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McNeilly O, Mann R, Hamidian M, Gunawan C. Emerging Concern for Silver Nanoparticle Resistance in Acinetobacter baumannii and Other Bacteria. Front Microbiol 2021; 12:652863. [PMID: 33936010 PMCID: PMC8085274 DOI: 10.3389/fmicb.2021.652863] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The misuse of antibiotics combined with a lack of newly developed ones is the main contributors to the current antibiotic resistance crisis. There is a dire need for new and alternative antibacterial options and nanotechnology could be a solution. Metal-based nanoparticles, particularly silver nanoparticles (NAg), have garnered widespread popularity due to their unique physicochemical properties and broad-spectrum antibacterial activity. Consequently, NAg has seen extensive incorporation in many types of products across the healthcare and consumer market. Despite clear evidence of the strong antibacterial efficacy of NAg, studies have raised concerns over the development of silver-resistant bacteria. Resistance to cationic silver (Ag+) has been recognised for many years, but it has recently been found that bacterial resistance to NAg is also possible. It is also understood that exposure of bacteria to toxic heavy metals like silver can induce the emergence of antibiotic resistance through the process of co-selection. Acinetobacter baumannii is a Gram-negative coccobacillus and opportunistic nosocomial bacterial pathogen. It was recently listed as the "number one" critical level priority pathogen because of the significant rise of antibiotic resistance in this species. NAg has proven bactericidal activity towards A. baumannii, even against strains that display multi-drug resistance. However, despite ample evidence of heavy metal (including silver; Ag+) resistance in this bacterium, combined with reports of heavy metal-driven co-selection of antibiotic resistance, little research has been dedicated to assessing the potential for NAg resistance development in A. baumannii. This is worrisome, as the increasingly indiscriminate use of NAg could promote the development of silver resistance in this species, like what has occurred with antibiotics.
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Affiliation(s)
- Oliver McNeilly
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Riti Mann
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mohammad Hamidian
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Cindy Gunawan
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
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Engelhardt H, Bollschweiler D. Cryo-Electron Microscopy of Extremely Halophilic Microbes. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Panáček A, Kvítek L, Smékalová M, Večeřová R, Kolář M, Röderová M, Dyčka F, Šebela M, Prucek R, Tomanec O, Zbořil R. Bacterial resistance to silver nanoparticles and how to overcome it. NATURE NANOTECHNOLOGY 2018; 13:65-71. [PMID: 29203912 DOI: 10.1038/s41565-017-0013-y] [Citation(s) in RCA: 472] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/04/2017] [Indexed: 05/20/2023]
Abstract
Silver nanoparticles have already been successfully applied in various biomedical and antimicrobial technologies and products used in everyday life. Although bacterial resistance to antibiotics has been extensively discussed in the literature, the possible development of resistance to silver nanoparticles has not been fully explored. We report that the Gram-negative bacteria Escherichia coli 013, Pseudomonas aeruginosa CCM 3955 and E. coli CCM 3954 can develop resistance to silver nanoparticles after repeated exposure. The resistance stems from the production of the adhesive flagellum protein flagellin, which triggers the aggregation of the nanoparticles. This resistance evolves without any genetic changes; only phenotypic change is needed to reduce the nanoparticles' colloidal stability and thus eliminate their antibacterial activity. The resistance mechanism cannot be overcome by additional stabilization of silver nanoparticles using surfactants or polymers. It is, however, strongly suppressed by inhibiting flagellin production with pomegranate rind extract.
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Affiliation(s)
- Aleš Panáček
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Libor Kvítek
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Monika Smékalová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Renata Večeřová
- Department of Microbiology, Palacký University Olomouc, Olomouc, Czech Republic
| | - Milan Kolář
- Department of Microbiology, Palacký University Olomouc, Olomouc, Czech Republic
| | - Magdalena Röderová
- Department of Microbiology, Palacký University Olomouc, Olomouc, Czech Republic
| | - Filip Dyčka
- Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Robert Prucek
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Ondřej Tomanec
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Olomouc, Czech Republic
| | - Radek Zbořil
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University Olomouc, Olomouc, Czech Republic.
