Nuclear Pore Complexes and Nucleocytoplasmic Transport - Methods

Nuclear Pore Complexes and Nucleocytoplasmic Transport - Methods
Author:
Publisher: Elsevier
Total Pages: 553
Release: 2014-05-20
Genre: Science
ISBN: 0124171788

Volume 122 of Methods in Cell Biology describes modern tools and techniques used to study nuclear pore complexes and nucleocytoplasmic transport in diverse eukaryotic model systems (including mammalian cells, Xenopus, C. elegans, yeast). The volume enables investigators to analyze nuclear pore complex structure, assembly, and dynamics; to evaluate protein and RNA trafficking through the nuclear envelope; and to design in vivo or in vitro assays appropriate to their research needs. Beyond the study of nuclear pores and transport as such, these protocols will also be helpful to scientists characterizing gene regulation, signal transduction, cell cycle, viral infections, or aging. The NPC being one of the largest multiprotein complexes in the cell, some protocols will also be of interest for people currently characterizing other macromolecular assemblies. This book is thus designed for laboratory use by graduate students, technicians, and researchers in many molecular and cellular disciplines. Describes modern tools and techniques used to study nuclear pore complexes and nucleocytoplasmic transport in diverse eukaryotic model systems (mammalian cells, Xenopus, C. elegans, yeast) Chapters are written by experts in the field Cutting-edge material

The Ins & Outs of Nucleocytoplasmic Transport

The Ins & Outs of Nucleocytoplasmic Transport
Author: Jeffrey Hsin Nien Tang
Publisher:
Total Pages: 103
Release: 2014
Genre:
ISBN:

The nuclear pore complex (NPC) is one of the largest known protein structures in the cell. Evolutionarily conserved in eukaryotes ranging from fungi to plants and animals, the NPC is the main transporter of molecules between the cell cytoplasm and nucleus. Maintaining the proper compartment-specific localization of proteins and RNA is crucial for normal cell function, and the nuclear pore accomplishes this task both robustly and efficiently. Over the past several decades, insight into the composition, organization, structure, and mechanism of the NPC has been gradually teased out through careful experimentation. However, many questions about the pore's function remain unanswered. In this dissertation, I describe efforts aimed at elucidating several aspects of the NPC. First, I investigate the transport properties of the pore, specifically looking at how the nuclear transport receptor importin-[beta] and the Ran GTPase interact not only with each other but also how they may affect the pore itself. The nucleoporin Nup153 is identified as an important player in the nuclear transport process which binds strongly to importin-[beta] in a Ran-sensitive manner. Using multiple experimental techniques, the properties of importin-[beta], and Nup153's interactions are characterized and shown to be capable of modulating the selective permeability barrier of the NPC. Next, I examine how members of a major class of nuclear pore proteins, the scaffold nucleoporins, are both structurally and functionally similar to the karyopherin family of soluble nuclear transport receptors. Structures of the proteins Nup188 and Nup192 are analyzed and shown to resemble those of karyopherins. Furthermore, in vitro assays indicate that at least a subset of the scaffold nucleoporins behave functionally as transport receptors, hinting at an evolutionary relationship between these two important classes of proteins. Finally, a calcium-mediated phenomenon affecting the permeability of the NPC is explored. I show that certain cytosolic proteases are activated by millimolar concentrations of calcium ion which leads irreversibly to an increase in the nuclear pore's permeability to large molecules. A model for physiological pathways implicated in this effect is proposed.

