Hydrocarbon-degrading filamentous fungi isolated from flare pit soils in northern and western Canada

Sixty-four species of filamentous fungi from five flare pits in northern and western Canada were tested for their ability to degrade crude oil using gas chromatographic analysis of residual hydrocarbons following incubation. Nine isolates were tested further using radiorespirometry to determine the extent of mineralization of model radiolabelled aliphatic and aromatic hydrocarbons dissolved in crude oil. Hydrocarbon biodegradation capability was observed in species representing six orders of the Ascomycota. Gas chromatography indicated that species capable of hydrocarbon degradation attacked compounds within the aliphatic fraction of crude oil, n-C12-n-C26; degradation of compounds within the aromatic fraction was not observed. Radiorespirometry, using n-[1-14C]hexadecane and [9-14C]phenanthrene, confirmed the gas chromatographic results and verified that aliphatic compounds were being mineralized, not simply transformed to intermediate metabolites. This study shows that filamentous fungi may play an integral role in the in situ biodegradation of aliphatic pollutants in flare pit soils.     

A route to RNA with an alkylating group at the 5''-triphosphate residue.

Reaction of ATP with N,N,N'-tris(2-chloroethyl), N' (p-formyl-phenyl)propylenediamine-1,3 (abbreviation C13R) afforded a gamma-ester of ATP (abbreviation C1RpppA) - the product of alkylation by an aliphatic nitrogen mustard residue of C13R. The alkylating activity of the aromatic nitrogen mustard residue of C1RpppA is suppressed by the electron-acceptor effect of the p-formyl group. C1RpppA is a substrate of RNA-polymerase, and affords RNA with C1RpppA-residues at the 5'-termini.     

Enhanced reactivity of amino-modified oligonucleotides by insertion of aromatic residue

We developed novel amino-modifying reagents, of which an amino group was connected with an aromatic residue by aliphatic linker. It was proved that the insertion of the aromatic residue could increase the reactivity of the amino group on oligonucleotides in comparison with conventional amino-modification.     

Full structural characterization of the lipid A components from the Agrobacterium tumefaciens strain C58 lipopolysaccharide fraction

For the first time, the complete structure of the lipid A from the lipopolysaccharide of an Agrobacterium species is here reported. In particular, the structure of the lipid A from A. tumefaciens strain C58, a soil pathogen bacterium strictly related to Rhizobiaceae, was determined. The structural study, carried out by chemical analysis, mass spectrometry, and nuclear magnetic resonance spectroscopy, revealed that lipid A fraction consisted of a mixture of species all sharing the bis-phosphorylated glucosamine disaccharide backbone that could be designated in two main structural motifs, according to the acylation pattern. The main species was a penta-acylated lipid A bearing two unsubstituted 14:0 (3-OH) fatty acids in ester linkage and two 16:0 (3-OH) in amide linkage; the one on GlcN II was O-acylated by a long chain fatty acid, 28:0 (27-OH). This in turn was esterified by a 3-hydroxy-butyroyl residue at its hydroxy group. The second species, in lesser amounts, was identified as a tetra-acylated lipid A and lacked the 14:0 (3-OH) residue on GlcN I. Other species deriving from these two lacked a phosphate group or 3-hydroxy-butyroyl residue or otherwise carried a 26:0 (25-OH) as long chain fatty acid. The lipid A structure of phytopathogen A. tumefaciens strain C58 presents deep structural analogies with lipid A of symbiotic Rhizobium, and the hypothesis is advanced that it can be a strategy of the bacterium to escape or attenuate the plant response.     

The initial binding of Cu(II) to some amino acids and dipeptides: a 13C nuclear-magnetic-resonance study.

