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Annual Review of Biochemistry Jun 2019The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein... (Review)
Review
The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein subunits, ∼110 MDa in humans), the NPC has remained one of the foremost challenges for structure determination. Structural studies have now provided atomic-resolution crystal structures of most nucleoporins. The acquisition of these structures, combined with biochemical reconstitution experiments, cross-linking mass spectrometry, and cryo-electron tomography, has facilitated the determination of the near-atomic overall architecture of the symmetric core of the human, fungal, and algal NPCs. Here, we discuss the insights gained from these new advances and outstanding issues regarding NPC structure and function. The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.
Topics: Active Transport, Cell Nucleus; Animals; Cell Nucleus; Cryoelectron Microscopy; Crystallography, X-Ray; Eukaryota; Humans; Models, Molecular; Nuclear Pore; Nuclear Pore Complex Proteins; Protein Conformation; Protein Subunits; RNA, Messenger
PubMed: 30883195
DOI: 10.1146/annurev-biochem-062917-011901 -
Cell Dec 2022Nuclear pore complexes (NPCs) are channels for nucleocytoplasmic transport of proteins and RNAs. However, it remains unclear whether composition, structure, and...
Nuclear pore complexes (NPCs) are channels for nucleocytoplasmic transport of proteins and RNAs. However, it remains unclear whether composition, structure, and permeability of NPCs dynamically change during the cleavage period of vertebrate embryos and affect embryonic development. Here, we report that the comprehensive NPC maturity (CNM) controls the onset of zygotic genome activation (ZGA) during zebrafish early embryogenesis. We show that more nucleoporin proteins are recruited to and assembled into NPCs with development, resulting in progressive increase of NPCs in size and complexity. Maternal transcription factors (TFs) transport into nuclei more efficiently with increasing CNM. Deficiency or dysfunction of Nup133 or Ahctf1/Elys impairs NPC assembly, maternal TFs nuclear transport, and ZGA onset, while nup133 overexpression promotes these processes. Therefore, CNM may act as a molecular timer for ZGA by controlling nuclear transport of maternal TFs that reach nuclear concentration thresholds at a given time to initiate ZGA.
Topics: Animals; Embryonic Development; Gene Expression Regulation, Developmental; Nuclear Pore; Nuclear Pore Complex Proteins; Transcription Factors; Zebrafish; Zygote; Genome
PubMed: 36493774
DOI: 10.1016/j.cell.2022.11.011 -
Cells Apr 2023The mitochondrial permeability transition pore (MPTP) is a calcium-dependent, ion non-selective membrane pore with a wide range of functions. Although the MPTP has been... (Review)
Review
The mitochondrial permeability transition pore (MPTP) is a calcium-dependent, ion non-selective membrane pore with a wide range of functions. Although the MPTP has been studied for more than 50 years, its molecular structure remains unclear. Short-term (reversible) opening of the MPTP protects cells from oxidative damage and enables the efflux of Ca ions from the mitochondrial matrix and cell signaling. However, long-term (irreversible) opening induces processes leading to cell death. Ca ions, reactive oxygen species, and changes in mitochondrial membrane potential regulate pore opening. The sensitivity of the pore to Ca ions changes as an organism ages, and MPTP opening plays a key role in the pathogenesis of many diseases. Most studies of the MPTP have focused on elucidating its molecular structure. However, understanding the mechanisms that will inhibit the MPTP may improve the treatment of diseases associated with its opening. To evaluate the functional state of the MPTP and its inhibitors, it is therefore necessary to use appropriate methods that provide reproducible results across laboratories. This review summarizes our current knowledge of the function and regulation of the MPTP. The latter part of the review introduces two optimized methods for evaluating the functional state of the pore under standardized conditions.
Topics: Mitochondrial Permeability Transition Pore; Mitochondrial Membrane Transport Proteins; Calcium; Mitochondria; Cell Death
PubMed: 37174672
DOI: 10.3390/cells12091273 -
Toxins Sep 2019Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins... (Review)
Review
Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins or highly potent virulence factors, they represent an attractive target for the development of molecules that neutralize their actions with high efficacy. There has been an assortment of inhibitors developed to specifically obstruct the activity of pore-forming proteins, in addition to vaccination and antibiotics that serve as a plausible treatment for the majority of diseases caused by bacterial infections. Here we review a wide range of potential inhibitors that can specifically and effectively block the activity of pore-forming proteins, from small molecules to more specific macromolecular systems, such as synthetic nanoparticles, antibodies, antibody mimetics, polyvalent inhibitors, and dominant negative mutants. We discuss their mechanism of inhibition, as well as advantages and disadvantages.
