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Chapter 24 : Bioenergetic Adaptations That Support Alkaliphily

Authors: Terry Ann Krulwich1, David B. Hicks2, Talia Swartz3, Masahiro Ito4
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Affiliations: 1: Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029; 2: Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029; 3: Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029; 4: Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan
Content Type: Monograph
Publication Year: 2007

Category: Applied and Industrial Microbiology; Environmental Microbiology

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Abstract:

Two themes that run through this chapter are the whole-cell, systems biology aspects of alkaliphile bioenergetics and the diverse ion transporters, pumps, and channels that participate in this system, many of which were first discovered in alkaliphiles and many of which have alkaliphile-specific roles or adaptations. All alkaliphiles examined to date, including both anaerobes and aerobes, do indeed maintain a cytoplasmic pH much lower than the external pH. The growing amount of comparative genomic data between alkaliphiles and neutrophiles has made it much easier to identify putative alkaliphile-specific deviations in conserved and functionally important residues or motifs in proteins of bioenergetic interest. Compelling genomic and biochemical evidence attest to the fact that extreme alkaliphiles experience a low proton motive force (PMF) at high pH. Alkaliphily in bacteria depends upon one or more Na/H antiporters that catalyze proton uptake in exchange for cytoplasmic Na. The specific properties of the antiporters of alkaliphilic that support its functions are not yet clear, but antiporter properties of interest in relation to alkaliphily have emerged for a different alkaliphile. The proton transfer might involve direct protein–protein interactions with a respiratory chain complex, as suggested by for mitochondria, and/or involve the abundant cardiolipin of the alkaliphile membrane.

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Bioenergetic Adaptations That Support Alkaliphily
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Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
/content/10.1128/9781555815813.ch24.ch24fig01
Figure 1.
The cytoplasmic pH, doubling time, and proton motive force of alkaliphilic OF4 growing at pH values from 7.5 to 11.2 in pH-controlled continuous cultures. Cells were grown in continuous cultures on malate-containing semidefined medium at the indicated, rigorously maintained pH values. Assays of the proton motive force parameters were conducted as described ( ). The closed and open circles indicate the doubling times (in minutes) in relation to the cytoplasmic pH at different growth pH; the numbers in parentheses are the values of the ΔpH, acid inside relative to the medium. The Δψ (closed triangles) and Δ (PMF in millivolt, open triangles) are also shown. (Modified from , with permission from Blackwell Publishing Ltd.)
10.1128/9781555815813/f0312-01_thmb.gif
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Image of Figure 1.
Figure 1.

The cytoplasmic pH, doubling time, and proton motive force of alkaliphilic OF4 growing at pH values from 7.5 to 11.2 in pH-controlled continuous cultures. Cells were grown in continuous cultures on malate-containing semidefined medium at the indicated, rigorously maintained pH values. Assays of the proton motive force parameters were conducted as described ( ). The closed and open circles indicate the doubling times (in minutes) in relation to the cytoplasmic pH at different growth pH; the numbers in parentheses are the values of the ΔpH, acid inside relative to the medium. The Δψ (closed triangles) and Δ (PMF in millivolt, open triangles) are also shown. (Modified from , with permission from Blackwell Publishing Ltd.)

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Figure 2.
Growth curves of wild-type alkaliphilic OF4 and a mutant disrupted in the S-layer-encoding gene . The two strains were compared at two concentrations, an optimal Na concentration, and a suboptimally low Na concentration at three different pH values on semidefined malate-containing medium at 30°C. Although not shown, the wild-type strain grew negligibly at pH 7.5 when the added Na was at 5 mM, a concentration that supported growth well at pH 10.5. (Modified from , with permission from the publisher.)
10.1128/9781555815813/f0314-01_thmb.gif
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Image of Figure 2.
Figure 2.

Growth curves of wild-type alkaliphilic OF4 and a mutant disrupted in the S-layer-encoding gene . The two strains were compared at two concentrations, an optimal Na concentration, and a suboptimally low Na concentration at three different pH values on semidefined malate-containing medium at 30°C. Although not shown, the wild-type strain grew negligibly at pH 7.5 when the added Na was at 5 mM, a concentration that supported growth well at pH 10.5. (Modified from , with permission from the publisher.)

