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Biomedical subjects

Michael Famulok

Publications and source records attributed to Michael Famulok.

At least 19 recordsLinked to original sources
PubMed2006

Inhibition of cytohesins by SecinH3 leads to hepatic insulin resistance.

G proteins are an important class of regulatory switches in all living systems. They are activated by guanine nucleotide exchange factors (GEFs), which facilitate the exchange of GDP for GTP. This activity makes GEFs attractive targets for modulating disease-relevant G-protein-controlled signalling networks. GEF inhibitors are therefore of interest as tools for elucidating the function of these proteins and for therapeutic intervention; however, only one small molecule GEF inhibitor, brefeldin A (BFA), is currently available. Here we used an aptamer displacement screen to identify SecinH3, a small molecule antagonist of cytohesins. The cytohesins are a class of BFA-resistant small GEFs for ADP-ribosylation factors (ARFs), which regulate cytoskeletal organization, integrin activation or integrin signalling. The application of SecinH3 in human liver cells showed that insulin-receptor-complex-associated cytohesins are required for insulin signalling. SecinH3-treated mice show increased expression of gluconeogenic genes, reduced expression of glycolytic, fatty acid and ketone body metabolism genes in the liver, reduced liver glycogen stores, and a compensatory increase in plasma insulin. Thus, cytohesin inhibition results in hepatic insulin resistance. Because insulin resistance is among the earliest pathological changes in type 2 diabetes, our results show the potential of chemical biology for dissecting the molecular pathogenesis of this disease.

ADP-Ribosylation Factors↗
PubMed2006

GGA1 is expressed in the human brain and affects the generation of amyloid beta-peptide.

The beta-amyloid peptide (Abeta) is a major component of Alzheimer disease (AD)-associated senile plaques and is generated by sequential cleavage of the beta-amyloid precursor protein (APP) by beta-secretase (BACE1) and gamma-secretase. BACE1 cleaves APP at the N terminus of the Abeta domain, generating a membrane-bound C-terminal fragment (CTF-beta) that can be subsequently cleaved by gamma-secretase within the transmembrane domain to release Abeta. Because BACE1 initiates Abeta generation, it represents a potential target molecule to interfere with Abeta production in therapeutic strategies for AD. BACE1 interacts with Golgi-localized, gamma-ear-containing, ADP ribosylation factor-binding (GGA) proteins that are involved in the subcellular trafficking of BACE1. Here, we show that GGA1 is preferentially expressed in neurons of the human brain. GGA1 was also detected in activated microglia surrounding amyloid plaques in AD brains. Functional analyses with cultured cells demonstrate that GGA1 is implicated in the proteolytic processing of APP. Overexpression of GGA1 or a dominant-negative variant reduced cleavage of APP by BACE1 as indicated by a decrease in CTF-beta generation. Importantly, overexpression of GGA1 reduced, whereas RNAi-mediated suppression of GGA1 increased the secretion of Abeta. The modulation of APP processing by GGA1 is independent of a direct interaction of both proteins. Because total cellular activity of BACE1 was not affected by GGA1 expression, our data indicate that changes in the subcellular trafficking of BACE1 or other GGA1-dependent proteins contribute to changes in APP processing and Abeta generation. Thus, GGA proteins might be involved in the pathogenesis of AD.

ADP-Ribosylation Factors↗
PubMed2006

DNA aptamer-mediated regulation of the hairpin ribozyme by human alpha-thrombin.

The combination of specific ligand-binding aptamers with hairpin ribozyme catalysis generates molecules that can be controlled by external factors. Here we have generated hairpin ribozymes that can be regulated by a short DNA aptamer specific for human alpha-thrombin. This was achieved by constructing a ribozyme variant harboring an RNA sequence complementary to the aptamer, to which the aptamer can hybridize forming a heteroduplex. In this way, the DNA aptamer completely abolishes the catalytic activity of the ribozyme, due to the formation of an inactive ribozyme conformation. However, in the presence of the aptamer's target protein human alpha-thrombin, the inhibitory effect of the DNA aptamer is competitively neutralized and the ribozyme is activated in a highly specific fashion. Protein-responsive allosteric ribozymes are proposed to act as tools with potential applications in medicine where fast detection of clinically relevant targets is required.

