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Systematic analysis to analyze the Drs2-I(S/R)TTK motif: comparative analysis bertween the interactome of Drs2 vs. drs2-5A by CS-MS.

ABSTRACT: The aim of the project was to systematically analyze the mechanism mediated by the Drs2 ISTTK motif in yeast, located in the N-terminal tail of the protein. Upon a GFP-specific pulldown, we carried-out a comparative analysis between the interactome of Drs2-GFP and drs2-5A-GFP (ISTTK>AAAAA) to identify proteins whose binding required to recognize directly, or in the near vicinity, the ISTTK motif of Drs2.

INSTRUMENT(S):

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Irene Pazos Capell

LAB HEAD: Oriol Gallego

PROVIDER: PXD038527 | Pride | 2023-03-08

REPOSITORIES: Pride

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			Action	DRS
	2019MX002_MAPU_001_01_10pto-ok.msf	Msf
	2019MX002_MAPU_001_01_10pto.raw	Raw
	2019MX002_MAPU_002_01_10pto.msf	Msf
	2019MX002_MAPU_002_01_10pto.raw	Raw
	2019MX002_MAPU_003_01_10pto.msf	Msf

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The regulation of ribosomal protein genes expression by the protein kinase DYRK1A contributes to the maintenance of ribosome mass and protein translation

Project description:Ribosomal protein genes (RPGs) coding sequences are highly conserved along evolution; however, promoter features and the machinery involved in their transcriptional regulation are not. In eukaryotes, the main genomic elements and players involved in RPG transcriptional regulation have been mostly characterized in Saccharomyces cerevisiae. However, given the lack of evolutionary conservation of the yeast factors, studies in higher eukaryotes have focused on searching for differential enrichment of transcription factor-binding motifs within the RPG promoters. Among them, the palindromic motif TCTCGCGAGA, which is currently acknowledged as a ZBTB33/KAISO motif, also matches the genomic sequence bound by the protein kinase DYRK1A. DYRK1A, a member of the human family of DYRK kinases, fulfills many diverse functions by phosphorylating a broad set of proteins involved in different cellular processes. One of such functions is to be a chromatin-associated kinase capable of regulating gene expression. Here, we analyze in-depth the presence of DYRK1A at the promoters of human and mouse RPGs and explore its functional consequences. Our results indicate that DYRK1A is a positive regulator of RPGs’ expression at the transcriptional level, and that this effect could, at least in part, contribute to the global reduction in ribosome amounts and protein synthesis observed when DYRK1A is silenced. Therefore, our results further expand the functional spectrum of the kinase as a contributor to the regulation of cell growth in mammalian cells.

2024-05-22 | PXD022966 | Pride

A trans-generational epigenetic process defines piRNA biogenesis in Drosophila virilis

Project description:Piwi interacting (pi)RNAs repress diverse transposable elements in the germ cells of metazoans and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two Drosophila virilis strains that show differential ability to generate piRNAs from several genomic regions. We found that active piRNA biogenesis correlates with high levels of histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Furthermore, piRNA biogenesis in the progeny requires the trans-generational inheritance of an epigenetic signal, presumably in form of homologous piRNAs that are generated in the maternal germline and deposited into the oocyte. The inherited piRNAs enhance piRNA biogenesis by installment of H3K9me3 mark on piRNA clusters and by promoting ping-pong processing of homologous transcripts into mature piRNAs. We submitted the resequencing data together with the functional genomic datasets because it was generated with the sole purpose of supporting those. The SRA accession numbers are SRR1536176 and SRR1536175. ChIP-seq against H3K9me3 and Pol2, Total RNA-seq, in Drosophila virilis Strain9 and Strain160 as well as crosses between them

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2024-12-02 | PXD047579 | Pride

Monitoring post-translational modifications and associated proteomes of WT-PML-V and two mutants from acute promyelocytic leukaemia patients refractory for arsenic therapy: A216T-PML-V and L217F-PML-V

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MAX-mutant small cell lung cancers exhibit impaired activities of MGA-dependent ncPRC1.6.

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2021-09-22 | PXD017658 | Pride

ChIP-seq on Znf417 and Znf587 overexpression 293T to verify Znf417 and Znf587 binding capacity at PBS-Lys elements.

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MYO19 interacts weakly with Miro2 GTPases on the mitochondrial outer membrane

Project description:MYO19 interacts with mitochondria through a unique C-terminal mitochondrial association domain (MyMOMA). The specific molecular mechanisms for localization of MYO19 to mitochondria are poorly understood. Using promiscuous biotinylation, we have identified ~100 candidate MYO19 interacting proteins, a subset of which were also identified in via affinity-capture experiments. We chose to further explore the interaction between MYO19 and the mitochondrial GTPase Miro2 by expressing mchr-Miro2 in combination with GFP-tagged fragments of the MyMOMA domain and assaying for recruitment of MYO19-GFP to mitochondria. Co-expression of MYO19898-970-GFP with mchr-Miro2 enhanced MYO19898-970-GFP localization to mitochondria. Mislocalizing Miro2 to filopodial tips or the cytosolic face of the nuclear envelope did not recruit MYO19898-970-GFP to either location. To address the kinetics of the Miro2/MYO19 interaction, we used FRAP analysis and permeabilization-activated reduction in fluorescence (PARF) analysis. MyMOMA constructs containing a putative membrane insertion motif but lacking the complete Miro2 interacting region, MYO19853-935-GFP, displayed slow exchange kinetics. MYO19898-970-GFP, which does not include the membrane-insertion motif, displayed rapid exchange kinetics, suggesting that the MYO19 and Miro2 interaction is weaker than between MYO19 and the mitochondrial outer membrane. Mutation of well-conserved, charged residues within MYO19 or within the switch I and II regions of Miro2 abolished the enhancement of MYO19898-970-GFP localization in cells ectopically expressing mchr-Miro2. Additionally, expressing mutant versions of Miro2 thought to represent particular nucleotide states indicated that the enhancement of MYO19898-970-GFP localization is dependent on Miro2 nucleotide state. Taken together, these data suggest a role for Miro2 in regulation and integration of actin- and microtubule-based mitochondrial activities.

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Agrobacterium tumefaciens 5A strain:5A

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Agrobacterium tumefaciens 5A strain:5A

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