SMART 7: recent updates to the protein domain annotation resource

SMART (Simple Modular Architecture Research Tool) is an online resource (http://smart.embl.de/) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 7 contains manually curated models for 1009 protein domains, 200 more than in the previous version. The current release introduces several novel features and a streamlined user interface resulting in a faster and more comfortable workflow. The underlying protein databases were greatly expanded, resulting in a 2-fold increase in number of annotated domains and features. The database of completely sequenced genomes now includes 1133 species, compared to 630 in the previous release. Domain architecture analysis results can now be exported and visualized through the iTOL phylogenetic tree viewer. ‘metaSMART’ was introduced as a novel subresource dedicated to the exploration and analysis of domain architectures in various metagenomics data sets. An advanced full text search engine was implemented, covering the complete annotations for SMART and Pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information

Crystal structures of the human Dysferlin inner DysF domain

Background: Mutations in dysferlin, the first protein linked with the cell membrane repair mechanism, causes a group of muscular dystrophies called dysferlinopathies. Dysferlin is a type two-anchored membrane protein, with a single C terminal trans-membrane helix, and most of the protein lying in cytoplasm. Dysferlin contains several C2 domains and two DysF domains which are nested one inside the other. Many pathogenic point mutations fall in the DysF domain region. Results: We describe the crystal structure of the human dysferlin inner DysF domain with a resolution of 1.9 Angstroms. Most of the pathogenic mutations are part of aromatic/arginine stacks that hold the domain in a folded conformation. The high resolution of the structure show that these interactions are a mixture of parallel ring/guanadinium stacking, perpendicular H bond stacking and aliphatic chain packing. Conclusions: The high resolution structure of the Dysferlin DysF domain gives a template on which to interpret in detail the pathogenic mutations that lead to disease

C19orf12 mutation leads to a pallido-pyramidal syndrome.

Pallido-pyramidal syndromes combine dystonia with or without parkinsonism and spasticity as part of a mixed neurodegenerative disorder. Several causative genes have been shown to lead to pallido-pyramidal syndromes, including FBXO7, ATP13A2, PLA2G6, PRKN and SPG11. Among these, ATP13A2 and PLA2G6 are inconsistently associated with brain iron deposition. Using homozygosity mapping and direct sequencing in a multiplex consanguineous Saudi Arabian family with a pallido-pyramidal syndrome, iron deposition and cerebellar atrophy, we identified a homozygous p.G53R mutation in C19orf12. Our findings add to the phenotypic spectrum associated with C19orf12 mutations

Drosophila CG3303 is an essential endoribonuclease linked to TDP-43-mediated neurodegeneration

Endoribonucleases participate in almost every step of eukaryotic RNA metabolism, acting either as degradative or biosynthetic enzymes. We previously identified the founding member of the Eukaryotic EndoU ribonuclease family, whose components display unique biochemical features and are flexibly involved in important biological processes, such as ribosome biogenesis, tumorigenesis and viral replication. Here we report the discovery of the CG3303 gene product, which we named DendoU, as a novel family member in Drosophila. Functional characterisation revealed that DendoU is essential for Drosophila viability and nervous system activity. Pan-neuronal silencing of dendoU resulted in fly immature phenotypes, highly reduced lifespan and dramatic motor performance defects. Neuron-subtype selective silencing showed that DendoU is particularly important in cholinergic circuits. At the molecular level, we unveiled that DendoU is a positive regulator of the neurodegeneration-associated protein dTDP-43, whose downregulation recapitulates the ensemble of dendoU-dependent phenotypes. This interdisciplinary work, which comprehends in silico, in vitro and in vivo studies, unveils a relevant role for DendoU in Drosophila nervous system physio-pathology and highlights that DendoU-mediated neurotoxicity is, at least in part, contributed by dTDP-43 loss-of-function

In silico characterization of boron transporter (BOR1) protein sequences in Poaceae species

