Genome Sequence of the 17β-Estradiol-Utilizing Bacterium Sphingomonas Strain KC8

Abstract

Sphingomonas strain KC8 is known for its ability to utilize 17β-estradiol, a natural estrogen and an environmental endocrine-disrupting compound, as the sole carbon and energy source. Here, we report the draft genome sequence of the strain KC8 (4,074,265 bp, with a GC content of 63.7%) and major findings from its annotation.

GENOME ANNOUNCEMENT

Estrogens are one of the most worrisome environmental endocrine-disrupting compounds because exposure to estrogens or estrogen-like chemicals is known to cause adverse health effects on wildlife (11, 13). As biodegradation is considered the major removal mechanism in human-made and natural environments, a better understanding of microbial transformation of estrogens is warranted (3). Among known estrogen-degrading isolates, Sphingomonas strain KC8 is of particular interest because strain KC8 can degrade 17β-estradiol into nonestrogenic end products (14). However, the degrading mechanism remains largely unclear. Here, we present the draft genome sequence of strain KC8. To our knowledge, this is the first genome report of estrogen-degrading bacteria.

The genome of KC8 was sequenced by a whole-genome shotgun strategy using Roche 454 GS-FLX Titanium pyrosequencing technology. A total of 217,810 reads and 85,408,792 bp of sequence were produced, providing about 21-fold coverage of the genome. Genome sequences were assembled in silico using Newbler Assembler 2.3 (Roche), resulting in 70 contigs (>1,000 bp in size) with an N₅₀ length of 142,404 bp. The protein-coding genes were predicted using Glimmer 3.02 (4), while tRNAscan-SE (9) and RNAmmer (8) were used to identify tRNA and rRNA, respectively. The genome sequence was also uploaded into Rapid Annotation using Subsystem Technology (RAST) (1) to check the annotated sequences. The functions of predicted protein-coding genes were then annotated through comparisons with the databases of NCBI-NR (2), COG (12), and KEGG (6).

The KC8 draft genome sequence has a total of 4,074,265 bp with an average GC content of 63.7%. It contains 3,950 predicted coding sequences (CDSs), one 16S-23S-5S operon, and 46 tRNAs. Using COG functional assignment, the majority of predicted proteins (89.4%) could be classified into 22 COG categories. According to subsystem-based annotation generated by RAST, strain KC8 has 369 subsystems. The four most abundant of the subsystems are related to amino acids and derivatives (number of CDSs = 328), carbohydrates (n = 264), protein metabolism (n = 213), and fatty acids, lipids, and isoprenoids (n = 199). In addition, a large number of the CDSs are found to be related to resistance to antibiotics and toxic compounds (n = 101), stress response (n = 125), and motility and chemotaxis (n = 128). These findings suggest that strain KC8 has a very diverse catabolic ability and a unique ability to adapt and/or survive in different environments.

According to the proposed estrogen and testosterone degradation pathways (5, 7, 10), several genes encoding the enzymes putatively involved in estrogen degradation, such as hydroxysteroid dehydrogenase, 3-ketosteroid-delta1-dehydrogenase, Rieske dioxygenase, and catechol 2,3-dioxygenase, were also observed in the genome of KC8. Further studies are needed to clone these genes to confirm their functions. In addition, a more detailed analysis of this genome and comparative genome analysis with other polycyclic aromatic hydrocarbon-degrading Sphingomonas members will reveal the unique biochemical and molecular characteristics of this strain.

Nucleotide sequence accession number.

The draft genome sequence of Sphingomonas strain KC8 has been deposited at GenBank under accession number AFMP01000000.