ABSTRACT
CRISPR drives prokaryotic adaptation to invasive nucleic acids such as phages and plasmids, using an RNA-mediated interference mechanism. Interference in type I CRISPR-Cas systems requires a targeting Cascade complex and a degradation machine, Cas3, which contains both nuclease and helicase activities. Here we report the crystal structures of Thermobifida fusca Cas3 bound to single-stranded (ss) DNA substrate and show that it is an obligate 3'-to-5' ssDNase that preferentially accepts substrate directly from the helicase moiety. Conserved residues in the HD-type nuclease coordinate two irons for ssDNA cleavage. We demonstrate ATP coordination and conformational flexibility of the SF2-type helicase domain. Cas3 is specifically guided toward Cascade-bound target DNA by a PAM sequence, through physical interactions with both the nontarget substrate strand and the CasA protein. The sequence of recognition events ensures well-controlled DNA targeting and degradation of foreign DNA by Cascade and Cas3.
Subject(s)
Actinomycetales/enzymology , CRISPR-Associated Proteins/metabolism , DNA Helicases/metabolism , Actinomycetales/chemistry , Actinomycetales/metabolism , Adenosine Triphosphate/metabolism , Base Sequence , CRISPR-Associated Proteins/chemistry , Crystallography, X-Ray , DNA Helicases/chemistry , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/metabolism , Models, Molecular , Molecular Sequence Data , Protein ConformationABSTRACT
The conserved transcriptional regulator heat shock factor 1 (Hsf1) is a key sensor of proteotoxic and other stress in the eukaryotic cytosol. We surveyed Hsf1 activity in a genome-wide loss-of-function library in Saccaromyces cerevisiae as well as ~78,000 double mutants and found Hsf1 activity to be modulated by highly diverse stresses. These included disruption of a ribosome-bound complex we named the Ribosome Quality Control Complex (RQC) comprising the Ltn1 E3 ubiquitin ligase, two highly conserved but poorly characterized proteins (Tae2 and Rqc1), and Cdc48 and its cofactors. Electron microscopy and biochemical analyses revealed that the RQC forms a stable complex with 60S ribosomal subunits containing stalled polypeptides and triggers their degradation. A negative feedback loop regulates the RQC, and Hsf1 senses an RQC-mediated translation-stress signal distinctly from other stresses. Our work reveals the range of stresses Hsf1 monitors and elucidates a conserved cotranslational protein quality control mechanism.
Subject(s)
Multiprotein Complexes/metabolism , Protein Biosynthesis , Ribosomes/metabolism , Saccharomyces cerevisiae/metabolism , Adenosine Triphosphatases/metabolism , Cell Cycle Proteins/metabolism , DNA-Binding Proteins/genetics , Heat-Shock Proteins/genetics , Peptides/metabolism , Proteasome Endopeptidase Complex/metabolism , RNA-Binding Proteins , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Stress, Physiological , Transcription Factors/genetics , Ubiquitin-Protein Ligases/metabolism , Valosin Containing ProteinABSTRACT
Natural products that elicit discomfort or pain represent invaluable tools for probing molecular mechanisms underlying pain sensation. Plant-derived irritants have predominated in this regard, but animal venoms have also evolved to avert predators by targeting neurons and receptors whose activation produces noxious sensations. As such, venoms provide a rich and varied source of small molecule and protein pharmacophores that can be exploited to characterize and manipulate key components of the pain-signalling pathway. With this in mind, here we perform an unbiased in vitro screen to identify snake venoms capable of activating somatosensory neurons. Venom from the Texas coral snake (Micrurus tener tener), whose bite produces intense and unremitting pain, excites a large cohort of sensory neurons. The purified active species (MitTx) consists of a heteromeric complex between Kunitz- and phospholipase-A2-like proteins that together function as a potent, persistent and selective agonist for acid-sensing ion channels (ASICs), showing equal or greater efficacy compared with acidic pH. MitTx is highly selective for the ASIC1 subtype at neutral pH; under more acidic conditions (pH < 6.5), MitTx massively potentiates (>100-fold) proton-evoked activation of ASIC2a channels. These observations raise the possibility that ASIC channels function as coincidence detectors for extracellular protons and other, as yet unidentified, endogenous factors. Purified MitTx elicits robust pain-related behaviour in mice by activation of ASIC1 channels on capsaicin-sensitive nerve fibres. These findings reveal a mechanism whereby snake venoms produce pain, and highlight an unexpected contribution of ASIC1 channels to nociception.
