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Terry A. Krulwich – One of the best experts on this subject based on the ideXlab platform.

  • Alkaliphilic bacteria with impact on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis
    Frontiers in bioengineering and biotechnology, 2015
    Co-Authors: Laura Preiss, David Hicks, Shino Suzuki, Thomas Meier, Terry A. Krulwich
    Abstract:

    Alkaliphilic bacteria typically grow well at pH 9, with the most extremophilic strains growing up to pH values as high as pH 12-13. Interest in extreme Alkaliphiles arises because they are sources of useful, stable enzymes, and the cells themselves can be used for biotechnological and other applications at high pH. In addition, alkaline hydrothermal vents represent an early evolutionary niche for Alkaliphiles and novel extreme Alkaliphiles have also recently been found in alkaline serpentinizing sites. A third focus of interest in Alkaliphiles is the challenge raised by the use of proton-coupled ATP synthases for oxidative phosphosphorylation by non-fermentative Alkaliphiles. This creates a problem with respect to tenets of the chemiosmotic model that remains the core model for the bioenergetics of oxidative phosphosphorylation. Each of these facets of alkaliphilic bacteria will be discussed with a focus on extremely alkaliphilic Bacillus strains. These alkaliphilic bacteria have provided a cogent experimental system to probe adaptations that enable their growth and oxidative phosphosphorylation at high pH. Adaptations are clearly needed to enable secreted or partially exposed enzymes or protein complexes to function at the high external pH. Also, Alkaliphiles must maintain a cytoplasmic pH that is significantly lower than the pH of the outside medium. This protects cytoplasmic components from an external pH that is alkaline enough to impair their stability or function. However, the pH gradient across the cytoplasmic membrane, with its orientation of more acidic inside than outside, is in the reverse of the productive orientation for bioenergetic work. The reversed gradient reduces the trans-membrane proton motive force available to energize ATP synthesis. Multiple strategies are hypothesized to be involved in enabling Alkaliphiles to circumvent the challenge of a low bulk proton-motive force energizing proton-coupled ATP synthesis at high pH.

  • Bioenergetic Adaptations That Support Alkaliphily
    Physiology and Biochemistry of Extremophiles, 2014
    Co-Authors: Terry A. Krulwich, David Hicks, Talia H. Swartz, Masahiro Ito
    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 Bacillus 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 proteinprotein interactions with a respiratory chaichain complex, as suggested by for mitochondria, and/or involve the abundant cardiolipin of the alkaliphile membrane.

  • 2.6 Adaptive Mechanisms of Extreme Alkaliphiles
    , 2011
    Co-Authors: Terry A. Krulwich, Masahiro Ito, Jun Liu, Makoto Fujisawa, Masato Morino, David B. Hicks
    Abstract:

    Prologue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 Cytoplasmic pH Homeostasis: The Central Challenge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 Growth of Extreme Alkaliphiles at Alkaline Cytoplasmic pH Values Not Tolerated by Neutralophiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 Na/H Antiporters: Key Participants in Cytoplasmic pH Homeostasis of Alkaliphiles . 124 Redundancy in the Cation/Proton Antiporter Complements of Alkaliphiles, and the Importance of Mrp-Type Antiporters in Alkaliphily . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 Additional Structural, Enzymatic, and Metabolic Strategies for Cytoplasmic pH Homeostasis, and Their Built-In Redundancies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 A Low Bulk Protonmotive Force (pmf) Resulting from Successful pH Homeostasis, and Its Bioenergetic Consequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 Strategies for Oxidative PhosPhosphorylation at Low Protonmotive Force . . . . . . . . . . . . . . . . . . . 132 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 Cross-References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

Isao Yumoto – One of the best experts on this subject based on the ideXlab platform.

