Biology subjects

Inaba, K.

Publications and source records attributed to Inaba, K..

24 records · Page 2Linked to original sources

bioRxiv2020

A unique adhesive motif of protein disulfide isomerase P5 supports its function via dimerization

P5, also known as PDIA6, is a PDI-family member that plays an important role in the ER quality control. Herein, we revealed that P5 dimerizes via a unique adhesive motif contained in the N-terminal thioredoxin-like domain. This motif is apparently similar to, but radically different from conventional leucine-zipper motifs, in that the former includes a periodic repeat of leucine or valine residues at the third or fourth position spanning five helical turns on 15-residue anti-parallel -helices, unlike the latter of which the leucine residues appear every two helical turns on [~]30-residue parallel -helices at dimer interfaces. A monomeric P5 mutant with the impaired adhesive motif showed structural instability and local unfolding, and behaved as an aberrant protein that induces the ER stress response. Disassembly of P5 to monomers compromised its ability to inactivate IRE1 via reduction of intermolecular disulfide bonds and its Ca2+-dependent regulation of chaperone function in vitro. Thus, the leucine-valine adhesive motif supports structure and physiological function of P5.

biochemistry↗

bioRxiv2020

Calaxin is essential for the transmission of Ca2+-dependent asymmetric waves in sperm flagella

Regulation of waveform asymmetry in sperm flagella is critical for changes in sperm swimming trajectory as seen during sperm chemotaxis towards eggs. Ca2+ is known as an important regulator of asymmetry in flagellar waveforms. A calcium sensor protein, calaxin, which is associated with the outer arm dynein, plays a key role in the sperm waveform regulation in a Ca2+-dependent manner. However, the molecular mechanism underlying the regulation of asymmetric waves by Ca2+ and calaxin remains unclear. We performed experiments using caged ATP to elucidate the formation and propagation of asymmetric flagellar waves in the sperm of the ascidian Ciona intestinalis. Demembranated sperm cells were suspended in a solution containing caged ATP and reactivated using UV flash photolysis. Initial bends were formed at the base and propagated towards the tip of flagella; however, the bend direction was different between asymmetric and symmetric waves. A calaxin inhibitor, repaglinide, had no effect on initial bend formation, but significantly inhibited the generation of the second flagellar bend in the reverse direction, resulting in the failure of asymmetric wave formation and propagation. These results suggest that calaxin plays a critical role in Ca2+-dependent transmission of flagellar asymmetric waveforms.

cell biology↗

bioRxiv2020

Cryo-EM structures of SERCA2b reveal the mechanism of regulation by the luminal extension tail

SERCA2b is a Ca2+-ATPase that pumps Ca2+ from the cytosol into the ER and maintains the cellular calcium homeostasis. Herein, we present cryo-EM structures of human SERCA2b in E1{middle dot}2Ca2+-AMPPCP and E2-BeF3- states at 2.9 and 2.8 [A] resolutions, respectively. The structures revealed that the luminal extension tail (LE) characteristic of SERCA2b runs parallel to the lipid-water boundary near the luminal ends of transmembrane (TM) helices TM10 and TM7, and approaches the luminal loop flanked by TM7 and TM8. Upon deletion of the LE, the cytosolic- and TM-domain arrangement of SERCA2b resembled that of SERCA1a, resulting in multiple conformations. The LE regulates the conformational transition between the E1{middle dot}2Ca2+-ATP and E2P states, explaining the different kinetic properties of SERCA2b from other isoforms lacking the LE. One sentence summaryCryo-EM structures of SERCA2b at 2.8-2.9 [A] resolutions reveal how the luminal extension tail regulates its activity.

biochemistry↗

bioRxiv2020

Biochemical characterizations of ER-resident peroxidases, GPx7 and GPx8, reveal their distinct and regulated oxidative activities

In the mammalian endoplasmic reticulum (ER), the diverse network comprising more than 20 members of the protein disulfide isomerase (PDI) family and more than five PDI oxidases has evolved to promote oxidative protein folding. While the canonical disulfide bond formation pathway constituted by Ero1 and PDI has been well studied so far, mechanistic and physiological bases of newly identified PDI oxidases, glutathione peroxidase-7 (GPx7) and -8 (GPx8), are only poorly understood. We here demonstrated that human GPx7 has much higher reactivity with H2O2 than human GPx8, leading to efficient PDI oxidation. GPx7 forms a catalytic tetrad at the redox active site to react with H2O2 efficiently and stabilize a resultantly generated sulfenylated species. While it was previously postulated that the GPx7 catalysis involved a highly reactive peroxidatic cysteine, a resolving cysteine was found to act to regulate the PDI oxidation activity of GPx7. The present study also revealed that GPx7 formed complexes preferentially with PDI and P5 in H2O2-treated cells. Altogether, human GPx7 functions as an H2O2-dependent PDI oxidase in cells whereas PDI oxidation may not be the central physiological role of human GPx8.

