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Recent Advances in the Study of Gas Vesicle Proteins and Application of Gas Vesicles in Biomedical Research. Life (Basel) 2022; 12:life12091455. [PMID: 36143491 PMCID: PMC9501494 DOI: 10.3390/life12091455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022] Open
Abstract
The formation of gas vesicles has been investigated in bacteria and haloarchaea for more than 50 years. These air-filled nanostructures allow cells to stay at a certain height optimal for growth in their watery environment. Several gvp genes are involved and have been studied in Halobacterium salinarum, cyanobacteria, Bacillus megaterium, and Serratia sp. ATCC39006 in more detail. GvpA and GvpC form the gas vesicle shell, and additional Gvp are required as minor structural proteins, chaperones, an ATP-hydrolyzing enzyme, or as gene regulators. We analyzed the Gvp proteins of Hbt. salinarum with respect to their protein–protein interactions, and developed a model for the formation of these nanostructures. Gas vesicles are also used in biomedical research. Since they scatter waves and produce ultrasound contrast, they could serve as novel contrast agent for ultrasound or magnetic resonance imaging. Additionally, gas vesicles were engineered as acoustic biosensors to determine enzyme activities in cells. These applications are based on modifications of the surface protein GvpC that alter the mechanical properties of the gas vesicles. In addition, gas vesicles have been decorated with GvpC proteins fused to peptides of bacterial or viral pathogens and are used as tools for vaccine development.
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Maeda K, Okuda Y, Enomoto G, Watanabe S, Ikeuchi M. Biosynthesis of a sulfated exopolysaccharide, synechan, and bloom formation in the model cyanobacterium Synechocystis sp. strain PCC 6803. eLife 2021; 10:66538. [PMID: 34127188 PMCID: PMC8205485 DOI: 10.7554/elife.66538] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/07/2021] [Indexed: 01/10/2023] Open
Abstract
Extracellularpolysaccharides of bacteria contribute to biofilm formation, stress tolerance, and infectivity. Cyanobacteria, the oxygenic photoautotrophic bacteria, uniquely produce sulfated extracellular polysaccharides among bacteria to support phototrophic biofilms. In addition, sulfated polysaccharides of cyanobacteria and other organisms have been focused as beneficial biomaterial. However, very little is known about their biosynthesis machinery and function in cyanobacteria. Here, we found that the model cyanobacterium, Synechocystis sp. strain PCC 6803, formed bloom-like cell aggregates embedded in sulfated extracellular polysaccharides (designated as synechan) and identified whole set of genes responsible for synechan biosynthesis and its transcriptional regulation, thereby suggesting a model for the synechan biosynthesis apparatus. Because similar genes are found in many cyanobacterial genomes with wide variation, our findings may lead elucidation of various sulfated polysaccharides, their functions, and their potential application in biotechnology. Bacteria are single-cell microorganisms that can form communities called biofilms, which stick to surfaces such as rocks, plants or animals. Biofilms confer protection to bacteria and allow them to colonize new environments. The physical scaffold of biofilms is a viscous matrix made of several molecules, the main one being polysaccharides, complex carbohydrates formed by many monosaccharides (single sugar molecules) joined together. Cyanobacteria, also known as blue-green algae, are a type of bacteria that produce oxygen and use sunlight as an energy source, just as plants and algae do. Cyanobacteria produce extracellular polysaccharides that contain sulfate groups. These sulfated polysaccharides are also produced by animals and algae but are not common in other bacteria or plants. One possible role of sulfated, extracellular polysaccharides in cyanobacteria is keeping cells together in the floating aggregates found in cyanobacterial blooms. These are visible discolorations of the water caused by an overgrowth of cyanobacteria that occur in lakes, estuaries and coastal waters. However, little is known about how these polysaccharides are synthesized in cyanobacteria and what their natural role is. Maeda et al. found a strain of cyanobacteria that formed bloom-like aggregates that were embedded in sulfated extracellular polysaccharides. Using genetic engineering techniques, the researchers identified a set of genes responsible for producing a sulfated extracellular polysaccharide and regulating its levels. They also found that cell aggregates of cyanobacteria can float without having intracellular gas vesicles, which was previously thought to enable blooms to float. The results of the present study could have applications for human health, since many sulfated polysaccharides have antiviral, antitumor or anti-inflammatory properties, and similar genes are found in many cyanobacteria. In addition, these findings could be useful for controlling toxic cyanobacterial blooms, which are becoming increasingly problematic for society.