Topics: Animals; Cell Membrane; Humans; Pore Forming Cytotoxic Proteins
PubMed: 31546810
DOI: 10.3390/toxins11090545 -
Microbiology (Reading, England) Mar 2022Pore-forming toxins (PFTs) are widely distributed in both Gram-negative and Gram-positive bacteria. PFTs can act as virulence factors that bacteria utilise in...
Pore-forming toxins (PFTs) are widely distributed in both Gram-negative and Gram-positive bacteria. PFTs can act as virulence factors that bacteria utilise in dissemination and host colonisation or, alternatively, they can be employed to compete with rival microbes in polymicrobial niches. PFTs transition from a soluble form to become membrane-embedded by undergoing large conformational changes. Once inserted, they perforate the membrane, causing uncontrolled efflux of ions and/or nutrients and dissipating the protonmotive force (PMF). In some instances, target cells intoxicated by PFTs display additional effects as part of the cellular response to pore formation. Significant progress has been made in the mechanistic description of pore formation for the different PFTs families, but in several cases a complete understanding of pore structure remains lacking. PFTs have evolved recognition mechanisms to bind specific receptors that define their host tropism, although this can be remarkably diverse even within the same family. Here we summarise the salient features of PFTs and highlight where additional research is necessary to fully understand the mechanism of pore formation by members of this diverse group of protein toxins.
Topics: Bacteria; Bacterial Toxins; Cell Membrane; Humans; Pore Forming Cytotoxic Proteins; Virulence Factors
PubMed: 35333704
DOI: 10.1099/mic.0.001154 -
Journal of Neurochemistry Jun 2016Regulated exocytosis is a multistage process involving a merger between the vesicle and the plasma membrane, leading to the formation of a fusion pore, a channel,... (Review)
Review
Regulated exocytosis is a multistage process involving a merger between the vesicle and the plasma membrane, leading to the formation of a fusion pore, a channel, through which secretions are released from the vesicle to the cell exterior. A stimulus may influence the pore by either dilating it completely (full-fusion exocytosis) or mediating a reversible closure (transient exocytosis). In neurons, these transitions are short-lived and not accessible for experimentation. However, in some neuroendocrine cells and astrocytes, initial fusion pores may reopen several hundred times, indicating their stability. Frequently, these pores are too narrow to pass luminal molecules to the extracellular space (unproductive exocytosis), but their diameter can dilate upon stimulation. To explain the stability of the initial narrow fusion pores, anisotropic membrane constituents with a non-axisymmetric shape were proposed to accumulate in the fusion pore membrane. Although the nature of these is unclear, they may consist of lipids and proteins, including SNAREs, which may facilitate and regulate the pre- and post-fusional stages of exocytosis. This review highlights models and experimental studies revealing mechanisms of fusion pore stabilization in a narrow, release unproductive state. The fusion pore is a channel that forms when the vesicle and the plasma membranes merge, and mediates the release of secretions from the vesicle lumen to the cell exterior. Frequently, these pores are too narrow to pass molecules to the extracellular space. Anisotropic membrane constituents with a non-axisymmetric shape were proposed to accumulate in the fusion pore membrane. This article is part of a mini review series on Chromaffin cells (ISCCB Meeting, 2015).
Topics: Animals; Calcium; Cell Membrane; Exocytosis; Humans; Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels; Membrane Fusion; Secretory Vesicles
PubMed: 26841731
DOI: 10.1111/jnc.13561 -
Journal of Colloid and Interface Science Nov 2022The spontaneous imbibition of a liquid within porous media, known as wicking, can display uncommon features in textiles and yarns. Yarns exhibited step-wise wicking...
UNLABELLED
The spontaneous imbibition of a liquid within porous media, known as wicking, can display uncommon features in textiles and yarns. Yarns exhibited step-wise wicking dynamics not captured by current models.
HYPOTHESIS
Wicking dynamics in yarns not only depend on inter-fiber pore filling, but are mainly determined by the pore-to-pore transition processes and the structure of the pore network.
EXPERIMENTS
Fast X-ray tomographic microscopy is employed to reveal the pore scale processes and neutron radiography for the macroscopic water uptake in yarns. A semi-empirical pore network model is presented that employs the measured pore network topology and pore scale dynamics to reproduce the experimentally observed wicking dynamics in yarns.
