60. Hicks AB, Wang Z, Wei Y, Kent R, Guffani AA, Banciu H et al (2003) A tenth atp gene in
the conserved atpI gene of a Bacillus atp operon have a role in Mg
2+ uptake. PNAS
100(18):10213–10218
61. Ko YH, Hong S, Pedersen PL (1999) Chemical mechanism of ATP synthase. Magnesium plays
a pivotal role in formation of the transition state where ATP is synthesized from ADP and
inorganic phosphate. J Biol Chem 274(41):28853–28856
62. McMillan DGG, Keis S, Dimroth P, Cook GM (2007) A specific adaptation in the alpha subunit
of thermoalkaliphilic F1F0-ATP synthase enables ATP synthesis at high pH but not at neutral
pH values. J Biol Chem 282:17395–17404
63. Preiss L, Hicks DB, Suzuki S, Meier T, Krulwich TA (2015) Alkaliphilic bacteria with impact
on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis.
Front Bioeng Biotechnol 3:75
64. Liu J, Fujisawa M, Hicks DB, Krulwich TA (2009) Characterization of the functionally critical
AXAXAXA and PXXEXXP motifs of the ATP synthase c-subunit from an alkaliphilic
Bacillus. J Biol Chem 284:8714–8725
65. Liberton M, Howard Berg R, Heuser J, Roth R, Pakrasi HB (2006) Ultrastructure of the
membrane systems in the unicellular cyanobacterium Synechocystic sp. strain PCC6803.
Protoplasma 227(2–4):129–138
66. Pogoryelov D, Yu J, Meier T, Vonck J, Dimroth P, Muller DJ (2005) The c15 ring of the
Spirulina platensis F-ATP synthase: F1/F0 symmetry mismatch is not obligatory. EMBO Rep 6
(11):1040–1044
67. Hicks DB, Liu J, Fujisawa M, Krulwich TA (2010) F1F0-ATP synthases of alkaliphilic
bacteria: lessons from their adaptations. Biochim Biophys Acta 1797:1362–1377
68. Pogoryelov D, Sudhir PR, Kovacs L, Gombos |, Brown I, Garab G (2003) Sodium dependency
of the photosynthetic electron transport in the alkaliphilic cyanobacterium Arthrospira
platensis. J Bioenerg Biomembr 35(5):427–437
69. Ferguson SA, Keis S, Cook GM (2006) Biochemical and molecular characterization of a Na
+ -
translocating F1F0-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum.
J Bacteriol 188(14):5045–5054
70. Stocker A, Keis S, Vonck J, Cook GM, Dimroth P (2007) The structural basis for unidirectional
rotation of thermoalkaliphilic F1-ATPase. Structure 15(8):904–914
71. Xu X, koyama N, Cui M, Yamagishi A, Nosoh Y, Oshima T (1991) Nucleotide sequence of the
gene encoding NADH dehydrogenase from an alkalophile, Bacillus sp. strain YN-1. J Biochem
109:678–683
72. Heikal A, Nakatani Y, Dunn E, Weimar MR, Day CL, Baker EN, Lott JS, Sazanov LA, Cook
GM (2014) Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane
protein with an essential role in energy generation. Mol Microbiol 91(5):950–964
73. Quirk PG, Hicks DB, Krulwich TA (1993) Cloning of the cta operon from allkaliphilic Bacillus
firmus OF4 and characterization OF the pH-regulated cytochrome caa 3 oxidase it encodes.
