Insufficiency of Copper Ion Homeostasis Causes Freeze-Thaw Injury of Yeast Cells as Revealed by Indirect Gene Expression Analysis

Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes, including frozen dough baking. Cell viability and fermentation activity after a freeze-thaw cycle were dramatically decreased due to freeze-thaw injury. Because this type of injury involves complex phenomena, the injury mechanisms are not fully understood. We examined freeze-thaw injury by indirect gene expression analysis during postthaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that genes involved in the homeostasis of metal ions were frequently contained in genes that were upregulated, depending on the freezing period. We assessed the phenotype of deletion mutants of the metal ion homeostasis genes that exhibited freezing period-dependent upregulation and found that the strains with deletion of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. We found that supplementation with copper ions during postthaw incubation increased intracellular superoxide dismutase activity and intracellular levels of reactive oxygen species were decreased. Moreover, cell viability was increased by supplementation with copper ions. These results suggest that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.Yeast (Saccharomyces cerevisiae) cells are exposed to various environmental stresses such as freeze-thaw, high-temperature, osmotic, and air-drying stresses during commercial processes. Freeze-thaw stress is important in the bread-making process, because frozen dough baking has become a major technology (3). Frozen dough baking improves labor conditions for bakers and enables them to provide fresh baked goods for consumers (3). Because frozen dough baking involves freeze-thaw treatment, it exposes yeast cells to freeze-thaw stress, which leads to a significant decrease in the fermentation ability and viability of yeast cells (called “freeze-thaw injury”) (8). The freeze-thaw injury of yeast cells depends on many factors, including freezing periods, freezing temperature, and the physiology of yeast cells (2, 5, 16, 17). Clarification of the changes in the cell physiology of yeast cells caused by freeze-thaw stress is important, because bakers are eager to extend the shelf life of frozen dough. In this study, we attempted to determine the changes in yeast cell physiology due to freeze-thaw injury by indirect gene expression analysis, which is described below.Freezing subjects yeast cells to low temperature, ice crystal formation in the cells, and dehydration from the cells. This causes both physical damage to cellular components, such as the cell wall, membrane, and proteins, and formation of reactive oxygen species (ROS) (13, 15). Superoxide anions and free radicals are generated in yeast cells during the freeze-thaw process (18), and ROS generation during the thawing process is increased, depending on the freezing period (5, 18). Oxidative stress generated by freeze-thaw treatment enhances the damage to cellular components (9, 25). Because modulation of intracellular levels of ROS after freeze-thaw treatment is required to protect against toxicity, ROS scavenging systems such as glutathione, catalase, and superoxide dismutase (SOD) are believed to be important for freeze-thaw tolerance of yeast cells (1, 2, 17). In particular, copper/zinc SOD (Cu/Zn SOD), which plays a role in oxygen radical detoxification, is necessary to confer full tolerance to freeze-thaw injury (18). Heavy metal ions, such as iron ions and copper ions, are important transition metals for the detoxification of oxygen radicals in yeast cells (6).Although there have been several studies on the mechanisms of freeze-thaw injury (5, 17, 18, 24), the mechanisms are complex and have not yet been fully elucidated. We therefore examined freeze-thaw injury by indirect gene expression analysis, which was conducted during postthaw incubation after freeze-thaw treatment using DNA microarray profiling. Indirect gene expression analysis may be advantageous for such an examination, because changes of gene expression may reflect the physiology of the freezing-state cell. We hypothesized that the genes involved in freeze-thaw injury may upregulate during postthaw incubation. To elucidate the physiological changes during freeze-thaw injury, we carried out indirect gene expression analysis using yeast cells after they had been frozen for different periods. The upregulated genes in the indirect gene expression analysis were extracted by clustering methods. We found that the genes involved in metal ion homeostasis were specifically upregulated. The importance of the genes extracted by the clustering was confirmed by phenotypic analysis using the deletion strains of the extracted genes. We also showed, by physiological analysis, that insufficiency of copper ion homeostasis causes freeze-thaw injury.     

Statistical Analysis of Multiplex Brain Gene Expression Images

Analysis of variance (ANOVA) was employed to investigate 9,000 gene expression patterns from brains of both normal mice and mice with a pharmacological model of Parkinson's disease (PD). The data set was obtained using voxelation, a method that allows high-throughput acquisition of 3D gene expression patterns through analysis of spatially registered voxels (cubes). This method produces multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. The ANOVA model was compared to the results from singular value decomposition (SVD) by using the first 42 singular vectors of the data matrix, a number equal to the rank of the ANOVA model. The ANOVA was also compared to the results from non-parametric statistics. Lastly, images were obtained for a subset of genes that emerged from the ANOVA as significant. The results suggest that ANOVA will be a valuable framework for insights into the large number of gene expression patterns obtained from voxelation.     

分析基因表达图式的新方法

随着基因组研究的深入进行,基因的分子生物学除了要寻找在生物学上重要的个别基因并研究其结构与功能外,更重要的应是了解整个基因组的功能活动,即细胞全部基因的表达图式.要解决如此复杂的问题就必须在研究方法上有所创新,基因表达系列分析法、cDNA微阵列分析法、DNA微芯片分析法等正是近几年发展起来的分析基因表达图式的新方法.     

