Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli

Abstract

Methanothermobacter thermautotrophicus strain DeltaH is a model hydrogenotrophic methanogen, for which the complete genome sequence and extensive biochemical information are available. Little is known, however, about how this organism regulates its cellular functions in response to environmental stimuli. In this study, whole-genome oligonucleotide microarrays were constructed for M. thermautotrophicus and used to gain insights into how this organism responds to different environmental stimuli, including hydrogen depletion, shifts in pH and temperature and the occurrence of toxics (hydrogen peroxide and ammonia). Our analysis confirmed that methanogenesis genes (including mtd, mer, frh and mcr) were upregulated under hydrogen-limited conditions, while some of them were affected by other environmental stimuli. Concerning stress responses of this organism, several unique features were revealed. First, there was no universal stress response in this organism. Second, genes for alternative redox enzymes, such as rubrerythrin, were upregulated under the oxidative stress, but those for typical antioxidant enzymes were not. Third, genes relevant to the modification of cell surface structures were differentially expressed under stress conditions. Finally, energy-requiring CO(2) assimilation systems were downregulated under stress conditions. These findings suggest that M. thermautotrophicus has complex transcriptional regulation mechanisms that facilitate it to survive in unstable ecosystems such as an anaerobic digester.

Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses

“…A study on Methanococcus maripaludis (17) showed that the genes coding for enzymes that reduce or oxidize the deazaflavin coenzyme F 420 were significantly upregulated under H 2 limitation. Similar results were observed in several other studies (16,(18)(19)(20)(21)(22)(23). A recent study on M. maripaludis grown syntrophically with Desulfovibrio vulgaris revealed that most of the genes for methanogenesis were upregulated, while those for biosynthetic functions declined compared to levels in monoculture (24).…”

The Methanogen-Specific Transcription Factor MsvR Regulates the fpaA-rlp-rub Oxidative Stress Operon Adjacent to msvR in Methanothermobacter thermautotrophicus

“…1A). Previous studies had shown that the fpaA-rlp-rub operon is upregulated during peroxide (oxidative) stress (10). In another methanogen, a homologue of the flavoprotein was shown to reduce O 2 (24).…”

“…Previous studies have shown peroxide stress has little effect on methane production and overall growth yield in the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus. The same study identified upregulation of the fpaA-rlp-rub operon (mth1350 to mth1352) believed to be involved in the detoxification of reactive oxygen species (10). This operon encodes a flavoprotein (fpaA), a rubrerythrin-like protein (rlp), and a rubredoxin (rub) (10,19).…”

“…The same study identified upregulation of the fpaA-rlp-rub operon (mth1350 to mth1352) believed to be involved in the detoxification of reactive oxygen species (10). This operon encodes a flavoprotein (fpaA), a rubrerythrin-like protein (rlp), and a rubredoxin (rub) (10,19). A homologue of the flavoprotein from the methanogen Methanobrevibacter arboriphilus has been demonstrated to reduce O 2 in the presence of H 2 and was reclassified as an F 420 H 2 oxidase (24).…”

Genomic composition and dynamics amongMethanomicrobialespredict adaptation to contrasting environments

“…Expression studies have shown that one of Mtd or Hmd takes on quantitatively greater importance in response to H 2 limitation, rapid growth rate and syntrophic growth (Hendrickson et al, 2007;Kato et al, 2008;Enoki et al, 2011;Walker et al, 2012). In this study, Mtd was found in all strains, while Hmd was only found in three (Figure 4).…”