RING-like Domains Research Articles

Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava.

The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein-protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.

The E3 ubiquitin ligase Pellino2 mediates priming of the NLRP3 inflammasome

The NLRP3 inflammasome has an important function in inflammation by promoting the processing of pro-IL-1β and pro-IL-18 to their mature bioactive forms, and by inducing cell death via pyroptosis. Here we show a critical function of the E3 ubiquitin ligase Pellino2 in facilitating activation of the NLRP3 inflammasome. Pellino2-deficient mice and myeloid cells have impaired activation of NLRP3 in response to toll-like receptor priming, NLRP3 stimuli and bacterial challenge. These functions of Pellino2 in the NLRP3 pathway are dependent on Pellino2 FHA and RING-like domains, with Pellino2 promoting the ubiquitination of NLRP3 during the priming phase of activation. We also identify a negative function of IRAK1 in the NLRP3 inflammasome, and describe a counter-regulatory relationship between IRAK1 and Pellino2. Our findings reveal a Pellino2-mediated regulatory signaling system that controls activation of the NLRP3 inflammasome.

Preparation of Patterned Ultrathin TiO2 Films by Langmuir–Blodgett Method Using Mixed Monolayers of Octadecylamine and 1H,1H-Perfluoro-1-dodecanol

An approach for the preparation of patterned ultrathin TiO2 films is demonstrated by using phase-separated Langmuir monolayers, wherein the mixed monolayer of long-chain alkylamine and perfluoroalcohol is formed on an aqueous subphase containing potassium titanium oxalate, followed by deposition onto a solid substrate as a single-layer Langmuir–Blodgett (LB) film. Atomic force microscope observation of the LB films shows that ring-like TiO2 domains are formed on the surface of the substrate and that the size and shape of the TiO2 domains can be tuned by concentration of spreading solution as well as mixing ratio of the two film materials. Subsequent heat-treatment at 500 °C results in TiO2 films of 1.6 nm in thickness maintaining the ring-like pattern.

The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers.

BackgroundThe N-end rule pathway is a part of the ubiquitin–dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-zinc-stabilized heart-shaped fold.ResultsUsing sequence and structure analysis we argue that the UBR-box fold emerged from a binuclear RING-like treble clef zinc finger. The RING-like core is preserved in the UBR-box and the metal-chelating motifs display significant sequence and structural similarity to B-box and ZZ domains. UBR-box domains retrieved in our analysis co-occur with a variety of other protein domains, suggestive of its involvement in diverse biological roles. The UBR-box is a unique family of RING-like treble clefs as it displays a distinct circular permutation at the zinc-knuckle of the first zinc-binding site unlike other documented permutations of the RING-like domains which occur at the second zinc-binding site. The circular permutation of the RING-like treble clef scaffold has possibly aided the gain of a novel and relatively deep cleft suited for binding N-degrons. The N- and C-terminal extensions to the circularly permuted RING-like region bind a third zinc ion, which likely provides additional stability to the domain by keeping the two halves of the permuted zinc-knuckle together.ConclusionsStructural modifications and extensions to the RING-like core have resulted in a novel UBR-box fold, which can recognize and target the type 1 N-degron containing proteins for ubiquitin-mediated proteolysis. The UBR-box appears to have emerged during the expansion of ubiquitin system pathway-related functions in eukaryotes, but is also likely to have other non-N-recognin functions as well.ReviewersThis article was reviewed by Eugene Koonin, Balaji Santhanam, Kira S. Makarova.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0066-5) contains supplementary material, which is available to authorized users.

Determinants of the Drosophila Odorant Receptor Pattern

In most olfactory systems studied to date, neurons that express the same odorant receptor (Or) gene are scattered across sensory epithelia, intermingled with neurons that express different Or genes. In Drosophila, olfactory sensilla that express the same Or gene are dispersed on the antenna and the maxillary palp. Here we show that Or identity is specified in a spatially stereotyped pattern by the cell-autonomous activity of the transcriptional regulators Engrailed and Dachshund. Olfactory sensilla then become highly motile and disperse beneath the epidermis. Thus, positional information and cell motility underlie the dispersed patterns of Drosophila Or gene expression.

Three-dimensional magnetic solitons

Results are presented on the theoretical investigation of various three-dimensional structures in magnets, such as cnoidal and spiral hedgehogs in the Heisenberg model, localized textures, structures with a degree of mapping equal to unity, antiferromagnetic ringlike domains (“targets”), three-dimensional sources, two-dimensional and three-dimensional vortex and spiral structures in multisublattice antiferromagnets. Structure and properties of hopfions in a uniaxial ferromagnet are described.