Aptamers, Nucleotide↗
PubMed2006

RNA aptamers selectively modulate protein recruitment to the cytoplasmic domain of beta-secretase BACE1 in vitro.

The beta-amyloid peptide (Abeta) is a major component of the Alzheimer's disease (AD)-associated senile plaques and is generated by sequential cleavage of the beta-amyloid precursor protein (APP) by beta-secretase and gamma-secretase. Since BACE1 initiates Abeta generation it represents a valuable target to interfere with Abeta production and treatment of AD. While the enzymatic activity of BACE1 resides in the extracellular domain, the protein also contains a short cytoplasmic tail (B1-CT). This domain serves as a binding site for at least two proteins, the copper chaperone for superoxide dismutase-1 (CCS), and the Golgi-localized, gamma-ear-containing, ADP ribosylation factor-binding (GGA1) protein, and contains a single phosphorylation site. However, the precise role of the B1-CT for the overall biological function of this protein is largely unknown. Functional studies focusing on the activity of this domain would strongly benefit from the availability of domain-specific inhibitors. Here we describe the isolation and characterization of RNA aptamers that selectively target the B1-CT. We show that these RNAs bind to authentic BACE1 and provide evidence that the binding site is restricted to the membrane-proximal half of the C terminus. Aptamer-binding specifically interferes with the recruitment of CCS, but still permits GGA1 association and casein kinase-dependent phosphorylation, consistent with selective binding site targeting within this short peptide. Because phosphorylation and GGA1 binding to B1-CT regulate BACE1 transport, these RNA inhibitors could be applied to investigate B1-CT activity without affecting the subcellular localization of BACE1.

ADP-Ribosylation Factors↗
PubMed2006

Discrimination of single mutations in cancer-related gene fragments with a surface acoustic wave sensor.

Here, we report on using a surface acoustic wave sensor for the highly sensitive and accurate detection of individual point mutations in cancer-related gene DNA fragments from single injections. Our sensor measures both the mass and viscosity signals and, thus, allows discriminating between mass effects resulting from hybridization of short DNA strands and viscosity effects due to increasing amounts of DNA deposited on the sensor. Single nucleotide exchanges or deletions are distinguished reliably and with exceeding simplicity from the wild-type sequences, on the basis of differences in their dissociation or association rates starting at low nanomolar concentrations. Mutant oligonucleotides were identified immediately from viewing the recorded signal and without further processing of the data. Multiple repeated binding cycles were possible over days without affecting sensitivity. To achieve signal amplification, our new bioassay can also apply multiple hybridization steps based on sandwich hybridizations. Kinetic evaluations gave insight into the physicochemical properties of the fragments used that explain the differences in their binding processes.

Acoustics↗
PubMed2006

Heteromerization of innexin gap junction proteins regulates epithelial tissue organization in Drosophila.

Gap junctions consist of clusters of intercellular channels, which enable direct cell-to-cell communication and adhesion in animals. Whereas deuterostomes, including all vertebrates, use members of the connexin and pannexin multiprotein families to assemble gap junction channels, protostomes such as Drosophila and Caenorhabditis elegans use members of the innexin protein family. The molecular composition of innexin-containing gap junctions and the functional significance of innexin oligomerization for development are largely unknown. Here, we report that heteromerization of Drosophila innexins 2 and 3 is crucial for epithelial organization and polarity of the embryonic epidermis. Both innexins colocalize in epithelial cell membranes. Innexin3 is mislocalized to the cytoplasm in innexin2 mutants and is recruited into ectopic expression domains defined by innexin2 misexpression. Conversely, RNA interference (RNAi) knockdown of innexin3 causes mislocalization of innexin2 and of DE-cadherin, causing cell polarity defects in the epidermis. Biochemical interaction studies, surface plasmon resonance analysis, transgenesis, and biochemical fractionation experiments demonstrate that both innexins interact via their C-terminal cytoplasmic domains during the assembly of heteromeric channels. Our data provide the first molecular and functional demonstration that innexin heteromerization occurs in vivo and reveal insight into a molecular mechanism by which innexins may oligomerize into heteromeric gap junction channels.

