Preliminary X-ray diffraction analysis of YcdB from Escherichia coli: a novel haem-containing and Tat-secreted periplasmic protein with a potential role in iron transport

YcdB is a periplasmic haem-containing protein from Escherichia coli that has a potential role in iron transport. It is currently the only reported haem-containing Tat-secreted substrate. Here, the overexpression, purification, crystallization and structure determination at 2.0 angstrom resolution are reported for the apo form of the protein. The apo-YcdB structure resembles those of members of the haem-dependent peroxidase family and thus confirms that YcdB is also a member of this family. Haem-soaking experiments with preformed apo-YcdB crystals have been optimized to successfully generate haem-containing YcdB crystals that diffract to 2.9 angstrom. Completion of model building and structure refinement are under way.

Thioquinolobactin, a pseudomonas siderophore with antifungal and anti-pythium activity

Under conditions of iron limitation Pseudomonas fluorescens ATCC 17400 produces two siderophores, pyoverdine, and a second siderophore quinolobactin, which itself results from the hydrolysis of the unstable molecule 8-hydroxy-4-methoxy-2-quinoline thiocarboxylic acid (thioquinolobactin). Pseudomonas fluorescens ATCC 17400 also displays a strong in vitro antagonism against the Oomycete Pythium, which is repressed by iron, suggesting the involvement of a siderophore(s). While a pyoverdine-negative mutant retains most of its antagonism, a thioquinolobactin-negative mutant only slowed-down Pythium growth, and a double pyoverdine-, thioquinolobactin-negative mutant, which does not produce any siderophore, totally lost its antagonism against Pythium. The siderophore thioquinolobactin could be purified and identified from spent medium and showed anti-Pythium activity, but it was quickly hydrolysed to quinolobactin, which we showed has no antimicrobial activity. Analysis of antagonism-affected transposon mutants revealed that genes involved in haem biosynthesis and sulfur assimilation are important for the production of thioquinolobactin and the expression of antagonism.

Feo - Transport of ferrous iron into bacteria

Bacteria commonly utilise a unique type of transporter, called Feo, to specifically acquire the ferrous (Fe2+) form of iron from their environment. Enterobacterial Feo systems are composed of three proteins: FeoA, a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor. We provide a review of the current literature combined with a bioinformatic assessment of bacterial Feo systems showing how they exhibit common features, as well as differences in organisation and composition which probably reflect variations in mechanisms employed and function.

Bacterial iron homeostasis

Iron is essential to virtually all organisms, but poses problems of toxicity and poor solubility. Bacteria have evolved various mechanisms to counter the problems imposed by their iron dependence, allowing them to achieve effective iron homeostasis under a range of iron regimes. Highly efficient iron acquisition systems are used to scavenge iron from the environment under iron-restricted conditions. In many cases, this involves the secretion and internalisation of extracellular ferric chelators called siderophores. Ferrous iron can also be directly imported by the G protein-like transporter, FcoB. For pathogens, host-iron complexes (transferrin, lactoferrin, haem, haemoglobin) are directly used as iron sources. Bacterial iron storage proteins (ferritin, bacterioferritin) provide intracellular iron reserves for use when external supplies are restricted, and iron detoxification proteins (Dps) are employed to protect the chromosome from iron-induced free radical damage. There is evidence that bacteria control their iron requirements in response to iron availability by downregulating the expression of iron proteins during iron-restricted growth. And finally, the expression of the iron homeostatic machinery is subject to iron-dependent global control ensuring that iron acquisition, storage and consumption are geared to iron availability and that intracellular levels of free iron do not reach toxic levels. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments

The distribution and activity of communities of sulfate-reducing bacteria (SRB) and methanogenic archaea in two contrasting Antarctic sediments were investigated. Methanogenesis dominated in freshwater Lake Heywood, while sulfate reduction dominated in marine Shallow Bay. Slurry experiments indicated that 90% of the methanogenesis in Lake Heywood was acetoclastic. This finding was supported by the limited diversity of clones detected in a Lake Heywood archaeal clone library, in which most clones were closely related to the obligate acetate-utilizing Methanosaeta concilii. The Shallow Bay archaeal clone library contained clones related to the C-1-utilizing Methanolobus and Methanococcoides and the H-2-utilizing Methanogenium. Oligonucleotide probing of RNA extracted directly from sediment indicated that archaea represented 34% of the total prokaryotic signal in Lake Heywood and that Methanosaeta was a major component (13.2%) of this signal. Archaea represented only 0.2% of the total prokaryotic signal in RNA extracted from Shallow Bay sediments. In the Shallow Bay bacterial clone library, 10.3% of the clones were SRB-like, related to Desulfotalea/Desulforhopalus, Desulfofaba, Desulfosarcina, and Desulfobacter as well as to the sulfur and metal oxidizers comprising the Desulfuromonas cluster. Oligonucleotide probes for specific SRB clusters indicated that SRB represented 14.7% of the total prokaryotic signal, with Desulfotalea/Desulforhopalus being the dominant SRB group (10.7% of the total prokaryotic signal) in the Shallow Bay sediments; these results support previous results obtained for Arctic sediments. Methanosaeta and Desulfotalea/Desulforhopalus appear to be important in Lake Heywood and Shallow Bay, respectively, and may be globally important in permanently low-temperature sediments.

The syntheses, structures and redox properties of phosphine-gold(I) and triruthenium-carbonyl cluster derivatives of tolans

The syntheses of several ethynyl-gold(I) phosphine substituted tolans (1,2-diaryl acetylenes) of general form [Au(C=CC6H4C=CC6H4X)(PPh3)] are described [X = Me (2a), OMe (2b), CO2Me (2c), NO2 (2d), CN (2e)]. These complexes react readily with [Ru-3(CO) 10(mu-dppm)] to give the heterometallic clusters [Ru3(mu-AuPPh3)(mu-eta(1), eta(2)-C2C6H4C, CC6H4X)(CO)(7)(mu-dppm)] (3a-e). The crystallographically determined molecular structures of 2b, 2d, 2e and 3a-e are reported here, that of 2a having been described on a previous occasion. Structural, spectroscopic and electrochemical studies were conducted and have revealed little electronic interaction between the remote substituent and the organometallic end-caps. (C) 2007 Elsevier B. V. All rights reserved.

Synthesis of a Mn-6 cluster and its self-assembly of an azido-bridged polymer

A rare mu(6)-oxo-centered Mn-6 mixed-valent cluster (1) is prepared and used as a secondary building unit for the self-assembly of its azido-bridged polymeric analogue (2) in a systematic way with the retention of the Mn-6 core of (1). Both complexes are characterized by X-ray single-crystal structure determination. The complex 1 was crystallized in a monoclinic system, space group P2(1), a = 11.252(5) A, b = 20.893(9) A, c = 12.301(6) A, and beta = 115.853(7)degrees, whereas the polymeric analogue was crystallized in an orthorhombic system, space group P2(1)2(1)2(1), a = 13.1941(8) A, b = 14.9897(9) A, and c = 27.8746(14) A. Variable-temperature magnetic behavior showed the presence of strong antiferromagnetic interaction in both cases.

A new tetrameric Cu-II cluster with square topology exhibiting ferro- and antiferromagnetic magnetic pathways: which is which?

[Cu4L2(bpy)(4)(H2O)(3)](ClO4)(4).2.5H(2)O, 1, a new tetranuclear Cu-II cluster showing square planar geometry, formed with aspartate bridging ligand (L) has been synthesized. The global magnetic coupling is ferromagnetic but theoretical DFT/B3LYP calculations are necessary to assign which Cu-L-Cu side is ferro or antiferromagnetically coupled.

Homogeneous and heterogeneous reactions of atmospheric mercury(II) with sulfur(IV)

Atmospheric models suggest that the reduction of Hg(II) to Hg(O) by S(W) prolongs the residence time of mercury. The redox reaction was investigated both in the aqueous phase (where the reductant is sulfite) and on particulate matter (where the reductant in SO2(g)). In both cases, one of the ultimate products is HgS. A mechanism is proposed involving formation of Hg(O) followed by mercury-induced disproportionation of SO2.

