Inflammation and Resolution Are Associated with Upregulation of Fatty Acid β-Oxidation in Zymosan-Induced Peritonitis

Inflammation is a fundamental defensive response to harmful stimuli. However, it can cause damage if it does not subside. To avoid such damage, organisms have developed a mechanism called resolution of inflammation. Here we applied an untargeted metabolomics approach to a sterile and self-resolving animal model of acute inflammation, namely zymosan-induced peritonitis in mice, to examine the effect of inflammation and resolution on the metabolomic profiles. Significant and time-dependent changes in metabolite profiles after zymosan administration were observed in both peritoneal wash fluid (PWF) and plasma. These metabolomic changes correlated well with inflammatory chemokine or cytokine production. In PWF, most of metabolites that could detected increased in zymosan-treated mice, which is suggestive of inflammation, oxidative stress and increased energy demands. In plasma, most metabolites in the central metabolic pathway (glycolysis and TCA cycle) were significantly downregulated after zymosan administration. The concentration of the ketone body 3-hydroxybutyric acid (3-HB) in plasma and PWF increased in zymosan-injected animals indicating upregulation of fatty acid β-oxidation. Increased 3-HB level was observed in the cells that infiltrated into the peritoneal cavity and these infiltrated cells might contribute, at least in part, to the production of 3-HB in the peritoneal cavity.     

Survival Response to Increased Ceramide Involves Metabolic Adaptation through Novel Regulators of Glycolysis and Lipolysis

The sphingolipid ceramide elicits several stress responses, however, organisms survive despite increased ceramide but how they do so is poorly understood. We demonstrate here that the AKT/FOXO pathway regulates survival in increased ceramide environment by metabolic adaptation involving changes in glycolysis and lipolysis through novel downstream targets. We show that ceramide kinase mutants accumulate ceramide and this leads to reduction in energy levels due to compromised oxidative phosphorylation. Mutants show increased activation of Akt and a consequent decrease in FOXO levels. These changes lead to enhanced glycolysis by upregulating the activity of phosphoglyceromutase, enolase, pyruvate kinase, and lactate dehydrogenase to provide energy. A second major consequence of AKT/FOXO reprogramming in the mutants is the increased mobilization of lipid from the gut through novel lipase targets, CG8093 and CG6277 for energy contribution. Ubiquitous reduction of these targets by knockdown experiments results in semi or total lethality of the mutants, demonstrating the importance of activating them. The efficiency of these adaptive mechanisms decreases with age and leads to reduction in adult life span of the mutants. In particular, mutants develop cardiac dysfunction with age, likely reflecting the high energy requirement of a well-functioning heart. The lipases also regulate physiological triacylglycerol homeostasis and are important for energy metabolism since midgut specific reduction of them in wild type flies results in increased sensitivity to starvation and accumulation of triglycerides leading to cardiac defects. The central findings of increased AKT activation, decreased FOXO level and activation of phosphoglyceromutase and pyruvate kinase are also observed in mice heterozygous for ceramide transfer protein suggesting a conserved role of this pathway in mammals. These data reveal novel glycolytic and non-autonomous lipolytic pathways in response to increased ceramide for sustenance of high energy demanding organ functions like the heart.     

Affinity Purification and Characterization of Functional Tubulin from Cell Suspension Cultures of Arabidopsis and Tobacco