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Briegel A, Oikonomou CM, Chang YW, Kjær A, Huang AN, Kim KW, Ghosal D, Nguyen HH, Kenny D, Ogorzalek Loo RR, Gunsalus RP, Jensen GJ. Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis. EMBO Rep 2017; 18:1660-1670. [PMID: 28729461 DOI: 10.15252/embr.201744070] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a peptidoglycan cell wall, is unknown. Here, we use electron cryotomography to visualize the archaellar basal body in vivo in Thermococcus kodakaraensis KOD1. Compared to the homologous bacterial type IV pilus (T4P), we observe structural similarities as well as several unique features. While the position of the cytoplasmic ATPase appears conserved, it is not braced by linkages that extend upward through the cell envelope as in the T4P, but rather by cytoplasmic components that attach it to a large conical frustum up to 500 nm in diameter at its base. In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome-excluding material and may function as a polar organizing center for the coccoid cells.
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Affiliation(s)
- Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andreas Kjær
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Audrey N Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ki Woo Kim
- School of Ecology and Environmental System, Kyungpook National University, Sangju, South Korea
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hong H Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dorothy Kenny
- Department of Microbiology, Immunology and Molecular Genetics, The UCLA DOE Institute, University of California, Los Angeles, CA, USA
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology and Molecular Genetics, The UCLA DOE Institute, University of California, Los Angeles, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA .,Howard Hughes Medical Institute, Pasadena, CA, USA
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Bollschweiler D, Schaffer M, Lawrence CM, Engelhardt H. Cryo-electron microscopy of an extremely halophilic microbe: technical aspects. Extremophiles 2017; 21:393-398. [PMID: 28050645 PMCID: PMC5329092 DOI: 10.1007/s00792-016-0912-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/19/2016] [Indexed: 11/30/2022]
Abstract
Most halophilic Archaea of the class Halobacteriaceae depend on the presence of several molar sodium chloride for growth and cell integrity. This poses problems for structural studies, particularly for electron microscopy, where the high salt concentration results in diminished contrast. Since cryo-electron microscopy of intact cells provides new insights into the cellular and molecular organization under close-to-live conditions, we evaluated strategies and conditions to make halophilic microbes available for investigations in situ. Halobacterium salinarum, the test organism for this study, usually grows at 4.3 M NaCl. Adaptation to lower concentrations and subsequent NaCl reduction via dialysis led to still vital cells at 3 M salt. A comprehensive evaluation of vitrification parameters, thinning of frozen cells by focused-ion-beam micromachining, and cryo-electron microscopy revealed that structural studies under high salt conditions are possible in situ.
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Affiliation(s)
- Daniel Bollschweiler
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Miroslava Schaffer
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - C Martin Lawrence
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Harald Engelhardt
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152, Martinsried, 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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Syutkin AS, Pyatibratov MG, Fedorov OV. Flagella of halophilic archaea: differences in supramolecular organization. BIOCHEMISTRY (MOSCOW) 2015; 79:1470-82. [PMID: 25749160 DOI: 10.1134/s0006297914130033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Archaeal flagella are similar functionally to bacterial flagella, but structurally they are completely different. Helical archaeal flagellar filaments are formed of protein subunits called flagellins (archaellins). Notwithstanding progress in studies of archaeal flagella achieved in recent years, many problems in this area are still unsolved. In this review, we analyze the formation of these supramolecular structures by the example of flagellar filaments of halophilic archaea. Recent data on the structure of the flagellar filaments demonstrate that their supramolecular organization differs considerably in different haloarchaeal species.
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Affiliation(s)
- A S Syutkin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Briegel A, Ortega DR, Huang A, Oikonomou CM, Gunsalus RP, Jensen GJ. Structural conservation of chemotaxis machinery across Archaea and Bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:414-9. [PMID: 25581459 PMCID: PMC4782749 DOI: 10.1111/1758-2229.12265] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/12/2014] [Accepted: 12/25/2014] [Indexed: 05/27/2023]
Abstract
Chemotaxis allows cells to sense and respond to their environment. In Bacteria, stimuli are detected by arrays of chemoreceptors that relay the signal to a two-component regulatory system. These arrays take the form of highly stereotyped super-lattices comprising hexagonally packed trimers-of-receptor-dimers networked by rings of histidine kinase and coupling proteins. This structure is conserved across chemotactic Bacteria, and between membrane-bound and cytoplasmic arrays, and gives rise to the highly cooperative, dynamic nature of the signalling system. The chemotaxis system, absent in eukaryotes, is also found in Archaea, where its structural details remain uncharacterized. Here we provide evidence that the chemotaxis machinery was not present in the last archaeal common ancestor, but rather was introduced in one of the waves of lateral gene transfer that occurred after the branching of Eukaryota but before the diversification of Euryarchaeota. Unlike in Bacteria, the chemotaxis system then evolved largely vertically in Archaea, with very few subsequent successful lateral gene transfer events. By electron cryotomography, we find that the structure of both membrane-bound and cytoplasmic chemoreceptor arrays is conserved between Bacteria and Archaea, suggesting the fundamental importance of this signalling architecture across diverse prokaryotic lifestyles.