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Figure 3.
A diagrammatic representation of the Na and proton cycles that support alkaline pH homeostasis, solute transport, and motility in extreme facultative alkaliphiles such as C-125 and OF4. Oxidative phosphorylation by OF4 is one of two processes that depend upon inward proton movements, as it utilizes a H-proton-pumping respiratory chain and a H-coupled ATP synthase; these complexes have alkaliphilic-specific features and function in a membrane that has a high content of cardiolipin (CL); the dashed lines around OXPHOS elements indicate a hypothesized use of kinetically sequestered proton transfers during OXPHOS at very high pH. The Δψ generated by respiration energizes a complement of Na/H antiporters: Mrp is shown as a multisub-unit antiporter and has a dominant role in pH homeostasis ( ), to which NhaC has also been shown to contribute ( ). Genomic evidence suggests that CPA1-type (Na/H) and MleN-type (2H malate/Na lactate) antiporters also contribute to alkaline pH homeostasis ( ). Na-coupled solute uptake and motility, as well as the voltage-gated channel Na BP play roles in Na reentry in support of pH homeostasis ( ). Na BP also has a role in motility and chemo-taxis ( ); the ABC transporter, NatCAB ( ), presumably plays a role under excessively high Na conditions; and AmhT has a role during growth on high-amine media but the transport mechanism is not yet established ( ).
10.1128/9781555815813/f0315-01_thmb.gif
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Image of Figure 3.
Figure 3.

A diagrammatic representation of the Na and proton cycles that support alkaline pH homeostasis, solute transport, and motility in extreme facultative alkaliphiles such as C-125 and OF4. Oxidative phosphorylation by OF4 is one of two processes that depend upon inward proton movements, as it utilizes a H-proton-pumping respiratory chain and a H-coupled ATP synthase; these complexes have alkaliphilic-specific features and function in a membrane that has a high content of cardiolipin (CL); the dashed lines around OXPHOS elements indicate a hypothesized use of kinetically sequestered proton transfers during OXPHOS at very high pH. The Δψ generated by respiration energizes a complement of Na/H antiporters: Mrp is shown as a multisub-unit antiporter and has a dominant role in pH homeostasis ( ), to which NhaC has also been shown to contribute ( ). Genomic evidence suggests that CPA1-type (Na/H) and MleN-type (2H malate/Na lactate) antiporters also contribute to alkaline pH homeostasis ( ). Na-coupled solute uptake and motility, as well as the voltage-gated channel Na BP play roles in Na reentry in support of pH homeostasis ( ). Na BP also has a role in motility and chemo-taxis ( ); the ABC transporter, NatCAB ( ), presumably plays a role under excessively high Na conditions; and AmhT has a role during growth on high-amine media but the transport mechanism is not yet established ( ).

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Figure 4.
The Mrp Na/H antiporter system. (A) The operon structure of a group 1 Mrp system that is encoded by a seven-gene operon ( ). (B) Unrooted tree (TreeView) of ClustalW (DSGene) analysis indicating that alkaliphiles contain a group 1 Mrp system that shows closer sequence similarity to each other than to Mrp systems from other gram-positive bacteria and to second Mrp systems found, in some cases, in the alkaliphiles themselves.
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Image of Figure 4.
Figure 4.

The Mrp Na/H antiporter system. (A) The operon structure of a group 1 Mrp system that is encoded by a seven-gene operon ( ). (B) Unrooted tree (TreeView) of ClustalW (DSGene) analysis indicating that alkaliphiles contain a group 1 Mrp system that shows closer sequence similarity to each other than to Mrp systems from other gram-positive bacteria and to second Mrp systems found, in some cases, in the alkaliphiles themselves.

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Figure 5.
The Na-coupled MotPS of alkaliphilic bacilli. (A) The operon of the two extreme alkaliphiles, C 125 and OF4. No stem loop is found between and in these two alkaliphiles, for which MotPS is the sole Mot (based, respectively, on genomic and genetic evidence; ). The stem loop is found in less alkaliphilic and nonalkaliphilic strains that also possess MotAB; the stem loop reduces transcription read-through between and (Terahara et al., submitted for publication). (B) Unrooted tree (TreeView) of ClustalW (DSGene) analysis of MotP from alkaliphiles is shown to cluster relative to homologous PomA from a Na-coupled Mot of and H-coupled MotA from moderately alkaliphilic and other bacilli.
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Image of Figure 5.
Figure 5.

The Na-coupled MotPS of alkaliphilic bacilli. (A) The operon of the two extreme alkaliphiles, C 125 and OF4. No stem loop is found between and in these two alkaliphiles, for which MotPS is the sole Mot (based, respectively, on genomic and genetic evidence; ). The stem loop is found in less alkaliphilic and nonalkaliphilic strains that also possess MotAB; the stem loop reduces transcription read-through between and (Terahara et al., submitted for publication). (B) Unrooted tree (TreeView) of ClustalW (DSGene) analysis of MotP from alkaliphiles is shown to cluster relative to homologous PomA from a Na-coupled Mot of and H-coupled MotA from moderately alkaliphilic and other bacilli.

