Na+ and flagella-dependent swimming of alkaliphilic Bacillus pseudofirmus OF4: a basis for poor motility at low pH and enhancement in viscous media in an “up-motile” variant

MotP Subunit is Critical for Ion Selectivity and Evolution of a K+-Coupled Flagellar Motor

The bacterial flagellar motor is a sophisticated nanomachine embedded in the cell envelope. The flagellar motor is driven by an electrochemical gradient of cations such as H⁺, Na⁺, and K⁺ through ion channels in stator complexes embedded in the cell membrane. The flagellum is believed to rotate as a result of electrostatic interaction forces between the stator and the rotor. In bacteria of the genus Bacillus and related species, the single transmembrane segment of MotB-type subunit protein (MotB and MotS) is critical for the selection of the H⁺ and Na⁺ coupling ions. Here, we constructed and characterized several hybrid stators combined with single Na⁺-coupled and dual Na⁺- and K⁺-coupled stator subunits, and we report that the MotP subunit is critical for the selection of K⁺. This result suggested that the K⁺ selectivity of the MotP/MotS complexes evolved from the single Na⁺-coupled stator MotP/MotS complexes. This finding will promote the understanding of the evolution of flagellar motors and the molecular mechanisms of coupling ion selectivity.

The Surface Layer Homology Domain-Containing Proteins of Alkaliphilic Bacillus pseudofirmus OF4 Play an Important Role in Alkaline Adaptation via Peptidoglycan Synthesis

It is well known that the Na⁺ cycle and the cell wall are essential for alkaline adaptation of Na⁺-dependent alkaliphilic Bacillus species. In Bacillus pseudofirmus OF4, surface layer protein A (SlpA), the most abundant protein in the surface layer (S-layer) of the cell wall, is involved in alkaline adaptation, especially under low Na⁺ concentrations. The presence of a large number of genes that encode S-layer homology (SLH) domain-containing proteins has been suggested from the genome sequence of B. pseudofirmus OF4. However, other than SlpA, the functions of SLH domain-containing proteins are not well known. Therefore, a deletion mutant of the csaB gene, required for the retention of SLH domain-containing proteins on the cell wall, was constructed to investigate its physiological properties. The csaB mutant strain of B. pseudofirmus OF4 had a chained morphology and alkaline sensitivity even under a 230 mM Na⁺ concentration at which there is no growth difference between the parental strain and the slpA mutant strain. Ultra-thin section transmission electron microscopy showed that a csaB mutant strain lacked an S-layer part, and its peptidoglycan (PG) layer was disturbed. The slpA mutant strain also lacked an S-layer part, although its PG layer was not disturbed. These results suggested that the surface layer homology domain-containing proteins of B. pseudofirmus OF4 play an important role in alkaline adaptation via peptidoglycan synthesis.

Nonconventional cation-coupled flagellar motors derived from the alkaliphilic Bacillus and Paenibacillus species

Prior to 2008, all previously studied conventional bacterial flagellar motors appeared to utilize either H⁺ or Na⁺ as coupling ions. Membrane-embedded stator complexes support conversion of energy using transmembrane electrochemical ion gradients. The main H⁺-coupled stators, known as MotAB, differ from Na⁺-coupled stators, PomAB of marine bacteria, and MotPS of alkaliphilic Bacillus. However, in 2008, a MotAB-type flagellar motor of alkaliphilic Bacillus clausii KSM-K16 was revealed as an exception with the first dual-function motor. This bacterium was identified as the first bacterium with a single stator-rotor that can utilize both H⁺ and Na⁺ for ion-coupling at different pH ranges. Subsequently, another exception, a MotPS-type flagellar motor of alkaliphilic Bacillus alcalophilus AV1934, was reported to utilize Na⁺ plus K⁺ and Rb⁺ as coupling ions for flagellar rotation. In addition, the alkaline-tolerant bacterium Paenibacillus sp. TCA20, which can utilize divalent cations such as Ca²⁺, Mg²⁺, and Sr²⁺, was recently isolated from a hot spring in Japan, which contains a high Ca²⁺ concentration. These findings show that bacterial flagellar motors isolated from unique environments utilize unexpected coupling ions. This suggests that bacteria that grow in different extreme environments adapt to local conditions and evolve their motility machinery.

