The inositol 5-phosphatase SHIP2 is an effector of RhoA and is involved in cell polarity and migration

Cell migration is essential for various physiological and pathological processes. Polarization in motile cells requires the coordination of several key signaling molecules, including RhoA small GTPases and phosphoinositides. Although RhoA participates in a front-rear polarization in migrating cells, little is known about the functional interaction between RhoA and lipid turnover. We find here that src-homology 2-containing inositol-5-phosphatase 2 (SHIP2) interacts with RhoA in a GTP-dependent manner. The association between SHIP2 and RhoA is observed in spreading and migrating U251 glioma cells. The depletion of SHIP2 attenuates cell polarization and migration, which is rescued by wild-type SHIP2 but not by a mutant defective in RhoA binding. In addition, the depletion of SHIP2 impairs the proper localization of phosphatidylinositol 3,4,5-trisphosphate, which is not restored by a mutant defective in RhoA binding. These results suggest that RhoA associates with SHIP2 to regulate cell polarization and migration.     

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding

Background

More than 7000 papers related to “protein refolding” have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource – “REFOLDdb” that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest.

Results

We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17^th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/.

Conclusion

REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

     

Autoregulation of Osteocyte Sema3A Orchestrates Estrogen Action and Counteracts Bone Aging

1. Download high-res image (184KB)
2. Download full-size image

     

Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation

Non-coding RNAs (ncRNAs) ubiquitously exist in normal and cancer cells. Despite their prevalent distribution, the functions of most long ncRNAs remain uncharacterized. The fission yeast Schizosaccharomyces pombe expresses >1800 ncRNAs annotated to date, but most unconventional ncRNAs (excluding tRNA, rRNA, snRNA and snoRNA) remain uncharacterized. To discover the functional ncRNAs, here we performed a combinatory screening of computational and biological tests. First, all S. pombe ncRNAs were screened in silico for those showing conservation in sequence as well as in secondary structure with ncRNAs in closely related species. Almost a half of the 151 selected conserved ncRNA genes were uncharacterized. Twelve ncRNA genes that did not overlap with protein-coding sequences were next chosen for biological screening that examines defects in growth or sexual differentiation, as well as sensitivities to drugs and stresses. Finally, we highlighted an ncRNA transcribed from SPNCRNA.1669, which inhibited untimely initiation of sexual differentiation. A domain that was predicted as conserved secondary structure by the computational operations was essential for the ncRNA to function. Thus, this study demonstrates that in silico selection focusing on conservation of the secondary structure over species is a powerful method to pinpoint novel functional ncRNAs.     

Evolutionary Origin of GnIH and NPFF in Chordates: Insights from Novel Amphioxus RFamide Peptides

Gonadotropin-inhibitory hormone (GnIH) is a newly identified hypothalamic neuropeptide that inhibits pituitary hormone secretion in vertebrates. GnIH has an LPXRFamide (X = L or Q) motif at the C-terminal in representative species of gnathostomes. On the other hand, neuropeptide FF (NPFF), a neuropeptide characterized as a pain-modulatory neuropeptide, in vertebrates has a PQRFamide motif similar to the C-terminal of GnIH, suggesting that GnIH and NPFF have diverged from a common ancestor. Because GnIH and NPFF belong to the RFamide peptide family in vertebrates, protochordate RFamide peptides may provide important insights into the evolutionary origin of GnIH and NPFF. In this study, we identified a novel gene encoding RFamide peptides and two genes of their putative receptors in the amphioxus Branchiostoma japonicum. Molecular phylogenetic analysis and synteny analysis indicated that these genes are closely related to the genes of GnIH and NPFF and their receptors of vertebrates. We further identified mature RFamide peptides and their receptors in protochordates. The identified amphioxus RFamide peptides inhibited forskolin induced cAMP signaling in the COS-7 cells with one of the identified amphioxus RFamide peptide receptors expressed. These results indicate that the identified protochordate RFamide peptide gene is a common ancestral form of GnIH and NPFF genes, suggesting that the origin of GnIH and NPFF may date back to the time of the emergence of early chordates. GnIH gene and NPFF gene may have diverged by whole-genome duplication in the course of vertebrate evolution.     

Effects of Ions and Membrane Potential on the Elongation of the Unicellular Green Alga Closterium

Cells of the unicellular green alga Closterium ehrenbergii elongatedexclusively at septa and for 4–5 hours after cell division.Cell elongation was strongly inhibited by a decrease in eitherthe external concentration of Ca²⁺ or pH, and was also inhibitedby several competitive Ca²⁺ channel blockers. Changes in concentrationsof other external ions had no effect on the elongation. Theaverage concentrations of ions in the intracellular fluid ofthe interphase cell before cell division was as follows (inmM): K⁺=56.5, Na⁺=4.8, Ca²⁺=2.4, Mg²⁺=1.3, Cl^–=59.5; thepH was 7.4. The levels of K⁺, Na⁺ and Cl^– ions decreasedsignificantly with cell elongation, suggesting that this process,which proceeds with water uptake, surpasses ion absorption.The plasma membrane potential (Vm) in both the interphase cellsand in the elongating cells was in the range of –90 to–105 mV (interior negative). The Vm was entirely determinedby the simple diffusion of K⁺. A decrease in the external concentrationof Ca²⁺ caused depolarization, probably by an indirect effectof low Ca²⁺. Changes in the extracellular level of H⁺ and othercations barely affected Vm. Thus, external Ca²⁺ and H⁺ are concludedto affect cell elongation but not via a change in the Vm acrossthe plasma membrane. (Received February 29, 1988; Accepted June 8, 1988)     

