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

Michelle A Allen, Federico M Lauro, Timothy J Williams, Dominic Burg, Khawar S Siddiqui, Davide De Francisci, Kevin W Y Chong, Oliver Pilak, Hwee H Chew, Matthew Z De Maere, Lily Ting, Marilyn Katrib (+12 others)
2009 The ISME Journal  
30 35 40 45 50 55 60 Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene
more » ... product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high "IQ" (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from εand δ-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine, to an Antarctic lake environment. Materials and Methods Genome sequencing, assembly, automated annotation DNA was isolated from M. burtonii DSM 6242 grown at 23°C [42]. The genome of M. burtonii was sequenced at the Joint Genome Institute (JGI) using a combination of 3 kb, 8 kb and 40 kb DNA libraries. All general aspects of library construction and sequencing can be found at the JGI's website (http://www.jgi.doe.gov/). The Phred/Phrap/Consed software package (www.phrap.com) was used to assemble all three libraries and to assess quality [43-45]. Possible mis-assemblies were corrected, and gaps between contigs were closed by editing in Consed, custom primer walks, or PCR amplification. The error rate of the completed genome sequence of M.burtonii is less than 1 in 50,000. Putative coding regions were identified using Critica [46], Generation and Glimmer [47], with automated annotation of proteins according to search results from the databases TIGRFam, PRIAM, Pfam, Smart, COGs, Swiss-Prot/TrEMBL and KEGG, as described for other JGI genomes [eg. 48]. Additional curation involved the calculation of homolog, paralog and ortholog gene relationships, and generation of genome statistics. A round of manual curation was performed on the predicted genes of M. burtonii by IMG staff in which 346 changes were made. This corresponds to 13.9% of 120 125 755 760 765 770 775 780
doi:10.1038/ismej.2009.45 pmid:19404327 fatcat:7fe7yj7jtbgfrprp4q2r7kw52u