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ACS Chemical Biology Mar 2017During development, the Hippo pathway regulates the balance between cell proliferation and apoptosis to control organ size. Appropriate Hippo signaling is associated... (Review)
Review
During development, the Hippo pathway regulates the balance between cell proliferation and apoptosis to control organ size. Appropriate Hippo signaling is associated with stem cell maintenance, while inappropriate signaling can result in tumorigenesis and cancer. Cellular and genetic investigations have identified core components and determined that complex formation and protein phosphorylation are crucial regulatory events. The recent spate of high-resolution structures of Hippo pathway components have begun to reveal the molecular mechanisms controlling these events, including the molecular determinates of complex formation between YAP and TEAD, the role of phosphorylation in controlling complex formation by Mob, and the conformational changes accompanying Mst1/2 kinase domain activation. We will review these advances and revisit previous structures to provide a comprehensive overview of the structural changes associated with the regulation of this pathway as well as discuss areas that could benefit from further mechanistic studies.
Topics: Drosophila Proteins; Intracellular Signaling Peptides and Proteins; Phosphorylation; Protein Conformation; Protein Serine-Threonine Kinases; Signal Transduction
PubMed: 28150487
DOI: 10.1021/acschembio.6b01058 -
Genetics Mar 2021Genetic approaches in the fruit fly, Drosophila melanogaster, have led to a major triumph in the field of sensory biology-the discovery of multiple large families of... (Review)
Review
Genetic approaches in the fruit fly, Drosophila melanogaster, have led to a major triumph in the field of sensory biology-the discovery of multiple large families of sensory receptors and channels. Some of these families, such as transient receptor potential channels, are conserved from animals ranging from worms to humans, while others, such as "gustatory receptors," "olfactory receptors," and "ionotropic receptors," are restricted to invertebrates. Prior to the identification of sensory receptors in flies, it was widely assumed that these proteins function in just one modality such as vision, smell, taste, hearing, and somatosensation, which includes thermosensation, light, and noxious mechanical touch. By employing a vast combination of genetic, behavioral, electrophysiological, and other approaches in flies, a major concept to emerge is that many sensory receptors are multitaskers. The earliest example of this idea was the discovery that individual transient receptor potential channels function in multiple senses. It is now clear that multitasking is exhibited by other large receptor families including gustatory receptors, ionotropic receptors, epithelial Na+ channels (also referred to as Pickpockets), and even opsins, which were formerly thought to function exclusively as light sensors. Genetic characterizations of these Drosophila receptors and the neurons that express them also reveal the mechanisms through which flies can accurately differentiate between different stimuli even when they activate the same receptor, as well as mechanisms of adaptation, amplification, and sensory integration. The insights gleaned from studies in flies have been highly influential in directing investigations in many other animal models.
Topics: Animals; Drosophila Proteins; Drosophila melanogaster; Ion Channels; Receptors, Cell Surface; Sensation; Sensory Receptor Cells; Signal Transduction
PubMed: 33683373
DOI: 10.1093/genetics/iyaa011 -
Science (New York, N.Y.) Jul 2023Gene expression is controlled by the precise activation and repression of transcription. Repression is mediated by specialized transcription factors (TFs) that recruit...
Gene expression is controlled by the precise activation and repression of transcription. Repression is mediated by specialized transcription factors (TFs) that recruit co-repressors (CoRs) to silence transcription, even in the presence of activating cues. However, whether CoRs can dominantly silence all enhancers or display distinct specificities is unclear. In this work, we report that most enhancers in can be repressed by only a subset of CoRs, and enhancers classified by CoR sensitivity show distinct chromatin features, function, TF motifs, and binding. Distinct TF motifs render enhancers more resistant or sensitive to specific CoRs, as we demonstrate by motif mutagenesis and addition. These CoR-enhancer compatibilities constitute an additional layer of regulatory specificity that allows differential regulation at close genomic distances and is indicative of distinct mechanisms of transcriptional repression.
Topics: Animals; Chromatin; Drosophila melanogaster; Drosophila Proteins; Enhancer Elements, Genetic; Gene Expression Regulation, Developmental; Repressor Proteins; Amino Acid Motifs
PubMed: 37440660
DOI: 10.1126/science.adf6149 -
Cellular and Molecular Life Sciences :... May 2021The Synaptotagmin (SYT) family of proteins play key roles in regulating membrane trafficking at neuronal synapses. Using both Ca-dependent and Ca-independent... (Review)
Review
The Synaptotagmin (SYT) family of proteins play key roles in regulating membrane trafficking at neuronal synapses. Using both Ca-dependent and Ca-independent interactions, several SYT isoforms participate in synchronous and asynchronous fusion of synaptic vesicles (SVs) while preventing spontaneous release that occurs in the absence of stimulation. Changes in the function or abundance of the SYT1 and SYT7 isoforms alter the number and route by which SVs fuse at nerve terminals. Several SYT family members also regulate trafficking of other subcellular organelles at synapses, including dense core vesicles (DCV), exosomes, and postsynaptic vesicles. Although SYTs are linked to trafficking of multiple classes of synaptic membrane compartments, how and when they interact with lipids, the SNARE machinery and other release effectors are still being elucidated. Given mutations in the SYT family cause disorders in both the central and peripheral nervous system in humans, ongoing efforts are defining how these proteins regulate vesicle trafficking within distinct neuronal compartments. Here, we review the Drosophila SYT family and examine their role in synaptic communication. Studies in this invertebrate model have revealed key similarities and several differences with the predicted activity of their mammalian counterparts. In addition, we highlight the remaining areas of uncertainty in the field and describe outstanding questions on how the SYT family regulates membrane trafficking at nerve terminals.