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Affiliation(s)
- Ariane Briegel
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
| | - Davi R. Ortega
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
| | - Audrey Huang
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
| | | | - Robert P. Gunsalus
- University of California Los Angeles, 609 Charles E. Young Dr. S., Los Angeles, CA 90095
| | - Grant J. Jensen
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
- Howard Hughes Medical Institute, 1200 E. California Blvd., Pasadena, CA 91125
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The Iho670 fibers of Ignicoccus hospitalis are anchored in the cell by a spherical structure located beneath the inner membrane. J Bacteriol 2014; 196:3807-15. [PMID: 25157085 DOI: 10.1128/jb.01861-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The Iho670 fibers of the hyperthermophilic crenarchaeon of Ignicoccus hospitalis were shown to contain several features that indicate them as type IV pilus-like structures. The application of different visualization methods, including electron tomography and the reconstruction of a three-dimensional model, enabled a detailed description of a hitherto undescribed anchoring structure of the cell appendages. It could be identified as a spherical structure beneath the inner membrane. Furthermore, pools of the fiber protein Iho670 could be localized in the inner as well as the outer cellular membrane of I. hospitalis cells and in the tubes/vesicles in the intermembrane compartment by immunological methods.
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Pyatibratov MG, Beznosov SN, Rachel R, Tiktopulo EI, Surin AK, Syutkin AS, Fedorov OV. Alternative flagellar filament types in the haloarchaeon Haloarcula marismortui. Can J Microbiol 2009; 54:835-44. [PMID: 18923552 DOI: 10.1139/w08-076] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many Archaea use rotation of helical flagellar filaments for swimming motility. We isolated and characterized the flagellar filaments of Haloarcula marismortui, an archaeal species previously considered to be nonmotile. Two Haloarcula marismortui phenotypes were discriminated--their filaments are composed predominantly of either FlaB or FlaA2 flagellin, and the corresponding genes are located on different replicons. FlaB and FlaA2 filaments differ in antigenicity and thermostability. FlaA2 filaments are distinctly thicker (20-22 nm) than FlaB filaments (16-18 nm). The observed filaments are nearly twice as thick as those of other characterized euryarchaeal filaments. The results suggest that the helicity of Haloarcula marismortui filaments is provided by a mechanism different from that in the related haloarchaeon Halobacterium salinarum, where 2 different flagellin molecules present in comparable quantities are required to form a helical filament.
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Affiliation(s)
- Michael G Pyatibratov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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Abstract
Prokaryotic cells move through liquids or over moist surfaces by swimming, swarming, gliding, twitching or floating. An impressive diversity of motility mechanisms has evolved in prokaryotes. Movement can involve surface appendages, such as flagella that spin, pili that pull and Mycoplasma 'legs' that walk. Internal structures, such as the cytoskeleton and gas vesicles, are involved in some types of motility, whereas the mechanisms of some other types of movement remain mysterious. Regardless of the type of motility machinery that is employed, most motile microorganisms use complex sensory systems to control their movements in response to stimuli, which allows them to migrate to optimal environments.
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Beznosov SN, Pyatibratov MG, Fedorov OV. On the multicomponent nature of Halobacterium salinarum flagella. Microbiology (Reading) 2007. [DOI: 10.1134/s002626170704008x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure. BMC Evol Biol 2007; 7:106. [PMID: 17605801 PMCID: PMC1914349 DOI: 10.1186/1471-2148-7-106] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 07/02/2007] [Indexed: 11/10/2022] Open
Abstract
Background As bacteria, motile archaeal species swim by means of rotating flagellum structures driven by a proton gradient force. Interestingly, experimental data have shown that the archaeal flagellum is non-homologous to the bacterial flagellum either in terms of overall structure, components and assembly. The growing number of complete archaeal genomes now permits to investigate the evolution of this unique motility system. Results We report here an exhaustive phylogenomic analysis of the components of the archaeal flagellum. In all complete archaeal genomes, the genes coding for flagellum components are co-localized in one or two well-conserved genomic clusters showing two different types of organizations. Despite their small size, these genes harbor a good phylogenetic signal that allows reconstruction of their evolutionary histories. These support a history of mainly vertical inheritance for the components of this unique motility system, and an interesting possible ancient horizontal gene transfer event (HGT) of a whole flagellum-coding gene cluster between Euryarchaeota and Crenarchaeota. Conclusion Our study is one of the few exhaustive phylogenomics analyses of a non-informational cell machinery from the third domain of life. We propose an evolutionary scenario for the evolution of the components of the archaeal flagellum. Moreover, we show that the components of the archaeal flagellar system have not been frequently transferred among archaeal species, indicating that gene fixation following HGT can also be rare for genes encoding components of large macromolecular complexes with a structural role.