Flagellum density regulates Proteus mirabilis swarmer cell motility in viscous environments

Proteus mirabilis is an opportunistic pathogen that is frequently associated with urinary tract infections. In the lab, P. mirabilis cells become long and multinucleate and increase their number of flagella as they colonize agar surfaces during swarming. Swarming has been implicated in pathogenesis; however, it is unclear how energetically costly changes in P. mirabilis cell morphology translate into an advantage for adapting to environmental changes. We investigated two morphological changes that occur during swarming--increases in cell length and flagellum density--and discovered that an increase in the surface density of flagella enabled cells to translate rapidly through fluids of increasing viscosity; in contrast, cell length had a small effect on motility. We found that swarm cells had a surface density of flagella that was ∼5 times larger than that of vegetative cells and were motile in fluids with a viscosity that inhibits vegetative cell motility. To test the relationship between flagellum density and velocity, we overexpressed FlhD(4)C(2), the master regulator of the flagellar operon, in vegetative cells of P. mirabilis and found that increased flagellum density produced an increase in cell velocity. Our results establish a relationship between P. mirabilis flagellum density and cell motility in viscous environments that may be relevant to its adaptation during the infection of mammalian urinary tracts and movement in contact with indwelling catheters.

A Bacillus flagellar motor that can use both Na+ and K+ as a coupling ion is converted by a single mutation to use only Na+

In bacteria, the sodium ion (Na(+)) cycle plays a critical role in negotiating the challenges of an extremely alkaline and sodium-rich environment. Alkaliphilic bacteria that grow optimally at high pH values use Na(+) for solute uptake and flagellar rotation because the proton (H(+)) motive force is insufficient for use at extremely alkaline pH. Only three types of electrically driven rotary motors exist in nature: the F-type ATPase, the V-type ATPase, and the bacterial flagellar motor. Until now, only H(+) and Na(+) have been reported as coupling ions for these motors. Here, we report that the alkaliphilic bacterium Bacillus alcalophilus Vedder 1934 can grow not only under a Na(+)-rich and potassium ion (K(+))-poor condition but also under the opposite condition in an extremely alkaline environment. In this organism, swimming performance depends on concentrations of Na(+), K(+) or Rb(+). In the absence of Na(+), swimming behavior is clearly K(+)- dependent. This pattern was confirmed in swimming assays of stator-less Bacillus subtilis and Escherichia coli mutants expressing MotPS from B. alcalophilus (BA-MotPS). Furthermore, a single mutation in BA-MotS was identified that converted the naturally bi-functional BA-MotPS to stators that cannot use K(+) or Rb(+). This is the first report that describes a flagellar motor that can use K(+) and Rb(+) as coupling ions. The finding will affect the understanding of the operating principles of flagellar motors and the molecular mechanisms of ion selectivity, the field of the evolution of environmental changes and stresses, and areas of nanotechnology.

The relationship between a coiled morphology and Mbl in alkaliphilic Bacillus halodurans C-125 at neutral pH values

The facultative alkaliphilic Bacillus halodurans C-125 can grow in a pH range from 6.8 to 10.8. The morphology of the cells grown at pH values above 7.5 is rod shaped, whereas, that gown at pH values less than 7.5 is coiled. Cytoplasmic membrane staining revealed that this coiled morphology was formed not by one filamentous cell, but by many chained bent/non-bent cells. Prokaryotic actin and tubulin homologs (MreB, Mbl MreBH, and FtsZ, respectively) are known to function as bacterial cytoskeleton proteins. The transcription levels of ftsZ, mreB, and mreBH genes were hardly affected by growth pH. However, the level of the mbl gene was significantly decreased at neutral pH values. Moreover, the expression level of the Mbl protein at pH 7.0 was about one-fourth of that at pH 10. Immunofluorescence microscopy (IFM) showed that the Mbl protein was localized as a helical structure in the rod-shaped cell grown at pH 10, whereas a helical structure was not observed in the cells grown at pH 7.0. Fluorescent vancomycin staining showed insertion of new peptidoglycan strands of sidewalls occurred in the cells grown at pH 7.0. These data suggested that a decrease in the expression level of the Mbl protein can influence the morphology of B. halodurans C-125 grown at pH 7.0 without influencing insertion of new peptidoglycan strands.