J Biol Chem 268(1):678–685
74. Brown KR, Allan BM, Do P, Hegg EL (2002) Identification of novel hemes generated by
heme A synthase: evidence for two successive monooxygenase reactions. Biochemist
41(36):10906–10913
75. Throne-Holst M, Hederstedt L (2000) The Bacillus subtilis ctaB paralogue, yjdK, can complement the heme A synthesis deficiency of a CtaB-deficient mutant. FEMS Microbiol Lett
183(2):247–251
76. Stothard P (2000) The sequence manipulation suite: JavaScript programs for analysing and
formatting protein and DNA sequences. BioTechniques 28:1102–1104
77. Matsuno T, Yumoto I (2015) Bioenergetics and the role of soluble cytochromes c for alkaline
adaptation in gram-negative alkaliphilic Pseudomonas. Biomed Res Int 2015:847945
Genomics of Alkaliphiles
155
the conserved atpI gene of a Bacillus atp operon have a role in Mg
2+ uptake. PNAS
100(18):10213–10218
61. Ko YH, Hong S, Pedersen PL (1999) Chemical mechanism of ATP synthase. Magnesium plays
a pivotal role in formation of the transition state where ATP is synthesized from ADP and
inorganic phosphate. J Biol Chem 274(41):28853–28856
62. McMillan DGG, Keis S, Dimroth P, Cook GM (2007) A specific adaptation in the alpha subunit
of thermoalkaliphilic F1F0-ATP synthase enables ATP synthesis at high pH but not at neutral
pH values. J Biol Chem 282:17395–17404
63. Preiss L, Hicks DB, Suzuki S, Meier T, Krulwich TA (2015) Alkaliphilic bacteria with impact
on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis.
Front Bioeng Biotechnol 3:75
64. Liu J, Fujisawa M, Hicks DB, Krulwich TA (2009) Characterization of the functionally critical
AXAXAXA and PXXEXXP motifs of the ATP synthase c-subunit from an alkaliphilic
Bacillus. J Biol Chem 284:8714–8725
65. Liberton M, Howard Berg R, Heuser J, Roth R, Pakrasi HB (2006) Ultrastructure of the
membrane systems in the unicellular cyanobacterium Synechocystic sp. strain PCC6803.
Protoplasma 227(2–4):129–138
66. Pogoryelov D, Yu J, Meier T, Vonck J, Dimroth P, Muller DJ (2005) The c15 ring of the
Spirulina platensis F-ATP synthase: F1/F0 symmetry mismatch is not obligatory. EMBO Rep 6
(11):1040–1044
67. Hicks DB, Liu J, Fujisawa M, Krulwich TA (2010) F1F0-ATP synthases of alkaliphilic
bacteria: lessons from their adaptations. Biochim Biophys Acta 1797:1362–1377
68. Pogoryelov D, Sudhir PR, Kovacs L, Gombos |, Brown I, Garab G (2003) Sodium dependency
of the photosynthetic electron transport in the alkaliphilic cyanobacterium Arthrospira
platensis. J Bioenerg Biomembr 35(5):427–437
69. Ferguson SA, Keis S, Cook GM (2006) Biochemical and molecular characterization of a Na
+ -
translocating F1F0-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum.
J Bacteriol 188(14):5045–5054
70. Stocker A, Keis S, Vonck J, Cook GM, Dimroth P (2007) The structural basis for unidirectional
rotation of thermoalkaliphilic F1-ATPase. Structure 15(8):904–914
71. Xu X, koyama N, Cui M, Yamagishi A, Nosoh Y, Oshima T (1991) Nucleotide sequence of the
gene encoding NADH dehydrogenase from an alkalophile, Bacillus sp. strain YN-1. J Biochem
109:678–683
72. Heikal A, Nakatani Y, Dunn E, Weimar MR, Day CL, Baker EN, Lott JS, Sazanov LA, Cook
GM (2014) Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane
protein with an essential role in energy generation. Mol Microbiol 91(5):950–964
73. Quirk PG, Hicks DB, Krulwich TA (1993) Cloning of the cta operon from allkaliphilic Bacillus
firmus OF4 and characterization OF the pH-regulated cytochrome caa 3 oxidase it encodes.
J Biol Chem 268(1):678–685
74. Brown KR, Allan BM, Do P, Hegg EL (2002) Identification of novel hemes generated by
heme A synthase: evidence for two successive monooxygenase reactions. Biochemist
41(36):10906–10913
75. Throne-Holst M, Hederstedt L (2000) The Bacillus subtilis ctaB paralogue, yjdK, can complement the heme A synthesis deficiency of a CtaB-deficient mutant. FEMS Microbiol Lett
183(2):247–251
76. Stothard P (2000) The sequence manipulation suite: JavaScript programs for analysing and
formatting protein and DNA sequences. BioTechniques 28:1102–1104
77. Matsuno T, Yumoto I (2015) Bioenergetics and the role of soluble cytochromes c for alkaline
adaptation in gram-negative alkaliphilic Pseudomonas. Biomed Res Int 2015:847945
Genomics of Alkaliphiles
155