Subject(s)
Elapid Venoms/chemistry , Elapid Venoms/pharmacology , Elapidae , Nerve Tissue Proteins/metabolism , Pain/chemically induced , Protein Multimerization , Sodium Channels/metabolism , Acid Sensing Ion Channels , Amino Acid Sequence , Animals , Capsaicin/pharmacology , Cells, Cultured , Hindlimb/drug effects , Hindlimb/physiopathology , Humans , Hydrogen-Ion Concentration , Ion Channel Gating/drug effects , Male , Mice , Mice, Knockout , Molecular Sequence Data , Nerve Tissue Proteins/agonists , Nerve Tissue Proteins/deficiency , Nerve Tissue Proteins/genetics , Nociception/drug effects , Nociception/physiology , Oocytes , Pain/metabolism , Pain/physiopathology , Protein Structure, Quaternary , Protons , Rats , Sensory Receptor Cells/drug effects , Sensory Receptor Cells/metabolism , Sodium Channel Agonists , Sodium Channels/deficiency , Sodium Channels/genetics , TRPV Cation Channels/metabolism , Xenopus laevisABSTRACT
Uridine insertion/deletion RNA editing in kinetoplastid mitochondria corrects encoded frameshifts in mRNAs. The genetic information for editing resides in small guide RNAs (gRNAs), which form anchor duplexes just downstream of an editing site and mediate editing within a single editing "block." Many mRNAs require multiple gRNAs; the observed overall 3' to 5' polarity of editing is determined by the formation of upstream mRNA anchors by downstream editing. Hel61, a mitochondrial DEAD-box protein, was previously shown to be involved in RNA editing, but the functional role was not clear. Here we report that down-regulation of Hel61 [renamed REH1 (RNA editing helicase 1)] expression in Trypanosoma brucei selectively affects editing mediated by two or more overlapping gRNAs but has no effect on editing within a single block. Down-regulation produces an increased abundance of the gRNA/edited mRNA duplex for the first editing block of the A6 mRNA. Recombinant REH1 has an ATP-dependent double strand RNA unwinding activity in vitro with a model gRNA-mRNA duplex. These data indicate that REH1 is involved in gRNA displacement either directly by unwinding the gRNA/edited mRNA duplex or indirectly, to allow the 5' adjacent upstream gRNA to form an anchor duplex with the edited mRNA to initiate another block of editing. Purified tagged REH1 is associated with the RNA editing core complex by RNA linkers and a colocalization of REH1, REL1, and two kinetoplast ribosomal proteins with the kinetoplast DNA was observed by immunofluorescence, suggesting that editing, transcription, and translation may be functionally linked.
Subject(s)
INDEL Mutation/genetics , Protozoan Proteins/metabolism , RNA Editing/genetics , RNA Helicases/metabolism , RNA, Guide, Kinetoplastida/metabolism , Trypanosoma brucei brucei/enzymology , Uridine/genetics , Adenosine Triphosphatases/metabolism , Carrier Proteins/metabolism , Down-Regulation/genetics , Intracellular Space/metabolism , Mitochondria/metabolism , Protein Transport , RNA Interference , RNA, Double-Stranded/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Protozoan/metabolism , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Ribosomal Proteins/metabolism , Trypanosoma brucei brucei/geneticsABSTRACT
Toxins have evolved to target regions of membrane ion channels that underlie ligand binding, gating, or ion permeation, and have thus served as invaluable tools for probing channel structure and function. Here, we describe a peptide toxin from the Earth Tiger tarantula that selectively and irreversibly activates the capsaicin- and heat-sensitive channel, TRPV1. This high-avidity interaction derives from a unique tandem repeat structure of the toxin that endows it with an antibody-like bivalency. The "double-knot" toxin traps TRPV1 in the open state by interacting with residues in the presumptive pore-forming region of the channel, highlighting the importance of conformational changes in the outer pore region of TRP channels during activation.
