Purification and biochemical characterization of a membrane-bound [NiFe]-hydrogenase from a hydrogen-oxidizing, lithotrophic bacterium, Hydrogenophaga sp. AH-24

Membrane-bound [NiFe]-hydrogenase from Hydrogenophaga sp. AH-24 was purified to homogeneity. The molecular weight was estimated as 100±10 kDa, consisting of two different subunits (62 and 37 kDa). The optimal pH values for H₂ oxidation and evolution were 8.0 and 4.0, respectively, and the activity ratio (H₂ oxidation/H₂ evolution) was 1.61 × 10² at pH 7.0. The optimal temperature was 75 °C. The enzyme was quite stable under air atmosphere (the half-life of activity was c . 48 h at 4 °C), which should be important to function in the aerobic habitat of the strain. The enzyme showed high thermal stability under anaerobic conditions, which retained full activity for over 5 h at 50 °C. The activity increased up to 2.5-fold during incubation at 50 °C under H₂. Using methylene blue as an electron acceptor, the kinetic constants of the purified membrane-bound homogenase (MBH) were V _max=336 U mg⁻¹, k _cat=560 s⁻¹, and k _cat/ K _m=2.24 × 10⁷ M⁻¹ s⁻¹. The MBH exhibited prominent electron paramagnetic resonance signals originating from [3Fe–4S]⁺ and [4Fe–4S]⁺ clusters. On the other hand, signals originating from Ni of the active center were very weak, as observed in other oxygen-stable hydrogenases from aerobic H₂-oxidizing bacteria. This is the first report of catalytic and biochemical characterization of the respiratory MBH from Hydrogenophaga .     

Cobalt(II) coordination polymers assembled from polycarboxylate and benzotriazole: Syntheses, structures and physical properties

Hydrothermal reactions of cobalt(II) salt with H₂CAM or H₂SDBA and HBTA in the presence of NaOH afford two interesting coordination polymers, Co₃(CAM)₂(BTA)₂ (1) and Co₃(SDBA)₂(BTA)₂ (2) (H₂CAM = camphoric acid, H₂SDBA = 4,4′-dicarboxybiphenyl sulfone, HBTA = benzotriazole), both of which have been structurally characterized by single-crystal X-ray, elemental analysis, infrared spectroscopy, and thermogravimetric analysis. Complexes 1 and 2 are isostructural and possess two-dimensional covalent network, comprising an unusual linear Co(II) chains of mixed T_d-O_h-T_d geometries. Temperature-dependent magnetic measurements indicate the existence of antiferromagnetic interactions in both 1 and 2.     

PKR-mediated degradation of STAT1 regulates osteoblast differentiation

The double-stranded RNA-dependent protein kinase (PKR) plays a critical role in various biological responses including antiviral defense, cell differentiation, apoptosis, and tumorigenesis. In this study, we investigated whether PKR could affect the post-translational modifications of STAT1 protein and whether these modifications regulate osteoblast differentiation. We demonstrated that PKR was necessary for the ubiquitination of STAT1 protein. The expressions of bone-related genes such as type I collagen, integrin binding sialoprotein, osteopontin, and osterix were suppressed in osteoblasts lacking PKR activity. In contrast, the expressions of interleukin-6 and matrix metalloproteinases 8 and 13 increased in PKR-mutated osteoblasts. The expression and degradation of STAT1 protein were regulated by PKR in a SLIM-dependent pathway. Inhibition of SLIM by RNA interference resulted in the decreased activity of Runx2 in osteoblasts. Stimulation of interleukin-6 expression and suppression of alkaline phosphatase activity were regulated through by SLIM-dependent pathway. However, expressions of bone-related genes and MMPs were regulated by SLIM-independent pathway. Our present results suggest that the aberrant accumulation of STAT1 protein induced by loss of PKR regulate osteoblast differentiation through both SLIM/STAT1-dependent and -independent pathways.     

