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1.  Structural mechanism of cytosolic DNA sensing by cGAS 
Nature  2013;498(7454):332-337.
Summary
Cytosolic DNA arising from intracellular bacteria or viral infections is a powerful pathogen-associated molecular pattern (PAMP) that leads to innate immune host defense by the production of type I interferon and inflammatory cytokines. Recognition of cytosolic DNA by the recently discovered cyclic-GMP-AMP (cGA) synthase (cGAS) induces the production of cGA to activate the stimulator of interferon genes (STING). Here we report the crystal structure of cGAS alone and in complex with DNA, ATP and GTP along with functional studies. Our results explain cGAS’ broad specificity DNA sensing, show how cGAS catalyzes di-nucleotide formation and indicate activation by a DNA-induced structural switch. cGAS possesses a remarkable structural similarity to the antiviral cytosolic dsRNA sensor 2’-5’oligoadenylate synthase (OAS1), but contains a unique zinc-thumb that recognizes B-form dsDNA. Our results mechanistically unify dsRNA and dsDNA innate immune sensing by OAS1 and cGAS nucleotidyl transferases.
doi:10.1038/nature12305
PMCID: PMC3768140  PMID: 23722159
2.  Sensing of viral nucleic acids by RIG-I: from translocation to translation 
The innate immune system is a first layer of defense against infection by pathogens. It responds to pathogens by activating host defense mechanisms via interferon and inflammatory cytokine expression. Pathogen associated molecular patterns (PAMPs) are sensed by specific pattern recognition receptors. Among those, the ATP dependent helicase related RIG-I like receptors RIG-I, MDA5 and LGP2 sense the presence of viral RNA in the cytoplasm of host cells. While the precise PAMPs and functions of MDA5 or LGP2 are still unclear, RIG-I senses predominantly viral RNA containing a 5’-triphosphate along with dsRNA regions. Here we review out current knowledge how these PAMPs are sensed and integrated by RIG-I, and how RIG-I’s innate immune function can be used in translational medical approaches.
doi:10.1016/j.ejcb.2011.01.015
PMCID: PMC3155743  PMID: 21496944
3.  Nuclear actin-related proteins take shape 
Bioarchitecture  2011;1(4):192-195.
The function of nuclear actin is poorly understood. It is known to be a discrete component of several chromatin-modifying complexes. Nevertheless, filamentous forms of actin are important for various nuclear processes as well. Nuclear actin is often associated with nuclear actin-related protein Arp4 and other actin-related proteins like Arp8 in the INO80 chromatin remodeler. We recently determined the crystal structure of S. cerevisiae Arp4 that explains why Arp4 is unable to form actin like filaments and shows that it is constitutively bound to an ATP nucleotide. More interestingly, in vitro activities of Arp4 and Arp8 seem to be directed towards stabilizing monomeric actin and to integrate it stoichiometrically into the INO80 complex. Based on this activity, we discuss possible roles of nuclear Arps in chromatin modifying complexes and in regulating more general aspects of nuclear actin dynamics.
doi:10.4161/bioa.1.4.17643
PMCID: PMC3210522  PMID: 22069513
actin-related proteins; chromatin remodeling; INO80 complex; nuclear actin
4.  Processive RNA decay by the exosome 
RNA Biology  2011;8(1):55-60.
RNA exosomes are large multi-subunit protein complexes involved in controlled and processive 3′ to 5′ RNA degradation. Exosomes form large molecular chambers and harbor multiple nuclease sites as well as RNA binding regions. This makes a quantitative kinetic analysis of RNA degradation with reliable parameter and error estimates challenging. For instance, recent quantitative biochemical assays revealed that degradation speed and efficiency depend on various factors, such as the type of RNA binding caps and the RNA length. We propose the combination of a differential equation model with Bayesian Markov Chain Monte Carlo (MCMC) sampling for a more robust and reliable analysis of such complex kinetic systems. Using the exosome as a paradigm, it is shown that conventional “best fit” approaches to parameter estimation are outperformed by the MCMC method. The parameter distribution returned by MCMC sampling allows for a reliable and meaningful comparison of the data from different time series. In the case of the exosome, we find that the cap structures of the exosome have a direct effect on the recruitment and degradation of RNA, and that these effects are RNA length-dependent. The described approach can be widely applied to any processive reaction with a similar kinetics like the XRN1-dependent RNA degradation, RNA/DNA synthesis by polymerases and protein synthesis by the ribosome.
doi:10.4161/rna.8.1.14067
PMCID: PMC3127079  PMID: 21282980
RNA degradation; exosome structure; processive enzymes; enzyme kinetics; bayesian inference; parameter estimation; Markov Chain Monte Carlo sampling
5.  Epitope interactions of monoclonal antibodies targeting CD20 and their relationship to functional properties 
mAbs  2013;5(1):22-33.