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Malapaka RRV, Adebayo LO, Tripp BC. A Deletion Variant Study of the Functional Role of the Salmonella Flagellin Hypervariable Domain Region in Motility. J Mol Biol 2007; 365:1102-16. [PMID: 17109884 DOI: 10.1016/j.jmb.2006.10.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 10/12/2006] [Accepted: 10/16/2006] [Indexed: 01/17/2023]
Abstract
The eubacterial flagellum is a complex structure with an elongated extracellular filament that is composed primarily of many subunits of a flagellin protein. The highly conserved N and C termini of flagellin are important in its export and self-assembly, whereas the middle sequence region varies greatly in size and composition in different species and is known to be deletion-tolerant. In Salmonella typhimurium phase 1 flagellin, this "hypervariable" region encodes two solvent-exposed domains, D2 and D3, that form a knob-like feature on flagella fibers. The functional role of this structural feature in motility remains unclear. We investigated the structural and physiological role of the hypervariable region in flagella assembly, stability and cellular motility. A library of random internal deletion variants of S. typhimurium flagellin was constructed and screened for functional variants using a swarming agar motility assay. The relative cellular motility and propulsive force of ten representative variants were determined in semi-solid and liquid medium using colony swarming motility assays, video microscopy and optical trapping of single cells. All ten variants exhibited diminished motility, with varying extents of motility observed for internal deletions less than 75 residues and nearly complete loss of motility for deletions greater than 100 residues. The mechanical stability of the variant flagella fibers also decreased with increasing size of deletion. Comparison of the variant sequences with the wild-type sequence and structure indicated that all deletions involved loss of hydrophobic core residues, and removal of both partial and complete segments of secondary structure in the D2 and D3 domains. Homology modeling predicted disruptions of secondary structures in each variant. The hypervariable region D2 and D3 domains appear to stabilize the folded conformation of the flagellin protein and contribute to the mechanical stability and propulsive force of the flagella fibers.
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Affiliation(s)
- Raghu Ram V Malapaka
- Department of Biological Sciences, College of Arts and Sciences, Western Michigan University, Kalamazoo, MI 49008-5410, USA
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Ng SYM, Chaban B, Jarrell KF. Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J Mol Microbiol Biotechnol 2006; 11:167-91. [PMID: 16983194 DOI: 10.1159/000094053] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The archaeal flagellum is a unique motility organelle. While superficially similar to the bacterial flagellum, several similarities have been reported between the archaeal flagellum and the bacterial type IV pilus system. These include the multiflagellin nature of the flagellar filament, N-terminal sequence similarities between archaeal flagellins and bacterial type IV pilins, as well as the presence of homologous proteins in the two systems. Recent advances in archaeal flagella research add to the growing list of similarities. First, the preflagellin peptidase that is responsible for processing the N-terminal signal peptide in preflagellins has been identified. The preflagellin peptidase is a membrane-bound enzyme topologically similar to its counterpart in the type IV pilus system (prepilin peptidase); the two enzymes are demonstrated to utilize the same catalytic mechanism. Second, it has been suggested that the archaeal flagellum and the bacterial type IV pilus share a similar mode of assembly. While bacterial flagellins and type IV pilins can be modified with O-linked glycans, N-linked glycans have recently been reported on archaeal flagellins. This mode of glycosylation, as well as the observation that the archaeal flagellum lacks a central channel, are both consistent with the proposed assembly model. On the other hand, the failure to identify other genes involved in archaeal flagellation by homology searches likely implies a novel aspect of the archaeal flagellar system. These interesting features remain to be deciphered through continued research. Such knowledge would be invaluable to motility and protein export studies in the Archaea.
