ABSTRACT
Diverse biological systems utilize fluctuations ("noise") in gene expression to drive lineage-commitment decisions. However, once a commitment is made, noise becomes detrimental to reliable function, and the mechanisms enabling post-commitment noise suppression are unclear. Here, we find that architectural constraints on noise suppression are overcome to stabilize fate commitment. Using single-molecule and time-lapse imaging, we find that-after a noise-driven event-human immunodeficiency virus (HIV) strongly attenuates expression noise through a non-transcriptional negative-feedback circuit. Feedback is established through a serial cascade of post-transcriptional splicing, whereby proteins generated from spliced mRNAs auto-deplete their own precursor unspliced mRNAs. Strikingly, this auto-depletion circuitry minimizes noise to stabilize HIV's commitment decision, and a noise-suppression molecule promotes stabilization. This feedback mechanism for noise suppression suggests a functional role for delayed splicing in other systems and may represent a generalizable architecture of diverse homeostatic signaling circuits.
Subject(s)
Feedback, Physiological , HIV-1/metabolism , RNA, Messenger/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , HEK293 Cells , HIV-1/genetics , Humans , Jurkat Cells , Models, Biological , RNA Precursors/metabolism , RNA Processing, Post-Transcriptional , RNA Splicing , Time-Lapse Imaging , tat Gene Products, Human Immunodeficiency Virus/geneticsABSTRACT
Mitochondrial fusion and division play important roles in the regulation of apoptosis. Mitochondrial fusion proteins attenuate apoptosis by inhibiting release of cytochrome c from mitochondria, in part by controlling cristae structures. Mitochondrial division promotes apoptosis by an unknown mechanism. We addressed how division proteins regulate apoptosis using inhibitors of mitochondrial division identified in a chemical screen. The most efficacious inhibitor, mdivi-1 (for mitochondrial division inhibitor) attenuates mitochondrial division in yeast and mammalian cells by selectively inhibiting the mitochondrial division dynamin. In cells, mdivi-1 retards apoptosis by inhibiting mitochondrial outer membrane permeabilization. In vitro, mdivi-1 potently blocks Bid-activated Bax/Bak-dependent cytochrome c release from mitochondria. These data indicate the mitochondrial division dynamin directly regulates mitochondrial outer membrane permeabilization independent of Drp1-mediated division. Our findings raise the interesting possibility that mdivi-1 represents a class of therapeutics for stroke, myocardial infarction, and neurodegenerative diseases.
Subject(s)
Dynamins/antagonists & inhibitors , Mitochondrial Membranes/drug effects , Mitochondrial Membranes/metabolism , Quinazolinones/pharmacology , bcl-2 Homologous Antagonist-Killer Protein/metabolism , bcl-2-Associated X Protein/metabolism , Animals , Apoptosis/drug effects , COS Cells , Chlorocebus aethiops , Dynamins/ultrastructure , Flow Cytometry , HeLa Cells , Humans , Mitochondria/drug effects , Mitochondria/metabolism , Permeability/drug effects , Quinazolinones/chemistry , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/drug effects , Structure-Activity RelationshipABSTRACT
Dynamin-related proteins (DRPs) are large self-assembling GTPases whose common function is to regulate membrane dynamics in a variety of cellular processes. Dnm1, which is a yeast DRP (Drp1/Dlp1 in humans), is required for mitochondrial division, but its mechanism is unknown. We provide evidence that Dnm1 likely functions through self-assembly to drive the membrane constriction event that is associated with mitochondrial division. Two regulatory features of Dnm1 self-assembly were also identified. Dnm1 self-assembly proceeded through a rate-limiting nucleation step, and nucleotide hydrolysis by assembled Dnm1 structures was highly cooperative with respect to GTP. Dnm1 formed extended spirals, which possessed diameters greater than those of dynamin-1 spirals but whose sizes, remarkably, were equal to those of mitochondrial constriction sites in vivo. These data suggest that Dnm1 has evolved to form structures that fit the dimensions of mitochondria.