Amino Acid Sequence↗
PubMed2005

Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs.

The noncoding RNA B2 and the RNA aptamer FC bind RNA polymerase (Pol) II and inhibit messenger RNA transcription initiation, but not elongation. We report the crystal structure of FC(*), the central part of FC RNA, bound to Pol II. FC(*) RNA forms a double stem-loop structure in the Pol II active center cleft. B2 RNA may bind similarly, as it competes with FC(*) RNA for Pol II interaction. Both RNA inhibitors apparently prevent the downstream DNA duplex and the template single strand from entering the cleft after DNA melting and thus interfere with open-complex formation. Elongation is not inhibited, as nucleic acids prebound in the cleft would exclude the RNA inhibitors. The structure also indicates that A-form RNA could interact with Pol II similarly to a B-form DNA promoter, as suggested for the bacterial transcription inhibitor 6S RNA.

Base Sequence↗
PubMed2005

A versatile toolbox for variable DNA functionalization at high density.

To broaden the applicability of chemically modified DNAs in nano- and biotechnology, material science, sensor development, and molecular recognition, strategies are required for introducing a large variety of different modifications into the same nucleic acid sequence at once. Here, we investigate the scope and limits for obtaining functionalized dsDNA by primer extension and PCR, using a broad variety of chemically modified deoxynucleotide triphosphates (dNTPs), DNA polymerases, and templates. All natural nucleobases in each strand were substituted with up to four different base-modified analogues. We studied the sequence dependence of enzymatic amplification to yield high-density functionalized DNA (fDNA) from modified dNTPs, and of fDNA templates, and found that GC-rich sequences are amplified with decreased efficiency as compared to AT-rich ones. There is also a strong dependence on the polymerase used. While family A polymerases generally performed poorly on "demanding" templates containing consecutive stretches of a particular base, family B polymerases were better suited for this purpose, in particular Pwo and Vent (exo-) DNA polymerase. A systematic analysis of fDNAs modified at increasing densities by CD spectroscopy revealed that single modified bases do not alter the overall B-type DNA structure, regardless of their chemical nature. A density of three modified bases induces conformational changes in the double helix, reflected by an inversion of the CD spectra. Our study provides a basis for establishing a generally applicable toolbox of enzymes, templates, and monomers for generating high-density functionalized DNAs for a broad range of applications.

Base Sequence↗
PubMed2005

Specific targeting of ultrasound contrast agent (USCA) for diagnostic application: an in vitro feasibility study based on SAW biosensor.

The present study described a new strategy to examine the interaction between the targeted ultrasound contrast agent (USCA) and its target under flow conditions with a surface acoustic wave (SAW) transducer. The sensing principle is based on the measurement of the phase change on the sensing element upon the binding of specific biomolecules. Love-wave biosensor array was consisting of sensor elements and reference elements. The sensor elements have been prepared by coating the sensor surface with tumor marker EDB-fibronectin by means of SAM technique and carbodiimide chemistry. Reference elements were left blank or coated with fibronectin and used to eliminate thermal drift, unspecific binding, and turbulence from injection of liquids by calculating the differential phase shift with respect to the sensor elements. The binding of targeted USCA to the sensor surface was constantly recorded by monitoring the phase shift on the sensor element. The binding of targeted USCA generated a high phase shift on the sensor elements, but almost no change on the reference elements. Control experiments using non-targeted and isotype-targeted USCA confirmed the specificity of binding due to anti-EDB-fibronectin scFv-antibody-fragment-EDB-fibronectin antigen interaction. The suitability of the SAW technique to monitor the specific binding behavior of targeted micron-sized USCA in real time has been well established.

