Efficient decoding of the UAG triplet as a full-fledged sense codon enhances the growth of a prfA-deficient strain of Escherichia coli

We previously reassigned the amber UAG stop triplet as a sense codon in Escherichia coli by expressing a UAG-decoding tRNA and knocking out the prfA gene, encoding release factor 1. UAG triplets were left at the ends of about 300 genes in the genome. In the present study, we showed that the detrimental effect of UAG reassignment could be alleviated by increasing the efficiency of UAG translation instead of reducing the number of UAGs in the genome. We isolated an amber suppressor tRNA(Gln) variant displaying enhanced suppression activity, and we introduced it into the prfA knockout strain, RFzero-q, in place of the original suppressor tRNA(Gln). The resulting strain, RFzero-q3, translated UAG to glutamine almost as efficiently as the glutamine codons, and it proliferated faster than the parent RFzero-q strain. We identified two major factors in this growth enhancement. First, the sucB gene, which is involved in energy regeneration and has two successive UAG triplets at the end, was expressed at a higher level in RFzero-q3 than RFzero-q. Second, the ribosome stalling that occurred at UAG in RFzero-q was resolved in RFzero-q3. The results revealed the importance of "backup" stop triplets, UAA or UGA downstream of UAG, to avoid the deleterious impact of UAG reassignment on the proteome.     

Structural study reveals that ser-354 determines substrate specificity on human histidine decarboxylase

Histamine is an important chemical mediator for a wide variety of physiological reactions. l-Histidine decarboxylase (HDC) is the primary enzyme responsible for histamine synthesis and produces histamine from histidine in a one-step reaction. In this study, we determined the crystal structure of human HDC (hHDC) complexed with the inhibitor histidine methyl ester. This structure shows the detailed features of the pyridoxal-5'-phosphate inhibitor adduct (external aldimine) at the active site of HDC. Moreover, a comparison of the structures of hHDC and aromatic l-amino acid (l-DOPA) decarboxylase showed that Ser-354 was a key residue for substrate specificity. The S354G mutation at the active site enlarged the size of the hHDC substrate-binding pocket and resulted in a decreased affinity for histidine, but an acquired ability to bind and act on l-DOPA as a substrate. These data provide insight into the molecular basis of substrate recognition among the group II pyridoxal-5'-phosphate-dependent decarboxylases.     

Deposition of micrometer particles in pulmonary airways during inhalation and breath holding

We investigated how breath holding increases the deposition of micrometer particles in pulmonary airways, compared with the deposition during inhalation period. A subject-specific airway model with up to thirteenth generation airways was constructed from multi-slice CT images. Airflow and particle transport were simulated by using GPU computing. Results indicate that breath holding effectively increases the deposition of 5μm particles for third to sixth generation (G3-G6) airways. After 10s of breath holding, the particle deposition fraction increased more than 5 times for 5μm particles. Due to a small terminal velocity, 1μm particles only showed a 50% increase in the most efficient case. On the other hand, 10μm particles showed almost complete deposition due to high inertia and high terminal velocity, leading to an increase of 2 times for G3-G6 airways. An effective breath holding time for 5μm particle deposition in G3-G6 airways was estimated to be 4-6s, for which the deposition amount reached 75% of the final deposition amount after 10s of breath holding.     

The effects of unsaturated fatty acids on lipid metabolism in HepG2 cells

We investigated the effects of stearic acid (saturated), oleic acid (monounsaturated), linoleic acid (n-6 polyunsaturated), and alpha-linolenic acid (n-3 polyunsaturated) on lipid metabolism in a hepatocyte-derived cell line, HepG2. HepG2 cells were cultured in medium supplemented with either stearic acid (0.1% w/v), oleic acid (0.1% v/v), linoleic acid (0.1% v/v), or alpha-linolenic acid (0.1% v/v). After 24 h, expression of lipid metabolism-associated genes was evaluated by real-time PCR. Alpha-linolenic acid showed a suppressive effect on the hepatic fatty acid de novo synthesis and fatty acid oxidation pathways, while linoleic acid also showed a tendency to suppress these pathways although the effect was weaker. Moreover, alpha-linolenic acid enhanced the expression of enzymes associated with reactive oxygen species (ROS) elimination. In contrast, oleic acid tended to promote fatty acid synthesis and oxidation. In conclusion, alpha-linolenic acid and linoleic acid may be expected to ameliorate hepatic steatosis by downregulating fatty acid de novo synthesis and fatty acid oxidation, and by upregulating ROS elimination enzymes. Oleic acid had no distinct effects for improving steatosis or oxidative stress.     