Several novel anti-CD20 monoclonal antibodies are currently in development with the aim of improving the treatment of B cell malignancies. Mutagenesis and epitope mapping studies have revealed differences between the CD20 epitopes recognized by these antibodies. Recently, X-ray crystallography studies confirmed that the Type I CD20 antibody rituximab and the Type II CD20 antibody obinutuzumab (GA101) differ fundamentally in their interaction with CD20 despite recognizing a partially overlapping epitope on CD20. The Type I CD20 antibodies rituximab and ofatumumab are known to bind to different epitopes. The differences suggest that the biological properties of these antibodies are not solely determined by their core epitope sequences, but also depend on other factors, such as the elbow hinge angle, the orientation of the bound antibody and differential effects mediated by the Fc region of the antibody. Taken together, these factors may explain differences in the preclinical properties and clinical efficacy of anti-CD20 antibodies.
doi:10.4161/mabs.22771
PMCID: PMC3564883  PMID: 23211638
Rituximab; obinutuzumab; ofatumumab; GA101; structure; type I; type II; non-Hodgkin lymphoma; immunotherapy; leukemia
6.  Swi2/Snf2 remodelers: hybrid views on hybrid molecular machines 
Summary
Swi2/Snf2 (switch / sucrose non-fermentable) enzymes form a large and diverse class of proteins and multiprotein assemblies that remodel nucleic acid:protein complexes, using the energy of ATP hydrolysis. The core Swi2/Snf2 type ATPase domain belongs to the “helicase and NTP driven nucleic acid translocase” superfamily 2 (SF2). It serves as a motor that functionally and structurally interacts with different targeting domains and functional modules to drive a plethora of different remodeling activities in chromatin structure and dynamics, transcription regulation and DNA repair. Recent progress on the interaction of Swi2/Snf2 enzymes and multiprotein assemblies with their substrate nucleic acids and proteins, using hybrid structural biology methods, sheds light onto mechanisms of the complex chemo-mechanical remodeling reactions. In the case of Mot1, a hybrid mechanism of remodeler and chaperone emerged.
doi:10.1016/j.sbi.2012.02.007
PMCID: PMC3323801  PMID: 22445226
7.  Cytosolic viral sensor RIG-I is a 5′-triphosphate dependent translocase on double stranded RNA 
Science (New York, N.Y.)  2009;323(5917):1070-1074.
RIG-I is a cytosolic multi-domain protein that detects viral RNA and elicits an antiviral immune response. Two N-terminal caspase activation and recruitment domains (CARDs) transmit the signal and the regulatory domain prevents signaling in the absence of viral RNA. 5′-triphosphate and double stranded (ds) RNA are two molecular patterns that enable RIG-I to discriminate pathogenic from self-RNA. However, the function of the ATPase domain that is also required for activity is less clear. Using single-molecule fluorescence assays we discovered a robust, ATP-powered dsRNA translocation activity of RIG-I. The CARDs dramatically suppress translocation in the absence of 5′f-triphosphate and the activation by 5′-triphosphate triggers RIG-I to translocate preferentially on dsRNA in cis. This functional integration of two RNA molecular patterns may provide a means to specifically sense and counteract replicating viruses.
