Genome Sequence of Sphingobium yanoikuyae XLDN2-5, an Efficient Carbazole-Degrading Strain

Abstract

Sphingobium yanoikuyae XLDN2-5 is an efficient carbazole-degrading strain. Carbazole-degrading genes are accompanied on both sides by two copies of IS6100 elements. Here, we describe the draft genome sequence of strain XLDN2-5, which may provide important clues as to how it recruited exogenous genes to establish pathways to degrade the xenobiotics.

GENOME ANNOUNCEMENT

The Sphingomonas genus was proposed by Yabuuchi et al. in 1990 and is characterized by an outer membrane that contains glycosphingolipids instead of lipopolysaccharide (13). By 2001, the Sphingomonas genus has been subdivided into four genera: Sphingomonas, Sphingobium, Novosphingobium, and Sphingopyxis (10). These genera are commonly referred to collectively as sphingomonads. Recently, sphingomonads have received increasing attention due to their biodegradative and biosynthetic capabilities and have been utilized for a wide range of biotechnological applications, from bioremediation of contaminants to production of extracellular polymers.

Sphingobium yanoikuyae XLDN2-5, a member of the sphingomonads, was isolated from petroleum-contaminated soils (3, 11) and is able to degrade carbazole efficiently. Moreover, this strain could also cometabolically catabolize dibenzofuran, dibenzothiophene, and benzothiophene (3, 4), which are among the most potent environmental pollutants (12). Carbazole is converted by carbazole 1,9a-dioxygenase, meta-cleavage enzyme, and hydrolase to anthranilate and 2-hydroxypenta-2,4-dienoate. Two gene clusters involved in the carbazole degradation by strain XLDN2-5 were identified and sequenced (5). The car gene cluster (carRAaBaBbCAc) and fdr gene are accompanied on both sides by two copies of IS6100 elements and organized as IS6100::ISSspI-ORF1-carRAaBaBbCAc-ORF8- IS6100-fdr-IS6100. The ant gene cluster (antRAcAdAbAa), which is involved in the conversion of anthranilate to catechol, is also sandwiched between two IS6100 elements as IS6100-antRAcAdAbAa-IS6100. Together the structure genes and IS6100 elements make up two catabolic transposons, responsible for carbazole degradation, indicating that the insertion sequence (IS6100) played an important role in the evolution of the carbazole-degrading pathway. Here, we describe the draft genome of Sphingobium yanoikuyae XLDN2-5.

The genome of this strain was sequenced using the 454 Life Sciences GS FLX system. The reads were assembled using the Newbler assembler, version 2.3. The contig N50 was approximately 73.7 kb, and the largest contig assembled was approximately 251.4 kb. This assembly generated 159 large contigs (>500 bp). The draft genome was 5,353,044 bases in length, with a mean GC content of 64.3%. The genome was annotated using the RAST annotation server (1) and the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (7). A total of 5,057 coding sequences and 52 structural RNAs were predicted.

As expected, strain XLDN2-5 encodes a diverse array of proteins with predicted roles in aromatic compound metabolism. We also identified mobile genetic elements, including insertion sequences, transposons, and plasmids, suggesting that the genome of strain XLDN2-5 has been extensively shaped by horizontal gene transfers. Strain XLDN2-5 contains at least one megaplasmid. The megaplasmid contains car and ant clusters, which are involved in carbazole degradation (5). In addition, we identified a gene cluster from strain XLDN2-5 responsible for the aerobic catechol degradation via a meta-cleavage pathway. The order of the genes in the meta-pathway of strain XLDN2-5 is carLM-catS-carJK-catR-carDEFGHIYX and remarkably different from that of plasmid-borne xyl (9), dmp (8), nah (6), and bph (2) pathways. Further genomic analyses may provide important clues about the functional capability of strain XLDN2-5.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AFXE00000000. The version described in this paper is the first version, AFXE01000000.