Protein expression profiling during chick retinal maturation: a proteomics-based approach

Background

We describe a biosensor platform for monitoring molecular interactions that is based on the combination of a defined nano-porous silicon surface, coupled to light interferometry. This platform allows the label-free detection of protein-protein and protein-DNA interactions in defined, as well as complex protein mixtures. The silicon surface can be functionalized to be compatible with traditional carboxyl immobilization chemistries, as well as with aldehyde-hydrazine bioconjugation chemistries.

Results

We demonstrate the utility of the new platform in measuring protein-protein interactions of purified products in buffer, in complex mixtures, and in the presence of different organic solvent spikes, such as DMSO and DMF, as these are commonly used in screening chemical compound libraries.

Conclusion

Nano-porous silicon, when combined with white light interferometry, is a powerful technique for the measurement of protein-protein interactions. In addition to studying the binary interactions of biomolecules in clean buffer systems, the newly developed surfaces are also suited for studying interactions in complex samples, such as plasma.     

Proteomic profiling of murine oocyte maturation

In an effort to better understand oocyte function, we utilized two-dimensional (2D) electrophoresis and mass spectrometry to identify proteins that are differentially expressed during murine oocyte maturation. Proteins from 500 germinal vesicle (GV) and metaphase II-(MII) arrested oocytes were extracted, resolved on 2D electrophoretic gels, and stained with silver. Analysis of the gels indicated that 12 proteins appeared to be differentially expressed between the GV and MII stage. These proteins were then cored from the 2D gels and identified by mass spectrometry as: transforming acidic coiled-coil protein 3 (TACC3), heat shock protein 105 (HSP105), programmed cell death six-interacting protein (PDCD6IP), stress-inducible phosphoprotein (STI1), importin alpha2, adenylsuccinate synthase (ADDS), nudix, spindlin, lipocalin, lysozyme, translationally controlled tumor protein (TCTP), and nucleoplasmin 2 (NPM2). Interestingly, PDCD6IP, importin alpha2, spindlin, and NPM2 appear slightly larger in mass and more acidic on the MII oocyte gel compared to the GV oocyte gel, suggesting that they may be post-translationally modified during oocyte maturation. Given NPM2 is an oocyte-restricted protein, we chose to further investigate its properties during oocyte maturation and preimplantation development. Real-Time RT-PCR showed that NPM2 mRNA levels rapidly decline at fertilization. Indirect immunofluorescence analysis showed that, with the exception of cortical localization in MII-arrested oocytes, NPM2 is localized to the nucleus of both GV stage oocytes and all stages of preimplantation embryos. We then performed one-dimensional (1D) western blot analysis of mouse oocytes and preimplantation embryos and found that, as implicated by the 2D gel comparison, NPM2 undergoes a phosphatase-sensitive electrophoretic mobility shift during the GV to MII transition. The slower migrating NPM2 form is also present in pronuclear embryos but by the two-cell stage, the majority of NPM2 exists as the faster migrating form, which persists to the blastocyst stage.     

Molecular analysis of maturation processes by protein and phosphoprotein profiling during in vitro maturation of bovine oocytes: a proteomic approach

Cellular maturation and differentiation processes are accompanied by the expression of specific proteins. Especially in oocytes, there is no reliable strict linear correlation between mRNA levels and the abundance of proteins. Furthermore, the activity of proteins is modulated by specific kinases and phosphatases which control cellular processes like cellular growth, differentiation, cell cycle and meiosis. During the meiotic maturation of oocytes, the activation of protein kinases, namely of the MPF and MAPK play a predominant role. Therefore, the present study was performed to analyze meiotic maturation at a molecular level, concerning alterations of the proteom and phosphoproteom during IVM. Using a proteomic approach by combining two-dimensional gel electrophoresis followed by selective protein and phosphoprotein staining and mass spectrometry, we identified proteins which were differentially expressed and/or phosphorylated during IVM. Furthermore, we used the MPF inhibitor butyrolactone I, to reveal new molecular effects which are potentially essential for successful maturation. The results show that approximately 550 protein spots could be visualized by the fluorescent dye Sypro ruby at any maturation stage (GV, M I, M II) investigated. From GV stage to M II, ProQ diamond staining indicate in GV 30%, in M I 50%, and in M II 45% of the spots were phosphorylated. The Identity of 40 spots could be established. These proteins belong to different families, for example, cytoskeleton, molecular chaperons, redox, energy and metabolism related proteins, nucleic acid binding proteins, cell cycle regulators, and protein kinases. Four of them were differentially expressed (alteration higher than factor 2) during IVM, namely tubulin beta-chain, cyclin E(2), protein disulfide isomerase and one of two different forms of peroxiredoxin 2. Seven proteins were differentially stained by ProQ diamond, indicating a differential phosphorylation. These are tubulin beta-chain, beta-actin, cyclin E(2), aldose reductase and UMP-synthase, protein disulfide isomerase 2, and peroxiredoxin 2. Furthermore, the results indicate that the phosphorylation of at least peroxiredoxin 2 respond to BL I treatment. This indicates that its phosphorylation is under the control of MPF or MAPK. In summary these results indicates that the reduction of cyclin Eexpression and the (partially) inactivation of peroxiredoxin 2 by phosphorylation, hence alterations in the peroxide levels which can mediate signal transduction are essential components for successful maturation.     