Subject(s)
Spider Venoms/metabolism , TRPV Cation Channels/metabolism , Xenopus Proteins/metabolism , Amino Acid Sequence , Animals , Cell Line , Cells, Cultured , Electrophysiological Phenomena , Humans , Models, Molecular , Molecular Sequence Data , Neurons/metabolism , Oocytes/metabolism , Rats , Spider Venoms/chemistry , TRPV Cation Channels/chemistry , Trigeminal Ganglion/cytology , Trigeminal Ganglion/metabolism , Xenopus Proteins/chemistryABSTRACT
U-insertion/deletion RNA editing of mitochondrial mRNAs in trypanosome mitochondria is mediated by a core complex (RECC) containing around 16-20 proteins which is linked to several other multiprotein complexes by RNA. There are two known subcomplexes in the RECC: the REL1 subcomplex which contains the REL1 RNA ligase, the MP63 zinc finger-containing protein and the REX2 U-specific 3'-5' exonuclease; and the REL2 subcomplex which contains the REL2 RNA ligase, the RET2 3' TUTase and the MP81 zinc finger-containing protein. In this study we have affinity isolated recombinant TAP-tagged Leishmania major RET2 and Leishmania tarentolae MP63, REL1 and REL2 proteins after expression in baculovirus-infected insect cells. Recombinant MP63 protein was found to stimulate several in vitro activities of recombinant REL1; these activities include autoadenylation, bridged ligation and even pre-cleaved gRNA-mediated U-insertion editing with RET2 which is in the REL2 subcomplex. There was no effect of recombinant MP63 on similar REL2 ligation activities. The specificity for REL1 is consistent with MP63 being a component of the REL1 subcomplex. These results suggest that in vivo the interaction of MP63 with REL1 may play a role in regulating the overall activity of RNA editing.
Subject(s)
Carbon-Oxygen Ligases/metabolism , Leishmania/metabolism , Mitochondria/metabolism , Protozoan Proteins/metabolism , RNA Editing , RNA-Binding Proteins/metabolism , Uridine/metabolism , Animals , Baculoviridae , Genetic Vectors , Leishmania/enzymology , Mitochondria/enzymology , Models, Biological , Models, Chemical , Protein Interaction Mapping , Protein Structure, Quaternary , Protozoan Proteins/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Zinc FingersABSTRACT
Native states of proteins are flexible, populating more than just the unique native conformation. The energetics and dynamics resulting from this conformational ensemble are inherently linked to protein function and regulation. Proteolytic susceptibility is one feature determined by this conformational energy landscape. As an attempt to investigate energetics of proteins on a proteomic scale, we challenged the Escherichia coli proteome with extensive proteolysis and determined which proteins, if any, have optimized their energy landscape for resistance to proteolysis. To our surprise, multiple soluble proteins survived the challenge. Maltose binding protein, a survivor from thermolysin digestion, was characterized by in vitro biophysical studies to identify the physical origin of proteolytic resistance. This experimental characterization shows that kinetic stability is responsible for the unusual resistance in maltose binding protein. The biochemical functions of the identified survivors suggest that many of these proteins may have evolved extreme proteolytic resistance because of their critical roles under stressed conditions. Our results suggest that under functional selection proteins can evolve extreme proteolysis resistance by modulating their conformational energy landscapes without the need to invent new folds, and that proteins can be profiled on a proteomic scale according to their energetic properties by using proteolysis as a structural probe.
Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Protein Conformation , Proteome/analysis , Carrier Proteins/chemistry , Carrier Proteins/metabolism , Hydrolysis , Maltose-Binding Proteins , Models, Molecular , Molecular Sequence Data , Thermodynamics , Thermolysin/metabolismABSTRACT
Bites and stings from venomous creatures can produce pain and inflammation as part of their defensive strategy to ward off predators or competitors. Molecules accounting for lethal effects of venoms have been extensively characterized, but less is known about the mechanisms by which they produce pain. Venoms from spiders, snakes, cone snails or scorpions contain a pharmacopoeia of peptide toxins that block receptor or channel activation as a means of producing shock, paralysis or death. We examined whether these venoms also contain toxins that activate (rather than inhibit) excitatory channels on somatosensory neurons to produce a noxious sensation in mammals. Here we show that venom from a tarantula that is native to the West Indies contains three inhibitor cysteine knot (ICK) peptides that target the capsaicin receptor (TRPV1), an excitatory channel expressed by sensory neurons of the pain pathway. In contrast with the predominant role of ICK toxins as channel inhibitors, these previously unknown 'vanillotoxins' function as TRPV1 agonists, providing new tools for understanding mechanisms of TRP channel gating. Some vanillotoxins also inhibit voltage-gated potassium channels, supporting potential similarities between TRP and voltage-gated channel structures. TRP channels can now be included among the targets of peptide toxins, showing that animals, like plants (for example, chilli peppers), avert predators by activating TRP channels on sensory nerve fibres to elicit pain and inflammation.