Single-Molecule Studies on Nuclear Pore Complex Structure and Function

Single-Molecule Studies on Nuclear Pore Complex Structure and Function
Author: Joseph M. Kelich
Publisher:
Total Pages: 115
Release: 2018
Genre:
ISBN:

Nuclear pore complexes (NPCs) are large macromolecular gateways embedded in the nuclear envelope of Eukaryotic cells that serve to regulate bi-directional trafficking of particles to and from the nucleus. NPCs have been described as creating a selectively permeable barrier mediating the nuclear export of key endogenous cargoes such as mRNA, and pre-ribosomal subunits as well as allow for the nuclear import of nuclear proteins and some viral particles. Remarkably, other particles that are not qualified for nucleocytoplasmic transport are repelled from the NPC, unable to translocate. The NPC is made up of over 30 unique proteins, each present in multiples of eight copies. The two primary protein components of the NPC can be simplified as scaffold nucleoporins which form the main structure of the NPC and the phenylalanine-glycine (FG) motif containing nucleoporins (FG-Nups) which anchor to the scaffold and together create the permeability barrier within the pore. Advances in fluorescence microscopy techniques including single-molecule and super-resolution microscopy have made it possible to label and visualize the dynamic components of the NPC as well as track the rapid nucleocytoplasmic transport process of importing and exporting cargoes. The focus of this dissertation will be on live cell fluorescence microscopy application in probing the dynamic components of the NPC as well as tracking the processes of nucleocytoplasmic transport.

Nuclear-Cytoplasmic Transport

Nuclear-Cytoplasmic Transport
Author: Weidong Yang
Publisher: Springer
Total Pages: 277
Release: 2018-07-27
Genre: Science
ISBN: 3319773097

Dysfunction of nuclear-cytoplasmic transport systems has been associated with many human diseases. Thus, understanding of how functional this transport system maintains, or through dysfunction fails to maintain remains the core question in cell biology. In eukaryotic cells, the nuclear envelope (NE) separates the genetic transcription in the nucleus from the translational machinery in the cytoplasm. Thousands of nuclear pore complexes (NPCs) embedded on the NE selectively mediate the bidirectional trafficking of macromolecules such as RNAs and proteins between these two cellular compartments. In this book, the authors integrate recent progress on the structure of NPC and the mechanism of nuclear-cytoplasmic transport system in vitro and in vivo.

Nuclear Pore Complexes in Genome Organization, Function and Maintenance

Nuclear Pore Complexes in Genome Organization, Function and Maintenance
Author: Maximiliano D’Angelo
Publisher: Springer
Total Pages: 245
Release: 2018-02-02
Genre: Medical
ISBN: 331971614X

The three-dimensional organization of the DNA inside the eukaryotic cell nucleus has emerged a critical regulator of genome integrity and function. Increasing evidence indicates that nuclear pore complexes (NPCs), the large protein channels that connect the nucleus to the cytoplasm, play a critical role in the establishment and maintenance of chromatin organization and in the regulation of gene activity. These findings, which oppose the traditional view of NPCs as channels with only one: the facilitation of nucleocytoplasmic molecule exchange, have completely transformed our understanding of these structures. This book describes our current knowledge of the role of NPCs in genome organization and gene expression regulation. It starts by providing an overview of the different compartments and structures of the nucleus and how they contribute to organizing the genome, then moves to examine the direct roles of NPCs and their components in gene expression regulation in different organisms, and ends by describing the function of nuclear pores in the infection and genome integration of HIV, in DNA repair and telomere maintenance, and in the regulation of chromosome segregation and mitosis. This book provides an intellectual backdrop for anyone interested in understanding how the gatekeepers of the nucleus contribute to safeguarding the integrity and function of the eukaryotic genome.

The Role of Nuclear Pore Complex Architecture in Nucleocytoplasmic Transport and Nuclear Envelope Structure

The Role of Nuclear Pore Complex Architecture in Nucleocytoplasmic Transport and Nuclear Envelope Structure
Author: Bryan Jeffrey Zeitler
Publisher:
Total Pages: 362
Release: 2007
Genre:
ISBN: 9780549172154

In order to dissect the function of NPC asymmetry, I constructed Saccharomyces cerevisiae mutants with asymmetric FG repeats either deleted or swapped. The mutant Nups localize properly within the NPC and exhibit exchanged binding specificity for the exportin Xpo1. Surprisingly, I was unable to detect any defects in the Kap95, Kap121, Xpo1, or mRNA transport pathways in cells expressing the mutant FG Nups. These findings suggest that the biased distribution of FG repeats is not required for major nucleocytoplasmic trafficking events across the NPC.