Subunit organization and Rab interactions of Vps-C protein complexes that control endolysosomal membrane traffic

Traffic through late endolysosomal compartments is regulated by sequential signaling of small G proteins of the Rab5 and Rab7 families. The Saccharomyces cerevisiae Vps-C protein complexes CORVET (class C core vacuole/endosome tethering complex) and HOPS (homotypic fusion and protein transport) interact with endolysosomal Rabs to coordinate their signaling activities. To better understand these large and intricate complexes, we performed interaction surveys to assemble domain-level interaction topologies for the eight Vps-C subunits. We identified numerous intersubunit interactions and up to six Rab-binding sites. Functional modules coordinate the major Rab interactions within CORVET and HOPS. The CORVET-specific subunits, Vps3 and Vps8, form a subcomplex and physically and genetically interact with the Rab5 orthologue Vps21. The HOPS-specific subunits, Vps39 and Vps41, also form a subcomplex. Both subunits bind the Rab7 orthologue Ypt7, but with distinct nucleotide specificities. The in vivo functions of four RING-like domains within Vps-C subunits were analyzed and shown to have distinct functions in endolysosomal transport. Finally, we show that the CORVET- and HOPS-specific subunits Vps3 and Vps39 bind the Vps-C core through a common region within the Vps11 C-terminal domain (CTD). Biochemical and genetic experiments demonstrate the importance of these regions, revealing the Vps11 CTD as a key integrator of Vps-C complex assembly, Rab signaling, and endosomal and lysosomal traffic.

Turning the RING Domain Protein MdmX into an Active Ubiquitin-Protein Ligase*

The related RING domain proteins MdmX and Mdm2 are best known for their role as negative regulators of the tumor suppressor p53. However, although Mdm2 functions as a ubiquitin ligase for p53, MdmX does not have appreciable ubiquitin ligase activity. In this study, we performed a mutational analysis of the RING domain of MdmX, and we identified two distinct regions that, when replaced by the respective regions of Mdm2, turn MdmX into an active ubiquitin ligase for p53. Mdm2 and MdmX form homodimers as well as heterodimers with each other. One of the regions identified localizes to the dimer interface indicating that subtle conformational changes in this region either affect dimer stability and/or the interaction with the ubiquitin-conjugating enzyme UbcH5b. The second region contains the cryptic nucleolar localization signal of Mdm2 but is also assumed to be involved in the interaction with UbcH5b. Here, we show that this region has a significant impact on the ability of respective MdmX mutants to functionally interact with UbcH5b in vitro supporting the notion that this region serves two distinct functional purposes, nucleolar localization and ubiquitin ligase activity. Finally, evidence is provided to suggest that the RING domain of Mdm2 not only binds to UbcH5b but also acts as an allosteric activator of UbcH5b.

Morphological Wetting Transitions at Ring-Shaped Surface Domains

The wetting behavior of ring-shaped (or annular) surface domains is studied both experimentally and theoretically. The ring-shaped domains are lyophilic and embedded in a lyophobic substrate. Liquid droplets deposited on these domains can attain a variety of morphologies depending on the liquid volume and on the dimensions of the ringlike surface domains. In the experiments, the liquid volume is changed in a controlled manner by varying the temperature of the sample. Such a volume change leads to a characteristic sequence of droplet shapes and to morphological wetting transitions between these shapes. The experimental observations are in good agreement with analytical and numerical calculations based on the minimization of the interfacial free energy. Small droplets form ringlike liquid channels (or filaments) that are confined to the ring-shaped domains and do not spread onto the lyophobic disks enclosed by these rings. As one increases the volume of the droplets, one finds two different morphologies depending on the width of the ring-shaped domains. For narrow rings, the droplets form nonaxisymmetric liquid channels with a pronounced bulge. For broad rings, the droplets form axisymmetric caps that cover both the lyophilic rings and the lyophobic disks.

Three-dimensional structure of different functional forms of the Vibrio cholerae hemolysin oligomer: a cryo-electron microscopic study.

Vibrio cholerae hemolysin (HlyA) is a 65-kDa water-soluble pore-forming toxin that causes lysis of eukaryotic cells by destroying selective permeability of the plasma membrane bilayer. The HlyA monomer self-assembles on the target cell surface to the more stable beta-barrel amphipathic heptamer, which inserts into the membrane bilayer to form a diffusion channel. Deletion of the 15-kDa beta-prism lectin domain at the C terminus generates a 50-kDa hemolysin variant (HlyA50) with an approximately 1,000-fold decrease in hemolytic activity. Because functional differences are eventually dictated by structural differences, we determined three-dimensional structures of 65- and 50-kDa HlyA oligomers, using cryo-electron microscopy and single-particle methods. Our study clearly shows that the HlyA oligomer has sevenfold symmetry but that the HlyA50 oligomer is an asymmetric molecule. The HlyA oligomer has bowl-like, arm-like, and ring-like domains. The bowl-like domain is coupled with the ring-like domain, and seven side openings are present just beneath the ring-like domain. Although a central channel is present in both HlyA and HlyA50 oligomers, they differ in pore size as well as in shape of the molecules and channel. These structural differences may be relevant to the striking difference in efficiencies of functional channel formation by the two toxin forms.