Subject(s)
Ion Channel Gating/drug effects , Pain/physiopathology , Spider Venoms/pharmacology , Spiders/chemistry , TRPV Cation Channels/agonists , TRPV Cation Channels/metabolism , Animals , Cell Line , Humans , Inflammation/chemically induced , Inflammation/metabolism , Inflammation/physiopathology , Mice , Neurons, Afferent/drug effects , Neurons, Afferent/metabolism , Pain/chemically induced , Pain/metabolism , Patch-Clamp Techniques , Rats , Spider Venoms/chemistry , Spiders/physiology , Substrate SpecificityABSTRACT
Uridine (U)-insertion/deletion RNA editing in trypanosome mitochondria involves an initial cleavage of the preedited mRNA at specific sites determined by the annealing of partially complementary guide RNAs. An involvement of two RNase III-containing core editing complex (L-complex) proteins, MP90 (KREPB1) and MP61 (KREPB3) in, respectively, U-deletion and U-insertion editing, has been suggested, but these putative enzymes have not been characterized or expressed in active form. Recombinant MP90 proteins from Trypanosoma brucei and Leishmania major were expressed in insect cells and cytosol of Leishmania tarentolae, respectively. These proteins were active in specifically cleaving a model U-deletion site and not a U-insertion site. Deletion or mutation of the RNase III motif abolished this activity. Full-round guide RNA (gRNA)-mediated in vitro U-deletion editing was reconstituted by a mixture of recombinant MP90 and recombinant RNA editing exonuclease I from L. major, and recombinant RNA editing RNA ligase 1 from L. tarentolae. MP90 is designated REN1, for RNA-editing nuclease 1.
Subject(s)
Protozoan Proteins/metabolism , RNA Editing , RNA-Binding Proteins/metabolism , RNA/metabolism , Recombinant Proteins/metabolism , Uridine/metabolism , Amino Acid Sequence , Animals , Base Sequence , Eosinophil Cationic Protein/metabolism , Gene Expression Regulation , Leishmania/genetics , Leishmania/metabolism , Mitochondria/genetics , Mitochondria/metabolism , Molecular Sequence Data , Protozoan Proteins/genetics , RNA/genetics , RNA Interference , RNA-Binding Proteins/genetics , Recombinant Proteins/genetics , Trypanosoma brucei brucei/genetics , Trypanosoma brucei brucei/metabolismABSTRACT
Condensins are essential protein complexes critical for mitotic chromosome organization. Little is known about the function of condensins during interphase, particularly in mammalian cells. Here we report the interphase-specific interaction between condensin I and the DNA nick-sensor poly(ADP-ribose) polymerase 1 (PARP-1). We show that the association between condensin I, PARP-1, and the base excision repair (BER) factor XRCC1 increases dramatically upon single-strand break damage (SSB) induction. Damage-specific association of condensin I with the BER factors flap endonuclease 1 (FEN-1) and DNA polymerase delta/epsilon was also observed, suggesting that condensin I is recruited to interact with BER factors at damage sites. Consistent with this, DNA damage rapidly stimulates the chromatin association of PARP-1, condensin I, and XRCC1. Furthermore, depletion of condensin in vivo compromises SSB but not double-strand break (DSB) repair. Our results identify a SSB-specific response of condensin I through PARP-1 and demonstrate a role for condensin in SSB repair.
