In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition

SILAC-Based Quantitative Proteomic Analysis of Drosophila Embryos

The fruit fly Drosophila melanogaster represents a classic genetic model organism that is amenable to a plethora of comprehensive analyses including proteomics. SILAC-based quantitative proteomics is a powerful method to investigate the translational and posttranslational regulation ongoing in cells, tissues, organs, and whole organisms. Here we describe a protocol for routine SILAC labeling of Drosophila adults within one generation to produce embryos with a labeling efficiency of over 92%. In combination with genetic selection markers, this method permits the quantification of translational and posttranslational changes in embryos mutant for developmental and disease-related genes.

Cloning of the Maternal Effector Gene org and Its Regulation by lncRNA ORG-AS in Chinese Tongue Sole (Cynoglossus semilaevis)

Maternal effector genes (MEGs) encode maternal RNA and protein, accumulating in the cytoplasm of oocytes. During oocyte development, MEGs participate in oocyte meiosis and promote oocyte development. And MEGs can also regulate maternal transcriptome stability and promote maternal–zygotic transition (MTZ) in early embryonic development. Long noncoding RNAs (lncRNAs), as new epigenetic regulators, can regulate gene expression at both the transcriptional and post-transcriptional levels through cis- or trans-regulation. The oogenesis-related gene org is a germ-cell-specific gene in fish, but the role of org in embryonic development and oogenesis has rarely been studied, and the knowledge of the lncRNA-mediated regulation of org is limited. In this study, we cloned and identified the org gene of Chinese tongue sole (Cynoglossus semilaevis), and we identified a lncRNA named lncRNA ORG-anti-sequence (ORG-AS), located at the reverse overlapping region of org. The results of qRT-PCR and FISH demonstrated that org was highly expressed during the early stages of embryonic development and oogenesis and was located in the cytoplasm of oocytes. ORG-AS was expressed at low levels in the ovary and colocalized with org in the cytoplasm of oocytes. In vitro experiments showed that overexpression of ORG-AS inhibited org expression. These results suggest that org, as a MEG in C. semilaevis, participates in the MTZ and the oogenesis. The lncRNA ORG-AS negatively regulates the gene expression of org through trans-regulation. These new findings broaden the function of MEGs in embryonic development and the oogenesis of bony fish and prove that lncRNAs are important molecular factors regulating org.

Emerging Roles of RNA-Binding Proteins in Neurodevelopment

Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.

Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition

In animal embryos, the maternal-to-zygotic transition (MZT) hands developmental control from maternal to zygotic gene products. We show that the maternal proteome represents more than half of the protein-coding capacity of Drosophila melanogaster’s genome, and that 2% of this proteome is rapidly degraded during the MZT. Cleared proteins include the post-transcriptional repressors Cup, Trailer hitch (TRAL), Maternal expression at 31B (ME31B), and Smaug (SMG). Although the ubiquitin-proteasome system is necessary for clearance of these repressors, distinct E3 ligase complexes target them: the C-terminal to Lis1 Homology (CTLH) complex targets Cup, TRAL, and ME31B for degradation early in the MZT and the Skp/Cullin/F-box-containing (SCF) complex targets SMG at the end of the MZT. Deleting the C-terminal 233 amino acids of SMG abrogates F-box protein interaction and confers immunity to degradation. Persistent SMG downregulates zygotic re-expression of mRNAs whose maternal contribution is degraded by SMG. Thus, clearance of SMG permits an orderly MZT.

Cao et al. show that 2% of the proteome is degraded in early Drosophila embryos, including a repressive ribonucleoprotein complex. Two E3 ubiquitin ligases separately act on distinct components of this complex to phase their clearance. Failure to degrade a key component, the Smaug RNA-binding protein, disrupts an orderly maternal-to-zygotic transition.

Using stable isotope tracers to monitor membrane dynamics in C. elegans

Membranes within an animal are composed of phospholipids, cholesterol, and proteins that together form a dynamic barrier. The types of lipids that are found within a membrane bilayer impact its biophysical properties including its fluidity, permeability, and susceptibility to damage. While membrane composition is very stable in healthy adults, aberrant membrane structure is seen in a wide and varied array of diseases as well as during natural aging. Despite the wide-reaching impacts of membrane composition, there is relatively little known about how membrane landscape is established and maintained over time. In vivo biochemical modeling of membrane lipids is needed to understand how these molecules interact in their natural configurations. Here, we have described analytical methods that increase the capacity to map the dynamics of individual membrane phospholipids using different types of mass spectrometry. Specifically, we describe novel stable isotope (¹³C and ¹⁵N) strategies to quantify the turnover of dozens of fatty acid tails and intact phospholipids simultaneously.

