Talk:Cell Nucleus

From CellBiology


2016

Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy

J Mol Biol. 2016 Jan 12. pii: S0022-2836(16)00023-1. doi: 10.1016/j.jmb.2016.01.004. [Epub ahead of print]

von Appen A1, Beck M2.

Abstract

Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review the recent progress in understanding the in situ architecture of the NPC with a specific focus on approaches using three-dimensional cryo electron microscopy. We discuss technological benefits and limitations and give an outlook toward obtaining a high-resolution structure of the NPC. Copyright © 2015. Published by Elsevier Ltd. KEYWORDS: cryoelectron microscopy; nuclear pore complex PMID 26791760


Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex

PLoS Biol. 2016 Feb 18;14(2):e1002365. doi: 10.1371/journal.pbio.1002365. eCollection 2016.

Obado SO1, Brillantes M1, Uryu K1, Zhang W1, Ketaren NE1, Chait BT1, Field MC2, Rout MP1.

Abstract

The nuclear pore complex (NPC) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression. The components of NPCs from several eukaryotic lineages have been determined, but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level. Significantly, recent evidence indicates that compositional similarity does not necessarily correspond to homologous architecture between NPCs from different taxa. To address this, we describe the interactome of the trypanosome NPC, a representative, highly divergent eukaryote. We identify numerous new NPC components and report an exhaustive interactome, allowing assignment of trypanosome nucleoporins to discrete NPC substructures. Remarkably, despite retaining similar protein composition, there are exceptional architectural dissimilarities between opisthokont (yeast and vertebrates) and excavate (trypanosomes) NPCs. Whilst elements of the inner core are conserved, numerous peripheral structures are highly divergent, perhaps reflecting requirements to interface with divergent nuclear and cytoplasmic functions. Moreover, the trypanosome NPC has almost complete nucleocytoplasmic symmetry, in contrast to the opisthokont NPC; this may reflect divergence in RNA export processes at the NPC cytoplasmic face, as we find evidence supporting Ran-dependent mRNA export in trypanosomes, similar to protein transport. We propose a model of stepwise acquisition of nucleocytoplasmic mechanistic complexity and demonstrate that detailed dissection of macromolecular complexes provides fuller understanding of evolutionary processes. PMID 26891179

2015

Lamins at the crossroads of mechanosignaling

Genes Dev. 2015 Feb 1;29(3):225-37. doi: 10.1101/gad.255968.114.

Osmanagic-Myers S1, Dechat T1, Foisner R2. Author information Abstract The intermediate filament proteins, A- and B-type lamins, form the nuclear lamina scaffold adjacent to the inner nuclear membrane. B-type lamins confer elasticity, while A-type lamins lend viscosity and stiffness to nuclei. Lamins also contribute to chromatin regulation and various signaling pathways affecting gene expression. The mechanical roles of lamins and their functions in gene regulation are often viewed as independent activities, but recent findings suggest a highly cross-linked and interdependent regulation of these different functions, particularly in mechanosignaling. In this newly emerging concept, lamins act as a "mechanostat" that senses forces from outside and responds to tension by reinforcing the cytoskeleton and the extracellular matrix. A-type lamins, emerin, and the linker of the nucleoskeleton and cytoskeleton (LINC) complex directly transmit forces from the extracellular matrix into the nucleus. These mechanical forces lead to changes in the molecular structure, modification, and assembly state of A-type lamins. This in turn activates a tension-induced "inside-out signaling" through which the nucleus feeds back to the cytoskeleton and the extracellular matrix to balance outside and inside forces. These functions regulate differentiation and may be impaired in lamin-linked diseases, leading to cellular phenotypes, particularly in mechanical load-bearing tissues. © 2015 Osmanagic-Myers et al.; Published by Cold Spring Harbor Laboratory Press. KEYWORDS: LINC complex; cytoskeleton; extracellular matrix; lamins; mechanosensing; mechanotransduction

PMID 25644599

2014

Nuclear physics (of the cell, not the atom)

Mol Biol Cell. 2014 Nov 5;25(22):3466-9. doi: 10.1091/mbc.E14-03-0790.

Pederson T1, Marko JF2.

