Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity

PloS One
Anna PopinakoVladimir O Popov

Abstract

Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl). To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed. The following adaptation strategies were observed: (1) strategies specific for halophilic and alkaliphilic proteins (an increase in the number of aspartate and glutamate residues and a decrease in the number of lysine residues on the protein surface), (2) strategies specific for halophilic proteins (an increase in the arginine content and a decrease in the number of hydrophobic residues on the solvent-accessible protein surface), (3) strategies specific for alkaliphilic proteins (an increase in the area of intersubunit hydrophobic contacts). Unique adaptation mechanism inherent in the ONRs from bacteria of genus Thioalkalivibrio was re...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Jun 20, 1993·Journal of Molecular Biology·R A LaskowskiJ M Thornton
Jun 23, 1998·The Journal of Biological Chemistry·G B McGaugheyA K Rappé
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Oct 12, 2000·Biophysical Chemistry·M MevarechL M Gloss
Mar 12, 2003·Journal of Molecular Biology·Satoshi FukuchiKen Nishikawa
Dec 6, 2003·International Journal of Systematic and Evolutionary Microbiology·Dimitry Yu SorokinJ Gijs Kuenen
Dec 31, 2003·Methods in Enzymology·András Fiser, Andrej Sali
Jun 29, 2004·Extremophiles : Life Under Extreme Conditions·Dominique MadernGiuseppe Zaccai
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Jul 5, 2006·Journal of Bioinformatics and Computational Biology·Anna KaryaginaAndrei Alexeevski
Jun 23, 2007·Nucleic Acids Research·K G TinaN Srinivasan
Aug 7, 2007·International Journal of Biological Macromolecules·Panagiotis L KastritisStavros J Hamodrakas
Aug 9, 2008·The Journal of Biological Chemistry·Vitaly A SelivanovTatyana V Votyakova
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
May 27, 2010·Nucleic Acids Research·M L HekkelmanG Vriend
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Oct 1, 2011·Nature Methods·Thomas Nordahl PetersenHenrik Nielsen
Oct 11, 2011·International Journal of Systematic and Evolutionary Microbiology·Dimitry Y SorokinGerard Muyzer
Dec 24, 2011·BMC Structural Biology·Alessandro SiglioccoloStefano Pascarella
Sep 14, 2013·Journal of Biomolecular Structure & Dynamics·Dmitry SuplatovVytas Svedas
Oct 24, 2013·Archaea : an International Microbiological Journal·Christopher J ReedCaryn Evilia
Mar 5, 2014·Biochimica Et Biophysica Acta·Giuseppe Graziano, Antonello Merlino
Sep 10, 2013·Journal of Chemical Theory and Computation·Romelia Salomon-FerrerRoss C Walker
Dec 22, 2015·Nature Communications·Andrew C WardenVictoria S Haritos
Feb 3, 2016·Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials·Guoshun ZhangYang Lu

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Methods Mentioned

BETA
differential
circular dichroism
X-ray

Software Mentioned

COFFEE
SignalP
PROCHECK
MEGA6
haONR
Chimera
MODELLER
Zebra
GeneDoc
STATISTICA

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