Cold Adaptation of the Antarctic Archaeon, Methanococcoides burtonii Assessed by Proteomics Using ICAT

Abstract

Using isotope coded affinity tag (ICAT) chromatography and liquid chromatography-mass spectrometry, 163 proteins were identified from the cold-adapted archaeon, Methanococcoides burtonii. 14 proteins were differentially expressed during growth at 4 degrees C and 23 degrees C. Knowledge of protein abundance, protein identity and gene arrangement was used to determine mechanisms of cold adaptation. Growth temperature was found to affect proteins involved in energy generation and biosynthesis linked to methanogenesis, membrane transport, transcription and protein folding, as well as affecting the expression of two hypothetical proteins. Pooling the data from this ICAT study with data from a previous two-dimensional gel electrophoresis study highlighted consistencies and differences between the two methods, and led us to conclude that the two approaches were generally complementary. This is the first report of ICAT applied to Archaea, or for the study of cold adaptation in any organism.

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

“…burtonii under laboratory growth conditions (Goodchild et al 2004a;Goodchild et al 2004b;Goodchild et al 2005; Burg D & Williams T, unpublished results).…”

“…BLAST searches against the NCBI nr database and the CAMERA Global Ocean Survey combined assembly ORF peptides database were performed (2 nd May 2008), and any proteins with matches of e-value smaller than 1 x 10 -5 were also discarded in order to obtain the final list of 117 proteins that are unique to M. burtonii. Conserved gene context analysis ) was also used to infer possible functions for 28 proteins that were known from proteomics analysis to be expressed in the cell (Goodchild et al 2004a;Goodchild et al 2004b;Goodchild et al 2005;Saunders et The other over-represented COGs from the Defense mechanisms category were COG0577…”

“…Manual annotation provided a functional annotation (ER4 or higher) for 91 of these (Table SI3). Previous proteomics analyses shows that 30 of the 158 CDSs are expressed in the cell ( [36][37][38] and D. Burg and T. Williams, unpublished results; a total of 1023 proteins detected by proteomics are identified in Table SI5). These include genes involved in diverse cellular processes (e.g.…”

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

“…Also, a peptidyl prolyl isomerase (Mbar_A2249) was upregulated in the phase 2 sample compared to levels in other samples. Although little is known regarding chaperone-like activity of the peptidyl prolyl isomerase, a study on Methanococcoides burtonii reported the upregulation of this protein when the organism was grown at 4°C compared to 26°C (43), therefore suggesting that this protein may play an important role in low-temperature adaptation of M. barkeri. Finally, a DnaK heat shock protein (Mbar_A3433) was found to be upregulated in phase 2, and a proteolysis protein (Mbar_A2503) was found to be upregulated in the phase 3 sample compared to phase 1 samples (Fig.…”

Life in the Cold: Proteomics of the Antarctic Bacterium Pseudoalteromonas haloplanktis

“…On the other hand the major heat shock proteins were identified as strongly cold-repressed proteins in the proteome of P. haloplanktis (or, in other words, they are up-regulated at 18°C). The overexpression of bacterial heat shock proteins at elevated temperatures is well recognized as being indicative of a heat-induced cellular stress (Rosen & Ron, 2002;Goodchild et al, 2005). Although this is obviously relevant for the Antarctic bacterium grown at 18 °C, the implications for the psychrophilic strain appear to be more complex.…”