scholarly journals Nuclear Import of TFIIB Is Mediated by Kap114p, a Karyopherin with Multiple Cargo-binding Domains

2005 ◽  
Vol 16 (7) ◽  
pp. 3200-3210 ◽  
Author(s):  
Jennifer L. Hodges ◽  
Jennifer H. Leslie ◽  
Nima Mosammaparast ◽  
Yurong Guo ◽  
Jeffrey Shabanowitz ◽  
...  
Keyword(s):  
Nuclear Import ◽  
Binding Sites ◽  
Binding Domains ◽  
Transcription Factor Iib ◽  
General Transcription Factor ◽  
Proteomic Approach ◽  
Evolutionarily Conserved ◽  
Import And Export ◽  
Transport Factors

Nuclear import and export is mediated by an evolutionarily conserved family of soluble transport factors, the karyopherins (referred to as importins and exportins). The yeast karyopherin Kap114p has previously been shown to import histones H2A and H2B, Nap1p, and a component of the preinitiation complex (PIC), TBP. Using a proteomic approach, we have identified several potentially new cargoes for Kap114p. These cargoes include another PIC component, the general transcription factor IIB or Sua7p, which interacted directly with Kap114p. Consistent with its role as a Sua7p import factor, deletion of KAP114 led to specific mislocalization of Sua7p to the cytoplasm. An interaction between Sua7p and TBP was also detected in cytosol, raising the possibility that both Sua7p and TBP can be coimported by Kap114p. We have also shown that Kap114p possesses multiple overlapping binding sites for its partners, Sua7p, Nap1p, and H2A and H2B, as well as RanGTP and nucleoporins. In addition, we have assembled an in vitro complex containing Sua7p, Nap1p, and histones H2A and H2B, suggesting that this Kap may import several proteins simultaneously. The import of more than one cargo at a time would increase the efficiency of each import cycle and may allow the regulation of coimported cargoes.

scholarly journals The mechanism of inhibition of Ran-dependent nuclear transport by cellular ATP depletion

2002 ◽  
Vol 157 (6) ◽  
pp. 963-974 ◽  
Author(s):  
Eric D. Schwoebel ◽  
Thai H. Ho ◽  
Mary Shannon Moore
Keyword(s):  
Nuclear Import ◽  
Nuclear Transport ◽  
Intact Cell ◽  
Transport Processes ◽  
Atp Depletion ◽  
Transport Pathways ◽  
Atp Production ◽  
Import And Export

Rran-dependent nuclear transport requires a nuclear pool of RanGTP both for the assembly of export complexes and the disassembly of import complexes. Accordingly, in order for these processes to proceed, Ran-dependent nuclear import and export assays in vitro require the addition of GTP to produce RanGTP. Notably, no ATP requirement can be detected for these transport processes in vitro. But in vivo, when cells are depleted of ATP by the addition of sodium azide and 2-deoxyglucose to block ATP production by oxidative phosphorylation and glycolysis, respectively, Ran-dependent nuclear import and export are rapidly inhibited. This raised the question of whether there is an ATP requirement for these nuclear transport pathways in an intact cell that has remained undetected in vitro. Here we report that the free (but not total) GTP concentration rapidly drops to an undetectable level upon ATP depletion as does the availability of RanGTP. Our conclusion is that the inhibition of Ran-dependent nuclear transport observed upon ATP depletion in vivo results from a shortage of RanGTP rather than the inhibition of some ATP-dependent process.

scholarly journals Nup2p Dynamically Associates with the Distal Regions of the Yeast Nuclear Pore Complex

2001 ◽  
Vol 153 (7) ◽  
pp. 1465-1478 ◽  
Author(s):  
David J. Dilworth ◽  
Adisetyantari Suprapto ◽  
Julio C. Padovan ◽  
Brian T. Chait ◽  
Richard W. Wozniak ◽  
...  
Keyword(s):  
Nuclear Pore Complex ◽  
Stationary Phases ◽  
Nucleocytoplasmic Transport ◽  
The Other ◽  
Nuclear Pore ◽  
Cytoplasmic Face ◽  
Import And Export ◽  
Ran Gtp ◽  
Transport Factors