doi:10.1126/science.1168352
PMCID: PMC3567915  PMID: 19119185
8.  Structural biology of the Mre11:Nbs1 complex structure yields insights into ataxia–telangiectasia–like disease mutations and DNA damage signaling 
Summary
The Mre11–Rad50–Nbs1 (MRN) complex tethers, processes and signals DNA double strand breaks, promoting genomic stability. To understand the functional architecture of MRN, we determined the crystal structures of the Schizosaccharomyces pombe Mre11 dimeric catalytic domain alone and in complex with a fragment of Nbs1. Two Nbs1 subunits stretch around the outside of Mre11’s nuclease domains, with one subunit additionally bridging and locking the Mre11 dimer via a highly conserved asymmetrical binding motif. Our results reveal that Mre11 forms a flexible dimer and suggest that Nbs1 is not only a checkpoint adaptor, but also functionally impacts on Mre11-Rad50. Clinical mutations in Mre11 are located along the Nbs1 interaction sites and weaken the Mre11–Nbs1 interaction. However, they differentially affect DNA repair and telomere maintenance in Saccharomyces cerevisiae, potentially providing insight into their different human disease pathologies.
doi:10.1038/nsmb.2323
PMCID: PMC3392456  PMID: 22705791
9.  Structure of Actin-related protein 8 and its contribution to nucleosome binding 
Nucleic Acids Research  2012;40(21):11036-11046.
Nuclear actin-related proteins (Arps) are subunits of several chromatin remodelers, but their molecular functions within these complexes are unclear. We report the crystal structure of the INO80 complex subunit Arp8 in its ATP-bound form. Human Arp8 has several insertions in the conserved actin fold that explain its inability to polymerize. Most remarkably, one insertion wraps over the active site cleft and appears to rigidify the domain architecture, while active site features shared with actin suggest an allosterically controlled ATPase activity. Quantitative binding studies with nucleosomes and histone complexes reveal that Arp8 and the Arp8–Arp4–actin-HSA sub-complex of INO80 strongly prefer nucleosomes and H3–H4 tetramers over H2A–H2B dimers, suggesting that Arp8 functions as a nucleosome recognition module. In contrast, Arp4 prefers free (H3–H4)2 over nucleosomes and may serve remodelers through binding to (dis)assembly intermediates in the remodeling reaction.
doi:10.1093/nar/gks842
PMCID: PMC3510490  PMID: 22977180
10.  The Mre11:Rad50 structure shows an ATP dependent molecular clamp in DNA double-strand break repair 
Cell  2011;145(1):54-66.
Summary
The MR (Mre11 nuclease and Rad50 ABC ATPase) complex is an evolutionarily conserved sensor for DNA double-strand breaks, highly genotoxic lesions linked to cancer development. MR can recognize and process DNA ends even if they are blocked and misfolded. To reveal its mechanism, we determined the crystal structure of the catalytic head of Thermotoga maritima MR and analyzed ATP dependent conformational changes. MR adopts an open form with a central Mre11 nuclease dimer and two peripheral Rad50 molecules, a form suited for sensing obstructed breaks. The Mre11 C-terminal helix-loop-helix domain binds Rad50 and attaches flexibly to the nuclease domain, enabling large conformational changes. ATP binding to the two Rad50 subunits induces a rotation of the Mre11 helix-loop-helix and Rad50 coiled-coil domains, creating a clamp conformation with increased DNA binding activity. The results suggest that MR is an ATP controlled transient molecular clamp at DNA double-strand breaks
doi:10.1016/j.cell.2011.02.038
PMCID: PMC3071652  PMID: 21458667
Rad50; Mre11; DNA double-strand break repair; X-ray crystallography; protein complex; homologous recombination; ABC ATPases
11.  Structure and mechanism of the Swi2/Snf2 remodeler Mot1 in complex with its substrate TBP 
Nature  2011;475(7356):403-407.
Swi2/Snf2-type ATPases broadly regulate genome-associated processes such as transcription, replication and repair by catalyzing disruption, assembly, or remodeling of nucleosomes or other protein:DNA complexes1,2. ATP-driven motor activity along DNA has been suggested to disrupt target protein:DNA interactions in the remodeling reaction3–5. However, the complex and highly specific remodeling reactions are poorly understood, mostly because we lack high-resolution structural information on how remodelers bind their substrate proteins. Mot1 (modifier of transcription 1, denoted BTAF1 in humans) is a Swi2/Snf2 enzyme that specifically displaces TATA box binding protein (TBP) from promoter DNA and globally regulates transcription by generating a highly dynamic TBP pool in the cell6,7. As a Swi2/Snf2 enzyme that functions as a single polypeptide and interacts with a relatively simple substrate, Mot1 offers an ideal system for a better understanding of this important enzyme family. To reveal how Mot1 specifically disrupts TBP:DNA, we combined crystal and electron microscopy structures of Mot1:TBP complexes with biochemical studies. Here we show that Mot1 wraps around TBP and appears to act like a bottle opener: a spring-like array of 16 HEAT (huntingtin, elongation factor 3, PP2A and lipid kinase TOR) repeats grips the DNA distal side of TBP via loop insertions, while the Swi2/Snf2 domain binds upstream DNA, positioned to weaken TBPs DNA interaction by DNA translocation. A “latch” subsequently blocks TBP’s DNA binding groove, acting as a chaperone to prevent DNA re-association for efficient promoter clearance. This work shows how a remodeling enzyme can combine both motor and chaperone activities to achieve functional specificity using a conserved Swi2/Snf2 translocase.