Abstract

The nucleus is physically distinct from the cytoplasm in ways that suggest new ideas and approaches for interrogating the operation of this organelle. Chemical bond formation and breakage underlie the lives of cells, but as this special issue of Molecular Biology of the Cell attests, the nonchemical aspects of cell nuclei present a new frontier to biologists and biophysicists. © 2014 Pederson and Marko. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). PMID 25368422

Super-resolution microscopy reveals LINC complex recruitment at nuclear indentation sites

Sci Rep. 2014 Dec 8;4:7362. doi: 10.1038/srep07362.

Versaevel M1, Braquenier JB2, Riaz M1, Grevesse T1, Lantoine J1, Gabriele S1. Author information Abstract Increasing evidences show that the actin cytoskeleton is a key parameter of the nuclear remodeling process in response to the modifications of cellular morphology. However, detailed information on the interaction between the actin cytoskeleton and the nuclear lamina was still lacking. We addressed this question by constraining endothelial cells on rectangular fibronectin-coated micropatterns and then using Structured Illumination Microscopy (SIM) to observe the interactions between actin stress fibers, nuclear lamina and LINC complexes at a super-resolution scale. Our results show that tension in apical actin stress fibers leads to deep nuclear indentations that significantly deform the nuclear lamina. Interestingly, indented nuclear zones are characterized by a local enrichment of LINC complexes, which anchor apical actin fibers to the nuclear lamina. Moreover, our findings indicate that nuclear indentations induce the formation of segregated domains of condensed chromatin. However, nuclear indentations and condensed chromatin domains are not irreversible processes and both can relax in absence of tension in apical actin stress fibers.

PMID 25482017

2013

Unit: Cell Biology (ANAT3231) Lecture Date: 2013-03-21 Lecture Time: 14:00 Venue: Matthews D Speaker: Dr Mark Hill

ID: 159017

The University has a system for automated recording of lectures called Lectopia. Lectopia requires login using your student number and unipass. I will be adding the link to each iLecture Audio following the Lecture. Due to the automated recording method, most lectures begin 4-5 minutes into MP3 recordings and occasionally stop before the end of the lecture.


Lecture 4 Audio Lecture Date: 2013-03-21 Lecture Time: 14:00 Venue: Matthews D Speaker: Dr Mark Hill


Recent PLoS Papers

  • PLOS Biology- A Case for a Functional Actin Network in the Nucleus
  • PLOS Biology- A Structural Analysis of Eukaryotic Membrane Evolution
  • PLOS Computational Biology- Charge as a Selection Criterion for Translocation through the Nuclear Po…
  • PLOS Computational Biology- Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of …
  • PLOS Computational Biology- Structure and Dynamics of Interphase Chromosomes
  • PLOS Genetics- A Meiotic Tapas Menu
  • PLOS Genetics- Chromosome Mechanics and Meiotic Engine Maintenance
  • PLOS ONE- 3D Ultrastructural Organization of Whole Chlamydomonas reinhardtii Cells Studied by Nanosc…
  • PLOS ONE- A Comparative Study of Drosophila and Human A-Type Lamins
  • PLOS ONE- Acute Manipulation of Diacylglycerol Reveals Roles in Nuclear Envelope Assembly & Endoplas…
  • PLOS ONE- Dissecting the Signaling Events That Impact Classical Nuclear Import and Target Nuclear Tr…
  • PLOS ONE- Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mo…
  • PLOS ONE- Human Nucleoporins Promote HIV-1 Docking at the Nuclear Pore, Nuclear Import and Integrati…
  • PLOS ONE- In Vivo Imaging of Single-Molecule Translocation Through Nuclear Pore Complexes by Pair Co…
  • PLOS ONE- In Vivo Imaging of Single-Molecule Translocation Through Nuclear Pore Complexes by Pair Co…-1
  • PLOS ONE- Mammalian Cells Change Volume during Mitosis
  • PLOS ONE- Mammalian Sperm Head Formation Involves Different Polarization of Two Novel LINC Complexes
  • PLOS ONE- Meiosis in Mice without a Synaptonemal Complex
  • PLOS ONE- Meiosis in Mice without a Synaptonemal Complex-1
  • PLOS ONE- Nuclear Distributions of NUP62 and NUP214 Suggest Architectural Diversity and Spatial Patt…
  • PLOS ONE- Nuclear Shield- A Multi-Enzyme Task-Force for Nucleus Protection
  • PLOS ONE- Protein Diffusion in Mammalian Cell Cytoplasm
  • PLOS ONE- Ribosome Distribution in HeLa Cells during the Cell Cycle

Online Textbooks

Molecular Cell Biology. 4th edition

Lodish H, Berk A, Zipursky SL, et al. New York: W. H. Freeman; 2000.

