scholarly journals A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

2012 ◽  
Vol 196 (6) ◽  
pp. 801-810 ◽  
Author(s):  
Kyle J. Roux ◽  
Dae In Kim ◽  
Manfred Raida ◽  
Brian Burke
Keyword(s):  
Fusion Protein ◽  
Mammalian Cells ◽  
Nuclear Lamina ◽  
Intermediate Filament Protein ◽  
Structural Element ◽  
Affinity Capture ◽  
Cellular Environment ◽  
A New Technique ◽  
Filament Protein

We have developed a new technique for proximity-dependent labeling of proteins in eukaryotic cells. Named BioID for proximity-dependent biotin identification, this approach is based on fusion of a promiscuous Escherichia coli biotin protein ligase to a targeting protein. BioID features proximity-dependent biotinylation of proteins that are near-neighbors of the fusion protein. Biotinylated proteins may be isolated by affinity capture and identified by mass spectrometry. We apply BioID to lamin-A (LaA), a well-characterized intermediate filament protein that is a constituent of the nuclear lamina, an important structural element of the nuclear envelope (NE). We identify multiple proteins that associate with and/or are proximate to LaA in vivo. The most abundant of these include known interactors of LaA that are localized to the NE, as well as a new NE-associated protein named SLAP75. Our results suggest BioID is a useful and generally applicable method to screen for both interacting and neighboring proteins in their native cellular environment.

scholarly journals Purification of desmin from adult mammalian skeletal muscle

1981 ◽  
Vol 195 (2) ◽  
pp. 345-356 ◽  
Author(s):  
J M O'Shea ◽  
R M Robson ◽  
M K Hartzer ◽  
T W Huiatt ◽  
W E Rathbun ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Average Diameter ◽  
Intermediate Filament Protein ◽  
Mammalian Skeletal Muscle ◽  
Cytoskeletal Function ◽  
10 Nm Filaments ◽  
And Function ◽  
Filament Protein

A method has been developed for preparation of purified desmin from mature mammalian (porcine) skeletal muscle. A crude desmin-containing fraction was prepared by modification of procedures used for isolation of smooth-muscle intermediate-filament protein [Small & Sobieszek (1977) J. Cell Sci. 23, 243-268]. The desmin was extracted in 1 M-acetic acid/20 mM-NaCl at 4 degrees C for 15h from the residue remaining after actomyosin extraction from washed myofibrils. Successive chromatography on hydroxyapatite and DEAE-Sepharose CL-6B in 6M-urea yielded desmin that was routinely more than 97% 55 000-dalton protein and that had no detectable actin contamination. Removal of urea by dialysis against 10mM-Tris/acetate (pH 8.5)/1 mM dithioerythritol and subsequent clarification at 134 000 g (rav. 5.9 cm) for 1 h results in a clear desmin solution. Dialysis of purified desmin against 100 mM-NaCl/1 mM-MgCl2/10 mM-imidazole/HCl, pH 7.0, at 2 degrees C resulted in the formation of synthetic desmin filaments have an average diameter of 9-11.5 nm. The present studies demonstrate that the relatively small amount of desmin in mature skeletal muscle can be isolated in sufficient quantity and purity to permit detailed studies of its properties and function. Although 10nm filaments have not been unequivocally demonstrated in mature muscle in vivo, that the purified skeletal-muscle desmin will form 10 nm filaments in vitro lends support to their possible existence and cytoskeletal function in mature skeletal-muscle cells.

scholarly journals The organization of engaged and quiescent translocons in the endoplasmic reticulum of mammalian cells

2004 ◽  
Vol 164 (7) ◽  
pp. 997-1007 ◽  
Author(s):  
Erik L. Snapp ◽  
Gretchen A. Reinhart ◽  
Brigitte A. Bogert ◽  
Jennifer Lippincott-Schwartz ◽  
Ramanujan S. Hegde
Keyword(s):  
Endoplasmic Reticulum ◽  
Mammalian Cells ◽  
Signal Recognition Particle ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Cellular Environment ◽  
Essential Components ◽  
Nascent Chain ◽  
Functional Components

