Open access
Announcement
27 March 2014

Genome Sequence of the Quorum-Quenching Rhodococcus erythropolis Strain R138

ABSTRACT

Rhodococcus erythropolis strain R138 was isolated from the rhizosphere of Solanum tuberosum and selected for its capacity to degrade N-acyl-homoserine lactones, quorum-sensing signals used as communication molecules by the potato pathogens Pectobacterium and Dickeya. Here, we report the genome sequence of Rhodococcus erythropolis strain R138.

GENOME ANNOUNCEMENT

Proteobacteria may use quorum-sensing (QS) signals, such as N-acyl-homoserine lactones (AHLs), to synchronize the gene expression at a population level. Several bacteria, including Rhodococcus erythropolis, are able to degrade AHLs, hence disrupting the expression of the QS-regulated functions (1, 2). These AHL-degrading bacteria were collectively named quorum-quenching bacteria (3). R. erythropolis expresses at least three enzymatic activities involved in AHL degradation: lactonase, opening the gamma-butyrolactone ring of the AHLs; amidase, cleaving AHLs into homoserine lactone and fatty acids; and reductase, converting the ketone function at the C-3 position of the fatty chain into hydroxyl (4, 5). Until now, only the lactonase-coding gene qsdA was characterized (5). The quorum-quenching Rhodococcus strains are proposed to be used as antibiofouling (6) and biocontrol (1, 7) agents. R. erythropolis strain R138 was isolated from the potato rhizosphere (7). It is able to degrade AHLs and limit the symptoms induced by the plant pathogen Pectobacterium atrosepticum on potato tubers (8). The growth and root colonization of R. erythropolis R138 are enhanced in the presence of gamma-caprolactone and gamma-heptanolactone, which are assimilated as a carbon source (9). In R. erythropolis R138, the lactonase QsdA is involved in the cleavage of AHLs, as well as that of gamma-caprolactone and gamma-heptanolactone (5, 10).
Here, we report the de novo genome assembly of R. erythropolis R138 by combining Illumina and 454-Roche technologies. Three genomic libraries were constructed: a 300-bp library used for paired-end 2 × 72 Illumina sequencing (Imagif, France), a 380-bp shotgun library used for single-read 454 sequencing, and a long paired-end library with an insert size of 8 kbp used for 454 sequencing (Eurofins MWG, Germany). Sequence reads with low quality (<0.05), ambiguous nucleotides (n > 2), and sequence lengths of <50 (454 mate-paired), 20 (454 single), or 70 (Illumina) nucleotides were discarded for the assembly. Assembly was carried out using the CLC Genomics Workbench version 5.1 (CLC bio, Aarhus, Denmark), with a read length of 0.5 and similarity of 0.8 as parameters. In total, 53,576,242 reads were obtained, corresponding to 4,010,660,803 bases, with an average length of 74.9 bp. The scaffolding was processed using SSPACE basic version 2.0 (11). The in silico finishing of the remaining gaps was carried out by mapping mate-pair reads (read length, 0.9; similarity, 0.95) on each of the 5-kbp contig ends. Next, the collected reads were used for de novo assembly (read length, 0.5; similarity, 0.8). Some additional gaps were resolved using Sanger sequencing of the PCR amplicons. The published sequence is composed of 12 contigs, with a sequence length from 5.5 kbp to 2.7 Mbp grouped in 3 scaffolds.
The R. erythropolis R138 genome consists of one circular chromosome (6,444,743 bp), a linear plasmid (247,675 bp), and a circular plasmid (84,151 bp). The G+C content percentages were homogenous among the replicons (from 60 to 62%). A total of 6,562 coding sequences were predicted using the Rapid Annotations using Subsystems Technology (RAST) version 4.0 automated pipeline (12).

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ASKF00000000.

ACKNOWLEDGMENTS

This work was supported by the Centre National de la Recherche Scientifique (CNRS) and has benefited from the facilities and expertise of the high-throughput sequencing platforms of Imagif (Centre de Recherche de Gif, France) and MWG (France).
We thank Xavier Latour (Université de Rouen, Evreux) for critical reading of the manuscript.

