Biology of the Cold Adapted Archaeon, Methanococcoides burtonii Determined by Proteomics Using Liquid Chromatography-Tandem Mass Spectrometry

Abstract

Genome sequence data of the cold-adapted archaeon, Methanococcoides burtonii, was linked to liquid chromatography-mass spectrometry analysis of the expressed-proteome to define the key biological processes functioning at 4 degrees C. 528 proteins ranging in pI from 3.5 to 13.2, and 3.5-230 kDa, were identified. 133 identities were for hypothetical proteins, and the analysis of these is described separately (Goodchild et al. manuscript in preparation). DNA replication and cell division involves eucaryotic-like histone and MC1-family DNA binding proteins, and 2 bacterial-like FtsZ proteins. Eucaryotic-like, core RNA polymerase machinery, a bacterial-like antiterminator, and numerous bacterial-like regulators enable transcription. Motility involves flagella synthesis regulated by a bacterial-like chemotaxis system. Lsmalpha and Lsmgamma were coexpressed raising the possibility of homo- and hetero-oligomeric complexes functioning in RNA processing. Expression of FKBP-type and cyclophilin-type peptidyl-prolyl cis-trans isomerases highlights the importance of protein folding, and novel characteristics of folding in the cold. Thirteen proteins from a superoperon system encoding proteasome and exosome subunits were expressed, supporting the functional interaction of transcription and translation pathways in archaea. Proteins involved in every step of methylotropic methanogenesis were identified. CO(2) appears to be fixed by a modified Calvin cycle, and by carbon monoxide dehydrogenase. Biosynthesis involves acetyl-CoA conversion to pyruvate by a non-oxidative pentose phosphate pathway, and gluconeogenesis for the conversion of pyruvate to carbohydrates. An incomplete TCA cycle may supply biosynthetic intermediates for amino acid biosynthesis. A novel finding was the expression of Tn11- and Tn12-family transposases, which has implications for genetic diversity and fitness of natural populations. Characteristics of the fundamental cellular processes inferred from the expressed-proteome highlight the evolutionary and functional complexity existing in this domain of life.

Identification of a large noncoding RNA in extremophilic eubacteria

“…3A). This operon could be considered a ''superoperon,'' which is a term that is sometimes used to denote long mRNAs that code for an eclectic mixture of proteins (44)(45)(46). Therefore, the precise role of OLE RNA cannot easily be deduced from the functions of its coexpressed neighbors.…”

Terrestrial models for extraterrestrial life: methanogens and halophiles at Martian temperatures

“…Given the abundance and diversity of Archaea in cold environments (Karner et al 2001;Feller & Gerday 2003), especially in the oceans, our understanding of the genetics and physiology of coldadapted Archaea is surprisingly scarce . Some insights have been obtained on the level of protein structure and function (Schleper et al 1997;Thomas et al 2001;Siddiqui et al 2002), gene regulation (Lim et al 2000;DasSarma 2006), tRNA modification (Noon et al 2004), membrane lipid composition (Nichols et al 2004 ;Gibson et al 2005), proteomics (Goodchild et al 2004a(Goodchild et al , b, 2005Saunders et al 2005) and genomics (Saunders et al 2003) by studying coldadapted Archaea.…”

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat

“…Fn1 did not contain genes encoding ATP citrate synthase and lyase (which catalyzes the cleavage of citrate into acetyl coenzyme A (acetylCoA) and oxaloacetate in a CoA-and ATP-dependent matter), suggesting that the TCA and reverse TCA cycles are not operative in Fn1. Instead, Fn1 contains an incomplete reverse TCA cycle as seen in methanogens (Goodchild et al, 2004). All six carbon fixation pathways known to date (Berg et al, 2010) were incomplete or undetectable in Fn1 (Supplementary Figure S5a).…”