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178. Matsuno T, Yoshimune K, Yumoto I (2011) Physiological function of soluble cytochrome
c-552 from alkaliphilic Pseudomonas alcaliphila AL15-21T. J Bioenerg Biomembr
43:473–481
179. Mulkidjanian AY, Dibrov P, Galperin MY (2008) The past and present of sodium energetics:
may the sodium-motive force be with you. Biochim Biophys Acta 1777:985–992
180. Liu X, Gong X, Hicks DB, Krulwich TA, Yu L, Yu CA (2007) Interaction between cytochrome caa3 and F1F0-ATP synthase of alkaliphilic Bacillus pseudofirmus OF4 is demonstrated by saturation transfer electron paramagnetic resonance and differential scanning
calorimetry assays. Biochemistry 46:306–313
181. Ling HL, Rahmat Z, Bakar FDA, Murad AMA, Illias RM (2018) Secretome analysis of
alkaliphilic bacterium Bacillus lehensis G1 in response to pH changes. Microbiol Res
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182. Saito H, Kobayashi H (2003) Bacterial responses to alkaline stress. Sci Prog 86:271–282
183. Serra-Cardona A, Canadell D, Ariño J (2015) Coordinate responses to alkaline pH stress in
budding yeast. Microb Cell 2:182–196
184. Canadell D, Garcia-Martinez J, Alepuz P, Perez-Ortin JE, Arino J (2015) Impact of high pH
stress on yeast gene expression: a comprehensive analysis of mRNA turnover during stress
responses. Biochim Biophys Acta 1849:653–664
185. Flahaut S, Hartke A, Giard JC, Auffray Y (1997) Alkaline stress response in Enterococcus
faecalis: adaptation, cross-protection, and changes in protein synthesis. Appl Environ
Microbiol 63:812–814
186. Clarke S, Stephenson RC, Lowenson JD (1992) Lability of asparagine and aspartic acid
residues in proteins and peptides. In: Ahern TJ, Manning MC (eds) Stability of protein
pharmaceuticals, part A: chemical and physical pathways of protein degradation. Plenum,
New York, pp 1–29
187. Shimizu T, Matsuoka Y, Shirasawa T (2005) Biological significance of isoaspartate and its
repair system. Biol Pharm Bull 28:1590–159610
188. Szymanska G, Leszyk JD, O’Connor CM (1998) Carboxyl methylation of deamidated calmodulin increases its stability in Xenopus oocyte cytoplasm: implications for protein repair.