SILAC-based quantitative proteomic analysis of Drosophila gastrula stage embryos mutant for fibroblast growth factor signalling

Quantitative proteomic analyses in combination with genetics provide powerful tools in developmental cell signalling research. Drosophila melanogaster is one of the most widely used genetic models for studying development and disease. Here we combined quantitative proteomics with genetic selection to determine changes in the proteome upon depletion of Heartless (Htl) Fibroblast-Growth Factor (FGF) receptor signalling in Drosophila embryos at the gastrula stage. We present a robust, single generation SILAC (stable isotope labelling with amino acids in cell culture) protocol for labelling proteins in early embryos. For the selection of homozygously mutant embryos at the pre-gastrula stage, we developed an independent genetic marker. Our analyses detected quantitative changes in the global proteome of htl mutant embryos during gastrulation. We identified distinct classes of downregulated and upregulated proteins, and network analyses indicate functionally related groups of proteins in each class. In addition, we identified changes in the abundance of phosphopeptides. In summary, our quantitative proteomic analysis reveals global changes in metabolic, nucleoplasmic, cytoskeletal and transport proteins in htl mutant embryos.

Quantifying post-transcriptional regulation in the development of Drosophila melanogaster

Even though proteins are produced from mRNA, the correlation between mRNA levels and protein abundances is moderate in most studies, occasionally attributed to complex post-transcriptional regulation. To address this, we generate a paired transcriptome/proteome time course dataset with 14 time points during Drosophila embryogenesis. Despite a limited mRNA-protein correlation (ρ = 0.54), mathematical models describing protein translation and degradation explain 84% of protein time-courses based on the measured mRNA dynamics without assuming complex post transcriptional regulation, and allow for classification of most proteins into four distinct regulatory scenarios. By performing an in-depth characterization of the putatively post-transcriptionally regulated genes, we postulate that the RNA-binding protein Hrb98DE is involved in post-transcriptional control of sugar metabolism in early embryogenesis and partially validate this hypothesis using Hrb98DE knockdown. In summary, we present a systems biology framework for the identification of post-transcriptional gene regulation from large-scale, time-resolved transcriptome and proteome data.

Monitoring Membrane Lipidome Turnover by Metabolic 15N Labeling and Shotgun Ultra-High-Resolution Orbitrap Fourier Transform Mass Spectrometry

Lipidomes undergo permanent extensive remodeling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic ¹⁵N labeling and shotgun ultra-high-resolution mass spectrometry (sUHR) to quantify the absolute (molar) abundance and determine the turnover rate of glycerophospholipids and sphingolipids by direct analysis of total lipid extracts. sUHR performed on a commercial Orbitrap Elite instrument at the mass resolution of 1.35 × 10⁶ (m/z 200) baseline resolved peaks of ¹³C isotopes of unlabeled and monoisotopic peaks of ¹⁵N labeled lipids (Δm = 0.0063 Da). Therefore, the rate of metabolic ¹⁵N labeling of individual lipid species could be determined without compromising the scope, accuracy, and dynamic range of full-lipidome quantitative shotgun profiling. As a proof of concept, we employed sUHR to determine the lipidome composition and fluxes of 62 nitrogen-containing membrane lipids in human hepatoma HepG2 cells.

Translational repression of the Drosophila nanos mRNA involves the RNA helicase Belle and RNA coating by Me31B and Trailer hitch

Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. In a comprehensive mass spectrometric analysis of the SRE-dependent repressor complex, we identified Smaug, Cup, Me31B, Trailer hitch, eIF4E, and PABPC, in agreement with earlier data. As a novel component, the RNA-dependent ATPase Belle (DDX3) was found, and its involvement in deadenylation and repression of nanos was confirmed in vivo. Smaug, Cup, and Belle bound stoichiometrically to the SREs, independently of RNA length. Binding of Me31B and Tral was also SRE-dependent, but their amounts were proportional to the length of the RNA and equimolar to each other. We suggest that "coating" of the RNA by a Me31B•Tral complex may be at the core of repression.