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Affiliation(s)
- Kaisei Maeda
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Yukiko Okuda
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.,Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
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Cai K, Xu BY, Jiang YL, Wang Y, Chen Y, Zhou CZ, Li Q. The model cyanobacteria Anabaena sp. PCC 7120 possess an intact but partially degenerated gene cluster encoding gas vesicles. BMC Microbiol 2020; 20:110. [PMID: 32375647 PMCID: PMC7204071 DOI: 10.1186/s12866-020-01805-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/27/2020] [Indexed: 11/23/2022] Open
Abstract
Background Bacterial gas vesicles, composed of two major gas vesicle proteins and filled with gas, are a unique class of intracellular bubble-like nanostructures. They provide buoyancy for cells, and thus play an essential role in the growth and survival of aquatic and soil microbes. Moreover, the gas vesicle could be applied to multimodal and noninvasive biological imaging as a potential nanoscale contrast agent. To date, cylinder-shaped gas vesicles have been found in several strains of cyanobacteria. However, whether the functional gas vesicles could be produced in the model filamentous cyanobacteria Anabaena sp. PCC 7120 remains controversial. Results In this study, we found that an intact gvp gene cluster indeed exists in the model filamentous cyanobacteria Anabaena sp. PCC 7120. Real-time PCR assays showed that the gvpA gene is constitutively transcribed in vivo, and its expression level is upregulated at low light intensity and/or high growth temperature. Functional expression of this intact gvp gene cluster enables the recombinant Escherichia coli to gain the capability of floatation in the liquid medium, thanks to the assembly of irregular gas vesicles. Furthermore, crystal structure of GvpF in combination with enzymatic activity assays of GvpN suggested that these two auxiliary proteins of gas vesicle are structurally and enzymatically conserved, respectively. Conclusions Our findings show that the laboratory strain of model filamentous cyanobacteria Anabaena sp. PCC 7120 possesses an intact but partially degenerated gas vesicle gene cluster, indicating that the natural isolate might be able to produce gas vesicles under some given environmental stimuli for better floatation.
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Affiliation(s)
- Kun Cai
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Bo-Ying Xu
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Ying Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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Huang R, Lin J, Gao D, Zhang F, Yi L, Huang Y, Yan X, Duan Y, Zhu X. Discovery of gas vesicles in Streptomyces sp. CB03234-S and potential effects of gas vesicle gene overexpression on morphological and metabolic changes in streptomycetes. Appl Microbiol Biotechnol 2019; 103:5751-5761. [DOI: 10.1007/s00253-019-09891-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 12/24/2022]
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Knitsch R, Schneefeld M, Weitzel K, Pfeifer F. Mutations in the major gas vesicle protein GvpA and impacts on gas vesicle formation in Haloferax volcanii. Mol Microbiol 2017; 106:530-542. [PMID: 28898511 DOI: 10.1111/mmi.13833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 11/28/2022]
Abstract
Gas vesicles are proteinaceous, gas-filled nanostructures produced by some bacteria and archaea. The hydrophobic major structural protein GvpA forms the ribbed gas vesicle wall. An in-silico 3D-model of GvpA of the predicted coil-α1-β1-β2-α2-coil structure is available and implies that the two β-chains constitute the hydrophobic interior surface of the gas vesicle wall. To test the importance of individual amino acids in GvpA we performed 85 single substitutions and analyzed these variants in Haloferax volcanii ΔA + Amut transformants for their ability to form gas vesicles (Vac+ phenotype). In most cases, an alanine substitution of a non-polar residue did not abolish gas vesicle formation, but the replacement of single non-polar by charged residues in β1 or β2 resulted in Vac- transformants. A replacement of residues near the β-turn altered the spindle-shape to a cylindrical morphology of the gas vesicles. Vac- transformants were also obtained with alanine substitutions of charged residues of helix α1 suggesting that these amino acids form salt-bridges with another GvpA monomer. In helix α2, only the alanine substitution of His53 or Tyr54, led to Vac- transformants, whereas most other substitutions had no effect. We discuss our results in respect to the GvpA structure and data available from solid-state NMR.