The adsorption and stability of sulfur containing amino acids on Cu{531}

The adsorption of L-CySteine and L-methionine amino acids on a chiral Cu{5 3 1} surface was investigated with high resolution X-ray photoelectron spectroscopy (XPS) and carbon K-edge near edge X-ray absorption fine structure (NEXAFS) Spectroscopy using synchrotron radiation. XPS shows that at 300 K L-cysteine adsorbs through two oxygen, a nitrogen and a sulfur atom, in a four point 'quadrangular footprint', whereas L-methionine adsorbs through only two oxygen and a nitrogen atom in a 'triangular footprint'. NEWS was used to clarify the adsorption geometry of both molecules, which suggests a binding orientation to the top layer and second layer atoms in two different orientations associated with adsorption sites on {1 1 0} and {3 1 1} microfacets; of the Cu{5 3 1} surface. (C) 2009 Elsevier B.V. All rights reserved.

A phosphorus analogue of Bis(eta(4)-cyclobutadiene)iron(0)

P makes it possible: The convenient oxidative synthesis of the 16-electron organophosphorus iron sandwich complex [Fe(4-P2C2tBu2)2] suggests that the elusive all-carbon complex [Fe(4-C4H4)2] is a viable synthetic target.

Building cluster and shading in urban canyon for hot dry climate - Part 1: Air and surface temperature measurements

Under low latitude conditions, minimization of solar radiation within the urban environment may often be a desirable criterion in urban design. The dominance of the direct component of the global solar irradiance under clear high sun conditions requires that the street solar access must be small. It is well known that the size and proportion of open spaces has a great influence on the urban microclimate This paper is directed towards finding the interaction between urban canyon geometry and incident solar radiation. The effect of building height and street width on the shading of the street surfaces and ground for different orientations have been examined and evaluated. It is aimed to explore the extent to which these parameters affect the temperature in the street. This work is based on air and surface temperature measurements taken in different urban street canyons in EL-Oued City (hot and and climate), Algeria. In general, the results show that there are less air temperature variations compared to the surface temperature which really depends on the street geometry and sky view factor. In other words, there is a big correlation between the street geometry, sky view factor and surface temperatures.

Building cluster and shading in urban canyon for hot dry climate Part 2: Shading simulations

Under low latitude conditions, minimisation of solar irradiance within the urban environment may often be an important criterion in urban design. This can be achieved when the obstruction angle is large (high H/W ratio, H = height, W = width). Solar access to streets can always be decreased by increasing H/W to larger values. It is shown in this paper that the street canyon orientation (and not only the H/W ratio) has a considerable effect on solar shading and urban microclimate. The paper demonstrates through a series of shading simulation and temperature measurements that a number of useful relationships can be developed between the geometry and the microclimate of urban street canyons. These relationships are potentially helpful to assist in the formulation of urban design guidelines governing street dimensions and orientations for use by urban designers.

Influence of sulfur amino acids on the volatile and nonvolatile components of cooked salmon (Salmo salar)

Volatile and nonvolatile compounds, which could contribute to flavor, were analyzed in salmon. One hundred twenty-three volatile compounds were identified in the headspace of two different samples of cooked salmon, including lipid-derived volatiles, Maillard-derived volatiles, sulfur volatiles, Strecker aldehydes, nitrogen heterocyclic compounds, terpenes, and trimethylamine. Significant differences between samples were found for 104 of the volatiles. Although the levels of free cysteine and methionine were low in the salmon, sulfur volatiles were formed in the cooked fish, demonstrating that there were sufficient sulfur amino acids present for their formation. Notable differences in sulfur compounds between the samples suggested that small changes in sulfur amino acids could be responsible. When this hypothesis was tested, salmon heated with cysteine had increased levels of many thiophenes, thiazoles, alicyclic sulfides, and nitrogen heterocycles. With the addition of methionine, levels of dimethyl sulfides, two alicyclic sulfides, pyrazines, some unsaturated aldehydes, and alcohols and 2-furanmethanethiol increased. The largest difference found among the nonvolatile (low molecular weight water-soluble) compounds was in inosine monophosphate.