  • Contribution of intracellular negative ion capacity to Donnan effect across the membrane in alkaliphilic Bacillus spp.
    Journal of bioenergetics and biomembranes, 2016
    Co-Authors: Toshitaka Goto, Toshinao Hirabayashi, Hajime Morimoto, Koji Yamazaki, Norio Inoue, Hidetoshi Matsuyama, Isao Yumoto
    Abstract:

    To elucidate the energy production mechanism of Alkaliphiles, the relationship between the H+ extrusion rate by the respiratory chain and the corresponding ATP synthesis rate was determined in the facultative alkaliphile Bacillus cohnii YN-2000 and compared with those in the obligate alkaliphile Bacillus clarkii DSM 8720T and the neutralophile Bacillus subtilis IAM 1026. Under high aeration condition, much higher ATP synthesis rates and larger Δψ in the alkaliphilic Bacillus spp. grown at pH 10 than those in the neutralophilic B. subtilis grown at pH 7 were observed. This high ATP productivity could be attributed to the larger Δψ in Alkaliphiles than in B. subtilis because the H+ extrusion rate in Alkaliphiles cannot account for the high ATP productivity. However, the large Δψ in the Alkaliphiles could not be explained only by the H+ translocation rate in the respiratory chain in Alkaliphiles. There is a possibility that the Donnan effect across the membrane has the potential to contribute to the large Δψ. To estimate the contribution of the Donnan effect to the large Δψ in alkaliphilic Bacillus spp. grown at pH 10, intracellular negative ion capacity was examined. The intracellular negative ion capacities in Alkaliphiles grown at pH 10 under high aeration condition corresponding to their intracellular pH (pH 8.1) were much higher than those in Alkaliphiles grown under low aeration condition. A proportional relationship is revealed between the negative ion capacity and Δψ in Alkaliphiles grown under different aeration conditions. This relationship strongly suggests that the intracellular negative ion capacity contributes to the formation of Δψ through the Donnan effect in alkaliphilic Bacillus spp. grown at pH 10.

  • Environmental and Taxonomic Biodiversities of Gram-Positive Alkaliphiles
    Physiology and Biochemistry of Extremophiles, 2014
    Co-Authors: Isao Yumoto
    Abstract:

    This chapter focuses on the environmental and taxonomic distributions of gram-positive Alkaliphiles. Garbeva et al. developed a polymerase chain reaction (PCR) system for studying the diversity of the species of Bacillus and related taxa using DNA directly obtained from soil. Detection of Bacillus halodurans by this procedure indicated that although the soil samples were slightly acidic, Bacillus halodurans might be one of the major Bacillus species in the soil samples used in that study. Microbial diversities of soda lakes in Africa, Europe, and North America have been detected on the basis of the analysis of DNA clone libraries produced by amplification of obtained DNA as well as from the isolation of microorganisms from the environments. The major gram-negative isolates are members of the gamma subdivision of Proteobacteria. Indigo-reducing bacteria have been isolated by Takahara and Tanabe and identified as Bacillus sp. they have been named Bacillus alcalophilus. This is the only species that can grow at 5°C among the currently known alkaliphilic Bacillus spp. The chapter provides facts that suggest that niches of Bacillus patagoniensis are in soil and in rhizosphere of certain plants. Some of the strains in this group were formally classified as Bacillus. In the next decade, the understanding of the distribution in the environment and of the taxonomic diversities of Alkaliphiles will proceed further not only by isolation of novel species of Alkaliphiles but also from results of analyses of DNA directly obtained from various environments.

  • 2 3 environmental distribution and taxonomic diversity of Alkaliphiles
    , 2010
    Co-Authors: Koki Horikoshi, Isao Yumoto, Kazuaki Yoshimune
    Abstract:

    Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Aims and Significance of Taxonomy of Alkaliphilic Fermicutes . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Environmental Distributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 Soil Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 Soda Lakes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 Gut of Insects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Groundwater . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Sea and Sea-Related Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Indigo Fermentation Liquor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Other Environments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Taxonomy of Isolated Alkaliphilic Firmicutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 Genus Bacillus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 Conclusions and Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 Cross-References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Gerard Muyzer – One of the best experts on this subject based on the ideXlab platform.

David Hicks – One of the best experts on this subject based on the ideXlab platform.

