An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics

Methanosarcina acetivorans produces acetate, formate, and methane when cultured with CO as the growth substrate [Rother M, Metcalf WW (2004) Proc Natl Acad Sci USA 101:], which suggests novel features of CO metabolism. Here we present a genome-wide proteomic approach to identify and quantify proteins differentially abundant in response to growth on CO versus methanol or acetate. The results indicate that oxidation of CO to CO2 supplies electrons for reduction of CO2 to a methyl group by steps and enzymes of the pathway for CO2 reduction determined for other methane-producing species. However, proteomic and quantitative RT-PCR results suggest that reduction of the methyl group to methane involves novel methyltransferases and a coenzyme F420H2:heterodisulfide oxidoreductase system that generates a proton gradient for ATP synthesis not previously described for pathways reducing CO2 to methane. Biochemical assays support a role for the oxidoreductase, and transcriptional mapping identified an unusual operon structure encoding the oxidoreductase. The proteomic results further indicate that acetate is synthesized from the methyl group and CO by a reversal of initial steps in the pathway for conversion of acetate to methane that yields ATP by substrate level phosphorylation. The results indicate that M. acetivorans utilizes a pathway distinct from all known CO2 reduction pathways for methane formation that reflects an adaptation to the marine environment. Finally, the pathway supports the basis for a recently proposed primitive CO-dependent energy-conservation cycle that drove and directed the early evolution of life on Earth.

New Algorithm for 15N/14N Quantitation with LC−ESI−MS Using an LTQ-FT Mass Spectrometer

A new algorithm (QN) for the (15)N /(14)N quantitation of relative protein abundances in complex proteomic samples is described. QN takes advantage of the high resolution, mass accuracy and throughput of the hybrid mass spectrometer LTQ-FT MS. Peptide quantitation is based on MS peak intensity (measured in the FT MS), while peptide identification is performed in the MS/MS mode (measured in the LTQ linear ion trap). Accuracy of the protein abundance is enhanced by a novel scoring procedure, allowing filtering of less reliable measurements of peptide abundances. The performance of QN is illustrated in the relative quantitative analysis of M. acetivorans C2A cultures grown with carbon monoxide vs methanol as substrate. Roughly 1,000 proteins were quantitated with an average CV of 9% for the protein abundance ratios. QN performs quantitation without manual intervention, does not require high processing power, and generates files compatible with the Guidelines for Proteomic Data Publication.

A Universal Denoising and Peak Picking Algorithm for LC−MS Based on Matched Filtration in the Chromatographic Time Domain

A new denoising and peak picking algorithm (MEND, matched filtration with experimental noise determination) for analysis of LC-MS data is described. The algorithm minimizes both random and chemical noise in order to determine MS peaks corresponding to sample components. Noise characteristics in the data set are experimentally determined and used for efficient denoising. MEND is shown to enable low-intensity peaks to be detected, thus providing additional useful information for sample analysis. The process of denoising, performed in the chromatographic time domain, does not distort peak shapes in the m/z domain, allowing accurate determination of MS peak centroids, including low-intensity peaks. MEND has been applied to denoising of LC-MALDI-TOF-MS and LC-ESI-TOF-MS data for tryptic digests of protein mixtures. MEND is shown to suppress chemical and random noise and baseline fluctuations, as well as filter out false peaks originating from the matrix (MALDI) or mobile phase (ESI). In addition, MEND is shown to be effective for protein expression analysis by allowing selection of a large number of differentially expressed ICAT pairs, due to increased signal-to-noise ratio and mass accuracy.

Computer simulation of affinity capillary electrophoresis

A computer-simulated model of affinity capillary electrophoresis is developed. Unlike existing models, it is able to describe the situation where the concentrations of sample molecules and ligand molecules are commensurable, or even the situation where the zones occupied by these molecules are not mixed initially. The model permits to study the dependence of the spatial and temporal distributions of sample molecules on various parameters such as reaction rate constants, concentrations of sample and reagent, electromigration velocities of sample and reagent and sample injection volume. A collection of peak shapes for different values of parameters is presented. The dependence of peak variance on the ratio of the time of analysis to the characteristic time of reaction is studied.

