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Koehler L, Flemming FE, Schrallhammer M. Towards an ecological understanding of the killer trait - A reproducible protocol for testing its impact on freshwater ciliates. Eur J Protistol 2019; 68:108-120. [PMID: 30826731 DOI: 10.1016/j.ejop.2019.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/04/2019] [Accepted: 02/04/2019] [Indexed: 11/19/2022]
Abstract
Paramecium strains with the ability to kill other paramecia often harbour intracellular bacteria belonging to the genera Caedibacter or Caedimonas. Central structures of this killer trait are refractile bodies (R-bodies) produced by the endosymbionts. Once ingested by a sensitive Paramecium, R-bodies presumably act as delivery system for an unidentified toxin which causes the death of endosymbiont-free paramecia while those infected gain resistance from their symbionts. The killer trait is therefore considered as competitive advantage for the hosts of R-body producers. While its effectiveness against paramecia is well documented, the effects on other aquatic ciliates are much less studied. In order to address the broadness of the killer trait, a reproducible killer test assay considering the effects on predatory ciliates (Climacostomum virens and Dileptus jonesi) as well as potential bacterivorous Paramecium competitors (Dexiostoma campyla, Euplotes aediculatus, Euplotes woodruffi, and Spirostomum teres) as possibly susceptible species was established. All used organisms were molecularly characterized to increase traceability and reproducibility. The absence of any lethal effects in both predators and competitors after exposure to killer paramecia strongly suggests a narrow action range for the killer trait. Thus, R-body producing bacteria provide their host with a complex, costly strategy to outcompete symbiont-free congeners only.
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Affiliation(s)
- Lars Koehler
- Institute of Biology II, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany; Institute of Hydrobiology, Technische Universität Dresden, 01217 Dresden, Germany
| | - Felicitas E Flemming
- Institute of Biology II, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Martina Schrallhammer
- Institute of Biology II, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany.
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Schrallhammer M, Castelli M, Petroni G. Phylogenetic relationships among endosymbiotic R-body producer: Bacteria providing their host the killer trait. Syst Appl Microbiol 2018; 41:213-220. [PMID: 29426636 DOI: 10.1016/j.syapm.2018.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/10/2018] [Accepted: 01/17/2018] [Indexed: 11/28/2022]
Abstract
R-body producing bacterial endosymbionts of Paramecium spp. transform their hosts into "killer" paramecia and provide them a selective advantage. This killer trait is connected to the presence of R-bodies, which are peculiar, tightly coiled protein ribbons capable of rapid unrolling. Based mainly on those two characteristics the respective obligate intracellular bacteria have been comprised in the genus Caedibacter and additional traits such as host species, subcellular localization, and R-body dimensions and mode of unrolling were used for species discrimination. Previous studies applying the full-cycle rRNA approach demonstrated the polyphyly of this assemblage. Following this approach, we obtained new sequences and in situ hybridizations for five strains of Caedibacter taeniospiralis and four strains associated to Caedibacter varicaedens and Caedibacter caryophilus. Detailed phylogenetic reconstructions confirm the association of C. taeniospiralis to Fastidiosibacteraceae and to Holosporales in case of the others. Therefore, we critically revise the taxonomy of the latter group. The high 16S rRNA gene sequence similarity among the type strains of Caedibacter varicaedens and C. caryophilus indicate that they should be classified within a single species for which we propose Caedimonas varicaedens comb. nov. owing to the priority of Caedibacter varicaedens. Moreover, we propose to establish the new family Caedimonadaceae fam. nov. to encompass Caedimonas varicaedens, "Ca. Paracaedimonas acanthamoebae" comb. nov. and "Ca. Nucleicultrix amoebiphila" within the order Holosporales.
