1, ALG7, and DPM1 genes, catalyze the transfer of sugars from nucleotide sugars to dolichol phosphate derivatives. The consensus sequence for the conserved peptide was Leu-Phe-Val-Xaa-Phe-Xaa-Xaa-Ile-Pro-Phe-Xaa-Phe-Tyr. A sequence resembling the conserved peptide was also found in the predicted SEC59 protein, which is suspected to participate in assembly of the lipid-linked precursor oligosaccharide, although its specific function is unknown. All of the identified sequences contain an isoleucine at position 8 and phenylalanine or tyrosine at positions 2, 5, and 12. We believe this peptide may be involved in dolichol recognition for the following reasons. (i) The conserved sequence occurs in potential membrane-spanning regions. (ii) The ALG7 and DPM1 proteins are known to recognize the isoprenoid region of dolichol phosphate specifically; this recognition presumably occurs in the membrane since dolichol is very hydrophobic. (iii) The consensus sequence is similar to a region of two halobacterial proteins implicated in binding of the isoprenoid region of retinal. (iv) If the consensus sequence is represented as an alpha-helix, the conserved residues lie on one face of the helix. An alpha-helical structure is likely since the conserved regions are in potential membrane-spanning domains.