Biosensing Techniques↗
PubMed2005

A ribozyme for the aldol reaction.

Directed in vitro evolution can create RNA catalysts for a variety of organic reactions, supporting the "RNA world" hypothesis, which proposes that metabolic transformations in early life were catalyzed by RNA molecules rather than proteins. Among the most fundamental carbon-carbon bond-forming reactions in nature is the aldol reaction, mainly catalyzed by aldolases that utilize either an enamine mechanism (class I) or a Zn(2+) cofactor (class II). We report on isolation of a Zn(2+)-dependent ribozyme that catalyzes an aldol reaction at its own modified 5' end with a 4300-fold rate enhancement over the uncatalyzed background reaction. The ribozyme can also act as an intermolecular catalyst that transfers a biotinylated benzaldehyde derivative to the aldol donor substrate, coupled to an external hexameric RNA oligonucleotide, supporting the existence of RNA-originated biosynthetic pathways for metabolic sugar precursors and other biomolecules.

Aldehydes↗
PubMed2005

GGA proteins regulate retrograde transport of BACE1 from endosomes to the trans-Golgi network.

Golgi-localized, gamma ear-containing, ADP ribosylation factor-binding (GGA) proteins have been shown to be implicated in the sorting of cargo proteins from the trans-Golgi network (TGN) to endosomal compartments. GGAs directly bind to DXXLL motifs in the cytoplasmic domains of cargo proteins. The Alzheimer-associated beta-secretase BACE1 also interacts with GGA proteins, but the functional relevance of this interaction was unknown. Here, we show that GGA1 regulates the retrograde transport of internalized BACE1 from endosomal compartments to the TGN by direct interaction in a phosphorylation-dependent manner. While phosphorylated BACE1 is efficiently transported from endosomes to the TGN, non-phosphorylated BACE1 enters a direct recycling route to the cell surface. Our data indicate that GGA proteins are not only involved in the sorting at the TGN but also mediate the retrograde transport of cargo proteins from endosomes to the TGN.

ADP-Ribosylation Factors↗
PubMed2005

Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector.

The hairpin ribozyme can catalyze the cleavage of RNA substrates by employing its conformational flexibility. To form a catalytic complex, the two domains A and B of the hairpin-ribozyme complex must interact with one another in a folding step called docking. We have constructed hairpin ribozyme variants harboring an aptamer sequence that can be allosterically induced by flavin mononucleotide (FMN). Domains A and B are separated by distinct bridge sequences that communicate the formation of the FMN-aptamer complex to domains A and B, facilitating their docking. In the presence of a short oligonucleotide that is complementary to the aptamer, catalytic activity of the ribozyme is completely abolished, due to the formation of an extended conformer that cannot perform catalysis. However, in the presence of the small molecule effector FMN, the inhibitory effect of the oligonucleotide is competitively neutralized and the ribozyme is activated 150-fold. We thus have established a new principle for the regulation of ribozyme catalysis in which two regulatory factors (an oligonucleotide and a small molecule) that switch the ribozyme's activity in opposite directions compete for the same binding site in the aptamer domain.

Allosteric Regulation↗
PubMed2005

Allosteric aptamers and aptazymes as probes for screening approaches.

Substantial effort is currently being devoted to engineering allosteric nucleic acids, aptamers and ribozymes for various applications in cellular and molecular biology, biotechnology and diagnostics. These molecular switches alter their different functional activities in response to specific binding molecules, including proteins, nucleic acids and small organic compounds. The interacting molecules trigger a response in the allosteric nucleic acid, which can be used for purposes such as real-time monitoring, high-throughput screening or gene expression control.

Allosteric Regulation↗