Novel three-dimensional 1H−13C−31P triple resonance experiments for sequential backbone correlations in nucleic acids

Summary Backbone-driven assignment methods that utilize covalent connectivities have greatly facilitated spectral assignments of proteins. In nucleic acids, ¹H–¹³C–³¹P correlations could play a similar role, and several related experiments (HCP) have recently been presented for backbone-driven sequential assignments in RNA. The three-dimensional extension of ¹H–³¹P Het-Cor (P,H-COSY-H,C-HMQC) and Het-TOCSY (P,H-TOCSY-H,C-HMQC) experiments presented here complements HCP experiments as tools for spectral assignments and extraction of dihydral angle constraints. By relying on ¹H–³¹P rather than ¹³C–³¹P couplings to generate cross peaks, the strongest connectivities are observed in different spectral regions, increasing the likelihood of resolving spectral overlap. In addition, semiquantitative estimates of ¹H–³¹P and ¹³C–³¹P couplings provide dihedral angle constraints for RNA structure determination.     

The C‐degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes

Protein termini are determinants of protein stability. Proteins bearing degradation signals, or degrons, at their amino‐ or carboxyl‐termini are eliminated by the N‐ or C‐degron pathways, respectively. We aimed to elucidate the function of C‐degron pathways and to unveil how normal proteomes are exempt from C‐degron pathway‐mediated destruction. Our data reveal that C‐degron pathways remove mislocalized cellular proteins and cleavage products of deubiquitinating enzymes. Furthermore, the C‐degron and N‐degron pathways cooperate in protein removal. Proteome analysis revealed a shortfall in normal proteins targeted by C‐degron pathways, but not of defective proteins, suggesting proteolysis‐based immunity as a constraint for protein evolution/selection. Our work highlights the importance of protein termini for protein quality surveillance, and the relationship between the functional proteome and protein degradation pathways.     

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

Synechococcus sp. represents an ecologically diverse group of cyanobacteria found in numerous environments, including hot-spring microbial mats, where they are spatially distributed along thermal, light and oxygen gradients. These thermophiles engage in photosynthesis and aerobic respiration during the day, but switch to fermentative metabolism and nitrogen fixation at night. The genome of Synechococcus OS-B′, isolated from Octopus Spring (Yellowstone National Park) contains a phn gene cluster encoding a phosphonate (Phn) transporter and a C–P lyase. A closely related isolate, Synechococcus OS-A, lacks this cluster, but contains genes encoding putative phosphonatases (Phnases) that appear to be active only in the presence of the Phn substrate. Both isolates grow well on several different Phns as a sole phosphorus (P) source. Interestingly, Synechococcus OS-B′ can use the organic carbon backbones of Phns for heterotrophic growth in the dark, whereas in the light this strain releases organic carbon from Phn as ethane or methane (depending on the specific Phn available); Synechococcus OS-A has neither of these capabilities. These differences in metabolic strategies for assimilating the P and C of Phn by two closely related Synechococcus spp. are suggestive of niche-specific constraints in the evolution of nutrient assimilation pathways and syntrophic relationships among the microbial populations of the hot-spring mats. Thus, it is critical to evaluate levels of various P sources, including Phn, in thermally active habitats and the potential importance of these compounds in the biogeochemical cycling of P and C (some Phn compounds also contain N) in diverse terrestrial environments.     

Phosphonate catabolism by <Emphasis Type="Italic">Campylobacter</Emphasis> spp.

The catabolism of phosphonates (Phn) by Campylobacter spp. was investigated employing nuclear magnetic resonance spectroscopy and cell culture techniques. The bacteria were capable of cleaving the Phn bonds of different compounds, including -aminomethylphosphonate, phosphonoacetate and phenylphosphonate (PhePhn). The kinetic parameters of these activities were determined in vivo in intact cells and in situ in whole-cell lysates. Cleavage of Phn-bearing compounds was associated with the cell-wall and cytosolic fractions. Results from substrate competition experiments suggested that at least two enzyme activities appeared to be involved in the cleavage of carbon–phosphate (C–P) bonds. In silico analyses indicated that no genes orthologous to those encoding C–P bond-cleaving enzymes in other bacteria were present in the Campylobacter jejuni genome. In most bacteria studied, Phn catabolism is induced under conditions of phosphate limitation; however, in Campylobacter spp. these activities were expressed in cells grown in media rich in phosphate. In chemically defined media, PhePhn supported bacterial growth and proliferation at concentrations above 100 M in the absence of phosphate. Thus, Phn utilisation may be a survival mechanism of Campylobacter spp. in milieux lacking sufficient phosphate. The expression of these enzyme activities in media abundant in phosphate suggested also that they may have other physiological roles.     

