Complete Genome Sequence of Pseudomonas aeruginosa Strain YL84, a Quorum-Sensing Strain Isolated from Compost Kok-Gan Chan, Wai-Fong Yin, Yan Lue Lim Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was isolated from compost. This strain was found to be a chitinase-producing quorum-sensing bacterium. Received 1 March 2014 Accepted 13 March 2014 Published 3 April 2014 Citation Chan K-G, Yin W-F, Lim YL. 2014. Complete genome sequence of Pseudomonas aeruginosa strain YL84, a quorum-sensing strain isolated from compost. Genome Announc. 2(2):e00246-14. doi:10.1128/genomeA.00246-14. Copyright © 2014 Chan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Kok-Gan Chan, [email protected].
P
seudomonas aeruginosa, which is from the Pseudomonadaceae family, is an aerobic, motile, and Gram-negative rod-shaped bacterium that exists in a wide range of ecological niches. P. aeruginosa is known to be a prevalent opportunistic human pathogen and is also one of the most important causative agents of hospital-acquired nosocomial infections, characteristically in immunocompromised individuals (1–3). The secretion of a vast multitude of virulence factors that are responsible for the diverse and overwhelming pathogenicity of P. aeruginosa is found to be controlled by a cell-to-cell signaling mechanism known as quorum sensing (1, 4). Quorum sensing is a cell-density-dependent communication system that relies on N-acylhomoserine lactone as the signaling molecule. It is used by a large number of Gram-negative bacteria to regulate population behavior (5, 6). Two types of quorumsensing systems have been described in P. aeruginosa, the las and rhl systems (7). Here, we report the complete genome sequence of a quorum-sensing P. aeruginosa strain, YL84, which was isolated from compost. Chitinase activity is also found in this isolate. Genomic DNA of P. aeruginosa YL84 was extracted using a MasterPure DNA purification kit (Epicentre, Inc., Madison, WI). Appropriately sheared genomic DNA was used to construct a SMRTbell library using P4 chemistry. Whole-genome sequencing was subsequently performed using a Pacific Biosciences RSII sequencing platform (Pacific Biosciences, Menlo Park, CA). Four single-molecule real-time (SMRT) cells were used in the sequencing process, yielding an average genome coverage of 210.43⫻. Primary filtering of the sequenced data was done in the PacBio Blade Center, and the filtered data were subsequently processed in the SMRT Portal. A total of 279,487 reads, with a mean read length of 5,261 bp, were obtained following the primary filtering. De novo assembly was performed using the hierarchical genome assembly process (11) (PacBio DevNet; Pacific Biosciences), which successfully assembled the genome into a single contig with a maximum contig length of 6,433,441 bp and an overall G⫹C content of 66.43%. The Rapid Annotations using Subsystems Technology (RAST) pipeline (8) was used to predict and annotate open reading frames (ORFs) of the genome, and 5,992 protein-coding ORFs with
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known protein functions were found to be present in the chromosome. ARAGORN (9) and RNAmmer (10) were used to identify tRNA and rRNA genes, respectively. From these analyses, 74 tRNAs and 12 rRNA operons, comprising four 5S, four 16S, and four 23S rRNA genes, were detected in the genome. The presence of both chitinase and chitin-binding proteins was identified from the annotated genome. The chitinase is predicted to be a 480-amino-acid protein that consists of a GH18 catalytic domain, a fibronectin type III (Fn 3) domain, and a chitin-binding domain, whereas the chitin-binding protein (CBP), CbpD, is a 389-amino-acid protein that belongs to family 33 of CBPs. Nucleotide sequence accession number. The results of this whole-genome shotgun project have been deposited at DDBJ/ EMBL/GenBank under the accession no. CP007147. ACKNOWLEDGMENT We thank the University of Malaya for the financial support given under the High Impact Research grant (UM-MOHE HIR Nature Microbiome grant UM.C/625/1/HIR/MOHE/CHAN/14/1, no. H-50001-A000027).
