Biology subjects

Ishikawa, T.

Publications and source records attributed to Ishikawa, T..

62 records · Page 4Linked to original sources

bioRxiv2019

Convergence of unisensory-evoked signals via multiple pathways to the cerebellum

The cerebellum receives signals directly from peripheral sensory systems and indirectly from the neocortex. To reveal how these different types of signals are processed in the cerebellar cortex, in vivo whole-cell recordings from granule cells and unit recordings from Purkinje cells were performed in mice in which primary somatosensory cortex (S1) could be optogenetically inhibited. Tactile stimulation of the upper lip produced two-phase granule cell responses (with latencies of [~] 8 ms and 28 ms), for which only the late phase was S1 dependent. Complex spikes and the late phase of simple spikes in Purkinje cells were also S1 dependent. These results indicate that individual granule cells integrate convergent inputs from the periphery and neocortex, and send their outputs to Purkinje cells, which then combine those signals with climbing fiber signals from the neocortex.

neuroscience↗

bioRxiv2019

Cortisol levels adter cold exposure are independent of adrenocorticotropic hormone stimulation

We previously showed that postmortem serum levels of adrenocorticotropic hormone (ACTH) were significantly higher in cases of hypothermia (cold exposure) than other causes of death. This study examined how the human hypothalamic-pituitary-adrenal axis, and specifically cortisol, responds to hypothermia.\n\nHuman samplesAutopsies on 205 subjects (147 men and 58 women; age 15-98 years, median 60 years) were performed within 3 days of death. Cause of death was classified as either hypothermia (cold exposure, n=14) or non-cold exposure (controls; n=191). Cortisol levels were determined in blood samples obtained from the left and right cardiac chambers and common iliac veins using a chemiluminescent enzyme immunoassay. Adrenal gland tissue samples were stained for cortisol using a rabbit anti-human polyclonal antibi.\n\nCell cultureAtT20, a mouse ACTH secretory cell line, and Y-1, a corticosterone secretory cell line derived from a mouse adrenal tumor, were analyzed in mono-and co-culture, and times courses of ACTH (in AtT20) and corticosterone (in Y-1) secretion were assessed after low temperature exposure mimicking hypothermia and compared with data for samples collected postmortem for other causes of death. However, no correlation between ACTH concentration and cortisol levels was observed in hypothermia cases. Immunohistologic analyses of samples from hypothermia cases showed that cortisol staining was localized primarily to the nucleus rather than the cytoplasm of cells in the zona fasciculata of the adrenal gland. During both mono-culture and co-culture, AtT20 cells secreted high levels of ACTH after 10-15 minutes of cold exposure, whereas corticosterone secretion by Y-1 cells increased slowly during the first 15-20 minutes of cold exposure. Similar to autopsy results, no correlation was detected between ACTH levels and corticosterone secretion, either in mono-culture or co-culture experiments. These results suggested that ACTH-independent cortisol secretion may function as a stress response during cold exposure.

biochemistry↗

bioRxiv2019

A new cryo-EM system for electron 3D crystallography by eEFD

A new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300 kV electron beam to a sample, filters out energy-loss electrons through the sample with an in-column energy filter, and allows rotational data collection on a fast camera. It also possesses motorized cryo-sample loading and automated liquid-nitrogen filling for cooling of multiple samples. To facilitate its use, we developed GUI programs for efficient operation and accurate structure analysis. Here we report on the performance of the system and first results for thin 3D crystals of the protein complexes, catalase and membrane protein complex ExbBD. Data quality is remarkably improved with this approach, which we name eEFD (electron energy-filtered diffraction of 3D crystals), compared with those collected at 200 kV without energy filtration. Key advances include precise control of the microscope and recordings of lens fluctuations, which the programs process and respond to. We also discuss the merits of higher-energy electrons and filtration of energy-loss electrons in electron 3D crystallography.

molecular biology↗

bioRxiv2018

Human RAD51 paralogue, SWSAP1, fosters RAD51 filament by regulating the anti-recombinase, FIGNL1 AAA+ ATPase

RAD51 assembly on single-stranded (ss)DNAs is a crucial step in the homology-dependent repair of DNA damage for genomic stability. The formation of the RAD51 filament is tightly regulated by various RAD51-interacting proteins. The familial breast cancer gene, BRCA2, as well as RAD52 and six RAD51 paralogues (SWSAP1, RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3) promote RAD51 assembly on ssDNAs in humans. However, the mechanisms underlying the differential control of RAD51 filament dynamics by these factors remain largely unknown. Here, we report a role for the human RAD51 paralogue, SWSAP1, as a novel regulator of RAD51 assembly. Swsap1-deficient cells show defects in DNA damage-induced RAD51 assembly during both mitosis and meiosis. Defective RAD51 assembly in SWSAP1-depleted cells is suppressed by the depletion of FIGNL1, an AAA+ ATPase, which binds to RAD51 as well as SWSAP1. Purified FIGNL1 promotes the dissociation of RAD51 from ssDNAs. The in vitro dismantling activity of FIGNL1 does not require its ATPase but depends on RAD51-binding, suggesting a novel mechanism of RAD51 filament remodelling. Purified SWSAP1 inhibits the RAD51-dismantling activity of FIGNL1. Taken together, our data suggest that SWSAP1 protects RAD51 filaments by antagonizing the anti-recombinase, FIGNL1.

molecular biology↗

bioRxiv2018

Microglial SIRPα regulates the emergence of CD11c+ microglia and demyelination damage in white matter