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Figure 6.
Alkaliphile-specific features of the ATP synthase and subunits. (A) A model indicating how features of the ATP synthase could contribute to kinetically sequestered movements of protons from the respiratory chain to the ATP synthase of an extremely alkaliphilic at pH ≥9.2. Protons in the bulk external phase are hypothesized to be blocked (hatched arrow) from entering the ATP synthase at pH ≥9.2 by gating that depends upon -subunit lysine and glycine. This gating prevents proton loss through the ATP synthase when extremely high-pH, low-PMF conditions prevail and accounts for failure of an imposed potential to energize ATP synthesis above pH 9.2. Protons are pumped into the bulk by both Complex III and Cta (the -type cytochrome oxidase), but some protons, as shown for cytochrome oxidase, are hypothesized to reach the ATP synthase without equilibration with the bulk, assisted by some combination of: (i) the alkaliphile-specific ATP synthase features (which are detailed in B–E and one of which is shown here as a cup-like proton-gathering element); (ii) special features of the cytochrome oxidase (indicated by the negatively charged region of CtaC, see Fig. 8 ); (iii) and the negatively charged membrane lipid environment (CL, cardiolipin). (B) Topological models illustrate positions of both the - and the -subunit features that are boxed. (Modified from Wang et al., 2004 , with permission from the publisher.). The features are: -loop, K180, G212, TMH1, T33, and P51. (C) Kyte–Doolittle hydropathy plots (Gene Runner) of different subunits. The boxed region is the hypothesized periplasmic loop between TMH2 and TMH3 (designated as “-loop”) corresponding to residues 128–137 ( Valiyaveetil and Fill-ingame, 1998 ), according to the ClustalW alignment (DS Gene). (D) An alignment showing the single, but probably interacting, amino acid features in TMH4 and TMH5 of the subunit, K180, and G212. (E) An alignment illustrating the features in the subunit displayed only by extreme alkaliphiles. Shown are a TMH1 feature, in which the glycines of the conserved XGXGXGXGX region are largely or completely replaced by alanines, the T33 residue instead of a conserved alanine, and P51 in place of a glycine or alanine in other bacteria. Numbering refers to OF4 at the top and to at the bottom. The accession numbers for the data shown are: AF330160, OF4; NP_244627, C-125 subunit; NP_244626, C-125 subunit; M84712, ; NC_006582, subunit; NC_006582, subunit; AF533147, . sp. strain TA2.A1; NP_693903, subunit; NP_693902, subunit; M20255, ; Z28592, ; NC_005957, subunit; NC_005957, subunit; NC_006510, subunit; NC_006510, subunit; NP_290377, subunit; NP_290376, subunit. (Modified from Wang et al., 2004 .)
10.1128/9781555815813/f0322-01_thmb.gif
10.1128/9781555815813/f0322-01.gif
Image of Figure 6.
Figure 6.

Alkaliphile-specific features of the ATP synthase and subunits. (A) A model indicating how features of the ATP synthase could contribute to kinetically sequestered movements of protons from the respiratory chain to the ATP synthase of an extremely alkaliphilic at pH ≥9.2. Protons in the bulk external phase are hypothesized to be blocked (hatched arrow) from entering the ATP synthase at pH ≥9.2 by gating that depends upon -subunit lysine and glycine. This gating prevents proton loss through the ATP synthase when extremely high-pH, low-PMF conditions prevail and accounts for failure of an imposed potential to energize ATP synthesis above pH 9.2. Protons are pumped into the bulk by both Complex III and Cta (the -type cytochrome oxidase), but some protons, as shown for cytochrome oxidase, are hypothesized to reach the ATP synthase without equilibration with the bulk, assisted by some combination of: (i) the alkaliphile-specific ATP synthase features (which are detailed in B–E and one of which is shown here as a cup-like proton-gathering element); (ii) special features of the cytochrome oxidase (indicated by the negatively charged region of CtaC, see Fig. 8 ); (iii) and the negatively charged membrane lipid environment (CL, cardiolipin). (B) Topological models illustrate positions of both the - and the -subunit features that are boxed. (Modified from Wang et al., 2004 , with permission from the publisher.). The features are: -loop, K180, G212, TMH1, T33, and P51. (C) Kyte–Doolittle hydropathy plots (Gene Runner) of different subunits. The boxed region is the hypothesized periplasmic loop between TMH2 and TMH3 (designated as “-loop”) corresponding to residues 128–137 ( Valiyaveetil and Fill-ingame, 1998 ), according to the ClustalW alignment (DS Gene). (D) An alignment showing the single, but probably interacting, amino acid features in TMH4 and TMH5 of the subunit, K180, and G212. (E) An alignment illustrating the features in the subunit displayed only by extreme alkaliphiles. Shown are a TMH1 feature, in which the glycines of the conserved XGXGXGXGX region are largely or completely replaced by alanines, the T33 residue instead of a conserved alanine, and P51 in place of a glycine or alanine in other bacteria. Numbering refers to OF4 at the top and to at the bottom. The accession numbers for the data shown are: AF330160, OF4; NP_244627, C-125 subunit; NP_244626, C-125 subunit; M84712, ; NC_006582, subunit; NC_006582, subunit; AF533147, . sp. strain TA2.A1; NP_693903, subunit; NP_693902, subunit; M20255, ; Z28592, ; NC_005957, subunit; NC_005957, subunit; NC_006510, subunit; NC_006510, subunit; NP_290377, subunit; NP_290376, subunit. (Modified from Wang et al., 2004 .)