Neonatal Maternal Deprivation Response and Developmental Changes in Gene Expression Revealed by Hypothalamic Gene Expression Profiling in Mice

Neonatal feeding problems are observed in several genetic diseases including Prader-Willi syndrome (PWS). Later in life, individuals with PWS develop hyperphagia and obesity due to lack of appetite control. We hypothesized that failure to thrive in infancy and later-onset hyperphagia are related and could be due to a defect in the hypothalamus. In this study, we performed gene expression microarray analysis of the hypothalamic response to maternal deprivation in neonatal wild-type and Snord116del mice, a mouse model for PWS in which a cluster of imprinted C/D box snoRNAs is deleted. The neonatal starvation response in both strains was dramatically different from that reported in adult rodents. Genes that are affected by adult starvation showed no expression change in the hypothalamus of 5 day-old pups after 6 hours of maternal deprivation. Unlike in adult rodents, expression levels of Nanos2 and Pdk4 were increased, and those of Pgpep1, Ndp, Brms1l, Mett10d, and Snx1 were decreased after neonatal deprivation. In addition, we compared hypothalamic gene expression profiles at postnatal days 5 and 13 and observed significant developmental changes. Notably, the gene expression profiles of Snord116del deletion mice and wild-type littermates were very similar at all time points and conditions, arguing against a role of Snord116 in feeding regulation in the neonatal period.     

Pattern Formation in the Arabidopsis Embryo Revealed by Position-Specific Lipid Transfer Protein Gene Expression

During Arabidopsis embryogenesis, the zygote divides asymmetrically in the future apical-basal axis; however, a radial axis is initiated only within the eight-celled embryo. Mutations in the GNOM, KNOLLE, and KEULE genes affect these processes: gnom zygotes tend to divide symmetrically; knolle embryos lack oriented cell divisions that initiate protoderm formation; and in keule embryos, an outer cell layer is present that consists of abnormally enlarged cells from early development. Pattern formation along the two axes is reflected by the position-specific expression of the Arabidopsis lipid transfer protein (AtLTP1) gene. In wild-type embryos, the AtLTP1 gene is expressed in the protoderm and initially in all protodermal cells; later, AtLTP1 expression is confined to the cotyledons and the upper end of the hypocotyl. Analysis of AtLTP1 expression in gnom, knolle, and keule embryos showed that gnom embryos also can have no or reversed apical-basal polarity, whereas radial polarity is unaffected. knolle embryos initially lack but eventually form a radial pattern, and keule embryos are affected in protoderm cell morphology rather than in the establishment of the radial pattern.     

Synaptic Protein Ubiquitination in Rat Brain Revealed by Antibody-based Ubiquitome Analysis

Protein ubiquitination is an essential post-translational modification regulating neurodevelopment, synaptic plasticity, learning, and memory, and its dysregulation contributes to the pathogenesis of neurological diseases. Here we report a systematic analysis of ubiquitinated proteome (ubiquitome) in rat brain using a newly developed monoclonal antibody that recognizes the diglycine tag on lysine residues in trypsinized peptides (K-GG peptides). Initial antibody specificity analysis showed that the antibody can distinguish K-GG peptides from linear GG peptides or pseudo K-GG peptides derived from iodoacetamide. To evaluate the false discovery rate of K-GG peptide matches during database search, we introduced a null experiment using bacterial lysate that contains no such peptides. The brain ubiquitome was then analyzed by this antibody enrichment with or without strong cation exchange (SCX) prefractionation. During SCX chromatography, although the vast majority of K-GG peptides were detected in the fractions containing at least three positive charged peptides, specific K-GG peptides with two positive charges (e.g., protein N-terminal acetylated and C-terminal non-K/R peptides) were also identified in early fractions. The reliability of C-terminal K-GG peptides was also extensively investigated. Finally, we collected a data set of 1786 K-GG sites on 2064 peptides in 921 proteins and estimated their abundance by spectral counting. The study reveals a wide range of ubiquitination events on key components in presynaptic region (e.g., Bassoon, NSF, SNAP25, synapsin, synaptotagmin, and syntaxin) and postsynaptic density (e.g., PSD-95, GKAP, CaMKII, as well as receptors for NMDA, AMPA, GABA, serotonin, and acetylcholine). We also determined ubiquitination sites on amyloid precursor protein and alpha synuclein that are thought to be causative agents in Alzhermer's and Parkinson's disorders, respectively. As K-GG peptides can also be produced from Nedd8 or ISG15 modified proteins, we quantified these proteins in the brain and found that their levels are less than 2% of ubiquitin. Together, this study demonstrates that a large number of neuronal proteins are modified by ubiquitination and provides a feasible method for profiling the ubiquitome in the brain.     

脑源性神经营养因子（BDNF）在成肌细胞中的稳定表达

将ｂｄｎｆ基因克隆入逆转录病毒载体ｐＬＮＣＸ,构建得到ｐＬＮＣ／ＢＤＮＦ,经ＰＡ３１７细胞包装后,感染大鼠成肌细胞Ｌ６ＴＧ,Ｇ４１８筛选２周后,得到稳定表达ｂｄｎｆ基因的细胞克隆Ｌ６ＴＧ／ＢＤＮＦ。ＤＮＡ印迹结果证实ｂｄｎｆ基因已经整合入Ｌ６ＴＧ染色体中,ＲＮＡ印迹和斑点印迹结果分别从ｍＲＮＡ水平和蛋白水平证明了ｂｄｎｆ基因的表达,且Ｌ６ＴＧ／ＢＤＮＦ培养上清中ＢＤＮＦ的含量约为２５ｎｇ（１０６细胞数每ｍｌ每２４ｈ）。     

Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression

Neural circuits in the medial entorhinal cortex (MEC) encode an animal’s position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.     

Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing

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