biochemistry↗

bioRxiv2019

An integrated approach unravels a crucial structural property for the function of the insect steroidogenic Halloween protein Noppera-bo

Ecdysteroids are the principal insect steroid hormones essential for insect development and physiology. In the last 18 years, several enzymes responsible for ecdysteroid biosynthesis, encoded by Halloween genes, have been identified and well characterized, both genetically and biochemically. However, none of these proteins have yet been characterized at the tertiary structure level. Here, we report an integrated in silico, in vitro, and in vivo analyses of the Halloween glutathione S-transferase (GST) protein, Noppera-bo (Nobo). We determine crystal structures of Drosophila melanogaster Nobo (DmNobo) complexed with glutathione and 17{beta}-estradiol, a DmNobo inhibitor. 17{beta}-estradiol almost fully occupied the putative ligand-binding pocket, and a prominent hydrogen bond formed between Asp113 of DmNobo and 17{beta}-estradiol. Asp113 is essential for inhibiting DmNobo enzymatic activity by 17{beta}-estradiol, as 17{beta}-estradiol does not inhibit and physically interacts less with the Asp113Ala DmNobo point mutant. Asp113 is highly conserved among Nobo proteins, but not among other GSTs, implying that Asp113 is important for endogenous Nobo function. Indeed, a homozygous nobo allele possessing the Asp113Ala point mutation exhibits embryonic lethality with undifferentiated cuticle structure, a phenocopy of complete loss-of-function nobo homozygotes. These results suggest that the nobo family of GST proteins has acquired a unique amino acid residue, which seems to be essential for binding an endogenous sterol substrate to regulate ecdysteroid biosynthesis. This is the first study to reveal the structural characteristics of insect steroidogenic Halloween proteins. This study also provides basic insight into applied entomology for developing a new type of insecticides that specifically inhibit ecdysteroid biosynthesis.\n\nSignificance StatementInsect molting and metamorphosis are drastic and dynamic biological processes and, therefore, have fascinated many scientists. Ecdysteroids represent one class of insect hormones that are indispensable for inducing molting and metamorphosis. It is well known that proteins responsible for catalyzing ecdysteroid biosynthesis reactions are encoded by \"Halloween\" genes, most of which have names of ghosts and phantoms. However, no studies have focused on the structural properties of these biosynthetic proteins. In this study, we addressed this unsolved issue and successfully unraveled a structural property that is crucial for the function of the fruit fly Halloween protein, Noppera-bo (a Japanese faceless ghost). This is the first study to reveal the structural characteristics of an insect steroidogenic Halloween protein.

biochemistry↗

bioRxiv2018

Microtubule dynamics is required for rapid coiling of haptonemata in haptophyte algae

A haptonema is an elongated microtubule-based motile organelle uniquely present in haptophytes. The most notable and rapid movement of a haptonema is \"coiling\", which occurs within a few milliseconds following mechanical stimulation in an unknown motor-independent mechanism. Here, we analyzed the coiling process in detail by high-speed filming and showed that haptonema coiling was initiated by left-handed twisting of the haptonema, followed by writhing to form a helix from the distal tip. On recovery from a mechanical stimulus, the helix slowly uncoiled from the proximal region. Electron microscopy showed that the seven microtubules in a haptonema were arranged mostly in parallel but that one of the microtubules often wound around the others in the extended state. The persistence lengths calculated from the curvature of the haptonematal microtubules indicated their unusual flexibility. A microtubule stabilizer, paclitaxel, inhibited coiling and induced right-handed twisting of the haptonema in the absence of Ca2+, suggesting changes in the microtubule surface lattice. Addition of Ca2+ caused bend propagation toward the proximal region. These results indicate that switching microtubule conformation with the aid of Ca2+-binding microtubule-associated proteins is responsible for rapid haptonematal coiling.\n\nSummary StatementMicroscopy observations and pharmacological experiments revealed that the rapid coiling of a non-motor microtubule-based motile organelle, the haptonema, is explained by conformational changes of microtubules, including twisting and writhing.

cell biology↗