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Affiliation(s)
- Martina Schrallhammer
- Institute of Biology II, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany.
| | - Michele Castelli
- Department of Veterinary Medicine, University of Milan, 20133 Milan, Italy; Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Giulio Petroni
- Department of Biology, University of Pisa, 56126 Pisa, Italy
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Stringent Expression Control of Pathogenic R-body Production in Legume Symbiont Azorhizobium caulinodans. mBio 2017; 8:mBio.00715-17. [PMID: 28743814 PMCID: PMC5527310 DOI: 10.1128/mbio.00715-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
R bodies are insoluble large polymers consisting of small proteins encoded by reb genes and are coiled into cylindrical structures in bacterial cells. They were first discovered in Caedibacter species, which are obligate endosymbionts of paramecia. Caedibacter confers a killer trait on the host paramecia. R-body-producing symbionts are released from their host paramecia and kill symbiont-free paramecia after ingestion. The roles of R bodies have not been explained in bacteria other than Caedibacter. Azorhizobium caulinodans ORS571, a microsymbiont of the legume Sesbania rostrata, carries a reb operon containing four reb genes that are regulated by the repressor PraR. Herein, deletion of the praR gene resulted in R-body formation and death of host plant cells. The rebR gene in the reb operon encodes an activator. Three PraR binding sites and a RebR binding site are present in the promoter region of the reb operon. Expression analyses using strains with mutations within the PraR binding site and/or the RebR binding site revealed that PraR and RebR directly control the expression of the reb operon and that PraR dominantly represses reb expression. Furthermore, we found that the reb operon is highly expressed at low temperatures and that 2-oxoglutarate induces the expression of the reb operon by inhibiting PraR binding to the reb promoter. We conclude that R bodies are toxic not only in paramecium symbiosis but also in relationships between other bacteria and eukaryotic cells and that R-body formation is controlled by environmental factors. Caedibacter species, which are obligate endosymbiotic bacteria of paramecia, produce R bodies, and R-body-producing endosymbionts that are released from their hosts are pathogenic to symbiont-free paramecia. Besides Caedibacter species, R bodies have also been observed in a few free-living bacteria, but the significance of R-body production in these bacteria is still unknown. Recent advances in genome sequencing technologies revealed that many Gram-negative bacteria possess reb genes encoding R-body components, and interestingly, many of them are animal and plant pathogens. Azorhizobium caulinodans, a microsymbiont of the tropical legume Sesbania rostrata, also possesses reb genes. In this study, we demonstrate that A. caulinodans has ability to kill the host plant cells by producing R bodies, suggesting that pathogenicity conferred by an R body might be universal in bacteria possessing reb genes. Furthermore, we provide the first insight into the molecular mechanism underlying the expression of R-body production in response to environmental factors, such as temperature and 2-oxoglutarate.
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Polka JK, Silver PA. A Tunable Protein Piston That Breaks Membranes to Release Encapsulated Cargo. ACS Synth Biol 2016; 5:303-11. [PMID: 26814170 DOI: 10.1021/acssynbio.5b00237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Movement of molecules across membranes in response to a stimulus is a key component of cellular programming. Here, we characterize and manipulate the response of a protein-based piston capable of puncturing membranes in a pH-dependent manner. Our protein actuator consists of modified R bodies found in a bacterial endosymbiont of paramecium. We express and purify R bodies from in E. coli; these pistons undergo multiple rounds of rapid extension and retraction. We developed a high throughput screen for mutants with altered pH sensitivity for tuning of the extension process. We show that the R bodies are capable of acting as synthetic pH-dependent pistons that can puncture E. coli membranes to release the trapped content. As such, these protein machines present a novel way to selectively rupture membrane compartments and will be important for programming cellular compartmentalization.
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Affiliation(s)
- Jessica K. Polka
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Pamela A. Silver
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
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A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria. G3-GENES GENOMES GENETICS 2013; 3:505-16. [PMID: 23450193 PMCID: PMC3583457 DOI: 10.1534/g3.112.005231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/09/2013] [Indexed: 12/29/2022]
Abstract
Bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. However, the diversity, occurrence, and mechanisms of these interactions often are not fully known. The obligate bacterial endosymbionts of Paramecium provide their hosts with the ability to kill sensitive Paramecium strains through the production of R-bodies, highly insoluble coiled protein ribbons. R-bodies have been observed in a number of free-living bacteria, where their function is unknown. We have performed an exhaustive survey of genes coding for homologs of Reb proteins (R-body components) in complete bacterial genomes. We found that reb genes are much more widespread than previously thought, being present in representatives of major Proteobacterial subdivisions, including many free-living taxa, as well as taxa known to be involved in various kinds of interactions with eukaryotes, from mutualistic associations to pathogenicity. Reb proteins display very good conservation at the sequence level, suggesting that they may produce functional R-bodies. Phylogenomic analysis indicates that reb genes underwent a complex evolutionary history and allowed the identification of candidates potentially involved in R-body assembly, functioning, regulation, or toxicity. Our results strongly suggest that the ability to produce R-bodies is likely widespread in Proteobacteria. The potential involvement of R-bodies in as yet unexplored interactions with eukaryotes and the consequent ecological implications are discussed.
