Structure of hydrogenase maturation protein HypF with reaction intermediates shows two active sites

[NiFe]-hydrogenases are multimeric proteins. The?large subunit contains the NiFe(CN)(2)CO bimetallic active center and the small subunit contains Fe-S clusters. Biosynthesis and assembly of the NiFe(CN)(2)CO active center requires six Hyp accessory proteins. The synthesis of the CN(-) ligands is?catalyzed by the combined actions of HypF and?HypE using carbamoylphosphate as a substrate.?We report the structure of Escherichia coli HypF(92-750) lacking the N-terminal acylphosphatase domain. HypF(92-750) comprises the novel Zn-finger domain, the nucleotide-binding YrdC-like domain, and the Kae1-like universal domain, also binding a nucleotide and a Zn(2+) ion. The two nucleotide-binding sites are sequestered in an internal cavity, facing each other and separated by ～14??. The YrdC-like domain converts carbamoyl moiety to a carbamoyl adenylate intermediate, which is channeled to the Kae1-like domain. Mutations within either nucleotide-binding site compromise hydrogenase maturation but do not affect the carbamoylphosphate phosphatase activity.     

Ribosomal DNA phylogenies of Cyathus: is the current infrageneric classification appropriate?

Phylogenetic relationships within the genus Cyathus (bird's nest fungi) were investigated with neighbor joining, maximum likelihood, weighted maximum parsimony and MrBayes analyses of ITS and LSU ribosomal DNA sequences datasets. Twenty-two taxa of Cyathus were used in the analyses based primarily on type and authentic specimens. The current infrageneric classification system of Brodie recognizes seven infrageneric groups based on morphological characters, including peridium plications and variations in peridium hair anatomy, peridiole structure and fruit-body color. These groups are not supported by molecular data. Instead the ITS and LSU datasets support recognition of three infrageneric groups herein named the ollum, pallidum and striatum groups. Morphological characters useful in distinguishing these groups include basidiospore size, fruit-body coloration and peridium anatomy. Cyathus africanus var. latisporus is considered a synonym of Cyathus jiayuguanensis, and a new combination Cyathus lanatus (Brodie) R.L. Zhao is proposed based on morphological and molecular data.     

Metabolism of adrenic acid to vasodilatory 1alpha,1beta-dihomo-epoxyeicosatrienoic acids by bovine coronary arteries

Adrenic acid (docosatetraenoic acid), an abundant fatty acid in the vasculature, is produced by a two-carbon chain elongation of arachidonic acid. Despite its abundance and similarity to arachidonic acid, little is known about its role in the regulation of vascular tone. Gas chromatography/mass spectrometric analysis of bovine coronary artery and endothelial cell lysates revealed arachidonic acid concentrations of 2.06 +/- 0.01 and 6.18 +/- 0.60 microg/mg protein and adrenic acid concentrations of 0.29 +/- 0.01 and 1.56 +/- 0.16 microg/mg protein, respectively. In bovine coronary arterial rings preconstricted with the thromboxane mimetic U-46619, adrenic acid (10(-9)-10(-5) M) induced concentration-related relaxations (maximal relaxation = 83 +/- 4%) that were similar to arachidonic acid relaxations. Adrenic acid relaxations were blocked by endothelium removal and the K(+) channel inhibitor, iberiotoxin (100 nM), and inhibited by the cyclooxygenase inhibitor, indomethacin (10 microM, maximal relaxation = 53 +/- 4%), and the cytochrome P-450 inhibitor, miconazole (10 microM, maximal relaxation = 52 +/- 5%). Reverse-phase HPLC and liquid chromatography/mass spectrometry isolated and identified numerous adrenic acid metabolites from coronary arteries including dihomo (DH)-epoxyeicosatrienoic acids (EETs) and DH-prostaglandins. DH-EET [16,17-, 13,14-, 10,11-, and 7,8- (10(-9)-10(-5) M)] induced similar concentration-related relaxations (maximal relaxations averaged 83 +/- 3%). Adrenic acid (10(-6) M) and DH-16,17-EET (10(-6) M) hyperpolarized coronary arterial smooth muscle. DH-16,17-EET (10(-8)-10(-6) M) activated iberiotoxin-sensitive, whole cell K(+) currents of isolated smooth muscle cells. Thus, in bovine coronary arteries, adrenic acid causes endothelium-dependent relaxations that are mediated by cyclooxygenase and cytochrome P-450 metabolites. The adrenic acid metabolite, DH-16,17-EET, activates smooth muscle K(+) channels to cause hyperpolarization and relaxation. Our results suggest a role of adrenic acid metabolites, specifically, DH-EETs as endothelium-derived hyperpolarizing factors in the coronary circulation.     