Subject(s)
Adenosine Triphosphatases/physiology , DNA Damage , DNA Repair , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/physiology , Multiprotein Complexes/physiology , Poly(ADP-ribose) Polymerases/genetics , Adenosine Triphosphatases/metabolism , Animals , Animals, Genetically Modified , Carrier Proteins , Cell Cycle Proteins , Cell Line , Chickens/genetics , Chromatin , Chromosomal Proteins, Non-Histone , DNA, Single-Stranded , HeLa Cells , Humans , Interphase , Mass Spectrometry , Mice/genetics , Mice, Knockout , Models, Biological , Multiprotein Complexes/metabolism , Nuclear Proteins , Poly(ADP-ribose) Polymerases/metabolism , Poly(ADP-ribose) Polymerases/physiology , Transfection , X-ray Repair Cross Complementing Protein 1 , Xenopus ProteinsABSTRACT
Uridine insertion/deletion RNA editing in trypanosomatid mitochondria is a posttranscriptional RNA modification phenomenon required for translation of mitochondrial mRNAs. This process involves guide RNA-mediated cleavage at a specific site, insertion or deletion of Us from the 3' end of the 5' mRNA fragment, and ligation of the two mRNA fragments. The Leishmania major RNA ligase-containing complex protein 2 expressed in insect cells has a 3'-5' exoribonuclease activity and was therefore renamed RNA editing exonuclease 1 (REX1). Recombinant REX1 specifically trims 3' overhanging Us and stops at a duplex region. Evidence is presented that REX1 is responsible for deletion of the 3' overhanging Us from the bridged mRNA 5' cleavage fragment and that RNA editing ligase 1 is responsible for the ligation of the two mRNA cleavage fragments in U-deletion editing. The evidence involves both in vivo down-regulation of REX1 expression in Trypanosoma brucei by RNA interference and the reconstitution of precleaved U-deletion in vitro editing with only two recombinant enzymes: recombinant REX1 and recombinant RNA editing ligase 1.
Subject(s)
Carbon-Oxygen Ligases/physiology , Mitochondrial Proteins/physiology , RNA Editing , Trypanosoma brucei brucei/genetics , Uridine/metabolism , Animals , Recombinant Proteins/pharmacologyABSTRACT
Smad proteins are critical intracellular mediators of the transforming growth factor-beta, bone morphogenic proteins (BMPs), and activin signaling. Upon ligand binding, the receptor-associated R-Smads are phosphorylated by the active type I receptor serine/threonine kinases. The phosphorylated R-Smads then form heteromeric complexes with Smad4, translocate into the nucleus, and interact with various transcription factors to regulate the expression of downstream genes. Interaction of Smad proteins with cellular partners in the cytoplasm and nucleus is a critical mechanism by which the activities and expression of the Smad proteins are modulated. Here we report a novel step of regulation of the R-Smad function at the inner nuclear membrane through a physical interaction between the integral inner nuclear membrane protein MAN1 and R-Smads. MAN1, through the RNA recognition motif, associates with R-Smads but not Smad4 at the inner nuclear membrane in a ligand-independent manner. Overexpression of MAN1 results in inhibition of R-Smad phosphorylation, heterodimerization with Smad4 and nuclear translocation, and repression of transcriptional activation of the TGFbeta, BMP2, and activin-responsive promoters. This repression of TGFbeta, BMP2, and activin signaling is dependent on the MAN1-Smad interaction because a point mutation that disrupts this interaction abolishes the transcriptional repression by MAN1. Thus, MAN1 represents a new class of R-Smad regulators and defines a previously unrecognized regulatory step at the nuclear periphery.
Subject(s)
DNA-Binding Proteins/metabolism , Membrane Proteins/metabolism , Nuclear Proteins/metabolism , Trans-Activators/metabolism , Transforming Growth Factor beta/metabolism , Bone Morphogenetic Protein 2 , Bone Morphogenetic Proteins/metabolism , Humans , Membrane Proteins/genetics , Nuclear Envelope/metabolism , Nuclear Proteins/genetics , Phosphorylation , Promoter Regions, Genetic , Signal Transduction , Smad ProteinsABSTRACT
The X gene of hepatitis B virus (HBV) is one of the major factors in HBV-induced hepatocarcinogenesis and is essential for the establishment of productive HBV replication in vivo. Recent studies have shown that the X gene product targets mitochondria and induces calcium flux, thereby activating Ca(+)-dependent signal transduction pathways. However, regulatory mechanisms of X gene expression have remained unclear. Previous studies had localized a minimal promoter activity to a 21-bp GC-rich sequence located 130 bp upstream of the X protein coding region and showed that there was a cellular protein bound to this DNA. Interestingly, the 21-bp sequence identified as an X gene minimal promoter does not contain any previously identified core promoter elements, such as a TATA box. To better understand the mechanisms of transcriptional initiation of the X gene, we set out to biochemically purify the binding protein(s) for the 21-bp DNA. We report here the identification of the X gene minimal promoter-binding activity as nuclear respiratory factor 1 (NRF1), a previously known transcription factor that activates the majority of nucleus-encoded mitochondrial genes and various housekeeping genes. Primer extension analyses of the X mRNAs show that mutations at the binding site specifically inactivate transcription from this promoter and that a dominant-negative NRF1 mutant and short interfering RNAs inhibit transcription from this promoter. Therefore, NRF1 specifically binds the 21-bp minimal promoter and positively contributes to transcription of the X gene. Simultaneous activation of the X gene and mitochondrial genes by NRF1 may allow the X protein to target mitochondria most efficiently.