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Affiliation(s)
- Regine Knitsch
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Marie Schneefeld
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Kerstin Weitzel
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Felicitas Pfeifer
- Microbiology and Archaea, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
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Diversity of KaiC-based timing systems in marine Cyanobacteria. Mar Genomics 2014; 14:3-16. [PMID: 24388874 DOI: 10.1016/j.margen.2013.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 11/19/2013] [Accepted: 12/18/2013] [Indexed: 12/21/2022]
Abstract
The coordination of biological activities into daily cycles provides an important advantage for the fitness of diverse organisms. Most eukaryotes possess an internal clock ticking with a periodicity of about one day to anticipate sunrise and sunset. The 24-hour period of the free-running rhythm is highly robust against many changes in the natural environment. Among prokaryotes, only Cyanobacteria are known to harbor such a circadian clock. Its core oscillator consists of just three proteins, KaiA, KaiB, and KaiC that produce 24-hour oscillations of KaiC phosphorylation, even in vitro. This unique three-protein oscillator is well documented for the freshwater cyanobacterium Synechococcus elongatus PCC 7942. Several physiological studies demonstrate a circadian clock also for other Cyanobacteria including marine species. Genes for the core clock components are present in nearly all marine cyanobacterial species, though there are large differences in the specific composition of these genes. In the first section of this review we summarize data on the model circadian clock from S. elongatus PCC 7942 and compare it to the reduced clock system of the marine cyanobacterium Prochlorococcus marinus MED4. In the second part we discuss the diversity of timing mechanisms in other marine Cyanobacteria with regard to the presence or absence of different components of the clock.
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Ramsay JP, Salmond GPC. Quorum sensing-controlled buoyancy through gas vesicles: Intracellular bacterial microcompartments for environmental adaptation. Commun Integr Biol 2012; 5:96-8. [PMID: 22482022 DOI: 10.4161/cib.18532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Gas vesicles are gas-filled microcompartments produced by many cyanobacteria and haloarchaea to regulate buoyancy and control positioning in the water column. Recently we identified the first case of gas vesicle production by a member of the Enterobacteriaceae, Serratia sp ATCC39006. Gas vesicle production enabled colonisation of the air-liquid interface and was positively regulated in low-oxygen conditions, suggesting development of these intracellular organelles is an adpative mechanism facilitating migration to the water surface. Vesicle production was also regulated by the intercellular communication molecule N‑butanoyl-L‑homoserine lactone (BHL) showing that gas vesicle production is controlled at the population level, through quorum sensing, with BHL acting as a morphogen. Gas vesicle production was also reciprocally regulated with flagella-driven swarming motility by the global regulatory protein RsmA, suggesting a fork in the regulatory pathway that controls induction of these distinct modes of mobility. Here we discuss these findings in the context of the interesting physiology of Serratia 39006 and highlight future prospects for gas vesicle research in this highly tractable strain.
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A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium. Proc Natl Acad Sci U S A 2011; 108:14932-7. [PMID: 21873216 DOI: 10.1073/pnas.1109169108] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gas vesicles are hollow intracellular proteinaceous organelles produced by aquatic Eubacteria and Archaea, including cyanobacteria and halobacteria. Gas vesicles increase buoyancy and allow taxis toward air-liquid interfaces, enabling subsequent niche colonization. Here we report a unique example of gas vesicle-mediated flotation in an enterobacterium; Serratia sp. strain ATCC39006. This strain is a member of the Enterobacteriaceae previously studied for its production of prodigiosin and carbapenem antibiotics. Genes required for gas vesicle synthesis mapped to a 16.6-kb gene cluster encoding three distinct homologs of the main structural protein, GvpA. Heterologous expression of this locus in Escherichia coli induced copious vesicle production and efficient cell buoyancy. Gas vesicle morphogenesis in Serratia enabled formation of a pellicle-like layer of highly vacuolated cells, which was dependent on oxygen limitation and the expression of ntrB/C and cheY-like regulatory genes within the gas-vesicle gene cluster. Gas vesicle biogenesis was strictly controlled by intercellular chemical signaling, through an N-acyl homoserine lactone, indicating that in this system the quorum-sensing molecule acts as a morphogen initiating organelle development. Flagella-based motility and gas vesicle morphogenesis were also oppositely regulated by the small RNA-binding protein, RsmA, suggesting environmental adaptation through physiological control of the choice between motility and flotation as alternative taxis modes. We propose that gas vesicle biogenesis in this strain represents a distinct mechanism of mobility, regulated by oxygen availability, nutritional status, the RsmA global regulatory system, and the quorum-sensing morphogen.
