Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

The genome sequence of the extremely thermophilic archaeon Methanococcus ja nnaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs front mesophilic Methanococcus species. Although the growth tempe ratures of the mesophiles are about 50 degrees C below that of M. jannaschi i, their genomic G + C contents are nearly identical. The properties most c orrelated with the proteins of the thermophile include higher residue volum e, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and few er uncharged polar residues (Ser, Thr, Asn, and Gln ). These are recurring themes, with all trends applying to 83-92% of the pr oteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature chang e are the same relatively conservative changes observed in all proteins, bu t in the case of the mesophile/thermophile comparison there is a directiona l bias. We identify 26 specific pairs of amino acids with a statistically s ignificant (P < 0.01) preferred direction of replacement.