The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition

Metazoan embryos undergo a maternal-to-zygotic transition (MZT) during which maternal gene products are eliminated and the zygotic genome becomes transcriptionally active. During this process, RNA-binding proteins (RBPs) and the microRNA-induced silencing complex (miRISC) target maternal mRNAs for degradation. In Drosophila, the Smaug (SMG), Brain tumor (BRAT), and Pumilio (PUM) RBPs bind to and direct the degradation of largely distinct subsets of maternal mRNAs. SMG has also been shown to be required for zygotic synthesis of mRNAs and several members of the miR-309 family of microRNAs (miRNAs) during the MZT. Here, we have carried out global analysis of small RNAs both in wild-type and in smg mutants. Our results show that 85% of all miRNA species encoded by the genome are present during the MZT. Whereas loss of SMG has no detectable effect on Piwi-interacting RNAs (piRNAs) or small interfering RNAs (siRNAs), zygotic production of more than 70 species of miRNAs fails or is delayed in smg mutants. SMG is also required for the synthesis and stability of a key miRISC component, Argonaute 1 (AGO1), but plays no role in accumulation of the Argonaute family proteins associated with piRNAs or siRNAs. In smg mutants, maternal mRNAs that are predicted targets of the SMG-dependent zygotic miRNAs fail to be cleared. BRAT and PUM share target mRNAs with these miRNAs but not with SMG itself. We hypothesize that SMG controls the MZT, not only through direct targeting of a subset of maternal mRNAs for degradation but, indirectly, through production and function of miRNAs and miRISC, which act together with BRAT and/or PUM to control clearance of a distinct subset of maternal mRNAs.

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches

During embryogenesis, organisms undergo considerable cellular remodelling requiring the combined action of thousands of proteins. In case of the well-studied model Drosophila melanogaster, transcriptomic studies, most notably from the modENCODE project, have described in detail changes in gene expression at the mRNA level across development. Although such data are clearly very useful to understand how the genome is regulated during embryogenesis, it is important to understand how changes in gene expression are reflected at the level of the proteome. In this study, we describe a combination of two quantitative label-free approaches, SWATH and data-dependent acquisition, to monitor changes in protein expression across a timecourse of D. melanogaster embryonic development. We demonstrate that both approaches provide robust and reproducible methods for the analysis of proteome changes. In a preliminary analysis of Drosophila embryogenesis, we identified several pathways, including the heat-shock response, nuclear protein import and energy production that are regulated during embryo development. In some cases changes in protein expression mirrored transcript levels across development, whereas other proteins showed signatures of post-transcriptional regulation. Taken together, our pilot study provides a solid platform for a more detailed exploration of the embryonic proteome.

Regulation and Function of Maternal Gene Products During the Maternal-to-Zygotic Transition in Drosophila

Drosophila late-stage oocytes and early embryos are transcriptionally silent. Thus, control of gene expression during these developmental periods is posttranscriptional and posttranslational. Global changes in the transcriptome and proteome occur during oocyte maturation, after egg activation and fertilization, and upon zygotic genome activation. We review the scale, content, and dynamics of these global changes; the factors that regulate these changes; and the mechanisms by which they are accomplished. We highlight the intimate relationship between the clearance of maternal gene products and the activation of the embryo's own genome, and discuss the fact that each of these complementary components of the maternal-to-zygotic transition can be subdivided into several phases that serve different biological roles and are regulated by distinct factors.

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

RNA sequencing (RNA-Seq) and MS-based shotgun proteomics are powerful high-throughput technologies for identifying and quantifying RNA transcripts and proteins, respectively. With the increasing affordability of these technologies, many projects have started to apply both to the same samples to achieve a more comprehensive understanding of biological systems. A major analytical challenge for such integrative projects is how to effectively leverage the complementary nature of RNA-Seq and shotgun proteomics data. RNA-Seq provides comprehensive information on mRNA abundance, alternative splicing, nucleotide variation, and structure alteration. Sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in cell and tissue samples and thus improve protein identification. Meanwhile, proteomics data provide essential confirmation of the validity and functional relevance of novel findings from RNA-Seq data. At the quantitative level, mRNA and protein levels are only modestly correlated, suggesting strong involvement of posttranscriptional regulation in controlling gene expression. Here, we review recent studies at the interface of RNA-Seq and proteomics data. We discuss goals, accomplishments, and challenges in RNA-Seq-based proteogenomics. We also examine the current status and future potential of parallel transcriptome and proteome quantification in revealing posttranscriptional regulatory mechanisms.

Ultrasensitive proteome analysis using paramagnetic bead technology

In order to obtain a systems-level understanding of a complex biological system, detailed proteome information is essential. Despite great progress in proteomics technologies, thorough interrogation of the proteome from quantity-limited biological samples is hampered by inefficiencies during processing. To address these challenges, here we introduce a novel protocol using paramagnetic beads, termed Single-Pot Solid-Phase-enhanced Sample Preparation (SP3). SP3 provides a rapid and unbiased means of proteomic sample preparation in a single tube that facilitates ultrasensitive analysis by outperforming existing protocols in terms of efficiency, scalability, speed, throughput, and flexibility. To illustrate these benefits, characterization of 1,000 HeLa cells and single Drosophila embryos is used to establish that SP3 provides an enhanced platform for profiling proteomes derived from sub-microgram amounts of material. These data present a first view of developmental stage-specific proteome dynamics in Drosophila at a single-embryo resolution, permitting characterization of inter-individual expression variation. Together, the findings of this work position SP3 as a superior protocol that facilitates exciting new directions in multiple areas of proteomics ranging from developmental biology to clinical applications.

Recent advances in quantitative neuroproteomics

The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.

Quantitative proteomic strategies for the identification of microRNA targets

MicroRNAs (miRNAs) are small noncoding RNAs, approximately 22 nucleotides in length, found in diverse organisms. They have emerged in recent years as key regulators of a broad spectrum of cellular functions. miRNAs regulate biological processes by inducing translational inhibition and degradation of their target mRNAs through base pairing to partially or fully complementary sites. In the field of miRNA research, the identification of the targets of individual miRNAs is of utmost importance. Our understanding of the molecular mechanisms by which individual miRNAs modulate cellular functions will remain incomplete until a full set of miRNA targets is identified and validated. Since a miRNA may regulate many of its targets at the translational level without affecting mRNA abundance, proteomic methods are best suited for revealing the full spectrum of miRNA targets. Quantitative proteomics is emerging as a powerful toolbox for identifying miRNA targets and for quantifying the contribution of translational repression by miRNAs. In this review, the authors summarize the quantitative proteomic approaches that have been employed for identification of miRNA targets and discuss current challenges as well as possible ways of overcoming them.

Integrative proteomic and transcriptomic analyses reveal multiple post-transcriptional regulatory mechanisms of mouse spermatogenesis

Mammalian spermatogenesis consists of many cell types and biological processes and serves as an excellent model for studying gene regulation at transcriptional and post-transcriptional levels. Many key proteins, miRNAs, and perhaps piRNAs have been shown to be involved in post-transcriptional regulation of spermatogenesis. However, a systematic method for assessing the relationship between protein and mRNA expression has not been available for studying mechanisms of post-transcriptional regulation. In the present study, we used the iTRAQ-based quantitative proteomic approach to identify 2008 proteins in mouse type A spermatogonia, pachytene spermatocytes, round spermatids, and elongative spermatids with high confidence. Of these proteins, 1194 made up four dynamically changing clusters, which reflect the mitotic amplification, meiosis, and post-meiotic development of germ cells. We identified five major regulatory mechanisms termed "transcript only," "transcript degradation," "translation repression," "translation de-repression," and "protein degradation" based on changes in protein level relative to changes in mRNA level at the mitosis/meiosis transition and the meiosis/post-meiotic development transition. We found that post-transcriptional regulatory mechanisms are related to the generation of piRNAs and antisense transcripts. Our results provide a valuable inventory of proteins produced during mouse spermatogenesis and contribute to elucidating the mechanisms of the post-transcriptional regulation of gene expression in mammalian spermatogenesis.

Regulation of developmental processes: insights from mass spectrometry-based proteomics

Mass spectrometry (MS)-based proteomics has become an indispensable tool for protein identification and quantification. In this paper, common MS workflows are described, with an emphasis on applications of MS-based proteomics in developmental biology. Progress has been made in the analysis of proteome changes during tissue differentiation and in various genetic perturbations. MS-based proteomics has been particularly useful for identifying novel protein interactions by affinity purification-mass spectrometry (AP-MS), many of which have been subsequently functionally validated and led to the discovery of previously unknown modes of developmental regulation. Quantitative proteomics approaches can be used to study posttranslational modifications (PTMs) of proteins such as phosphorylation, to reveal the dynamics of intracellular signal transduction. Integrative approaches combine quantitative MS-based proteomics with other high-throughput methods, with the promise of a systems level understanding of developmental regulation.