Topics: Animals; Calcium; Drosophila; Drosophila Proteins; Exocytosis; Humans; Neurotransmitter Agents; Protein Isoforms; Synaptic Vesicles; Synaptotagmins
PubMed: 33619613
DOI: 10.1007/s00018-021-03788-9 -
Developmental Biology Apr 2022The ability of stem cells to divide asymmetrically is crucial for cell-type diversity and tissue homeostasis. Drosophila neural stem cells, also knowns as neuroblasts,... (Review)
Review
The ability of stem cells to divide asymmetrically is crucial for cell-type diversity and tissue homeostasis. Drosophila neural stem cells, also knowns as neuroblasts, utilize asymmetric cell division to self-renew and give rise to differentiated daughter cells. Drosophila neuroblasts relies on the polarized protein complexes on the apical and basal cortex to govern cell polarity and asymmetry. Here, we review recent advances in our understanding of the neuroblast polarity focusing on how actin cytoskeleton, phosphoinositide lipids and liquid-liquid phase separation regulate the asymmetric cell division of Drosophila neuroblasts.
Topics: Animals; Cell Division; Drosophila; Drosophila Proteins; Neural Stem Cells; Neurons
PubMed: 35181298
DOI: 10.1016/j.ydbio.2022.02.006 -
PloS One 2021During formation of the Hedgehog (Hh) signaling proteins, cooperative activities of the Hedgehog INTein (Hint) fold and Sterol Recognition Region (SRR) couple...
During formation of the Hedgehog (Hh) signaling proteins, cooperative activities of the Hedgehog INTein (Hint) fold and Sterol Recognition Region (SRR) couple autoproteolysis to cholesterol ligation. The cholesteroylated Hh morphogens play essential roles in embryogenesis, tissue regeneration, and tumorigenesis. Despite the centrality of cholesterol in Hh function, the full structure of the Hint-SRR ("Hog") domain that attaches cholesterol to the last residue of the active Hh morphogen remains enigmatic. In this work, we combine molecular dynamics simulations, photoaffinity crosslinking, and mutagenesis assays to model cholesterolysis intermediates in the human Sonic Hedgehog (hSHH) protein. Our results provide evidence for a hydrophobic Hint-SRR interface that forms a dynamic, non-covalent cholesterol-Hog complex. Using these models, we suggest a unified mechanism by which Hh proteins can recruit, sequester, and orient cholesterol, and offer a molecular basis for the effects of disease-causing hSHH mutations.
Topics: Animals; Cholesterol; Drosophila Proteins; Drosophila melanogaster; HEK293 Cells; Hedgehog Proteins; Humans; Molecular Dynamics Simulation; Protein Domains
PubMed: 33630857
DOI: 10.1371/journal.pone.0246814 -
Proteins Jun 2024Understanding the emergence and structural characteristics of de novo and random proteins is crucial for unraveling protein evolution and designing novel enzymes....
Understanding the emergence and structural characteristics of de novo and random proteins is crucial for unraveling protein evolution and designing novel enzymes. However, experimental determination of their structures remains challenging. Recent advancements in protein structure prediction, particularly with AlphaFold2 (AF2), have expanded our knowledge of protein structures, but their applicability to de novo and random proteins is unclear. In this study, we investigate the structural predictions and confidence scores of AF2 and protein language model-based predictor ESMFold for de novo and conserved proteins from Drosophila and a dataset of comparable random proteins. We find that the structural predictions for de novo and random proteins differ significantly from conserved proteins. Interestingly, a positive correlation between disorder and confidence scores (pLDDT) is observed for de novo and random proteins, in contrast to the negative correlation observed for conserved proteins. Furthermore, the performance of structure predictors for de novo and random proteins is hampered by the lack of sequence identity. We also observe fluctuating median predicted disorder among different sequence length quartiles for random proteins, suggesting an influence of sequence length on disorder predictions. In conclusion, while structure predictors provide initial insights into the structural composition of de novo and random proteins, their accuracy and applicability to such proteins remain limited. Experimental determination of their structures is necessary for a comprehensive understanding. The positive correlation between disorder and pLDDT could imply a potential for conditional folding and transient binding interactions of de novo and random proteins.
