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

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Joint Genome Institute (JGI)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1153914
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Bacteriology; Journal Volume: 189; Journal Issue: 4
Country of Publication:
United States
Language:
English

Citation Formats

D. L.,Maeder, I.,Anderson, T. S.,Brettin, D. C.,Bruce, P.,Gilna, C. S.,Han, A.,Lapidus, W. W.,Metcalf, E.,Saunders, R.,Tapia, and K. R.,Sowers. The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes. United States: N. p., 2007. Web. doi:10.1128/JB.01858-06.
D. L.,Maeder, I.,Anderson, T. S.,Brettin, D. C.,Bruce, P.,Gilna, C. S.,Han, A.,Lapidus, W. W.,Metcalf, E.,Saunders, R.,Tapia, & K. R.,Sowers. The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes. United States. doi:10.1128/JB.01858-06.
D. L.,Maeder, I.,Anderson, T. S.,Brettin, D. C.,Bruce, P.,Gilna, C. S.,Han, A.,Lapidus, W. W.,Metcalf, E.,Saunders, R.,Tapia, and K. R.,Sowers. Wed . "The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes". United States. doi:10.1128/JB.01858-06.
@article{osti_1153914,
title = {The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes},
author = {D. L.,Maeder and I.,Anderson and T. S.,Brettin and D. C.,Bruce and P.,Gilna and C. S.,Han and A.,Lapidus and W. W.,Metcalf and E.,Saunders and R.,Tapia and K. R.,Sowers},
abstractNote = {},
doi = {10.1128/JB.01858-06},
journal = {Journal of Bacteriology},
number = 4,
volume = 189,
place = {United States},
year = {Wed Jan 31 00:00:00 EST 2007},
month = {Wed Jan 31 00:00:00 EST 2007}
}
  • We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. All three genomes share a conserved double origin of replication and many gene clusters. M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcinae 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 proximal semi-genome. Of the 3680 open reading frames in M. barkeri,more » 678 had paralogs with better than 80% similarity to both M. acetivorans and M. mazei while 128 nonhypothetical orfs were unique (non-paralogous) amongst these species including a complete formate dehydrogenase operon, two genes required for N-acetylmuramic acid synthesis, a 14 gene gas vesicle cluster and a bacterial P450-specific ferredoxin reductase cluster not previously observed or characterized in this genus. A cryptic 36 kbp plasmid sequence was detected in M. barkeri that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143 nt motif. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the large M. acetivorans is the result of multiple gene-scale insertions and duplications uniformly distributed in that genome, while M. barkeri is characterized by localized inversions associated with the loss of gene content. In contrast, the relatively short M. mazei most closely approximates the ancestral organizational state.« less
  • Methanosarcina barkeri 227 and Methanosarcina mazei S-6 grew with acetate as the substrate; little effect of H/sub 2/ on the rate of aceticlastic growth was found in the presence of various H/sub 2/ pressures between 2 and 810 Pa. Physical (H/sub 2/ addition or flushing the headspace to remove H/sub 2/) and biological (H/sub 2/-producing or -utilizing bacteria in cocultures) methods were used for controlling H/sub 2/ pressure in Methanosarcina cultures growing on acetate. Added H/sub 2/ (ca. 100 Pa) was removed rapidly (a few hours) by M. barkeri and slowly (within a day) by M. mazei. When the H/submore » 2/ produced by the aceticlastic methanogens was removed by coculturing with an H/sub 2/-using Desulfovibrio sp., the H/sub 2/ pressure was about 2.2 Pa. Under these conditions the stoichiometry of aceticlastic methanogenesis did not change. H/sub 2/-grown inocula of M. barkeri grew with acetate as the sole catabolic substrate if the inoculum culture was transferred during logarithmic growth to acetate-containing medium or if the transfer was accomplished with 1 or 2 days after exhaustion of H/sub 2/. H/sub 2/-grown cultures incubated for 4 or more days after exhaustion of H/sub 2/ were able to grow with H/sub 2/ but not with acetate as the sole catabolic substrate. Addition of small quantities of H/sub 2/ to acetate-containing medium permitted these cultures to initiate growth on acetate.« less
  • Summary Methanosarcina barkeri can grow only under strictly anoxic conditions because enzymes in methane formation pathways of are very oxygen sensitive. However, it has been determined that M. barkeri can survive oxidative stress. To obtain further knowledge of cellular changes in M. barkeri in responsive to oxidative and other environmental stress, a first whole-genome M. barkeri oligonucleotide microarray was constructed according to the draft genome sequence that contains 5072 open reading frames (ORFs) and was used to investigate the global transcriptomic response of M. barkeri to oxidative stress and heat shock. The result showed that 552 genes in the M.more » barkeri genome were responsive to oxidative stress, while 177 genes responsive to heat-shock, respectively using a cut off of 2.5 fold change. Among them, 101 genes were commonly responsive to both environmental stimuli. In addition to various house-keeping genes, large number of functionally unknown genes (38-57% of total responsive genes) was regulated by both stress conditions. The result showed that the Hsp60 (GroEL) system, which was previously thought not present in archaea, was up-regulated and may play important roles in protein biogenesis in responsive to heat shock in M. barkeri. No gene encoding superoxide dismutase, catalase, nonspecific peroxidases or thioredoxin reductase was differentially expressed when subjected to oxidative stress. Instead, significant downregulation of house-keeping genes and up-regulation of genes encoding transposase was found in responsive to oxidative stress, suggesting that M. barkeri may be adopting a passive protective mechanism by slowing down cellular activities to survive the stress rather than activating a means against oxidative stress.« less
  • Here, while a few studies on the variations in mRNA expression and half-lives measured under different growth conditions have been used to predict patterns of regulation in bacterial organisms, the extent to which this information can also play a role in defining metabolic phenotypes has yet to be examined systematically. Here we present the first comprehensive study for a model methanogen. As a result, we use expression and half-life data for the methanogen Methanosarcina acetivorans growing on fast- and slow-growth substrates to examine the regulation of its genes. Unlike Escherichia coli where only small shifts in half-lives were observed, wemore » found that most mRNA have significantly longer half-lives for slow growth on acetate compared to fast growth on methanol or trimethylamine. Interestingly, half-life shifts are not uniform across functional classes of enzymes, suggesting the existence of a selective stabilization mechanism for mRNAs. Using the transcriptomics data we determined whether transcription or degradation rate controls the change in transcript abundance. Degradation was found to control abundance for about half of the metabolic genes underscoring its role in regulating metabolism. Genes involved in half of the metabolic reactions were found to be differentially expressed among the substrates suggesting the existence of drastically different metabolic phenotypes that extend beyond just the methanogenesis pathways. By integrating expression data with an updated metabolic model of the organism (iST807) significant differences in pathway flux and production of metabolites were predicted for the three growth substrates. In conclusion, this study provides the first global picture of differential expression and half-lives for a class II methanogen, as well as provides the first evidence in a single organism that drastic genome-wide shifts in RNA half-lives can be modulated by growth substrate. We determined which genes in each metabolic pathway control the flux and classified them as regulated by transcription (e.g. transcription factor) or degradation (e.g. post-transcriptional modification). We found that more than half of genes in metabolism were controlled by degradation. Our results suggest that M. acetivorans employs extensive post-transcriptional regulation to optimize key metabolic steps, and more generally that degradation could play a much greater role in optimizing an organism’s metabolism than previously thought.« less
  • Cited by 5