Growth-phase-dependent gene expression profiling of poplar (Populus alba x Populus tremula var. glandulosa) suspension cells

Complex sequences of morphological and biochemical changes occur during the developmental course of a batch plant cell culture. However, little information is available about the changes in gene expression that could explain these changes, because of the difficulties involved in isolating specific cellular events or developmental phases in the overlapping phases of cell growth. In an attempt to obtain such information we have examined the global growth phase-dependent gene expression of poplar cells in suspension cultures by cDNA microarray analysis. Our results reveal that significant changes occur in the expression of genes with functions related to protein synthesis, cell cycling, hormonal responses and cell wall biosynthesis, as cultures progress from initiation to senescence, that are highly correlated with observed developmental and physiological changes in the cells. Genes encoding protein kinases, calmodulin and proteins involved in both ascorbate metabolism and water-limited stress responses also showed strong stage-specific expression patterns. Our report provides fundamental information on molecular mechanisms that control cellular changes throughout the developmental course of poplar cell cultures.     

The C. elegans heterochronic gene lin-46 affects developmental timing at two larval stages and encodes a relative of the scaffolding protein gephyrin

The succession of developmental events in the C. elegans larva is governed by the heterochronic genes. When mutated, these genes cause either precocious or retarded developmental phenotypes, in which stage-specific patterns of cell division and differentiation are either skipped or reiterated, respectively. We identified a new heterochronic gene, lin-46, from mutations that suppress the precocious phenotypes caused by mutations in the heterochronic genes lin-14 and lin-28. lin-46 mutants on their own display retarded phenotypes in which cell division patterns are reiterated and differentiation is prevented in certain cell lineages. Our analysis indicates that lin-46 acts at a step immediately downstream of lin-28, affecting both the regulation of the heterochronic gene pathway and execution of stage-specific developmental events at two stages: the third larval stage and adult. We also show that lin-46 is required prior to the third stage for normal adult cell fates, suggesting that it acts once to control fates at both stages, and that it affects adult fates through the let-7 branch of the heterochronic pathway. Interestingly, lin-46 encodes a protein homologous to MoeA of bacteria and the C-terminal domain of mammalian gephyrin, a multifunctional scaffolding protein. Our findings suggest that the LIN-46 protein acts as a scaffold for a multiprotein assembly that controls developmental timing, and expand the known roles of gephyrin-related proteins to development.     

Vectors for the expression of tagged proteins in Drosophila.

Regulated expression systems have been extremely useful in developmental studies, allowing the expression of specific proteins in defined spatial and temporal patterns. If these proteins are fused to an appropriate molecular tag, then they can be purified or visualized without the need to raise specific antibodies. If the tag is inherently fluorescent, then the proteins can even be visualized directly, in living tissue. We have constructed a series of P element-based transformation vectors for the most widely used expression system in Drosophila, GAL4/UAS. These vectors provide a series of useful tags for antibody detection, protein purification, and/or direct visualization, together with a convenient multiple cloning site into which the cDNA of interest can be inserted.     

The MsK family of alfalfa protein kinase genes encodes homologues of shaggy/glycogen synthase kinase-3 and shows differential expression patterns in plant organs and development

This paper reports on the isolation of a novel class of plant serine/threonine protein kinase genes, MsK-1 , MsK-2 and MsK-3 . They belong to the superfamily of cdc2 -like genes, but show highest identity to the Drosophila shaggy and rat GSK-3 proteins (66–70%). All of these kinases share a highly conserved catalytic protein kinase domain. Different amino-terminal extensions distinguish the different proteins. The different plant kinases do not originate from differential processing of the same gene as is found for shaggy , but are encoded by different members of a gene family. Similarly to the shaggy kinases, the plant kinases show different organ-specific and stage-specific developmental expression patterns. Since the shaggy kinases play an important role in intercellular communication in Drosophila development, the MsK kinases are expected to perform a similar function in plants.     

Overlapping expression patterns among the genes encoding Arabidopsis chromosomal high mobility group (HMG) proteins

High mobility group (HMG) proteins are usually considered ubiquitous components of the eukaryotic chromatin. Using HMG gene promoter-GUS reporter gene fusions we have examined the expression of the reporter gene in transgenic Arabidopsis plants. These experiments have revealed that the different HMGA and HMGB promoters display overlapping patterns of activity, but they also show tissue- and developmental stage-specific differences. Moreover, leader introns that are present in some of the HMGB genes can modulate reporter gene expression. The differential HMG gene expression supports the view that the various HMG proteins serve partially different architectural functions in plant chromatin.     

