GENOME ANNOUNCEMENT
Genome Sequence of Pseudomonas putida Strain SJTE-1, a Bacterium Capable of Degrading Estrogens and Persistent Organic Pollutants Rubing Liang, Huan Liu, Fei Tao, Yang Liu, Chen Ma, Xipeng Liu, and Jianhua Liu State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
Pseudomonas putida strain SJTE-1 can utilize 17-estradiol and other environmental estrogens/toxicants, such as estrone, and naphthalene as sole carbon sources. We report the draft genome sequence of strain SJTE-1 (5,551,505 bp, with a GC content of 62.25%) and major findings from its annotation, which could provide insights into its biodegradation mechanisms.
E
strogens are one of the most dangerous environmental endocrine-disrupting compounds, due to their strong carcinogenicity and pathogenicity for wildlife (3, 16, 18). Biodegradation is considered to be a major and efficient strategy to remove these chemicals (5, 13). Although some estrogen-degrading bacteria have been isolated, the degrading mechanisms vary in different strains and remain poorly characterized (8, 10, 15). Pseudomonas putida strain SJTE-1 was isolated from soil and was determined to be capable of utilizing 17-estradiol as the sole carbon source and then converting it into nonestrogenic products. It can also use and degrade other estrogens and estrogenic chemicals, such as estrone, estriol, naphthalene, phenanthrene, and fluorine (unpublished data). Therefore, strain SJTE-1 may play an important role in the bioremediation of estrogen-polluted environments; its genome sequencing will provide great insights into its genetic variability and assist in the study of its biodegradation mechanisms. Here, we report the draft genome sequence of P. putida SJTE-1, obtained with the 454 GS-FLX (Roche) system (total of 67,499 reads averaging 400 bp) and Solexa paired-end sequencing (total of 8,605,720 reads, 151 bp each). The gaps were closed by specific PCR and Sanger sequencing. Genome sequences were assembled in silico using the AMOScmp program, resulting in 152 contigs (⬎500 bp in size) with an N50 length of 79,005 bp. The proteincoding genes were predicted using Glimmer 3.0 (4); tRNA and rRNA were identified with tRNAscan-SE (12) and RNAmmer (11). The genome sequence was annotated using the databases of RAST (1) and PGAAP (14). The functions of predicted proteincoding genes were annotated with the NCBI-NR (2), COG (17), and KEGG (9) databases. The SJTE-1 draft genome sequence has a total of 5,551,505 bp with an average GC content of 62.25%. It contains 4,915 predicted coding sequences (CDSs), one 16S-23S-5S operon, and 52 tRNAs. Using COG functional assignment, the majority of predicted proteins (89.7%) could be classified into 22 COG categories. There are 412 subsystems represented in the genome, and the metabolic network of SJTE-1 was reconstructed (1). The five most abundant subsystems are related to amino acids (n ⫽ 642 CDSs), carbohydrates (n ⫽ 436), cofactors, vitamins, and pigments (n ⫽ 361), miscellaneous (n ⫽ 279), and protein metabolism (n ⫽ 215). In addition, many CDSs are involved in membrane transport (n ⫽ 176), metabolism of aromatic compounds (n ⫽ 125), stress response (n ⫽ 108), motility and chemotaxis (n ⫽ 122), and virulence, disease, and defense (n ⫽ 116). These findings suggest that
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strain SJTE-1 has very diverse catabolic abilities and a unique ability to adapt and survive in different environments. According to the proposed steroid degradation pathways (6, 7, 19), several enzymes putatively involved in estrogen degradation were also observed in the SJTE-1 genome, such as hydroxysteroid dehydrogenase, 3-ketosteroid-delta-dehydrogenase, Rieske dioxygenase, and catechol 2,3-dioxygenase. Further studies will be performed to confirm their functions in strain SJTE-1, and more detailed genome analysis will reveal the unique biochemical and molecular characteristics of strain SJTE-1. Nucleotide sequence accession numbers. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AKCL00000000. The version described in this paper is the first version, with accession number AKCL01000000. ACKNOWLEDGMENTS We acknowledge Shanghai Personal Biotechnology Co., Ltd., for genome sequence and draft map gap closing. This work was supported in part by the National Basic Research Program of China (grant no. 2009CB118906), the National Natural Science Foundation of China (grants no. 21135004/B050901, 30870512/C050103, 31070090/C010302, and 30900010/C010201), and the New Teacher Programs Foundation of the Ministry of Education of China (grant no. 20090073120066).
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Received 14 June 2012 Accepted 26 June 2012 Address correspondence to Jianhua Liu,
[email protected]. R.L. and H.L. contributed equally to this work. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01060-12
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