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Khurana H, Sharma M, Verma H, Lopes BS, Lal R, Negi RK. Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential. Genomics 2020; 112:3191-3200. [PMID: 32512145 DOI: 10.1016/j.ygeno.2020.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
| | - Bruno Silvester Lopes
- School of Medicine, Medical Sciences and Nutrition, Medical Microbiology, 0:025 Polwarth Building, Aberdeen AB25 2ZD, UK
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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Molecular characterization and in silico analysis of ectoine biosynthesis genes from the deep sea halophilic eubacteria, Bacillus clausii NIOT-DSB04. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ray AE, Connon SA, Neal AL, Fujita Y, Cummings DE, Ingram JC, Magnuson TS. Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment. Front Microbiol 2018; 9:1689. [PMID: 30174652 PMCID: PMC6107796 DOI: 10.3389/fmicb.2018.01689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/06/2018] [Indexed: 01/11/2023] Open
Abstract
The capability of microorganisms to alter metal speciation offers potential for the development of new strategies for immobilization of toxic metals in the environment. A metal-reducing microbe, "Pelosinus lilae" strain UFO1, was isolated under strictly anaerobic conditions from an Fe(III)-reducing enrichment established with uncontaminated soil from the Department of Energy Oak Ridge Field Research Center, Tennessee. "P. lilae" UFO1 is a rod-shaped, spore-forming, and Gram-variable anaerobe with a fermentative metabolism. It is capable of reducing the humic acid analog anthraquinone-2,6-disulfonate (AQDS) using a variety of fermentable substrates and H2. Reduction of Fe(III)-nitrilotriacetic acid occurred in the presence of lactate as carbon and electron donor. Ferrihydrite was not reduced in the absence of AQDS. Nearly complete reduction of 1, 3, and 5 ppm Cr(VI) occurred within 24 h in suspensions containing 108 cells mL-1 when provided with 10 mM lactate; when 1 mM AQDS was added, 3 and 5 ppm Cr(VI) were reduced to 0.1 ppm within 2 h. Strain UFO1 is a novel species within the bacterial genus Pelosinus, having 98.16% 16S rRNA gene sequence similarity with the most closely related described species, Pelosinus fermentans R7T. The G+C content of the genomic DNA was 38 mol%, and DNA-DNA hybridization of "P. lilae" UFO1 against P. fermentans R7T indicated an average 16.8% DNA-DNA similarity. The unique phylogenetic, physiologic, and metal-transforming characteristics of "P. lilae" UFO1 reveal it is a novel isolate of the described genus Pelosinus.
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Affiliation(s)
- Allison E. Ray
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Idaho National Laboratory, Idaho Falls, ID, United States
| | - Stephanie A. Connon
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- California Institute of Technology, Pasadena, CA, United States
| | - Andrew L. Neal
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Yoshiko Fujita
- Idaho National Laboratory, Idaho Falls, ID, United States
| | - David E. Cummings
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Jani C. Ingram
- Idaho National Laboratory, Idaho Falls, ID, United States
| | - Timothy S. Magnuson
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
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Muschallik L, Molinnus D, Bongaerts J, Pohl M, Wagner T, Schöning MJ, Siegert P, Selmer T. (R,R)-Butane-2,3-diol dehydrogenase from Bacillus clausii DSM 8716 T: Cloning and expression of the bdhA-gene, and initial characterization of enzyme. J Biotechnol 2017; 258:41-50. [PMID: 28793235 DOI: 10.1016/j.jbiotec.2017.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/09/2017] [Accepted: 07/21/2017] [Indexed: 12/01/2022]
Abstract
The gene encoding a putative (R,R)-butane-2,3-diol dehydrogenase (bdhA) from Bacillus clausii DSM 8716T was isolated, sequenced and expressed in Escherichia coli. The amino acid sequence of the encoded protein is only distantly related to previously studied enzymes (identity 33-43%) and exhibited some uncharted peculiarities. An N-terminally StrepII-tagged enzyme variant was purified and initially characterized. The isolated enzyme catalyzed the (R)-specific oxidation of (R,R)- and meso-butane-2,3-diol to (R)- and (S)-acetoin with specific activities of 12U/mg and 23U/mg, respectively. Likewise, racemic acetoin was reduced with a specific activity of up to 115U/mg yielding a mixture of (R,R)- and meso-butane-2,3-diol, while the enzyme reduced butane-2,3-dione (Vmax 74U/mg) solely to (R,R)-butane-2,3-diol via (R)-acetoin. For these reactions only activity with the co-substrates NADH/NAD+ was observed. The enzyme accepted a selection of vicinal diketones, α-hydroxy ketones and vicinal diols as alternative substrates. Although the physiological function of the enzyme in B. clausii remains elusive, the data presented herein clearly demonstrates that the encoded enzyme is a genuine (R,R)-butane-2,3-diol dehydrogenase with potential for applications in biocatalysis and sensor development.