doi:10.1038/nature10215
PMCID: PMC3276066  PMID: 21734658
12.  Syk Kinase-Coupled C-type Lectin Receptors Engage Protein Kinase C-δ to Elicit Card9 Adaptor-Mediated Innate Immunity 
Immunity  2012;36(1-2):32-42.
Summary
C-type lectin receptors (CLRs) that couple with the kinase Syk are major pattern recognition receptors for the activation of innate immunity and host defense. CLRs recognize fungi and other forms of microbial or sterile danger, and they induce inflammatory responses through the adaptor protein Card9. The mechanisms relaying CLR proximal signals to the core Card9 module are unknown. Here we demonstrated that protein kinase C-δ (PKCδ) was activated upon Dectin-1-Syk signaling, mediated phosphorylation of Card9 at Thr231, and was responsible for Card9-Bcl10 complex assembly and canonical NF-κB control. Prkcd−/− dendritic cells, but not those lacking PKCα, PKCβ, or PKCθ, were defective in innate responses to Dectin-1, Dectin-2, or Mincle stimulation. Moreover, Candida albicans-induced cytokine production was blocked in Prkcd−/− cells, and Prkcd−/− mice were highly susceptible to fungal infection. Thus, PKCδ is an essential link between Syk activation and Card9 signaling for CLR-mediated innate immunity and host protection.
Highlights
► Dectin-1-Syk stimulation activates PKCδ in dendritic cells ► PKCδ controls Card9-Bcl10 complex assembly for canonical NF-κB activation ► Prkcd−/− cells are defective in Dectin-1-, Dectin-2-, or Mincle-triggered responses ► PKCδ is essential for innate antifungal immunity and host protection in vivo
doi:10.1016/j.immuni.2011.11.015
PMCID: PMC3477316  PMID: 22265677
13.  ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex 
Nucleic Acids Research  2011;40(2):914-927.
DNA double-strand breaks (DSBs) threaten genome stability in all kingdoms of life and are linked to cancerogenic chromosome aberrations in humans. The Mre11:Rad50 (MR) complex is an evolutionarily conserved complex of two Rad50 ATPases and a dimer of the Mre11 nuclease that senses and processes DSBs and tethers DNA for repair. ATP binding and hydrolysis by Rad50 is functionally coupled to DNA-binding and tethering, but also regulates Mre11's nuclease in processing DNA ends. To understand how ATP controls the interaction between Mre11 and Rad50, we determined the crystal structure of Thermotoga maritima (Tm) MR trapped in an ATP/ADP state. ATP binding to Rad50 induces a large structural change from an open form with accessible Mre11 nuclease sites into a closed form. Remarkably, the NBD dimer binds in the Mre11 DNA-binding cleft blocking Mre11's dsDNA-binding sites. An accompanying large swivel of the Rad50 coiled coil domains appears to prepare the coiled coils for DNA tethering. DNA-binding studies show that within the complex, Rad50 likely forms a dsDNA-binding site in response to ATP, while the Mre11 nuclease module retains a ssDNA-binding site. Our results suggest a possible mechanism for ATP-dependent DNA tethering and DSB processing by MR.
doi:10.1093/nar/gkr749
PMCID: PMC3258140  PMID: 21937514
14.  Quantitative analysis of processive RNA degradation by the archaeal RNA exosome 
Nucleic Acids Research  2010;38(15):5166-5176.
