Miki Imanishi

Autoinhibition regulates the motility of the C. elegans intraflagellar transport motor OSM-3

OSM-3 is a Kinesin-2 family member from Caenorhabditis elegans that is involved in intraflagellar transport (IFT), a process essential for the construction and maintenance of sensory cilia. In this study, using a single-molecule fluorescence assay, we show that bacterially expressed OSM-3 in solution does not move processively (multiple steps along a microtubule without dissociation) and displays low microtubule-stimulated adenosine triphosphatase (ATPase) activity. However, a point mutation (G444E) in a predicted hinge region of OSM-3s coiled-coil stalk as well as a deletion of that hinge activate ATPase activity and induce robust processive movement. These hinge mutations also cause a conformational change in OSM-3, causing it to adopt a more extended conformation. The motility of wild-type OSM-3 also can be activated by attaching the motor to beads in an optical trap, a situation that may mimic attachment to IFT cargo. Our results suggest that OSM-3 motility is repressed by an intramolecular interaction that involves folding about a central hinge and that IFT cargo binding relieves this autoinhibition in vivo. Interestingly, the G444E allele in C. elegans produces similar ciliary defects to an osm-3–null mutation, suggesting that autoinhibition is important for OSM-3s biological function.

Cytosolic Targeting of Macromolecules Using a pH-Dependent Fusogenic Peptide in Combination with Cationic Liposomes

pH-Sensitive peptides and polymers have been employed as additives to enhance the cytosolic delivery of drugs and genes by facilitating their endosomal escape. However, little attention has been paid to the intracellular fate of these peptides and polymers. In this study, we explored the possibility of utilizing GALA, a pH-sensitive fusogenic peptide, as a cytosol-targeting vehicle. In combination with cationic liposomes, Lipofectamine 2000 (LF2000), the feasibility of this approach for the cytosolic targeting of proteins and nanoparticles was exemplified through the delivery of avidin (68 kDa) and streptavidin-coated quantum dots (15-20 nm) in serum-containing medium. The use of cationic liposomes is critical to enhance the cell-surface adhesion of the GALA conjugates and eventual endosomal uptake. Circular dichroism studies suggest that the GALA can be liberated from cationic liposomes at a reducing pH to form a helical structure and this may eventually lead to disruption of the endosomal membrane to achieve an efficient leakage of the GALA conjugates into the cytosol.

New Redesigned Zinc‐Finger Proteins: Design Strategy and Its Application

The design of DNA-binding proteins for the specific control of the gene expression is one of the big challenges for several research laboratories in the post-genomic era. An artificial transcription factor with the desired DNA binding specificity could work as a powerful tool and drug to regulate the target gene. The zinc-finger proteins, which typically contain many fingers linked in a tandem fashion, are some of the most intensively studied DNA-binding proteins. In particular, the Cys(2)His(2)-type zinc finger is one of the most common DNA-binding motifs in eukaryotes. A simple mode of DNA recognition by the Cys(2)His(2)-type zinc-finger domain provides an ideal framework for designing proteins with new functions. Our laboratory has utilized several design strategies to create new zinc-finger peptides/proteins by redesigning the Cys(2)His(2)-type zinc-finger motif. This review focuses on the aspects of design strategies, mainly from our recent results, for the creation of artificial zinc-finger proteins, and discusses the possible application of zinc-finger technology for gene regulation and gene therapy.

Octa-Arginine Mediated Delivery of Wild-Type Lnk Protein Inhibits TPO-Induced M-MOK Megakaryoblastic Leukemic Cell Growth by Promoting Apoptosis

Background Lnk plays a non-redundant role by negatively regulating cytokine signaling of TPO, SCF or EPO. Retroviral expression of Lnk has been shown to suppress hematopoietic leukemic cell proliferation indicating its therapeutic value in cancer therapy. However, retroviral gene delivery carries risks of insertional mutagenesis. To circumvent this undesired consequence, we fused a cell permeable peptide octa-arginine to Lnk and evaluated the efficacy of inhibition of leukemic cell proliferation in vitro. Methodology/Principal Findings In this study, proliferation assays, flow cytometry, Western Blot analyses were performed on wild-type (WT), mutant Lnk R8 or BSA treated M-MOK cells. We found that delivered WT, but not mutant Lnk R8 blocked TPO-induced M-MOK megakaryoblastic leukemic cell proliferation. In contrast, WT Lnk R8 showed no growth inhibitive effect on non-hematopoietic HELA or COS-7 cell. Moreover, we demonstrated that TPO-induced M-MOK cell growth inhibition by WT Lnk R8 was dose-dependent. Penetrated WT Lnk R8 induced cell cycle arrest and apoptosis. Immunoprecipitation and Western blots data indicated WT Lnk R8 interacted with endogeneous Jak2 and downregulated Jak-Stat and MAPK phosphorylation level in M-MOK cells after TPO stimulation. Treatment with specific inhibitors (TG101348 and PD98059) indicated Jak-Stat and MAPK pathways were crucial for TPO-induced proliferation of M-MOK cells. Further analyses using TF-1 and HEL leukemic cell-lines showed that WT Lnk R8 inhibited Jak2-dependent cell proliferation. Using cord blood-derived CD34+ stem cells, we found that delivered WT Lnk R8 blocked TPO-induced megakaryopoiesis in vitro. Conclusions/Significance Intracellular delivery of WT Lnk R8 fusion protein efficiently inhibited TPO-induced M-MOK leukemic cell growth by promoting apoptosis. WT Lnk R8 protein delivery may provide a safer and more practical approach to inhibit leukemic cell growth worthy of further development.