Protein translocons of the mammalian endoplasmic reticulum are composed of numerous functional components whose organization during different stages of the transport cycle in vivo remains poorly understood. We have developed generally applicable methods based on fluorescence resonance energy transfer (FRET) to probe the relative proximities of endogenously expressed translocon components in cells. Examination of substrate-engaged translocons revealed oligomeric assemblies of the Sec61 complex that were associated to varying degrees with other essential components including the signal recognition particle receptor TRAM and the TRAP complex. Remarkably, these components not only remained assembled but also had a similar, yet distinguishable, organization both during and after nascent chain translocation. The persistence of preassembled and complete translocons between successive rounds of transport may facilitate highly efficient translocation in vivo despite temporal constraints imposed by ongoing translation and a crowded cellular environment.

scholarly journals Cytotoxic T-Lymphocyte Epitopes Fused to Anthrax Toxin Induce Protective Antiviral Immunity

1999 ◽  
Vol 67 (7) ◽  
pp. 3290-3296 ◽  
Author(s):  
Amy M. Doling ◽  
Jimmy D. Ballard ◽  
Hao Shen ◽  
Kaja Murali Krishna ◽  
Rafi Ahmed ◽  
...  
Keyword(s):  
Fusion Protein ◽  
T Lymphocyte ◽  
Mammalian Cells ◽  
Protective Antigen ◽  
Cytotoxic T Lymphocyte ◽  
Lethal Factor ◽  
Antiviral Immunity ◽  
Anthrax Toxin ◽  
Listeriolysin O

ABSTRACT We have investigated the use of the protective antigen (PA) and lethal factor (LF) components of anthrax toxin as a system for in vivo delivery of cytotoxic T-lymphocyte (CTL) epitopes. During intoxication, PA directs the translocation of LF into the cytoplasm of mammalian cells. Here we demonstrate that antiviral immunity can be induced in BALB/c mice immunized with PA plus a fusion protein containing the N-terminal 255 amino acids of LF (LFn) and an epitope from the nucleoprotein (NP) of lymphocytic choriomeningitis virus. We also demonstrate that BALB/c mice immunized with a single LFn fusion protein containing NP and listeriolysin O protein epitopes in tandem mount a CTL response against both pathogens. Furthermore, we show that NP-specific CTL are primed in both BALB/c and C57BL/6 mice when the mice are immunized with a single fusion containing two epitopes, one presented by Ld and one presented by Db. The data presented here demonstrate the versatility of the anthrax toxin delivery system and indicate that this system may be used as a general approach to vaccinate outbred populations against a variety of pathogens.

scholarly journals Cdk5 Regulates the Organization of Nestin and Its Association with p35

2003 ◽  
Vol 23 (14) ◽  
pp. 5090-5106 ◽  
Author(s):  
Cecilia M. Sahlgren ◽  
Andrey Mikhailov ◽  
Samuli Vaittinen ◽  
Hanna-Mari Pallari ◽  
Hannu Kalimo ◽  
...  
Keyword(s):  
Ectopic Expression ◽  
Dominant Negative ◽  
Myoblast Differentiation ◽  
Intermediate Filament Protein ◽  
Nestin Expression ◽  
Specific Expression ◽  
Elevated Expression ◽  
Myoblast Cell ◽  
Filament Protein