REFERENCES

1.
d'Angelo-Picard C, Faure D, Penot I, and Dessaux Y. 2005. Diversity of N-acyl homoserine lactone-producing and -degrading bacteria in soil and tobacco rhizosphere. Environ. Microbiol. 7:1796–1808.
2.
Uroz S, D'Angelo-Picard C, Carlier A, Elasri M, Sicot C, Petit A, Oger P, Faure D, and Dessaux Y. 2003. Novel bacteria degrading N-acylhomoserine lactones and their use as quenchers of quorum-sensing-regulated functions of plant-pathogenic bacteria. Microbiology 149:1981–1989.
3.
Dong YH, Wang LH, Xu JL, Zhang HB, Zhang XF, and Zhang LH. 2001. Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature 411:813–817.
4.
Uroz S, Chhabra SR, Cámara M, Williams P, Oger P, and Dessaux Y. 2005. N-acylhomoserine lactone quorum-sensing molecules are modified and degraded by Rhodococcus erythropolis W2 by both amidolytic and novel oxidoreductase activities. Microbiology 151:3313–3322.
5.
Uroz S, Oger PM, Chapelle E, Adeline MT, Faure D, and Dessaux Y. 2008. A Rhodococcus qsdA-encoded enzyme defines a novel class of large-spectrum quorum-quenching lactonases. Appl. Environ. Microbiol. 74:1357–1366.
6.
Kim SR, Oh HS, Jo SJ, Yeon KM, Lee CH, Lim DJ, Lee CH, and Lee JK. 2013. Biofouling control with bead-entrapped quorum quenching bacteria in membrane bioreactors: physical and biological effects. Environ. Sci. Technol. 47:836–842.
7.
Cirou A, Diallo S, Kurt C, Latour X, and Faure D. 2007. Growth promotion of quorum-quenching bacteria in the rhizosphere of Solanum tuberosum. Environ. Microbiol. 9:1511–1522.
8.
Cirou A, Raffoux A, Diallo S, Latour X, Dessaux Y, and Faure D. 2011. Gamma-caprolactone stimulates growth of quorum-quenching Rhodococcus populations in a large-scale hydroponic system for culturing Solanum tuberosum. Res. Microbiol. 162:945–950.
9.
Cirou A, Mondy S, An S, Charrier A, Sarrazin A, Thoison O, Dubow M, and Faure D. 2012. Efficient biostimulation of native and introduced quorum-quenching Rhodococcus erythropolis populations is revealed by a combination of analytical chemistry, microbiology, and pyrosequencing. Appl. Environ. Microbiol. 78:481–492.
10.
Barbey C, Crépin A, Cirou A, Budin-Verneuil A, Orange N, Feuilloley M, Faure D, Dessaux Y, Burini JF, and Latour X. 2012. Catabolic pathway of Gamma-caprolactone in the biocontrol agent Rhodococcus erythropolis. J. Proteome Res. 11:206–216.
11.
Boetzer M, Henkel CV, Jansen HJ, Butler D, and Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578–579.
12.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, and Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 2Number 21 May 2014
eLocator: 10.1128/genomea.00224-14

History

Received: 26 February 2014
Accepted: 13 March 2014
Published online: 27 March 2014

Contributors

Authors

Anthony Kwasiborski
Institut des Sciences du Végétal, CNRS, Gif-sur-Yvette, France
Samuel Mondy
Institut des Sciences du Végétal, CNRS, Gif-sur-Yvette, France
Amélie Beury-Cirou
Comité Nord Plant de Pomme de Terre (CNPPT), Semences, Innovation, Protection Recherche et Environnement (SIPRE), Achicourt, France
Denis Faure
Institut des Sciences du Végétal, CNRS, Gif-sur-Yvette, France

Notes

Address correspondence to Denis Faure, [email protected].

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.
  • Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy