Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea

Handle URI:
http://hdl.handle.net/10754/626952
Title:
Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea
Authors:
Takahashi, Masateru; Takahashi, Etsuko; Joudeh, Luay I.; Marini, Monica ( 0000-0001-8182-5239 ) ; Das, Gobind ( 0000-0003-0942-681X ) ; Elshenawy, Mohamed ( 0000-0002-8599-8388 ) ; Akal, Anastassja; Sakashita, Kosuke ( 0000-0002-7118-5511 ) ; Alam, Intikhab; Tehseen, Muhammad ( 0000-0001-9834-2372 ) ; Sobhy, Mohamed Abdelmaboud; Stingl, Ulrich ( 0000-0002-0684-2597 ) ; Merzaban, Jasmeen S. ( 0000-0002-7276-2907 ) ; Di Fabrizio, Enzo M. ( 0000-0001-5886-4678 ) ; Hamdan, Samir ( 0000-0001-5192-1852 )
Abstract:
The 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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Physical Sciences and Engineering (PSE) Division; Chemical and Biological Engineering Program; Bioscience Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; KAUST Catalysis Center (KCC)
Citation:
Takahashi 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.
Publisher:
FASEB
Journal:
The FASEB Journal
Issue Date:
24-Jan-2018
DOI:
10.1096/fj.201700862rr
Type:
Article
ISSN:
0892-6638; 1530-6860
Sponsors:
The 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.
Additional Links:
http://www.fasebj.org/doi/10.1096/fj.201700862RR
Appears in Collections:
Articles; Bioscience Program; Physical Sciences and Engineering (PSE) Division; Chemical and Biological Engineering Program; KAUST Catalysis Center (KCC); Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorTakahashi, Masateruen
dc.contributor.authorTakahashi, Etsukoen
dc.contributor.authorJoudeh, Luay I.en
dc.contributor.authorMarini, Monicaen
dc.contributor.authorDas, Gobinden
dc.contributor.authorElshenawy, Mohameden
dc.contributor.authorAkal, Anastassjaen
dc.contributor.authorSakashita, Kosukeen
dc.contributor.authorAlam, Intikhaben
dc.contributor.authorTehseen, Muhammaden
dc.contributor.authorSobhy, Mohamed Abdelmabouden
dc.contributor.authorStingl, Ulrichen
dc.contributor.authorMerzaban, Jasmeen S.en
dc.contributor.authorDi Fabrizio, Enzo M.en
dc.contributor.authorHamdan, Samiren
dc.date.accessioned2018-01-30T08:08:08Z-
dc.date.available2018-01-30T08:08:08Z-
dc.date.issued2018-01-24en
dc.identifier.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.en
dc.identifier.issn0892-6638en
dc.identifier.issn1530-6860en
dc.identifier.doi10.1096/fj.201700862rren
dc.identifier.urihttp://hdl.handle.net/10754/626952-
dc.description.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.en
dc.description.sponsorshipThe 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.en
dc.publisherFASEBen
dc.relation.urlhttp://www.fasebj.org/doi/10.1096/fj.201700862RRen
dc.rightsArchived with thanks to The FASEB Journalen
dc.subjectDNA polymerase engineeringen
dc.subjecthalophilic enzymesen
dc.subjectthermophilic enzymesen
dc.subjectstructure dynamismen
dc.subjectstructural adaptationen
dc.titleDynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Seaen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.contributor.departmentChemical and Biological Engineering Programen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.identifier.journalThe FASEB Journalen
dc.eprint.versionPost-printen
dc.contributor.institutionFort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USAen
kaust.authorTakahashi, Masateruen
kaust.authorTakahashi, Etsukoen
kaust.authorJoudeh, Luay I.en
kaust.authorMarini, Monicaen
kaust.authorDas, Gobinden
kaust.authorElshenawy, Mohameden
kaust.authorAkal, Anastassjaen
kaust.authorSakashita, Kosukeen
kaust.authorAlam, Intikhaben
kaust.authorTehseen, Muhammaden
kaust.authorSobhy, Mohamed Abdelmabouden
kaust.authorStingl, Ulrichen
kaust.authorMerzaban, Jasmeen S.en
kaust.authorDi Fabrizio, Enzo M.en
kaust.authorHamdan, Samiren
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