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Affiliation(s)
- Lukas Muschallik
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Denise Molinnus
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Torsten Wagner
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Michael J Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Thorsten Selmer
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany.
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Ito M, Takahashi Y. Nonconventional cation-coupled flagellar motors derived from the alkaliphilic Bacillus and Paenibacillus species. Extremophiles 2016; 21:3-14. [PMID: 27771767 DOI: 10.1007/s00792-016-0886-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/10/2016] [Indexed: 12/21/2022]
Abstract
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.
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Affiliation(s)
- Masahiro Ito
- Faculty of Life Sciences, Toyo University, Oura-gun, Gunma, 374-0193, Japan. .,Bio-nano Electronics Research Center, Toyo University, Kawagoe, Saitama, 350-8585, Japan.
| | - Yuka Takahashi
- Bio-nano Electronics Research Center, Toyo University, Kawagoe, Saitama, 350-8585, Japan
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Brander S, Mikkelsen JD, Kepp KP. Characterization of an alkali- and halide-resistant laccase expressed in E. coli: CotA from Bacillus clausii. PLoS One 2014; 9:e99402. [PMID: 24915287 PMCID: PMC4051777 DOI: 10.1371/journal.pone.0099402] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 05/13/2014] [Indexed: 01/25/2023] Open
Abstract
The limitations of fungal laccases at higher pH and salt concentrations have intensified the search for new extremophilic bacterial laccases. We report the cloning, expression, and characterization of the bacterial cotA from Bacillus clausii, a supposed alkalophilic ortholog of cotA from B. subtilis. Both laccases were expressed in E. coli strain BL21(DE3) and characterized fully in parallel for strict benchmarking. We report activity on ABTS, SGZ, DMP, caffeic acid, promazine, phenyl hydrazine, tannic acid, and bilirubin at variable pH. Whereas ABTS, promazine, and phenyl hydrazine activities vs. pH were similar, the activity of B. clausii cotA was shifted upwards by ∼0.5–2 pH units for the simple phenolic substrates DMP, SGZ, and caffeic acid. This shift is not due to substrate affinity (KM) but to pH dependence of catalytic turnover: The kcat of B. clausii cotA was 1 s−1 at pH 6 and 5 s−1 at pH 8 in contrast to 6 s−1 at pH 6 and 2 s−1 at pH 8 for of B. subtilis cotA. Overall, kcat/KM was 10-fold higher for B. subtilis cotA at pHopt. While both proteins were heat activated, activation increased with pH and was larger in cotA from B. clausii. NaCl inhibited activity at acidic pH, but not up to 500–700 mM NaCl in alkaline pH, a further advantage of the alkali regime in laccase applications. The B. clausii cotA had ∼20 minutes half-life at 80°C, less than the ∼50 minutes at 80°C for cotA from B. subtilis. While cotA from B. subtilis had optimal stability at pH∼8, the cotA from B. clausii displayed higher combined salt- and alkali-resistance. This resistance is possibly caused by two substitutions (S427Q and V110E) that could repel anions to reduce anion-copper interactions at the expense of catalytic proficiency, a trade-off of potential relevance to laccase optimization.