Subject(s)
DNA-Binding Proteins/metabolism , Gene Expression Regulation, Viral , Hepatitis B virus/metabolism , Promoter Regions, Genetic/physiology , Trans-Activators/metabolism , Transcription, Genetic , Amino Acid Sequence , Base Sequence , Cell Line, Tumor , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , HeLa Cells , Hepatitis B virus/genetics , Humans , Molecular Sequence Data , Nuclear Respiratory Factor 1 , Nuclear Respiratory Factors , Promoter Regions, Genetic/genetics , Trans-Activators/chemistry , Trans-Activators/genetics , Viral Regulatory and Accessory ProteinsABSTRACT
DOCK180 protein plays a key role during development, cell motility, and phagocytosis. It forms a complex with another protein ELMO, and this complex acts as a guanine nucleotide exchange factor (GEF) for Rac. However, DOCK180-containing complexes have not been purified by unbiased biochemical approaches, and the nature and subcellular localization of these complexes remain unclear. Here, we show that a large fraction of endogenous DOCK180 is present as a 700kDa nuclear complex with ELMO proteins. In addition, this nuclear DOCK180/ELMO complex has functional Rac-GEF activity. Furthermore, endogenous DOCK180 could be found in complexes with different ELMO isoforms (ELMO1, 2 or 3) in different cell lines, depending on the ELMO isoforms expressed. These studies suggest that DOCK180 may associate with different ELMO proteins to form cell-type specific complexes and may have functions in both the nucleus and the cytoplasm.
Subject(s)
Adaptor Proteins, Signal Transducing , Caenorhabditis elegans Proteins/metabolism , Carrier Proteins/metabolism , Cell Nucleus/metabolism , Cytoplasm/metabolism , Cytoskeletal Proteins/metabolism , rac GTP-Binding Proteins/metabolism , Animals , Apoptosis Regulatory Proteins , Binding Sites , CHO Cells , Cell Extracts/analysis , Cricetinae , Cricetulus , HeLa Cells , Humans , Protein Binding , Protein Isoforms/metabolism , Tissue DistributionABSTRACT
The human activator-recruited cofactor (ARC), a family of large transcriptional coactivator complexes related to the yeast Mediator, was recently identified based on functional association with the activation domains of multiple cellular and viral transcriptional activators, including the herpes simplex viral activator VP16, sterol regulatory element binding protein, and NF-kappaB. Here we describe the biochemical purification and cloning of the 92-kDa ARC/Mediator subunit, ARC92, that is specifically targeted by the activation domain of the VP16 transactivator. Affinity chromatography using the VP16 activation domain followed by peptide microsequencing led to the identification of ARC92 as a specific cellular interaction partner of the VP16 activation domain. ARC92 associates with the VP16 activation domain in vitro and in vivo, and the VP16 binding domain of ARC92 is a strong competitive inhibitor of Gal4-VP16 in vivo. Moreover, small interfering RNA-mediated knockdown of ARC92 in human cells results in selective inhibition of Gal4-VP16 gene activation. Taken together, our results suggest that ARC92 is a direct and specific target of the VP16 transactivator that serves in the context of the ARC/Mediator coactivator as an important transducer of transcription activating signals from the VP16 activation domain to the RNA polymerase II transcriptional machinery.