Isotope label-aided mass spectrometry reveals the influence of environmental factors on metabolism in single eggs of fruit fly

In order to investigate the influence of light/dark cycle on the biosynthesis of metabolites during oogenesis, here we demonstrate a simple experimental protocol which combines in-vivo isotopic labeling of primary metabolites with mass spectrometric analysis of single eggs of fruit fly (Drosophila melanogaster). First, fruit flies were adapted to light/dark cycle using artificial white light. Second, female flies were incubated with an isotopically labeled sugar (¹³C₆-glucose) for 12 h – either during the circadian day or the circadian night, at light or at dark. Third, eggs were obtained from the incubated female flies, and analyzed individually by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS): this yielded information about the extent of labeling with carbon-13. Since the incorporation of carbon-13 to uridine diphosphate glucose (UDP-glucose) in fruit fly eggs is very fast, the labeling of this metabolite was used as an indicator of the biosynthesis of metabolites flies/eggs during 12-h periods, which correspond to circadian day or circadian night. The results reveal that once the flies adapted to the 12-h-light/12-h-dark cycle, the incorporation of carbon-13 to UDP-glucose present in fruit fly eggs was not markedly altered by an acute perturbation to this cycle. This effect may be due to a relationship between biosynthesis of primary metabolites in developing eggs and an alteration to the intake of the labeled substrate – possibly related to the change of the feeding habit. Overall, the study shows the possibility of using MALDI-MS in conjunction with isotopic labeling of small metazoans to unravel the influence of environmental cues on primary metabolism.

Stable isotope labeling with amino acids in Drosophila for quantifying proteins and modifications

Drosophila melanogaster is a common animal model for genetics studies, and quantitative proteomics studies of the fly are emerging. Here, we present in detail the development of a procedure to incorporate stable isotope-labeled amino acids into the fly proteome. In the method of stable isotope labeling with amino acids in Drosophila melanogaster (SILAC fly), flies were fed with SILAC-labeled yeast grown with modified media, enabling near complete labeling in a single generation. Biological variation in the proteome among individual flies was evaluated in a series of null experiments. We further applied the SILAC fly method to profile proteins from a model of fragile X syndrome, the most common cause of inherited mental retardation in human. The analysis identified a number of altered proteins in the disease model, including actin-binding protein profilin and microtubulin-associated protein futsch. The change of both proteins was validated by immunoblotting analysis. Moreover, we extended the SILAC fly strategy to study the dynamics of protein ubiquitination during the fly life span (from day 1 to day 30), by measuring the level of ubiquitin along with two major polyubiquitin chains (K48 and K63 linkages). The results show that the abundance of protein ubiquitination and the two major linkages do not change significantly within the measured age range. Together, the data demonstrate the application of the SILAC principle in D. melanogaster, facilitating the integration of powerful fly genomics with emerging proteomics.

Translational regulation of the cell cycle: when, where, how and why?

Translational regulation contributes to the control of archetypal and specialized cell cycles, such as the meiotic and early embryonic cycles. Late meiosis and early embryogenesis unfold in the absence of transcription, so they particularly rely on translational repression and activation of stored maternal mRNAs. Here, we present examples of cell cycle regulators that are translationally controlled during different cell cycle and developmental transitions in model organisms ranging from yeast to mouse. Our focus also is on the RNA-binding proteins that affect cell cycle progression by recognizing special features in untranslated regions of mRNAs. Recent research highlights the significance of the cytoplasmic polyadenylation element-binding protein (CPEB). CPEB determines polyadenylation status, and consequently translational efficiency, of its target mRNAs in both transcriptionally active somatic cells as well as in transcriptionally silent mature Xenopus oocytes and early embryos. We discuss the role of CPEB in mediating the translational timing and in some cases spindle-localized translation of critical regulators of Xenopus oogenesis and early embryogenesis. We conclude by outlining potential directions and approaches that may provide further insights into the translational control of the cell cycle.