A characteristic subset of microglia expressing CD11c appears in response to brain damage. However, the functional role of CD11c+ microglia, as well as the mechanism of its induction, are poorly understood. Here we report that the genetic ablation of signal regulatory protein (SIRP), a membrane protein, induced CD11c+ microglia in the brain white matter. Mice lacking CD47, a physiological ligand of SIRP, and microglia-specific SIRP knockout mice exhibited the same phenotype, suggesting the interaction between microglial SIRP and CD47 on neighbouring cells suppressed the emergence of CD11c+ microglia. A lack of SIRP did not cause detectable damage in the white matter, but resulted in the increased expression of genes characteristic of the repair phase after demyelination. In addition, cuprizone-induced demyelination was alleviated by the microglia-specific ablation of SIRP. Thus, microglial SIRP suppresses the induction of CD11c+ microglia that have the potential to accelerate the repair of damaged white matter.

neuroscience↗

bioRxiv2018

Phylogeny and distinct properties of major intrinsic proteins in the genomes of six Phytophthora species suggest their novel functions in Phytophthora

ABSTRACTMajor intrinsic proteins (MIPs), commonly known as aquaporins, facilitate the membrane diffusion of water and some other non- polar solutes. MIPs might be involved in host-pathogen interactions. Herein, we identified 17, 24, 27, 19, 19, and 22 full-length MIPs, respectively, in the genomes of six Phytophthora species, P. infestans, P. parasitica, P. sojae, P. ramorum, P. capsici, and P. cinnamomi. These Phytophthora species are devastating plant pathogens and members of oomycetes, a distinct lineage of fungus-like eukaryotic microbes. Phylogenetic analysis showed that the Phytophthora MIPs (PMIPs) formed a completely distinct clade from their counterparts in other taxa and were clustered into nine subgroups. Sequence and structural properties indicated that the primary selectivity-related constrictions, including aromatic arginine (ar/R) selectivity filter and Froger’s positions in PMIPs were distinct from those in other taxa. The substitutions in the conserved Asn-Pro-Ala motifs in loops B and E of many PMIPs were also divergent from those in plants. We further deciphered group-specific consensus sequences/motifs in different loops and transmembrane helices of PMIPs, which were distinct from those in plants, animals, and microbes. The data collectively supported the notion that PMIPs might have novel functions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2018

GONST2 transports GDP-Mannose for sphingolipid glycosylation in the Golgi apparatus of Arabidopsis

The Golgi lumen is the site of many different glycosylation events, including cell wall polysaccharide biosynthesis and lipid glycosylation. Transporters are necessary for the import of the substrates required for glycosylation (nucleotide sugars) from the cytosol where they are synthesized. Plants use four GDP-linked sugars to glycosylate macromolecules: GDP-L-Fucose, GDP-D-Mannose, GDP-L-Galactose and GDP-D-Glucose. Of the predicted fifty-one members of the nucleotide sugar transporter/triose phosphate transporter family in Arabidopsis, only four appear to contain the conserved motif needed for the transport of GDP-linked sugars, GOLGI LOCALIZED NUCLEOTIDE SUGAR TRANSPORTER (GONST) 1-4. Previously, we have demonstrated that GONST1 provides GDP-D-Mannose for glycosylation of a class of sphingolipids, the glycosylinositolphosphorylceramides (GIPCs). Here, we characterize its closest homologue, GONST2, and conclude that it also specifically provides substrate for GIPC glycosylation. Expression of GONST2 driven by the GONST1 promoter is able to rescue the severe growth phenotype of gonst1. Loss of GONST2 exacerbates the gonst1 constitutive hypersensitive response, as well as the reduced cell wall cellulose content. The gonst2 mutant grows normally under standard conditions, but has enhanced resistance to the powdery mildew-causing fungus Golovinomyces orontii.

plant biology↗

bioRxiv2018

SETD3 protein is the actin-specific histidine N-methyltransferase

Protein histidine methylation is rarely studied posttranslational modification of unknown biochemical importance. In vertebrates, only a few methylhistidne-containing proteins have been reported so far, including {beta}-actin as an essential example. The evolutionary conserved methylation of {beta}-actin H73 residue is catalyzed by a specific histidine N-methyltransferase that has never been identified molecularly. In the present investigation, we have purified actin-specific histidine N-methyltransferase from rat muscles about 1200-fold. Its activity was studied by the radiochemical assay employing either homogeneous recombinant human {beta}-actin produced in E. coli or its mutated form exhibiting substitution of H73 by Ala residue (H73A) as substrates. Three polypeptides of {approx}65, 75 and 90 kDa coeluting with the enzyme activity were identified in the preparation. Mass spectrometry analysis of these polypeptides resulted in the identification of SETD3 methyltransferase as the only plausible candidate. Rat SETD3 and its human ortholog were expressed in COS-7 cells, purified to homogeneity and shown to catalyze methylation of {beta}-actin at H73 residue as confirmed by mass spectrometry analysis. The SETD3 enzyme was active towards a synthetic peptide corresponding to residues 69-77 of {beta}-actin, but not to its mutated form exhibiting His-to-Ala substitution. Finally, Setd3-deficient HAP1 cells were devoid of methylated H73 in {beta}-actin and exhibited phenotypic changes, including a decrease in F-actin content and an increased glycolytic activity. We conclude that SETD3 is the actin-specific histidine N-methyltransferase. The data show for the first time the molecular identity of protein histidine N-methyltransferase in vertebrates and throw new light on the substrate specificity of SET-domain-containing enzymes.

biochemistry↗