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Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste Gun-Seok Park, Sung-Jun Hong, Chang-Hyun Lee, Abdur Rahim Khan, Ihsan Ullah, Byung Kwon Jung, JungBae Choi, Yunyoung Kwak, Chang-Gi Back, Hee-Young Jung, Jae-Ho Shin School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
Received 16 October 2014 Accepted 17 October 2014 Published 26 November 2014 Citation Park G-S, Hong S-J, Lee C-H, Khan AR, Ullah I, Jung BK, Choi JB, Kwak Y, Back C-G, Jung H-Y, Shin J-H. 2014. Draft genome sequence of Chryseobacterium sp. strain P1-3, a keratinolytic bacterium isolated from poultry waste. Genome Announc. 2(6):e01237-14. doi:10.1128/genomeA.01237-14. Copyright © 2014 Park et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Jae-Ho Shin, [email protected].
K
eratin, the major component of animal hair, nail, feathers, and wool, is the most abundant fibrous protein in the epithelial cells of vertebrates (1). The insoluble protein is tightly packed in an ␣-helix structure (␣-keratin) or -sheet structure (-keratin) into a supercoiled polypeptide chain with cysteine bridges (2). Keratin shows resistance to proteolysis due not only to the disulfide bonds, but also to the structurally limited interior space with hydrophobic interactions between nonpolar residues (3). The proteolytic resistance of keratin has been considered to be a critical factor disturbing the process of keratin waste treatment (4). To date, some keratinolytic microorganisms producing various proteases have been reported, such as Bacillus (5), fungi (6), thermophilic bacteria (7), and even Chryseobacterium (8). The keratinolytic proteases from these organisms may have important uses for the biodegradation of keratin-containing waste from industry (9). The genus Chryseobacterium, belonging to a member of family Flavobacteriaceae, is a non-spore-forming, nonmotile, rodshaped Gram-negative bacterium. Chryseobacterium species have been known to possess strong proteolytic activity with typical morphological characteristics, such as translucent circular and yellow pigmented colonies (10). A strong keratin degrader, strain Chryseobacterium sp. P1-3 was isolated from a poultry waste dumping ground in Iksan, Jeonbuk, Republic of Korea (S. J. Hong, unpublished data). The genomic DNA of the strain P1-3 was sequenced to enlarge the enzymatic hydrolysis efficacy for keratin waste treatment. The genome was sequenced using an Ion Torrent personal genome machine (PGM) sequencer with a 316 v2 chip (11). The sequence reads were assembled using Mimicking Intelligent Read Assembly (MIRA) 4.0 (12). The draft genome is composed of 45 contigs (⬎728 bp). The genome size is 4,628,764 bp at 78.0-fold coverage with a G⫹C content of 37.0%. The assembled contigs were annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) version 2.6 software on NCBI (http://www.ncbi.nlm .nih.gov/genome/annotation_prok/) and the Rapid Annotation using Subsystem Technology (RAST) server (13). The genome contains a total of 4,087 genes, consisting of 3,119 protein-coding
November/December 2014 Volume 2 Issue 6 e01237-14
sequences (CDSs), 882 pseudo genes, 20 rRNA (5S, 16S, 23S) genes, 65 tRNA genes, and 1 ncRNA gene. Predicted genes were functionally assigned via 311 RAST subsystems. In regard to the keratinolytic activity, a total of 32 open reading frames are identified as proteases, including metalloproteases and serine proteases. The genome sequence of Chryseobacterium sp. strain P1-3 may contribute to a better understanding of keratin degradation and also provide potential applications for the treatment of keratin wastes. Nucleotide sequence accession number. The draft genome sequence of strain Chryseobacterium sp. P1-3 has been deposited at DDBJ/EMBL/GenBank under the accession no. JPEQ00000000. ACKNOWLEDGMENT This research was supported by the Kyungpook National University Research Fund, 2013.
