The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes

Abstract

We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcina spp. in the region proximal to the origin of replication, with interspecies gene similarities as high as 95%. However, it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the distal semigenome. Of the 3,680 open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80% identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs were unique (nonorthologous) among these species, including a complete formate dehydrogenase operon, genes required for N-acetylmuramic acid synthesis, a 14-gene gas vesicle cluster, and a bacterial-like P450-specific ferredoxin reductase cluster not previously observed or characterized for this genus. A cryptic 36-kbp plasmid sequence that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143-nucleotide motif was detected in M. barkeri. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the relatively large M. acetivorans genome is the result of uniformly distributed multiple gene scale insertions and duplications, while the M. barkeri genome is characterized by localized inversions associated with the loss of gene content. In contrast, the short M. mazei genome most closely approximates the putative ancestral organizational state of these species.Biological methanogenesis by the methane-producing archaea has a significant role in the global carbon cycle. This process is one of several anaerobic degradative processes that complement aerobic degradation by utilizing alternative electron acceptors in habitats where O 2 is not available (39). The efficiency of this microbial process is directly dependent upon the interaction of three metabolically distinct groups of microorganisms: the fermentative and acetogenic bacteria and the methanogenic archaea. The methanogenic archaea have two pivotal roles in methanogenic consortia (28). By consuming hydrogen for methanogenesis and effectively lowering its partial pressure by the process of interspecies hydrogen exchange, the methanogens provide a thermodynamically favorable environment for the fermentative and acetogenic species to utilize protons as electron acceptors. This interaction enables fermenters to conserve more energy by producing a more oxidized product, acetate, which is also a substrate for methanogenesis. The second role of the methanogens is the fermentation of acetate, which accounts for 70% of the global methane produced by biological methane production (28). The net effect of these microbial interactions is the diversion of protons to hydrogen and carbon to acetate, which ultimately yields methane and carbon dioxide via methanogenesis.The genus M...

Regulation of putative methyl‐sulphide methyltransferases in Methanosarcina acetivorans C2A

“…To remove contaminating chromosomal DNA, the RNA preparation was digested with TURBO DNA-free (Ambion, Austin, TX). This RNA preparation (5 mg) was then treated with 20 units of tobacco acid pyrophosphatase (Maeder et al, 2006) (Epicentre, Madison, WI) for 1 h at 37°C in the presence of 80 units of RNasin (Promega, Madison, WI). A negative control was included where the tobacco acid pyrophosphatase was replaced with RNase-free water (TAP -control).…”

“…Although homologues for the MtsA/B system are present in M. barkeri Fusaro and Methanosarcina mazei Gö1, they are absent in M. acetivorans C2A. Therefore, this organism must use novel enzymes for the utilization/ production of DMS (Deppenmeier et al, 2002;Galagan et al, 2002;Maeder et al, 2006). Because the production of DMS occurs concomitantly with the upregulation of MA0859, MA4384 and MA4558 during growth on CO (Rother et al, 2007;Moran et al, 2008), these open reading frames (ORFs) might encode DMS-specific methyltransferases.…”

Unusual phyletic distribution of peptidases as a tool for identifying potential drug targets

“…Horizontal transfer in the opposite direction appears to have occurred in the huge genome of Methanosarcina acetivorans [13], including the only archaean genes for homologues of thermolysin (peptidase family M4) and clostripain (peptidase family C11): both peptidase families are otherwise only known from bacteria. The closely related M. barkeri is equally a 'kleptomaniac' for foreign genes [14], but this genome contains a real surprise. Multicellular eukaryotes have to kill their own cells during development and to recycle tissues.…”

Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment

“…For instance, comparative genomics of M. barkeri Fursaro, M. acetivorans C16 and M. mazei Gö1 revealed that large fluctuations in genome size (up to~1.7 Mb) were likely caused by gene insertions, localized inversions and transpositions (Maeder et al, 2006). In addition, gene gain from bacterial taxa is common in at least some Methanosarcina spp.…”