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Schrallhammer M, Galati S, Altenbuchner J, Schweikert M, Görtz HD, Petroni G. Tracing the role of R-bodies in the killer trait: Absence of toxicity of R-body producing recombinant E. coli on paramecia. Eur J Protistol 2012; 48:290-6. [DOI: 10.1016/j.ejop.2012.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/16/2012] [Accepted: 01/17/2012] [Indexed: 10/28/2022]
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Lim CK, Hassan KA, Tetu SG, Loper JE, Paulsen IT. The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5. PLoS One 2012; 7:e39139. [PMID: 22723948 PMCID: PMC3377617 DOI: 10.1371/journal.pone.0039139] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 05/18/2012] [Indexed: 11/18/2022] Open
Abstract
One of the most important micronutrients for bacterial growth is iron, whose bioavailability in soil is limited. Consequently, rhizospheric bacteria such as Pseudomonas fluorescens employ a range of mechanisms to acquire or compete for iron. We investigated the transcriptomic and proteomic effects of iron limitation on P. fluorescens Pf-5 by employing microarray and iTRAQ techniques, respectively. Analysis of this data revealed that genes encoding functions related to iron homeostasis, including pyoverdine and enantio-pyochelin biosynthesis, a number of TonB-dependent receptor systems, as well as some inner-membrane transporters, were significantly up-regulated in response to iron limitation. Transcription of a ribosomal protein L36-encoding gene was also highly up-regulated during iron limitation. Certain genes or proteins involved in biosynthesis of secondary metabolites such as 2,4-diacetylphloroglucinol (DAPG), orfamide A and pyrrolnitrin, as well as a chitinase, were over-expressed under iron-limited conditions. In contrast, we observed that expression of genes involved in hydrogen cyanide production and flagellar biosynthesis were down-regulated in an iron-depleted culture medium. Phenotypic tests revealed that Pf-5 had reduced swarming motility on semi-solid agar in response to iron limitation. Comparison of the transcriptomic data with the proteomic data suggested that iron acquisition is regulated at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Chee Kent Lim
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Joyce E. Loper
- USDA-ARS Horticultural Crops Research Laboratory and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- * E-mail:
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Schrallhammer M, Schweikert M. The Killer Effect of Paramecium and Its Causative Agents. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-3-540-92677-1_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Görtz HD, Fokin SI. Diversity of Endosymbiotic Bacteria inParamecium. ENDOSYMBIONTS IN PARAMECIUM 2009. [DOI: 10.1007/978-3-540-92677-1_6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Heruth DP, Pond FR, Dilts JA, Quackenbush RL. Characterization of genetic determinants for R body synthesis and assembly in Caedibacter taeniospiralis 47 and 116. J Bacteriol 1994; 176:3559-67. [PMID: 8206833 PMCID: PMC205544 DOI: 10.1128/jb.176.12.3559-3567.1994] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Caedibacter taeniospiralis, an obligate bacterial endosymbiont of Paramecium tetraurelia, confers a killing trait upon its host paramecium. Type 51 R bodies (refractile inclusion bodies) are synthesized by these endosymbionts and are required for expression of the killing trait. The nucleotide sequence of the genetic determinants for type 51 R body synthesis and assembly was determined for C. taeniospiralis 47 and 116. Three independently transcribed genes (rebA, rebB, and rebC) were characterized. To date these are the only genes from C. taeniospiralis to be sequenced and characterized. DNA regulatory regions are recognized by Escherichia coli, and codon usage appears similar to that in E. coli. A fourth open reading frame with appropriate regulatory sequences was found within the reb locus, but no evidence was obtained to suggest that this putative gene is expressed in E. coli. The R body-encoding sequences from both strains are identical. Two-dimensional gel electrophoresis of deletion derivatives shows that two polymerization events are involved in R body assembly. One polymerization event requires only RebB and RebC; the other requires all three proteins. Expression of RebC is necessary for the posttranslational modification of RebA and RebB into species with three and two different molecular weights, respectively. In the presence of RebC, each species of RebB with a different molecular weight has six different isoelectric points.