Nek2 expression and localization in porcine oocyte during maturation

We studied the role of the Ser/Thr protein kinase Nek2 on meiosis progression by using in vitro porcine oocyte maturation system. Nek2 is a candidate of a mammalian homologue of NIMA, which was found in Aspergillus nidulans as an essential molecule for mitosis progression. We cloned porcine Nek2 cDNA, and examined the mRNA and protein expression levels during meiosis progression. The expression levels did not change through the oocyte maturation, but fluorescence microscopy observation of Nek2 in the oocytes at various maturation steps showed that Nek2 was detected only at metaphase II, but not before metaphase II. At metaphase II, Nek2 was found exclusively on the chromosomes. These results suggest that Nek2 changes the cellular localization during maturation and accumulates on the chromosomes to play a role on the entry and progression of metaphase II.     

Cloning and expression profiling of testis-expressed microRNAs

Using a new small RNA cloning method, we identified 141 miRNAs from the mouse testis, of which 29 were novel. The 141 miRNAs were mapped onto all chromosomes except the Y chromosome and 2/3 of these miRNA genes exist as clusters. ∼ 70% of these miRNA genes were located in intronic or intergenic regions, whereas the remaining miRNAs were derived from exonic sequences. We further validated these cloned miRNAs by examining their expression in multiple mouse organs including developing testes and also in purified spermatogenic cells using semi-quantitative PCR analyses. Our expression profiling assays revealed that 60% of the testis-expressed miRNAs were ubiquitously expressed and the remaining are either preferentially (35%) or exclusively (5%) expressed in the testis. We also observed a lack of strand selection during testicular miRNA biogenesis, characterized by paired expression of both the 5′ strands and 3′ strands derived from the same precursor miRNAs. The present work identified numerous miRNAs preferentially or exclusively expressed in the testis, which would be interesting targets for further functional studies.     

Changes in protein synthesis and phosphorylation patterns during bovine oocyte maturation in vitro

Sequential protein synthesis and protein phosphorylation patterns were generated by radiolabelling bovine cumulus-oocyte complexes after various periods of culture with [35S]methionine and [32P]orthophosphate respectively. The radiolabelled oocytes were assessed for their nuclear status and used individually for gel electrophoresis. Marked changes in the protein synthesis patterns were observed exclusively after germinal vesicle breakdown (GVBD), whereas oocytes which remained in the germinal vesicle stage showed a consistent protein synthesis pattern. The changes were observed after 8 and 16 h or culture, shortly after GVBD and before first polar body extrusion. From 3 h of culture, dominant phosphoprotein bands with apparent molecular weights of 24,000 and two between 50,000 and 60,000 were observed. The latter bands displayed slight molecular weight changes, which were not closely time related. After GVBD, the phosphoprotein band with Mr 19,000 was no longer observed. This study demonstrates that specific changes in protein synthesis and protein phosphorylation are programmed during bovine oocyte maturation.     

Distribution and expression of phosphorylated histone H3 during porcine oocyte maturation

Phosphorylation modification of core histones is correlated well with diverse chromatin-based cell activities. However, its distribution pattern and primary roles during mammalian oocyte meiosis are still in dispute. In this study, by performing immunofluorescence and Western blotting, spatial distribution and temporal expression of phosphorylated serine 10 or 28 on histone H3 during porcine oocyte meiotic maturation were examined and distinct subcellular distribution patterns between them were presented. Low expression of phosphorylated H3/ser10 was detected in germinal vesicle. Importantly, following gradual dephosphorylation from germinal vesicle (GV) to late germinal vesicle (L-GV) stage, a transient phosphorylation at the periphery of condensed chromatin was re-established at early germinal vesicle breakdown (E-GVBD) stage, and then the dramatically increased signals covered whole chromosomes from pre-metaphase I (Pre-MI) to metaphase II (MII). Similarly, hypophosphorylation of serine 28 on histone H3 was also monitored from GV to E-GVBD, indicating dephosphorylation of histone H3 maybe involved in the regulation of meiotic resumption. Moreover, the rim staining on the chromosomes and high levels of H3/ser28 phosphorylation were observed in Pre-MI, MI, and MII stage oocytes. Based on above results, such stage-dependent dynamics of phosphorylation of H3/ser 10 and 28 may play specific roles during mammalian oocyte maturation.     

Study of newly synthesized proteins during bovine oocyte maturation in vitro using image analysis of two-dimensional gel electrophoresis

To investigate protein synthesis during bovine oocyte maturation in vitro, oocytes were put in culture with 35S-methionine for 4 hr periods from time zero to 28 hr. Pools of 10 oocytes were then prepared for two-dimensional gel electrophoresis (2-DE). For each time interval, three gels were obtained, digitalized, and analyzed to detect proteins. Then, the gel containing the most proteins was chosen as the reference gel and compared with the others. An averaged gel was created with proteins present in at least two gels of the three. Our results indicate that the rate of protein synthesis is higher at the beginning of maturation until the appearance of metaphase I (MI, 8-12 hr) and then it decreases and stays relatively constant. Percentages of initial proteins (0-4 hr) and remaining present during the progression decrease progressively from 100% to 53%. In contrast, when we compare proteins synthesized from the 4 to 8 hr period with proteins from the 8 to 12 or the 12 to 16 hr intervals, percentages of overall protein matching are stable with values of 81 and 79%, respectively. Comparison of proteins from 20 to 24 hr with proteins from 16 to 20 or 24 to 28 hr intervals also gives stable percentages of overall protein matching with values of 83 and 84%, respectively. Furthermore, a higher number of new proteins is observed at 4-8 hr (n=130) and 16-20 hr (n=136) of maturation. Thus, three major patterns of protein synthesis were observed during bovine oocyte maturation in vitro: one at the beginning of maturation (0-4 hr), another one in the middle (4-16 hr), and the last one after the completion of MI stage (16-28 hr).