FINDINGS
The yarn pore system is a sparse network of long and narrow pores that promotes step-wise uptake dynamics. Wicking in yarns displays fast pore filling events in the order of seconds and long waiting times between filling events up to several minutes while navigating the pore network. As main result, we find that a few filling events directly determine the macroscopic behavior of wicking in the sparse pore network of yarns. It is necessary to consider pore-to-pore transition waiting times and the pore network structure to explain the characteristics of wicking dynamics in yarns.
Topics: Capillary Action; Textiles
PubMed: 35714401
DOI: 10.1016/j.jcis.2022.04.060 -
Neuron Jan 2018Microglia exhibit two modes of motility: they constantly extend and retract their processes to survey the brain, but they also send out targeted processes to envelop...
Microglia exhibit two modes of motility: they constantly extend and retract their processes to survey the brain, but they also send out targeted processes to envelop sites of tissue damage. We now show that these motility modes differ mechanistically. We identify the two-pore domain channel THIK-1 as the main K channel expressed in microglia in situ. THIK-1 is tonically active, and its activity is potentiated by P2Y receptors. Inhibiting THIK-1 function pharmacologically or by gene knockout depolarizes microglia, which decreases microglial ramification and thus reduces surveillance, whereas blocking P2Y receptors does not affect membrane potential, ramification, or surveillance. In contrast, process outgrowth to damaged tissue requires P2Y receptor activation but is unaffected by blocking THIK-1. Block of THIK-1 function also inhibits release of the pro-inflammatory cytokine interleukin-1β from activated microglia, consistent with K loss being needed for inflammasome assembly. Thus, microglial immune surveillance and cytokine release require THIK-1 channel activity.
Topics: Adenosine Triphosphate; Animals; Cell Movement; Cell Polarity; Cell Shape; Cell Surface Extensions; Chemotaxis; Inflammasomes; Interleukin-1beta; Membrane Potentials; Mice; Mice, Knockout; Microglia; Potassium; Potassium Channels, Tandem Pore Domain; Rats; Rats, Sprague-Dawley; Receptors, Purinergic P2Y12; Transcriptome
PubMed: 29290552
DOI: 10.1016/j.neuron.2017.12.002 -
FEBS Letters Nov 2018Membrane fusion and fission are fundamental processes in living organisms. Membrane fusion occurs through the formation of a fusion pore, which is the structure that... (Review)
Review
Membrane fusion and fission are fundamental processes in living organisms. Membrane fusion occurs through the formation of a fusion pore, which is the structure that connects two lipid membranes during their fusion. Fusion pores can form spontaneously, but cells endow themselves with a set of proteins that make the process of fusion faster and regulatable. The fusion pore starts with a narrow diameter and dilates relatively slowly; it may fluctuate in size or can even close completely, producing a transient vesicle fusion (kiss-and-run), or can finally expand abruptly to release all vesicle contents. A set of proteins control the formation, dilation, and eventual closure of the fusion pore and, therefore, the velocity at which the contents of secretory vesicles are released to the extracellular medium. Thus, the regulation of fusion pore expansion or closure is key to regulate the release of neurotransmitters and hormones. Here, we review the phases of the fusion pore and discuss the implications in the modes of exocytosis.
Topics: Animals; Cell Membrane; Exocytosis; Extracellular Space; Hormones; Humans; Membrane Fusion; Neurotransmitter Agents; Secretory Vesicles
PubMed: 30169901
DOI: 10.1002/1873-3468.13234 -
Neurotherapeutics : the Journal of the... Jul 2022The nuclear pore complex (NPC) is a large multimeric structure that is interspersed throughout the membrane of the nucleus and consists of at least 33 protein... (Review)
Review
The nuclear pore complex (NPC) is a large multimeric structure that is interspersed throughout the membrane of the nucleus and consists of at least 33 protein components. Individual components cooperate within the nuclear pore to facilitate selective passage of materials between the nucleus and cytoplasm while simultaneously performing pore-independent roles throughout the cell. NPC dysfunction is a hallmark of neurodegenerative disorders including Alzheimer's disease, Huntington's disease, and amyotrophic lateral sclerosis (ALS). NPC components can become mislocalized or altered in expression in neurodegeneration. These alterations in NPC structure are often detrimental to the neuronal function and ultimately lead to neuronal loss. This review highlights the importance of nucleocytoplasmic transport and NPC integrity and how dysfunction of such may contribute to neurodegeneration.
Topics: Humans; Nuclear Pore; Active Transport, Cell Nucleus; Amyotrophic Lateral Sclerosis; Cytoplasm; Cell Nucleus
PubMed: 36070178
DOI: 10.1007/s13311-022-01293-w