Genetic mapping and embryonic expression of a novel, maternally transcribed gene Mem3

Interrogating the transcriptome of oocytes and preimplantation embryos

During its growth phase, a mouse oocyte accumulates RNA that is the sole template for new protein synthesis in the transcriptionally silent interval between growth completion and transcriptional activation of the embryonic genome. Over this transcriptionally silent interval, almost half the quantity of RNA accumulated in the full-grown oocyte is degraded, while stable messages undergo major transcript-specific polyadenylation fluctuations associated with timely translation of new proteins. These processes, in the background of substantial RNA degradation, create unique pitfalls for transcriptome analysis. Three particular challenges are discussed herein. (1) Systematic errors of relative quantification occur if standard approaches are used, wherein samples are normalized to a constant quantity of RNA, or when computational analyses are normalized to an apparent "constant" endogenous to the sample. We show that use of a fixed quantity of exogenous RNA per oocyte or embryo alleviates this problem. (2) Comparison of large-scale expression analyses from widely disparate platforms highlights how the differing protocols produce correspondingly different lists of genes with significant changes in transcript abundance. Only with careful attention to the differences among experiments can such discrepancies be understood. (3) The complete assessment of changes in expression requires correspondingly comprehensive assessment of the role of isoform-specific changes.

Gene expression during the oocyte-to-embryo transition in mammals

The seminal question in modern developmental biology is the origins of new life arising from the unification of sperm and egg. The roots of this question begin from 19th to 20th century embryologists studying fertilization and embryogenesis. Although the revolution of molecular biology has yielded significant insight into the complexity of this process, the overall orchestration of genes, molecules, and cells is still not fully formed. Early mammalian development, specifically the oocyte-to-embryo transition, is essentially under "maternal command" from factors deposited in the cytoplasm during oocyte growth, independent of de novo transcription from the nascent embryo. Many of the advances in understanding this developmental period occurred in tandem with application of new methods and techniques from molecular biology, from protein electrophoresis to sequencing and assemblies of whole genomes. From this bed of knowledge, it appears that precise control of mRNA translation is a key regulator coordinating the molecular and cellular events occurring during oocyte-to-embryo transition. Notably, oocyte transcriptomes share, yet retain some uniqueness, common genetic motifs among all chordates. The common genetic motifs typically define fundamental processes critical for cellular maintenance, whereas the unique genetic features may be a source of variation and a substrate for sexual selection, genetic drift, or gene flow. One purpose for this complex interplay among genes, proteins, and cells may allow for evolution to transform and act upon the underlying processes, at molecular, structural and organismal levels, to increase diversity, which is the ultimate goal of sexual reproduction.

Arabidopsis VPS35, a retromer component, is required for vacuolar protein sorting and involved in plant growth and leaf senescence

The retromer complex is responsible for retrograde transport, which is coordinated with anterograde transport in the secretory pathway including vacuolar protein sorting. Yeast VPS35 is a component of the retromer complex that is essential for recognition of specific cargo molecules. The physiological function of VPS35 has not been determined in vacuolar protein sorting in higher organisms. Arabidopsis thaliana has three VPS35 homologs designated VPS35a, VPS35b and VPS35c. We isolated four vps35 mutants (vps35a-1, vps35b-1, vps35b-2 and vps35c-1) and then generated four double mutants and one triple mutant. vps35a-1 vps35c-1 exhibited no unusual phenotypes. On the other hand, vps35b-1 vps35c-1 and the triple mutant (vps35a-1 vps35b-2 vps35c-1) exhibited severe phenotypes: dwarfism, early leaf senescence and fragmentation of protein storage vacuoles (PSVs). In addition, these mutants mis-sorted storage proteins by secreting them out of the cells and accumulated a higher level of vacuolar sorting receptor (VSR) than the wild type. VPS35 was localized in pre-vacuolar compartments (PVCs), some of which contained VSR. VPS35 was immunoprecipitated with VPS29/MAG1, another component of the retromer complex. Our findings suggest that VPS35, mainly VPS35b, is involved in sorting proteins to PSVs in seeds, possibly by recycling VSR from PVCs to the Golgi complex, and is also involved in plant growth and senescence in vegetative organs.

Retromer: multipurpose sorting and specialization in polarized transport

Retromer is an evolutionary conserved protein complex required for endosome-to-Golgi retrieval of lysosomal hydrolases' receptors. A dimer of two sorting nexins-typically, SNX1 and/or SNX2-deforms the membrane and thus cooperates with retromer to ensure cargo sorting. Research in various model organisms indicates that retromer participates in sorting of additional molecules whose proper transport has important repercussions in development and disease. The role of retromer as well as SNXs in endosomal protein (re)cycling and protein targeting to specialized plasma membrane domains in polarized cells adds further complexity and has implications in growth control, the establishment of developmental patterns, cell adhesion, and migration. This chapter will discuss the functions of retromer described in various model systems and will focus on relevant aspects in polarized transport.