ABSTRACT The intermediate filament protein nestin is characterized by its specific expression during the development of neuronal and myogenic tissues. We identify nestin as a novel in vivo target for cdk5 and p35 kinase, a critical signaling determinant in development. Two cdk5-specific phosphorylation sites on nestin, Thr-1495 and Thr-316, were established, the latter of which was used as a marker for cdk5-specific phosphorylation in vivo. Ectopic expression of cdk5 and p35 in central nervous system progenitor cells and in myogenic precursor cells induced elevated phosphorylation and reorganization of nestin. The kinetics of nestin expression corresponded to elevated expression and activation of cdk5 during differentiation of myoblast cell cultures and during regeneration of skeletal muscle. In the myoblasts, a disassembly-linked phosphorylation of Thr-316 indicated active phosphorylation of nestin by cdk5. Moreover, cdk5 occurred in physical association with nestin. Inhibition of cdk5 activity—either by transfection with dominant-negative cdk5 or by using a specific cdk5 inhibitor—blocked myoblast differentiation and phosphorylation of nestin at Thr-316, and this inhibition markedly disturbed the organization of nestin. Interestingly, the interaction between p35, the cdk5 activator, and nestin appeared to be regulated by cdk5. In differentiating myoblasts, p35 was not complexed with nestin phosphorylated at Thr-316, and inhibition of cdk5 activity during differentiation induced a marked association of p35 with nestin. These results demonstrate that there is a continuous turnover of cdk5 and p35 activity on a scaffold formed by nestin. This association is likely to affect the organization and operation of both cdk5 and nestin during development.

scholarly journals Vimentin protects cells against nuclear rupture and DNA damage during migration

2019 ◽  
Vol 218 (12) ◽  
pp. 4079-4092 ◽  
Author(s):  
Alison E. Patteson ◽  
Amir Vahabikashi ◽  
Katarzyna Pogoda ◽  
Stephen A. Adam ◽  
Kalpana Mandal ◽  
...  
Keyword(s):  
Dna Damage ◽  
Mammalian Cells ◽  
Nuclear Shape ◽  
Null Mouse ◽  
Intermediate Filament Protein ◽  
Cell Periphery ◽  
Damage Repair ◽  
Repair Mechanisms ◽  
Filament Protein ◽  
Nuclear Rupture

Mammalian cells frequently migrate through tight spaces during normal embryogenesis, wound healing, diapedesis, or in pathological situations such as metastasis. Nuclear size and shape are important factors in regulating the mechanical properties of cells during their migration through such tight spaces. At the onset of migratory behavior, cells often initiate the expression of vimentin, an intermediate filament protein that polymerizes into networks extending from a juxtanuclear cage to the cell periphery. However, the role of vimentin intermediate filaments (VIFs) in regulating nuclear shape and mechanics remains unknown. Here, we use wild-type and vimentin-null mouse embryonic fibroblasts to show that VIFs regulate nuclear shape and perinuclear stiffness, cell motility in 3D, and the ability of cells to resist large deformations. These changes increase nuclear rupture and activation of DNA damage repair mechanisms, which are rescued by exogenous reexpression of vimentin. Our findings show that VIFs provide mechanical support to protect the nucleus and genome during migration.

Prolonged in-vivo half-life of factor VIIa by fusion to albumin

2008 ◽  
Vol 99 (04) ◽  
pp. 659-667 ◽  
Author(s):  
Thomas Weimer ◽  
Wilfried Wormsbächer ◽  
Ulrich Kronthaler ◽  
Wiegand Lang ◽  
Uwe Liebing ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Half Life ◽  
Mammalian Cells ◽  
Factor Viia ◽  
Therapeutic Option ◽  
Human Albumin ◽  
Pharmacokinetic Studies ◽  
Wild Type

SummaryFor the treatment of haemophilia patients with inhibitors, recombinant factor VIIa (rFVIIa) is available as a therapeutic option to control bleeding episodes with a good balance of safety and efficacy. However, the short in-vivo half-life of approximately 2.5 hours makes multiple injections necessary, which is inconvenient for both physicians and patients. Here we describe the generation of a recombinant FVIIa molecule with an extended half-life based on genetic fusion to human albumin. The recombinant FVII albumin fusion protein (rVII-FP) was expressed in mammalian cells and upon activation displayed a FVII activity close to that of wild type FVIIa. Pharmacokinetic studies in rats demonstrated that the half-life of the activated recombinant FVII albumin fusion protein (rVIIa-FP) was extended six- to sevenfold compared with wild type rFVIIa. The in-vitro and in-vivo efficacy was evaluated and was found to be comparable to a commercially available rFVIIa (NovoSeven®). The results of this study demonstrate that it is feasible to develop a half-life extended FVIIa molecule with haemostatic properties very similar to the wild-type factor.