Analysis of 13C labeling enrichment in microbial culture applying metabolic tracer experiments using gas chromatography-combustion-isotope ratio mass spectrometry

The applicability of gas chromatography–combustion–isotope ratio mass spectrometry (GC–C–IRMS) for the quantification of ¹³C enrichment of proteinogenic amino acids in metabolic tracer experiments was evaluated. Measurement of the ¹³C enrichment of proteinogenic amino acids from cell hydrolyzates of Corynebacterium glutamicum growing on different mixtures containing between 0.5 and 10% [1-¹³C]glucose shows the significance of kinetic isotope effects in metabolic flux studies at low degree of labeling. We developed a method to calculate the ¹³C enrichment. The approach to correct for these effects in metabolic flux studies using δ¹³C measurement by GC–C–IRMS uses two parallel experiments applying substrate with natural abundance and ¹³C-enriched tracer substrate, respectively. The fractional enrichment obtained in natural substrate is subtracted from that of the enriched one. Tracer studies with C. glutamicum resulted in a statistically identical relative fractional enrichment of ¹³C in proteinogenic amino acids over the whole range of applied concentrations of [1-¹³C]glucose. The current findings indicate a great potential of GC–C–IRMS for labeling quantification in ¹³C metabolic flux analysis with low labeling degree of tracer substrate directly in larger scale bioreactors.     

Bioremediation potential of glyphosate-degrading microorganisms in eutrophicated Ecuadorian water bodies

Phosphonate compounds are the basis of many xenobiotic pollutants, such as Glyphosate (N-(phosphonomethyl-glycine). Only procaryotic microorganisms and the lower eukaryotes are capable of phosphonate biodegradation through C–P lyase pathways. Thus, the aim of this study was to determine the presence of C–P lyase genes in Ecuadorian freshwater systems as a first step towards assessing the presence of putative glyphosate degraders. To that end, two Nested PCR assays were designed to target the gene that codifies for the subunit J (phnJ), which breaks the C-P bond that is critical for glyphosate mineralization. The assays designed in this study led to the detection of phnJ genes in 7 out of 8 tested water bodies. The amplified fragments presented 85–100% sequence similarity with phnJ genes that belong to glyphosate-degrading microorganisms. Nine sequences were not reported previously in the GenBank. The presence of phosphonate degraders was confirmed by isolating three strains able to grow using glyphosate as a unique carbon source. According to the 16S sequence, these strains belong to the Pantoea, Pseudomonas, and Klebsiella genera. Performing a Nested PCR amplification of phnJ genes isolated from eutrophicated water bodies, prior to isolation, may be a cost-effective strategy for the bioprospection of new species and/or genes that might have new properties for biotech industries, laying the groundwork for additional research.     

Benthic oxygen flux in the highly productive subarctic Lake Myvatn, Iceland: In situ benthic flux chamber study

In situ paired light and dark-stirred benthic flux chambers were used to estimate dissolved oxygen flux across the sediment–water interface in Lake Mývatn, Iceland. Three sampling stations were selected, each station reflecting a specific sedimentary environment, benthic communities, and water depth. During this study the phytoplankton density was low. Spatial and seasonal variations of bottom DO concentration and DO flux have been observed during this study. The oxygen consumption rate at all study sites had a mean of –89 (±44) mmol m^–2 d^–1 while the oxygen production rate due to benthic algae had a mean of 131 (±103) mmol m^–2 d^–1. There was a strong correlation (r=0.91) between oxygen consumption rate and temperature. This was presumably because of the temperature influence on rates of microbial and macrobenthic processes. The mean benthic primary production rate at all study sites was 1216 (±957) mg C m^–2 d^–1 between June 2000 and February 2001. Annual gross benthic primary production was estimated from the gross mean daily benthic DO production (P) and Redfield's C:O₂ ratio of 106:138 to be 420 g C m^–2 y^–1 at station HO, 250 g C m^–2 y^–1 at B2 and 340 g C m^–2 y^–1 at station 95. Thus, the mean gross benthic primary production was estimated as 1151 mg C m^–2 d^–1 at station HO, 685 mg C m^–2 d^–1 at station B2, and 932 mg C m^–2 d^–1 at station 95.     