REFERENCES 1. Gradišar H, Friedrich J, Križaj I, Jerala R. 2005. Similarities and specificities of fungal keratinolytic proteases: comparison of keratinases of Paecilomyces marquandii and Doratomyces microsporus to some known proteases. Appl. Environ. Microbiol. 71:3420 –3426. http://dx.doi.org/ 10.1128/AEM.71.7.3420-3426.2005. 2. Parry DAD, North ACT. 1998. Hard ␣-keratin intermediate filament chains: substructure of the N- and C-terminal domains and the predicted structure and function of the C-terminal domains of type I and type II chains. J. Struct. Biol. 122:67–75. http://dx.doi.org/10.1006/jsbi.1998.3967. 3. Hanukoglu I, Ezra L. 2014. Proteopedia entry: coiled-coil structure of keratins. Biochem. Mol. Biol. Educ. 42:93–94. http://dx.doi.org/10.1002/ bmb.20746. 4. Korniłłowicz-Kowalska T, Bohacz J. 2011. Biodegradation of keratin waste: theory and practical aspects. Waste Manag. 31:1689 –1701. http:// dx.doi.org/10.1016/j.wasman.2011.03.024. 5. Macedo AJ, da Silva WOB, Gava R, Driemeier D, Henriques JAP, Termignoni C. 2005. Novel keratinase from Bacillus subtilis S14 exhibiting remarkable dehairing capabilities. Appl. Environ. Microbiol. 71: 594 –596. http://dx.doi.org/10.1128/AEM.71.1.594-596.2005. 6. Gradišar H, Kern S, Friedrich J. 2000. Keratinase of Doratomyces microsporus. Appl. Microbiol. Biotechnol. 53:196 –200. http://dx.doi.org/ 10.1007/s002530050008. 7. Riessen S, Antranikian G. 2001. Isolation of Thermoanaerobacter kerati-
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on November 14, 2015 by guest
Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a GⴙC content of 37.0% and 4,087 proteincoding genes.
Park et al.
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9. 10.
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Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348 –352. http:// dx.doi.org/10.1038/nature10242. 12. Chevreux B. 2005. MIRA: an automated genome and EST assembler. Uprecht-Karls University, Heidelberg, Germany. 13. 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.
Genome Announcements
November/December 2014 Volume 2 Issue 6 e01237-14
Downloaded from http://genomea.asm.org/ on November 14, 2015 by guest
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nophilus sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity. Extremophiles 5:399 – 408. http://dx.doi.org/10.1007/ s007920100209. Riffel A, Brandelli A, Bellato CdM, Souza GH, Eberlin MN, Tavares FC. 2007. Purification and characterization of a keratinolytic metalloprotease from Chryseobacterium sp. kr6. J. Biotechnol. 128:693–703. http:// dx.doi.org/10.1016/j.jbiotec.2006.11.007. Shih JCH. 1993. Recent development in poultry waste digestion and feather utilization—a review. Poult. Sci. 72:1617–1620. http://dx.doi.org/ 10.3382/ps.0721617. Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. 1994. NOTES: new perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int. J. Syst. Bacteriol. 44:827– 831. http://dx.doi.org/ 10.1099/00207713-44-4-827. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF,
Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste Gun-Seok Park, Sung-Jun Hong, Chang-Hyun Lee, Abdur Rahim Khan, Ihsan Ullah, Byung Kwon Jung, JungBae Choi, Yunyoung Kwak, Chang-Gi Back, Hee-Young Jung, Jae-Ho Shin School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
Received 16 October 2014 Accepted 17 October 2014 Published 26 November 2014 Citation Park G-S, Hong S-J, Lee C-H, Khan AR, Ullah I, Jung BK, Choi JB, Kwak Y, Back C-G, Jung H-Y, Shin J-H. 2014. Draft genome sequence of Chryseobacterium sp. strain P1-3, a keratinolytic bacterium isolated from poultry waste. Genome Announc. 2(6):e01237-14. doi:10.1128/genomeA.01237-14. Copyright © 2014 Park et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Jae-Ho Shin, [email protected].
K
eratin, the major component of animal hair, nail, feathers, and wool, is the most abundant fibrous protein in the epithelial cells of vertebrates (1). The insoluble protein is tightly packed in an ␣-helix structure (␣-keratin) or -sheet structure (-keratin) into a supercoiled polypeptide chain with cysteine bridges (2). Keratin shows resistance to proteolysis due not only to the disulfide bonds, but also to the structurally limited interior space with hydrophobic interactions between nonpolar residues (3). The proteolytic resistance of keratin has been considered to be a critical factor disturbing the process of keratin waste treatment (4). To date, some keratinolytic microorganisms producing various proteases have been reported, such as Bacillus (5), fungi (6), thermophilic bacteria (7), and even Chryseobacterium (8). The keratinolytic proteases from these organisms may have important uses for the biodegradation of keratin-containing waste from industry (9). The genus Chryseobacterium, belonging to a member of family Flavobacteriaceae, is a non-spore-forming, nonmotile, rodshaped Gram-negative