Complete Genome Sequence of an Aerobic Hyper-thermophilic Crenarchaeon, Aeropyrum pernix K1

Abstract

The complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1, which optimally grows at 95 degrees C, has been determined by the whole genome shotgun method with some modifications. The entire length of the genome was 1,669,695 bp. The authenticity of the entire sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2,694 open reading frames (ORFs) were assigned. By similarity search against public databases, 633 (23.5%) of the ORFs were related to genes with putative function and 523 (19.4%) to the sequences registered but with unknown function. All the genes in the TCA cycle except for that of alpha-ketoglutarate dehydrogenase were included, and instead of the alpha-ketoglutarate dehydrogenase gene, the genes coding for the two subunits of 2-oxoacid:ferredoxin oxidoreductase were identified. The remaining 1,538 ORFs (57.1%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs suggested that a considerable member of ORFs were generated by sequence duplication. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 47 tRNA genes including 14 genes with intron structures. All the assigned ORFs and RNA coding regions occupied 89.12% of the whole genome. The data presented in this paper are available on the internet homepage (http://www.mild.nite.go.jp).

Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota

“…3). These data are in line with the presence of the biotindependent carboxylases in all Sulfolobales studied so far (Norris et al, 1989;Burton et al, 1999;Ishii et al, 1996;Chuakrut et al, 2003;Hügler et al, 2003a, b;Menendez et al, 1999) as well as with the absence of these proteins and the corresponding genes in the sequenced Desulfurococcales genomes (Hügler et al, 2003a;Jahn et al, 2007;Anderson et al, 2009;Brügger et al, 2007;Kawarabayasi et al, 1999;Podar et al, 2008;Ravin et al, 2009).…”

“…It can grow aerobically or anaerobically by nitrate respiration (Blöchl et al, 1997). The sequence and the annotation of its genome are not available yet, and it is not known if this species contains the genes encoding biotin-dependent carboxylases, though the sequenced genomes of members of the Desulfurococcales lack them (Anderson et al, 2009;Brügger et al, 2007;Kawarabayasi et al, 1999;Podar et al, 2008;Ravin et al, 2009). Moreover, autotrophic pathways functioning in Pyrodictiaceae are completely unknown.…”

Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney

“…In the phylum Crenarchaeota, A. pernix strain K1 T is unique in its strictly aerobic, sulfur-independent and neutrophilic growth. The complete genome sequence of this archaeon was determined for the first time in Crenarchaeota (Kawarabayasi et al, 1999), and a number of molecular biological characterizations of its hyperthermophilic enzymes have been reported (e.g. Sako et al, 1997;Yamano et al, 1999; Tachibana et al, 2000;Hansen et al, 2002;Daimon et al, 2002;Jeon & Ishikawa, 2002).…”

Gene expression and characterization of two 2‐oxoacid:ferredoxin oxidoreductases from Aeropyrum pernix K1

“…Aeropyrum pernix has two putative heterodimeric OFORs, one OFOR, Ape2126/2128, being encoded in open reading frames (ORFs) ape2126 and ape2128, and the other OFOR, Ape1473/1472, in ORFs ape1473 and ape1472, as deduced on recent genome analysis [14]. Since OFORs are usually classified into four categories (POR, VOR, KOR, and IOR) according to the 2-oxoacid specificity, the functions of these two putative OFORs from A. pernix are interesting.…”