Charge block-driven liquid-liquid phase separation: A mechanism of how phosphorylation regulates phase behavior of disordered proteins.

Phosphorylation regulates protein function by modulating stereospecific interactions between protein-protein or enzyme-ligand. On the other hand, many bioinformatics studies have demonstrated that phosphorylation preferably occurs in intrinsically disordered regions (IDRs), which do not have any secondary and tertiary structures. Although studies have demonstrated that phosphorylation changes the phase behavior of IDRs, the mechanism, which is distinct from the "stereospecific" effect, had not been elucidated. Here, we describe how phosphorylation in IDRs regulates the protein function by modulating phase behavior. Mitotic phosphorylation in the IDRs of Ki-67 and NPM1 promotes or suppresses liquid-liquid phase separation, respectively, by altering the "charge blockiness" along the polypeptide chain. The phosphorylation-mediated regulation of liquid-liquid phase separation by enhancing or suppressing "charge blockiness," rather than by modulating stereospecific interactions, may provide one of the general mechanisms of protein regulation by posttranslational modifications and the role of multiple phosphorylations.

Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association.

Bombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, we show that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa are responsible for self-association and RNA binding, respectively, but N-IDR is also required for full RNA-binding activity. Both domains are essential for Vasa body assembly in vivo and droplet formation in vitro via phase separation. FAST-iCLIP reveals that BmVasa preferentially binds transposon mRNAs. Loss of Siwi function derepresses transposons but has marginal effects on BmVasa-RNA binding. This study shows that BmVasa assembles nuage by phase separation via its ability to self-associate and bind newly exported transposon mRNAs. This unique property of BmVasa allows transposon mRNAs to be sequestered and enriched in nuage, resulting in effective Siwi-dependent transposon repression and Ago3-piRISC biogenesis.

Ultrastructural Assessment and Proteomic Analysis in Myofibrillogenesis in the Heart Primordium After Heartbeat Initiation in Rats.

Myofibrillogenesis is an essential process for cardiogenesis and is closely related to excitation-contraction coupling and the maintenance of heartbeat. It remains unclear whether the formation of myofibrils and sarcomeres is associated with heartbeat initiation in the early embryonic heart development. Here, we investigated the association between the ultrastructure of myofibrils assessed by transmission electron microscopy and their proteomic profiling assessed by data-independent acquisition mass spectrometry (DIA-MS) in the rat heart primordia before and after heartbeat initiation at embryonic day 10.0, when heartbeat begins in rats, and in the primitive heart tube at embryonic day 11.0. Bundles of myofilaments were scattered in a few cells of the heart primordium after heartbeat initiation, whereas there were no typical sarcomeres in the heart primordia both before and after heartbeat initiation. Sarcomeres with Z-lines were identified in cells of the primitive heart tube, though myofilaments were not aligned. DIA-MS proteome analysis revealed that only 43 proteins were significantly upregulated by more than 2.0 fold among a total of 7,762 detected proteins in the heart primordium after heartbeat initiation compared with that before heartbeat initiation. Indeed, of those upregulated proteins, 12 (27.9%) were constituent proteins of myofibrils and 10 (23.3%) were proteins that were accessories and regulators for myofibrillogenesis, suggesting that upregulated proteins that are associated with heartbeat initiation were enriched in myofibrillogenesis. Collectively, our results suggest that the establishment of heartbeat is induced by development of bundles of myofilaments with upregulated proteins associated with myofibrillogensis, whereas sarcomeres are not required for the initial heartbeat.

Cell cycle-specific phase separation regulated by protein charge blockiness.

Dynamic morphological changes of intracellular organelles are often regulated by protein phosphorylation or dephosphorylation1-6. Phosphorylation modulates stereospecific interactions among structured proteins, but how it controls molecular interactions among unstructured proteins and regulates their macroscopic behaviours remains unknown. Here we determined the cell cycle-specific behaviour of Ki-67, which localizes to the nucleoli during interphase and relocates to the chromosome periphery during mitosis. Mitotic hyperphosphorylation of disordered repeat domains of Ki-67 generates alternating charge blocks in these domains and increases their propensity for liquid-liquid phase separation (LLPS). A phosphomimetic sequence and the sequences with enhanced charge blockiness underwent strong LLPS in vitro and induced chromosome periphery formation in vivo. Conversely, mitotic hyperphosphorylation of NPM1 diminished a charge block and suppressed LLPS, resulting in nucleolar dissolution. Cell cycle-specific phase separation can be modulated via phosphorylation by enhancing or reducing the charge blockiness of disordered regions, rather than by attaching phosphate groups to specific sites.