The roles of JK-1 (FAM134B) expressions in colorectal cancer

The aims of the present study are to investigate the clinicopathological correlations of JK-1(FAM134B) expression and its relationship to carcinogenesis in a colorectal adenoma–adenocarcinoma model. JK-1(FAM134B) protein expression was studied in a colon cancer cell line by Western blot and immunocytochemistry. JK-1(FAM134B) expression profiles at mRNA and protein levels were investigated in cancer tissues from 236 patients with colorectal adenocarcinoma and 32 patients with colorectal adenoma using real-time polymerase chain reaction and immunohistochemistry. The findings were then correlated with the clinicopathological features of these tumours. JK-1(FAM134B) protein was demonstrated in the colon cancer cells by Western blot. The protein was located in the nuclei of the tumour cells at both cellular and tissue levels. In colorectal adenocarcinomas, lower levels of JK-1(FAM134B) protein expression were associated with younger age (p=0.032), larger tumour size (p=0.004), advanced cancer stages (p=0.016) and higher rates of cancer recurrence (p=0.04). Also, lower levels of JK-1(FAM134B) mRNA expression were associated with advanced cancer stages (p=0.02) and presence of lymphovascular invasion (p=0.014). Higher JK-1(FAM134B) mRNA and protein expression levels were identified in adenomas and non-neoplastic mucosae, compared to carcinomas (p=0.005). To conclude, JK-1(FAM134B) mRNA expression and JK1 (FAM134B) protein levels varied with the different stages of progression of colorectal tumours. The expression levels of the gene were associated with clinicopathological features in patients with colorectal adenocarcinoma suggesting that JK-1(FAM134B) gene has roles in controlling some steps in the development of the invasive phenotypes from colorectal adenoma to early staged as well as advanced staged colorectal adenocarcinomas.     

The Influence of Oxygen on [NiFe]–Hydrogenase Cofactor Biosynthesis and How Ligation of Carbon Monoxide Precedes Cyanation

The class of [NiFe]–hydrogenases is characterized by a bimetallic cofactor comprising low–spin nickel and iron ions, the latter of which is modified with a single carbon monoxide (CO) and two cyanide (CN⁻) molecules. Generation of these ligands in vivo requires a complex maturation apparatus in which the HypC–HypD complex acts as a ‘construction site’ for the Fe–(CN)₂CO portion of the cofactor. The order of addition of the CO and CN^– ligands determines the ultimate structure and catalytic efficiency of the cofactor; however much debate surrounds the succession of events. Here, we present an FT–IR spectroscopic analysis of HypC–HypD isolated from a hydrogenase–competent wild–type strain of Escherichia coli. In contrast to previously reported samples, HypC–HypD showed spectral contributions indicative of an electron–rich Fe–CO cofactor, at the same time lacking any Fe–CN^– signatures. This immature iron site binds external CO and undergoes oxidative damage when in contact with O₂. Binding of CO protects the site against loss of spectral features associated with O₂ damage. Our findings strongly suggest that CO ligation precedes cyanation in vivo. Furthermore, the results provide a rationale for the deleterious effects of O₂ on in vivo cofactor biosynthesis.     

Characterization of Sugar and Polyphenolic Diversity in Floral Nectar of Different ‘Oblačinska’ Sour Cherry Clones

‘Obla?inska’ sour cherry, an autochthonous cultivar, is the most planted cultivar in Serbian orchards. Since fruit trees in temperate zone reward insects by producing nectar which ‘quality’ affects the efficiency of insect pollination, the aim of this study was analyzing of sugars and polyphenolics in floral nectar of 16 ‘Obla?inska’ sour cherry clones with different yielding potential. The contents of sugars and sugar alcohols were analyzed by ion chromatography, while polyphenolic profile was established using liquid chromatography/mass spectrometry technique. Fourteen sugars and six sugar alcohols were detected in nectar samples and the most abundant were fructose, glucose, and sucrose. Eleven polyphenols were quantified using available standards, while another 17 were identified according to their exact masses and characteristic fragmentations. Among quantified polyphenols, rutin, naringenin, and chrysin were the most abundant in nectar. Principal component analysis showed that some polyphenol components (naringin, naringenin, and rutin) together with sugars had high impact of spatial distribution of nectar samples on score plot.     

