197. Hicks WM, Kotlajich MV, Visick JE (2005) Recovery from long-term stationary phase and
stress survival in Escherichia coli require the L-isoaspartyl protein carboxyl methyltransferase
at alkaline pH. Microbiology 151:2151–2158
198. Dahl JU, Koldewey P, Salmon L, Horowitz S, Bardwell JCA, Jakob U (2015) HdeB functions
as an acid-protective chaperone in bacteria. J Biol Chem 290:65–75
199. Hong W, Wu YE, Fu X, Chang Z (2012) Chaperone-dependent mechanisms for acid resistance in enteric bacteria. Trends Microbiol 20:328–335
200. Kern R, Malki A, Abdallah J, Tagourti J, Richarme G (2007) Escherichia coli HdeB is an acid
stress chaperone. J Bacteriol 189:603–610
201. Taglicht D, Padan E, Oppenheim AB, Schuldiner S (1987) An alkaline shiftinduces the
heatshock response in Escherichia coli. J Bacteriol 169:885–887
202. Horikoshi K, Akiba T (1982) Alkalophilic microorganisms: a new microbial world. Springer,
Heidelberg
203. Verdolino V, Cammi R, Munk BH, Schlegel HB (2008) Calculation of pKa values of
nucleobases and the guanine oxidation products guanidinohydantoin and spiroiminodihydantoin using density functional theory and a polarizable continuum model. J Phys
Chem B 112:16860–16873
204. Goodson M, Rowbury RJ (1990) Habituation to alkali and increased UV-resistance in DNA
repair-proficient and -deficient strains of Escherichia coli grown at pH 9.0. Lett Appl
Microbiol 11:123–125
205. Dubnovitsky AP, Kapetaniou EG, Papageorgiou AC (2005) Enzyme adaptation to alkaline
pH: atomic resolution (1.08 Å) structure of phosphoserine aminotransferase from Bacillus
alcalophilus. Protein Sci 14:97–110
206. Mamo G, Thunnissen M, Hatti-Kaul R, Mattiasson B (2009) An alkaline active xylanase:
insights into mechanisms of high pH catalytic adaptation. Biochimie 91:1187–1196
207. Shirai T, Ishida H, Noda J, Yamane T, Ozaki K, Hakamada Y, Ito S (2001) Crystal structure of
alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme. J Mol Biol
310:1079–1087
208. Shirai T, Suzuki A, Yamane T, Ashida T, Kobayashi T, Hitomi J, Ito S (1997) High-resolution
crystal structure of M-protease: phylogeny aided analysis of the highalkaline adaptation
mechanism. Protein Eng 10:627–634
209. Zhao Y, Zhang Y, Cao Y, Qi J, Mao L, Xue Y et al (2011) Structural analysis of alkaline
β-mannanase from alkaliphilic Bacillus sp. N16-5: implications for adaptation to alkaline
conditions. PLoS One 6(1):e14608. https://doi.org/10.1371/journal.pone.0014608
210. Geiger T, Clarke S (1987) Deamidation, isomerization, and racemization at asparaginyl and
aspartyl residues in peptides: succinimide-linked reactions that contribute to protein degradation. J Biol Chem 262:785–794
211. Tyler-Cross R, Schirch V (1991) Effects of amino acid sequence, buffers, and ionic strength on
the rate and mechanism of deamidation of asparagine residues in small peptides. J Biol Chem
266:22549–22556
212. Gulich S, Linhult M, Nygren PA, Hober S (2000) Stability towards alkaline conditions can be
engineered into a protein ligand. J Biotechnol 80:169–178
213. Gulich S, Linhult M, Stahl S, Hober S (2002) Engineering streptococcal protein G for
increased alkaline stability. Protein Eng 15:835–842
214. Krulwich TA (2005) Extreme alkaliphiles: experts at alkaline pH homeostasis and able to grow
when cytoplasmic pH rises above the limit for growth of non-alkaliphiles. In: International
symposium on extremophiles and their applications, pp 220–227
215. Schmidt A, Schlacher A, Steiner W, Schwab H, Kratky C (1998) Structure of the xylanase
from Penicillium simplicissimum. Protein Sci 7:2081–2088
216. Mamo G, Hatti-Kaul R, Mattiasson B (2006) A thermostable alkaline active endo-β-1-4xylanase from Bacillus halodurans S7: purification and characterization. Enzym Microb
Technol 39:1492–1498