Enhanced glucose metabolism through activation of HIF-1α covers the energy demand in a rat embryonic heart primordium after heartbeat initiation.

The initiation of heartbeat is an essential step in cardiogenesis in the heart primordium, but it remains unclear how intracellular metabolism responds to increased energy demands after heartbeat initiation. In this study, embryos in Wistar rats at embryonic day 10, at which heartbeat begins in rats, were divided into two groups by the heart primordium before and after heartbeat initiation and their metabolic characteristics were assessed. Metabolome analysis revealed that increased levels of ATP, a main product of glucose catabolism, and reduced glutathione, a by-product of the pentose phosphate pathway, were the major determinants in the heart primordium after heartbeat initiation. Glycolytic capacity and ATP synthesis-linked mitochondrial respiration were significantly increased, but subunits in complexes of mitochondrial oxidative phosphorylation were not upregulated in the heart primordium after heartbeat initiation. Hypoxia-inducible factor (HIF)-1α was activated and a glucose transporter and rate-limiting enzymes of the glycolytic and pentose phosphate pathways, which are HIF-1α-downstream targets, were upregulated in the heart primordium after heartbeat initiation. These results suggest that the HIF-1α-mediated enhancement of glycolysis with activation of the pentose phosphate pathway, potentially leading to antioxidant defense and nucleotide biosynthesis, covers the increased energy demand in the beating and developing heart primordium.

Siwi levels reversibly regulate secondary piRISC biogenesis by affecting Ago3 body morphology in Bombyx mori.

Silkworm ovarian germ cells produce the Siwi-piRNA-induced silencing complex (piRISC) through two consecutive mechanisms, the primary pathway and the secondary ping-pong cycle. Primary Siwi-piRISC production occurs on the outer mitochondrial membrane in an Ago3-independent manner, where Tudor domain-containing Papi binds unloaded Siwi via its symmetrical dimethylarginines (sDMAs). Here, we now show that secondary Siwi-piRISC production occurs at the Ago3-positive nuage Ago3 bodies, in an Ago3-dependent manner, where Vreteno (Vret), another Tudor protein, interconnects unloaded Siwi and Ago3-piRISC through their sDMAs. Upon Siwi depletion, Ago3 is phosphorylated and insolubilized in its piRISC form with cleaved RNAs and Vret, suggesting that the complex is stalled in the intermediate state. The Ago3 bodies are also enlarged. The aberrant morphology is restored upon Siwi re-expression without Ago3-piRISC supply. Thus, Siwi depletion aggregates the Ago3 bodies to protect the piRNA intermediates from degradation until the normal cellular environment returns to re-initiate the ping-pong cycle. Overall, these findings reveal a unique regulatory mechanism controlling piRNA biogenesis.

Response to exercise-induced blood pressure elevation is blunted in wrist-cuff automated oscillometric measurement in healthy young college students.

BACKGROUND: A wrist-cuff automated oscillometric device is portable and useful for self-monitoring of blood pressure (BP) at home and outdoors when an upper arm device is not available. Although the height of the forearm in wrist BP measurement is acknowledged to be the major cause of measurement error, it remains unclear whether exercise affects subsequent wrist BP measurement. METHODS AND RESULTS: Ninety-seven healthy college students (median age of 20 years with an age range of 19 to 36 years, 70.1% males) participated in this study. Care was taken to keep the position of the wrist at a level near the upper arm level in BP measurement. At rest, BP measured by a wrist-cuff oscillometric device (Omron HEM-6183) was generally acceptable when it was compared with BP measured by an upper arm oscillometric device (Omron HEM-7130-HP) and with BP measured by the auscultatory method using a mercury sphygmomanometer. However, the ratio of systolic BP measured by oscillometric devices just after a two-step exercise test to that before exercise on the wrist (1.22 ± 0.14) was significantly lower than the ratio on the upper arm (1.27 ± 0.14), and the difference was significantly correlated with exercise-induced increase in pulse rate (Spearman's ρ = 0.23), suggesting a possible role of autonomic nerve activity in the blunted response to exercise-induced BP elevation in wrist BP measurement. CONCLUSIONS: The results indicate that the blunted response to exercise-induced BP elevation should be considered in wrist BP measurement when using a wrist-cuff oscillometric device.