RNA exosomes are large multisubunit assemblies involved in controlled RNA processing. The archaeal exosome possesses a heterohexameric processing chamber with three RNase-PH-like active sites, capped by Rrp4- or Csl4-type subunits containing RNA-binding domains. RNA degradation by RNA exosomes has not been studied in a quantitative manner because of the complex kinetics involved, and exosome features contributing to efficient RNA degradation remain unclear. Here we derive a quantitative kinetic model for degradation of a model substrate by the archaeal exosome. Markov Chain Monte Carlo methods for parameter estimation allow for the comparison of reaction kinetics between different exosome variants and substrates. We show that long substrates are degraded in a processive and short RNA in a more distributive manner and that the cap proteins influence degradation speed. Our results, supported by small angle X-ray scattering, suggest that the Rrp4-type cap efficiently recruits RNA but prevents fast RNA degradation of longer RNAs by molecular friction, likely by RNA contacts to its unique KH-domain. We also show that formation of the RNase-PH like ring with entrapped RNA is not required for high catalytic efficiency, suggesting that the exosome chamber evolved for controlled processivity, rather than for catalytic chemistry in RNA decay.
doi:10.1093/nar/gkq238
PMCID: PMC2926604  PMID: 20392821
15.  Structure and DNA binding activity of the mouse condensin hinge domain highlight common and diverse features of SMC proteins 
Nucleic Acids Research  2010;38(10):3454-3465.
Structural Maintenance of Chromosomes (SMC) proteins are vital for a wide range of processes including chromosome structure and dynamics, gene regulation and DNA repair. Eukaryotes have three SMC complexes, consisting of heterodimeric pairs of six different SMC proteins along with several specific regulatory subunits. In addition to their other functions, all three SMC complexes play distinct roles in DNA repair. Cohesin (SMC1–SMC3) is involved in DNA double-strand break repair, condensin (SMC2–SMC4) participates in single-strand break (SSB) repair, and the SMC5–SMC6 complex functions in various DNA repair pathways. SMC proteins consist of N- and C-terminal domains that fold back onto each other to create an ATPase ‘head’ domain, connected to a central ‘hinge’ domain via long coiled-coils. The hinge domain mediates dimerization of SMC proteins and binds DNA, but it is not clear to what purpose this activity serves. We studied the structure and function of the condensin hinge domain from mouse. While the SMC hinge domain structure is largely conserved from prokaryotes to eukaryotes, its function seems to have diversified throughout the course of evolution. The condensin hinge domain preferentially binds single-stranded DNA. We propose that this activity plays a role in the SSB repair function of the condensin complex.
doi:10.1093/nar/gkq038
PMCID: PMC2879519  PMID: 20139420
16.  The regulatory domain of the RIG-I family ATPase LGP2 senses double-stranded RNA 
Nucleic Acids Research  2009;37(6):2014-2025.
RIG-I and MDA5 sense cytoplasmic viral RNA and set-off a signal transduction cascade, leading to antiviral innate immune response. The third RIG-I-like receptor, LGP2, differentially regulates RIG-I- and MDA5-dependent RNA sensing in an unknown manner. All three receptors possess a C-terminal regulatory domain (RD), which in the case of RIG-I senses the viral pattern 5′-triphosphate RNA and activates ATP-dependent signaling by RIG-I. Here we report the 2.6 Å crystal structure of LGP2 RD along with in vitro and in vivo functional analyses and a homology model of MDA5 RD. Although LGP2 RD is structurally related to RIG-I RD, we find it rather binds double-stranded RNA (dsRNA) and this binding is independent of 5′-triphosphates. We identify conserved and receptor-specific parts of the RNA binding site. Latter are required for specific dsRNA binding by LGP2 RD and could confer pattern selectivity between RIG-I-like receptors. Our data furthermore suggest that LGP2 RD modulates RIG-I-dependent signaling via competition for dsRNA, another pattern sensed by RIG-I, while a fully functional LGP2 is required to augment MDA5-dependent signaling.
doi:10.1093/nar/gkp059
PMCID: PMC2665237  PMID: 19208642
17.  Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle 
Nucleic Acids Research  2008;36(6):1881-1890.
