Quantitative proteomics reveals the dynamics of protein changes during Drosophila oocyte maturation and the oocyte-to-embryo transition

The onset of development is marked by two major, posttranscriptionally controlled, events: oocyte maturation (release of the prophase I primary arrest) and egg activation (release from the secondary meiotic arrest). Using quantitative mass spectrometry, we previously described proteome remodeling during Drosophila egg activation. Here, we describe our quantitative mass spectrometry-based analysis of the changes in protein levels during Drosophila oocyte maturation. This study presents the first quantitative survey, to our knowledge, of proteome changes accompanying oocyte maturation in any organism and provides a powerful resource for identifying both key regulators and biological processes driving this critical developmental window. We show that Muskelin, found to be up-regulated during oocyte maturation, is required for timely nurse cell nuclei clearing from mature egg chambers. Other proteins up-regulated at maturation are factors needed not only for late oogenesis but also completion of meiosis and early embryogenesis. Interestingly, the down-regulated proteins are predominantly involved in RNA processing, translation, and RNAi. Integrating datasets on the proteome changes at oocyte maturation and egg activation uncovers dynamics in proteome remodeling during the change from oocyte to embryo. Notably, 66 proteins likely act uniquely during late oogenesis, because they are up-regulated at maturation and down-regulated at activation. We find down-regulation of this class of proteins to be mediated partially by APC/C[superscript CORT], a meiosis-specific form of the E3 ligase anaphase promoting complex/cyclosome (APC/C).National Institutes of Health (U.S.) (Grant GM39341

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

The oocyte-to-embryo transition marks the onset of development. The initial phase of this profound change from the differentiated oocyte to the totipotent embryo occurs in the absence of both transcription and mRNA degradation. Here we combine global polysome profiling, ribosome-footprint profiling, and quantitative mass spectrometry in a comprehensive approach to delineate the translational and proteomic changes that occur during this important transition in Drosophila. Our results show that PNG kinase is a critical regulator of the extensive changes in the translatome, acting uniquely at this developmental window. Analysis of the proteome in png mutants provided insights into the contributions of translation to changes in protein levels, revealing a compensatory dynamic between translation and protein turnover during proteome remodeling at the return to totipotency. The proteome changes additionally suggested regulators of meiosis and early embryogenesis, including the conserved H3K4 demethylase LID, which we demonstrated is required during this period despite transcriptional inactivity.National Institutes of Health (U.S.) (Grant GM39341

Comprehensive histone phosphorylation analysis and identification of Pf14-3-3 protein as a histone H3 phosphorylation reader in malaria parasites

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Comprehensive histone phosphorylation analysis and identification of Pf14-3-3 protein as a histone H3 phosphorylation reader in malaria parasites

The important role of histone posttranslational modifications, particularly methylation and acetylation, in Plasmodium falciparum gene regulation has been established. However, the role of histone phosphorylation remains understudied. Here, we investigate histone phosphorylation utilizing liquid chromatography and tandem mass spectrometry to analyze histones extracted from asexual blood stages using two improved protocols to enhance preservation of PTMs. Enrichment for phosphopeptides lead to the detection of 14 histone phospho-modifications in P. falciparum. The majority of phosphorylation sites were observed at the N-terminal regions of various histones and were frequently observed adjacent to acetylated lysines. We also report the identification of one novel member of the P. falciparum histone phosphosite binding protein repertoire, Pf14-3-3I. Recombinant Pf14-3-3I protein bound to purified parasite histones. In silico structural analysis of Pf14-3-3 proteins revealed that residues responsible for binding to histone H3 S10ph and/or S28ph are conserved at the primary and the tertiary structure levels. Using a battery of H3 specific phosphopeptides, we demonstrate that Pf14-3-3I preferentially binds to H3S28ph over H3S10ph, independent of modification of neighbouring residues like H3S10phK14ac and H3S28phS32ph. Our data provide key insight into histone phosphorylation sites. The identification of a second member of the histone modification reading machinery suggests a widespread use of histone phosphorylation in the control of various nuclear processes in malaria parasites