scholarly journals Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells

2019 ◽  
Author(s):  
Koos Rooijers ◽  
Corina M. Markodimitraki ◽  
Franka J. Rang ◽  
Sandra S. de Vries ◽  
Alex Chialastri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
Single Cells ◽  
Critical Role ◽  
Nuclear Lamina ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Expression Variability ◽  
The Impact

AbstractThe epigenome plays a critical role in regulating gene expression in mammalian cells. However, understanding how cell-to-cell heterogeneity in the epigenome influences gene expression variability remains a major challenge. Here we report a novel method for simultaneous single-cell quantification of protein-DNA contacts with DamID and transcriptomics (scDamID&T). This method enables quantifying the impact of protein-DNA contacts on gene expression from the same cell. By profiling lamina-associated domains (LADs) in human cells, we reveal different dependencies between genome-nuclear lamina (NL) association and gene expression in single cells. In addition, we introduce the E. coli methyltransferase, Dam, as an in vivo marker of chromatin accessibility in single cells and show that scDamID&T can be utilized as a general technology to identify cell types in silico while simultaneously determining the underlying gene-regulatory landscape. With this strategy the effect of chromatin states, transcription factor binding, and genome organization on the acquisition of cell-type specific transcriptional programs can be quantified.

scholarly journals Artemisinins target the intermediate filament protein vimentin for human cytomegalovirus inhibition

2020 ◽  
Vol 295 (44) ◽  
pp. 15013-15028 ◽  
Author(s):  
Sujayita Roy ◽  
Arun Kapoor ◽  
Fei Zhu ◽  
Rupkatha Mukhopadhyay ◽  
Ayan Kumar Ghosh ◽  
...  
Keyword(s):  
Intermediate Filament ◽  
Hcmv Infection ◽  
Intermediate Filament Protein ◽  
Biological Assays ◽  
Human Foreskin Fibroblasts ◽  
Hcmv Replication ◽  
Human Cmv ◽  
Filament Protein

The antimalarial agents artemisinins inhibit cytomegalovirus (CMV) in vitro and in vivo, but their target(s) has been elusive. Using a biotin-labeled artemisinin, we identified the intermediate filament protein vimentin as an artemisinin target, validated by detailed biochemical and biological assays. We provide insights into the dynamic and unique modulation of vimentin, depending on the stage of human CMV (HCMV) replication. In vitro, HCMV entry and viral progeny are reduced in vimentin-deficient fibroblasts, compared with control cells. Similarly, mouse CMV (MCMV) replication in vimentin knockout mice is significantly reduced compared with controls in vivo, confirming the requirement of vimentin for establishment of infection. Early after HCMV infection of human foreskin fibroblasts vimentin level is stable, but as infection proceeds, vimentin is destabilized, concurrent with its phosphorylation and virus-induced calpain activity. Intriguingly, in vimentin-overexpressing cells, HCMV infection is reduced compared with control cells. Binding of artesunate, an artemisinin monomer, to vimentin prevents virus-induced vimentin degradation, decreasing vimentin phosphorylation at Ser-55 and Ser-83 and resisting calpain digestion. In vimentin-deficient fibroblasts, the anti-HCMV activity of artesunate is reduced compared with controls. In summary, an intact and stable vimentin network is important for the initiation of HCMV replication but hinders its completion. Artesunate binding to vimentin early during infection stabilizes it and antagonizes subsequent HCMV-mediated vimentin destabilization, thus suppressing HCMV replication. Our target discovery should enable the identification of vimentin-binding sites and compound moieties for binding.

scholarly journals Viscoelastic properties of vimentin compared with other filamentous biopolymer networks.

