Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea
Joudeh, Luay I.
Sobhy, Mohamed Abdelmaboud
Di Fabrizio, Enzo M.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Physical Sciences and Engineering (PSE) Division
Chemical and Biological Engineering Program
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
KAUST Catalysis Center (KCC)
MetadataShow full item record
AbstractThe deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein’s surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt-induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of KOD DNA polymerase.—Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., Akal, A., Sakashita, K., Alam, I., Tehseen, M., Sobhy, M. A., Stingl, U., Merzaban, J. S., Di Fabrizio, E., Hamdan, S. M. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.
CitationTakahashi M, Takahashi E, Joudeh LI, Marini M, Das G, et al. (2018) Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea. The FASEB Journal: fj.201700862RR. Available: http://dx.doi.org/10.1096/fj.201700862rr.
SponsorsThe authors thank the King Abdullah University of Science and Technology (KAUST) BioScience Core Laboratory for providing Pfu polymerase. This research was funded by the Saudi Economic and Development Company (SEDCO) Research Excellence Project and baseline funding from KAUST to S.M.H. The authors declare no conflicts of interest.
JournalThe FASEB Journal
- Structure and activity of malate dehydrogenase from the extreme halophilic bacteria of the Dead Sea. 1. Conformation and interaction with water and salt between 5 M and 1 M NaCl concentration.
- Authors: Pundak S, Eisenberg H
- Issue date: 1981 Sep 1
- Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii.
- Authors: Pieper U, Kapadia G, Mevarech M, Herzberg O
- Issue date: 1998 Jan 15
- Electrostatic contributions to the stability of halophilic proteins.
- Authors: Elcock AH, McCammon JA
- Issue date: 1998 Jul 24
- The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation.
- Authors: Winter JA, Christofi P, Morroll S, Bunting KA
- Issue date: 2009 Aug 22
- A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea.
- Authors: Sayed A, Ghazy MA, Ferreira AJ, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JA, Bajic VB, Siam R, El-Dorry H
- Issue date: 2014 Jan 17