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Highlights
• NPM1/NPM1c induce the autophagy-lysosome pathway by activating the master regulator TFEB
• NPM1/NPM1c bind to GABARAP proteins via an atypical module in their N-terminal regions
• The pro-autophagic activity of NPM1c depends on this GABARAP binding module
Summary
The nucleolar scaffold protein NPM1 is a multifunctional regulator of cellular homeostasis, genome integrity, and stress response. NPM1 mutations, known as NPM1c variants promoting its aberrant cytoplasmic localization, are the most frequent genetic alterations in acute myeloid leukemia (AML). A hallmark of AML cells is their dependency on elevated autophagic flux. Here, we show that NPM1 and NPM1c induce the autophagy-lysosome pathway by activating the master transcription factor TFEB, thereby coordinating the expression of lysosomal proteins and autophagy regulators. Importantly, both NPM1 and NPM1c bind to autophagy modifiers of the GABARAP subfamily through an atypical binding module preserved within its N terminus. The propensity of NPM1c to induce autophagy depends on this module, likely indicating that NPM1c exerts its pro-autophagic activity by direct engagement with GABARAPL1. Our data report a non-canonical binding mode of GABARAP family members that drives the pro-autophagic potential of NPM1c, potentially enabling therapeutic options.
The pyruvate oxidases from Escherichia coli (EcPOX) and Lactobacillus plantarum (LpPOX) are both thiamin-dependent flavoenzymes. Their sequence and structure are closely related, and they catalyse similar reactions—but they differ in their activity pattern: LpPOX is always highly active, EcPOX only when activated by lipids or limited proteolysis, both involving the protein's C-terminal 23 residues (the ‘α-peptide’). Here, we relate the redox-induced infrared (IR) difference spectrum of EcPOX to its unusual activation mechanism. The IR difference spectrum of EcPOX is marked by contributions from the protein backbone, reflecting major conformational changes. A rare sulfhydryl (−SH) difference signal indicates changes in the vicinity of cysteines. We could pin the Cys–SH difference signal to Cys88 and Cys494, both being remote from the moving α-peptide and the redox-active flavin cofactor. Yet, when the α-peptide is proteolytically removed, the Cys–SH difference signal disappears, together with several difference signals in the amide range. The remaining IR signature of the permanently activated EcPOXΔ23 is strikingly similar to the simpler signature of LpPOX. The loss of the α-peptide ‘transforms’ the catalytically complex EcPOX into the catalytically ‘simpler’ LpPOX.
Understanding the functional roles of cells in neuronal circuits and behavior requires the ability to control neuronal activity in an acute and precise way. The field of optogenetics offers a variety of molecular tools to excite or inhibit neurons with light. In the last decade, several strategies have been proposed for reversible silencing of neurotransmission. These tools vary widely in their mechanisms: ranging from opsin-based light-driven ion pumps or anion channels, which are known to hyperpolarize the cell, to alter ionic gradients or cellular biochemistry; over metabotropic receptors, to tools damaging the neurotransmitter release machinery, that allow only long-term silencing as their recovery requires de novo synthesis of targeted proteins. Therefore, the optogenetic toolbox still lacks tools that combine fast activation and fast reversibility with the ability of long-term silencing.
In this study, the optogenetic tool optoSynC (optogenetic synaptic vesicle clustering) was characterized in depth. optoSynC utilizes the light-induced homo-oligomerization of Arabidopsis thaliana cryptochrome 2 (CRY2) for silencing synaptic transmission via clustering of synaptic vesicles (SVs). CRY2 was targeted to the SV membrane by fusion to the SV transmembrane protein synaptogyrin-1 (SNG-1). The silencing kinetics of optoSynC were determined with analyses of swimming and crawling behavior in Caenorhabditis elegans (C. elegans). Pan-neuronally expressed optoSynC reduced swimming locomotion by 80% within 30 s following photo-stimulation (τon ~7.2 s). Locomotion recovered within 15 min in darkness (τoff ~6.5 min). Analysis of crawling behavior indicated even faster activation within 2 s and an almost complete inhibition of the LITE-1-mediated escape response. This escape response occurs at high blue light intensities and results in an increased velocity, which was not detected after optoSynC activation. However, optoSynC can exert its full effect at significantly lower intensities (25 µW/mm²) and is so light-sensitive that it can even be activated at 1.4 µW/mm². optoSynC could be fully recovered and reactivated at least twice without decreased efficiency. With a combination of pharmacological analysis and optogenetics, it has been demonstrated that optoSynC can inhibit neurotransmitter release for several hours. To realize its full potential, optoSynC should be expressed in an sng-1 mutant background. Expression along with endogenous SNG-1 decreases the effectiveness of optoSynC by 50%. Specific expression of optoSynC in cholinergic or GABAergic neurons could robustly inhibit swimming behavior by 55% and 30%, respectively. Moreover, optoSynC can selectively inhibit individual neurons like the nociceptive neuron pair PVD. When PVD is photoactivated by Chrimson, a red-light activatable channelrhodopsin, forward locomotion increases. Activation of optoSynC reduced this behavior by 50%. Besides my experiments in C. elegans, my cooperation partners Dr. Holger Dill and Yilmaz Arda Ateş demonstrated silencing of neurotransmission with optoSynC in zebrafish, and Dr. Shigeki Watanabe and Brady D. Goulden in murine hippocampal neurons.