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells

Background

During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole embryos. Here we report the first such analysis for primordial germ cells (PGCs), the progenitors of the germ-line stem cells.

Results

We purified PGCs from Drosophila embryos, defined their proteome and transcriptome, and assessed the content, scale and dynamics of their MZT. Transcripts encoding proteins that implement particular types of biological functions group into nine distinct expression profiles, reflecting coordinate control at the transcriptional and posttranscriptional levels. mRNAs encoding germ-plasm components and cell-cell signaling molecules are rapidly degraded while new transcription produces mRNAs encoding the core transcriptional and protein synthetic machineries. The RNA-binding protein Smaug is essential for the PGC MZT, clearing transcripts encoding proteins that regulate stem cell behavior, transcriptional and posttranscriptional processes. Computational analyses suggest that Smaug and AU-rich element binding proteins function independently to control transcript elimination.

Conclusions

The scale of the MZT is similar in the soma and PGCs. However, the timing and content of their MZTs differ, reflecting the distinct developmental imperatives of these cell types. The PGC MZT is delayed relative to that in the soma, likely because relief of PGC-specific transcriptional silencing is required for zygotic genome activation as well as for efficient maternal transcript clearance.

MSQuant: a platform for stable isotope-based quantitative proteomics

Quantitative approaches in proteomics are emerging as a powerful tool to probe the dynamics of protein expression across biological conditions. Thereby, quantification helps to recognize proteins with potential biological relevance, which greatly aids in the design of follow-up experiments. Although multiple methods have been established that are based on stable-isotope labeling and label-free approaches, one of the remaining bottlenecks is the analysis and quantification of proteins in large datasets. MSQuant is a platform for protein quantification, capable of handling multiple labeling strategies and supporting several vendor data formats. Here, we report on the use and versatility of MSQuant.

Transcript clearance during the maternal-to-zygotic transition

In all animals, a key event in the transition from maternal control of development to control by products of the zygotic genome is the elimination of a significant fraction of the mRNAs loaded into the egg by the mother. Clearance of these maternal mRNAs is accomplished by two activities: the first is maternally encoded while the second requires zygotic transcription. Recent advances include identification of RNA-binding proteins that function as specificity factors to direct the maternal degradation machinery to its target mRNAs; small RNAs-most notably microRNAs-that function as components of the zygotically encoded activity; signaling pathways that trigger production and/or activation of the clearance mechanism in early embryos; and mechanisms for spatial control of transcript clearance.

Metabolic labeling of model organisms using heavy nitrogen (15N)

Quantitative proteomics aims to identify and quantify proteins in cells or organisms that have been obtained from different biological origin (e.g., "healthy vs. diseased"), that have received different treatments, or that have different genetic backgrounds. Protein expression levels can be quantified by labeling proteins with stable isotopes, followed by mass spectrometric analysis. Stable isotopes can be introduced in vitro by reacting proteins or peptides with isotope-coded reagents (e.g., iTRAQ, reductive methylation). A preferred way, however, is the metabolic incorporation of heavy isotopes into cells or organisms by providing the label, in the form of amino acids (such as in SILAC) or salts, in the growth media. The advantage of in vivo labeling is that it does not suffer from side reactions or incomplete labeling that might occur in chemical derivatization. In addition, metabolic labeling occurs at the earliest possible moment in the sample preparation process, thereby minimizing the error in quantitation. Labeling with the heavy stable isotope of nitrogen (i.e., (15)N) provides an efficient way for accurate protein quantitation. Where the application of SILAC is mostly restricted to cell culture, (15)N labeling can be used for micro-organisms as well as a number of higher (multicellular) organisms. The most prominent examples of the latter are Caenorhabditis elegans and Drosophila (fruit fly), two important model organisms for a range of regulatory processes underlying developmental biology. Here we describe in detail the labeling with (15)N atoms, with a particular focus on fruit flies and C. elegans. We also describe methods for the identification and quantitation of (15)N-labeled proteins by mass spectrometry and bioinformatic analysis.

Genome-wide analysis of mRNA decay patterns during early Drosophila development

BACKGROUND

The modulation of mRNA levels across tissues and time is key for the establishment and operation of the developmental programs that transform the fertilized egg into a fully formed embryo. Although the developmental mechanisms leading to differential mRNA synthesis are heavily investigated, comparatively little attention is given to the processes of mRNA degradation and how these relate to the molecular programs controlling development.

