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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 101:16929-16934], 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 C[O.sub.2] supplies electrons for reduction of C[O.sub.2] to a methyl group by steps and enzymes of the pathway for C[O.sub.2] 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 [F.sub.420][H.sub.2]:heterodisulfide oxidoreductase system that generates a proton gradient for ATP synthesis not previously described for pathways reducing C[O.sub.2] 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 C[O.sub.2] 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. anaerobic | Archaea | carbon monoxide

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.

Electroinjection analysis has been demonstrated to provide reaction kinetics information. Reactants are injected continuously from opposite ends of the capillary for the duration of the experiment, and reaction product formation occurs at the boundary where the zones merge. The width of the product signal measured by the detector depends on the ratio of the fluxes of reactants. The boundary moves toward the detector where the products are measured. A sharp peak at the edge of the main flat product signal peak was observed and most probably corresponds to the metastable intermediate product of reaction, a unique capability of this technique. A theoretical explanation and an experimental verification of the possibile use of electroinjection analysis for the study of reaction kinetics is given.