In situ 1H NMR study of the biodegradation of xenobiotics: application to heterocyclic compounds

In vivo or in situ nuclear magnetic resonance (NMR) offers a powerful tool to study the degradation of xenobiotics by microorganisms. Most studies reported are based on the use of heteronuclei, and experiments with xenobiotics have been limited because specifically labeled xenobiotics are not commercially available, with the exception of ¹⁹F and ³¹P. ¹H NMR is, thus, of great interest in this area. To avoid problems caused by the presence of water and intrinsic metabolite signals, some studies were performed using a deuterated medium or specific detection of protons linked to the ¹³C–¹⁵N enriched pattern. We report here the application of in situ ¹H NMR, performed directly on culture media, to study the metabolism of heterocyclic compounds. In this review, we show that a common pathway is involved in the biodegradation of morpholine, piperidine, and thiomorpholine by Mycobacterium aurum MO1 and Mycobacterium sp. RP1. In all cases, the first step is the cleavage of the C–N bond, which results in an amino acid. Thiomorpholine is first oxidized to sulfoxide before the opening of the ring. The second step is the deamination of the intermediate amino acid, which leads to the formation of a diacid. We have shown that the cleavage of the C–N bond and the oxidation of thiomorpholine are initiated by reactions involving a cytochrome P450. Journal of Industrial Microbiology & Biotechnology (2001) 26, 2–8. Received 27 December 1999/ Accepted in revised form 08 May 2000     

Cyclohexane-1,2-dione hydrolase: A new tool to degrade alicyclic compounds

Alicyclic alcohols are naturally occurring compounds which can be degraded by microorganisms via cleavage of the ring C–C bond. Denitrifying Azoarcus sp. strain 22Lin grows on cyclohexane-1,2-diol which serves as electron donor and carbon source. The diol is converted to cyclohexane-1,2-dione followed by hydrolysis to the corresponding semialdehyde and oxidation to adipate. The latter two reactions are catalyzed by the thiamine diphosphate-dependent flavoenzyme cyclohexane-1,2-dione hydrolase, the first α-ketolase known so far. Biochemical and structural properties of this new member of the thiamine diphosphate enzyme family will be presented.     

Unusual P450 reactions in plant secondary metabolism

Plant cytochromes P450 (P450s) participate in a variety of biochemical pathways to produce a vast diversity of plant natural products. The number of P450 genes in plant genomes is estimated to be up to 1% of the total gene annotations of each plant species, implying that plants are huge sources for various P450-dependent reactions. Plant P450s catalyze a wide variety of monooxygenation/hydroxylation reactions in secondary metabolism, and some of them are involved in unusual reactions such as methylenedioxy-bridge formation, phenol coupling reactions, oxidative rearrangement of carbon skeletons, and oxidative C–C bond cleavage. Here, we summarize unusual P450 reactions in various plant secondary metabolisms, and describe their proposed reaction mechanisms.     

Activated sludge encapsulation in gellan gum microbeads for gasoline biodegradation

A two-phase dispersion technique, termed emulsification–internal gelation, is proposed for encapsulation of activated sludge in gellan gum microbeads. The influence of emulsion parameters on size distribution of microbeads was investigated. Mean diameter of microbeads varied within a range of 34–265 µm as a descending function of emulsion stirring rate (1,000–5,000 rpm), emulsification time (10–40 min), and emulsifier concentration (0–0.1% w/w), and as an ascending function of disperse phase volume fraction (0.08–0.25). Encapsulated sludge expressed a high biodegradation activity compared with non-encapsulated sludge cultures even at 4.4 times lower level of overall biomass loading. Over 90% of gasoline at an initial concentration of 35 and 70 mg l^–1 was removed by both encapsulated and non-encapsulated sludge cultures in sealed serum bottles within 7 days. Encapsulation of activated sludge in gellan gum microbeads enhanced the biological activity of microbial populations in the removal of gasoline hydrocarbons. The results of this study demonstrated the feasibility of the production of size-controlled gellan gum-encapsulated sludge microbeads and their use in the biodegradation of gasoline.     