RESULTS

Here we combine timed collection of Drosophila embryos and unfertilized eggs with genome-wide microarray technology to determine the degradation patterns of all mRNAs present during early fruit fly development. Our work studies the kinetics of mRNA decay, the contributions of maternally and zygotically encoded factors to mRNA degradation, and the ways in which mRNA decay profiles relate to gene function, mRNA localization patterns, translation rates and protein turnover. We also detect cis-regulatory sequences enriched in transcripts with common degradation patterns and propose several proteins and microRNAs as developmental regulators of mRNA decay during early fruit fly development. Finally, we experimentally validate the effects of a subset of cis-regulatory sequences and trans-regulators in vivo.

CONCLUSIONS

Our work advances the current understanding of the processes controlling mRNA degradation during early Drosophila development, taking us one step closer to the understanding of mRNA decay processes in all animals. Our data also provide a valuable resource for further experimental and computational studies investigating the process of mRNA decay.

The SILAC fly allows for accurate protein quantification in vivo

Stable isotope labeling by amino acids in cell culture (SILAC) is widely used to quantify protein abundance in tissue culture cells. Until now, the only multicellular organism completely labeled at the amino acid level was the laboratory mouse. The fruit fly Drosophila melanogaster is one of the most widely used small animal models in biology. Here, we show that feeding flies with SILAC-labeled yeast leads to almost complete labeling in the first filial generation. We used these "SILAC flies" to investigate sexual dimorphism of protein abundance in D. melanogaster. Quantitative proteome comparison of adult male and female flies revealed distinct biological processes specific for each sex. Using a tudor mutant that is defective for germ cell generation allowed us to differentiate between sex-specific protein expression in the germ line and somatic tissue. We identified many proteins with known sex-specific expression bias. In addition, several new proteins with a potential role in sexual dimorphism were identified. Collectively, our data show that the SILAC fly can be used to accurately quantify protein abundance in vivo. The approach is simple, fast, and cost-effective, making SILAC flies an attractive model system for the emerging field of in vivo quantitative proteomics.

When peptides fly: advances in Drosophila proteomics

In the past decade, improvements in genome annotation, protein fractionation methods and mass spectrometry instrumentation resulted in rapid growth of Drosophila proteomics. This review presents the current status of proteomics research in the fly. Areas that have seen major advances in recent years include efforts to map and catalog the Drosophila proteome and high-throughput as well as targeted studies to analyze protein-protein interactions and post-translational modifications. Stable isotope labeling of flies and other applications of quantitative proteomics have opened up new possibilities for functional analyses. It is clear that proteomics is becoming an indispensable tool in Drosophila systems biology research that adds a unique dimension to studying gene function.

MSQuant, an open source platform for mass spectrometry-based quantitative proteomics

Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environment, called MSQuant, which allows visualization and validation of peptide identification results directly on the raw mass spectrometric data. MSQuant iteratively recalibrates MS data thereby significantly increasing mass accuracy leading to fewer false positive peptide identifications. Algorithms to increase data quality include an MS(3) score for peptide identification and a post-translational modification (PTM) score that determines the probability that a modification such as phosphorylation is placed at a specific residue in an identified peptide. MSQuant supports relative protein quantitation based on precursor ion intensities, including element labels (e.g., (15)N), residue labels (e.g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net .

Worms from venus and mars: proteomics profiling of sexual differences in Caenorhabditis elegans using in vivo 15N isotope labeling

Hermaphrodites of the nematode Caenorhabditis elegans produce both sperm and oocytes in the same germline. To investigate the process underlying spermatogenesis and oogenesis separately, we used a quantitative proteomics approach applied to two mutant worm lines (fem-3(q20) and fem-1(hc17)) developing only male and female germlines, respectively. We used stable isotopic labeling of whole animals by feeding them either (14)N or (15)N labeled Escherichia coli. This way, we could confidently identify and quantify 1040 proteins in two independent experiments. Of these, approximately 400 proteins showed significant differential expression between female-like and male-like animals. As expected, proteins linked to oogenesis were found to be highly upregulated in the feminized worms, whereas proteins involved in spermatogenesis were found to be highly upregulated in the masculinized worms. This was complemented by many proteins strongly enriched in either mutant. Although the function of the majority of these proteins is unknown, their expression profile indicates that they have an as yet unrecognized role in the development and/or function of the female- and male germline in C. elegans. We show that members of several protein complexes as well as functionally similar proteins show comparable abundance ratios, indicating coregulation of protein expression. Additional analysis comparing our protein data to a previously published microarray data set shows that mRNA and protein expression are poorly correlating. We provide one of the first examples of a large-scale quantitative proteomics experiment in C. elegans and show the potential and feasibility of an approach enabling system-wide accurate quantitative proteomics experiments in this model organism.

