Changes of chlorine isotope composition characterize bacterial dehalogenation of dichloromethane

Fractionation of dichloromethane (DCM) molecules with different chlorine isotopes by aerobic methylobacteria Methylobacterium dichloromethanicum DM4 and Albibacter methylovorans DM10; cell-free extract of strain DM4; and transconjugant Iethylobacterium extorquens AI1/pME 8220, expressing the dcmA gene for DCM dehalogenase but unable to grow on DCM, was studied. Kinetic indices of DCM isotopomers for chlorine during bacterial dehalogenation and diffusion were compared. A two-step model is proposed, which suggests diffusional DCM transport to bacterial cells.     

Analysis of the key functional genes in new aerobic degraders of dichloromethane

The genes of dichloromethane (CH₂C1₂, DCM) degradation have been characterized in the aerobic degraders “Gottschalkia methylica” DM15, “Ancylobacter dichloromethanicus” DM16, and Methylobac- terium extorquens DM17, isolated from different regions of Russia. The sequencing of the structural gene dcmA of DCM dehalogenase, followed by phylogenetic analysis, showed that the new degraders possess A-type dehalogenases. The DcmAs of the strains DM15 and DM17 were identical to the known orthologous proteins of Methylorhabdus multivorans DM 13 and Methylobacterium dichloromethanicum DM4, respectively. DcmA of the degrader DM16 differed by three amino acid substitutions from DcmA of strain DM4. In agreement with the organization of the cluster of DCM degradation genes in M. dichloromethanicum DM4, the regulatory gene dcmR and the open reading frame orf353, flanking dcmA, were identified in the new degraders. The similarity of DCM degradation genes in aerobic degraders of different taxonomic position and geographical origin suggests their distribution among methylotrophic bacteria by means of horizontal transfer.     

Effects of DNA-damaging Agents on Aerobic Methylobacteria Capable and Incapable of Utilizing Dichloromethane

Methylobacterium dichloromethanicum DM4, a degrader of dichloromethane (DCM), was more tolerant to the effect of H₂O₂ and UV irradiation than Methylobacterium extorquens AM1, which does not consume DCM. The addition of CH₂Cl₂ to methylobacteria with active serine, ribulose monophosphate, and ribulose bisphosphate pathways of C₁ metabolism, grown on methanol, resulted in a 1.1- to 2.5-fold increase in the incorporation of [α-³²P]dATP into DNA by the Klenow fragment (exo^?). Since DCM dehalogenase was not induced in this process, the increase in the total lengths of DNA gaps resulted from the action of DCM rather than S-chloromethylglutathione (intermediate of primary dehalogenation). The degree of DNA damage in the presence of CH₂Cl₂ was lower in DCM degraders than methylobacteria incapable of degrading this pollutant. This suggests that DCM degraders possess a more efficient mechanism of DNA repair.     

Physiological and Biochemical Analysis of the Transformants of Aerobic Methylobacteria Expressing the dcmA Gene of Dichloromethane Dehalogenase

Transformants of Methylobacterium dichloromethanicum DM4 (DM4-2cr^–/pME 8220 and DM4-2cr^–/pME8221) and of Methylobacterium extorquens AM1 (AM1/pME8220 and AM1/pME8221) that express the dcm A gene of dichloromethane dehalogenase undergo lysis when incubated in the presence of dichloromethane and are sensitive to acidic shock. The lysis of the transformants was found to be related neither to the accumulation of Cl^– ions, CH₂O, or HCOOH, nor to the impairment of glutathione synthesis or to the disturbance of intracellular pH homeostasis. The (exo^–) Klenow fragment–mediated incorporation of [-³²P]dATP into the DNA of the transformants DM4-2cr^–/pME8220 and AM1/pME8220 was considerably greater when the transformed cells were incubated with CH₂Cl₂ than when they were incubated with CH₃OH, indicating the occurrence of a significant increase in the total length of gaps. At the same time, the strain AM1 (which lacks dichloromethane dehalogenase) and the dichloromethane-degrading strain DM4 incubated with CH₂Cl₂ showed an insignificant increase in the total length of the gaps. The transformed cells are likely to lyse due to the relatively inefficient repair of DNA lesions that are induced in response to the alkylating action of S-chloromethylglutathione, an intermediate product of CH₂Cl₂ degradation. The data obtained suggest that the bacterial mineralization of dichloromethane requires an efficient DNA repair system.     