Hydrodynamics and mass transfer of the coaxial jet mixer in flow injection analysis

A coaxial jet mixer that was previously proposed for rapid and efficient mixing under laminar flow conditions has been studied both theoretically and experimentally. A mathematical model that consists of a set of Navie-Stokes equations that determine the flow velocities and three diffusion-convection reaction equations that determine the reactant and product concentrations has been developed. Equations are solved with the help of finite difference techniques for different flow conditions. The quality of sample and reagent mixing is characterized by the mean product concentration and the amount of product produced. Theoretical results are compared with experimental ones for the mixing of bromothymol blue (a pH indicator) in the outer capillary with NaOH in the inner capillary of the jet mixer.

[The use of ocular drug films of propolis in the sequelae of ophthalmic herpes]

There was studied the therapeutic efficiency of ocular medical propolis films (OMF) in 35 patients with postherpetic trophic keratitis and in 20 with postherpetic nebula. OMF were applied behind the lower eyelid at bedtime during 10-15 days. All the patients endured the propolis films well. OMF accelerated the cornea epithelization. Epitheliopathy and micropoint edema of cornea epithelium rapidly disappeared. Time of patients recovery reduced nearly twice (P,001) in comparison with the control group--from 14.1 to 7.6 days. On the average their visual acuity increased in two times--from 0.12 to 0.27 (P > 0.001).

Investigation of the electroosmotic flow effect on the efficiency of capillary electrophoresis

The influence of the electroosmotic flow profile on the efficiency and resolution of capillary electrophoresis is studied. The mathematical model is formulated and the set of equations is solved numerically. The results of the analysis are applicable to a wide range of buffer concentrations and capillary diameters. The temperature dependence of electrophoretic mobility, viscosity and thermal conductivity and the dependence of electrical conductivity on temperature and ion concentration in the double layer are taken into account. It is shown that there exists a region of buffer concentrations and capillary diameters where the influence of the electroosmotic flow profile on the efficiency and resolution is much greater than that of the temperature dependence of the electrophoretic mobility. The results are especially essential for small buffer concentrations or capillary diameters comparable with the double electrical layer thickness.

[Characteristics of recovery process in kidney tubule epithelium of white rats with advanced mercuric chloride-induced necrotic nephrosis]

Paraffin and semithin sections were used to study the peculiarities of recovery process in kidney tubules of white rats at various intervals (3 days to 5 months). Koss reaction for evaluation of calcium saline level was used after subcutaneous injection of large doses of sublimate (0.6 mg/100 g of b.w.). The study revealed the expressed destruction of tubules to be followed by rapid (3 days after nephrotoxin injection) calcification of cellular detritus.

[Changes in the nucleoli of epithelial cells of the kidney tubules in mercuric chloride-induced experimental kidney tubular necrosis]

Electron-microscopic studies of epithelial cells of uric tubules in white rat kidneys after i.m. injections of mercury dichloride (0.4 mg/100 of body weight) given every 24, 48 and 72 hours showed the affected epithelial cells to have nonspecific changes in tubule ultrastructure, i.e. dissociation and segregation of tubule components as well as degranulation, fragmentation and hypertrophy. The dissociation of nucleolus components is followed by the damage of an essential part of cell mitochondrial apparatus and becomes irreversible. In some damaged cells degranulation is accompanied by the nucleolus decay into separate solid fragments formed of fibrous tissue. The enlargement of nucleolus fragments in the absence of proribosomes speaks in favour of the depression of proribosome formation process while the ability to synthesize p-RNA in comparatively slight.

[Correlations of intracellular and cellular regeneration of the epithelium of the kidney tubules in necronephrosis]

The study of radioautographs in ultrathin and semithin sections extracted from animal tissues and following the impulsive as well as long-term injection of 3H-thymidine was made. Intracellular regeneration processes (external cell membrane synthesis, DNA reparation, restoration of the lost albumin-synthesizing complex and cytoskeleton) turned to develop in proximal canals of epithelial cells. The processes were aimed at the liquidation of distortions preventing cell from entering mitosis.

[Isolation of viruses of antigenic complexes of California encephalitis and Bunyamwera (Bunyaviridae, Bunuavirus) from mosquitoes in northeast Asia]

Studies in suckling mice and by direct solid-phase enzyme immunoassay were carried out with 111,1 thousand Aedes mosquitoes collected in July, 1986, in tundra, forest-tundra, and northern taiga of Kamchatka region and Chukotka autonomous district of Magadan region (North-Pacific natural area within 69 degrees-53 degrees North and 156 degrees-177 degrees East). Eleven strains were isolated of which 7 were classified as members of the California encephalitis complex (Tahyna-like strains) and 4 as members of the Bunyamwera complex (Batai-like strains). According to electron-microscopic studies of 2 strains (one from each antigenic complex), both were classified as belonging to the family of Bunyaviridae. Strains of both complexes were isolated in all landscape zones examined--tundra, forest-tundra, northern taiga. Virus-neutralizing antibodies to them were found in human and reindeer sera also in all the landscape zones, to Tahyna virus in 11%-61%, to Batain virus in 2%-6% blood specimens. No antibody to Uukuniemi virus was found.