Molecular Biology of the Cell

4th edition. Alberts B, Johnson A, Lewis J, et al. New York: Garland Science; 2002.

JCB Annotated Video Collection

Chromosomes

http://jcb.rupress.org/site/misc/annotatedvideo.xhtml#Chromosomes

TopoII α is mobile http://jcb.rupress.org/cgi/content/abstract/158/1/23

The DNA-decatenating protein topoisomerase II has been proposed as a stable scaffold for mitotic chromosomes. Although Tavormina et al. do not rule out this idea, they show that a fluorescent version of DNA topoisomerase II α (topoII α) protein turns over rapidly. This may allow topoIIα, which is concentrated toward the axes of mitotic chromosome arms, to quickly reach and relieve areas of chromosomal strain that develop during mitosis. In another study examining the localization of topoII, Christensen et al. come to similar conclusions.

The nuclear envelope may help retard origin firing http://jcb.rupress.org/content/152/2/385.full

Time-lapse microscopy of GFP-marked origins allows Heun et al. to show that late-firing origins are enriched in a zone immediately adjacent to the nuclear envelope during G1, at which time a modified chromatin structure may be established to retard origin firing.

Nuclear pores

Nuclear pore complexes are fixed in place http://jcb.rupress.org/cgi/content/abstract/154/1/71

Daigle et al. report that nuclear pore complexes (NPCs) undergo limited movements that match the deformations of the nuclear envelope as tracked using a grid of bleached nuclear lamins. NPCs are therefore remarkably stable complexes, and are probably anchored to a protein network in the nuclear envelope.

Nucleoporins reassemble around post-mitotic chromatin

A conserved nuclear pore subcomplex was characterized and tracked by Belgareh et al., who found that the proteins were recruited during telophase in a rim pattern surrounding the chromosomes. A low level of staining was also apparent on the kinetochores throughout mitosis.

Nucleoli

Nucleolar re-formation after mitosis http://jcb.rupress.org/cgi/content/abstract/153/5/1097

Savino et al. follow the re-formation of nucleoli after mitosis. Prenucleolar bodies (PNB) form on the chromosome surface and nucleolar material flows along links between PNBs and towards a developing nucleolar organizer region (NOR). Eventually this leads to the fusion of nucleoli to form a single entity.

Processing complexes may help reassemble nucleoli http://jcb.rupress.org/cgi/content/abstract/150/3/433

Nucleolar reassembly during telophase is shown by Dundr et al. to require mitotically preserved processing complexes.

Speckles

A splicing factor has limited mobility http://jcb.rupress.org/cgi/content/abstract/150/1/41

Based on the limited mobility of a splicing factor, Kruhlak et al. determine that the factor undergoes frequent but transient interactions with relatively immobile nuclear binding sites, both when associated with speckles and when dispersed in the nucleoplasm. This a 3-D video that should be viewed using red/green 3-D glasses.

References

Connecting the nucleus to the cytoskeleton by SUN-KASH bridges across the nuclear envelope

Curr Opin Cell Biol. 2013 Feb;25(1):57-62. doi: 10.1016/j.ceb.2012.10.014. Epub 2012 Nov 10.

Tapley EC, Starr DA. Author information

Abstract

The nuclear-cytoskeleton connection influences many aspects of cellular architecture, including nuclear positioning, the stiffness of the global cytoskeleton, and mechanotransduction. Central to all of these processes is the assembly and function of conserved SUN-KASH bridges, or LINC complexes, that span the nuclear envelope. Recent studies provide details of the higher order assembly and targeting of SUN proteins to the inner nuclear membrane. Structural studies characterize SUN-KASH interactions that form the central link of the nuclear-envelope bridge. KASH proteins at the outer nuclear membrane link the nuclear envelope to the cytoskeleton where forces are generated to move nuclei. Significantly, SUN proteins were recently shown to contribute to the progression of laminopathies. Copyright © 2012 Elsevier Ltd. All rights reserved.