The initial binding of Cu2+ ot L-lysine, L-histidine, glycyl-histidine and histidyl-glycine in aqueous solutions was examined by 13C nuclear magnetic resonance spectroscopy. The measurements were carried out in a substantially improved way employing the pulse Fourier transform technique. Spectra of both high quality and resolution were obtained. Cu2+ complex formation with L-lysine occurred with the alpha-amino and carboxyl group attributable to the well expressed broadening effect of the 13C signals of the alpha-carbon atom and the carboxyl atom. The epsilon-amino group was not involved. Measurements of the Cu chelates using L-histidine and glycyl-histidine and histidyl-glycine confirmed the ambidentate nature of the histidine residue. It was concluded that an equilibrium exists between two Cu-complex species designated as histamine-like and histamine-like/glycine-like species. In the homogeneous histamine-like Cu complex, the Cu2+ is exclusively bound with 4 nitrogens, while in the other species one oxygen of the glycyl carboxyl group is involved in the Cu2+ binding. Blocking of this carboxyl groups by peptide bonding as found in histidyl-glycine favoured the formation of a Cu complex where the imidazole carbons of the histidyl residue were the most influenced species.     

Galactosyltransferase activities in mitochondria outer membrane: biosynthesis of galactosylated proteins

1. Mitochondria outer membranes prepared from mouse livers were purified on a discontinuous sucrose gradient. Control in electron microscopy and marker enzymes assays confirmed purity and homogeneity of this fraction. 2. Purified mitochondria outer membranes exhibited significant UDP-galactose: glycoprotein galactosyltransferase activities when incubated with endogenous or exogenous glycoprotein acceptors in presence of detergent (Nonidet P40). 3. Some properties of two distinct mitochondrial galactosyltransferases, acting respectively on ovomucoid and ovine asialo-mucin were investigated. 4. Transfer of galactose on ovomucoid was maximal for a pH of 7.6 at 33 degrees C whereas asialo-mucin galactosyltransferase exhibited an optimum pH of 5.6 for an optimal temperature of 46 degrees C. 5. These two distinct membrane-bound enzymes were both inhibited by diacylglycerophospholipids whereas lysophospholipids modulated both enzymes in a different way: at 5 mM lysophosphatidylcholine, asialo-mucin galactosyltransferase was slightly stimulated while ovomucoid galactosyltransferase was markedly activated. 6. The most important activating effect on ovomucoid galactosyltransferase was obtained with a phospholipid containing a long aliphatic side chain linked by an ester bond in sn-1 of glycerol, an hydroxyl group or hydrogen atoms in sn-2 and a phosphorylcholine head group in sn-3.     

Synthesis of oligodeoxyribonucleotide derivatives, containing perfluoroarylazide group at C8-atom of deoxyadenosine and their use in photomodification of DNA fragments

Heptadeoxynucleotides were obtained that contained an aliphatic amino group in position 8 of the deoxyadenosine residue: ALNH2 CTTTCT, CTCALNH2 CTT, and ACACTCALNH2 where L = NH(CH2)n, n = 3, 5, or 7. A 4-azidotetrafluorobenzoyl residue was attached to the amino group in the oligonucleotides, and photomodification of a DNA target by the resulting reagents was carried out. It was shown that the length of the spacer influences the photomodification extent of the target; a spacer with n = 5 is optimum. The maximum modification extent (65%) was reached when a reagent containing a photoreactive group at the 5'-terminal deoxyadenosine residue was used.     

Identification of sn-2-omega-hydroxycarboxylate-containing phospholipids in a lipid extract from bovine brain

Phospholipids having both a long-chain acyl (palmitoyl or stearoyl) and a short-chain hydroxycarboxylyl (C3-C9) residue were identified by GC-MS in a fraction with PAF-like activity from a bovine brain lipid extract. The hydroxyl group in the hydroxycarboxylate residue was determined to be at the omega-position by comparison of the mass spectra of the tert-butyl-dimethylsilyl derivatives of these compounds with those of synthetic hydroxybutyrate-containing phosphatidylcholines. The co-existence of short-chain hydroxycarboxylate-, monocarboxylate- and dicarboxylate-containing phospholipids in the bovine brain lipid extract suggested that these compounds were formed by peroxidation of membrane phospholipids, especially phosphatidylcholines.     