Boron (B) is essential for the plant growth and development, and its primary function is connected with formation of the cell wall. Moreover, boron toxicity is a shared problem in semiarid and arid regions. In this study, boron transporter protein (BOR1) sequences from some Poaceae species (Hordeum vulgare subsp. vulgare, Zea mays, Brachypodium distachyon, Oryza sativa subsp. japonica, Oryza sativa subsp. indica, Sorghum bicolor, Triticum aestivum) were evaluated by bioinformatics tools. Physicochemical analyses revealed that most of BOR1 proteins were basic character and had generally aliphatic amino acids. Analysis of the domains showed that transmembrane domains were identified constantly and three motifs were detected with 50 amino acids length. Also, the motif SPNPWEPGSYDHWTVAKDMFNVPPAYIFGAFIPATMVAGLYYFDHSVASQ was found most frequently with 25 repeats. The phylogenetic tree showed divergence into two main clusters. B. distachyon species were clustered separately. Finally, this study contributes to the new BOR1 protein characterization in grasses and create scientific base for in silico analysis in future

STRING v10: protein-protein interaction networks, integrated over the tree of life

The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks

Characterization of gibberellin 2-oxidase isoforms in coconut (Cocos nucifera L.)

Gibberellins (GAs) are plant hormones that are essential for many developmental processes in plants, including seed germination, stem elongation, leaf expansion, trichome development, pollen maturation and the induction of flowering. Gibberellin 2-oxidase (GA2-ox) regulates plant growth by inactivating endogenous bioactive GAs through 2β-hydroxylation. There is no information about GA2-ox encoding genes or their functions in coconut. In this study, we have identified 10 transcripts encoding different isoforms of GA2-ox from coconut leaf transcriptome data. Sequence comparison and phylogenetic analysis revealed that these 10 transcripts represented different types of GA2-ox. The secondary structure, three dimensional structure and active sites of these 10 isoforms were predicted. Docking studies of different active GAs with these isoforms was also carried out

Integrative meta-analysis of protein interaction data identified multiple GID/MRCTLH protein complexes in plants

GID/MRCTLH is a protein complex involved in the regulation of several cellular processes through the polyubiquitination and proteosome degradation. It has been described in yeast and mammals. Genes coding for homologous proteins are also present in plant genomes but have been little studied. BLAST analyses revealed that genes coding for members of the GID/MRCTLH complex are found in multiple copies in plants, compared to mammals and yeast. The potential structure of the Arabidopsis GID/MRCTLH complex was estimated based on the Arabidopsis protein interaction database Interactome 2.0. According to these data, Arabidopsis may contain two GID/MRCTLH complexes instead of the one described in yeast and mammals. The structure of the two Arabidopsis complexes seem to be similar to the yeast GID complex, and seem to interact with several other proteins out of the complex. These data suggest that, similarly to yeast and mammals, the plant GID/MRCTLH complexes are involved in the regulation of several cellular processes through proteosome protein degradation

Brassica oleracea L. var. acephala ABA biosynthesis genes (NCED2 and NCED3) in silico interactome analysis

Brassicaceae are industrially important flowering plants and in the same time often used for human consumption. Brassicae species are known heavy metal accumulators and therefore evaluated as potential phytoextraction plants. However, a detail analysis of heavy metal correlated genes, correlating to abscisic acid synthesis, is still not available. ABA (Abscisic acid) signaling genes from Brassica oleracea, NCED2/3 are known to be correlated to heavy metal stresses, including cupper, arsenic and cadmium. NCED2/3 proteins control the plants developmental processes and response to environmental stresses such as drought, heat stress, cold tolerance, and primarily, heavy metal influence. Through a simple in silico approach, we have confirmed that NCED2/3 proteins share more than 65% similarity, as confirmed by phylogenetic analysis and 3D structure models. After the domain and interactome prediction, we revealed that NCED2/3 strongly correlates with BoXDIX1, ABA3, BoZE and BoZCD proteins, therefore indicating new roles to NCED2/3 proteins, which is the involvement in the pigmentation and photoprotection processes of Brassica oleracea