Featured Article - February 2010
Short description: Salt-loving archaea use small negative amino acids to survive hostile conditions.
Some organisms thrive in very salty conditions such as the Great Salt Lake in Utah or the Dead Sea at the mouth of the river Jordan. Salt-loving (halophilic) archaea have evolved to cope with this environment and their proteins have adapted to what would normally be destabilizing conditions.
Halophilic proteins have a characteristic, biased, amino-acid composition, favoring glutamic acids and shunning lysines on their surface. This results in an increased negative surface charge, but how does this help the proteins maintain their structure in salty conditions? Oscar Millet and team report in PLoS Biology that the small size of these amino acids is the key to survival.
The team carried out extensive site-directed mutagenesis on three proteins: a halophile, the homologous domain from a mesophile (an organism that thrives in the absence of salt) and an unrelated mesophile protein. Specifically, they looked at the 1A domain of NAD+-dependent DNA ligase N from the halophilic archaeon Haloferax volcanii; the homologous domain from the mesophilic bacterium Escherichia coli and the IgG-binding domain of protein L (ProtL) from another mesophile, Streptococcus magnus.
Millet and colleagues mutated the surface residues aspartic acid, glutamic acid, lysine, arginine, serine and glutamine, and grouped the mutations into three types —charge-preserving, size-preserving, and mutations that change both shape and size — in order to study their structural and thermodynamic effects.
In particular, they made multiple mutations in the mesophilic ProtL domain and determined the high-resolution NMR structures of two highly mutated forms. Kx6E is made by mutating six lysine residues to glutamic acid, and is only stable in halophilic conditions. Its structure was solved in 500 mM sodium chloride (PDB 2KAC). Kx5Q by contrast has five lysines replaced with glutamines (PDB 2JZP) and was solved in low salt conditions. Despite the different buffer conditions, the structures are very similar to the wild type (PDB 1HZ6), and no new inter-side-chain interactions are seen, so the halophilicity of Kx6E must originate elsewhere.
Millet's team used the structural data to calculate the solvent-accessible area of the proteins, and found that the increase in halophilicity correlated well with a decrease in side-chain solvent-accessible area. Thus the abundance of glutamic acids at the surface of halophilic proteins can be explained in terms of their size, rather than their charge. Their smaller size decreases the solvent-accessible area, meaning that fewer water molecules are needed to solvate the protein. This appears to be the key to haloadaptation.
But that leaves the puzzle of why small charged residues are preferred and not small neutral residues. This is probably because these charged residues reduce protein aggregation and lower the isoelectric point for solubility.
X. Tadeo et al. Structural basis for the aminoacid composition of proteins from halophilic archea.
PLoS Biol. 7, e1000257 (2009). doi:10.1371/journal.pbio.1000257