DNA microarray analysis of Methanosarcina mazei Gö1 reveals adaptation to different methanogenic substrates

Abstract

Methansarcina mazei Gö1 DNA arrays were constructed and used to evaluate the genomic expression patterns of cells grown on either of two alternative methanogenic substrates, acetate or methanol, as sole carbon and energy source. Analysis of differential transcription across the genome revealed two functionally grouped sets of genes that parallel the central biochemical pathways in, and reflect many known features of, acetate and methanol metabolism. These include the acetate-induced genes encoding acetate activating enzymes, acetyl-CoA synthase/CO dehydrogenase, and carbonic anhydrase. Interestingly, additional genes expressed at significantly higher levels during growth on acetate included two energy-conserving complexes (the Ech hydrogenase, and the A1A0-type ATP synthase). Many previously unknown features included the induction by acetate of genes coding for ferredoxins and flavoproteins, an aldehyde:ferredoxin oxidoreductase, enzymes for the synthesis of aromatic amino acids, and components of iron, cobalt and oligopeptide uptake systems. In contrast, methanol-grown cells exhibited elevated expression of genes assigned to the methylotrophic pathway of methanogenesis. Expression of genes for components of the translation apparatus was also elevated in cells grown in the methanol medium relative to acetate, and was correlated with the faster growth rate observed on the former substrate. These experiments provide the first comprehensive insight into substrate-dependent gene expression in a methanogenic archaeon. This genome-wide approach, coupled with the complementary molecular and biochemical tools, should greatly accelerate the exploration of Methanosarcina cell physiology, given the present modest level of our knowledge of these large archaeal genomes.

Electron Transport in the Pathway of Acetate Conversion to Methane in the Marine Archaeon Methanosarcina acetivorans

“…Of these 60 proteins from M. acetivorans, the patterns of differential abundance for 57 proteins were in agreement with the transcriptional profile of M. mazei (17). Furthermore, the methods reported here for M. acetivorans identified 20 differentially abundant proteins previously determined by 2-D gel/MS (26) for which the differential abundance patterns of all 20 proteins were in agreement with the 2-D gel/MS analyses.…”

“…Transcriptional profiling of acetate-grown compared methanol-grown M. mazei cells (17) showed that the pathway of acetate conversion to methane is similar to that previously determined for other freshwater Methanosarcina species (7,9,12). However, M. acetivorans was isolated from marine sediments (38) where it functions to convert acetate to methane during the anaerobic decomposition of giant kelp (39 way and assessing metabolic flexibility in response to the environment.…”

“…Fundamental to this understanding is the identification of novel proteins essential to the pathway for methane formation from acetate. Transcriptional profiling of the freshwater species Methanosarcina mazei (17) has identified genes up-regulated in response to growth with acetate compared to growth with methanol, suggesting roles for the encoded proteins that are specific to the pathway for acetate conversion to methane. The results show that the pathway in M. mazei is similar to that previously proposed for other freshwater Methanosarcina species (8)(9)(10)29).…”

Inhibitory effects of saturated fatty acids on methane production by methanogenic <i>Archaea</i>

“…The second hypothesis tested was, therefore, that SFA act anti-methanogenic in methanogenic Archaea independent of the metabolic pathway used to form CH 4 . For that purpose, Methanosarcina mazei, able to grow without H 2 and CO 2 as substrates (Hovey et al, 2005), was cultivated on methanol to test whether this methanogenic pathway is also inhibited. A key coenzyme for any kind of methanogenesis and thus common to all methanogenic Archaea is the methyl-coenzyme M reductase (MCR) (Thauer, 1998).…”

“…A key coenzyme for any kind of methanogenesis and thus common to all methanogenic Archaea is the methyl-coenzyme M reductase (MCR) (Thauer, 1998). The genes encoding MCR are expressed to the same level irrespective if M. mazei forms CH 4 from acetate or from methanol even though numerous, mainly methanol-pathways specific, genes show different expression levels in the cells grown on methanol as compared to the cells grown on acetate (Hovey et al, 2005). This enzyme is involved in the release of CH 4 from methyl-coenzyme M by formation of a heterodisulfide of 2-mercaptoethanesulfonic acid (HS-CoM), i.e.…”