Kinase-active Interleukin-1 Receptor-associated Kinases Promote Polyubiquitination and Degradation of the Pellino Family: DIRECT EVIDENCE FOR PELLINO PROTEINS BEING UBIQUITIN-PROTEIN ISOPEPTIDE LIGASES

Members of the Pellino family are interleukin-1 receptor-associated kinase (IRAK)-interacting proteins that possess RING-like domains. The presence of these domains led to the suggestion that Pellino proteins are ubiquitin-protein isopeptide ligases (E3). However, no conclusive data currently exist to prove this proposal. This study provides the first direct evidence that Pellino proteins possess E3 activity. Recombinant forms of Pellino1 and Pellino2 and both spliced variants of Pellino3 are shown in an in vitro ubiquitination assay to be E3 ligases that catalyze Lys(63)-linked polyubiquitination, with Pellino3 exhibiting the greatest ligase activity. Whereas the Pellino proteins cause polyubiquitination of IRAK-1, we also show that kinase-active members of the IRAK family (IRAK-1 and IRAK-4) promote reciprocal polyubiquitination of the Pellino proteins and that this is associated with IRAK-induced degradation of the Pellino family. In contrast, IRAK-2 (which lacks a functional kinase domain) and kinase-dead forms of IRAK-1 and IRAK-4 fail to degrade the Pellino proteins. We show that these kinase-inactive IRAK proteins can associate with Pellino proteins, thus excluding the possibility that their inability to regulate Pellino degradation is due to lack of association with the Pellino proteins. The physiological relevance of IRAK-induced degradation of Pellino proteins is confirmed by the demonstration that lipopolysaccharide causes degradation of endogenous forms of Pellino3 in peripheral blood mononuclear cells. In summary, this study not only demonstrates Pellino proteins to be E3 ligases that can catalyze Lys(63)-linked polyubiquitination but also shows bidirectional signaling between the IRAK and Pellino families and highlights a novel function for IRAK kinase activity.

Orientationally Controlled Nanoporous Cylindrical Domains in Polystyrene-b-poly(ferrocenylethylmethylsilane) Block Copolymer Films

The self-assembly of thin films of organometallic cylinder-forming amorphous polystyrene-block-polyferrocenylsilane diblock copolymers is described. By varying film thickness and/or the conditions of toluene during evaporation annealing, well-ordered arrays of hexagonally packed iron-rich cylindrical microdomains oriented either parallel to or normal to the substrate were produced. In the latter case, when the film thickness was very small (12−15 nm), well-defined nanoporous cylindrical domains were found. This unique morphology persists in UV ozone etched films where inorganic, ring-like cylindrical domains were produced. By varying the rate of solvent evaporation from solvent-swollen films, control over the orientation, order, and size of the cylindrical microdomains was achieved and variation of the fundamental morphology was observed.

A Novel Zinc Finger Protein Interacts with Receptor-interacting Protein (RIP) and Inhibits Tumor Necrosis Factor (TNF)- and IL1-induced NF-κB Activation

Receptor-interacting protein (RIP) is a serine/threonine protein kinase that is critically involved in tumor necrosis factor receptor-1 (TNF-R1)-induced NF-kappa B activation. In a yeast two-hybrid screening for potential RIP-interacting proteins, we identified ZIN (zinc finger protein inhibiting NF-kappa B), a novel protein that specifically interacts with RIP. ZIN contains four RING-like zinc finger domains at the middle and a proline-rich domain at the C terminus. Overexpression of ZIN inhibits RIP-, IKK beta-, TNF-, and IL1-induced NF-kappa B activation in a dose-dependent manner in 293 cells. Domain mapping experiments indicate that the RING-like zinc finger domains of ZIN are required for its interaction with RIP and inhibition of RIP-mediated NF-kappa B activation. Overexpression of ZIN also potentiates RIP- and TNF-induced apoptosis. Moreover, immunofluorescent staining indicates that ZIN is a cytoplasmic protein and that it colocalizes with RIP. Our findings suggest that ZIN is an inhibitor of TNF- and IL1-induced NF-kappa B activation pathways.

Chain and ring structures in smectic phases of molecules with transverse dipoles

Systems of hard spherocylinders with central transverse point dipoles are studied by Monte Carlo simulation. The dipoles are seen to stabilise the formation of the smectic-A phase relative to the nematic phase; the nematic phase disappears altogether at low temperatures. In the smectic-A phase the cores of the molecules align parallel to the layer normal with the dipoles in the plane. At high temperatures the dipoles are orientationally disordered; as the temperature is lowered ring-like domains appear, and then elongated antiferroelectric chain-like domains form. We analyse these results in the context of recent studies on two-dimensional vortex-antivortex systems.

A superadditive time coordinate for the closed bosonic string

The possibility of using the moduli of ringlike domains on the world sheet to define a conformal invariant notion of time intervals for closed bosonic strings is investigated. It is demonstrated that time intervals for neighboring domains on the world sheet defined in this way in general do not add up, rather they behave superadditive.

A variational approach to closed bosonic strings on bordered Riemann surfaces

Polyakov's path integral for bosonic closed strings defined on a bordered Riemann surface is investigated by variational methods. It is demonstrated that boundary variations are generated by the Virasoro operators. The investigation is performed for both, simply connected Riemann surfaces as well as ringlike domains. It is shown that the form of the variational operator is the same on both kinds of surfaces. The Virasoro algebra arises as a consistency condition for the variation.