Aquifex pyrophilus is one of the hyperthermophilic bacteria that can g
row at temperatures up to 95 degrees C. To obtain information about it
s genomic structure, random sequencing was performed on plasmid librar
ies containing 0.5-2kb genomic DNA fragments of A. pyrophilus. Compari
son of the obtained sequence tags with known proteins revealed that 12
3 tags showed strong similarity to previously identified proteins in t
he PIR or Genebank databases. These included three proteases, two amin
o acid racemases, and three enzymes utilizing oxygen as substrate. Alt
hough the GC ratio of the genome is about 30%, the codon usage of A. p
yrophilus showed biased occurrence of G and C at the third position of
codons, especially those for amino acids such as asparagine, aspartic
acid, cysteine, glutamine, glutamic, acid, histidine, lysine, and tyr
osine. A higher ratio of positively charged amino acids in A. pyrophil
us proteins as compared with proteins from mesophiles suggested that A
quifex proteins might contain increased ion-pair interaction that coul
d help to maintain heat stability.