Subject(s)
Trans-Activators/metabolism , Transcription Factors/metabolism , Base Sequence , Cell Nucleus/metabolism , Cloning, Molecular , DNA Primers , DNA, Complementary/genetics , HeLa Cells , Humans , Mediator Complex , Molecular Sequence Data , Polymerase Chain Reaction , RNA Polymerase II , RNA, Small Interfering/genetics , Recombinant Fusion Proteins/metabolism , Recombinant Proteins/metabolism , Trans-Activators/genetics , Transcription Factors/genetics , Transcription, Genetic , Transcriptional Activation/genetics , TransfectionABSTRACT
ATRX syndrome is characterized by X-linked mental retardation associated with alpha-thalassemia. The gene mutated in this disease, ATRX, encodes a plant homeodomain-like finger and a SWI2/SNF2-like ATPase motif, both of which are often found in chromatin-remodeling enzymes, but ATRX has not been characterized biochemically. By immunoprecipitation from HeLa extract, we found that ATRX is in a complex with transcription cofactor Daxx. The following evidence supports that ATRX and Daxx are components of an ATP-dependent chromatin-remodeling complex: (i) Daxx and ATRX can be coimmunoisolated by antibodies specific for each protein; (ii) a proportion of Daxx cofractionates with ATRX as a complex of 1 MDa by gel-filtration analysis; (iii) in extract from cells of a patient with ATRX syndrome, the level of the Daxx-ATRX complex is correspondingly reduced; (iv) a proportion of ATRX and Daxx colocalize in promyelocytic leukemia nuclear bodies, with which Daxx had previously been located; and (v) the ATRX complex displays ATP-dependent activities that resemble those of other chromatin-remodeling complexes, including triple-helix DNA displacement and alteration of mononucleosome disruption patterns. But unlike the previously described SWI/SNF or NURD complexes, the ATRX complex does not randomize DNA phasing of the mononucleosomes, suggesting that it may remodel chromatin differently. Taken together, the results suggest that ATRX functions in conjunction with Daxx in a novel chromatin-remodeling complex. The defects in ATRX syndrome may result from inappropriate expression of genes controlled by this complex.
Subject(s)
Carrier Proteins/metabolism , Cell Nucleus/metabolism , Chromatin/metabolism , DNA Helicases/metabolism , Intracellular Signaling Peptides and Proteins , Leukemia, Promyelocytic, Acute/metabolism , Nuclear Proteins/metabolism , Adaptor Proteins, Signal Transducing , Adenosine Triphosphate/metabolism , Co-Repressor Proteins , Fluorescent Antibody Technique , Humans , Molecular Chaperones , X-linked Nuclear ProteinABSTRACT
The SWI/SNF family of chromatin-remodeling complexes has been discovered in many species and has been shown to regulate gene expression by assisting transcriptional machinery to gain access to their sites in chromatin. Several complexes of this family have been reported for humans. In this study, two additional complexes are described that belong to the same SWI/SNF family. These new complexes contain as many as eight subunits identical to those found in other SWI/SNF complexes, and they possess a similar ATP-dependent nucleosome disruption activity. But unlike known SWI/SNFs, the new complexes are low in abundance and contain an extra subunit conserved between human and yeast SWI/SNF complexes. This subunit, ENL, is a homolog of the yeast SWI/SNF subunit, ANC1/TFG3. Moreover, ENL is a fusion partner for the gene product of MLL that is a common target for chromosomal translocations in human acute leukemia. The resultant MLL-ENL fusion protein associates and cooperates with SWI/SNF complexes to activate transcription of the promoter of HoxA7, a downstream target essential for oncogenic activity of MLL-ENL. Our data suggest that human SWI/SNF complexes show considerable heterogeneity, and one or more may be involved in the etiology of leukemia by cooperating with MLL fusion proteins.
Subject(s)
Chromatin/genetics , Chromosomal Proteins, Non-Histone/genetics , DNA-Binding Proteins/genetics , Proto-Oncogenes , Transcription Factors/genetics , Amino Acid Sequence , Chromatin/metabolism , Chromosomal Proteins, Non-Histone/chemistry , Chromosomal Proteins, Non-Histone/metabolism , Cloning, Molecular , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Histone-Lysine N-Methyltransferase , Homeodomain Proteins/genetics , Humans , Macromolecular Substances , Molecular Sequence Data , Myeloid-Lymphoid Leukemia Protein , Neoplasm Proteins/genetics , Nuclear Proteins/chemistry , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Promoter Regions, Genetic , Protein Subunits , Saccharomyces cerevisiae Proteins/genetics , Sequence Homology, Amino Acid , Species Specificity , Transcription Factors/chemistry , Transcription Factors/metabolism , Translocation, Genetic , Tumor Cells, CulturedABSTRACT
Depletion of CD4(+) T cells is the hallmark of HIV infection and AIDS progression. In addition to the direct killing of the viral-infected cells, HIV infection also leads to increased apoptosis of predominantly uninfected bystander cells. This is mediated in part through the HIV-1 Tat protein, which is secreted by the infected cells and taken up by uninfected cells. Using an affinity-purification approach, a specific and direct interaction of Tat with tubulin and polymerized microtubules has been detected. This interaction does not affect the secretion and uptake of Tat, but is critical for Tat to induce apoptosis. Tat binds tubulin/microtubules through a four-amino-acid subdomain of its conserved core region, leading to the alteration of microtubule dynamics and activation of a mitochondria-dependent apoptotic pathway. Bim, a pro-apoptotic Bcl-2 relative and a transducer of death signals initiated by perturbation of microtubule dynamics, facilitates the Tat-induced apoptosis. Our findings reveal a strategy by which Tat induces apoptosis by targeting the microtubule network. Thus HIV-1 Tat joins a growing list of pathogen-derived proteins that target the cytoskeleton of host cells.