[Electron microscopic-radioautographic study of RNA synthesis in the epithelial cells of the kidney urinary tubules of white rats in corrosive sublimate poisoning]

Radioautographic study of ultrathin selections of proximal white rat renal canals labeled with 3H-uridine revealed diffuse transition of peripheral and paranuclear heterochromatin to be observed in nuclei of undamaged epithelia cells and those affected by partial necrosis in case of sublimate nephrosis. Nucleus degranulation as well as decrease in its size accompanied by inhibition of RNA synthesis is also observed. Nucleus reparation being observed 48 hours after subcutaneous injection of 0.4/0.1 kg corrosive sublimate in some cells and characterized by the appearance of granular component as well as the increase of nucleolar vacuole count is usually revealed in case of decondensation form of peripheral and paranuclear chromatin in the enlarged nuclei.

[Autoradiographic research on RNA biosynthesis in renal tissue in the early period of corrosive sublimate-induced necronephrosis]

Study of 3H-uridine autoradiographs in semithin methacrylate renal sections of white rats showed pronounced decrease of uridine mark in all cellular types of renal tissue following 24 hours after the administration of 0.5 mg corrosive sublimate per 100 g bw. The period was marked by the development of anuria in animals. 48 hours later increase of uridine mark level in renal cortical substance was observed. Epithelial cells being contiguous with necrosed zone of non- and partially damaged but kept-alive urinary small canals became hypertrophic and synthesized RNA actively preceding their mitotic division.

[Electron microscopic and radioautographic study of DNA synthesis in kidney tubule epithelial cells in white rats with sublimate-induced necronephrosis]

Electron microscopic analysis of 3H-thymidine radioautographs of ultrathin sections from the white rat kidney has revealed that 72 hours after subcutaneous injection of 0.5 mg per 100 g body weight of mercury bichloride, the damaged and partially necrotized epithelial cell became capable of DNA synthesis. However, due to the reduction of cellular organelle count the process was less intensive, as compared to that in insignificantly damaged cells. The presence in the cytoplasm of many damaged epithelial cells capable of DNA synthesis and free ribosomes demonstrates that the RNA and free ribosome biogenesis is an earlier cell regenerative reaction than DNA synthesis.

[Autoradiographic study of DNA synthesis in epithelial cells of albino rat kidney tubules as affected by corrosive sublimate nephrosis]

The analysis of 3H-thymidine radioautographs of semithin (0.5 micron) methacrylate sections of white rat kidney has shown that 72 h after corrosive sublimate injection in a dose of 0.5 mg/100 g bw, pronounced heterogeneity of impulse thymidine mark distribution stipulated by asynchronous DNA replication in damaged nephrocytes was noted. Thymidine mark is to be observed in some heavily damaged nephrocytes, retaining around the nucleus a negligible amount of cytoplasm. Thymidine mark concentration in the peripheral zone of nuclei typical only of nephrocytes with increased cytoplasm amount testifies to the fact that during S-period repairing processes take place in the damaged nephrocytes, leading to normalization of nuclear-cytoplasmic shifts.

[Characteristics of destructive-regenerative processes in the kidneys of albino rats in conditions of necronephrosis caused by corrosive sublimate]

Study of serial semi-thin (0.5 micron) metacrylate and paraffinic (8 microns) of rat kidney sections 6, 12, 24 and 48 h after subcutaneous injection of mercury bichloride at a dose of 0.6 mg/100 g bw has revealed that injury to different parts of the canalicular nephron is of heterogeneous character. The proximal part of the nephron demonstrates both complete and partial necrosis of nephrocyte cytoplasm. The distal parts of the nephron and collecting tubules are characterized by partial necrosis of the apical cytoplasm. Within the period between 12 and 24 h after the mercury bichloride injection, intracellular reparative processes are observed, in addition to destruction, in partially damaged but viable nephrocytes, which is confirmed by the enlargement of the nucleolic size. Regeneration of the tubular epithelium due to cellular restoration was unmarked 24 h after the mercury bichloride injection.