A Functional Approach To Uncover the Low-Temperature Adaptation Strategies of the Archaeon Methanosarcina barkeri

Gunnigle, Eoin; McCay, Paul B.; Fuszard, Matthew; Botting, Catherine H.; Abram, Florence; O'Flaherty, Vincent

doi:10.1128/aem.03787-12

Cited by 26 publications

(15 citation statements)

References 50 publications

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“…This indicated that the cold adaptation of the two pathways may be at the mRNA level, namely, mtaA1 and mtaC1B1 expression was more cold adaptive than that of ackA and pta at the transcriptional level. A recent proteomics study (29) also showed the upregulation of the MtaC protein in the 15°C culture of Methanosarcina barkeri. mtaA1 and mtaC1B1 transcripts possessed high stabilities at both temperatures, while the pta-ackA transcript possessed reduced stability at low temperatures.…”

Section: Resultsmentioning

confidence: 99%

Mechanism for Stabilizing mRNAs Involved in Methanol-Dependent Methanogenesis of Cold-Adaptive Methanosarcina mazei zm-15

Cao

Jiang

et al. 2014

Appl Environ Microbiol

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Methylotrophic methanogenesis predominates at low temperatures in the cold Zoige wetland in Tibet. To elucidate the basis of cold-adapted methanogenesis in these habitats, Methanosarcina mazei zm-15 was isolated, and the molecular basis of its cold activity was studied. For this strain, aceticlastic methanogenesis was reduced 7.7-fold during growth at 15°C versus 30°C. Methanol-derived methanogenesis decreased only 3-fold under the same conditions, suggesting that it is more cold adaptive. Reverse transcription-quantitative PCR (RT-qPCR) detected <2-fold difference in the transcript abundances of mtaA1, mtaB1, and mtaC1, the methanol methyltransferase (Mta) genes, in 30°C versus 15°C culture, while ackA and pta mRNAs, encoding acetate kinase (Ack) and phosphotransacetylase (Pta) in aceticlastic methanogenesis, were 4.5-and 6.8-fold higher in 30°C culture than in 15°C culture. The in vivo half-lives of mtaA1 and mtaC1B1 mRNAs were similar in 30°C and 15°C cultures. However, the ptaackA mRNA half-life was significantly reduced in 15°C culture compared to 30°C culture. Using circularized RNA RT-PCR, large 5= untranslated regions (UTRs) (270 nucleotides [nt] and 238 nt) were identified for mtaA1 and mtaC1B1 mRNAs, while only a 27-nt 5= UTR was present in the pta-ackA transcript. Removal of the 5= UTRs significantly reduced the in vitro half-lives of mtaA1 and mtaC1B1 mRNAs. Remarkably, fusion of the mtaA1 or mtaC1B1 5= UTRs to pta-ackA mRNA increased its in vitro half-life at both 30°C and 15°C. These results demonstrate that the large 5= UTRs significantly enhance the stability of the mRNAs involved in methanol-derived methanogenesis in the cold-adaptive M. mazei zm-15.

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Section: Resultsmentioning

confidence: 99%

Mechanism for Stabilizing mRNAs Involved in Methanol-Dependent Methanogenesis of Cold-Adaptive Methanosarcina mazei zm-15

Cao

Jiang

et al. 2014

Appl Environ Microbiol

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“…Species of Methanosarcina are metabolically versatile and can grow on methanol (+/ − H 2 ) or methylamines in addition to acetate or H 2 -CO 2 (Maestrojuán and Boone, 1991;Gunnigle et al, 2013). The ability to use different methanogenic substrates would be advantageous for Methanosarcina under the substrate limited conditions of peat.…”

Section: Active Archaeal Taxa In Anoxic Microcosmsmentioning

confidence: 99%

Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens

et al. 2016

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Syntrophic bacteria drive the anaerobic degradation of certain fermentation products (e.g., butyrate, ethanol, propionate) to intermediary substrates (e.g., H 2 , formate, acetate) that yield methane at the ecosystem level. However, little is known about the in situ activities and identities of these syntrophs in peatlands, ecosystems that produce significant quantities of methane. The consumption of butyrate, ethanol or propionate by anoxic peat slurries at 5 and 15°C yielded methane and CO 2 as the sole accumulating products, indicating that the intermediates H 2 , formate and acetate were scavenged effectively by syntrophic methanogenic consortia. 16S rRNA stable isotope probing identified novel species/strains of Pelobacter and Syntrophomonas that syntrophically oxidized ethanol and butyrate, respectively. Propionate was syntrophically oxidized by novel species of Syntrophobacter and Smithella, genera that use different propionate-oxidizing pathways. Taxa not known for a syntrophic metabolism may have been involved in the oxidation of butyrate (Telmatospirillum-related) and propionate (unclassified Bacteroidetes and unclassified Fibrobacteres). Gibbs free energies (ΔGs) for syntrophic oxidations of ethanol and butyrate were more favorable than ΔGs for syntrophic oxidation of propionate. As a result of the thermodynamic constraints, acetate transiently accumulated in ethanol and butyrate treatments but not in propionate treatments. Aceticlastic methanogens (Methanosarcina, Methanosaeta) appeared to outnumber hydrogenotrophic methanogens (Methanocella, Methanoregula), reinforcing the likely importance of aceticlastic methanogenesis to the overall production of methane. ΔGs for acetogenesis from H 2 to CO 2 approximated to − 20 kJ mol − 1 when acetate concentrations were low, indicating that acetogens may have contributed to the flow of carbon and reductant towards methane.

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“…Recently, spectral counting, differential isotopic labelling strategies as well as label‐free quantitation were employed to study oxidative stress, the impact of individual mutations, or the exponential‐stationary growth phase transition, respectively, in Haloferax . Additional publications cover topics at the intersection of proteomics and the stress response for other archaea …”

Section: Introductionmentioning

confidence: 99%

The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label‐Free Mass Spectrometry

et al. 2019

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In-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii has been performed under standard, low/high salt, and low/high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high-pH/reversed-phase fractionated samples indicates 61.1% proteome coverage (2509 proteins), which is close to the maximum recorded values in archaea. Identified proteins match to the predicted proteome in their physicochemical properties, with only a small bias against low-molecular-weight and membrane-associated proteins. Cells grown under low and high salt stress as well as low and high temperature stress are quantitatively compared to standard cultures by sequential window acquisition of all theoretical mass spectra (SWATH-MS). A total of 2244 proteins, or 54.7% of the predicted proteome, are quantified across all conditions at high reproducibility, which allowed for global analysis of protein expression changes under these stresses. Of these, 2034 are significantly regulated under at least one stress condition. KEGG pathway enrichment analysis shows that several major cellular pathways are part of H. volcanii's universal stress response. In addition, specific pathways (purine, cobalamin, and tryptophan) are affected by temperature stress. The most strongly downregulated proteins under all stress conditions, zinc finger protein HVO_2753 and ribosomal protein S14, are found oppositely regulated to their immediate genetic neighbors from the same operon.

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A Functional Approach To Uncover the Low-Temperature Adaptation Strategies of the Archaeon Methanosarcina barkeri

Cited by 26 publications

References 50 publications

Mechanism for Stabilizing mRNAs Involved in Methanol-Dependent Methanogenesis of Cold-Adaptive Methanosarcina mazei zm-15

Mechanism for Stabilizing mRNAs Involved in Methanol-Dependent Methanogenesis of Cold-Adaptive Methanosarcina mazei zm-15

Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens

The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label‐Free Mass Spectrometry

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