Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018
Abstract
Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod / nif / noeM gene clusters from C. taiwanensis LMG19424 T and “ Cupriavidus neocalidonicus” STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterialmore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); French National Research Agency (ANR)
- OSTI Identifier:
- 1960100
- Alternate Identifier(s):
- OSTI ID: 1969972
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Name: Frontiers in Microbiology Journal Volume: 14; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Media SA
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Betaproteobacteria; root-nodule bacteria; bacteriophage; filamentous phage; symbiosis
Citation Formats
Klonowska, Agnieszka, Ardley, Julie, Moulin, Lionel, Zandberg, Jaco, Patrel, Delphine, Gollagher, Margaret, Marinova, Dora, Reddy, T. B. K., Varghese, Neha, Huntemann, Marcel, Woyke, Tanja, Seshadri, Rekha, Ivanova, Natalia, Kyrpides, Nikos, and Reeve, Wayne. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Switzerland: N. p., 2023.
Web. doi:10.3389/fmicb.2023.1082107.
Klonowska, Agnieszka, Ardley, Julie, Moulin, Lionel, Zandberg, Jaco, Patrel, Delphine, Gollagher, Margaret, Marinova, Dora, Reddy, T. B. K., Varghese, Neha, Huntemann, Marcel, Woyke, Tanja, Seshadri, Rekha, Ivanova, Natalia, Kyrpides, Nikos, & Reeve, Wayne. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Switzerland. https://doi.org/10.3389/fmicb.2023.1082107
Klonowska, Agnieszka, Ardley, Julie, Moulin, Lionel, Zandberg, Jaco, Patrel, Delphine, Gollagher, Margaret, Marinova, Dora, Reddy, T. B. K., Varghese, Neha, Huntemann, Marcel, Woyke, Tanja, Seshadri, Rekha, Ivanova, Natalia, Kyrpides, Nikos, and Reeve, Wayne. Tue .
"Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018". Switzerland. https://doi.org/10.3389/fmicb.2023.1082107.
@article{osti_1960100,
title = {Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018},
author = {Klonowska, Agnieszka and Ardley, Julie and Moulin, Lionel and Zandberg, Jaco and Patrel, Delphine and Gollagher, Margaret and Marinova, Dora and Reddy, T. B. K. and Varghese, Neha and Huntemann, Marcel and Woyke, Tanja and Seshadri, Rekha and Ivanova, Natalia and Kyrpides, Nikos and Reeve, Wayne},
abstractNote = {Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod / nif / noeM gene clusters from C. taiwanensis LMG19424 T and “ Cupriavidus neocalidonicus” STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.},
doi = {10.3389/fmicb.2023.1082107},
journal = {Frontiers in Microbiology},
number = ,
volume = 14,
place = {Switzerland},
year = {Tue Feb 28 00:00:00 EST 2023},
month = {Tue Feb 28 00:00:00 EST 2023}
}
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Two different evolutionary lines of filamentous phages in Ralstonia solanacearum: their effects on bacterial virulence
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A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey
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Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility
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Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes
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Biodiversity of Mimosa pudica rhizobial symbionts (Cupriavidus taiwanensis, Rhizobium mesoamericanum) in New Caledonia and their adaptation to heavy metal-rich soils
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Diversity and Geographic Distribution of Microsymbionts Associated With Invasive Mimosa Species in Southern China
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Prospects for inferring very large phylogenies by using the neighbor-joining method
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Type I secretion system—it takes three and a substrate
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Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge
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Two Lineages of Pseudomonas aeruginosa Filamentous Phages: Structural Uniformity over Integration Preferences
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Legume Symbiotic Nitrogen Fixation by -Proteobacteria Is Widespread in Nature
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DNA–DNA hybridization values and their relationship to whole-genome sequence similarities
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Enzyme-specific profiles for genome annotation: PRIAM
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Novel Burkholderia bacteria isolated from Lebeckia ambigua – A perennial suffrutescent legume of the fynbos
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Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil
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