Hindering biofilm formation with zosteric acid

The antifoulant, zosteric acid, was synthesized using a non-patented process. Zosteric acid at 500 mg l(-1) caused a reduction of bacterial (Escherichia coli, Bacillus cereus) and fungal (Aspergillus niger, Penicillium citrinum) coverage by 90% and 57%, respectively. Calculated models allowed its antifouling activity to be predicted at different concentrations. Zosteric acid counteracted the effects of some colonization-promoting factors. Bacterial and fungal wettability was not affected, but the agent increased bacterial motility by 40%. A capillary accumulation test showed that zosteric acid did not act as a chemoeffector for E. coli, but stimulated a chemotactic response. Along with enhanced swimming migration of E. coli in the presence of zosteric acid, staining showed an increased production of flagella. Reverse transcriptase-PCR revealed an increased transcriptional level of the fliC gene and isolation and quantification of flagellar proteins demonstrated a higher flagellin amount. Biofilm experiments confirmed that zosteric acid caused a significant decrease in biomass (-92%) and thickness (-54%).

Industrial applications of alkaliphiles and their enzymes--past, present and future

Alkaliphiles are microorganisms that can grow in alkaline environments, i.e. pH >9.0. Their enzymes, especially extracellular enzymes, are able to function in their catalytic activities under high alkaline pH values because of their stability under these conditions. Proteases, protein degrading enzymes, are one of the most produced enzymes in industry. Among proteases, alkaline proteases, which are added to some detergents, are the most produced. Other alkaline enzymes, e.g. alkaline cellulases, alkaline amylases, and alkaline lipases, are also adjuncts to detergents for improving cleaning efficiency. Alkaline enzymes often show activities in a broad pH range, thermostability, and tolerance to oxidants compared to neutral enzymes. Alkaliphilic Bacillus species are the most characterized organisms among alkaliphiles. They produce so many extracellular alkaline-adapted enzymes that they are often good sources for industrial enzymes. As a patent strain, the whole genome sequence of alkaliphilic Bacillus halodurans C-125 has been sequenced for the first time. In addition, an increasing number of whole genomic sequences and structural analyses of proteins in alkaliphiles, development of genetic engineering techniques and physiological analyses will reveal the alkaline adaptation mechanisms of alkaliphilic Bacillus species and the structural basis of their enzymatic functions. This information opens up the possibility of new applications. In this paper we describe, first, the physiologies of environmental adaptations, and then the applications of enzymes and microorganisms themselves in alkaliphilic Bacillus species.

Motility and chemotaxis in alkaliphilic Bacillus species

Alkaliphilic Bacillus species grow at pH values up to approximately 11. Motile alkaliphilic Bacillus use electrochemical gradients of Na(+) (sodium-motive force) to power ion-coupled, flagella-mediated motility as opposed to the electrochemical gradients of H(+) (proton-motive force) used by most neutralophilic bacteria. Membrane-embedded stators of bacterial flagella contain ion channels through which either H(+) or Na(+) flow to energize flagellar rotation. Stators of the major H(+)-coupled type, MotAB, are distinguishable from Na(+)-coupled stators, PomAB of marine bacteria and MotPS of alkaliphilic Bacillus. Dual ion-coupling capacity is found in neutralophilic Bacillus strains with both MotAB and MotPS. There is also a MotAB variant that uses both coupling ions, switching as a function of pH. Chemotaxis of alkaliphilic Bacillus depends upon flagellar motility but also requires a distinct voltage-gated NaChBac-type channel. The two alkaliphile Na(+) channels provide new vistas on the diverse adaptations of sensory responses in bacteria.