The Aeration-Dependent Effect of Vitamin B12 on DNA Biosynthesis in Methylobacterium dichloromethanicum

The effect of vitamin B₁₂ (cobalamin) on DNA biosynthesis in Methylobacterium dichloromethanicum was studied. When cultivated in media with methanol or dichloromethane, the bacterium produced approximately 10 g corrinoids per gram dry biomass, compared to about 7 g/g when cultivated on ethanol or succinate. Exogenous adenosylcobalamin (AdoCbl) stimulated DNA biosynthesis in M. dichloromethanicum cells grown under poor aeration, the effect being mediated by AdoCbl-dependent ribonucleotide reductase. In vitro studies showed that M. dichloromethanicumalso has AdoCbl-independent ribonucleotide reductase. Under good aeration, exogenous AdoCbl had no effect on DNA biosynthesis, while hydroxyurea suppressed it. These data suggest that AdoCbl-independent ribonucleotide reductase, which is likely to be activated by oxygen, plays an important part in DNA biosynthesis when M. dichloromethanicum is cultured with good aeration, whereas AdoCbl-dependent ribonucleotide reductase is active under conditions of poor aeration.     

Functional activity of thyroid gland in male rats with acute and mild streptozotocin diabetes

Type 1 diabetes mellitus (DM1) and dysfunction of the thyroid gland (TG) are the most common endocrine diseases, which are interrelated. However, the molecular mechanisms of thyroid dysfunction in DM1 and the role of adenylyl cyclase signaling system (ACSS) in this process remain poorly understood. Typically for studying etiology and pathogenesis of thyroid diseases in DM1 the models of acute DM1 induced by high doses of streptozotocin (STZ) are used. At the same time, a suitable model for this purpose is the model of mild DM1 initiated by moderate doses of STZ, which more closely resembles human DM1. The aim of this study was a comparative study of the functional state of the thyroid gland in rats with 30-day acute DM1 induced by injection of STZ at a dose of 65 mg/kg, and in rats with 30- and 210-day mild DM1 induced by three consecutive injections of STZ at medium doses (30–40 mg/kg). For this purpose in diabetic animals the levels of thyroid hormones and TSH and the functional activity of hormone-sensitive ACSS in membranes isolated from thyroid gland were studied. It was shown that in blood of rats with acute DM1 the levels of fT₄, fT₃, and tT₃ were decreased by 45, 23 and 19%, respectively, while the level of TSH did not change significantly. In rats with the 30-day mild DM1 the concentration of fT₄ was decreased by 32%, while the levels of tT₄, tT₃, and TSH were similar to that in control. In rats with prolonged mild DM1 after 150 and 210 days following the first treatment with STZ the levels of tT₄, fT₄, and tT₃ were significantly reduced, but the concentration of TSH in rats with 210-day mild DM1 was increased by 119%. The results obtained in the study of thyroid status and TSH levels in rats with prolonged mild DM1 are in good agreement with the data obtained in the study of thyroid diseases in patients with DM1. It was found that the AC basal activity in the membranes isolated from the thyroid gland of diabetic rats did not change, except for the rats with the prolonged mild DM1 where this activity was increased by 21%. In all groups of diabetic rats the decrease of AC stimulating effects of GppNHp (10^?5 M) and TSH (10^?8 M) was found, and in the rats with prolonged mild DM1 the AC effect of PACAP-38 (10^?6 M) was also reduced. The decrease of AC effect of TSH varied among different groups of the diabetic animals: in the rats with acute DM1 this effect was reduced by 46% and in the rats with 30- and 210-day mild DM1-by 18 and 34%. Thus, it was concluded that the key cause of the thyroid resistance to TSH under conditions of DM1 is a weakening of the signal transduction generated by TSH via the ACSS.     

Effect of glucose on the biosynthesis of the membranes of bacillus

In the presence of glucose in complex media, the following changes in the characters of the membranes of Bacillus subtilis and Bacillus cereus were observed. (1) The activity of succinate dehydrogenase and the amount of cytochromes of the membranes were greatly reduced. (2) The ratio of lipid to protein in the membranes was decreased and a membrane subfraction, which had a density of around 1.2 (B. subtilis) and 1.24 g/cm³ (B. cereus), was newly formed (B. subtilis) or increased (B. cereus). (3) The phospholipid and diglyceride contents in the membranes were reduced.Polyacrylamide gel electrophoresis of proteins of the two types (plus and minus glucose) of the membranes show that the patterns were very different between the two types of membranes, though the lost or newly formed membrane protein components were not observed.The cytochrome content was not increased when the cells were grown in glucose medium supplemented with haemin, therefore, glucose or its metabolite may not be involved in the inhibition of haem biosynthesis.     