Purification of a NifEN protein complex that contains bound molybdenum and a FeMo-Co precursor from an Azotobacter vinelandii DeltanifHDK strain

The NifEN protein complex serves as a molecular scaffold where some of the steps for the assembly of the iron-molybdenum cofactor (FeMo-co) of nitrogenase take place. A His-tagged version of the NifEN complex has been previously purified and shown to carry two identical [4Fe-4S] clusters of unknown function and a [Fe-S]-containing FeMo-co precursor. We have improved the purification of the his-NifEN protein from a DeltanifHDK strain of Azotobacter vinelandii and have found that the amounts of iron and molybdenum within NifEN were significantly higher than those reported previously. In an in vitro FeMo-co synthesis system with purified components, the NifEN protein served as a source of both molybdenum and a [Fe-S]-containing FeMo-co precursor, showing significant FeMo-co synthesis activity in the absence of externally added molybdate. Thus, the NifEN scaffold protein, purified from DeltanifHDK background, contained the Nif-Bco-derived Fe-S cluster and molybdenum, although these FeMo-co constituents were present at different levels within the protein complex.     

Evidence for an oxygen-sensitive iron-sulfur cluster in an immature large subunit species of Escherichia coli [NiFe]-hydrogenase 2

Lung cancer is the most common cause of cancer-related death worldwide. Stromal cancer-associated fibroblasts (CAFs) play crucial roles in carcinogenesis, proliferation, invasion, and metastasis of non-small cell lung carcinoma, and targeting of CAFs could be a novel strategy for cancer treatment. However, the characteristics of human CAFs still remain to be better defined. In this study, we established patient-matched CAFs and normal fibroblasts (NFs), from tumoral and non-tumoral portions of resected lung tissue from lung cancer patients. CAFs showed higher α-smooth muscle actin (α-SMA) expression than NFs, and CAFs clearly enhanced collagen gel contraction. Furthermore, we employed three-dimensional co-culture assay with A549 lung cancer cells, where CAFs were more potent in inducing collagen gel contraction. Hematoxylin and eosin staining of co-cultured collagen gel revealed that CAFs had the potential to increase invasion of A549 cells compared to NFs. These observations provide evidence that lung CAFs have the tumor-promoting capacity distinct from NFs.     

Mushroom diversity in sustainable shade tea forest and the effect of fire damage

A survey of the biodiversity of wild macrofungi, including edible species yields, was carried out from 1 May to 30 September 2007 at four different forest types (in mainly Miang tea forest). The plots 100 m², comprised a tea garden with a few planted canopy tree species (37.2% canopy cover), a cultivated sustainable tea forest (80.2% canopy cover), an abandoned sustainable tea forest (89.8% canopy cover), and an abandoned sustainable tea forest that had suffered fire damage (72.9% canopy cover). All visible mushrooms were collected during weekly forays. Macro-characters of the fungi were annotated and photographed by digital camera and the fungi were identified to genera and morphospecies (e.g. Agaricus sp.1, Agaricus sp.2). The fresh weight of wild edible mushrooms produced in the plots was also recorded during this period. The biodiversity of macrofungi in abandoned sustainable tea forest was highest with 115 species in 47 genera, followed by cultivated sustainable tea forest with 85 species in 42 genera and fire damaged abandoned sustainable tea forest with 48 species in 25 genera, while only 19 species belonging to 15 genera were found in the tea garden. Twenty-one species belonging to nine genera with a total of 60.9 kg of edible fungi were collected throughout this study. The fresh weight of edible mushrooms was recorded with the highest fresh weight (25.3 kg) collected from the abandoned sustainable tea forest, followed by 18.2 kg in the cultivated sustainable tea forest, while in the fire damaged sustainable tea forest 16.4 kg were collected and only 1 kg was collected in the tea garden. Abandoned sustainable tea forest contained a greater shade tree biodiversity and higher canopy cover than other plots. This area has a generally higher humidity, a greater ground litter cover, a greater number of microhabitats, a greater number of trees that can form mycorrhizal associations and this probably accounts for the higher diversity of macrofungi and production of edible mushrooms. The fire damaged sustainable tea forest had lower mushroom diversity and edible mushroom production possibly due to the loss of litter and lower tree diversity. The tea garden supported a poor diversity of mushrooms and almost no edible mushrooms. Shade tea forest (Miang tea forest) is a good method to produce tea in a sustainable way as it maintains diversity of mushrooms and other organisms and could be developed as an alternative to shade coffee.