bacterium. Chryseobacterium species have been known to possess strong proteolytic activity with typical morphological characteristics, such as translucent circular and yellow pigmented colonies (10). A strong keratin degrader, strain Chryseobacterium sp. P1-3 was isolated from a poultry waste dumping ground in Iksan, Jeonbuk, Republic of Korea (S. J. Hong, unpublished data). The genomic DNA of the strain P1-3 was sequenced to enlarge the enzymatic hydrolysis efficacy for keratin waste treatment. The genome was sequenced using an Ion Torrent personal genome machine (PGM) sequencer with a 316 v2 chip (11). The sequence reads were assembled using Mimicking Intelligent Read Assembly (MIRA) 4.0 (12). The draft genome is composed of 45 contigs (⬎728 bp). The genome size is 4,628,764 bp at 78.0-fold coverage with a G⫹C content of 37.0%. The assembled contigs were annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) version 2.6 software on NCBI (http://www.ncbi.nlm .nih.gov/genome/annotation_prok/) and the Rapid Annotation using Subsystem Technology (RAST) server (13). The genome contains a total of 4,087 genes, consisting of 3,119 protein-coding
November/December 2014 Volume 2 Issue 6 e01237-14
sequences (CDSs), 882 pseudo genes, 20 rRNA (5S, 16S, 23S) genes, 65 tRNA genes, and 1 ncRNA gene. Predicted genes were functionally assigned via 311 RAST subsystems. In regard to the keratinolytic activity, a total of 32 open reading frames are identified as proteases, including metalloproteases and serine proteases. The genome sequence of Chryseobacterium sp. strain P1-3 may contribute to a better understanding of keratin degradation and also provide potential applications for the treatment of keratin wastes. Nucleotide sequence accession number. The draft genome sequence of strain Chryseobacterium sp. P1-3 has been deposited at DDBJ/EMBL/GenBank under the accession no. JPEQ00000000. ACKNOWLEDGMENT This research was supported by the Kyungpook National University Research Fund, 2013.
REFERENCES 1. Gradišar H, Friedrich J, Križaj I, Jerala R. 2005. Similarities and specificities of fungal keratinolytic proteases: comparison of keratinases of Paecilomyces marquandii and Doratomyces microsporus to some known proteases. Appl. Environ. Microbiol. 71:3420 –3426. http://dx.doi.org/ 10.1128/AEM.71.7.3420-3426.2005. 2. Parry DAD, North ACT. 1998. Hard ␣-keratin intermediate filament chains: substructure of the N- and C-terminal domains and the predicted structure and function of the C-terminal domains of type I and type II chains. J. Struct. Biol. 122:67–75. http://dx.doi.org/10.1006/jsbi.1998.3967. 3. Hanukoglu I, Ezra L. 2014. Proteopedia entry: coiled-coil structure of keratins. Biochem. Mol. Biol. Educ. 42:93–94. http://dx.doi.org/10.1002/ bmb.20746. 4. Korniłłowicz-Kowalska T, Bohacz J. 2011. Biodegradation of keratin waste: theory and practical aspects. Waste Manag. 31:1689 –1701. http:// dx.doi.org/10.1016/j.wasman.2011.03.024. 5. Macedo AJ, da Silva WOB, Gava R, Driemeier D, Henriques JAP, Termignoni C. 2005. Novel keratinase from Bacillus subtilis S14 exhibiting remarkable dehairing capabilities. Appl. Environ. Microbiol. 71: 594 –596. http://dx.doi.org/10.1128/AEM.71.1.594-596.2005. 6. Gradišar H, Kern S, Friedrich J. 2000. Keratinase of Doratomyces microsporus. Appl. Microbiol. Biotechnol. 53:196 –200. http://dx.doi.org/ 10.1007/s002530050008. 7. Riessen S, Antranikian G. 2001. Isolation of Thermoanaerobacter kerati-
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on November 14, 2015 by guest
Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a GⴙC content of 37.0% and 4,087 proteincoding genes.
Park et al.
8.
9. 10.
2 genomea.asm.org
Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348 –352. http:// dx.doi.org/10.1038/nature10242. 12. Chevreux B. 2005. MIRA: an automated genome and EST assembler. Uprecht-Karls University, Heidelberg, Germany. 13. 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.
Genome Announcements
November/December 2014 Volume 2 Issue 6 e01237-14
Downloaded from http://genomea.asm.org/ on November 14, 2015 by guest
11.
nophilus sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity. Extremophiles 5:399 – 408. http://dx.doi.org/10.1007/ s007920100209. Riffel A, Brandelli A, Bellato CdM, Souza GH, Eberlin MN, Tavares FC. 2007. Purification and characterization of a keratinolytic metalloprotease from Chryseobacterium sp. kr6. J. Biotechnol. 128:693–703. http:// dx.doi.org/10.1016/j.jbiotec.2006.11.007. Shih JCH. 1993. Recent development in poultry waste digestion and feather utilization—a review. Poult. Sci. 72:1617–1620. http://dx.doi.org/ 10.3382/ps.0721617. Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. 1994. NOTES: new perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int. J. Syst. Bacteriol. 44:827– 831. http://dx.doi.org/ 10.1099/00207713-44-4-827. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF,