Endocytosis Is Crucial for Cell Polarity and Apical Membrane Recycling in the Filamentous Fungus Aspergillus oryzae

Establishing the occurrence of endocytosis in filamentous fungi was elusive in the past mainly due to the lack of reliable indicators of endocytosis. Recently, however, it was shown that the fluorescent dye N-(3-triethylammoniumpropyl)-4-(p-diethyl-aminophenyl-hexatrienyl)pyridinium dibromide (FM4-64) and the plasma membrane protein AoUapC (Aspergillus oryzae UapC) fused to enhanced green fluorescent protein (EGFP) were internalized from the plasma membrane by endocytosis. Although the occurrence of endocytosis was clearly demonstrated, its physiological importance in filamentous fungi still remains largely unaddressed. We generated a strain in which A. oryzae end4 (Aoend4), the A. oryzae homolog of Saccharomyces cerevisiae END4/SLA2, was expressed from the Aoend4 locus under the control of a regulatable thiA promoter. The growth of this strain was severely impaired, and its hyphal morphology was altered in the Aoend4-repressed condition. Moreover, in the Aoend4-repressed condition, neither FM4-64 nor AoUapC-EGFP was internalized, indicating defective endocytosis. Furthermore, the localization of a secretory soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) was abnormal in the Aoend4-repressed condition. Aberrant accumulation of cell wall components was also observed by calcofluor white staining and transmission electron microscopy analysis, and several genes that encode cell wall-building enzymes were upregulated, indicating that the regulation of cell wall synthesis is abnormal in the Aoend4-repressed condition, whereas Aopil1 disruptants do not display the phenotype exhibited in the Aoend4-repressed condition. Our results strongly suggest that endocytosis is crucial for the hyphal tip growth in filamentous fungi.The filamentous fungus Aspergillus oryzae has been used in industrial fermentation processes and is regarded to be safe for humans. A. oryzae can secrete several proteins, such as alpha-amylase, into the medium. Thus, A. oryzae is a potential host for heterologous protein production. Since the completion of A. oryzae genome sequencing (18) in recent years, many applied and basic studies have been conducted on A. oryzae using its genome sequencing data. In particular, studies on vesicular trafficking, including the secretory pathway, are of increasing importance because they are closely related to protein production. For example, endoplasmic reticulum and vacuole dynamics and systematic soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein analyses have been performed in A. oryzae (16, 19, 23, 30, 31, 32). However, endocytosis, an intracellular trafficking pathway, has not been studied as well in A. oryzae as in other filamentous fungi.Endocytosis is an important cellular process that occurs, for example, in signal transduction and reconstruction of cell polarity and is conserved in eukaryotic cells. The detailed mechanism of endocytosis has been well studied in model organisms such as yeasts. Many proteins are involved in the endocytic process, which is regulated spatiotemporally (12). Saccharomyces cerevisiae END4/SLA2 (synthetic lethal with ABP1) is an endocytosis-associated gene that has been studied in detail (3, 6, 22, 27, 35, 43, 44). End4p/Sla2p is essential for fluid-phase and receptor-mediated endocytosis and actin assembly and polarization (27). The protein has the epsin N-terminal homology (ENTH) and the AP180 N-terminal homology (ANTH) domains, which bind to phosphatidylinositol-4,5-bisphosphate in the plasma membrane in the N-terminal region, and the I/LWEQ domain, which is proposed to be the actin-binding domain in the C-terminal region; it also functions as an adaptor that connects the invaginated plasma membrane and actin cytoskeleton, which plays an important role in endocytosis, to generate force for invaginating the plasma membrane into the intracellular space and forming endocytic pits (13, 33). Abp1p (actin-binding protein) forms actin patches by polymerization of the actin cytoskeleton. It is suggested that endocytosis occurs at the sites in which Abp1p localizes, i.e., cortical actin patches (21, 22). Hence, Abp1p has been used as a tool to investigate the subcellular space in which endocytosis occurs (21).Establishing the existence of endocytosis in filamentous fungi was elusive in the past mainly due to the lack of reliable indicators of endocytosis (28). However, it has been confirmed that the fluorescent dye N-(3-triethylammoniumpropyl)-4-(p-diethyl-aminophenyl-hexatrienyl)pyridinium dibromide (FM4-64) and the plasma membrane protein AoUapC (Aspergillus oryzae UapC [uric acid-xanthine permease]) fused to enhanced green fluorescent protein (EGFP) were internalized from the plasma membrane by endocytosis (8, 25). Moreover, recently, in Aspergillus nidulans, the localization of components required for endocytosis has been analyzed in living hyphae (1, 37, 41). ActA and FimA, which are actin and fimbrin, respectively, are mostly localized in the hyphal tip region (41). Furthermore, AbpA, an actin-binding protein, is primarily localized in the apical region and is used as an endocytic site marker. AmpA, the amphiphysin homolog in A. nidulans, and SlaB, the End4p/Sla2p homolog, are also localized in sites in which AbpA is localized (1). These endocytic components are localized near the hyphal tip regions but slightly away from the apex where exocytosis preferentially occurs (37). Although the occurrence of endocytosis was clearly demonstrated and the localization of endocytic components was analyzed, the physiological importance of endocytosis in filamentous fungi still remains largely unaddressed.In this report, we analyzed the physiological significance of endocytosis by generating strains that conditionally express A. oryzae end4 (Aoend4), the A. oryzae homolog of S. cerevisiae END4/SLA2. Hyphae grown in the Aoend4-repressed condition displayed aberrant morphology; endocytic defects in AoUapC-EGFP and FM4-64; abnormal apical recycling of EGFP-fused AoSnc1, which is a vesicle SNARE required for secretion; and abnormal cell wall synthesis. These results suggest that endocytosis plays crucial roles in the physiology of hyphal growth.     

