Methanococcus maripaludis S2
Refseq: NC_005791
NCBI taxonomy ID: 267377
Overview
Our laboratories have made substantial progress in the physiology and systems biology of the hydrogenotrophic methanogens. We focus on the species Methanococcus maripaludis, which we developed as the premier model for the hydrogenotrophic methanogens. M. maripaludis is distinguished by rapid and reliable growth in the laboratory and an excellent set of genetic tools. Its genome is small (1.7 Mb) and straight-forward to study and both transcriptomics and proteomics have been highly effective. Our recent progress (detailed below) includes the generation of the first comprehensive transcriptome map for a hydrogenotrophic methanogen. We have also conducted extensive studies of the proteome, which have culminated in the generation of a peptide atlas (described below). We expect to generate an initial regulatory network model by the end of the current grant period. Hence, we have established a solid basis for continued systems biological studies.
Foundation for Systems Biology of Methanococcus maripaludis S2
Genome Sequence and Annotations
Methanococcus maripaludis possesses a small, circular genome of 1.66 Mb in length with no extrachromosomal elements. The genome has a low, 33%, GC content. Open reading frame predictions indicate 1722 orfs. The maripaludis genome is relatively simple with few repeated sequences, though it contains three copies of the 16S and 23S ribosomal genes. Interestingly, while the genome of the closely related Methanocaldococcus jannaschii contains a number of inteins, maripaludis appears to lack inteins entirely, even in orfs that are otherwise highly homologous to their M. jannaschii counterparts.
The complete M. maripaludis genome sequence is available at NCBI, and its accession number is NC_005791. The sequence was obtained at the University of Washington Genome Center under the direction of Maynard Olson. The computational phase of the annotation was carried out at the Oak Ridge National Laboratory under the supervision of Frank Larimer.
[Content from HP of John Leigh Lab at UW]
Transcriptome structure and Peptide Atlas
We determined transcriptome structure (TS) of Methanococcus maripaludis by high-resolution tiling microarray (Agilent e-Array) which contained 244K of 60-mer probes tiling every 14 nt. The transcript boundaries were identified by integrating relative expression changes of probes complementary to the site across the growth curve, their log intensities in reference-RNA, and their correlation of growth-related transcriptional change. Using the Gaggle Genome Browser, the tiling array data was plotted against coordinates on the genome and demarcation of a transcript unit was manually curated. This analysis identified 1,005 transcriptional units of which 294 were polycistronic transcripts and 711 were monocistronic, in which 769 transcription start sites (TSSs) and 689 transcription termination sites (TTSs) were determined (Table 1).