The clustering of SVs as the mode of action of optoSynC could be confirmed using transmission electron microscopy. Analysis of micrographs of cholinergic synapses stimulated with and without light revealed that distances of neighboring synaptic vesicles in the cytosol were reduced by around 14% after photoactivation. Distances of docked SVs at the plasma membrane remained unaffected. However, near the dense projection, docked SVs accumulated, while other docked SVs were depleted after optoSynC activation. Activation of optoSynC increased the appearances of SVs and dense core vesicles (DCVs) in micrographs. It is unclear whether sizes became physically larger due to lateral pressure by CRY2 aggregates in the SV membrane or if oligomer formation only altered their appearance in micrographs. optoSynC did not accumulate in the plasma membrane to the extent that abnormal structures at the plasma membrane or dense projection were observed. Recycling of SVs remained unaffected by optoSynC as no unusual number of large vesicles was determined. Therefore, optoSynC inhibits neuronal activity mainly by clustering of cytosolic SVs.
To study the precise sequence and timing of events of vesicle mobilization, it is necessary to introduce known stops in the synaptic vesicle cycle which can be achieved by optoSynC. The C. elegans mutation dyn-1(ts-) is a temperature-sensitive dynamin mutation that blocks the recycling of SVs from the plasma membrane and early endosomes at temperatures exceeding 25 °C. By expressing optoSynC in dyn-1(ts-) animals, a novel assay was established, enabling the transfer of SVs between different stages in the SV cycle. Cluster formation of reserve pool SVs blocks the SV cycle before the process of docking and priming begins, while the SV cycle is blocked after the fusion of SVs at high temperatures. It could be demonstrated that behavior returned 15 min after optoSynC activation while animals without optoSynC remained immobile. Unfortunately, the time scale of the recovery from inhibition by optoSynC is too long to effectively study vesicle mobilization.
Lipid acquisition and transport are fundamental processes in all organisms, but many of the key players remain unidentified. In this study, we investigate the lipid-cycling mechanism of the minimal model organism Mycoplasma pneumoniae. We show that the essential protein P116 can extract lipids from the environment but also self- sufficiently deposit them into both eukaryotic cell membranes and liposomes. Our structures and molecular dynamics simulation reveal the mechanism by which the N- terminal region of P116, which resembles an SMP domain, perturbs the membrane, while a hydrophobic pocket exploits the chemical gradient to collect the lipids. Filling of P116 with cargo leads to a conformational change that modulates membrane affinity without consumption of ATP. We show that the Mycoplasmas have one integrated lipid acquisition and delivery machinery that shortcuts the complex multi-protein pathways used by higher developed organisms.
Mycoplasma pneumoniae is a human pathogen causing atypical community-acquired pneumonia. It is a model for a minimal cell, known for its non-canonical use of surface proteins for host-cell adhesion through ectodomain shedding and antigenic variation to evade the host cell immune response. Mpn444 is an essential mycoplasma surface protein implicated in both processes. It is one of 46 lipoproteins of M. pneumoniae, none of which have been structurally or functionally characterized. Here, we report the structure of Mpn444 at 3.04 Å as well as the molecular architecture of the trimeric Mpn444 complex. Our experimental structure displays striking similarity to structure predictions of several other essential lipoproteins in M. pneumoniae and other related Mycoplasma species, suggesting it to have a specialized and conserved function. The essentiality and involvement of Mpn444 in host immune evasion makes our structure a target for the development of new treatment strategies against mycoplasma infections.
Mycoplasma pneumoniae is a human pathogen causing atypical community-acquired pneumonia. It is a model for a minimal cell, known for its non-canonical use of surface proteins for host-cell adhesion through ectodomain shedding and antigenic variation to evade the host cell immune response. Mpn444 is an essential mycoplasma surface protein implicated in both processes. It is one of 46 lipoproteins of M. pneumoniae, none of which have been structurally or functionally characterized. Here, we report the structure of Mpn444 at 3.04 Å as well as the molecular architecture of the trimeric Mpn444 complex. Our experimental structure displays striking similarity to structure predictions of several other essential lipoproteins in M. pneumoniae and other related Mycoplasma species, suggesting it to have a specialized and conserved function. The essentiality and involvement of Mpn444 in host immune evasion makes our structure a target for the development of new treatment strategies against mycoplasma infections.
