We present GENECODIS, a web-based tool that integrates different sources of information to search for annotations that frequently co-occur in a set of genes and rank them by statistical significance. The analysis of concurrent annotations provides significant information for the biologic interpretation of high-throughput experiments and may outperform the results of standard methods for the functional analysis of gene lists. GENECODIS is publicly available at http:// genecodis.dacya.ucm.es/.

Strigolactones (SLs) are phytohormones that play a central role in regulating shoot branching. SL perception and signaling involves the F-box protein MAX2 and the hydrolase DWARF14 (D14), proposed to act as an SL receptor. We used strong loss-offunction alleles of the Arabidopsis thaliana D14 gene to characterize D14 function from early axillary bud development through to lateral shoot outgrowth and demonstrated a role of this gene in the control of flowering time. Our data show that D14 distribution in vivo overlaps with that reported for MAX2 at both the tissue and subcellular levels, allowing physical interactions between these proteins. Our grafting studies indicate that neither D14 mRNA nor the protein move over a long range upwards in the plant. Like MAX2, D14 is required locally in the aerial part of the plant to suppress shoot branching. We also identified a mechanism of SLinduced, MAX2-dependent proteasome-mediated degradation of D14. This negative feedback loop would cause a substantial drop in SL perception, which would effectively limit SL signaling duration and intensity.

Inosine-5′-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches.

Mice from the inbred C57BL/6 strain have been commonly used for the generation and analysis of transgenic and knockout animal models. However, several C57BL/6 substrains exist, and these are genetically and phenotypically different. In addition, each of these substrains can be purchased from different animal providers and, in some cases, they have maintained their breeding stocks separated for a long time, allowing genetic differences to accumulate due to individual variability and genetic drift. With the aim of describing the differences in the genotype of several C57BL/6 substrains, we applied the Illumina(®) Mouse Medium Density Linkage Mapping panel, with 1,449 single nucleotide polymorphisms (SNPs), to individuals from ten C57BL/6-related strains: C57BL/6JArc, C57BL/6J from The Jackson Lab, C57BL/6J from Crl, C57BL6/JRccHsd, C57BL/6JOlaHsd, C57BL/6JBomTac, B6(Cg)-Tyr ( c-2j )/J, C57BL/6NCrl, C57BL/6NHsd and C57BL/6NTac. Twelve SNPs were found informative to discriminate among the mouse strains considered. Mice derived from the original C57BL/6J: C57BL/6JArc, C57BL/6J from The Jackson Lab and C57BL/6J from Crl, were indistinguishable. Similarly, all C57BL/6N substrains displayed the same genotype, whereas the additional substrains showed intermediate cases with substrain-specific polymorphisms. These results will be instrumental for the correct genetic monitoring and appropriate mouse colony handling of different transgenic and knockout mice produced in distinct C57BL/6 inbred substrains.

No abstract

The web server is freely available at http://csbg.cnb.csic.es/mbrole. It was tested in the main web browsers.

Metabolites Biological Role (MBROLE) is a server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms. Since its release in 2011, MBROLE has been used by different groups worldwide to analyse metabolomics experiments from a variety of organisms. Here we present the latest version of the system, MBROLE2, accessible at http://csbg.cnb.csic.es/mbrole2. MBROLE2 has been supplemented with 10 databases not available in the previous version, which allow analysis over a larger, richer set of vocabularies including metabolite–protein and drug–protein interactions. This new version performs automatic conversion of compound identifiers from different databases, thus simplifying usage. In addition, the user interface has been redesigned to generate an interactive, more intuitive representation of the results.

Class I A phosphoinositide 3-kinases (PI3Ks) are heterodimeric enzymes composed of a p85 regulatory and a p110 catalytic subunit that induce the formation of 3-polyphosphoinositides, which mediate cell survival, division, and migration. There are two ubiquitous PI3K isoforms p110␣ and p110␤ that have nonredundant functions in embryonic development and cell division. However, whereas p110␣ concentrates in the cytoplasm, p110␤ localizes to the nucleus and modulates nuclear processes such as DNA replication and repair. At present, the structural features that determine p110␤ nuclear localization remain unknown. We describe here that association with the p85␤ regulatory subunit controls p110␤ nuclear localization. We identified a nuclear localization signal (NLS) in p110␤ C2 domain that mediates its nuclear entry, as well as a nuclear export sequence (NES) in p85␤. Deletion of p110␤ induced apoptosis, and complementation with the cytoplasmic C2-NLS p110␤ mutant was unable to restore cell survival. These studies show that p110␤ NLS and p85␤ NES regulate p85␤/p110␤ nuclear localization, supporting the idea that nuclear, but not cytoplasmic, p110␤ controls cell survival.The phosphoinositide 3-kinase (PI3K) family is divided into four groups (I A , I B , II, and III) according to structural features and substrate specificity. Of these, only class I enzymes catalyze the production of PI(3,4,5)P 3 and PI(3,4)P 2 in vivo. Class I A PI3Ks are heterodimeric proteins consisting of a p110 catalytic subunit (p110␣, p110␤, and p110␦) and an associated p85 regulatory subunit (p85␣, p85␤, and p55␥) (14,18,21,22,53). p110␥ (class I B PI3K) is structurally similar but associates with a distinct class of regulatory subunits. The catalytic subunits p110␣ and p110␤ are expressed ubiquitously, whereas p110␦ and p110␥ are more abundant in hematopoietic cells (14,44,53).Despite the similarity in sequence, expression patterns, and regulatory subunits, p110␣ and p110␤ have distinct functions in cell proliferation, cell cycle progression, and development (5,6,12,26,(32)(33)(34)(35)47). p110␣ has a key role in insulin action and cell cycle entry (12, 13), whereas p110␤ is reported to play a pivotal role in DNA replication, S phase progression, and DNA repair (32,34,35). Activating mutations of p110␣, but not of p110␤, have been found in human cancer; nonetheless, p110␤ drives tumorigenesis in PTEN-defective cells and induces focus formation in fibroblasts (8,9,26,29). Moreover, overexpression of p110␤ is found in specific tumor types (7,54,58). Previous studies showed that part of the specific functions of p110␣ and p110␤ result from their distinct subcellular localization and activation requirements (34, 35), highlighting the emergence of subcellular localization as a major mechanism to govern cell responses (30). Previous reports showed that p85/p110 complex can translocate to the nucleus regulating cell survival, particularly in neuronal cell lines (37). In addition, p110␤, but not p110␣, localizes to the nucleus in several cell types. The...