Remodelling protein nucleic acid interfaces is an important biological task, which is often carried out by nucleic acid stimulated ATPases of the Swi2/Snf2 superfamily. Here we study the mechano-chemical cycle of such an ATPase, namely the catalytic domain of the Sulfolobus solfataricus Rad54 homologue (SsoRad54cd), by means of fluorescence resonance energy transfer (FRET). The results of the FRET studies show that the enzyme can be found in (at least) two different possible conformations in solution. An open conformation, consistent with a recently reported crystal structure, is converted into a closed conformation after DNA binding. Upon subsequent binding of ATP no further change in conformation can be detected by the FRET measurements. Instead, a FRET detectable conformational change occurs after ATP hydrolysis and prior to ADP release, suggesting a powerstroke that is linked to phosphate release. Based on these data we will present a new model for the mechano-chemical cycle of this enzyme. This scheme in turn provides a working model for understanding the function of other members of the Swi2/Snf2 family.
doi:10.1093/nar/gkn040
PMCID: PMC2346605  PMID: 18267970
18.  Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures 
Nucleic Acids Research  2006;34(15):4160-4167.
Proteins with sequence similarity to the yeast Snf2 protein form a large family of ATPases that act to alter the structure of a diverse range of DNA–protein structures including chromatin. Snf2 family enzymes are related in sequence to DExx box helicases, yet they do not possess helicase activity. Recent biochemical and structural studies suggest that the mechanism by which these enzymes act involves ATP-dependent translocation on DNA. Crystal structures suggest that these enzymes travel along the minor groove, a process that can generate the torque or energy in remodelling processes. We review the recent structural and biochemical findings which suggest a common mechanistic basis underlies the action of many of both Snf2 family and DExx box helicases.
doi:10.1093/nar/gkl540
PMCID: PMC1616948  PMID: 16935875
19.  Structural and functional analysis of Mre11-3 
Nucleic Acids Research  2004;32(6):1886-1893.
The Mre11, Rad50 and Nbs1 proteins make up the conserved multi-functional Mre11 (MRN) complex involved in multiple, critical DNA metabolic processes including double-strand break repair and telomere maintenance. The Mre11 protein is a nuclease with broad substrate recognition, but MRN-dependent processes requiring the nuclease activity are not clearly defined. Here, we report the functional and structural characterization of a nuclease-deficient Mre11 protein termed mre11-3. Importantly, the hmre11-3 protein has wild-type ability to bind DNA, Rad50 and Nbs1; however, nuclease activity was completely abrogated. When expressed in cell lines from patients with ataxia telangiectasia-like disorder (ATLD), hmre11-3 restored the formation of ionizing radiation-induced foci. Consistent with the biochemical results, the 2.3 Å crystal structure of mre11-3 from Pyrococcus furiosus revealed an active site structure with a wild-type-like metal-binding environment. The structural analysis of the H85L mutation provides a detailed molecular basis for the ability of mre11-3 to bind but not hydrolyze DNA. Together, these results establish that the mre11-3 protein provides an excellent system for dissecting nuclease-dependent and independent functions of the Mre11 complex.
doi:10.1093/nar/gkh343
PMCID: PMC390353  PMID: 15047855
20.  Mre11 and Rad50 from Pyrococcus furiosus: Cloning and Biochemical Characterization Reveal an Evolutionarily Conserved Multiprotein Machine 
Journal of Bacteriology  2000;182(21):6036-6041.
The processing of DNA double-strand breaks is a critical event in nucleic acid metabolism. This is evidenced by the severity of phenotypes associated with deficiencies in this process in multiple organisms. The core component involved in double-strand break repair in eukaryotic cells is the Mre11-Rad50 protein complex, which includes a third protein, p95, in humans and Xrs2 in yeasts. Homologues of Mre11 and Rad50 have been identified in all kingdoms of life, while the Nbs1 protein family is found only in eukaryotes. In eukaryotes the Mre11-Rad50 complex has nuclease activity that is modulated by the addition of ATP. We have isolated the Mre11 and Rad50 homologues from the thermophilic archaeon Pyrococcus furiosus and demonstrate that the two proteins exist in a large, heat-stable complex that possesses single-strand endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. These findings verify the identification of the P. furiosus Rad50 and Mre11 homologues and demonstrate that functional homologues with similar biochemical properties exist in all kingdoms of life.