Sex and the single embryo: early deveiopment in the Mediterranean fruit fly, Ceratitis capitata

Background

In embryos the maternal-to-zygotic transition (MTZ) integrates post-transcriptional regulation of maternal transcripts with transcriptional activation of the zygotic genome. Although the molecular mechanisms underlying this event are being clarified in Drosophila melanogaster, little is know about the embryogenic processes in other insect species. The recent publication of expressed sequence tags (ESTs) from embryos of the global pest species Ceratitis capitata (medfly) has enabled the investigation of embryogenesis in this species and has allowed a comparison of the embryogenic processes in these two related dipteran species, C. capitata and D. melanogaster, that shared a common ancestor 80-100 mya.

Results

Using a novel PCR-based sexing method, which takes advantage of a putative LTR retrotransposon MITE insertion on the medfly Y chromosome, the transcriptomes of individual early male and female embryos were analysed using RT-PCR. This study is focused on two crucial aspects of the onset of embryonic development: sex determination and cellular blastoderm formation. Together with the three known medfly genes (Cctransformer, Cctransformer2 and Ccdoublesex), the expression patterns of other medfly genes that are similar to the D. melanogaster sex-determination genes (sisterlessA, groucho, deadpan, Sex-lethal, female lethal d, sans fille and intersex) and four cellular blastoderm formation genes (Rho1, spaghetti squash, slow-as-molasses and serendipity-α) were analyzed, allowing us to sketch a preliminary outline of the embryonic process in the medfly. Furthermore, a putative homologue of the Zelda gene has been considered, which in D. melanogaster encodes a DNA-binding factor responsible for the maternal-to-zygotic transition.

Conclusions

Our novel sexing method facilitates the study of i) when the MTZ transition occurs in males and females of C. capitata, ii) when and how the maternal information of "female-development" is reprogrammed in the embryos and iii) similarities and differences in the regulation of gene expression in C. capitata and D. melanogaster. We suggest a new model for the onset of the sex determination cascade in the medfly: the maternally inherited Cctra transcripts in the female embryos are insufficient to produce enough active protein to inhibit the male mode of Cctra splicing. The slow rate of development and the inefficiency of the splicing mechanism in the pre-cellular blastoderm facilitates the male-determining factor (M) activity, which probably acts by inhibiting CcTRA protein activity.

Quantitative proteomics by metabolic labeling of model organisms

In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on genetics and genomics approaches, it is important that methods become available to extend this to the relevant protein level. Mass spectrometry-based proteomics is increasingly becoming the standard to comprehensively analyze proteomes. An important transition has been made recently by moving from charting static proteomes to monitoring their dynamics by simultaneously quantifying multiple proteins obtained from differently treated samples. Especially the labeling with stable isotopes has proved an effective means to accurately determine differential expression levels of proteins. Among these, metabolic incorporation of stable isotopes in vivo in whole organisms is one of the favored strategies. In this perspective, we will focus on methodologies to stable isotope label a variety of model organisms in vivo, ranging from relatively simple organisms such as bacteria and yeast to Caenorhabditis elegans, Drosophila, and Arabidopsis up to mammals such as rats and mice. We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life.

The maternal-to-zygotic transition: a play in two acts

All animal embryos pass through a stage during which developmental control is handed from maternally provided gene products to those synthesized from the zygotic genome. This maternal-to-zygotic transition (MZT) has been extensively studied in model organisms, including echinoderms, nematodes, insects, fish,amphibians and mammals. In all cases, the MZT can be subdivided into two interrelated processes: first, a subset of maternal mRNAs and proteins is eliminated; second, zygotic transcription is initiated. The timing and scale of these two events differ across species, as do the cellular and morphogenetic processes that sculpt their embryos. In this article, we discuss conserved and distinct features within the two component processes of the MZT.