Topics: Animals; Protein Folding; Conserved Sequence; Drosophila Proteins; Databases, Protein; Models, Molecular; Computational Biology; Proteins; Intrinsically Disordered Proteins; Protein Conformation; Amino Acid Sequence; Algorithms; Drosophila
PubMed: 38226524
DOI: 10.1002/prot.26652 -
Current Biology : CB Aug 2023Bilateral symmetry defines much of the animal kingdom and is crucial for numerous functions of bilaterian organisms. Genetic approaches have discovered highly conserved...
Bilateral symmetry defines much of the animal kingdom and is crucial for numerous functions of bilaterian organisms. Genetic approaches have discovered highly conserved patterning networks that establish bilateral symmetry in early embryos, but how this symmetry is maintained throughout subsequent morphogenetic events remains largely unknown. Here we show that the terminal patterning system-which relies on Ras/ERK signaling through activation of the Torso receptor by its ligand Trunk-is critical for preserving bilateral symmetry during Drosophila body axis elongation, a process driven by cell rearrangements in the two identical lateral regions of the embryo and specified by the dorsal-ventral and anterior-posterior patterning systems. We demonstrate that fluctuating asymmetries in this rapid convergent-extension process are attenuated in normal embryos over time, possibly through noise-dissipating forces from the posterior midgut invagination and movement. However, when Torso signaling is attenuated via mutation of Trunk or RNAi directed against downstream Ras/ERK pathway components, body axis elongation results in a characteristic corkscrew phenotype, which reflects dramatic reorganization of global tissue flow and is incompatible with viability. Our results reveal a new function downstream of the Drosophila terminal patterning system in potentially active control of bilateral symmetry and should motivate systematic search for similar symmetry-preserving regulatory mechanisms in other bilaterians.
Topics: Animals; Body Patterning; Morphogenesis; Drosophila; Drosophila Proteins; Gastrulation; Gene Expression Regulation, Developmental; Embryo, Nonmammalian
PubMed: 37562404
DOI: 10.1016/j.cub.2023.07.050 -
Journal of Molecular Biology Sep 2018Genomes of metazoan organisms possess a large number of genes encoding cell surface and secreted (CSS) proteins that carry out crucial functions in cell adhesion and...
Genomes of metazoan organisms possess a large number of genes encoding cell surface and secreted (CSS) proteins that carry out crucial functions in cell adhesion and communication, signal transduction, extracellular matrix establishment, nutrient digestion and uptake, immunity, and developmental processes. We developed the FlyXCDB database (http://prodata.swmed.edu/FlyXCDB) that provides a comprehensive resource to investigate extracellular (XC) domains in CSS proteins of Drosophila melanogaster, the most studied insect model organism in various aspects of animal biology. More than 300 Drosophila XC domains were discovered in Drosophila CSS proteins encoded by over 2500 genes through analyses of computational predictions of signal peptide, transmembrane (TM) segment, and GPI-anchor signal sequence, profile-based sequence similarity searches, gene ontology, and literature. These domains were classified into six classes mainly based on their molecular functions, including protein-protein interactions (class P), signaling molecules (class S), binding of non-protein molecules or groups (class B), enzyme homologs (class E), enzyme regulation and inhibition (class R), and unknown molecular function (class U). Main cellular functions such as cell adhesion, cell signaling, and extracellular matrix composition were described for the most abundant domains in each functional class. We assigned cell membrane topology categories (E, secreted; S, type I/III single-pass TM; T, type II single-pass TM; M, multi-pass TM; and G, GPI-anchored) to the products of genes with XC domains and investigated their regulation by mechanisms such as alternative splicing and stop codon readthrough.
Topics: Amino Acid Sequence; Animals; Disulfides; Drosophila; Drosophila Proteins; Female; Ligands; Male; Membrane Proteins; Models, Molecular; Protein Binding; Protein Domains; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Protein Interaction Maps; Signal Transduction
PubMed: 29890119
DOI: 10.1016/j.jmb.2018.06.002 -
Journal of the American Chemical Society Jun 2018Cells survive fluctuations in osmolality by accumulating and depleting highly soluble, usually neutral, small organic compounds. Natural selection has converged on a...
Cells survive fluctuations in osmolality by accumulating and depleting highly soluble, usually neutral, small organic compounds. Natural selection has converged on a small set of such molecules, called osmolytes. The biophysical characterization of osmolytes, with respect to proteins, has centered on tertiary structure stability. Data about their effect on protein assemblies, whose formation is driven by surface interactions, is lacking. Here, we investigate the effects of osmolytes and related molecules on the stabilities of a protein and a protein complex. The results demonstrate that osmolytes are not differentiated from other cosolutes by their stabilizing influences on protein tertiary structure but by their compatibility with the interactions between protein surfaces that organize the cellular interior.
Topics: Animals; Bacterial Proteins; Drosophila; Drosophila Proteins; Organic Chemicals; Osmolar Concentration; Protein Binding; Protein Multimerization; Static Electricity; Streptococcus; src Homology Domains
PubMed: 29842777
DOI: 10.1021/jacs.8b03903