Time-course of hormonal induction of mitochondrial glycerophosphate dehydrogenase biogenesis in rat liver

Thyroid hormones are important regulators of mitochondrial metabolism. Due to their complex mechanism of action, the timescale of different responses varies from minutes to days. In this work, we studied selective T3 induction of the inner mitochondrial membrane enzyme-glycerophosphate dehydrogenase (mGPDH) in liver of euthyroid rats. We correlated the kinetics of the T3 level in blood, the mRNA level in liver, the activity and amount of mGPDH in liver mitochondria after a single dose of T3. The T3 level reached maximum after 1 h (80 nmol/l) and subsequently rapidly decreased. mGPDH mRNA increased also relatively fast, reaching a maximum after 12 h and fell to the control level after 72 h. An increase of mGPDH activity could be already found after 6 h and reached a maximum after 24 h in accordance with the increase in mGPDH content (2.4-fold vs. 2.7-fold induction). After 72 h, the mGPDH activity showed a significant 30% decrease. When the rats received three subsequent doses of T3, the increase of mGPDH activity was 2-fold higher than after a single T3 dose. The results demonstrate that mGPDH displays rapid induction as well as decay upon disappearance of a hormonal stimulus, indicating a rather short half-life of this inner mitochondrial membrane enzyme.

IL-1 and LPS but not IL-6 inhibit differentiation and downregulate PPAR gamma in brown adipocytes

Brown adipose tissue (BAT) is well recognized as a heat-producing organ of rodents and generally all young mammals. There is good experimental evidence that its thermogenic activity plays a role also during development of fever and that this activation is mediated exclusively via an adrenergic pathway. However, we have shown that brown adipocytes highly express receptors for pyrogenic factors (IL-1, LPS) and that after their activation, brown adipocytes are capable of responding by production of IL-6 and IL-1alpha. In this study we examined the effect of chronic treatment of mouse brown adipocytes in primary culture with pyrogens (IL-1beta, IL-6 and LPS) on their ability to differentiate into mature adipocytes. We found that treatment with IL-1beta or LPS, but not with IL-6, inhibited the differentiation of brown adipocytes, which was accompanied by a 2.5-10-fold decrease in PPARgamma mRNA. The anti-adipogenic effect of IL-1beta and LPS could thus be mediated via downregulation of PPARgamma levels, similar to the anti-adipogenic action of another pyrogenic cytokine--TNFalpha. We also found that pretreatment of brown adipocytes with IL-1beta or LPS led to a more pronounced (2-4-fold) induction of IL-6 transcripts upon whole 24h time course of adrenergic stimulation. These results support the view that BAT functions not only as an effector but also as a mediator of the febrile response; while the thermogenic activity is associated with terminally differentiated cells, earlier developmental states of brown adipocytes seem to be able to play a mediatory role.

Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos

We have adapted the whole-mount in situ hybridization technique to perform high-throughput gene expression analysis in mouse embryos. A large-scale screen for genes showing specific expression patterns in the mid-gestation embryo was carried out, and a large number of genes controlling development were isolated. From 35760 clones of a 9.5 d.p.c. cDNA library, a total of 5348 cDNAs, enriched for rare transcripts, were selected and analyzed by whole-mount in situ hybridization. Four hundred and twenty-eight clones revealed specific expression patterns in the 9.5 d.p.c. embryo. Of 361 tag-sequenced clones, 198 (55%) represent 154 known mouse genes. Thirty-nine (25%) of the known genes are involved in transcriptional regulation and 33 (21%) in inter- or intracellular signaling. A large number of these genes have been shown to play an important role in embryogenesis. Furthermore, 24 (16%) of the known genes are implicated in human disorders and three others altered in classical mouse mutations. Similar proportions of regulators of embryonic development and candidates for human disorders or mouse mutations are expected among the 163 new mouse genes isolated. Thus, high-throughput gene expression analysis is suitable for isolating regulators of embryonic development on a large-scale, and in the long term, for determining the molecular anatomy of the mouse embryo. This knowledge will provide a basis for the systematic investigation of pattern formation, tissue differentiation and organogenesis in mammals.

Expression of Melk, a new protein kinase, during early mouse development

A new gene named maternal embryonic leucine zipper kinase, Melk, has been recently identified (Heyer et al. [1997] Mol. Reprod. Dev. 47:148-156). As a basis for further study of the function of the gene, we have examined the expression of Melk across a wide range of embryonic stages, from the ovulated egg and 2-cell embryo through the gastrulation and early organogenesis stages, by in situ hybridization and immunohistochemistry. Melk is expressed in a spatially and temporally specific pattern during mammalian embryogenesis. The strongest expression was detected during maturation of oocytes and preimplantation development. Given its expression pattern, Melk may play an important role during preimplantation embryonic development. Dev Dyn 1999;215:344-351.