Dietary fat modulation of apoA-II metabolism and prevention of senile amyloidosis in the senescence- accelerated mouse

Senescence-accelerated mouse-prone (SAMP1; SAMP1@Umz) is an animal model of senile amyloidosis with apolipoprotein A-II (apoA-II) amyloid fibril (AApoAII) deposits. This study was undertaken to investigate the effects of dietary fats on AApoAII deposits in SAMP1 mice when purified diets containing 4% fat as butter, safflower oil, or fish oil were fed to male mice for 26 weeks. The serum HDL cholesterol was significantly lower (P < 0.01) in mice on the diet containing fish oil (7.4 +/- 3.0 mg/dl) than in mice on the butter diet (38.7 +/- 12.5 mg/dl), which in turn had significantly lower (P < 0.01) HDL levels than mice on the safflower oil diet (51.9 +/- 5.6 mg/dl). ApoA-II was also significantly lower (P < 0.01) in mice on the fish oil diet (7.6 +/- 2.7 mg/dl) than on the butter (26.9 +/- 7.3 mg/dl) or safflower oil (21.6 +/- 3.7 mg/dl) diets. The mice fed fish oil had a significantly greater ratio (P < 0.01) of apoA-I to apoA-II, and a smaller HDL particle size than those fed butter and safflower oil. Severe AApoAII deposits in the spleen, heart, skin, liver, and stomach were shown in the fish oil group compared with those in the butter and safflower oil groups (fish oil > butter > safflower oil group, P < 0.05). These findings suggest that dietary fats differ in their effects on serum lipoprotein metabolism, and that dietary lipids may modulate amyloid deposition in SAMP1 mice.     

Bile acid regulation of hepatic physiology: IV. Bile acids and death receptors

Toxic bile acids facilitate Fas and tumor necrosis factor-associated apoptosis-inducing ligand (TRAIL) death-receptor oligomerization and activation. Bile acid modulation of death-receptor signaling is multifactorial and includes trafficking of Fas to the cell surface, enhancing TRAIL-R2/DR5 expression, and suppression of function of cFLIP, an antiapoptotic protein modulating death-receptor function. Because bile acid-associated death receptor-mediated apoptosis is a common mechanism for cholestatic hepatocyte injury, inhibition of death receptors and their cascades may prove useful in attenuating liver injury during cholestasis.     