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Affiliation(s)
- Søren Brander
- Technical University of Denmark, DTU Chemical Engineering, Kongens Lyngby, Denmark
- Technical University of Denmark, DTU Chemistry, Kongens Lyngby, Denmark
| | - Jørn D. Mikkelsen
- Technical University of Denmark, DTU Chemical Engineering, Kongens Lyngby, Denmark
| | - Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, Kongens Lyngby, Denmark
- * E-mail:
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Combined effect of improved cell yield and increased specific productivity enhances recombinant enzyme production in genome-reduced Bacillus subtilis strain MGB874. Appl Environ Microbiol 2011; 77:8370-81. [PMID: 21965396 DOI: 10.1128/aem.06136-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome reduction strategies to create genetically improved cellular biosynthesis machineries for proteins and other products have been pursued by use of a wide range of bacteria. We reported previously that the novel Bacillus subtilis strain MGB874, which was derived from strain 168 and has a total genomic deletion of 874 kb (20.7%), exhibits enhanced production of recombinant enzymes. However, it was not clear how the genomic reduction resulted in elevated enzyme production. Here we report that deletion of the rocDEF-rocR region, which is involved in arginine degradation, contributes to enhanced enzyme production in strain MGB874. Deletion of the rocDEF-rocR region caused drastic changes in glutamate metabolism, leading to improved cell yields with maintenance of enzyme productivity. Notably, the specific enzyme productivity was higher in the reduced-genome strain, with or without the rocDEF-rocR region, than in wild-type strain 168. The high specific productivity in strain MGB874 is likely attributable to the higher expression levels of the target gene resulting from an increased promoter activity and plasmid copy number. Thus, the combined effects of the improved cell yield by deletion of the rocDEF-rocR region and the increased specific productivity by deletion of another gene(s) or the genomic reduction itself enhanced the production of recombinant enzymes in MGB874. Our findings represent a good starting point for the further improvement of B. subtilis reduced-genome strains as cell factories for the production of heterologous enzymes.
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McDonald GD, Storrie-Lombardi MC. Biochemical constraints in a protobiotic earth devoid of basic amino acids: the "BAA(-) world". ASTROBIOLOGY 2010; 10:989-1000. [PMID: 21162678 DOI: 10.1089/ast.2010.0484] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
It has been hypothesized in this journal and elsewhere, based on surveys of published data from prebiotic synthesis experiments and carbonaceous meteorite analyses, that basic amino acids such as lysine and arginine were not abundant on prebiotic Earth. If the basic amino acids were incorporated only rarely into the first peptides formed in that environment, it is important to understand what protobiotic chemistry is possible in their absence. As an initial test of the hypothesis that basic amino acid negative [BAA(-)] proteins could have performed at least a subset of protobiotic chemistry, the current work reports on a survey of 13 archaeal and 13 bacterial genomes that has identified 61 modern gene sequences coding for known or putative proteins not containing arginine or lysine. Eleven of the sequences found code for proteins whose functions are well known and important in the biochemistry of modern microbial life: lysine biosynthesis protein LysW, arginine cluster proteins, copper ion binding proteins, bacterial flagellar proteins, and PE or PPE family proteins. These data indicate that the lack of basic amino acids does not prevent peptides or proteins from serving useful structural and biochemical functions. However, as would be predicted from fundamental physicochemical principles, we see no fossil evidence of prebiotic BAA(-) peptide sequences capable of interacting directly with nucleic acids.
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Affiliation(s)
- Gene D McDonald
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.
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Alcaraz LD, Moreno-Hagelsieb G, Eguiarte LE, Souza V, Herrera-Estrella L, Olmedo G. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics 2010; 11:332. [PMID: 20504335 PMCID: PMC2890564 DOI: 10.1186/1471-2164-11-332] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 05/26/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus. RESULTS Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches. CONCLUSIONS The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches.
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Affiliation(s)
- Luis David Alcaraz
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN Campus Guanajuato, Guanajuato, México.
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Fujinami S, Terahara N, Krulwich TA, Ito M. Motility and chemotaxis in alkaliphilic Bacillus species. Future Microbiol 2010; 4:1137-49. [PMID: 19895217 DOI: 10.2217/fmb.09.76] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
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.
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Affiliation(s)
- Shun Fujinami
- NITE Bioresource Information Center, Department of Biotechnology, National Institute of Technology and Evaluation, Nishihara, Shibuya-ku, Tokyo, Japan.
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Mutations alter the sodium versus proton use of a Bacillus clausii flagellar motor and confer dual ion use on Bacillus subtilis motors. Proc Natl Acad Sci U S A 2008; 105:14359-64. [PMID: 18796609 DOI: 10.1073/pnas.0802106105] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Antibacterial activity of cyclodextrins against Bacillus strains. Arch Microbiol 2008; 190:605-9. [DOI: 10.1007/s00203-008-0415-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 06/28/2008] [Accepted: 07/09/2008] [Indexed: 01/23/2023]
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