PMID 23149102


Samp1 is a component of TAN lines and is required for nuclear movement

J Cell Sci. 2012 Mar 1;125(Pt 5):1099-105. doi: 10.1242/jcs.087049. Epub 2012 Feb 20.

Borrego-Pinto J, Jegou T, Osorio DS, Auradé F, Gorjánácz M, Koch B, Mattaj IW, Gomes ER. Author information

Abstract

The position of the nucleus is regulated in different developmental stages and cellular events. During polarization, the nucleus moves away from the future leading edge and this movement is required for proper cell migration. Nuclear movement requires the LINC complex components nesprin-2G and SUN2, which form transmembrane actin-associated nuclear (TAN) lines at the nuclear envelope. Here we show that the nuclear envelope protein Samp1 (NET5) is involved in nuclear movement during fibroblast polarization and migration. Moreover, we demonstrate that Samp1 is a component of TAN lines that contain nesprin-2G and SUN2. Finally, Samp1 associates with SUN2 and lamin A/C, and the presence of Samp1 at the nuclear envelope requires lamin A/C. These results support a role for Samp1 in the association between the LINC complex and lamins during nuclear movement.

PMID 22349700

http://jcs.biologists.org/content/125/5/1099.long

Actin-based motility drives baculovirus transit to the nucleus and cell surface

J Cell Biol. 2010 Jul 26;190(2):187-95.

Ohkawa T, Volkman LE, Welch MD.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Comment in:

Nat Rev Mol Cell Biol. 2010 Sep;11(9):606. Nat Rev Microbiol. 2010 Sep;8(9):612. Abstract Most viruses move intracellularly to and from their sites of replication using microtubule-based mechanisms. In this study, we show that nucleocapsids of the baculovirus Autographa californica multiple nucleopolyhedrovirus undergo intracellular motility driven by actin polymerization. Motility requires the viral P78/83 capsid protein and the host Arp2/3 complex. Surprisingly, the virus directs two sequential and coordinated phases of actin-based motility. Immediately after cell entry, motility enables exploration of the cytoplasm and collision with the nuclear periphery, speeding nuclear entry and the initiation of viral gene expression. Nuclear entry itself requires transit through nuclear pore complexes. Later, after the onset of early gene expression, motility is required for accumulation of a subpopulation of nucleocapsids in the tips of actin-rich surface spikes. Temporal coordination of actin-based nuclear and surface translocation likely enables rapid transmission to neighboring cells during infection in insects and represents a distinctive evolutionary strategy for overcoming host defenses.

PMID: 20660627 http://www.ncbi.nlm.nih.gov/pubmed/20660627

http://jcb.rupress.org/content/190/2/187.long

http://jcb.rupress.org/content/suppl/2010/07/26/jcb.201001162.DC1


Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution

Biol Direct. 2010 Feb 4;5:7.


Cavalier-Smith T.

Department of Zoology, University of Oxford, South Parks Road, Oxford OX13PS, UK. tom.cavalier-smith@zoo.ox.ac.uk

Abstract BACKGROUND: The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis.

RESULTS: I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate.

CONCLUSION: Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.


"Recently De Duve [367] reappraised the evidence for eukaryotic origins in the light of modern molecular cell biology and now accepts that peroxisomes were early offshoots of the endomembrane system [3,11] and that theories that he and I once espoused of a separate symbiotic origin for them are entirely superfluous. According to the coevolutionary theory of the eukaryote cell, cytoskeleton, endomembranes, peroxisomes, cilia and genetic systems are part of a unified whole, within which food came first and sex was an afterthought [3]. The autogenous origin of all these structures was far more radical than the minor tinkering when the resulting phagotroph converted an engulfed but undigested proteobacterium into a mitochondrion - another afterthought [20]; ultrastructurally and functionally mitochondria are still easily recognisable as slightly modified negibacteria. Intracellular coevolution is strongly exemplified between the endomembrane system and cytoskeleton; and in the way that internalization of membrane-attached DNA revolutionised DNA segregation [70]; in how the origin of centromeres led to other eukaryotic chromosomal properties through mutation pressure [70]; in the way the origin of motor ATPases provided selective forces for nuclear origins; and the origins of coat proteins by duplications both diversified endomembranes into ER, Golgi, endosomes [4] and yielded NPCs and ciliary transport particles [374] necessary for the simultaneous origin of cilia from astral microtubules attached orthogonally to the cell surface by transitional fibres [4]."