Structure of an acetyl-CoA binding protein from Staphylococcus aureus representing a novel subfamily of GCN5-related N-acetyltransferase-like proteins

We have determined the solution NMR structure of SACOL2532, a putative GCN5-like N-acetyltransferase (GNAT) from Staphylococcus aureus. SACOL2532 was shown to bind both CoA and acetyl-CoA, and structures with and without bound CoA were determined. Based on analysis of the structure and sequence, a subfamily of small GCN5-related N-acetyltransferase (GNAT)-like proteins can be defined. Proteins from this subfamily, which is largely congruent with COG2388, are characterized by a cysteine residue in the acetyl-CoA binding site near the acetyl group, by their small size in relation to other GNATs, by a lack of obvious substrate binding site, and by a distinct conformation of bound CoA in relation to other GNATs. Subfamily members are found in many bacterial and eukaryotic genomes, and in some archaeal genomes. Whereas other GNATs transfer the acetyl group of acetyl-CoA directly to an aliphatic amine, the presence of the conserved cysteine residue suggests that proteins in the COG2388 GNAT-subfamily transfer an acetyl group from acetyl-CoA to one or more presently unidentified aliphatic amines via an acetyl (cysteine) enzyme intermediate. The apparent absence of a substrate-binding region suggests that the substrate is a macromolecule, such as another protein, or that a second protein subunit providing a substrate-binding region must combine with SACOL2532 to make a fully functional N-acetyl transferase.     

Aggregation and C and N contents of soil organic matter fractions in a permanent raised-bed planting system in the Highlands of Central Mexico

Permanent raised bed planting with crop residue retention is a form of conservation agriculture that has been proposed as an alternative to conventional tillage for wheat production systems in the Central Highlands of Mexico. A field experiment comparing permanent and tilled raised beds with different residue management under rainfed conditions was started at El Batán (State of Mexico, Mexico) in 1999. The percentage of small and large macroaggregates and mean weight diameter (MWD) was significantly larger in permanent raised beds compared to conventionally tilled raised beds both with full crop residue retention (average for maize and wheat), while the percentages free microaggregates was lower. The percentages of small and large macroaggregates and mean weight diameter (MWD) was significantly larger in permanent raised beds with residue retention compared to permanent raised beds with removal of the residue (average for maize and wheat), while the percentages free microaggregates and silt and clay fraction was lower. Cultivation of maize significantly reduced the large macroaggregates, while wheat reduced the silt and clay fraction (average over all systems). Cultivation of maize reduced the C and N content of the free microaggregates compared to soil cultivated with wheat, while removal of plant residue reduced the C and N content of the silt and clay fraction compared to soil where residue was retained. The C and N content of the coarse particulate organic matter (cPOM) and microaggregates within the macroaggregates was significantly larger in permanent raised beds compared to conventionally tilled raised beds both with full residue retention, while C and N content of the cPOM was significantly lower when residue was removed or partially removed compared to the soil where the residue was retained. The δ ¹³C ‰ signatures of the macroaggregates, microaggregates, the silt and clay fraction, cPOM and microaggregates within the macroaggregates were not affected by tillage or residue management when wheat was the last crop, but removal of residue reduced the δ ¹³C ‰ signatures of the macro-, microaggregates and microaggregates within the macroaggregates significantly compared to soil where the residue was retained. Retaining only 30–50% of the organic residue still improved the soil structure considerably compared to plots where it was removed completely. Permanent raised beds without residue retention, however, is a practice leading to soil degradation. Kelly Lichter and Bram Govaerts contributed equally to this publication.     