The Liver

The Liver
Author: Irwin M. Arias
Publisher: John Wiley & Sons
Total Pages: 1156
Release: 2020-03-09
Genre: Medical
ISBN: 1119436826

Bridging the gap between basic scientific advances and the understanding of liver disease — the extensively revised new edition of the premier text in the field. The latest edition of The Liver: Biology and Pathobiology remains a definitive volume in the field of hepatology, relating advances in biomedical sciences and engineering to understanding of liver structure, function, and disease pathology and treatment. Contributions from leading researchers examine the cell biology of the liver, the pathobiology of liver disease, the liver’s growth, regeneration, metabolic functions, and more. Now in its sixth edition, this classic text has been exhaustively revised to reflect new discoveries in biology and their influence on diagnosing, managing, and preventing liver disease. Seventy new chapters — including substantial original sections on liver cancer and groundbreaking advances that will have significant impact on hepatology — provide comprehensive, fully up-to-date coverage of both the current state and future direction of hepatology. Topics include liver RNA structure and function, gene editing, single-cell and single-molecule genomic analyses, the molecular biology of hepatitis, drug interactions and engineered drug design, and liver disease mechanisms and therapies. Edited by globally-recognized experts in the field, this authoritative volume: Relates molecular physiology to understanding disease pathology and treatment Links the science and pathology of the liver to practical clinical applications Features 16 new “Horizons” chapters that explore new and emerging science and technology Includes plentiful full-color illustrations and figures The Liver: Biology and Pathobiology, Sixth Edition is an indispensable resource for practicing and trainee hepatologists, gastroenterologists, hepatobiliary and liver transplant surgeons, and researchers and scientists in areas including hepatology, cell and molecular biology, virology, and drug metabolism.

Nuclear Pore Proteins in Regulation of Chromatin State and Gene Expression

Nuclear Pore Proteins in Regulation of Chromatin State and Gene Expression
Author: Terra Kuhn
Publisher:
Total Pages: 250
Release: 2019
Genre:
ISBN:

Nuclear pore complexes are best known for their regulation of nucleocytoplasmic transport as integral components of the eukaryotic nuclear envelope. Over the years, their importance in regulation of genome function has become apparent. Many of the 30 individual nuclear pore proteins, Nups, have been found to play distinct roles interacting with and regulating various genomic targets, especially in a cell-type specific manner. The mechanism behind this regulation is often unknown. We have developed a method by which to study the roles of Nups on chromatin using an ectopic-tethering system. Drosophila melanogaster provide a powerful tool with which to combine many genetic elements of interest together in individual organisms quickly and efficiently, and additionally has allowed for powerful high-resolution visualization of chromatin structure perturbations through the imaging of their larval salivary gland polytene chromosomes. Using this system we observed that tethering Nups to chromatin was sufficient to induce chromatin decondensation, visualized by robust and reproducible loss of DNA and histone fluorescene signal associated with Nup binding. Additionally we observed recruitment of chromatin-remodeling complex PBAP, and reliance on PBAP for the observed Nup-induced decondensation, suggesting an important functional relationship between these proteins. We then took our findings and hypotheses generated from this ectopic-tethering imaging system to next conduct functional biochemical analysis of these proteins in Drosophila S2 cell culture. We found that nucleoporin Elys has a robust biochemical interaction with components of PBAP in an endogenous context, supporting the recruitment of these proteins we observed via immunofluorescence. Additionally, MNase experiments determined that Elys was critical for facilitating the formation and/or maintenance of open chromatin, both genome-wide and on a local nucleosomal level at Elys target genes. Together these results demonstrate the importance of nucleoporins in regulation of chromatin structure, and provide one mechanism to explain this phenomenon. These findings are of particular interest in the fields of chromatin biology and the study of nuclear pore protein function, demonstrating a possible explanation for not only associations of NPCs with decondensed chromatin at the nuclear periphery, but also regulation of Nup target gene expression, through regulation of chromatin accessibility.