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Affiliation(s)
- Sandy Y M Ng
- Department of Microbiology and Immunology, Queen's University, Kingston, Canada
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Cavalier-Smith T. Rooting the tree of life by transition analyses. Biol Direct 2006; 1:19. [PMID: 16834776 PMCID: PMC1586193 DOI: 10.1186/1745-6150-1-19] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 07/11/2006] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed--the most difficult problems in phylogeny. Protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution; ribosome-related and DNA-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it within eubacteria but in contradictory places. Palaeontology shows that eubacteria are much more ancient than eukaryotes, and, together with phylogenetic evidence that archaebacteria are sisters not ancestral to eukaryotes, implies that the root is not within the neomura. Transition analysis, involving comparative/developmental and selective arguments, can polarize major transitions and thereby systematically exclude the root from major clades possessing derived characters and thus locate it; previously the 20 shared neomuran characters were thus argued to be derived, but whether the root was within eubacteria or between them and archaebacteria remained controversial. RESULTS I analyze 13 major transitions within eubacteria, showing how they can all be congruently polarized. I infer the first fully resolved prokaryote tree, with a basal stem comprising the new infrakingdom Glidobacteria (Chlorobacteria, Hadobacteria, Cyanobacteria), which is entirely non-flagellate and probably ancestrally had gliding motility, and two derived branches (Gracilicutes and Unibacteria/Eurybacteria) that diverged immediately following the origin of flagella. Proteasome evolution shows that the universal root is outside a clade comprising neomura and Actinomycetales (proteates), and thus lies within other eubacteria, contrary to a widespread assumption that it is between eubacteria and neomura. Cell wall and flagellar evolution independently locate the root outside Posibacteria (Actinobacteria and Endobacteria), and thus among negibacteria with two membranes. Posibacteria are derived from Eurybacteria and ancestral to neomura. RNA polymerase and other insertions strongly favour the monophyly of Gracilicutes (Proteobacteria, Planctobacteria, Sphingobacteria, Spirochaetes). Evolution of the negibacterial outer membrane places the root within Eobacteria (Hadobacteria and Chlorobacteria, both primitively without lipopolysaccharide): as all phyla possessing the outer membrane beta-barrel protein Omp85 are highly probably derived, the root lies between them and Chlorobacteria, the only negibacteria without Omp85, or possibly within Chlorobacteria. CONCLUSION Chlorobacteria are probably the oldest and Archaebacteria the youngest bacteria, with Posibacteria of intermediate age, requiring radical reassessment of dominant views of bacterial evolution. The last ancestor of all life was a eubacterium with acyl-ester membrane lipids, large genome, murein peptidoglycan walls, and fully developed eubacterial molecular biology and cell division. It was a non-flagellate negibacterium with two membranes, probably a photosynthetic green non-sulphur bacterium with relatively primitive secretory machinery, not a heterotrophic posibacterium with one membrane.
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Malapaka VRR, Tripp BC. A theoretical model of Aquifex pyrophilus flagellin: implications for its thermostability. J Mol Model 2006; 12:481-93. [PMID: 16411078 DOI: 10.1007/s00894-005-0075-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Accepted: 10/17/2005] [Indexed: 10/25/2022]
Abstract
Aquifex pyrophilus is a flagellated hyperthermophilic eubacterial species that grows optimally at 85 degrees C. The thermostable A. pyrophilus flagellar filament is primarily composed of a single protein called flagellin (FlaA). The N- and C-terminal sequence regions of FlaA are important for self-assembly and share high sequence similarity with mesophilic bacterial flagellins. We have developed a predictive 3D-structure of FlaA, using the published structure of mesophilic Salmonella typhimurium flagellin (FliC) as a template and analyzed it with respect to possible determinants of thermostability. A sequence comparison of FlaA and FliC revealed a +7.0% increase in FlaA hydrophobic residues, a +0.6% increase in charged residues and a corresponding decrease of -6.0% in polar residues. The FlaA N- and C-termini also have higher proportions of hydrophobic and charged residues at the expense of polar residues and higher non-polar surface areas. Thus, a predominant stabilizing factor in FlaA appears to be increased hydrophobicity, which often confers greater rigidity to proteins. Fewer intramolecular ion pairs were observed in FlaA than FliC, although an increase in the positive charge potential of the FlaA D0 and D1 domains was also observed; increased intermolecular salt bridges may also contribute to the thermal stability of the oligomeric flagellar fiber. [Figure: see text].
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Affiliation(s)
- V Raghu Ram Malapaka
- Department of Biological Sciences, Mailstop 5410, 1903 West Michigan Avenue, Western Michigan University, Kalamazoo, MI 49008-5410, USA
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