Signal Transduction Using an Artificial Receptor System that Undergoes Dimerization Upon Addition of a Bivalent Leucine‐Zipper Ligand

Dimerization and clustering of biological receptors on the plasma membrane lead to activation and subsequent signal transduction. If this dimerization event could be artificially controlled, it would be a valuable tool for studying signal transduction and modulating cellular functions. Previous studies have applied antibodies that recognize pre-incorporated tags on cell-surface receptors to stimulate receptor dimerization. Dimerization of receptors expressing a single-chain antibody against fluorescein by adding fluorescein-modified albumins were also reported. 4] Although antibodies are specific and have high ligand-binding affinities, their bulky structures may limit the design of ligand-receptor recognition systems. Other approaches caused intracellular cross-linking using FK506and FKBP-tagged intracellular signaling domains of receptors to form dimers when FKBP binds FK506. These approaches often employed multiple intracellular FKBP domains, which could lead to the assembly of more than two intracellular domains upon the addition of dimeric FK506. Possible steric interference of FKBP multimers might induce interaction of intracellular domains different from those of the wild-type receptors. Herein, we propose a novel approach to controlled receptor activation that employs a leucine-zipper coiled-coil as a recognition element to stimulate dimerization (Figure 1). This approach provides flexibility in the selection of the different combinations of leucine zippers, as recognition elements, and the linkers tethering them to the receptors being studied. To demonstrate the feasibility of this approach, we used a heterodimeric coiled-coil developed by Hodges and coworkers (E/K coil). This recognition motif has already been used to fluorescently label cell-surface proteins. 8] Peptide probes K3 (= (KIAALKE)3) and K4 (= (KIAALKE)4), labeled with a fluorophore, specifically stained the surfaceexposed tag sequence E3 (= (EIAALEK)3) attached to the N-terminus of the proteins. Recognition of these peptides is quick (< 1 min) with a high affinity (Kd = 64 nm for K3 and 6 nm for K4), which should also allow for efficient dimerization of receptor proteins. Considering that the K4 peptide showed a higher affinity to E3 than K3, we designed a system using bivalent K4 ligands to bring together cell-surface receptors bearing the E3 tag (Figure 1). One recent study employed an extracellular leucine-zipper dimerization domain of epidermal growth factor receptor (EGFR). This previous work used a constitutively dimerized leucinezipper–EGFR fusion to analyze the mechanism of an intracellular EGFR activating factor. On the other hand, our approach could increase the flexibility in selection of combinations of leucine zippers as recognition elements and in the linkers tethering them to the receptors. In addition, this method should provide an additional level of control by allowing a triggered dimerization event in biochemical and cell-biological experiments. EGFR is a representative receptor tyrosine kinase (RTK) that regulates proliferation, motility, and survival in normal cells, and is also implicated in many human cancers. Binding of EGF promotes dimerization of the EGFR, which causes phosphorylation of the cytoplasmic domain and activation of downstream signaling pathways. 10, 12, 13] The extracellular region of EGFR contains four subdomains (domains I–IV). 12] We designed an EGFR receptor lacking domains I–III and a part of domain IV (which are responsible for binding to EGF and dimerization) but included hemagglutinin A (HA) and E3 tags (E3-EGFR; tags are for the Figure 1. Scheme of artificial EGFR activation by a helical peptide through coiled-coil formation.

Design of novel zinc finger proteins: towards artificial control of specific gene expression.

In this review, we summarize design strategies for generating proteins with desired sequences such as long contiguous base pairs and diverse sequence specificities based on the nature of Cys(2)-His(2) zinc finger proteins. Recent progress towards artificial DNA binding proteins has been achieved by structure-based design processes and by selection strategies. Indeed, a multi-zinc finger protein with an 18 (or 27)-base pair address, and new zinc finger proteins for diverse DNA target sites (TATA-box and p53 binding site) have been created successfully. Such novel zinc finger proteins will probably be useful tools in molecular biology and potentially in human medicine.