Interaction of cytochrome P-450 with hydrocarbons

Hydrocarbons of different structures interact with microsomal and solubilized cytochrome P-450 from liver of phenobarbital-pretreated rats forming a high spin enzyme-substrate type complex. The affinity of cytochrome P-450 for hydrocarbons increases with increasing lipophilicity independently of the chemical structure. The binding capacity of microsomal P-450 for aliphatic hydrocarbons is generally higher than for aromates. Mutual influence in binding of two different hydrocarbons by microsomal P-450 is stronger among aromatic than among aliphatic hydrocarbons; in both cases it appears to be effected rather by specific interaction of both substances with the binding site than by a nonspecific influence on the microsomal membrane. Only one fraction of low spin form of solubilized cytochrome P-450 from rat liver interacts with hydrocarbons. The binding capacity for aromatic and aliphatic substances corresponds to that found in microsomes. The affinity for the most lipiphilic substrate, perhydrophenanthrene, is equal in microsomal and solubilized preparation; with decreasing lipophilicity the affinity of solubilized P-450 decreases faster than in microsomes. The LM2 fraction of cytochrome P-450 from phenobarbital-pretreated rabbits interacts only with aliphatic hydrocarbons with wide variation of the binding capacity. The affinity is generally one order of magnitude lower than in microsomes. Active fractions of solubilized P-450 from both species are rapidly converted to P-420 by dithionite. The extent of this conversion is strongly reduced by saturation with substrate.     

Structural characterization and functional properties of a novel lipomannan variant isolated from a Corynebacterium glutamicum pimB′ mutant

The genus Corynebacterium is part of the phylogenetic group nocardioform actinomycetes, which also includes the genus Mycobacterium. Members of this phylogenetic group have a characteristic cell envelope structure, which is dominated by complex lipids and amongst these, lipoglycans are of particular interest. The disruption of NCgl2106 in C. glutamicum resulted in a mutant devoid of monoacylated phosphatidyl-myo-inositol dimannoside (Ac(1)PIM(2)) resulting in the accumulation of Ac(1)PIM(1) and cessation of phosphatidyl-myo-inositol (PI) based lipomannan (Cg-LM, now also termed 'Cg-LM-A') and lipoarabinomannan (Cg-LAM) biosynthesis. Interestingly, SDS-analysis of the lipoglycan fraction from the mutant revealed the synthesis of a single novel lipoglycan, now termed 'Cg-LM-B'. Further chemical analyses established the lipoglycan possessed an alpha-D: -glucopyranosyluronic acid-(1 --> 3)-glycerol (GlcAGroAc(2)) based anchor which was then further glycosylated by 8-22 mannose residues, with Man(12-20)GlcAGroAC(2) molecular species being the most abundant, to form a novel lipomannan structure (Cg-LM-B). The deletion of NCgl2106 in C. glutamicum has now provided a useful strain, in addition with a deletion mutant of NCgl0452 in C. glutamicum for the purification of Cg-LM-A and Cg-LM-B. Interestingly, both Cg-LM species induced a similar production of TNF-alpha by a human macrophage cell line suggesting that the phospho-myo-inositol residue of the PI-anchor does not play a key role in lipoglycan pro-inflammatory activity.     

Synthesis of isotope labeled oligonucleotides and their use in an NMR study of a protein-DNA complex.

The synthesis of an oligonucleotide labeled with 13C at the thymine methyl and 15N at the exocyclic amino groups of the cytosines is described. 13CH3I and 15NH4OH were used as sources of the labels. The labeled oligonucleotide was characterized by several NMR techniques. The duplex possesses a labeled functional group in the major groove at every base pair which makes it a very suitable probe for the study of sequence-specific protein-DNA interaction. The labeled thymine methyl group facilitates the detection of hydrophobic contacts with aliphatic side-chains of proteins. This is demonstrated in an NMR study of a complex between the glucocorticoid receptor DNA-binding domain and the labeled oligomer, which revealed a hydrophobic contact between a thymine methyl group and the methyl groups of a valine residue. There are indications for small differences between the solution structure the X-ray structure of the complex.     