Age-Specific Differentiations during the Development of the Rat Submandibular Gland

Histological observations indicate that the rodent submanfibular salivary gland does not complete its development until adulthood. Reports in the literature based upon enzyme studies suggest that the gland may pass through several stages of differentiation from birth to adulthood. Considering that proteases appear late in the developmental sequence and could cause apparent changes in enzyme concentrations, a methodology free of possible protease-mediated artefacts has been developed to analyze the patterns of protein accumulations. Analysis of total trichloroacetic acid-precipitable proteins on acrylamide gradient slab gels with sodium dodecyl sulphate and urea indicated that there are stage-specific patterns, and that certain protein species are prominent in early stages, but become unresolvable in later stages where different species have assumed prominence. Direct analysis of stage-specific gene expression as indicated by patterns of short-term protein synthesis also suggest that some of the major synthetic activities change qualitatively as development progresses. These alterations are discussed in the light of the changing cellular populations within the gland and certain correlations are proposed. These studies support the view that the submandibular gland exhibits several distinguishable differentiated states in the course of its development.     

小菜蛾热休克蛋白基因的鉴定及其表达模式分析

热休克蛋白(heat shock protein, HSP)在昆虫应对外界胁迫刺激时起着重要作用。为了系统研究小菜蛾Plutella xylostella HSP基因家族, 根据家蚕的HSP蛋白序列, 采用本地Blast程序对小菜蛾全基因组数据库进行同源序列检索, 从小菜蛾基因组数据库中鉴定了25个HSP基因, 包括2个HSP90、 8个HSP70和15个sHSP（small heat shock protein, sHSP）基因。小菜蛾、 家蚕Bombyx mori、 黑腹果蝇Drosophila melanogaster和赤拟谷盗Tribolium castaneum的HSP系统进化分析显示, 昆虫的小分子量热休克蛋白sHSP具有很强的种属特异性, HSP70家族的保守性比sHSP强。小菜蛾HSP基因表达模式分析显示, 与敏感品系对比, 抗性品系（抗毒死蜱和抗氟虫氰品系）中HSP基因具有不同的表达模式。小菜蛾1, 2和3龄幼虫HSP基因表达模式较为接近, 而与4龄幼虫中的表达模式相差较大; 4龄幼虫和蛹中的表达模式相近; 雌成虫和雄成虫中的表达模式显著不同, 与果蝇精子形成有关的两个热休克蛋白HSP23和HSP27基因［分别为CCG003980.1 (Px23.5)和CCG005412.2 (Px27.5)］, 在小菜蛾雄成虫中的表达量显著高于雌成虫。研究结果表明小菜蛾HSP基因不仅在杀虫剂抗性、 发育分化, 甚至在生殖上均可能起着重要的作用。本研究为深入研究小菜蛾HSP与生长发育、 抗逆行为的相互关系奠定了基础。     

Differential expression of sex-related fat body proteins during the larval–pupal developmental stages of the silkworm (Bombyx mori)

The silkworm fat body is the site of many intermediary metabolic processes, and a source of sustenance for growth throughout the life cycle. Fat body proteins are responsible for storing nutrients, providing energy, and regulating hormones, and they have been identified using proteomic approaches. However, detailed differential expression of sex-related fat body proteins has not previously been evaluated. In the present study, we characterized the differential expression of sex-related fat body proteins, by using 2-dimensional gel electrophoresis (2-DE) followed by mass spectrometry identification and bioinformatics methods. We extracted the fat body proteins from 5-day-old fifth instar larvae (L5), 10-day-old fifth instar larvae (corresponding to the end of spinning [LE]), and 0-day-old pupae (P0) of the multivoltine silkworm variety “Da Zao”. We confirmed the presence of 11 important sex-specific expression proteins and 14 stage-specific expression proteins. We accurately identified 13 of these specific expression proteins, including actin, calponin-like protein, 75 kDa subunit NADH, receptor for activated protein kinase C from Bombyx mori (BmRACK), IMP (inosine monophosphate) cyclohydrolase, tropomyosin 1, β-tubulin, hypothetical protein, antichymotrypsin precursor, and 30 K protein precursor. We showed that BmRACK was differentially expressed between male and female silkworms. We discuss the biological roles of the specific expression proteins during the larval–pupal developmental stages.     

Epigenomic Landscape of Human Fetal Brain,Heart, and Liver

The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. We identified 40,181 active enhancers, with a large portion showing tissue-specific and developmental stage-specific patterns, pointing to their roles in controlling the ordered spatiotemporal expression of the developmental genes in early human embryos. Moreover, using sequential ChIP-seq, we showed that all three organs have hundreds to thousands of bivalent domains that are marked by both H3K4me3 and H3K27me3, probably to keep the progenitor cells in these organs ready for immediate differentiation into diverse cell types during subsequent developmental processes. Our work illustrates the potentially critical roles of tissue-specific and developmental stage-specific epigenomes in regulating the spatiotemporal expression of developmental genes during early human embryonic development.