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Affiliation(s)
- D P Heruth
- Department of Microbiology, School of Medicine, University of South Dakota, Vermillion 57069
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Abstract
Until 10 years ago, R bodies were known only as diagnostic features by which endosymbionts of paramecia were identified as kappa particles. They were thought to be limited to the cytoplasm of two species in the Paramecium aurelia species complex. Now, R bodies have been found in free-living bacteria and other Paramecium species. The organisms now known to form R bodies include the cytoplasmic kappa endosymbionts of P. biaurelia and P. tetraurelia, the macronuclear kappa endosymbionts of P. caudatum, Pseudomonas avenae (a free-living plant pathogen), Pseudomonas taeniospiralis (a hydrogen-oxidizing soil microorganism), Rhodospirillum centenum (a photosynthetic bacterium), and a soil bacterium, EPS-5028, which is probably a pseudomonad. R bodies themselves fall into five distinct groups, distinguished by size, the morphology of the R-body ribbons, and the unrolling behavior of wound R bodies. In recent years, the inherent difficulties in studying the organization and assembly of R bodies by the obligate endosymbiont kappa, have been alleviated by cloning and expressing genetic determinants for these R bodies (type 51) in Escherichia coli. Type 51 R-body synthesis requires three low-molecular-mass polypeptides. One of these is modified posttranslationally, giving rise to 12 polypeptide species, which are the major structural subunits of the R body. R bodies are encoded in kappa species by extrachromosomal elements. Type 51 R bodies, produced in Caedibacter taeniospiralis, are encoded by a plasmid, whereas bacteriophage genomes probably control R-body synthesis in other kappa species. However, there is no evidence that either bacteriophages or plasmids are present in P. avenae or P. taeniospiralis. No sequence homology was detected between type 51 R-body-encoding DNA and DNA from any R-body-producing species, except C. varicaedens 1038. The evolutionary relatedness of different types of R bodies remains unknown.
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12
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Gibson I. A comparison of the refractile bodies (R-bodies) of certain bacteria—III. Nucleotide sequence homologies and R-body function. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/0739-6260(84)90039-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Jurand A, Rudman BM, Preer JR. Prelethal symptoms of the killing action of some non-kappa killers in theParamecium aurelia complex. ACTA ACUST UNITED AC 1982. [DOI: 10.1002/jez.1402200202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jurand A, Preer JR, Rudman BM. Further investigations on the prelethal effects of the killing action of kappa containing killer stocks ofParamecium aurelia. ACTA ACUST UNITED AC 1978. [DOI: 10.1002/jez.1402060105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Koizumi S, Kobayashi S. A study on the mate-killer toxin by microinjection in Paramecium. Genet Res (Camb) 1976; 27:179-85. [PMID: 1278682 DOI: 10.1017/s0016672300016384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
SUMMARYThe killing action by mu toxin, which is contained in the cytoplasm of stock 540,Paramecium primaurelia, was demonstrated against the various stocks of paramecia by means of microinjection. Most of the toxin is present in the soluble fraction of the host cytoplasm. The toxin was precipitated by ammonium sulphate at 50–80% saturation, and was almost completely inactivated by incubation at 60 °C for 30 min. Pre-autogamous paramecia were more sensitive than post-autogamous ones to the toxin. Paramecia which bear endosymbionts were generally resistant to the mate-killer toxin.
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Preer JR, Preer LB, Jurand A. Kappa and other endosymbionts in Paramecium aurelia. BACTERIOLOGICAL REVIEWS 1974; 38:113-63. [PMID: 4599970 PMCID: PMC413848 DOI: 10.1128/br.38.2.113-163.1974] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Preer JR, Preer LB, Rudman B, Jurand A. Isolation and composition of bacteriophage-like particles from kappa of killer Paramecia. MOLECULAR & GENERAL GENETICS : MGG 1971; 111:202-8. [PMID: 5563933 DOI: 10.1007/bf00433105] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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