Discovery of Thermophiles Rich in Protein Disulfide Bonds

Initial structural evidence for disulfide bonding in P. aerophilum. (Adapted from Toth, et al.)
Initial structural evidence for disulfide bonding in P. aerophilum. (Adapted from Toth, et al.)

A simple cysteine-counting procedure detects disulfide bonding in hyperthermophiles. (Adapted from Mallick, et al.)
A simple cysteine-counting procedure detects disulfide bonding in hyperthermophiles. (Adapted from Mallick, et al.)

The cytosolic environment of most well-studied organisms is chemically reducing. As a result, stabilizing disulfide bonds are generally absent from cytosolic proteins, though they are abundant in extracellular proteins, including those that are secreted and those that reside in the bacterial periplasmic space. However, this simplistic textbook view of protein disulfide bonding is apparently violated by certain organisms. Based upon a crystal structure of a hyperthermophilic protein he determined as a student in 2000, Eric Toth predicted that certain thermophiles are able to use disulfide bonding to stabilize their proteins against extreme conditions. This claim was supported by Parag Mallick in 2002 using computational approaches, and has since been validated by multiple subsequent studies. The various studies included: a simple cysteine-counting exercise (which showed that hyperthermophilic archaea show a clear abundance of proteins having an even number of cysteine residues), genome-wide sequence-structure mapping calculations (which showed a striking tendency of cysteine residues to be near other cysteine residues in these organisms), and 2D oxidized-reduced SDS gels (which showed an abundance of proteins and protein-complexes held together by disulfide bonds.

A genome-wide sequence-structure mapping approach shows clear evidence for widespread disulfide bonding in hyperthermophiles. The right panel highlights the tendency of cysteine residues to be mapped into proximity of other cysteine residues in proteins from P. aerophilum. (Adapted from Mallick, et al. and Beeby, et al.)
A genome-wide sequence-structure mapping approach shows clear evidence for widespread disulfide bonding in hyperthermophiles. The right panel highlights the tendency of cysteine residues to be mapped into proximity of other cysteine residues in proteins from P. aerophilum. (Adapted from Mallick, et al. and Beeby, et al.)

The widespread occurrence of disulfide bonds in these organisms helps explain the puzzle of how their proteins are stabilized under such extreme conditions. It also paints a picture of protein disulfide bonding and cellular redox state that is more complex than previously anticipated. Our future efforts aim to exploit the expected presence of disulfide bonds in proteins from these organisms to boost protein structure prediction algorithms.

A 2D (oxidized-reduced) SDS gel of P. aerophilum lysate. (Adapted from Boutz, et al.)
A 2D (oxidized-reduced) SDS gel of P. aerophilum lysate. (Adapted from Boutz, et al.)

A current archaeal tree colored by optimal growth temperature (red) and predicted protein disulfide abundance (green) based on genomic calculations. The Crenarchaea are blue. (Adapted from Jorda, et al.)
A current archaeal tree colored by optimal growth temperature (red) and predicted protein disulfide abundance (green) based on genomic calculations. The Crenarchaea are blue. (Adapted from Jorda, et al.)

References:

2011

Jorda J, Yeates TO
Widespread disulfide bonding in proteins from thermophilic archaea.
Archaea. 2011. 2011:409156. 2011 PMID: 21941460
PMC3177088 10.1155/2011/409156

2007

Boutz DR, Cascio D, Whitelegge J, Perry LJ, Yeates TO
Discovery of a thermophilic protein complex stabilized by topologically interlinked chains.
J. Mol. Biol.. May 2007. 368(5):1332-44. 2007 PMID: 17395198
PMC1955483 10.1016/j.jmb.2007.02.078 NIHMS22846

2005

Beeby M, O’Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO
The genomics of disulfide bonding and protein stabilization in thermophiles.
PLoS Biol.. Sep 2005. 3(9):e309. 2005 PMID: 16111437
PMC1188242 10.1371/journal.pbio.0030309

2002

Mallick P, Boutz DR, Eisenberg D, Yeates TO
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds.
Proc. Natl. Acad. Sci. U.S.A.. Jul 2002. 99(15):9679-84. 2002 PMID: 12107280
PMC124975 10.1073/pnas.142310499

structural, computational, and synthetic biology