A study of inhomogeneity of bilayer lipid membranes by measuring the higher harmonics of the transmembrane current

The higher harmonics of the alternating current in bilayer lipid membranes induced by a sinusoidal voltage applied to the membrane were measured. The bilayer lipid membranes were prepared from diphytanoylphosphatidylcholine in decane and tetradecane; a 16-bit analog-to-digital converter was used for the measurements. A sinusoidal voltage was formed with a 16-bit digital-to-analog converter. The dynamic measurement range reached 90 dB. The coefficients α and β of the expansion of capacitance C in terms of the membrane voltage U—C = C ₀(1 + αU ² + βU ⁴)—were determined from the measurement results. It was shown within the framework of the electrostriction model that a certain ratio of the coefficients α and β characterizes the inhomogeneity of the membrane with respect to its thickness and Young’s modulus of elasticity.     

Identification and biochemical characterization of the plasma-membrane H+-ATPase in guard cells of Vicia faba L.

The plasma-membrane H⁺-pump in guard cells generates the driving force for the rapid ion fluxes required for stomatal opening. Since our electrophysio-logical studies revealed a two fold higher pump-current density in guard cells than in mesophyll cells of Vicia faba L. we elucidated the biochemical properties of this proton-translocating ATPase in plasma-membrane vesicles isolated from both cell types. The capability of the H⁺ —ATPase to create an H⁺ gradient is maintained in plasma-membrane vesicles derived from purified guard cells via blender maceration, high-pressure homogenization and polymer separation. The H⁺-pumping activity of these vesicles coincides with the presence of two polypeptides of approx. 100 and 92 kDa which are recognized by a monoclonal antibody raised against the plasma-membrane H⁺-ATPase from Zea mays L. coleoptiles. Comparison of H⁺-pumping activities of isolated membranes revealed an approximately two fold higher activity in guard cells than in mesophyll cells with respect to the total membrane protein content. Furthermore, we demonstrated by western blotting that the difference in pump activities resulted from a higher abundance of the electroenzyme per unit membrane protein in guard-cell plasma membranes. We suggest that the high H⁺-pump capacity is necessary to enable guard cells to respond to sudden changes in the environment by a change in stomatal aperture.     

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

Background

Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared.

Methodology/Principal Findings

The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid).

Conclusion/Significance

These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.     

Changes of chlorine isotope composition characterize bacterial dehalogenation of dichloromethane

Fractionation of dichloromethane (DCM) molecules with different chlorine isotopes by aerobic methylobacteria Methylobacterium dichloromethanicum DM4 and Albibacter nethylovorans DM10; cell-free extract of strain DM4; and transconjugant Methylobacterium evtorquens Al1/pME 8220, expressing the dcmA gene for DCM dehalogenase but unable to grow on DCM, was studied. Kinetic indices of DCM isotopomers for chlorine during bacterial dehalogenation and diffusion were compared. A two-step model is proposed, which suggests diffusional DCM transport to bacterial cells.     

Adaptation of aerobic methylobacteria to dichloromethane degradation

A shortening of the lag phase in dichloromethane (DCM) consumption was observed in the methylobacteria Methylopila helvetica DM6 and Albibacter methylovorans DM10 after prior growth on methanol with the presence of 1.5% NaCl. Neither heat nor acid stress accelerated methylobacterium adaptation to DCM consumption. Sodium azide (1 mM) and potassium cyanide (1 mM) inhibited consumption of DCM by these degraders but not by transconjugants Methylobacterium extorquens AM1, expressing DCM dehalogenase but unable to grow on DCM. This indicates that the degrader strains possess energy-dependent systems of transport of DCM or chloride anions produced during DCM dehalogenation. Inducible proteins were found in the membrane fraction of A. methylovorans DM10 cells adapted to DCM and elevated NaCl concentration.     