Subject(s)
Apoptosis , Carrier Proteins/metabolism , Gene Products, tat/metabolism , HIV-1/metabolism , Membrane Proteins , Proto-Oncogene Proteins c-bcl-2/metabolism , Proto-Oncogene Proteins , Animals , Apoptosis Regulatory Proteins , Bcl-2-Like Protein 11 , CD4-Positive T-Lymphocytes/metabolism , Cell Death , Cell Line , Cytoplasm/metabolism , Cytoskeleton/metabolism , Dimerization , Dose-Response Relationship, Drug , Electrophoresis, Polyacrylamide Gel , Female , Flow Cytometry , G1 Phase , Glutathione Transferase/metabolism , Humans , Jurkat Cells , Mice , Mice, Inbred C57BL , Microscopy, Fluorescence , Microtubules/metabolism , Mitochondria/metabolism , Mutation , Protein Binding , Protein Structure, Tertiary , Retroviridae/genetics , Transfection , Tubulin/metabolism , tat Gene Products, Human Immunodeficiency VirusABSTRACT
There is considerable interest in the developmental, temporal and tissue-specific patterns of DNA replication in metazoans. Site-specific DNA replication at the chorion loci in Drosophila follicle cells leads to extensive gene amplification, and the organization of the cis-acting DNA elements that regulate this process may provide a model for how such regulation is achieved. Two elements important for amplification of the third chromosome chorion gene cluster, ACE3 and Ori-beta, are directly bound by Orc (origin recognition complex), and two-dimensional gel analysis has revealed that the primary origin used is Ori-beta (refs 7-9). Here we show that the Drosophila homologue of the Myb (Myeloblastosis) oncoprotein family is tightly associated with four additional proteins, and that the complex binds site-specifically to these regulatory DNA elements. Drosophila Myb is required in trans for gene amplification, showing that a Myb protein is directly involved in DNA replication. A Drosophila Myb binding site, as well as the binding site for another Myb complex member (p120), is necessary in cis for replication of reporter transgenes. Chromatin immunoprecipitation experiments localize both proteins to the chorion loci in vivo. These data provide evidence that specific protein complexes bound to replication enhancer elements work together with the general replication machinery for site-specific origin utilization during replication.
Subject(s)
DNA Replication , DNA-Binding Proteins/metabolism , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , Proto-Oncogene Proteins c-myb/metabolism , Animals , Binding Sites , Chromatin/genetics , Chromatin/metabolism , DNA Footprinting , DNA-Binding Proteins/genetics , Enhancer Elements, Genetic/genetics , Female , Gene Amplification , Genes, Insect/genetics , Macromolecular Substances , Origin Recognition Complex , Precipitin Tests , Protein Binding , Regulatory Sequences, Nucleic Acid/genetics , Replication Origin , Substrate Specificity , Transgenes/geneticsABSTRACT
Drosophila TATA-box-binding protein (TBP)-related factor 2 (TRF2) is a member of a family of TBP-related factors present in metazoan organisms. Recent evidence suggests that TRF2s are required for proper embryonic development and differentiation. However, true target promoters and the mechanisms by which TRF2 operates to control transcription remain elusive. Here we report the antibody affinity purification of a Drosophila TRF2-containing complex that contains components of the nucleosome remodelling factor (NURF) chromatin remodelling complex as well as the DNA replication-related element (DRE)-binding factor DREF. This latter finding led us to potential target genes containing TRF2-responsive promoters. We have used a combination of in vitro and in vivo assays to show that the DREF-containing TRF2 complex directs core promoter recognition of the proliferating cell nuclear antigen (PCNA) gene. We also identified additional TRF2-responsive target genes involved in DNA replication and cell proliferation. These data suggest that TRF2 functions as a core promoter-selectivity factor responsible for coordinating transcription of a subset of genes in Drosophila.