REFERENCES 1. Van Delden C, Iglewski BH. 1998. Cell-to-cell signaling and Pseudomonas aeruginosa infections. Emerg. Infect. Dis. 4:551–560. http://dx.doi.org /10.3201/eid0404.980405. 2. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV. 2000. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959 –964. http://dx.doi.org /10.1038/35023079. 3. Bodey GP, Bolivar R, Fainstein V, Jadeja L. 1983. Infections caused by Pseudomonas aeruginosa. Rev. Infect. Dis. 5:279 –313. http://dx.doi.org/1 0.1093/clinids/5.2.279. 4. de Kievit TR, Iglewski BH. 2000. Bacterial quorum sensing in pathogenic relationships. Infect. Immun. 68:4839 – 4849. http://dx.doi.org/10.1128/I AI.68.9.4839-4849.2000. 5. Bassler BL. 1999. How bacteria talk to each other: regulation of gene expression by quorum sensing. Curr. Opin. Microbiol. 2:582–587. http: //dx.doi.org/10.1016/S1369-5274(99)00025-9. 6. Williams P, Winzer K, Chan WC, Cámara M. 2007. Look who’s talking: communication and quorum sensing in the bacterial world. Philos. Trans.
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Chan et al.
R. Soc. Lond. B Biol. Sci. 362:1119 –1134. http://dx.doi.org/10.1098/rstb. 2007.2039. 7. Pearson JP, Pesci EC, Iglewski BH. 1997. Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes. J. Bacteriol. 179:5756 –5767. 8. 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, Zagnitko O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186 /1471-2164-9-75.
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9. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11–16. http://dx.doi.org/10.1093/nar/gkh152. 10. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100 –3108. http://dx.doi.org/10.1093 /nar/gkm160. 11. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563–569. http://dx.doi.org/10.1 038/nmeth.2474.
Genome Announcements
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Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was isolated from compost. This strain was found to be a chitinase-producing quorum-sensing bacterium. Received 1 March 2014 Accepted 13 March 2014 Published 3 April 2014 Citation Chan K-G, Yin W-F, Lim YL. 2014. Complete genome sequence of Pseudomonas aeruginosa strain YL84, a quorum-sensing strain isolated from compost. Genome Announc. 2(2):e00246-14. doi:10.1128/genomeA.00246-14. Copyright © 2014 Chan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Kok-Gan Chan, [email protected].
P
seudomonas aeruginosa, which is from the Pseudomonadaceae family, is an aerobic, motile, and Gram-negative rod-shaped bacterium that exists in a wide range of ecological niches. P. aeruginosa is known to be a prevalent opportunistic human pathogen and is also one of the most important causative agents of hospital-acquired nosocomial infections, characteristically in immunocompromised individuals (1–3). The secretion of a vast multitude of virulence factors that are responsible for the diverse and overwhelming pathogenicity of P. aeruginosa is found to be controlled by a cell-to-cell signaling mechanism known as quorum sensing (1, 4). Quorum sensing is a cell-density-dependent communication system that relies on N-acylhomoserine lactone as the signaling molecule. It is used by a large number of Gram-negative bacteria to regulate population behavior (5, 6). Two types of quorumsensing systems have been described in P. aeruginosa, the las and rhl systems (7). Here, we report the complete genome sequence of a quorum-sensing P. aeruginosa strain, YL84, which was isolated from compost. Chitinase activity is also found in this isolate. Genomic DNA of P. aeruginosa YL84 was extracted using a MasterPure DNA purification kit (Epicentre, Inc., Madison, WI). Appropriately sheared genomic DNA was used to construct a SMRTbell library using P4 chemistry. Whole-genome sequencing was subsequently performed using a Pacific Biosciences RSII sequencing