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Figure 7.
Segments of alkaliphile membrane proteins just outside the membrane surface, including a functionally important segment of cytochrome oxidase, show evident sequence adaptations relative to homologous regions from nonalkaliphiles. The content of acidic and basic residues and overall charge is displayed for the external segments of: the stress protein FtsH; the CtaC subunit of the -type cytochrome oxidase; and the smaller subunit, MotB (nonalkaliphiles except for ) or MotP (alkaliphiles) of the membrane-embedded flagellar stator-force generator.
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Image of Figure 7.
Figure 7.

Segments of alkaliphile membrane proteins just outside the membrane surface, including a functionally important segment of cytochrome oxidase, show evident sequence adaptations relative to homologous regions from nonalkaliphiles. The content of acidic and basic residues and overall charge is displayed for the external segments of: the stress protein FtsH; the CtaC subunit of the -type cytochrome oxidase; and the smaller subunit, MotB (nonalkaliphiles except for ) or MotP (alkaliphiles) of the membrane-embedded flagellar stator-force generator.

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Figure 8.
An imposed potential of the same magnitude as respiration-generated Δψ values energizes ATP synthesis by OF4 below but not above pH 9.2, whereas respiration-energized ATP synthesis is more robust and resistant to small drops in the Δψ>pH 9.2 than below. (A) The efficacy of an imposed potential (a valinomycin-mediated K+ diffusion potential of –160 mV) to energize ATP synthesis, AIB uptake, and Na efflux (an assessment of aggregate Na/H antiport) in energy-depleted whole cells that are reenergized by addition of malate. (Modified from Guffanti and Krulwich, 1992 , with permission from the publisher.) (B) The effect of downward titration of the Δψ on respiration-dependent ATP synthesis by ADP + P-loaded membrane vesicles from OF4 at pH 7.8 or 9.5. Ascorbate-phenazine methosulfate is the electron donor, potassium-containing buffers are present both inside and outside the vesicles, and Δψ is reduced by addition of the concentrations of valinomycin shown in parentheses. (Modified from Guffanti and Krulwich, 1994 ,)
10.1128/9781555815813/f0324-02_thmb.gif
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Image of Figure 8.
Figure 8.

An imposed potential of the same magnitude as respiration-generated Δψ values energizes ATP synthesis by OF4 below but not above pH 9.2, whereas respiration-energized ATP synthesis is more robust and resistant to small drops in the Δψ>pH 9.2 than below. (A) The efficacy of an imposed potential (a valinomycin-mediated K+ diffusion potential of –160 mV) to energize ATP synthesis, AIB uptake, and Na efflux (an assessment of aggregate Na/H antiport) in energy-depleted whole cells that are reenergized by addition of malate. (Modified from Guffanti and Krulwich, 1992 , with permission from the publisher.) (B) The effect of downward titration of the Δψ on respiration-dependent ATP synthesis by ADP + P-loaded membrane vesicles from OF4 at pH 7.8 or 9.5. Ascorbate-phenazine methosulfate is the electron donor, potassium-containing buffers are present both inside and outside the vesicles, and Δψ is reduced by addition of the concentrations of valinomycin shown in parentheses. (Modified from Guffanti and Krulwich, 1994 ,)

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
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Tables

Bioenergetic Adaptations That Support Alkaliphily
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Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
/content/10.1128/9781555815813.ch24.ch24tab01
Table 1.
Alkaliphilic OF4 pH homeostasis after a sudden alkaline shift in the external pH
Generic image for table
Table 1.

Alkaliphilic OF4 pH homeostasis after a sudden alkaline shift in the external pH

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24
/content/10.1128/9781555815813.ch24.ch24tab02
Table 2.
Alkaliphile-specific sequence features of the and subunits of ATP synthase are required for robust OXPHOS at high pH and prevention of proton loss to the outside
Generic image for table
Table 2.

Alkaliphile-specific sequence features of the and subunits of ATP synthase are required for robust OXPHOS at high pH and prevention of proton loss to the outside

Citation: Krulwich T, Hicks D, Swartz T, Ito M. 2007. Bioenergetic Adaptations That Support Alkaliphily, p 311-329. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch24

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