Microtubules assemble into several distinct arrays that play important roles in cell division and cell morphogenesis. To decipher the mechanisms that regulate the dynamics and organization of this versatile cytoskeletal component, it is essential to establish in vitro assays that use functional tubulin. Although plant tubulin has been purified previously from protoplasts by reversible taxol-induced polymerization, a simple and efficient purification method has yet to be developed. Here, we used a Tumor Overexpressed Gene (TOG) column, in which the tubulin-binding domains of a yeast (Saccharomyces cerevisiae) TOG homolog are immobilized on resin, to isolate functional plant tubulin. We found that several hundred micrograms of pure tubulin can readily be purified from cell suspension cultures of tobacco (Nicotiana tabacum) and Arabidopsis (Arabidopsis thaliana). The tubulin purified by the TOG column showed high assembly competence, partly because of low levels of polymerization-inhibitory phosphorylation of α-tubulin. Compared with porcine brain tubulin, Arabidopsis tubulin is highly dynamic in vitro at both the plus and minus ends, exhibiting faster shrinkage rates and more frequent catastrophe events, and exhibits frequent spontaneous nucleation. Furthermore, our study shows that an internal histidine tag in α-tubulin can be used to prepare particular isotypes and specifically engineered versions of α-tubulin. In contrast to previous studies of plant tubulin, our mass spectrometry and immunoblot analyses failed to detect posttranslational modification of the isolated Arabidopsis tubulin or detected only low levels of posttranslational modification. This novel technology can be used to prepare assembly-competent, highly dynamic pure tubulin from plant cell cultures.Microtubules (MTs) are important cytoskeletal polymers that are conserved in eukaryotic cells and are assembled from α- and β-tubulin heterodimers (Desai and Mitchison, 1997). In plants, MTs have important functions in essential cellular processes, such as cell division, and in cell morphogenesis. MTs in plant cells adopt several distinct higher order arrays and are remodeled in response to the cell cycle, developmental programs, and environmental cues (Hashimoto, 2015). Genetic, molecular, and cell biological approaches have been used to identify cellular factors that regulate the organization and dynamics of plant MTs. Considerable effort has been devoted to simulating the organization of cortical MT arrays by computational modeling.Cell-free in vitro studies are essential for the biochemical characterization of various MT regulators and for elucidating the mechanistic principles underlying the versatility of this dynamic polymer in cellular functions. The purification of sufficient amounts of assembly-competent tubulin is a prerequisite for these in vitro studies. Tubulin is traditionally purified from mammalian brains, since these tissues contain sufficiently high concentrations of tubulin to allow MT assembly in crude cell extracts. Polymerized MTs and their associated MT-binding proteins are separated from other cellular proteins by sedimentation. Pelleted MTs are then depolymerized upon drug washout under MT-destabilizing conditions, such as high concentrations of salt and calcium and low temperature. A few rounds of assembly-disassembly cycles highly enrich for tubulin and copurify MT-associated proteins, which can subsequently be removed by column chromatography (Borisy et al., 1975). Tubulin has also been purified from several plant sources (Morejohn and Fosket, 1982; Mizuno, 1985; Jiang et al., 1992; Bokros et al., 1993; Moore et al., 1997). However, since tubulin concentrations are low in plant cells, taxol, which stabilizes MTs, is generally included in the polymerization buffer, and cytoplasm-rich miniprotoplasts, which lack vacuoles, are sometimes used as starting material (Hamada et al., 2013). Since it is technically challenging to isolate assembly-competent pure tubulin from nonneural sources (Sackett et al., 2010), general plant science laboratories may hesitate to prepare plant tubulin themselves.Although the primary amino acid sequences of eukaryotic tubulins are fairly well conserved and the biophysical mechanisms of MT assembly and disassembly are thought to be similar for all MTs, the kinetics of MT dynamic instability differ for MTs assembled from animal and plant tubulin (Moore et al., 1997). Interactions with MT-interacting proteins may differ for tubulins isolated from different biological sources, as reported for the MT-dependent activation of kinesin (Alonso et al., 2007). Posttranslational modifications of tubulin, which generate distinct tubulin signatures and may modulate the functions of MT-interacting proteins, such as kinesin (Sirajuddin et al., 2014), are extensive in brain tubulin (Janke, 2014) but may be quantitatively and qualitatively different in plant tubulin. Furthermore, MT nucleation by the γ-tubulin ring complex shows a strong preference for tubulin from the same species (Kollman et al., 2015). Thus, it is important to use plant tubulin, and not brain tubulin, for in vitro studies of plant MTs.Tubulin is folded by a series of molecular chaperones to form an αβ-tubulin heterodimer in which one structural GTP is embedded in the interdimer interface (Lundin et al., 2010). The requirement of these eukaryote-specific chaperones precludes the use of prokaryotic expression systems for synthesizing properly folded and functional tubulin. Bacterially synthesized tubulin can be folded in rabbit reticulocyte lysate to produce functional tubulin, but with moderate yields (Shah et al., 2001). A yeast (Saccharomyces cerevisiae) expression system has been developed to produce modified yeast tubulin (Uchimura et al., 2006; Johnson et al., 2011), but this system is not suitable for the synthesis of animal (Sirajuddin et al., 2014) and plant (our unpublished data) tubulin. A baculovirus-insect cell expression system was recently reported to yield functional human tubulin (Minoura et al., 2013).Tubulin-binding proteins have been used to develop affinity-purification columns. The TOG domains (named after the human MT regulator, colonic and hepatic Tumor Overexpressed Gene [ch-TOG]) are among the best-characterized tubulin-binding domains. ch-TOG and orthologs from other eukaryotes bind to the growing plus ends of MTs and accelerate MT growth (Al-Bassam and Chang, 2011). TOG domains from the yeast ortholog Stu2 were recently used to affinity purify assembly-competent tubulin from fungal and animal sources (Widlund et al., 2012). In this study, we demonstrate that a TOG-based affinity column can be used to purify functional tubulin from tobacco (Nicotiana tabacum) and Arabidopsis (Arabidopsis thaliana). We examined the posttranslational modifications of the isolated tubulins by mass spectrometry and immunoblot analysis and showed that a His-tagged Arabidopsis tubulin isotype could be purified using this column. These results show that wild-type and recombinant functional tubulin from plant sources can be isolated efficiently.     