The 3′-Phosphoadenosine 5′-Phosphosulfate Transporters,PAPST1 and 2, Contribute to the Maintenance and Differentiation of Mouse Embryonic Stem Cells

Recently, we have identified two 3′-phosphoadenosine 5′-phosphosulfate (PAPS) transporters (PAPST1 and PAPST2), which contribute to PAPS transport into the Golgi, in both human and Drosophila. Mutation and RNA interference (RNAi) of the Drosophila PAPST have shown the importance of PAPST-dependent sulfation of carbohydrates and proteins during development. However, the functional roles of PAPST in mammals are largely unknown. Here, we investigated whether PAPST-dependent sulfation is involved in regulating signaling pathways required for the maintenance of mouse embryonic stem cells (mESCs), differentiation into the three germ layers, and neurogenesis. By using a yeast expression system, mouse PAPST1 and PAPST2 proteins were shown to have PAPS transport activity with an apparent K_m value of 1.54 µM or 1.49 µM, respectively. RNAi-mediated knockdown of each PAPST induced the reduction of chondroitin sulfate (CS) chain sulfation as well as heparan sulfate (HS) chain sulfation, and inhibited mESC self-renewal due to defects in several signaling pathways. However, we suggest that these effects were due to reduced HS, not CS, chain sulfation, because knockdown of mouse N-deacetylase/N-sulfotransferase, which catalyzes the first step of HS sulfation, in mESCs gave similar results to those observed in PAPST-knockdown mESCs, but depletion of CS chains did not. On the other hand, during embryoid body formation, PAPST-knockdown mESCs exhibited abnormal differentiation, in particular neurogenesis was promoted, presumably due to the observed defects in BMP, FGF and Wnt signaling. The latter were reduced as a result of the reduction in both HS and CS chain sulfation. We propose that PAPST-dependent sulfation of HS or CS chains, which is regulated developmentally, regulates the extrinsic signaling required for the maintenance and normal differentiation of mESCs.     

Insight into the Regulation of Glycan Synthesis in Drosophila Chaoptin Based on Mass Spectrometry

Background

A variety of N-glycans attached to protein are known to involve in many important biological functions. Endoplasmic reticulum (ER) and Golgi localized enzymes are responsible to this template-independent glycan synthesis resulting glycoforms at each asparagine residues. The regulation mechanism such glycan synthesis remains largely unknown.

Methodology/Principal Findings

In order to investigate the relationship between glycan structure and protein conformation, we analyzed a glycoprotein of Drosophila melanogaster, chaoptin (Chp), which is localized in photoreceptor cells and is bound to the cell membrane via a glycosylphosphatidylinositol anchor. Detailed analysis based on mass spectrometry revealed the presence of 13 N-glycosylation sites and the composition of the glycoform at each site. The synthetic pathway of glycans was speculated from the observed glycan structures and the composition at each N-glycosylation site, where the presence of novel routes were suggested. The distribution of glycoforms on a Chp polypeptide suggested that various processing enzymes act on the exterior of Chp in the Golgi apparatus, although virtually no enzyme can gain access to the interior of the horseshoe-shaped scaffold, hence explaining the presence of longer glycans within the interior. Furthermore, analysis of Chp from a mutant (RNAi against dolichyl-phosphate α-d-mannosyltransferase), which affects N-glycan synthesis in the ER, revealed that truncated glycan structures were processed. As a result, the distribution of glycoforms was affected for the high-mannose-type glycans only, whereas other types of glycans remained similar to those observed in the control and wild-type.

Conclusions/Significance

These results indicate that glycan processing depends largely on the backbone structure of the parent polypeptide. The information we obtained can be applied to other members of the LRR family of proteins.     

Deadenylation is a widespread effect of miRNA regulation

miRNAs silence gene expression by repressing translation and/or by promoting mRNA decay. In animal cells, degradation of partially complementary miRNA targets occurs via deadenylation by the CAF1-CCR4-NOT1 deadenylase complex, followed by decapping and subsequent exonucleolytic digestion. To determine how generally miRNAs trigger deadenylation, we compared mRNA expression profiles in D. melanogaster cells depleted of AGO1, CAF1, or NOT1. We show that ~60% of AGO1 targets are regulated by CAF1 and/or NOT1, indicating that deadenylation is a widespread effect of miRNA regulation. However, neither a poly(A) tail nor mRNA circularization are required for silencing, because mRNAs whose 3′ ends are generated by a self-cleaving ribozyme are also silenced in vivo. We show further that miRNAs trigger mRNA degradation, even when binding by 40S ribosomal subunits is inhibited in cis. These results indicate that miRNAs promote mRNA decay by altering mRNP composition and/or conformation, rather than by directly interfering with the binding and function of ribosomal subunits.     