  • Alkaliphilic bacteria with impact on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis
    Frontiers in bioengineering and biotechnology, 2015
    Co-Authors: Laura Preiss, David Hicks, Shino Suzuki, Thomas Meier, Terry A. Krulwich
    Abstract:

    Alkaliphilic bacteria typically grow well at pH 9, with the most extremophilic strains growing up to pH values as high as pH 12-13. Interest in extreme Alkaliphiles arises because they are sources of useful, stable enzymes, and the cells themselves can be used for biotechnological and other applications at high pH. In addition, alkaline hydrothermal vents represent an early evolutionary niche for Alkaliphiles and novel extreme Alkaliphiles have also recently been found in alkaline serpentinizing sites. A third focus of interest in Alkaliphiles is the challenge raised by the use of proton-coupled ATP synthases for oxidative phosphorylation by non-fermentative Alkaliphiles. This creates a problem with respect to tenets of the chemiosmotic model that remains the core model for the bioenergetics of oxidative phosphorylation. Each of these facets of alkaliphilic bacteria will be discussed with a focus on extremely alkaliphilic Bacillus strains. These alkaliphilic bacteria have provided a cogent experimental system to probe adaptations that enable their growth and oxidative phosphorylation at high pH. Adaptations are clearly needed to enable secreted or partially exposed enzymes or protein complexes to function at the high external pH. Also, Alkaliphiles must maintain a cytoplasmic pH that is significantly lower than the pH of the outside medium. This protects cytoplasmic components from an external pH that is alkaline enough to impair their stability or function. However, the pH gradient across the cytoplasmic membrane, with its orientation of more acidic inside than outside, is in the reverse of the productive orientation for bioenergetic work. The reversed gradient reduces the trans-membrane proton motive force available to energize ATP synthesis. Multiple strategies are hypothesized to be involved in enabling Alkaliphiles to circumvent the challenge of a low bulk proton-motive force energizing proton-coupled ATP synthesis at high pH.

  • Bioenergetic Adaptations That Support Alkaliphily
    Physiology and Biochemistry of Extremophiles, 2014
    Co-Authors: Terry A. Krulwich, David Hicks, Talia H. Swartz, Masahiro Ito
    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 Bacillus 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.

  • Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4.
    Environmental microbiology, 2011
    Co-Authors: Benjamin Janto, Masahiro Ito, David Hicks, Jun Liu, Oliver J. Fackelmayer, Azad Ahmed, Sarah Pagni, Terry Ann Smith, Joshua P. Earl, Liam D. H. Elbourne
    Abstract:

    Summary Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions.

Gaël Erauso – One of the best experts on this subject based on the ideXlab platform.

  • Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., two novel anaerobic alkaliphilic species isolated from the serpentinite-hosted Prony Bay Hydrothermal Field (New Caledonia)
    Systematic and Applied Microbiology, 2021
    Co-Authors: Anne Postec, Marianne Quemeneur, Aurélien Lecoeuvre, Nicolas Chabert, Manon Joseph, Gaël Erauso
    Abstract:

    Two novel anaerobic alkaliphilic strains, designated as LacT T and LacV T , were isolated from the Prony Bay Hydrothermal Field (PBHF, New Caledonia). Cells were motile, Gram-positive, terminal endosporeforming rods, displaying a straight to curved morphology during the exponential phase. Strains LacT T and LacV T were mesophilic (optimum 30°C), moderately alkaliphilic (optimum pH 8.2 and 8.7, respectively) and halotolerant (optimum 2% and 2.5% NaCl, respectively). Both strains were able to ferment yeast extract, peptone and casamino acids, but only strain LacT T could use sugars (glucose, maltose and sucrose). Both strains disproportionated crotonate into acetate and butyrate. Phylogenetic analysis revealed that strains LacT T and LacV T shared 96.4% 16S rRNA gene sequence identity and were most closely related to A. peptidifermentans Z-7036, A. namsaraevii X-07-2 and A. hydrothermalis FatMR1 (95.7%-96.3%). Their genome size was of 3.29 Mb for strain LacT T and 3.06 Mb for strain LacV T with a G + C content of 36.0 and 33.9 mol%, respectively. The ANI value between both strains was 73.2 %. Finally, strains LacT T (=DSM 100337 = JCM 30643) and LacV T (=DSM 100017 = JCM 30644) are proposed as two novel species of the genus Alkaliphilus, order Clostridiales, phylum Firmicutes, Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., respectively. The genomes of the three Alkaliphilus species isolated from PBHF were consistently detected in the PBHF chimney metagenomes, although at very low abundance, but not significantly in the metagenomes of other serpentinizing systems (marine or terrestrial) worldwide, suggesting they represent indigenous members of the PBHF microbial ecosystem.