Subject(s)
GTP Phosphohydrolases/chemistry , GTP Phosphohydrolases/metabolism , Mitochondria/metabolism , Mitochondrial Proteins/chemistry , Mitochondrial Proteins/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Dimerization , GTP Phosphohydrolases/genetics , Mitochondrial Proteins/genetics , Mutation , Osmolar Concentration , Protein Conformation , Saccharomyces cerevisiae Proteins/geneticsABSTRACT
Dynamin-related proteins (DRPs) compose a diverse family of proteins that function, through GTPase stimulated self-assembly, to remodel cellular membranes. The molecular mechanism by which DRPs mediate membrane remodeling events and the specific role of their GTPase cycle is still not fully understood. Although DRPs are members of the GTPase superfamily, they possess unique kinetic properties. In particular, they have relatively low affinity for guanine nucleotides and, under conditions that favor self-assembly, they have high rates of GTP turnover. Established fixed time point assays used for the analysis of assembly stimulated GTPase activity are prone to inaccuracies due to substrate depletion and are also limited by lack of time resolution. We describe a simple, continuous, coupled GTP regenerating assay that tackles the limitations of the fixed time point assays and can be used for the kinetic analysis of DRP GTP hydrolysis under unassembled and assembled conditions.
Subject(s)
Dynamins/analysis , GTP Phosphohydrolases/analysis , Dynamin I/analysis , Guanosine Diphosphate/metabolism , Guanosine Triphosphate/metabolism , L-Lactate Dehydrogenase/metabolism , NAD/analysis , Pyruvate Kinase/metabolismABSTRACT
We examined the role of ATP hydrolysis by the Arp2/3 complex in building the leading edge of a cell by studying the effects of hydrolysis defects on the behavior of the complex in the lamellipodial actin network of Drosophila S2 cells and in a reconstituted, in vitro, actin-based motility system. In S2 cells, nonhydrolyzing Arp2 and Arp3 subunits expanded and delayed disassembly of lamellipodial actin networks and the effect of mutant subunits was additive. Arp2 and Arp3 ATP hydrolysis mutants remained in lamellipodial networks longer and traveled greater distances from the plasma membrane, even in networks still containing wild-type Arp2/3 complex. In vitro, wild-type and ATP hydrolysis mutant Arp2/3 complexes each nucleated actin and built similar dendritic networks. However, networks constructed with Arp2/3 hydrolysis-defective mutants were more resistant to disassembly by cofilin. Our results indicate that ATP hydrolysis on both Arp2 and Arp3 contributes to dissociation of the complex from the actin network but is not strictly necessary for lamellipodial network disassembly.
Subject(s)
Actin Cytoskeleton/enzymology , Actin-Related Protein 2-3 Complex/metabolism , Adenosine Triphosphate/metabolism , Pseudopodia/enzymology , Actin-Related Protein 2/genetics , Actin-Related Protein 2/metabolism , Actin-Related Protein 2-3 Complex/genetics , Actin-Related Protein 3/genetics , Actin-Related Protein 3/metabolism , Animals , Cell Line , Cofilin 1/metabolism , Drosophila , Genotype , Hydrolysis , Microscopy, Fluorescence , Mutation , Phenotype , Profilins/metabolism , RNA Interference , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Time Factors , TransfectionABSTRACT
Mitochondria are dynamic organelles that undergo cycles of fission and fusion. The yeast dynamin-related protein Dnm1 has been localized to sites of mitochondrial division. Using cryo-EM, we have determined the three-dimensional (3D) structure of Dnm1 in a GTP-bound state. The 3D map showed that Dnm1 adopted a unique helical assembly when compared with dynamin, which is involved in vesicle scission during endocytosis. Upon GTP hydrolysis, Dnm1 constricted liposomes and subsequently dissociated from the lipid bilayer. The magnitude of Dnm1 constriction was substantially larger than the decrease in diameter previously reported for dynamin. We postulate that the larger conformational change is mediated by a flexible Dnm1 structure that has limited interaction with the underlying bilayer. Our structural studies support the idea that Dnm1 has a mechanochemical role during mitochondrial division.
Subject(s)
GTP Phosphohydrolases/chemistry , Mitochondria/metabolism , Mitochondrial Proteins/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Cryoelectron Microscopy , Dynamins/chemistry , Guanosine Triphosphate/metabolism , Lipid Bilayers/metabolism , Models, Biological , Protein Structure, TertiaryABSTRACT
The dynamin-related GTPase, Dnm1, self-assembles into punctate structures that are targeted to the outer mitochondrial membrane where they mediate mitochondrial division. Post-targeting, Dnm1-dependent division is controlled by the actions of the WD repeat protein, Mdv1, and the mitochondrial tetratricopeptide repeat-like outer membrane protein, Fis1. Our previous studies suggest a model where at this step Mdv1 functions as an adaptor linking Fis1 with Dnm1. To gain insight into the exact role of the Fis1.Mdv1.Dnm1 complex in mitochondrial division, we performed a structure-function analysis of the Mdv1 adaptor. Our analysis suggests that dynamic interactions between Mdv1 and Dnm1 play a key role in division by regulating Dnm1 self-assembly.