Conversion of aliphatic nitriles by the arylacetonitrilase from <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis> EBC191

The conversion of aliphatic nitriles by the arylacetonitrilase from Pseudomonas fluorescens EBC191 (NitA) was analyzed. The nitrilase hydrolysed a wide range of aliphatic mono- and dinitriles and showed a preference for unsaturated aliphatic substrates containing 5–6 carbon atoms. In addition, increased reaction rates were also found for aliphatic nitriles carrying electron withdrawing substituents (e.g. chloro- or hydroxy-groups) close to the nitrile group. Aliphatic dinitriles were attacked only at one of the nitrile groups and with most of the tested dinitriles the monocarboxylates were detected as major products. In contrast, fumarodinitrile was converted to the monocarboxylate and the monocarboxamide in a ratio of about 65:35. Significantly different relative amounts of the two products were observed with two nitrilase variants with altered reaction specifities. NitA converted some aliphatic substrates with higher rates than 2-phenylpropionitrile, which is one of the standard substrates for arylacetonitrilases. This indicated that the traditional classification of nitrilases as “arylacetonitrilases”, “aromatic” or “aliphatic” nitrilases might require some corrections. This was also suggested by the construction of some variants of NitA which were modified in an amino acid residue which was previously suggested to be essential for the conversion of aliphatic substrates by a homologous nitrilase.     

Organic matter humification in olive oil mill wastewater by abiotic catalysis with manganese(IV) oxide

The chemical changes occurring in an olive oil mill wastewater (OMW) sample digested catalytically with MnO(2) for 30 and 60 days were evaluated comparatively with those occurring in the same OMW left standing for the same time in an open-air lagoon. Both treatments increased the pH and electrical conductivity and decreased the contents of dry matter, total organic C and total N, and C/N ratio of OMW. The humic acid (HA)-like fraction isolated from the fresh OMW was characterized by a marked aliphatic character, small O and acidic functional group contents, marked presence of proteinaceous materials, partially modified lignin moieties and polysaccharides-like structures, extended molecular heterogeneity, and small degrees of aromatic ring polycondensation, polymerization and humification. With increasing the time of either lagooning or catalytic digestion, a loss of aliphatic materials and an increase of extraction yield, oxygenation, acidic functional groups, carbohydrates and aromaticity occurred in the HA-like fractions. The more evident changes measured for the HA-like fractions from catalytically-digested OMW, with respect to those from lagooned OMW, indicated that MnO(2) was able to catalyze organic matter humification in OMW.     

Application of composted urban residue enhanced the performance of afforested shrub species in a degraded semiarid land

Improvement of physical-chemical soil quality is a key step for carrying out revegetation programs of degraded lands in Mediterranean semiarid areas. Organic residue addition may restore the quality of these areas. A field experiment was conducted in a silt-loam soil (Typic Petrocalcid) from a degraded semiarid Mediterranean area to evaluate the effect of the addition of a composted urban residue on soil aggregate stability, bulk density and chemical properties and on the establishment of Pistacia lentiscus and Retama sphaerocarpa seedlings. The composted residue was applied at a rate of 6.7 kg m(-2) before planting. The nutrient content (NPK), total organic C and water soluble C were increased and bulk density was decreased, in the rhizosphere soil of both shrub species, by the composted residue. The addition of composted residue significantly increased the soil aggregate stability by about 22% for both shrub species. The beneficial effect of the composted residue on soil quality still persisted 18 months after addition. Eighteen months after planting, the addition of composted residue to soil had increased significantly the production of shoot biomass by P. lentiscus and R. sphaerocarpa, by about 160% and 320% respectively, compared to control values. Composted residue addition to soil can be considered an effective preparation method of a degraded area for carrying out successful revegetation programs with Mediterranean shrubs under semiarid conditions.     