Ouabain-insensitive Na+-stimulated ATPase activity of basolateral plasma membranes from guinea-pig kidney cortex cells: II. Effect of Ca2+

The ouabain-insensitive, Mg²⁺-dependent, Na⁺-stimulated ATPase activity present in fresh basolateral plasma membranes from guinea-pig kidney cortex cells (prepared at pH 7.2) can be increased by the addition of micromolar concentrations of Ca²⁺ to the assay medium. The Ca²⁺ involved in this effect seems to be associated with the membranes in two different ways: as a labile component, which can be quickly and easily ‘deactivated’ by reducing the free Ca²⁺ concentration of the assay medium to values lower than 1 μM; and as a stable component, which can be ‘deactivated’ by preincubating the membranes for periods of 3–4 h with 2 mM EDTA or EGTA. Both components are easily activated by micromolar concentrations of Ca²⁺. The $\text{K}{}_{\mathrm{<mtext>a</mtext>}}$ of the system for Na⁺ is the same, 8 mM, whether only the stable component or both components, stable and labile, are working. In other words, the activating effect of Ca²⁺ on the Na⁺-stimulated ATPase is on the $\text{V}{}_{\mathrm{<mtext>max</mtext>}}$, and not on the $\text{K}{}_{\mathrm{<mtext>a</mtext>}}$ of the system for Na⁺. The activating effect of Ca²⁺ may be related to some conformational change produced by the interaction of this ion with the membranes, since it can also be obtained by resuspending the membranes at pH 7.8 or by ageing the preparations. Changes in the Ca²⁺ concentration may modulate the ouabain-insensitive, Na⁺-stimulated ATPase activity. This modulation could regulate the magnitude of the extrusion of Na⁺ accompanied by Cl^? and water that these cells show, and to which the Na⁺-ATPase has been associated as being responsible for the energy supply of this mode of Na⁺ extrusion.     

Porous membranes for reconstitution of ion channels

Functional biological synthetic composite (BSC) membranes were made using phospholipids, biological membrane proteins and permeable synthetic supports or membranes. Lipid bilayers were formed on porous polycarbonate (PC), polyethylene terephthalate (PETE) and poly (l-lactic acid) (PLLA) membranes and in 10-100 μm laser-drilled pores in a 96-well plastic plate as measured by increased resistance or decreased currents. Bilayers in 50 μm and smaller pores were stable for up to 4 h as measured by resistance changes or a current after gramicidin D reconstitution. Biological membrane transport reconstitution was then carried out. Using vesicles containing Kv1.5 K⁺ channels, K⁺ currents and decreased resistance were measured across bilayers in 50 μm pores in the plastic plate and PLLA membranes, respectively, which were inhibited by compound B, a Kv1.5 K⁺ channel inhibitor. Functional reconstitution of Kv1.5 K⁺ channels was successful. Incorporation of membrane proteins in functional form in stable permeable membrane-supported lipid bilayers is a simple technology to create BSC membranes that mimic biological function which is readily adaptable for high throughput screening.     

Analysis of calorimetric data for isodesmic self-associating systems.

ATP and respiration (NADH)-driven NAD(P)⁺ transhydrogenase (EC 1.6.1.1) activities are low in membranes from Escherichia coli cultured on yeast extract medium (17 and 21 nmol/min × mg) but high on glucose (82 and 142 nmol/min × mg). The ATPase and respiratory activities in both cases appeared comparable. Growth of the bacteria in yeast extract medium followed by washing and replacement into a glucose medium showed that after 3 h the energy-linked and energy-independent NAD(P)⁺ transhydrogenase (reduction of acetylpyridine NAD⁺ by NADPH) activities had appeared simultaneously. Incorporation of chloramphenicol or omission of glucose in the induction medium resulted in no increase in these activities indicating that de novo protein synthesis is required for the induction of energy-linked and -independent NAD(P)⁺ transhydrogenase. It was found that the K_m values for acetylpyridine NAD⁺ and NADPH for the energy-independent reaction in membranes from glucose grown cells (143 and 62 μm) were similar to those in membranes from cells grown on glucose-yeast extract (135 and 45 μm), respectively, but the maximum velocity at infinite acetyl pyridine NAD⁺ and NADPH increased from 353 to 2175 nmol/min × mg. Furthermore, the membrane-bound NAD(P)⁺ transhydrogenase in glucose-yeast extract grown cells showed substrate inhibition at high NADPH and low acetyl pyridine NAD⁺ levels. Further kinetic data demonstrate that the mechanism of the energy-independent NAD(P)⁺ transhydrogenase in E. coli is similar to that of the mitochondrial enzyme and exhibits similar responses to competitive inhibitors at the NAD⁺ and NADPH sites.