Molecular characterization of a novel tubby gene family member, TULP3, in mouse and humans

Tubby and related proteins are derived from a small family of novel genes. The carboxytermini of this family are highly conserved across a number of species including humans, mice, Caenorhabditis elegans, Arabidopsis, rice, and maize. Splicing defects in both tub and another member of the gene family, TULP1 (tubby-like protein 1), lead to phenotypes of retinal degeneration in mice and humans, respectively. We describe here the isolation of the human and mouse homologs of a new family member, TULP3. The cDNAs code for proteins of 442 and 460 amino acids, respectively. The level of identity between the human TULP3 and the mouse homolog is 69%, lower than that observed for the homologs of the other family members (96% for human and mouse TUB), and is higher at the amino- and carboxytermini than in the central region of the protein. Phylogenetically, TULP3 is the family member most closely related to TUB. Also, like TUB, it has a wider pattern of tissue expression than either TULP1 or TULP2. TULP3 is detected at high levels in human RNA from testis, ovaries, thyroid, and spinal chord. Tulp3 is also highly expressed in mouse RNA from eyes and adipose depots, tissues not tested in the human Northern analysis. We also report that TULP3 maps to human chromosome 12p13. The murine homolog, Tulp3, maps to the telomere of mouse chromosome 6.

Abnormal nonshivering thermogenesis in mice with inherited defects of fatty acid oxidation

When placed in the cold (4 degreesC), BALB/cByJ mice of both genders rapidly lose body temperature as compared with the control strain, C57BL/6J. This sensitivity to cold resembles that previously described for mice with a defect in nonshivering thermogenesis due to the targeted inactivation of the brown adipocyte-specific mitochondrial uncoupling protein gene, Ucp1. Genetic mapping of the trait placed the gene on chromosome 5 near Acads, a gene encoding the short chain acyl CoA dehydrogenase, which is mutated in BALB/cByJ mice. The analysis of candidate genes in the region indicated a defect only in the expression of Acads. Confirmation of the importance of fatty acid oxidation to thermogenesis came from our finding that mice carrying the targeted inactivation of the long chain acyl CoA dehydrogenase gene (Acadl) are also sensitive to the cold. Both of these mutations attenuate the induction of genes normally responsive to adrenergic signaling in brown adipocytes. These results suggest that the action of fatty acids as regulators of gene expression has been perturbed in the mutant mice. From a clinical perspective, it is important to determine whether defects in thermogenesis may be a phenotype in human neonates with inherited deficiencies in fatty acid beta-oxidation.

A membrane coat complex essential for endosome-to-Golgi retrograde transport in yeast

We have recently characterized three yeast gene products (Vps35p, Vps29p, and Vps30p) as candidate components of the sorting machinery required for the endosome-to-Golgi retrieval of the vacuolar protein sorting receptor Vps10p (Seaman, M.N.J., E.G. Marcusson, J.-L. Cereghino, and S.D. Emr. 1997. J. Cell Biol. 137:79-92). By genetic and biochemical means we now show that Vps35p and Vps29p interact and form part of a multimeric membrane-associated complex that also contains Vps26p, Vps17p, and Vps5p. This complex, designated here as the retromer complex, assembles from two distinct subcomplexes comprising (a) Vps35p, Vps29p, and Vps26p; and (b) Vps5p and Vps17p. Density gradient fractionation of Golgi/endosomal/vesicular membranes reveals that Vps35p cofractionates with Vps5p/Vps17p in a vesicle-enriched dense membrane fraction. Furthermore, gel filtration analysis indicates that Vps35p and Vps5p are present on a population of vesicles and tubules slightly larger than COPI/coatomer-coated vesicles. We also show by immunogold EM that Vps5p is localized to discrete regions at the rims of the prevacuolar endosome where vesicles appear to be budding. Size fractionation of cytosolic and recombinant Vps5p reveals that Vps5p can self-assemble in vitro, suggesting that Vps5p may provide the mechanical impetus to drive vesicle formation. Based on these findings we propose a model in which Vps35p/Vps29p/Vps26p function to select cargo for retrieval, and Vps5p/Vps17p assemble onto the membrane to promote vesicle formation. Conservation of the yeast retromer complex components in higher eukaryotes suggests an important general role for this complex in endosome-to-Golgi retrieval.

A new method for isolating tyrosine kinase substrates used to identify fish, an SH3 and PX domain-containing protein, and Src substrate

We describe a method for identifying tyrosine kinase substrates using anti-phosphotyrosine antibodies to screen tyrosine-phosphorylated cDNA expression libraries. Several potential Src substrates were identified including Fish, which has five SH3 domains and a recently discovered phox homology (PX) domain. Fish is tyrosine-phosphorylated in Src-transformed fibroblasts (suggesting that it is a target of Src in vivo) and in normal cells following treatment with several growth factors. Treatment of cells with cytochalasin D also resulted in rapid tyrosine phosphorylation of Fish, concomitant with activation of Src. These data suggest that Fish is involved in signalling by tyrosine kinases, and imply a specialized role in the actin cytoskeleton.