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Strunk T, Hamacher K, Hoffgaard F, Engelhardt H, Zillig MD, Faist K, Wenzel W, Pfeifer F. Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo. Mol Microbiol 2011; 81:56-68. [PMID: 21542854 DOI: 10.1111/j.1365-2958.2011.07669.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Gas vesicles are gas-filled protein structures increasing the buoyancy of cells. The gas vesicle envelope is mainly constituted by the 8 kDa protein GvpA forming a wall with a water excluding inner surface. A structure of GvpA is not available; recent solid-state NMR results suggest a coil-α-β-β-α-coil fold. We obtained a first structural model of GvpA by high-performance de novo modelling. Attenuated total reflection (ATR)-Fourier transform infrared spectroscopy (FTIR) supported this structure. A dimer of GvpA was derived that could explain the formation of the protein monolayer in the gas vesicle wall. The hydrophobic inner surface is mainly constituted by anti-parallel β-strands. The proposed structure allows the pinpointing of contact sites that were mutated and tested for the ability to form gas vesicles in haloarchaea. Mutations in α-helix I and α-helix II, but also in the β-turn affected the gas vesicle formation, whereas other alterations had no effect. All mutants supported the structural features deduced from the model. The proposed GvpA dimers allow the formation of a monolayer protein wall, also consistent with protease treatments of isolated gas vesicles.
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Affiliation(s)
- Timo Strunk
- Institute for Nanotechnology, Karlsruhe Institute of Technology, PO Box 3640, D-76021 Karlsruhe, Germany
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Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One 2010; 5:e9605. [PMID: 20333302 PMCID: PMC2841640 DOI: 10.1371/journal.pone.0009605] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 02/11/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
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Affiliation(s)
- Amber L. Hartman
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Cédric Norais
- Institut de Génétique et Microbiologie, Université Paris-Sud, Paris, France
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jonathan H. Badger
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Stéphane Delmas
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Sam Haldenby
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Ramana Madupu
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Jeffrey Robinson
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Qinghu Ren
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Todd M. Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Julie Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Mecky Pohlschroder
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Charles Daniels
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Thorsten Allers
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan A. Eisen
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
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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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Maeder DL, Anderson I, Brettin TS, Bruce DC, Gilna P, Han CS, Lapidus A, Metcalf WW, Saunders E, Tapia R, Sowers KR. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol 2006; 188:7922-31. [PMID: 16980466 PMCID: PMC1636319 DOI: 10.1128/jb.00810-06] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. The genome of M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcina spp. in the region proximal to the origin of replication, with interspecies gene similarities as high as 95%. However, it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the distal semigenome. Of the 3,680 open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80% identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs were unique (nonorthologous) among these species, including a complete formate dehydrogenase operon, genes required for N-acetylmuramic acid synthesis, a 14-gene gas vesicle cluster, and a bacterial-like P450-specific ferredoxin reductase cluster not previously observed or characterized for this genus. A cryptic 36-kbp plasmid sequence that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143-nucleotide motif was detected in M. barkeri. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the relatively large M. acetivorans genome is the result of uniformly distributed multiple gene scale insertions and duplications, while the M. barkeri genome is characterized by localized inversions associated with the loss of gene content. In contrast, the short M. mazei genome most closely approximates the putative ancestral organizational state of these species.
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Affiliation(s)
- Dennis L Maeder
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 701 E. Pratt Street, Baltimore, MD 21202, USA
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14
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Dunton PG, Walsby AE. The diameter and critical collapse pressure of gas vesicles in Microcystis are correlated with GvpCs of different length. FEMS Microbiol Lett 2006; 247:37-43. [PMID: 15927745 DOI: 10.1016/j.femsle.2005.04.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 04/15/2005] [Accepted: 04/17/2005] [Indexed: 10/25/2022] Open
Abstract
In cyanobacteria the protein on the outside of the gas vesicle, GvpC, is characterised by the presence of a 33 amino acid residue repeat (33RR), which in some genera is highly conserved. The number of 33RRs correlates with the diameter of the gas vesicle and inversely with its strength. Gas vesicles isolated from Microcystis aeruginosa strain PCC 7806 were found to be wider and have a lower critical collapse pressure than those from Microcystis sp. strain BC 8401. The entire gas-vesicle gene cluster of the latter strain was sequenced and compared with the published sequence of the former: the sequences of nine of the ten gvp genes differed by only 1-5% between the two strains; the only substantial difference was in gvpC which in strain BC 8401 lacked a 99-nucleotide section encoding a 33RR. This observation further narrows the correlation of gas vesicle width to the number of 33RRs and suggests how Microcystis strains might be used in experimental manipulation of gas vesicle width and strength.