Unnatural Amino Acid Mutagenesis Reveals Dimerization As a Negative Regulatory Mechanism of VHR’s Phosphatase Activity

<i>Vaccinia</i> H1-related (VHR) phosphatase is a dual specificity phosphatase that is required for cell-cycle progression and plays a role in cell growth of certain cancers. Therefore, it represents a potential drug target. VHR is structurally and biochemically well characterized, yet its regulatory principles are still poorly understood. Understanding its regulation is important, not only to comprehend VHR’s biological mechanisms and roles but also to determine its potential and druggability as a target in cancer. Here, we investigated the functional role of the unique “variable insert” region in VHR by selectively introducing the photo-cross-linkable amino acid <i>para-</i>benzoylphenylalanine (<i>p</i>BPA) using the amber suppression method. This approach led to the discovery of VHR dimerization, which was further confirmed using traditional chemical cross-linkers. Phe68 in VHR was discovered as a residue involved in the dimerization. We demonstrate that VHR can dimerize inside cells, and that VHR catalytic activity is reduced upon dimerization. Our results suggest that dimerization could occlude the active site of VHR, thereby blocking its accessibility to substrates. These findings indicate that the previously unknown transient self-association of VHR acts as a means for the negative regulation of its catalytic activity

Homology-based structural models of Pf14-3-3 proteins.

<p>A) The highest scoring models of Pf14-3-3I and Pf14-3-3II are displayed alongside the structure of human 14-3-3 zeta co-crystallized with phosphorylated histone (H3S10ph) peptide. Ribbon diagrams are coloured blue to red from their N- to C-termini. The phosphorylated histone peptide in the human structure is coloured gray for carbon, blue for nitrogen, red for oxygen, orange for phosphate. B) The above Pf14-3-3I structure (green), Pf14-3-3II structure (cyan), and the human 14-3-3 zeta structure co-crystallized with an ARKSphTGGK peptide (magenta, from 2C1N). The four residues involved in phosphorylated residue binding for each 14-3-3 protein are displayed as sticks. The phosphoserine side-chain from the bound peptide in the human structure is also displayed as sticks. Nitrogen is blue, oxygen is red, phosphate is orange, and carbon is gray.</p

Subcellular location of 14-3-3 in asexual blood stage parasites.

<p>A) Cellular localization of Pf14-3-3I was investigated by probing cytoplasmic and nuclear fraction prepared from asynchronous 3D7 parasite culture with anti-14-3-3I antibody in western blot analysis. Aldolase and histone H3 antibodies were used to check the purity of cytoplasmic and nuclear fraction respectively. Protein extract from non infected red blood cells (RBC) was used as control to show that anti Pf14-3- antibody does not recognized mammalian homologues present in human erythrocytes. B) Using anti-14-3-3I antibody in immunofluorescence assay, the Pf14-3-3I protein was localized in both nuclear and cytoplasmic compartments.</p

Sequence alignment of 14-3-3 proteins.

<p>Amino acid sequences of Pf14-3-3I (PF3D7_0818200), Pf14-3-3II (PF3D7_1362100), human 14-3-3 zeta (NP_003397), <i>Nicotiana tobaccum</i> 14-3-3-like protein C (P93343), and <i>Cryptosporidium parvum</i> epsilon (cdg3_1290) aligned by ClustalW2. Residues involved in the binding of phosphorylated residues are marked with (#). Residues involved in stabilizing homo- or hetero-dimerization are marked with (*).</p

Improved extraction methods preserve histone phosphorylation.

<p>A) Coomassie-stained gel demonstrating the purity of extracted histone sample by acid extraction protocol. The high-salt extraction protocol yields similar high purity sample (data not shown). B) Western blot analysis performed on acid extracted histone with commercially available antibodies against H3 core, H3S10ph, H3T11ph, and H3S28ph modifications. These antibodies yielded a single band corresponding to the expected size of histone H3 (∼17 kDa) when developed with Super Signal West FEMTO Chemiluminescent Substrate.</p

List of biotinylated H3-peptides used for ELISA binding assay.

<p>List of biotinylated H3-peptides used for ELISA binding assay.</p