An experimental test of the hypothesis of non‐homeostatic consumer stoichiometry in a plant litter–microbe system

Stoichiometric homeostasis of heterotrophs is a common, but not always well‐examined premise in ecological stoichiometry. We experimentally evaluated the relationship between substrate (plant litter) and consumer (microorganisms) stoichiometry for a tropical terrestrial decomposer system. Variation in microbial C : P and N : P ratios tracked that of the soluble litter fraction, but not that of bulk leaf litter material. Microbial N and P were not isometrically related, suggesting higher rates of P than N sequestration in microbial biomass. Shifts in microbial stoichiometry were related to changes in microbial community structure. Our results indicate that P in dissolved form is a major driver of terrestrial microbial stoichiometry, similar to aquatic environments. The demonstrated relative plasticity in microbial C : P and N : P and the critical role of P have important implications for theoretical modelling and contribute to a process‐based understanding of stoichiometric relationships and the flow of elements across trophic levels in decomposer systems.     

Degradation of the Herbicide Glyphosate by Members of the Family Rhizobiaceae

Several strains of the family Rhizobiaceae were tested for their ability to degrade the phosphonate herbicide glyphosate (isopropylamine salt of N-phosphonomethylglycine). All organisms tested (seven Rhizobium meliloti strains, Rhizobium leguminosarum, Rhizobium galega, Rhizobium trifolii, Agrobacterium rhizogenes, and Agrobacterium tumefaciens) were able to grow on glyphosate as the sole source of phosphorus in the presence of the aromatic amino acids, although growth on glyphosate was not as fast as on P_i. These results suggest that glyphosate degradation ability is widespread in the family Rhizobiaceae. Uptake and metabolism of glyphosate were studied by using R. meliloti 1021. Sarcosine was found to be the immediate breakdown product, indicating that the initial cleavage of glyphosate was at the C—P bond. Therefore, glyphosate breakdown in R. meliloti 1021 is achieved by a C—P lyase activity.     

Microbial cells as catalysts for stereoselective red–ox reactions

Enzyme catalyzed reactions are commonly used at laboratory or industrial scale. Contrarily, the whole cell catalyzed reactions are restricted to special cases. The tremendous advances in the last years in Molecular Biology and more specifically in Metabolic Engineering and Directed Enzyme Evolution have opened the door to create tailor-made microorganisms or “designer bugs” for industrial purposes. Whole cell catalysts can be much more readily and inexpensively prepared than purified enzymes and the enzymes – inside the cells – are protected from the external environment and stabilized by the intracellular medium. Three situations have traditionally been considered convenient to select the use of whole cell catalyzed processes against the free enzyme catalyzed process: i) when the enzyme is intracellular; ii) when the enzyme needs a cofactor to carry out the catalytic act and iii) in the development of multienzymatic processes. Red–ox reactions represent the molecular basis for energy generation in the cell. These reactions are catalyzed by intracellular enzymes and are cofactor dependent as red–ox reactions need electron carriers as helpers in reduction reactions (gain of electrons) or oxidation (loss of electrons).In this review we present an overview of the state of the art of red–ox biotransformations catalyzed by whole cells — wild-type or genetically engineered microorganisms. Stereoselective reductions, hydroxylations of arenes and unfunctionalized alkanes, alkene monooxygenation, and Baeyer–Villiger reactions are among the processes described along the text, focusing in their chemo-, regio- and stereoselectivity.     

Combined anticancer therapy with imidazoacridinone analogue C‐1305 and paclitaxel in human lung and colon cancer xenografts—Modulation of tumour angiogenesis

The acridanone derivative 5‐dimethylaminopropylamino‐8‐hydroxytriazoloacridinone (C‐1305) has been described as a potent inhibitor of cancer cell growth. Its mechanism of action in in vitro conditions was attributed, among others, to its ability to bind and stabilize the microtubule network and subsequently exhibit its tumour‐suppressive effects in synergy with paclitaxel (PTX). Therefore, the objective of the present study was to analyse the effects of the combined treatment of C‐1305 and PTX in vivo. In addition, considering the results of previous genomic analyses, particular attention was given to the effects of this treatment on tumour angiogenesis. Treatment with C‐1305 revealed antitumor effect in A549 lung cancer cells, and combined treatment with PTX showed tendency to anticancer activity in HCT116 colon cancer xenografts. It also improved tumour blood perfusion in both tumour models. The plasma level of CCL2 was increased and that of PDGF was decreased after combined treatment with C‐1305 and PTX. The experimental results showed that the levels of FGF1, TGF‐β and Ang‐4 decreased, whereas the levels of ERK1/2 and Akt phosphorylation increased in HCT116 tumour tissue following combined treatment with both drugs. The results of in vitro capillary‐like structure formation assay demonstrated the inhibiting effect of C‐1305 on this process. Although previous in vitro and in vivo studies suggested a positive effect of C‐1305 on cancer cells, combined treatment of HCT116 human colon and A549 lung cancer cells with both PTX and C‐1305 in vivo showed that the antitumor activity was restricted and associated with the modulation of tumour angiogenesis.     