Quantitative proteomics indicate a strong correlation of mitotic phospho-/dephosphorylation with non-structured regions of substrates.

Protein phosphorylation plays a critical role in the regulation and progression of mitosis. >40,000 phosphorylated residues and the associated kinases have been identified to date via proteomic analyses. Although some of these phosphosites are associated with regulation of either protein-protein interactions or the catalytic activity of the substrate protein, the roles of most mitotic phosphosites remain unclear. In this study, we examined structural properties of mitotic phosphosites and neighboring residues to understand the role of heavy phosphorylation in non-structured domains. Quantitative mass spectrometry analysis of mitosis-arrested and non-arrested HeLa cells revealed >4100 and > 2200 residues either significantly phosphorylated or dephosphorylated, respectively, at mitotic entry. The calculated disorder scores of amino acid sequences of neighboring individual phosphosites revealed that >70% of dephosphorylated phosphosites exist in disordered regions, whereas 50% of phosphorylated sites exist in non-structured domains. A clear inverse correlation was observed between probability of phosphorylation in non-structured domain and increment of phosphorylation in mitosis. These results indicate that at entry to mitosis, a significant number of phosphate groups are removed from non-structured domains and transferred to more-structured domains. Gene ontology term analysis revealed that mitosis-related proteins are heavily phosphorylated, whereas RNA-related proteins are both dephosphorylated and phosphorylated, suggesting that heavy phosphorylation/dephosphorylation in non-structured domains of RNA-binding proteins plays a role in dynamic rearrangement of RNA-containing organelles, as well as other intracellular environments.

N-terminal dual lipidation-coupled molecular targeting into the primary cilium.

The primary cilium functions as an "antenna" for cell signaling, studded with characteristic transmembrane receptors and soluble protein factors, raised above the cell surface. In contrast to the transmembrane proteins, targeting mechanisms of nontransmembrane ciliary proteins are poorly understood. We focused on a pathogenic mutation that abolishes ciliary localization of retinitis pigmentosa 2 protein and revealed a dual acylation-dependent ciliary targeting pathway. Short N-terminal sequences which contain myristoylation and palmitoylation sites are sufficient to target a marker protein into the cilium in a palmitoylation-dependent manner. A Golgi-localized palmitoyltransferase DHHC-21 was identified as the key enzyme controlling this targeting pathway. Rapid turnover of the targeted protein was ensured by cholesterol-dependent membrane fluidity, which balances highly and less-mobile populations of the molecules within the cilium. This targeting signal was found in a set of signal transduction molecules, suggesting a general role of this pathway in proper ciliary organization, and dysfunction in ciliary disorders.

Nanoscale Mosaic Works: Tetragonal Lattices of Iso-Oriented Heterogeneous Nanocubes.

Tetragonal 2D lattices are spontaneously formed by the self-assembly of homogeneous nanocubes. However, ordered arrays consisting of differently sized rectangular nanoblocks have not been achieved because the regulation of the assembly is weakened by the combination of binary units. In the present work, ordered arrays comprising binary nanocubes were investigated using the combination of 10 nm Pt nanocubes and 20 nm BaTiO3 nanocubes. Heterogeneous but ordered 2D tetragonal lattices were successfully produced using differently sized rectangular nanoblocks. The highly ordered self-assembly in the heterogeneous system requires the matching of the size ratio of binary nanocubes with the buffer effect of oleic acid covering the building units.

Successful embolisation of intrahepatic portosystemic venous shunt using AMPLATZER Vascular Plug II.

An intrahepatic portosystemic venous shunt is a relatively rare abnormality that can cause encephalopathy owing to hyperammonaemia. Two patients with encephalopathy owing to intrahepatic portosystemic venous shunts were treated with transcatheter emboli sation using the AMPLATZER Vascular Plug II. Both patients achieved complete obliteration, which was confirmed on dynamic CT. Their symptoms that had been related to portalsystemic encephalopathy subsequently improved after the intervention. No short-term complications were observed in either patient. We recommend that the AMPLATZER Vascular Plug II be used for embolis ation owing to its superior safety and utility when compared with metallic coils or other liquid embolic materials.

