Amino acid substitutions in cold-adapted proteins from Halorubrum lacusprofundi, an extremely halophilic microbe from antarctica

Abstract

The halophilic Archaeon Halorubrum lacusprofundi, isolated from the perennially cold and hypersaline Deep Lake in Antarctica, was recently sequenced and compared to 12 Haloarchaea from temperate climates by comparative genomics. Amino acid substitutions for 604 H. lacusprofundi proteins belonging to conserved haloarchaeal orthologous groups (cHOGs) were determined and found to occur at 7.85% of positions invariant in proteins from mesophilic Haloarchaea. The following substitutions were observed most frequently: (a) glutamic acid with aspartic acid or alanine; (b) small polar residues with other small polar or non-polar amino acids; (c) small non-polar residues with other small non-polar residues; (d) aromatic residues, especially tryptophan, with other aromatic residues; and (e) some larger polar residues with other similar residues. Amino acid substitutions for a cold-active H. lacusprofundi β-galactosidase were then examined in the context of a homology modeled structure at residues invariant in homologous enzymes from mesophilic Haloarchaea. Similar substitutions were observed as in the genome-wide approach, with the surface accessible regions of β-galactosidase displaying reduced acidity and increased hydrophobicity, and internal regions displaying mainly subtle changes among smaller non-polar and polar residues. These findings are consistent with H. lacusprofundi proteins displaying amino acid substitutions that increase structural flexibility and protein function at low temperature. We discuss the likely mechanisms of protein adaptation to a cold, hypersaline environment on Earth, with possible relevance to life elsewhere.

Figure 1. Amino acid substitution matrix of selected core haloarchaeal orthologous proteins for invariant residues in mesophilic versus cold-adapted H. lacusprofundi.

Amino acids conserved in 604 protein families in 12 mesophilic sequences are indicated on the right-axis, H. lacusprofundi amino acids are on left-axis, and the number of amino acid substitutions on the vertical axis, with the floor placed at 35 amino acids, to emphasize higher peaks.

Figure 2. Amino acid substitution matrix of selected core haloarchaeal orthologous proteins for invariant negatively and positively charged and polar and small non-polar residues in mesophilic versus corresponding cold-adapted H. lacusprofundi proteins.

Amino acids conserved in 604 protein families in 12 mesophilic sequences are indicated on the right-axis, H. lacusprofundi amino acids are on left-axis, and the number of amino acid substitutions on the vertical axis, with higher peaks (>10) colored for emphasis.

Figure 3. Amino acid substitution matrix of selected core haloarchaeal orthologous proteins for invariant non-polar residues in mesophilic versus cold-adapted H. lacusprofundi proteins.

Amino acids conserved in 604 protein families in 12 mesophilic sequences are shown on the right-axis, H. lacusprofundi amino acids are on left-axis, and the number of amino acid substitutions on the vertical axis, with higher peaks (>10) colored for emphasis.

Figure 4. Model of H. lacusprofundi β-galactosidase highlighting differences with mesophilic Haloarchaea.

The protein backbone is colored gray, substitutions of surface residues are shown colored red, and substitutions of internal residues are shown colored dark blue. The protein structure was illustrated using Swiss-PDBViewer .