A flipped ion pair at the dynein–microtubule interface is critical for dynein motility and ATPase activation

Dynein is a motor protein that moves on microtubules (MTs) using the energy of adenosine triphosphate (ATP) hydrolysis. To understand its motility mechanism, it is crucial to know how the signal of MT binding is transmitted to the ATPase domain to enhance ATP hydrolysis. However, the molecular basis of signal transmission at the dynein–MT interface remains unclear. Scanning mutagenesis of tubulin identified two residues in α-tubulin, R403 and E416, that are critical for ATPase activation and directional movement of dynein. Electron cryomicroscopy and biochemical analyses revealed that these residues form salt bridges with the residues in the dynein MT-binding domain (MTBD) that work in concert to induce registry change in the stalk coiled coil and activate the ATPase. The R403-E3390 salt bridge functions as a switch for this mechanism because of its reversed charge relative to other residues at the interface. This study unveils the structural basis for coupling between MT binding and ATPase activation and implicates the MTBD in the control of directional movement.     

Analysis of metabolite profile data using batch-learning self-organizing maps

Novel tools are needed for efficient analysis and visualization of the massive data sets associated with metabolomics. Here, we describe a batch-learning self-organizing map (BL-SOM) for metabolome informatics that makes the learning process and resulting map independent of the order of data input. This approach was successfully used in analyzing and organizing the metabolome data forArabidopsis thaliana cells cultured under salt stress. Our 6 × 4 matrix presented patterns of metabolite levels at different time periods. A negative correlation was found between the levels of amino acids and metabolites related to glycolysis metabolism in response to this stress. Therefore, BL-SOM could be an excellent tool for clustering and visualizing high dimensional, complex metabolome data in a single map.     

Noncovalent binding of small ubiquitin-related modifier (SUMO) protease to SUMO is necessary for enzymatic activities and cell growth

SUMO proteases possess two enzymatic activities to hydrolyze the C-terminal region of SUMOs (hydrolase activity) and to remove SUMO from SUMO-conjugated substrates (isopeptidase activity). SUMO proteases bind to SUMOs noncovalently, but the physiological roles of the binding in the functions of SUMO proteases are not well understood. In this study we found that SUMO proteases (Axam, SENP1, and yeast Ulp1) show different preferences for noncovalent binding to various SUMOs (SUMO-1, -2, -3, and yeast Smt3) and that the hydrolase and isopeptidase activities of SUMO proteases are dependent on their binding to SUMOs through salt bridge. Expression of Smt3 suppressed the phenotype of yeast mutant lacking smt3, which exhibits growth arrest, and the binding of Ulp1 to Smt3 was essential for this rescue activity. Although expression of an Smt3 mutant (smt3R64E(GG)), which conjugates to substrate but loses the ability to bind to Ulp1, rescued the phenotype of yeast lacking smt3 partially, the mutant cells showed an increment in the doubling time and a delay of desumoylation of Smt3-conjugated Cdc3. These results indicate that the noncovalent binding of SUMO protease to SUMO through salt bridge is essential for the enzymatic activities and that the balance between sumoylation and desumoylation is important for cell growth control.     