Dissecting in vivo steady-state dynamics of karyopherin-dependent nuclear transport.

Karyopherin-dependent molecular transport through the nuclear pore complex is maintained by constant recycling pathways of karyopherins coupled with the Ran-dependent cargo catch-and-release mechanism. Although many studies have revealed the bidirectional dynamics of karyopherins, the entire kinetics of the steady-state dynamics of karyopherin and cargo is still not fully understood. In this study, we used fluorescence recovery after photobleaching and fluorescence loss in photobleaching on live cells to provide convincing in vivo proof that karyopherin-mediated nucleocytoplasmic transport of cargoes is bidirectional. Continuous photobleaching of the cytoplasm of live cells expressing NLS cargoes led to progressive decrease of nuclear fluorescence signals. In addition, experimentally obtained kinetic parameters of karyopherin complexes were used to establish a kinetic model to explain the entire cargo import and export transport cycles facilitated by importin ß. The results strongly indicate that constant shuttling of karyopherins, either free or bound to cargo, ensures proper balancing of nucleocytoplasmic distribution of cargoes and establishes effective regulation of cargo dynamics by RanGTP.

The use of susceptibility-weighted imaging for epileptic focus localization in acute-stage pediatric encephalopathy: a case report.

BACKGROUND: Susceptibility-weighted imaging is a novel high-spatial-resolution three-dimensional gradient-echo magnetic resonance imaging technique with phase postprocessing that accentuates the paramagnetic properties of blood products. The use of susceptibility-weighted imaging for epileptic focus localization in the acute stage of encephalopathy in a child has not been documented. PATIENTS: We report three pediatric patients with status epilepticus in the setting of fever, in whom susceptibility-weighted imaging showed transient prominence of the focal venous vasculature. RESULTS: Conventional cranial T1- and T2-weighted images and diffusion-weighted images showed no abnormalities. The prominence of the focal venous vasculature in these patients, as demonstrated by susceptibility-weighted imaging, was consistent with the epileptic focuses suggested by both clinical symptoms and electroencephalograph findings and resolved completely without neurological sequelae in all patients. CONCLUSIONS: Susceptibility-weighted imaging may facilitate assessing epileptic focus localization in the acute stage of encephalopathy in children.

Imaging of congenital lipoid adrenal hyperplasia.

This article describes the specific radiological findings of congenital lipoid adrenal hyperplasia (lipoid CAH) in a phenotypic female and karyotypic 46XY infant. Radiological examination showed enlarged bilateral adrenal glands with fatty accumulation and spared medulla. These findings are key to differentiating lipoid CAH from the diseases that cause adrenal insufficiency during early infancy, including other forms of congenital adrenal hyperplasia.

The diagnosis of lung cancer using 1064-nm excited near-infrared multichannel Raman spectroscopy.

PURPOSE: Raman spectroscopy is based on Raman scattering of light from molecules. Because the wavelength of Raman scattered light depends on molecular composition, Raman spectra provide highly useful information about molecular composition. It has already been shown that Raman spectroscopy is potentially useful for the clinical diagnosis of malignant tumors. However, this technique had never been applied to the diagnosis of lung cancers, primarily because of interference from the strong fluorescence emitted from lung tissues. Our purpose was to examine the effectiveness of near-infrared Raman spectroscopy for the diagnosis of lung cancers. METHODS: We constructed a new near-infrared multichannel Raman system that is capable of measuring high signal-to-noise ratio, fluorescence-free Raman spectra of lung tissues within a measurement time of 1 second. Using this system, we collected a total of 210 Raman spectra from cancerous and non-cancerous lung tissues and analyzed these spectra by a least-squares fitting procedure for cancer diagnosis. RESULTS: The resultant sensitivity of cancer prediction was as high as 91%, with 97% specificity and an error margin of p<0.0001 according to Fisher's exact test. CONCLUSIONS: A method of diagnosing lung cancer efficiently and objectively using Raman spectroscopy has thus been established.