PMCID: PMC94736  PMID: 11029422
21.  Reversible and Controllable Nanolocomotion of an RNA-Processing Machinery 
Nano Letters  2010;10(12):5123-5130.
Molecular motors have inspired many avenues of research for nanotechnology but most molecular motors studied so far allow only unidirectional movement. The archaeal RNA-exosome is a reversible motor that can either polymerize or degrade an RNA strand, depending on the chemical environments. We developed a single molecule fluorescence assay to analyze the real time locomotion of this nanomachine on RNA. Despite the multimeric structure, the enzyme followed the Michaelis−Menten kinetics with the maximum speed of ∼3 nucleotides/s, showing that the three catalytic cylinders do not fire cooperatively. We also demonstrate rapid directional switching on demand by fluidic control. When the two reaction speeds are balanced on average, the enzyme shows a memory of the previous reaction it catalyzed and stochastically switches between primarily polymerizing and primarily degrading behaviors. The processive, reversible, and controllable locomotion propelled by this nanomachine has a promising potential in environmental sensing, diagnostic, and cargo delivery applications.
doi:10.1021/nl103754z
PMCID: PMC2999004  PMID: 21082788
Archaeal exosome; RNA degradation; RNA polymerization; nanolocomotion; nanomotor; single molecule FRET technique
23.  In Vivo Ligands of MDA5 and RIG-I in Measles Virus-Infected Cells 
PLoS Pathogens  2014;10(4):e1004081.
RIG-I-like receptors (RLRs: RIG-I, MDA5 and LGP2) play a major role in the innate immune response against viral infections and detect patterns on viral RNA molecules that are typically absent from host RNA. Upon RNA binding, RLRs trigger a complex downstream signaling cascade resulting in the expression of type I interferons and proinflammatory cytokines. In the past decade extensive efforts were made to elucidate the nature of putative RLR ligands. In vitro and transfection studies identified 5′-triphosphate containing blunt-ended double-strand RNAs as potent RIG-I inducers and these findings were confirmed by next-generation sequencing of RIG-I associated RNAs from virus-infected cells. The nature of RNA ligands of MDA5 is less clear. Several studies suggest that double-stranded RNAs are the preferred agonists for the protein. However, the exact nature of physiological MDA5 ligands from virus-infected cells needs to be elucidated. In this work, we combine a crosslinking technique with next-generation sequencing in order to shed light on MDA5-associated RNAs from human cells infected with measles virus. Our findings suggest that RIG-I and MDA5 associate with AU-rich RNA species originating from the mRNA of the measles virus L gene. Corresponding sequences are poorer activators of ATP-hydrolysis by MDA5 in vitro, suggesting that they result in more stable MDA5 filaments. These data provide a possible model of how AU-rich sequences could activate type I interferon signaling.
Author Summary
RIG-I-like receptors (RLRs) are helicase-like molecules that detect cytosolic RNAs that are absent in the non-infected host. Upon binding to specific RNA patterns, RLRs elicit a signaling cascade that leads to host defense via the production of antiviral molecules. To understand how RLRs sense RNA, it is important to characterize the nature and origin of RLR-associated RNA from virus-infected cells. While it is well established that RIG-I binds 5′-triphosphate containing double-stranded RNA, the in vivo occurring ligand for MDA5 is poorly characterized. A major challenge in examining MDA5 agonists is the apparently transient interaction between the protein and its ligand. To improve the stability of interaction, we have used an approach to crosslink MDA5 to RNA in measles virus-infected cells. The virus-infected cells were treated with the photoactivatable nucleoside analog 4-thiouridine, which is incorporated in newly synthesized RNA. Upon 365 nm UV light exposure of living cells, a covalent linkage between the labeled RNA and the receptor protein is induced, resulting in a higher RNA recovery from RLR immunoprecipitates. Based on next generation sequencing, bioinformatics and in vitro approaches, we observed a correlation between the AU-composition of viral RNA and its ability to induce an MDA5-dependent immune response.
doi:10.1371/journal.ppat.1004081
PMCID: PMC3990713  PMID: 24743923
24.  Activating FLT3 Mutants Show Distinct Gain-of-Function Phenotypes In Vitro and a Characteristic Signaling Pathway Profile Associated with Prognosis in Acute Myeloid Leukemia 
PLoS ONE  2014;9(3):e89560.