1991 ◽  
Vol 113 (1) ◽  
pp. 155-160 ◽  
Author(s):  
P A Janmey ◽  
U Euteneuer ◽  
P Traub ◽  
M Schliwa
Keyword(s):  
Viscoelastic Properties ◽  
Intermediate Filament Protein ◽  
Linear Polymers ◽  
Cell Integrity ◽  
Interphase Cell ◽  
Shear Moduli ◽  
Lower Shear ◽  
Cytoplasmic Filaments ◽  
Filament Protein

The cytoplasm of vertebrate cells contains three distinct filamentous biopolymers, the microtubules, microfilaments, and intermediate filaments. The basic structural elements of these three filaments are linear polymers of the proteins tubulin, actin, and vimentin or another related intermediate filament protein, respectively. The viscoelastic properties of cytoplasmic filaments are likely to be relevant to their biologic function, because their extreme length and rodlike structure dominate the rheologic behavior of cytoplasm, and changes in their structure may cause gel-sol transitions observed when cells are activated or begin to move. This paper describes parallel measurements of the viscoelasticity of tubulin, actin, and vimentin polymers. The rheologic differences among the three types of cytoplasmic polymers suggest possible specialized roles for the different classes of filaments in vivo. Actin forms networks of highest rigidity that fluidize at high strains, consistent with a role in cell motility in which stable protrusions can deform rapidly in response to controlled filament rupture. Vimentin networks, which have not previously been studied by rheologic methods, exhibit some unusual viscoelastic properties not shared by actin or tubulin. They are less rigid (have lower shear moduli) at low strain but harden at high strains and resist breakage, suggesting they maintain cell integrity. The differences between F-actin and vimentin are optimal for the formation of a composite material with a range of properties that cannot be achieved by either polymer alone. Microtubules are unlikely to contribute significantly to interphase cell rheology alone, but may help stabilize the other networks.

Human α-synemin interacts directly with vinculin and metavinculin

2008 ◽  
Vol 409 (3) ◽  
pp. 657-667 ◽  
Author(s):  
Ning Sun ◽  
David R. Critchley ◽  
Denise Paulin ◽  
Zhenlin Li ◽  
Richard M. Robson
Keyword(s):  
Mammalian Cells ◽  
Striated Muscle ◽  
Splice Variants ◽  
Focal Adhesions ◽  
Muscle Cells ◽  
Intermediate Filament Protein ◽  
Tail Domain ◽  
Protein Protein Interaction

Synemin is a very large, unique member of the IF (intermediate filament) protein superfamily. Association of synemin with the major IF proteins, desmin and/or vimentin, within muscle cells forms heteropolymeric IFs. We have previously identified interactions of avian synemin with α-actinin and vinculin. Avian synemin, however, is expressed as only one form, whereas human synemin is expressed as two major splice variants, namely α- and β-synemins. The larger α-synemin contains an additional 312-amino-acid insert (termed SNTIII) located near the end of the long C-terminal tail domain. Whether α- and β-synemins have different cellular functions is unclear. In the present study we show, by in vitro protein–protein interaction assays, that SNTIII interacts directly with both vinculin and metavinculin. Furthermore, SNTIII interacts with vinculin in vivo, and this association is promoted by PtdIns(4,5)P2. SNTIII also specifically co-localizes with vinculin within focal adhesions when transiently expressed in mammalian cells. In contrast, other regions of synemin show distinct localization patterns in comparison with those of SNTIII, without labelling focal adhesions. Our results indicate that α-synemin, but not β-synemin, interacts with both vinculin and metavinculin, thereby linking the heteropolymeric IFs to adhesion-type junctions, such as the costameres located within human striated muscle cells.

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