Bile acids activate EGF receptor via a TGF-alpha-dependent mechanism in human cholangiocyte cell lines

Bile acids transactivate the EGF receptor (EGFR) in cholangiocytes. However, the mechanisms by which bile acids transactivate the EGFR remain unknown. Our aims were to examine the effects of bile acids on EGFR activation in human cholangiocyte cell lines KMBC and H-69. Bile acids stimulated cell growth and induced EGFR phosphorylation in a ligand-dependent manner. Although cells constitutively expressed several EGFR ligands, only transforming growth factor-alpha (TGF-alpha) antisera effectively blocked bile acid-induced EGFR phosphorylation. Consistent with the concept that matrix metalloproteinase (MMP) activity is requisite for TGF-alpha membrane release and ligand function, bile acid transactivation of EGFR and cell growth was blocked by an MMP inhibitor. In conclusion, bile acids activate EGFR via a TGF-alpha-dependent mechanism, and this EGFR activation promotes cellular growth.     

Mitochondria play a central role in apoptosis induced by alpha-tocopheryl succinate,an agent with antineoplastic activity: comparison with receptor-mediated pro-apoptotic signaling

alpha-Tocopheryl succinate (alpha-TOS) is a semisynthetic vitamin E analogue with high pro-apoptotic and anti-neoplastic activity [Weber, T et al. (2002) Clin. Cancer Res. 8, 863-869]. Previous studies suggested that it acts through destabilization of subcellular organelles, including mitochondria, but compelling evidence is missing. Cells treated with alpha-TOS showed altered mitochondrial structure, generation of free radicals, activation of the sphingomyelin cycle, relocalization of cytochrome c and Smac/Diablo, and activation of multiple caspases. A pan-caspase inhibitor suppressed caspase-3 and -6 activation and phosphatidyl serine externalization, but not decrease of mitochondrial membrane potential or generation of radicals. For alpha-TOS, but not Fas or TRAIL, apoptosis was suppressed by caspase-9 inhibition, while TRAIL- and Fas-resistant cells overexpressing cFLIP or CrmA were susceptible to alpha-TOS. The central role of mitochondria was confirmed by resistance of mtDNA-deficient cells to alpha-TOS, by regulation of alpha-TOS apoptosis by Bcl-2 family members, and by anti-apoptotic activity of mitochondrially targeted radical scavengers. Co-treatment with alpha-TOS and anti-Fas IgM showed their cooperative effect, probably by signaling via different, convergent pathways. These data provide an insight into the molecular mechanism, by which alpha-TOS kills malignant cells, and advocate its testing as a potential anticancer agent or adjuvant.     

Over-reduced states of the Mn-cluster in cucumber leaves induced by dark-chilling treatment

Oxygen evolution is inhibited when leaves of chilling-sensitive plants like cucumber are treated at 0 degrees C in the dark. The activity is restored by moderate illumination at room temperature. We examined the changes in the redox state of the Mn-cluster in cucumber leaves in the processes of dark-chilling inhibition and subsequent light-induced reactivation by means of thermoluminescence (TL). A TL B-band arising from S(2)Q(B)(-) charge recombination in PSII was observed upon single-flash illumination of untreated leaves, whereas four flashes were required to yield the B-band after dark-chilling treatment for 24 h. This three-step delay indicates that over-reduced states of the Mn-cluster such as the S(-2) state were formed during the treatment. Fitting analysis of the flash-number dependence of the TL intensities showed that the Mn-cluster was more reduced with a longer period of the treatment and that S(-3) was the lowest S-state detectable in the dark-chilled leaves. Measurements of the Mn content by atomic absorption spectroscopy showed that Mn atoms were gradually released from PSII during the dark-chilling treatment but re-bound to PSII by illumination at 30 degrees C. Thus, dark-chilling inhibition of oxygen evolution can be ascribed to the disintegration of the Mn-cluster due to its over-reduction. The observation of the S(-3) state in the present in vivo system strongly suggests that S(-3), which has been observed only by addition of exogenous reductants into in vitro preparations, is indeed a redox intermediate of the Mn-cluster in the processes of its disintegration and photoactivation.