About 30% of patients with acute myeloid leukemia (AML) harbour mutations of the receptor tyrosine kinase FLT3, mostly internal tandem duplications (ITD) and point mutations of the second tyrosine kinase domain (TKD). It was the aim of this study to comprehensively analyze clinical and functional properties of various FLT3 mutants.
In 672 normal karyotype AML patients FLT3-ITD, but not FLT3-TKD mutations were associated with a worse relapse free and overall survival in multivariate analysis. In paired diagnosis-relapse samples FLT3-ITD showed higher stability (70%) compared to FLT3-TKD (30%). In vitro, FLT3-ITD induced a strong activating phenotype in Ba/F3 cells. In contrast, FLT3-TKD mutations and other point mutations – including two novel mutations – showed a weaker but clear gain-of-function phenotype with gradual increase in proliferation and protection from apoptosis. The pro-proliferative capacity of the investigated FLT3 mutants was associated with cell surface expression and tyrosine 591 phosphorylation of the FLT3 receptor. Western blot experiments revealed STAT5 activation only in FLT3-ITD positive cell lines, in contrast to FLT3-non-ITD mutants, which displayed an enhanced signal of AKT and MAPK activation. Gene expression analysis revealed distinct difference between FLT3-ITD and FLT3-TKD for STAT5 target gene expression as well as deregulation of SOCS2, ENPP2, PRUNE2 and ART3.
FLT3-ITD and FLT3 point mutations show a gain-of-function phenotype with distinct signalling properties in vitro. Although poor prognosis in AML is only associated with FLT3-ITD, all activating FLT3 mutations can contribute to leukemogenesis and are thus potential targets for therapeutic interventions.
doi:10.1371/journal.pone.0089560
PMCID: PMC3946485  PMID: 24608088
25.  NK cells from an AML patient have recovered in remission and reached comparable cytolytic activity to that of a healthy monozygotic twin mediated by the single-chain triplebody SPM-2 
Background
The capacity of patient’s Natural Killer cells (NKs) to be activated for cytolysis is an important prerequisite for the success of antibody-derived agents such as single-chain triplebodies (triplebodies) in cancer therapy. NKs recovered from AML patients at diagnosis are often found to be reduced in peripheral blood titers and cytolytic activity. Here, we had the unique opportunity to compare blood titers and cytolytic function of NKs from an AML patient with those of a healthy monozygotic twin. The sibling’s NKs were compared with the patient’s drawn either at diagnosis or in remission after chemotherapy. The cytolytic activities of NKs from these different sources for the patient’s autologous AML blasts and other leukemic target cells in conjunction with triplebody SPM-2, targeting the surface antigens CD33 and CD123 on the AML cells, were compared.
Methods
Patient NKs drawn at diagnosis were compared to NKs drawn in remission after chemotherapy and a sibling’s NKs, all prepared from PBMCs by immunomagnetic beads (MACS). Redirected lysis (RDL) assays using SPM-2 and antibody-dependent cellular cytotoxicity (ADCC) assays using the therapeutic antibody RituximabTM were performed with the enriched NKs. In addition, MACS-sorted NKs were analyzed for NK cell activating receptors (NCRs) by flow cytometry, and the release of TNF-alpha and IFN-gamma from blood samples of both siblings after the addition of the triplebody were measured in ELISA-assays.
Results
Patient NKs isolated from peripheral blood drawn in remission produced comparable lysis as NKs from the healthy twin against the patient’s autologous bone marrow (BM) blasts, mediated by SPM-2. The NCR receptor expression profiles on NKs from patient and twin were similar, but NK cell titers in peripheral blood were lower for samples drawn at diagnosis than in remission.
Conclusions
Peripheral blood NK titers and ex vivo cytolytic activities mediated by triplebody SPM-2 were comparable for cells drawn from an AML patient in remission and a healthy twin. If these results can be generalized, then NKs from AML patients in remission are sufficient in numbers and cytolytic activity to make triplebodies promising new agents for the treatment of AML.
doi:10.1186/1479-5876-11-289
PMCID: PMC3842817  PMID: 24237598
Single chain triplebody (triplebodies); Antibody-dependent cellular cytotoxicity (ADCC); Natural killer (NK) cells; Acute myeloid leukemia (AML); Cancer immunotherapy

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