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Affiliation(s)
- Peter G Dunton
- School of Biological Sciences, University of Bristol, UK
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Oren A, Pri-El N, Shapiro O, Siboni N. Gas vesicles isolated fromHalobacteriumcells by lysis in hypotonic solution are structurally weakened. FEMS Microbiol Lett 2006; 252:337-41. [PMID: 16213677 DOI: 10.1016/j.femsle.2005.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2005] [Revised: 09/06/2005] [Accepted: 09/09/2005] [Indexed: 11/17/2022] Open
Abstract
Analysis of pressure-collapse curves of Halobacterium cells containing gas vesicles and of gas vesicles released from such cells by hypotonic lysis shows that the isolated gas vesicles are considerably weaker than those present within the cells: their mean critical collapse pressure was around 0.049-0.058 MPa, as compared to 0.082-0.095 MPa for intact cells. The hypotonic lysis procedure, which is widely used for the isolation of gas vesicles from members of the Halobacteriaceae, thus damages the mechanical properties of the vesicles. The phenomenon can possibly be attributed to the loss of one or more structural gas vesicle proteins such as GvpC, the protein that strengthens the vesicles built of GvpA subunits: Halobacterium GvpC is a highly acidic, typically "halophilic" protein, expected to denature in the absence of molar concentrations of salt.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, Israel.
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Abstract
Cyanobacteria such as Synechococcus elongatus PCC 7942, Thermosynechococcus elongatus BP-1, and Synechocystis species strain PCC 6803 have an endogenous timing mechanism that can generate and maintain a 24 h (circadian) periodicity to global (whole genome) gene expression patterns. This rhythmicity extends to many other physiological functions, including chromosome compaction. These rhythmic patterns seem to reflect the periodicity of availability of the primary energy source for these photoautotrophic organisms, the Sun. Presumably, eons of environmentally derived rhythmicity--light/dark cycles--have simply been mechanistically incorporated into the regulatory networks of these cyanobacteria. Genetic and biochemical experimentation over the last 15 years has identified many key components of the primary timing mechanism that generates rhythmicity, the input pathways that synchronize endogenous rhythms to exogenous rhythms, and the output pathways that transduce temporal information from the timekeeper to the regulators of gene expression and function. Amazingly, the primary timing mechanism has evidently been extracted from S. elongatus PCC 7942 and can also keep time in vitro. Mixing the circadian clock proteins KaiA, KaiB, and KaiC from S. elongatus PCC 7942 in vitro and adding ATP results in a circadian rhythm in the KaiC protein phosphorylation state. Nonetheless, many questions still loom regarding how this circadian clock mechanism works, how it communicates with the environment and how it regulates temporal patterns of gene expression. Many details regarding structure and function of the individual clock-related proteins are provided here as a basis to discuss these questions. A strong, data-intensive foundation has been developed to support the working model for the cyanobacterial circadian regulatory system. The eventual addition to that model of the metabolic parameters participating in the command and control of this circadian global regulatory system will ultimately allow a fascinating look into whole-cell physiology and metabolism and the consequential organization of global gene expression patterns.
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Affiliation(s)
- Stanly B Williams
- Department of Biology, Life Science Building, University of Utah, Salt Lake City, UT 84112, USA
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Shukla HD, DasSarma S. Complexity of gas vesicle biogenesis in Halobacterium sp. strain NRC-1: identification of five new proteins. J Bacteriol 2004; 186:3182-6. [PMID: 15126480 PMCID: PMC400621 DOI: 10.1128/jb.186.10.3182-3186.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of Halobacterium sp. strain NRC-1 contains a large gene cluster, gvpMLKJIHGFEDACNO, that is both necessary and sufficient for the production of buoyant gas-filled vesicles. Due to the resistance of gas vesicles to solubilization, only the major gas vesicle protein GvpA and a single minor protein, GvpC, were previously detected. Here, we used immunoblotting analysis to probe for the presence of gas vesicle proteins corresponding to five additional gvp gene products. Polyclonal antisera were raised in rabbits against LacZ-GvpF, -GvpJ, and -GvpM fusion proteins and against synthetic 15-amino-acid peptides from GvpG and -L. Immunoblotting analysis was performed on cell lysates of wild-type Halobacterium sp. strain NRC-1, gas vesicle-deficient mutants, and purified gas vesicles, after purification of LacZ fusion antibodies on protein A and beta-galactosidase affinity columns. Our results show the presence of five new gas vesicle proteins (GvpF, GvpG, GvpJ, GvpL, and GvpM), bringing the total number of proteins identified in the organelles to seven. Two of the new gas vesicle proteins are similar to GvpA (GvpJ and GvpM), and two proteins contain predicted coiled-coil domains (GvpF and GvpL). GvpL exhibited a multiplet ladder on sodium dodecyl sulfate-polyacrylamide gels indicative of oligomerization and self-assembly. We discuss the possible functions of the newly discovered gas vesicle proteins in biogenesis of these unique prokaryotic flotation organelles.
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Affiliation(s)
- Hem Dutt Shukla
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA
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