Biology subjects

Papadopoulos, D. K.

Publications and source records attributed to Papadopoulos, D. K..

4 recordsLinked to original sources

bioRxiv2020

Identification of a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the Endoplasmic Reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Here, we show that NBAS fulfils an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 co-regulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER protective function by ensuring quality control of ER-translated mRNAs. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/954453v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@172e4a3org.highwire.dtl.DTLVardef@9769org.highwire.dtl.DTLVardef@d478c1org.highwire.dtl.DTLVardef@143e0f9_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LINBAS is an NMD factor that localizes to the membrane of the endoplasmic reticulum (ER) C_LIO_LINBAS has dual, independent, roles in Golgi-to-ER retrograde transport and in ER-NMD C_LIO_LINBAS recruits the core NMD factor UPF1 to the membrane of the ER C_LIO_LIThe ER-NMD pathway targets for degradation mRNAs that are translated at the ER C_LI

molecular biology↗

bioRxiv2019

Ordered patterning of the sensory system is susceptible to stochastic features of gene expression

Sensory neuron numbers and positions are precisely organized to accurately map environmental signals in the brain. However, this precision must emerge from biochemical processes within and between cells that are stochastic. We measured intrinsic noise in senseless protein output, a key determinant of sensory fate, during Drosophila development. Perturbing microRNA regulation or genomic locus of senseless transcription produced distinct noise signatures. Genomic location altered protein stochasticity in an allelic-pairing dependent manner (transvection). This generated sensory pattern disorder without perturbing protein abundance. In contrast, loss of microRNA repression of senseless increased protein abundance but not sensory pattern disorder. This suggests that gene expression stochasticity is a critical feature that must be constrained during development to allow rapid yet accurate cell fate resolution. One Sentence SummaryLife on the Margin: balancing speed and accuracy during animal development.

developmental biology↗

bioRxiv2019

Yorkie controls tube length and apical barrier integrity in the developing Drosophila airways

Epithelial organ size and shape depend on cell shape changes, cell-matrix communication and apical membrane growth. The Drosophila embryonic tracheal network is an excellent model to study these processes. Here, we show that the transcriptional co-activator of the Hippo pathway, Yorkie (YAP in vertebrates), plays distinct roles in the developing Drosophila airways. Yorkie exerts a cytoplasmic function by binding Drosophila Twinstar, the orthologue of the vertebrate actin-severing protein Cofilin, to regulate F-actin levels and apical cell membrane size, which are required for proper tracheal tube elongation. Second, Yorkie controls water-tightness of tracheal tubes by transcriptional regulation of the enzyme{delta} -aminolevulinate synthase (Alas). We conclude that Yorkie has a dual role in tracheal development to ensure proper tracheal growth and functionality. Short SummaryThis work identified an alternative role of the transcriptional co-activator Yorkie (Yki) in controlling water impermeability and tube size of the developing Drosophila airways. Tracheal impermeability is triggered by Yki-mediated transcriptional regulation of{delta} -aminolevulinate synthase, Alas, whereas tube elongation is controlled by binding of Yki to the actin severing factor Twinstar.

developmental biology↗

bioRxiv2017

Control of Hox transcription factor concentration and cell-to-cell variability by an auto-regulatory switch

The variability in transcription factor concentration among cells is an important developmental determinant, yet how variability is controlled remains poorly understood. Studies of variability have focused predominantly on monitoring mRNA production noise. Little information exists about transcription factor protein variability, since this requires the use of quantitative methods with single-molecule sensitivity. Using Fluorescence Correlation Spectroscopy (FCS), we characterized the concentration and variability of 14 endogenously tagged TFs in live Drosophila imaginal discs. For the Hox TF Antennapedia we investigated whether protein variability results from random stochastic events or is developmentally regulated. We found that Antennapedia transitioned from low concentration/high variability early, to high concentration/low variability later, in development. FCS and temporally resolved genetic studies uncovered that Antennapedia itself is necessary and sufficient to drive a developmental regulatory switch from auto-activation to auto-repression, thereby reducing variability. This switch is controlled by progressive changes in relative concentrations of preferentially activating and repressing Antennapedia isoforms, which bind chromatin with different affinities. Mathematical modelling demonstrated that the experimentally supported auto-regulatory circuit can explain the increase of Antennapedia concentration and suppression of variability over time.

genetics↗