Nucleocytoplasmic transport is mediated by the interplay between soluble transport factors and nucleoporins resident within the nuclear pore complex (NPC). Understanding this process demands knowledge of components of both the soluble and stationary phases and the interface between them. Here, we provide evidence that Nup2p, previously considered to be a typical yeast nucleoporin that binds import- and export-bound karyopherins, dynamically associates with the NPC in a Ran-facilitated manner. When bound to the NPC, Nup2p associates with regions corresponding to the nuclear basket and cytoplasmic fibrils. On the nucleoplasmic face, where the Ran–GTP levels are predicted to be high, Nup2p binds to Nup60p. Deletion of NUP60 renders Nup2p nucleoplasmic and compromises Nup2p-mediated recycling of Kap60p/Srp1p. Depletion of Ran–GTP by metabolic poisoning, disruption of the Ran cycle, or in vitro by cell lysis, results in a shift of Nup2p from the nucleoplasm to the cytoplasmic face of the NPC. This mobility of Nup2p was also detected using heterokaryons where, unlike nucleoporins, Nup2p was observed to move from one nucleus to the other. Together, our data support a model in which Nup2p movement facilitates the transition between the import and export phases of nucleocytoplasmic transport.

scholarly journals Splicing factor SRSF1 expands the regulatory logic of microRNA expression

2020 ◽  
Author(s):  
Marija Dargyte ◽  
Julia Philipp ◽  
Christina D. Palka ◽  
Michael D. Stone ◽  
Jeremy R. Sanford
Keyword(s):  
Binding Sites ◽  
Regulatory Elements ◽  
Mrna Splicing ◽  
Splicing Factor ◽  
Stem Loop ◽  
Microrna Biogenesis ◽  
Evolutionarily Conserved ◽  
Rna Interaction

AbstractThe serine and arginine-rich splicing factor SRSF1 is an evolutionarily conserved, essential pre-mRNA splicing factor. Through a global protein-RNA interaction survey we discovered SRSF1 binding sites 25-50nt upstream from hundreds of pre-miRNAs. Using primary miRNA-10b as a model we demonstrate that SRSF1 directly regulates microRNA biogenesis both in vitro and in vivo. Selective 2’ hydroxyl acylation analyzed by primer extension (SHAPE) defined a structured RNA element located upstream of the precursor miRNA-10b stem loop. Our data support a model where SRSF1 promotes initial steps of microRNA biogenesis by relieving the repressive effects of cis-regulatory elements within the leader sequence.

scholarly journals Growth-regulated Hsp70 phosphorylation regulates stress responses and prion maintenance

2019 ◽  
Author(s):  
Chung-Hsuan Kao ◽  
Seung Ryu ◽  
Min J. Kim ◽  
Xuemei Wen ◽  
Oshadi Wimalarathne ◽  
...  
Keyword(s):  
Stress Responses ◽  
Normal Growth ◽  
Serine Phosphorylation ◽  
Metal Exposure ◽  
Active Growth ◽  
Binding Domains ◽  
Evolutionarily Conserved ◽  
Heat Shock Responses

AbstractMaintenance of protein homeostasis in eukaryotes during normal growth and stress conditions requires the functions of Hsp70 chaperones and associated co-chaperones. Here we investigate an evolutionarily-conserved serine phosphorylation that occurs at the site of communication between the nucleotide-binding and substrate-binding domains of Hsp70. Ser151 phosphorylation in yeast Hsp70 (Ssa1) is promoted by cyclin-dependent kinase (Cdk1) during normal growth and dramatically affects heat shock responses, a function conserved with Hsc70 S153 phosphorylation in human cells. Phospho-mimic forms of Ssa1 (S151D) also fail to relocalize in response to starvation conditions, do not associate in vivo with Hsp40 co-chaperones, Ydj1 and Sis1, and do not catalyze refolding of denatured proteins in vitro in cooperation with Ydj1 and Hsp104. S151 phosphorylation strongly promotes survival of heavy metal exposure and reduces Sup35-dependent [PSI+] prion activity, however, consistent with proposed roles for Ssa1 and Hsp104 in generating self-nucleating seeds of misfolded proteins. Taken together, these results suggest that Cdk1 downregulates Hsp70 function during periods of active growth, reducing propagation of aggregated proteins despite potential costs to overall chaperone efficiency.

scholarly journals Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site

2019 ◽  
Vol 116 (35) ◽  
pp. 17280-17289 ◽  
Author(s):  
Edmond R. Watson ◽  
Christy R. R. Grace ◽  
Wei Zhang ◽  
Darcie J. Miller ◽  
Iain F. Davidson ◽  
...  
Keyword(s):  
Binding Sites ◽  
Protein Quality ◽  
Ex Vivo ◽  
Anaphase Promoting Complex ◽  
Ubiquitin Chain ◽  
Binding Domains ◽  
C Terminus ◽  
Enzymatic Cascades ◽  
Multistep Process

Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub’s C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at “exosites.” However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.

scholarly journals NF-κB Is Transported into the Nucleus by Importin α3 and Importin α4

2005 ◽  
Vol 280 (16) ◽  
pp. 15942-15951 ◽  
Author(s):  
Riku Fagerlund ◽  
Leena Kinnunen ◽  
Matthias Köhler ◽  
Ilkka Julkunen ◽  
Krister Melén
Keyword(s):  
Nuclear Import ◽  
Binding Sites ◽  
Site Directed Mutagenesis ◽  
Nuclear Localization Signals ◽  
Inactive Form ◽  
Tnf Α ◽  
Importin Α ◽  
Close Relatives ◽  
Armadillo Repeats

NF-κB transcription factors are retained in the cytoplasm in an inactive form until they are activated and rapidly imported into the nucleus. We identified importin α3 and importin α4 as the main importin α isoforms mediating TNF-α-stimulated NF-κB p50/p65 heterodimer translocation into the nucleus. Importin α3 and α4 are close relatives in the human importin α family. We show that importin α3 isoform also mediates nuclear import of NF-κB p50 homodimer in nonstimulated cells. Importin α3 is shown to directly bind to previously characterized nuclear localization signals (NLSs) of NF-κB p50 and p65 proteins. Importin α molecules are known to have armadillo repeats that constitute the N-terminal and C-terminal NLS binding sites. We demonstrate by site-directed mutagenesis that NF-κB p50 binds to the N-terminal and p65 to the C-terminal NLS binding site of importin α3.In vitrocompetition experiments and analysis of cellular NF-κB suggest that NF-κB binds to importin α only when it is free of IκBα. The present study demonstrates that the nuclear import of NF-κB is a highly regulated process mediated by a subset of importin α molecules.

scholarly journals RIP-140 interacts with multiple nuclear receptors by means of two distinct sites.

1996 ◽  
Vol 16 (11) ◽  
pp. 6029-6036 ◽  
Author(s):  
F L'Horset ◽  
S Dauvois ◽  
D M Heery ◽  
V Cavaillès ◽  
M G Parker
Keyword(s):  
Nuclear Receptors ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Target Genes ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Vitro Binding ◽  
Mutant Receptors

We have characterized two distinct binding sites, called site 1 and site 2, in the nuclear protein RIP-140 which interact with the ligand binding domain of the estrogen receptor both in solution and when the receptor is bound to DNA. Both sites are capable of independently interacting with other nuclear receptors, including the thyroid hormone and retinoic acid receptors, but they are not identical since the interaction with retinoid X receptor is mediated primarily by site 1. The interaction is enhanced by agonists but not by antagonists, and the in vitro binding activities to a number of mutant receptors correlate with their abilities to stimulate transcription in vivo. When RIP-140 is fused to heterologous DNA binding domains, it is able to stimulate the transcription of reporter genes in both yeast and mammalian cells. Thus, RIP-140 is likely to function as a bridging protein between receptors and the basal transcription machinery and thereby stimulate the transcription of target genes.

EVALUATION OF TISSUE STEROID BINDING IN VITRO

1971 ◽  
Vol 68 (1_Suppl) ◽  
pp. S223-S246 ◽  
Author(s):  
C. R. Wira ◽  
H. Rochefort ◽  
E. E. Baulieu
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Experimental System ◽  
Specific Protein ◽  
Coupling Mechanism ◽  
Target Tissue ◽  
Protein Binding Sites ◽  
Definition Of ◽  
Hormone Specificity

ABSTRACT The definition of a RECEPTOR* in terms of a receptive site, an executive site and a coupling mechanism, is followed by a general consideration of four binding criteria, which include hormone specificity, tissue specificity, high affinity and saturation, essential for distinguishing between specific and nonspecific binding. Experimental approaches are proposed for choosing an experimental system (either organized or soluble) and detecting the presence of protein binding sites. Techniques are then presented for evaluating the specific protein binding sites (receptors) in terms of the four criteria. This is followed by a brief consideration of how receptors may be located in cells and characterized when extracted. Finally various examples of oestrogen, androgen, progestagen, glucocorticoid and mineralocorticoid binding to their respective target tissues are presented, to illustrate how researchers have identified specific corticoid and mineralocorticoid binding in their respective target tissue receptors.

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