Cytoplasmic pH measurement and homeostasis in bacteria and archaea

Of all the molecular determinants for growth, the hydronium and hydroxide ions are found naturally in the widest concentration range, from acid mine drainage below pH 0 to soda lakes above pH 13. Most bacteria and archaea have mechanisms that maintain their internal, cytoplasmic pH within a narrower range than the pH outside the cell, termed "pH homeostasis." Some mechanisms of pH homeostasis are specific to particular species or groups of microorganisms while some common principles apply across the pH spectrum. The measurement of internal pH of microbes presents challenges, which are addressed by a range of techniques under varying growth conditions. This review compares and contrasts cytoplasmic pH homeostasis in acidophilic, neutralophilic, and alkaliphilic bacteria and archaea under conditions of growth, non-growth survival, and biofilms. We present diverse mechanisms of pH homeostasis including cell buffering, adaptations of membrane structure, active ion transport, and metabolic consumption of acids and bases.

Mutations alter the sodium versus proton use of a Bacillus clausii flagellar motor and confer dual ion use on Bacillus subtilis motors

Bacterial flagella contain membrane-embedded stators, Mot complexes, that harness the energy of either transmembrane proton or sodium ion gradients to power motility. Use of sodium ion gradients is associated with elevated pH and sodium concentrations. The Mot complexes studied to date contain channels that use either protons or sodium ions, with some bacteria having only one type and others having two distinct Mot types with different ion-coupling. Here, alkaliphilic Bacillus clausii KSM-K16 was shown to be motile in a pH range from 7 to 11 although its genome encodes only one Mot (BCl-MotAB). Assays of swimming as a function of pH, sodium concentration, and ion-selective motility inhibitors showed that BCl-MotAB couples motility to sodium at the high end of its pH range but uses protons at lower pH. This pattern was confirmed in swimming assays of a statorless Bacillus subtilis mutant expressing either BCl-MotAB or one of the two B. subtilis stators, sodium-coupled Bs-MotPS or proton-coupled Bs-MotAB. Pairs of mutations in BCl-MotB were identified that converted the naturally bifunctional BCl-MotAB to stators that preferentially use either protons or sodium ions across the full pH range. We then identified trios of mutations that added a capacity for dual-ion coupling on the distinct B. subtilis Bs-MotAB and Bs-MotPS motors. Determinants that alter the specificity of bifunctional and single-coupled flagellar stators add to insights from studies of other ion-translocating transporters that use both protons and sodium ions.

The voltage-gated Na+ channel NaVBP co-localizes with methyl-accepting chemotaxis protein at cell poles of alkaliphilic Bacillus pseudofirmus OF4

Na(V)BP, found in alkaliphilic Bacillus pseudofirmus OF4, is a member of the bacterial voltage-gated Na(+) channel superfamily. The alkaliphile requires Na(V)BP for normal chemotaxis responses and for optimal pH homeostasis during a shift to alkaline conditions at suboptimally low Na(+) concentrations. We hypothesized that interaction of Na(V)BP with one or more other proteins in vivo, specifically methyl-accepting chemotaxis proteins (MCPs), is involved in activation of the channel under the pH conditions that exist in the extremophile and could underpin its role in chemotaxis; MCPs transduce chemotactic signals and generally localize to cell poles of rod-shaped cells. Here, immunofluorescence microscopy and fluorescent protein fusion studies showed that an alkaliphile protein (designated McpX) that cross-reacts with antibodies raised against Bacillus subtilis McpB co-localizes with Na(V)BP at the cell poles of B. pseudofirmus OF4. In a mutant in which Na(V)BP-encoding ncbA is deleted, the content of McpX was close to the wild-type level but McpX was significantly delocalized. A mutant of B. pseudofirmus OF4 was constructed in which cheAW expression was disrupted to assess whether this mutation impaired polar localization of McpX, as expected from studies in Escherichia coli and Salmonella, and, if so, whether Na(V)BP would be similarly affected. Polar localization of both McpX and Na(V)BP was decreased in the cheAW mutant. The results suggest interactions between McpX and Na(V)BP that affect their co-localization. The inverse chemotaxis phenotype of ncbA mutants may result in part from MCP delocalization.