Zn(II) Binding and DNA Binding Properties of Ligand-Substituted CXHH-Type Zinc Finger Proteins

CCHH-type zinc fingers are among the most common DNA binding motifs found in eukaryotes. In a previous report, we substituted the second ligand cysteine residue with aspartic acid, producing a Zn(II)-responsive transcription factor; this indicates that a ligand substitution is a possible design target of an engineered zinc finger peptide. Despite the importance of Zn(II) binding with respect to the folding and DNA binding properties of a zinc finger peptide, no study about the effects of ligand substitution on both Zn(II) binding and DNA binding properties has been reported. Here, we substituted a conserved cysteine (C) with other zinc-coordinated amino acid residues, histidine (H), aspartic acid (D), and glutamic acid (E), to create CXHH-type zinc finger peptides (X = C, H, D, and E). The Zn(II)-dependent conformational change was observed in all peptides; however, the Zn(II) binding affinity and metal coordination geometry of the peptides were different. Gel mobility shift assays showed that the Zn(II)-bound forms of the ligand-substituted derivatives retain DNA binding ability, while the DNA binding affinity decreased in the following manner: CCHH > CDHH > CEHH ≫ CHHH. The DNA binding sequence preferences of the ligand-substituted derivatives were similar to that of the wild type in the context of the full three-finger DNA-binding domain of transcription factor Zif268. These results indicate that artificial zinc finger proteins with various DNA binding affinities that respond to a diverse range of Zn(II) concentrations can be designed by substituting the Zn(II) ligand.

Multiconnection of identical zinc finger: implication for DNA binding affinity and unit modulation of the three zinc finger domain.

Cys(2)-His(2)-type zinc finger proteins have a tandemly repeated array structure consisting of independent finger modules. They are expected to elevate the DNA binding affinity and specificity by increasing the number of finger modules. To investigate the relation between the number and the DNA binding affinity of the zinc finger, we have designed the two- to four-finger peptides by connecting the central zinc finger (finger 2) of Sp1 with the canonical linker sequence, Thr-Gly-Glu-Lys-Pro. Gel mobility shift assays reveal that the cognate three- and four-finger peptides, Sp1(zf222) and Sp1(zf2222), strongly bind to the predicted target sequences, but the two-finger peptide, Sp1(zf22), does not. Of special interest is the fact that the dissociation constant for Sp1(zf2222) binding to the target DNA is comparable to that for Sp1(zf222). The methylation interference, DNase I and hydroxyl radical footprintings, and circular permutation analyses demonstrate that Sp1(zf2222) binds to its target site with three successive zinc fingers and the binding of the fourth zinc finger is inhibited by DNA bending induced by the binding of the three-finger domain. The present results strongly indicate that the zinc finger protein binds to DNA by the three-finger domain as one binding unit. In addition, this information provides the basis for the design of a novel multifinger protein with high affinity and specificity for long DNA sequences, such as chromosomal DNAs.

Rapid Transcriptional Activity in Vivo and Slow DNA Binding in Vitro by an Artificial Multi-Zinc Finger Protein

Artificial transcription factors targeting any desired genes are very attractive but require specific DNA binding domains in order to address a single site for each gene promoter. By connecting various zinc fingers recognizing the corresponding 3-4 bp DNA, DNA binding domains for the desired and long sequences can be created. Though such a long sequence recognition is a marvelous property, we have found that as the number of finger motifs increases, the equilibrium time with the target sequence is significantly longer as detected by in vitro EMSA experiments. In this study, we created 3- and 9-finger-type artificial transcription factors and compared the kinetics of the transcriptional activation in vivo as to whether or not a significant delay in the activation is observed for the 9-finger type. By using a ligand-inducing system, we demonstrated for the first time that finger multimerization does not affect the kinetics of the transcriptional activity; the 9-finger type artificial transcription factor activated the reporter gene as quickly as the 3-figner type. Our results suggest that the drawback of finger multimerization, i.e., the equilibrium time is prolonged depending on the number of finger motifs, can be surmounted in terms of its use for transcription factors in vivo. There is much interest in creating therapeutic molecules, and these findings suggest the significant potential of multi-zinc finger proteins as a tool for an artificial gene regulator.

Positive and negative cooperativity of modularly assembled zinc fingers.

One simple and widespread method to create engineered zinc fingers targeting the desired DNA sequences is to modularly assemble multiple finger modules pre-selected to recognize each DNA triplet. However, it has become known that a sufficient DNA binding affinity is not always obtained. In order to create successful zinc finger proteins, it is important to understand the context-dependent contribution of each finger module to the DNA binding ability of the assembled zinc finger proteins. Here, we have created finger-deletion mutants of zinc finger proteins and examined the DNA bindings of these zinc fingers to clarify the contributions of each finger module. Our results indicate that not only a positive cooperativity but also a context-dependent reduction in the DNA binding activity can be induced by assembling zinc finger modules.