Population regulation of the euonymus gall midgeMasakimyia pustulae Yukawa andSunose (Diptera: Cecidomyiidae) by hymenopterous parasitoids

Yearly population fluctuations of M. pustulae were investigated at 19 sites in Kyushu. In sites where a platygastrid is the only parasitoid of the midge, the percentage parasitism was very low in the incipient stage of the outbreak of the midge populations. After the number of midges reached a peak, the midge populations declined as the percentage parasitism increased, and then the outbreak ceased. On the other hand, in several populations no outbreak was found and the percentage parasitism was constantly at a high level. Therefore, the immediate cause for the outbreak seemed to be a decline of the percentage parasitism. Like the midge, the platygastrid has one generation each year, and its females also emerge in spring to deposit their eggs within host eggs. The decline of the percentage parasitism seemed to be mainly affected by the time lag between emergence periods of M. pustulae and the platygastrid. In the midge populations parasitized by both the platygastrid and a eulophid (Chrysonotomyia sp.), an extinction of the population was observed, resulting from parasitism by the latter, Chrysonotomyia sp. is polyphagous and multivoltine, and is a late parasitoid, as discussed byAskew (1975). When the density of the midges is very low, the platygastrid may leave the host eggs unparasitized, while Chrysonotomyia sp. may not, because the mature galls are conspicuous.     

Interfractional diaphragm changes during breath-holding in stereotactic body radiotherapy for liver cancer

Aim and background

IGRT based on bone matching may produce a large target positioning error in terms of the reproducibility of expiration breath-holding on SBRT for liver cancer. We evaluated the intrafractional and interfractional errors using the diaphragm position at the end of expiration by utilising Abches and analysed the factor of the interfractional error.

Evaluation of mitochondrial redox status and energy metabolism of X-irradiated HeLa cells by LC/UV,LC/MS/MS and ESR

To evaluate the metabolic responses in tumour cells exposed to ionizing radiation, oxygen consumption rate (OCR), cellular lipid peroxidation, cellular energy status (intracellular nucleotide pool and ATP production), and mitochondrial reactive oxygen species (ROS), semiquinone (SQ), and iron–sulphur (Fe?S) cluster levels were evaluated in human cervical carcinoma HeLa cells at 12 and 24?h after X-irradiation. LC/MS/MS analysis showed that levels of 8-iso PGF_2α and 5-iPF_2α-VI, lipid peroxidation products of membrane arachidonic acids, were not altered significantly in X-irradiated cells, although mitochondrial ROS levels and OCR significantly increased in the cells at 24?h after irradiation. LC/UV analysis revealed that intracellular AMP, ADP, and ATP levels increased significantly after X-irradiation, but adenylate energy charge (adenylate energy charge (AEC)?=?[ATP?+?0.5?×?ADP]/[ATP?+?ADP?+?AMP]) remained unchanged after X-irradiation. In low-temperature electron spin resonance (ESR) spectra of HeLa cells, the presence of mitochondrial SQ at g?=?2.004 and Fe–S cluster at g?=?1.941 was observed and X-irradiation enhanced the signal intensity of SQ but not of the Fe–S cluster. Furthermore, this radiation-induced increase in SQ signal intensity disappeared on treatment with rotenone, which inhibits electron transfer from Fe–S cluster to SQ in complex I. From these results, it was suggested that an increase in OCR and imbalance in SQ and Fe–S cluster levels, which play a critical role in the mitochondrial electron transport chain (ETC), occur after X-irradiation, resulting in an increase in ATP production and ROS leakage from the activated mitochondrial ETC.     

Calmodulin-dependent protein kinase II (CaMKII) mediates radiation-induced mitochondrial fission by regulating the phosphorylation of dynamin-related protein 1 (Drp1) at serine 616

Mitochondrial dynamics are suggested to be indispensable for the maintenance of cellular quality and function in response to various stresses. While ionizing radiation (IR) stimulates mitochondrial fission, which is mediated by the mitochondrial fission protein, dynamin-related protein 1 (Drp1), it remains unclear how IR promotes Drp1 activation and subsequent mitochondrial fission. Therefore, we conducted this study to investigate these concerns. First, we found that X-irradiation triggered Drp1 phosphorylation at serine 616 (S616) but not at serine 637 (S637). Reconstitution analysis revealed that introduction of wild-type (WT) Drp1 recovered radiation-induced mitochondrial fission, which was absent in Drp1-deficient cells. Compared with cells transfected with WT or S637A Drp1, the change in mitochondrial shape following irradiation was mitigated in S616A Drp1-transfected cells. Furthermore, inhibition of CaMKII significantly suppressed Drp1 S616 phosphorylation and mitochondrial fission induced by IR. These results suggest that Drp1 phosphorylation at S616, but not at S637, is prerequisite for radiation-induced mitochondrial fission and that CaMKII regulates Drp1 phosphorylation at S616 following irradiation.