UDP-glucose:3-deoxyanthocyanidin 5-O-glucosyltransferase from Sinningia cardinalis

3-Deoxyanthocyanins are rare anthocyanin pigments produced by some mosses, ferns, and higher plants. The enzymes and genes responsible for biosynthesis of 3-deoxyanthocyanins have not been well characterized. We identified a novel gene encoding UDP-glucose:3-deoxyanthocyanidin 5-O-glucosyltransferase (dA5GT) from Sinningia cardinalis, which accumulates abundant 3-deoxyanthocyanins in its petals. Five candidate genes (ScUGT1 to ScUGT5) were isolated from an S. cardinalis flower cDNA by degenerate PCR targeted for the UGT88 clade. ScUGT1, ScUGT3, and ScUGT5 exhibited 45–47% identity with rose anthocyanidin 5,3-O-glucosyltransferase, which catalyzes glucosylation at the 5- and 3-position of 3-hydroxyanthocyanidin. Based on its temporal and spatial gene expression patterns, and enzymatic activity assays of the recombinant protein, ScUGT5 was screened as a dA5GT candidate. Recombinant ScUGT5 protein expressed in Escherichia coli was used to analyze the detailed enzymatic properties. The results demonstrated that ScUGT5 specifically transferred a glucosyl moiety to 3-deoxyanthocyanidins in the presence of UDP-glucose, but not to other flavonoid compounds, such as 3-hydroxyanthocyanidins, flavones, flavonols, or flavanones.     

Self-assembly of 3-D 4d-4f coordination frameworks based on pyridine-3,5-dicarboxylic acid: Syntheses, crystal structures and luminescence

The hydrothermal reactions of H₂PDC, AgNO₃ with Eu₂O₃ or Tb(NO₃)₃·6H₂O gave rise to two novel three-dimensional 4d-4f heterometallic metal-organic coordination polymers, AgEu(PDC)₂ (1) and AgTb(PDC)₂ (2) (H₂PDC = pyridine-3,5-dicarboxylic acid), and characterized by elemental analysis, IR, thermal analysis and single-crystal X-ray diffraction. Complexes 1 and 2 crystallize in the monoclinic system, P2/c space group; the structure determination reveal that both of them are isostructural and feature an unusual three-dimensional heterometallic network structure in which infinite lanthanide-carboxylate chains are linked by [Ag(PDC)₂]³⁻ metalloligands to form a mixed-metal coordination network. Moreover, the luminescent properties of two complexes have also been investigated at room temperature.     

Site‐directed mutagenesis of rat thioltransferase: Effects of essential cysteine residues for the protection against oxidative stress

A cDNA of rat liver thioltransferase was cloned and then expressed using pMAL‐c expression vector in Escherichia coli. Recombinant rat liver thioltransferase was expressed as a fusion protein with maltose‐binding protein and then purified by amylose resin column chromatography to be homogeneity on 12.5% SDS‐polyacrylamide gel electrophoretic analysis. The expressed proteins were shown as two bands at around 53 and 41 kDa, suggesting that the high molecular one was a fusion protein of recombinant thioltransferase (11.7 plus 41 kDa) and the other (smaller one) was a maltose‐binding protein (41 kDa). A recombinant thioltransferase catalyzed a thiol/disulfide exchange reaction in the same way as thioltransferases purified from various sources. Compared with wild type, the mutants C23A, C26A, C79A, and C83A showed 0%, 17%, 82%, and 86% in the enzymatic activity, respectively. In addition, wild‐type‐transfected bacteria expressed in bacterial cells showed a strong resistance to H₂O₂ treatment as well as the case of active mutants (C79A and C83A), but inactive mutants (C23A and C26A) showed no resistance to H₂O₂ treatment as same as mocktransfection. Thioltransferase can be important for survival of bacterial cells under oxidative stress. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 24:60–65, 2010; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20312