An essential role for Cdk1 in S phase control is revealed via chemical genetics in vertebrate cells

In vertebrates Cdk1 is required to initiate mitosis; however, any functionality of this kinase during S phase remains unclear. To investigate this, we generated chicken DT40 mutants, in which an analog-sensitive mutant cdk1 as replaces the endogenous Cdk1, allowing us to specifically inactivate Cdk1 using bulky ATP analogs. In cells that also lack Cdk2, we find that Cdk1 activity is essential for DNA replication initiation and centrosome duplication. The presence of a single Cdk2 allele renders S phase progression independent of Cdk1, which suggests a complete overlap of these kinases in S phase control. Moreover, we find that Cdk1 inhibition did not induce re-licensing of replication origins in G2 phase. Conversely, inhibition during mitosis of Cdk1 causes rapid activation of endoreplication, depending on proteolysis of the licensing inhibitor Geminin. This study demonstrates essential functions of Cdk1 in the control of S phase, and exemplifies a chemical genetics approach to target cyclin-dependent kinases in vertebrate cells.     

A Prognostic Score for Patients with Intermediate-Stage Hepatocellular Carcinoma Treated with Transarterial Chemoembolization

Background

Intermediate-stage hepatocellular carcinoma (HCC), defined according to the Barcelona Clinic Liver Cancer (BCLC) staging system, is a heterogeneous condition with variable clinical benefits from transarterial chemoembolization (TACE). This study aimed to develop a simple validated prognostic score based on the predictive factors for survival in patients with intermediate-stage HCC treated with TACE.

Methods

Three-hundred and fifty patients with intermediate-stage HCC undergoing initial TACE at Chiba University Hospital (training cohort; n = 187) and two affiliated hospitals (validation cohort; n = 163) were included. Following variables were entered into univariate and multivariate Cox regression models to develop a points-based clinical scoring system: gender, age, etiology, pretreatment, Child–Pugh score, aspartate aminotransferase, creatinine, C-reactive protein, alfa-fetoprotein, size of the largest lesion, and number and location of lesions.

Results

The number of lesions and the Child–Pugh score were identified as independent prognostic factors in the training cohort. The development of a 0–7-point prognostic score, named the Chiba HCC in intermediate-stage prognostic (CHIP) score, was based on the sum of three subscale scores (Child–Pugh score = 0, 1, 2, or 3, respectively, number of lesions = 0, 2, or 3, respectively, HCV-RNA positivity = 0 or 1, respectively). The generated scores were then differentiated into five groups (0–2 points, 3 points, 4 points, 5 points, and 6–7 points) by the median survival time (65.2, 29.2, 24.3, 13.1, and 8.4 months, respectively; p < 0.0001). These results were confirmed in the external validation cohort (p < 0.0001).

Conclusions

The CHIP score is easy-to-use and may assist in finding an appropriate treatment strategy for intermediate-stage HCC.     

The Essential Functions of Human Rad51 Are Independent of ATP Hydrolysis

Genetic recombination and the repair of double-strand DNA breaks in Saccharomyces cerevisiae require Rad51, a homologue of the Escherichia coli RecA protein. In vitro, Rad51 binds DNA to form an extended nucleoprotein filament and catalyzes the ATP-dependent exchange of DNA between molecules with homologous sequences. Vertebrate Rad51 is essential for cell proliferation. Using site-directed mutagenesis of highly conserved residues of human Rad51 (hRad51) and gene targeting of the RAD51 locus in chicken DT40 cells, we examined the importance of Rad51's highly conserved ATP-binding domain. Mutant hRad51 incapable of ATP hydrolysis (hRad51K-133R) binds DNA less efficiently than the wild type but catalyzes strand exchange between homologous DNAs. hRad51 does not need to hydrolyze ATP to allow vertebrate cell proliferation, form nuclear foci, or repair radiation-induced DNA damage. However, cells expressing hRad51K-133R show greatly reduced targeted integration frequencies. These findings show that ATP hydrolysis is involved in DNA binding by hRad51 and suggest that the extent of DNA complexed with hRad51 in nucleoprotein influences the efficiency of recombination.