The β-barrel assembly machinery (BAM) mediates the folding and insertion of the majority of outer membrane proteins (OMPs) in gram-negative bacteria. BAM is a penta-heterooligomeric complex consisting of the central β-barrel BamA and four interacting lipoproteins BamB, C, D, and E. The conformational switching of BamA between inward-open (IO) and lateral-open (LO) conformations is required for substrate recognition and folding. However, the mechanism for the lateral gating or how the structural details observed in vitro correspond with the cellular environment remains elusive. In this study, we addressed these questions by characterizing the conformational heterogeneity of BamAB, BamACDE, and BamABCDE complexes in detergent micelles and/or Escherichia coli using pulsed dipolar electron spin resonance spectroscopy (PDS). We show that the binding of BamB does not induce any visible changes in BamA, and the BamAB complex exists in the IO conformation. The BamCDE complex induces an IO to LO transition through a coordinated movement along the BamA barrel. However, the extracellular loop 6 (L6) is unaffected by the presence of lipoproteins and exhibits large segmental dynamics extending to the exit pore. PDS experiments with the BamABCDE complex in intact E. coli confirmed the dynamic behavior of both the lateral gate and the L6 in the native environment. Our results demonstrate that the BamCDE complex plays a key role in the function by regulating lateral gating in BamA.
Lipopolysaccharides (LPS) confer resistance against harsh conditions, including antibiotics, in Gram-negative bacteria. The lipopolysaccharide transport (Lpt) complex, consisting of seven proteins (A-G), exports LPS across the cellular envelope. LptB2FG forms an ATP-binding cassette transporter that transfers LPS to LptC. How LptB2FG couples ATP binding and hydrolysis with LPS transport to LptC remains unclear. We observed the conformational heterogeneity of LptB2FG and LptB2FGC in micelles and/or proteoliposomes using pulsed dipolar electron spin resonance spectroscopy. Additionally, we monitored LPS binding and release using laser-induced liquid bead ion desorption mass spectrometry. The β-jellyroll domain of LptF stably interacts with the LptG and LptC β-jellyrolls in both the apo and vanadate-trapped states. ATP binding at the cytoplasmic side is allosterically coupled to the selective opening of the periplasmic LptF β-jellyroll domain. In LptB2FG, ATP binding closes the nucleotide binding domains, causing a collapse of the first lateral gate as observed in structures. However, the second lateral gate, which forms the putative entry site for LPS, exhibits a heterogeneous conformation. LptC binding limits the flexibility of this gate to two conformations, likely representing the helix of LptC as either released from or inserted into the transmembrane domains. Our results reveal the regulation of the LPS entry gate through the dynamic behavior of the LptC transmembrane helix, while its β-jellyroll domain is anchored in the periplasm. This, combined with long-range ATP-dependent allosteric gating of the LptF β-jellyroll domain, may ensure efficient and unidirectional transport of LPS across the periplasm.
K + is the most abundant cytosolic cation in bacteria, and its homeostasis is vital for bacterial survival, playing roles in many essential processes like pH homeostasis, protein synthesis and osmoregulation. When surrounding K + concentrations become very low, bacteria require an active high-affinity uptake system to ensure sufficient cellular K + levels. In many prokaryotes, this system is the K + pump KdpFABC. Peculiarly, KdpFABC forms a functional chimera between a channel-like subunit (KdpA) and a P-type ATPase (KdpB), and for a long time, the mechanism of how transport and ATP hydrolysis between these subunits are coordinated remained unclear. By applying a combination of cryo-EM, biochemical assays, and MD simulations, we have been able to shed light on a unique transport mechanism that combines both the channel and P-type ATPase subunits.
At high K + levels, KdpFABC needs to be inhibited to prevent excessive K + accumulation. This is achieved by a phosphorylation of the serine residue in the TGES 162 motif in the A domain of the pump subunit KdpB, which was shown to stall the complex in the E1P intermediate. Using cryo-EM studies under turnover conditions, we illuminated how stalling in this high-energy intermediate is possible.
Furthermore, we identify a previously uncharacterized atypical serine kinase domain in the sensor histidine kinase KdpD as the responsible kinase for KdpB phosphorylation, giving it a dual role in transcriptional and post-translational regulation of the Kdp system.