J Biol Chem 273:28516–28523
189. Riggs DL, Gomez SV, Julian RR (2017) Sequence and solution effects on the prevalence of
d-isomers produced by deamidation. ACS Chem Biol 12:2875–2882
190. Yang H, Zubarev RA (2010) Mass spectrometric analysis of asparagine deamidation and
aspartate isomerization in polypeptides. Electrophoresis 31:1764–1772
191. Visick JE, Clarke S (1995) Repair, refold, recycle: how bacteria can deal with spontaneous and
environmental damage to proteins. Mol Microbiol 16:835–845
192. Li C, Clarke S (1992) Distribution of an L-isoaspartyl protein methyltransferase in eubacteria.
J Bacteriol 174:355–361
193. Visick JE, Cai H, Clarke S (1998) The L-isoaspartyl protein repair methyltransferase enhances
survival of aging Escherichia coli subjected to secondary environmental stresses. J Bacteriol
180:2623–2629
194. Johnson BA, Shirokawa JM, Aswad DW (1989) Deamidation of calmodulin at neutral and
alkaline pH: quantitative relationships between ammonia loss and the susceptibility of calmodulin to modification by protein carboxyl methyltransferase. Arch Biochem Biophys
268:276–286
195. Suh MJ, Alami H, Clark DJ, Parmar PP, Robinson JM, Huang ST et al (2008) Widespread
occurrence of non-enzymatic deamidations of asparagine residues in Yersinia pestis proteins
resulting from alkaline pH membrane extraction conditions. Open Proteomics J 1:106–115
196. Yan Q, Huang M, Lewis MJ, Hu P (2018) Structure based prediction of asparagine
deamidation propensity in monoclonal antibodies. MAbs 10:901–912
130
G. Mamo
proton motive force under low-aeration alkaline conditions in alkaliphilic bacteria. Front
Microbiol 9:2331. https://doi.org/10.3389/fmicb.2018.02331
178. Matsuno T, Yoshimune K, Yumoto I (2011) Physiological function of soluble cytochrome
c-552 from alkaliphilic Pseudomonas alcaliphila AL15-21T. J Bioenerg Biomembr
43:473–481
179. Mulkidjanian AY, Dibrov P, Galperin MY (2008) The past and present of sodium energetics:
may the sodium-motive force be with you. Biochim Biophys Acta 1777:985–992
180. Liu X, Gong X, Hicks DB, Krulwich TA, Yu L, Yu CA (2007) Interaction between cytochrome caa3 and F1F0-ATP synthase of alkaliphilic Bacillus pseudofirmus OF4 is demonstrated by saturation transfer electron paramagnetic resonance and differential scanning
calorimetry assays. Biochemistry 46:306–313
181. Ling HL, Rahmat Z, Bakar FDA, Murad AMA, Illias RM (2018) Secretome analysis of
alkaliphilic bacterium Bacillus lehensis G1 in response to pH changes. Microbiol Res
215:46–54
182. Saito H, Kobayashi H (2003) Bacterial responses to alkaline stress. Sci Prog 86:271–282
183. Serra-Cardona A, Canadell D, Ariño J (2015) Coordinate responses to alkaline pH stress in
budding yeast. Microb Cell 2:182–196
184. Canadell D, Garcia-Martinez J, Alepuz P, Perez-Ortin JE, Arino J (2015) Impact of high pH
stress on yeast gene expression: a comprehensive analysis of mRNA turnover during stress
responses. Biochim Biophys Acta 1849:653–664
185. Flahaut S, Hartke A, Giard JC, Auffray Y (1997) Alkaline stress response in Enterococcus
faecalis: adaptation, cross-protection, and changes in protein synthesis. Appl Environ
Microbiol 63:812–814
186. Clarke S, Stephenson RC, Lowenson JD (1992) Lability of asparagine and aspartic acid
residues in proteins and peptides. In: Ahern TJ, Manning MC (eds) Stability of protein
pharmaceuticals, part A: chemical and physical pathways of protein degradation. Plenum,
New York, pp 1–29
187. Shimizu T, Matsuoka Y, Shirasawa T (2005) Biological significance of isoaspartate and its
repair system. Biol Pharm Bull 28:1590–159610
188. Szymanska G, Leszyk JD, O’Connor CM (1998) Carboxyl methylation of deamidated calmodulin increases its stability in Xenopus oocyte cytoplasm: implications for protein repair.
J Biol Chem 273:28516–28523
189. Riggs DL, Gomez SV, Julian RR (2017) Sequence and solution effects on the prevalence of
d-isomers produced by deamidation. ACS Chem Biol 12:2875–2882
190. Yang H, Zubarev RA (2010) Mass spectrometric analysis of asparagine deamidation and
aspartate isomerization in polypeptides. Electrophoresis 31:1764–1772
191. Visick JE, Clarke S (1995) Repair, refold, recycle: how bacteria can deal with spontaneous and
environmental damage to proteins. Mol Microbiol 16:835–845
192. Li C, Clarke S (1992) Distribution of an L-isoaspartyl protein methyltransferase in eubacteria.
J Bacteriol 174:355–361
193. Visick JE, Cai H, Clarke S (1998) The L-isoaspartyl protein repair methyltransferase enhances
survival of aging Escherichia coli subjected to secondary environmental stresses. J Bacteriol
180:2623–2629
194. Johnson BA, Shirokawa JM, Aswad DW (1989) Deamidation of calmodulin at neutral and
alkaline pH: quantitative relationships between ammonia loss and the susceptibility of calmodulin to modification by protein carboxyl methyltransferase. Arch Biochem Biophys
268:276–286
195. Suh MJ, Alami H, Clark DJ, Parmar PP, Robinson JM, Huang ST et al (2008) Widespread
occurrence of non-enzymatic deamidations of asparagine residues in Yersinia pestis proteins
resulting from alkaline pH membrane extraction conditions. Open Proteomics J 1:106–115
196. Yan Q, Huang M, Lewis MJ, Hu P (2018) Structure based prediction of asparagine
deamidation propensity in monoclonal antibodies. MAbs 10:901–912
130
G. Mamo