Challenges and Adaptations of Life in Alkaline Habitats
131
stress survival in Escherichia coli require the L-isoaspartyl protein carboxyl methyltransferase
at alkaline pH. Microbiology 151:2151–2158
198. Dahl JU, Koldewey P, Salmon L, Horowitz S, Bardwell JCA, Jakob U (2015) HdeB functions
as an acid-protective chaperone in bacteria. J Biol Chem 290:65–75
199. Hong W, Wu YE, Fu X, Chang Z (2012) Chaperone-dependent mechanisms for acid resistance in enteric bacteria. Trends Microbiol 20:328–335
200. Kern R, Malki A, Abdallah J, Tagourti J, Richarme G (2007) Escherichia coli HdeB is an acid
stress chaperone. J Bacteriol 189:603–610
201. Taglicht D, Padan E, Oppenheim AB, Schuldiner S (1987) An alkaline shiftinduces the
heatshock response in Escherichia coli. J Bacteriol 169:885–887
202. Horikoshi K, Akiba T (1982) Alkalophilic microorganisms: a new microbial world. Springer,
Heidelberg
203. Verdolino V, Cammi R, Munk BH, Schlegel HB (2008) Calculation of pKa values of
nucleobases and the guanine oxidation products guanidinohydantoin and spiroiminodihydantoin using density functional theory and a polarizable continuum model. J Phys
Chem B 112:16860–16873
204. Goodson M, Rowbury RJ (1990) Habituation to alkali and increased UV-resistance in DNA
repair-proficient and -deficient strains of Escherichia coli grown at pH 9.0. Lett Appl
Microbiol 11:123–125
205. Dubnovitsky AP, Kapetaniou EG, Papageorgiou AC (2005) Enzyme adaptation to alkaline
pH: atomic resolution (1.08 Å) structure of phosphoserine aminotransferase from Bacillus
alcalophilus. Protein Sci 14:97–110
206. Mamo G, Thunnissen M, Hatti-Kaul R, Mattiasson B (2009) An alkaline active xylanase:
insights into mechanisms of high pH catalytic adaptation. Biochimie 91:1187–1196
207. Shirai T, Ishida H, Noda J, Yamane T, Ozaki K, Hakamada Y, Ito S (2001) Crystal structure of
alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme. J Mol Biol
310:1079–1087
208. Shirai T, Suzuki A, Yamane T, Ashida T, Kobayashi T, Hitomi J, Ito S (1997) High-resolution
crystal structure of M-protease: phylogeny aided analysis of the highalkaline adaptation
mechanism. Protein Eng 10:627–634
209. Zhao Y, Zhang Y, Cao Y, Qi J, Mao L, Xue Y et al (2011) Structural analysis of alkaline
β-mannanase from alkaliphilic Bacillus sp. N16-5: implications for adaptation to alkaline
conditions. PLoS One 6(1):e14608. https://doi.org/10.1371/journal.pone.0014608
210. Geiger T, Clarke S (1987) Deamidation, isomerization, and racemization at asparaginyl and
aspartyl residues in peptides: succinimide-linked reactions that contribute to protein degradation. J Biol Chem 262:785–794
211. Tyler-Cross R, Schirch V (1991) Effects of amino acid sequence, buffers, and ionic strength on
the rate and mechanism of deamidation of asparagine residues in small peptides. J Biol Chem
266:22549–22556
212. Gulich S, Linhult M, Nygren PA, Hober S (2000) Stability towards alkaline conditions can be
engineered into a protein ligand. J Biotechnol 80:169–178
213. Gulich S, Linhult M, Stahl S, Hober S (2002) Engineering streptococcal protein G for
increased alkaline stability. Protein Eng 15:835–842
214. Krulwich TA (2005) Extreme alkaliphiles: experts at alkaline pH homeostasis and able to grow
when cytoplasmic pH rises above the limit for growth of non-alkaliphiles. In: International
symposium on extremophiles and their applications, pp 220–227
215. Schmidt A, Schlacher A, Steiner W, Schwab H, Kratky C (1998) Structure of the xylanase
from Penicillium simplicissimum. Protein Sci 7:2081–2088
216. Mamo G, Hatti-Kaul R, Mattiasson B (2006) A thermostable alkaline active endo-β-1-4xylanase from Bacillus halodurans S7: purification and characterization. Enzym Microb
Technol 39:1492–1498
Challenges and Adaptations of Life in Alkaline Habitats
131