platform (Pacific Biosciences, Menlo Park, CA). Four single-molecule real-time (SMRT) cells were used in the sequencing process, yielding an average genome coverage of 210.43⫻. Primary filtering of the sequenced data was done in the PacBio Blade Center, and the filtered data were subsequently processed in the SMRT Portal. A total of 279,487 reads, with a mean read length of 5,261 bp, were obtained following the primary filtering. De novo assembly was performed using the hierarchical genome assembly process (11) (PacBio DevNet; Pacific Biosciences), which successfully assembled the genome into a single contig with a maximum contig length of 6,433,441 bp and an overall G⫹C content of 66.43%. The Rapid Annotations using Subsystems Technology (RAST) pipeline (8) was used to predict and annotate open reading frames (ORFs) of the genome, and 5,992 protein-coding ORFs with
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known protein functions were found to be present in the chromosome. ARAGORN (9) and RNAmmer (10) were used to identify tRNA and rRNA genes, respectively. From these analyses, 74 tRNAs and 12 rRNA operons, comprising four 5S, four 16S, and four 23S rRNA genes, were detected in the genome. The presence of both chitinase and chitin-binding proteins was identified from the annotated genome. The chitinase is predicted to be a 480-amino-acid protein that consists of a GH18 catalytic domain, a fibronectin type III (Fn 3) domain, and a chitin-binding domain, whereas the chitin-binding protein (CBP), CbpD, is a 389-amino-acid protein that belongs to family 33 of CBPs. Nucleotide sequence accession number. The results of this whole-genome shotgun project have been deposited at DDBJ/ EMBL/GenBank under the accession no. CP007147. ACKNOWLEDGMENT We thank the University of Malaya for the financial support given under the High Impact Research grant (UM-MOHE HIR Nature Microbiome grant UM.C/625/1/HIR/MOHE/CHAN/14/1, no. H-50001-A000027).
REFERENCES 1. Van Delden C, Iglewski BH. 1998. Cell-to-cell signaling and Pseudomonas aeruginosa infections. Emerg. Infect. Dis. 4:551–560. http://dx.doi.org /10.3201/eid0404.980405. 2. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV. 2000. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959 –964. http://dx.doi.org /10.1038/35023079. 3. Bodey GP, Bolivar R, Fainstein V, Jadeja L. 1983. Infections caused by Pseudomonas aeruginosa. Rev. Infect. Dis. 5:279 –313. http://dx.doi.org/1 0.1093/clinids/5.2.279. 4. de Kievit TR, Iglewski BH. 2000. Bacterial quorum sensing in pathogenic relationships. Infect. Immun. 68:4839 – 4849. http://dx.doi.org/10.1128/I AI.68.9.4839-4849.2000. 5. Bassler BL. 1999. How bacteria talk to each other: regulation of gene expression by quorum sensing. Curr. Opin. Microbiol. 2:582–587. http: //dx.doi.org/10.1016/S1369-5274(99)00025-9. 6. Williams P, Winzer K, Chan WC, Cámara M. 2007. Look who’s talking: communication and quorum sensing in the bacterial world. Philos. Trans.
Genome Announcements
genomea.asm.org 1
Chan et al.
R. Soc. Lond. B Biol. Sci. 362:1119 –1134. http://dx.doi.org/10.1098/rstb. 2007.2039. 7. Pearson JP, Pesci EC, Iglewski BH. 1997. Roles of Pseudomonas aeruginosa las and rhl quorum-sensing systems in control of elastase and rhamnolipid biosynthesis genes. J. Bacteriol. 179:5756 –5767. 8. 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, Zagnitko O. 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186 /1471-2164-9-75.
2 genomea.asm.org
9. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11–16. http://dx.doi.org/10.1093/nar/gkh152. 10. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100 –3108. http://dx.doi.org/10.1093 /nar/gkm160. 11. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563–569. http://dx.doi.org/10.1 038/nmeth.2474.
Genome Announcements
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