Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii

CRIBI Biotechnology Centre, Department of Biology, University of Padua, Via U. Bassi 58/B, 35121 Padova, Italy.
Environmental Microbiology (Impact Factor: 6.2). 11/2010; 13(8):2018-38. DOI: 10.1111/j.1462-2920.2010.02367.x
Source: PubMed


Methanococcoides burtonii is a member of the Archaea that was isolated from Ace Lake in Antarctica and is a valuable model for studying cold adaptation. Low temperature transcriptional regulation of global gene expression, and the arrangement of transcriptional units in cold-adapted archaea has not been studied. We developed a microarray for determining which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Approximately 55% of genes were found to be arranged in operons that range in length from 2 to 23 genes, and mRNA abundance tended to increase with operon length. Analysing microarray data previously obtained by others for Halobacterium salinarum revealed a similar correlation between operon length and mRNA abundance, suggesting that operons may play a similar role more broadly in the Archaea. More than 500 genes were differentially expressed at levels up to ≈ 24-fold. A notable feature was the upregulation of genes involved in maintaining RNA in a state suitable for translation in the cold. Comparison between microarray experiments and results previously obtained using proteomics indicates that transcriptional regulation (rather than translation) is primarily responsible for controlling gene expression in M. burtonii. In addition, certain genes (e.g. involved in ribosome structure and methanogenesis) appear to be regulated post-transcriptionally. This is one of few experimental studies describing the genome-wide distribution and regulation of operons in archaea.

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    • "Studies on cold adaptations of the mesophilic [8]–[10] and psychrophillic bacteria [11], [12] indicated that they are widely heterogeneous in their genomes content and encompass broad ranges of complex network strategies to survive at low temperature. Most cold adaptation comprehensive studies were mainly performed by applying high-throughput genome sequencing [4], [5], [11] and other omics technologies such as proteomics [13], [14] and transcriptomics [15]. In E. coli, it has been shown that under different perturbations (cold, heat, lactose diauxie, and oxidative stress) the metabolite profiles are much more stress-specific when compared with transcriptomic changes [16]. "
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    ABSTRACT: Arctic Mesorhizobium sp. N33 isolated from nodules of Oxytropis arctobia in Canada's eastern Arctic has a growth temperature range from 0°C to 30°C and is a well-known cold-adapted rhizobia. The key molecular mechanisms underlying cold adaptation in Arctic rhizobia remains totally unknown. Since the concentration and contents of metabolites are closely related to stress adaptation, we applied GC-MS and NMR to identify and quantify fatty acids and water soluble compounds possibly related to low temperature acclimation in strain N33. Bacterial cells were grown at three different growing temperatures (4°C, 10°C and 21°C). Cells from 21°C were also cold-exposed to 4°C for different times (2, 4, 8, 60 and 240 minutes). We identified that poly-unsaturated linoleic acids 18∶2 (9, 12) & 18∶2 (6, 9) were more abundant in cells growing at 4 or 10°C, than in cells cultivated at 21°C. The mono-unsaturated phospho/neutral fatty acids myristoleic acid 14∶1(11) were the most significantly overexpressed (45-fold) after 1hour of exposure to 4°C. As reported in the literature, these fatty acids play important roles in cold adaptability by supplying cell membrane fluidity, and by providing energy to cells. Analysis of water-soluble compounds revealed that isobutyrate, sarcosine, threonine and valine were more accumulated during exposure to 4°C. These metabolites might play a role in conferring cold acclimation to strain N33 at 4°C, probably by acting as cryoprotectants. Isobutyrate was highly upregulated (19.4-fold) during growth at 4°C, thus suggesting that this compound is a precursor for the cold-regulated fatty acids modification to low temperature adaptation.
    PLoS ONE 12/2013; 8(12):e84801. DOI:10.1371/journal.pone.0084801 · 3.23 Impact Factor
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    • "Much of the microbial research in Antarctic terrestrial and aquatic ecosystems has focused on the bacterial populations, and to a lesser extent on the archaea [3,4] and viruses [5,6]. In contrast, eukaryotic microorganisms have received much less attention [7]. "
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    ABSTRACT: The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts.
    Biology 03/2013; 2(1):331-40. DOI:10.3390/biology2010331
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    • "However, it is when comparing global responses of an organism to two or more test conditions that transcriptome studies identify profiles of differentially expressed targets in good approximation to that obtained using other “omics” technologies. For instance, reasonably good correlations are observed between differential transcript abundance and differential protein abundance for wild type M. maripaludis versus a mutant deficient in Ehb hydrogenase activity [50], for acetate versus methanol grown M. acetivorans [10] and for M. burtonii grown at 4°C versus 23°C [33]. Thus, methanogens use the regulation of transcript abundance as a major point of gene regulation in response to the environment. "
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    ABSTRACT: Methane-producing Archaea are of interest due to their contribution to atmospheric change and for their roles in technological applications including waste treatment and biofuel production. Although restricted to anaerobic environments, methanogens are found in a wide variety of habitats, where they commonly live in syntrophic relationships with bacterial partners. Owing to tight thermodynamic constraints of methanogenesis alone or in syntrophic metabolism, methanogens must carefully regulate their catabolic pathways including the regulation of RNA transcripts. The transcriptome is a dynamic and important control point in microbial systems. This paper assesses the impact of mRNA (transcriptome) studies on the understanding of methanogenesis with special consideration given to how methanogenesis is regulated to cope with nutrient limitation, environmental variability, and interactions with syntrophic partners. In comparison with traditional microarray-based transcriptome analyses, next-generation high-throughput RNA sequencing is greatly advantageous in assessing transcription start sites, the extent of 5' untranslated regions, operonic structure, and the presence of small RNAs. We are still in the early stages of understanding RNA regulation but it is already clear that determinants beyond transcript abundance are highly relevant to the lifestyles of methanogens, requiring further study.
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