Abstract
BackgroundThe archaeon, Methanosarcina acetivorans strain C2A forms methane, a potent greenhouse gas, from a variety of one-carbon substrates and acetate. Whereas the biochemical pathways leading to methane formation are well understood, little is known about the expression of the many of the genes that encode proteins needed for carbon flow, electron transfer and/or energy conservation. Quantitative transcript analysis was performed on twenty gene clusters encompassing over one hundred genes in M. acetivorans that encode enzymes/proteins with known or potential roles in substrate conversion to methane.ResultsThe expression of many seemingly "redundant" genes/gene clusters establish substrate dependent control of approximately seventy genes for methane production by the pathways for methanol and acetate utilization. These include genes for soluble-type and membrane-type heterodisulfide reductases (hdr), hydrogenases including genes for a vht-type F420 non-reducing hydrogenase, molybdenum-type (fmd) as well as tungsten-type (fwd) formylmethanofuran dehydrogenases, genes for rnf and mrp-type electron transfer complexes, for acetate uptake, plus multiple genes for aha- and atp-type ATP synthesis complexes. Analysis of promoters for seven gene clusters reveal UTR leaders of 51-137 nucleotides in length, raising the possibility of both transcriptional and translational levels of control.ConclusionsThe above findings establish the differential and coordinated expression of two major gene families in M. acetivorans in response to carbon/energy supply. Furthermore, the quantitative mRNA measurements demonstrate the dynamic range for modulating transcript abundance. Since many of these gene clusters in M. acetivorans are also present in other Methanosarcina species including M. mazei, and in M. barkeri, these findings provide a basis for predicting related control in these environmentally significant methanogens.
Highlights
The archaeon, Methanosarcina acetivorans strain C2A forms methane, a potent greenhouse gas, from a variety of one-carbon substrates and acetate
M. acetivorans possesses four gene clusters annotated for formylmethanofuran dehydrogenase, three gene sets annotated for hydrogenase, five distinct clusters of genes encoding membrane-bound and/or soluble-type heterodisulfide reductase enzymes, and two gene clusters encoding distinct membrane bound ATP sythase complexes
Gene redundancy in the M. acetivorans genome The M. acetivorans genome contains many seemingly redundant copies of genes annotated with roles in methanogenesis [5]
Summary
The archaeon, Methanosarcina acetivorans strain C2A forms methane, a potent greenhouse gas, from a variety of one-carbon substrates and acetate. Whereas the biochemical pathways leading to methane formation are well understood, little is known about the expression of the many of the genes that encode proteins needed for carbon flow, electron transfer and/or energy conservation. Methanosarcina acetivorans strain C2A is a mesophilic anaerobic archaean isolated from a kelp-degrading enrichment of marine origin [1] It is one of the more metabolically versatile methanogens in that it can use acetate as well as one-carbon substrates including mono-methylamine, di-methylamine, tri-methyl amine, methanol, or carbon monoxide as a sole source of carbon and energy. Little is yet known about the expression of the genes encoding the described pathway enzymes or accessory proteins needed for electron and carbon flow. Orthologs of many of these genes are present in other described Methanosarcinaceae species including M. acetivorans, M. mazei, and M. barkeri (Table 1, described below), plus in other methanogenic species
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