Porphyromonas gingivalis DPP-7 represents a novel type of dipeptidylpeptidase

A novel dipeptidylpeptidase (DPP-7) was purified from the membrane fraction of Porphyromonas gingivalis. This enzyme, with an apparent molecular mass of 76 kDa, has the specificity for both aliphatic and aromatic residues in the P1 position. Although it belongs to the serine class of peptidases, it does not resemble other known dipeptidylpeptidases. Interestingly, the amino acid sequence around the putative active site serine residue shows significant similarity to the C-terminal region of the Staphylococcus aureus V-8 endopeptidase. The genes encoding homologues of DPP-7 were found in genomes of Xylella fastidiosa, Shewanella putrefaciens, and P. gingivalis. It is likely that at least in P. gingivalis, DPP-7 and its homologue, in concert with other di- and tripeptidases, serve nutritional functions by providing dipeptides to this asaccharolytic bacterium.     

Properties of cell wall-associated DD-carboxypeptidase of Enterococcus hirae (Streptococcus faecium) ATCC 9790 extracted with alkali.

DD-Carboxypeptidase (DD-CPase) activity of Enterococcus hirae (Streptococcus faecium) ATCC 9790 was extracted from intact bacteria and from the insoluble residue (crude cell wall fraction) of mechanically disrupted bacteria by a brief treatment at pH 10.0 (10 mM glycine-NaOH) at 0 degrees C or by extraction with any of several detergents. Extractions with high salt concentrations failed to remove DD-CPase activity from the crude wall fraction. In contrast to N-acetylmuramoylhydrolase (both muramidase 2 and muramidase 1) activities, DD-CPase activity failed to bind to insoluble cell walls or peptidoglycan matrices. Thus, whereas muramidase 1 and muramidase 2 activities can be considered to be cell wall proteins, the bulk of the data are consistent with the interpretation that the DD-CPase of this species is a membrane protein that is sometimes found in the cell wall fraction, presumably because of hydrophobic interactions with other proteins and cell wall polymers. The binding of [14C]penicillin to penicillin-binding protein 6 (43 kilodaltons) was proportional to DD-CPase activity. Kinetic parameters were also consistent with the presence of only one DD-CPase (penicillin-binding protein 6) in E. hirae.     

Protein-binding patterns of the antitumor antibiotic cryptophycin 52 as measured with a two-phase partitioning system

Exposure of murine leukemia L1210 cells to the antitumor antibiotic cryptophycin 52 (C52) resulted in a rapid and dose-dependent increase in cell-surface hydrophobicity, as measured with a two-phase partitioning system. This effect was not observed with inactive drug analogs that lacked an epoxy residue. While the C52 has distinctly hydrophobic properties, the drug does not uniformly bind to all proteins. Affinity for human high- and low-density lipoprotein and albumin was demonstrated, but the drug binds only to the albumin fraction of mouse plasma, in spite of the high HDL level in the latter species.     

Molecular Basis for Recognition of Nucleoside Triphosphate by Gene 4 Helicase of Bacteriophage T7

The translocation of DNA helicases on single-stranded DNA and the unwinding of double-stranded DNA are fueled by the hydrolysis of nucleoside triphosphates (NTP). Although most helicases use ATP in these processes, the DNA helicase encoded by gene 4 of bacteriophage T7 uses dTTP most efficiently. To identify the structural requirements of the NTP, we determined the efficiency of DNA unwinding by T7 helicase using a variety of NTPs and their analogs. The 5-methyl group of thymine was critical for the efficient unwinding of DNA, although the presence of a 3′-ribosyl hydroxyl group partially overcame this requirement. The NTP-binding pocket of the protein was examined by randomly substituting amino acids for several amino acid residues (Thr-320, Arg-504, Tyr-535, and Leu-542) that the crystal structure suggests interact with the nucleotide. Although positions 320 and 542 required aliphatic residues of the appropriate size, an aromatic side chain was necessary at position 535 to stabilize NTP for efficient unwinding. A basic side chain of residue 504 was essential to interact with the 4-carbonyl of the thymine base of dTTP. Replacement of this residue with a small aliphatic residue allowed the accommodation of other NTPs, resulting in the preferential use of dATP and the use of dCTP, a nucleotide not normally used. Results from this study suggest that the NTP must be stabilized by specific interactions within the NTP-binding site of the protein to achieve efficient hydrolysis. These interactions dictate NTP specificity.