Emergence of brown adipocytes in white fat in mice is under genetic control. Effects on body weight and adiposity

The mRNA levels for the mitochondrial uncoupling protein (UCP1) in fat tissues of A/J and C57BL/6J inbred strains of mice varied in a regional-specific manner after stimulation of adrenergic signaling by cold exposure or treatment with a beta3-adrenergic agonist. While the differences between strains were minimal in interscapular brown fat, large differences occurred in white fat tissues, particularly in retroperitoneal fat. Among the AXB recombinant inbred strains, the Ucp1 mRNA levels varied up to 130-fold. This large induction at the mRNA level was accompanied by a corresponding increase in brown adipocytes as revealed by immunohistology with anti-UCP1 antibodies. A high capacity to induce brown fat in areas of traditional white fat had no impact on the ability to gain weight in response to high fat and sucrose diets, but did correlate with the loss of weight in response to treatment with a beta3-adrenergic agonist (CL 316,243). This genetic variation in mice provides an experimental approach to identify genes controlling the induction of brown adipocytes in white fat tissues.

cDNA libraries from single human preimplantation embryos

In this paper, the construction, evaluation, and application of cDNA libraries from eight unfertilized oocytes and single four-cell-, seven-cell-, and blastocyst-stage embryos are described. Rapid, reproducible, and efficient procedures for the construction of PCR-based cDNA libraries from fewer than 10 cells were first developed in small populations of fibroblast cells. The human embryo libraries display complexities sufficient (between 10(5) and 10(6) clones) to represent the entire active gene population at these early stages of human development. The ubiquitous cytoskeletal elements, beta-actin, keratin-18, and alpha-tubulin, were detected at the expected frequency. Sequencing of consecutively picked random clones, without selection, showed the presence of a variety of sequences, such as the human transposable element, LINE-1 and Alu repeat sequences, housekeeping genes, and tissue-specific genes, such as alpha-globin and FMR-1. In addition to cDNAs corresponding to known ESTs (expressed sequence tags) in the GenBank and dbEST databases, a high proportion of novel sequences were detected. Applications of the libraries to several areas of interest, such as expression of CpG-island-containing "tissue-specific" genes, developmental genes expressed in a stage-specific manner, and a search for monoallelic expression of imprinted genes, are described. The libraries are a valuable resource for the study of gene expression during human preimplantation development and obviate the need for research on the human embryos themselves.

Maid: a maternally transcribed novel gene encoding a potential negative regulator of bHLH proteins in the mouse egg and zygote

We isolated an abundant novel cDNA SSEC-8 from a subtraction cDNA library enriched for maternal transcripts that are still present in the mouse 2 cell stage embryo. This gene is evolutionarily conserved and maps to the distal region of mouse chromosome 2. The deduced polypeptide sequence of the encoded protein contains a conserved helix-loop-helix (HLH) motif without a basic DNA binding domain, suggesting that it functions as a negative regulator of basic (b) HLH transcription factors. Gel mobility shift assays show that in vitro translated protein prevents the E12/MyoD bHLH dimer from binding to DNA. Also, transient overexpression of this protein in C2C12 cells reduced the transcription of a CAT-reporter regulated by an E12/MyoD driven enhancer. The 3'-UTR contains consensus sequences of cytoplasmic polyadenylation elements (CPE's), and the length of its poly (A) tail changes during oocyte maturation, indicating that its expression is controlled by timely activation of translation. This new gene, Maid, models the translational and transcriptional regulation of gene expression during the transition from gamete to embryo.

Spindlin, a major maternal transcript expressed in the mouse during the transition from oocyte to embryo

Timely translation of maternal transcripts and post-translational modification of their gene products control the initial development of preimplantation-stage embryos. We have isolated and characterized a gene encoding a stage-specific embryonic protein. This novel gene, spindlin (Spin), is an abundant maternal transcript present in the unfertilized egg and 2-cell, but not 8-cell, stage embryo. Spin exhibits high homology to a multicopy gene, Y-linked spermiogenesis-specific transcript (Ssty), and together they form a new gene family expressed during gametogenesis. We find that spindlin associates with the meiotic spindle and is modified by phosphorylation in a cell-cycle-dependent fashion. Furthermore, it comigrates with the previously described 30x10(3) Mr metaphase complex which is posttranslationally modified during the first mitotic cell cycle. Our data suggest that spindlin plays a role in cell-cycle regulation during the transition from gamete to embryo.