Abstract and subjects
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.