Tight Junctions of the Blood–Brain Barrier

1. The blood–brain barrier is essential for the maintainance and regulation of the neural microenvironment. The blood–brain barrier endothelial cells comprise an extremely low rate of transcytotic vesicles and a restrictive paracellular diffusion barrier. The latter is realized by the tight junctions between the endothelial cells of the brain microvasculature, which are subject of this review. Morphologically, blood–brain barrier-tight junctions are more similar to epithelial tight junctions than to endothelial tight junctions in peripheral blood vessels.2. Although blood–brain barrier-tight junctions share many characteristics with epithelial tight junctions, there are also essential differences. However, in contrast to tight junctions in epithelial systems, structural and functional characteristics of tight junctions in endothelial cells are highly sensitive to ambient factors.3. Many ubiquitous molecular constituents of tight junctions have been identified and characterized including claudins, occludin, ZO-1, ZO-2, ZO-3, cingulin, and 7H6. Signaling pathways involved in tight junction regulation comprise, among others, G-proteins, serine, threonine, and tyrosine kinases, extra- and intracellular calcium levels, cAMP levels, proteases, and TNF. Common to most of these pathways is the modulation of cytoskeletal elements which may define blood–brain barrier characteristics. Additionally, cross-talk between components of the tight junction– and the cadherin–catenin system suggests a close functional interdependence of the two cell–cell contact systems.4. Recent studies were able to elucidate crucial aspects of the molecular basis of tight junction regulation. An integration of new results into previous morphological work is the central intention of this review.     

The synthesis of polyoxygenated, enantiomerically pure cyclopentane derivatives on route to neplanocin A stereoisomers via alkylidenecarbene species prepared from sugar templates

Our new method for the generation of alkylidenecarbenes, based on the reaction of trimethylsilylazide/Bu₂SnO with α-cyanomesylates, has been applied to the synthesis of enantiomerically pure polyhydroxylated cyclopentane derivatives from conveniently functionalized sugar intermediates prepared from d-mannose. The stereoselectivity of the 1,5 C–H insertion reaction leading to the major trans-isomers (8a,b) has been assigned by ¹H RMN spectroscopic data, and correctly rationalized by a computational analysis at DFT level. Compounds 8a and 8b have been designed as suitable intermediates for the synthesis of neplanocin A enantiomer.     

Performance of trichlorfon degradation by a novel <Emphasis Type="Italic">Bacillus tequilensis</Emphasis> strain PA F-3 and its proposed biodegradation pathway

The novel trichlorfon (TCF)-degrading bacterium PA F-3, identified as Bacillus tequilensis, was isolated from pesticide-polluted soils by using an effective screening and domesticating procedure. The TCF biodegradation pathways of PA F-3 were also systematically elucidated. As revealed by high-performance liquid chromatography, the TCF residues in the mineral salt medium demonstrated that PA F-3 can utilize TCF as its sole carbon source and reach the highest degradation of 71.1 % at an initial TCF concentration of 200 mg/L within 5 days. The TCF degradation conditions were optimized using response surface methodology as follows: temperature, 28 °C; inoculum amount, 4 %; and initial TCF concentration, 125 mg/L. Biodegradation treatments supplemented with exogenous carbon sources and yeast extract markedly increased the microbial dry weights and TCF-degrading performance of PA F-3, respectively. Meanwhile, five metabolic products of TCF were identified through gas chromatography/mass spectrometry, and a biodegradation pathway was proposed. Results indicated that deoxidation and dehydration (including the cleavage of the P–C phosphonate bond and the C–O bond) were the preferred metabolic reactions of TCF in this TCF-degrading bacterium.