PMID: 20132544 http://www.ncbi.nlm.nih.gov/pubmed/20132544


Lipid microdomains in cell nucleus

Mol Biol Cell. 2008 Dec;19(12):5289-95. Epub 2008 Oct 15.

Cascianelli G, Villani M, Tosti M, Marini F, Bartoccini E, Magni MV, Albi E.

Department of Clinical and Experimental Medicine, Physiopathology Section, University School of Medicine, University of Perugia, Policlinico Monteluce, 06100 Perugia, Italy.

Abstract It is known that nuclear lipids play a role in proliferation, differentiation, and apoptotic process. Cellular nuclei contain high levels of phosphatidylcholine and sphingomyelin, which are partially linked with cholesterol and proteins to form lipid-protein complexes. These lipids are also associated with transcription factors and newly synthesized RNA but, up to date, their organization is still unknown. The aim of the present work was to study if these specific lipid-protein interactions could be nuclear membrane microdomains and to evaluate their possible role. The results obtained demonstrate for the first time the existence of nuclear microdomains characterized by a specific lipid composition similar to that of intranuclear lipid-protein complexes previously described. Nuclear microdomain lipid composition changes during cell proliferation when the content of newly synthesized RNA increases. Because previous data show a correlation between nuclear lipids and transcription process, the role of nuclear microdomains in cellular functions is discussed.

PMID: 18923143


Spatial organization of active and inactive genes and noncoding DNA within chromosome territories

J Cell Biol. 2002 May 13;157(4):579-89. Epub 2002 May 6.

Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA.

Medical Research Council Human Genetics Unit, Edinburgh EH4 2XU, United Kingdom.

Abstract

The position of genes within the nucleus has been correlated with their transcriptional activity. The interchromosome domain model of nuclear organization suggests that genes preferentially locate at the surface of chromosome territories. Conversely, high resolution analysis of chromatin fibers suggests that chromosome territories do not present accessibility barriers to transcription machinery. To clarify the relationship between the organization of chromosome territories and gene expression, we have used fluorescence in situ hybridization to analyze the spatial organization of a contiguous approximately 1 Mb stretch of the Wilms' tumor, aniridia, genitourinary anomalies, mental retardation syndrome region of the human genome and the syntenic region in the mouse. These regions contain constitutively expressed genes, genes with tissue-restricted patterns of expression, and substantial regions of intergenic DNA. We find that there is a spatial organization within territories that is conserved between mouse and humans: certain sequences do preferentially locate at the periphery of the chromosome territories in both species. However, we do not detect genes necessarily at the periphery of chromosome territories or at the surface of subchromosomal domains. Intraterritory organization is not different among cell types that express different combinations of the genes under study. Our data demonstrate that transcription of both ubiquitous and tissue-restricted genes is not confined to the periphery of chromosome territories, suggesting that the basal transcription machinery and transcription factors can readily gain access to the chromosome interior.

PMID: 11994314 http://www.ncbi.nlm.nih.gov/pubmed/11994314

http://jcb.rupress.org/content/157/4/579.long


2011 NSW Cell and Developmental Biology Meeting

All current Cell Biology Students are welcome to attend this meeting!
Next Monday 21st of March 2011

NAB Auditorium at the Garvan Institute 384 Victoria Street, Darlinghurst (02) 9295 8100 Map starting at 12:30 pm

Plenary talks will be given by:

Prof Kai Simons (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany)

“Lipid rafts as a membrane organizing principle”

Prof Patrick Tam (Children’s Medical Research Institute, Westmead)

“Gene activity influencing the morphogenesis of the mouse embryonic foregut”

A/Prof Peter Noakes (Queensland Brain Institute, University of Queensland)

“Neuregulin potentiates agrin-induced acetylcholine receptor clustering via muscle specific kinase phosphorylation”