Draft Genome Sequence of Pseudomonas stutzeri Strain 19, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons

ABSTRACT

Pseudomonas stutzeri strain 19 is a Gram-negative bacterium capable of degrading aromatic hydrocarbons. The draft genome of P. stutzeri 19 is estimated to be 5.1 Mb, containing 4,652 protein-coding genes and a G+C content of 63.3%. Multiple genes responsible for the degradation of aromatics are present in this strain.

GENOME ANNOUNCEMENT

Pseudomonas stutzeri strain 19 was isolated from a wastewater sample from Dayton, OH, USA. P. stutzeri 19 was shown, through gas chromatography-mass spectrometry (GC-MS) analysis, to efficiently metabolize toluene, xylenes, and 1,2,4-trimethyl benzene. Comparative BLAST analysis (http://blast.ncbi.nlm.nih.gov/Blast.cgi) of the 16S rRNA gene of P. stutzeri 19, identified using RNAmmer (1), showed 99% similarity with P. stutzeri DSM 4166 and P. stutzeri A1501, while Rapid Annotations using Subsystems Technology (RAST) identified P. stutzeri A1501 as the closest neighbor, with a score of 507. The genome of P. stutzeri was chosen for sequencing due to its ability to degrade recalcitrant aromatics and grow in harsh hydrocarbon-containing environments.

Whole-genome shotgun sequencing was performed on a Roche 454-GS Junior platform, producing 334,879 reads. Newbler assembly (version 2.9) was used to align reads, creating 136 large (>500-bp) contigs with an average size of 37,500 bp, an N₅₀ of 104,286, and an L₅₀ of 15. The draft genome sequence was 5,100,040 bp in length, with a G+C content of 63.3%. The largest contig extended for 263,585 bp. The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/) predicted 4,895 genes, 4,652 coding sequences (CDSs), and 54 tRNAs. Rapid genome annotations using the RAST server (2) assigned the protein-coding sequences to 512 subsystems, of which amino acids and derivatives (n = 439 CDSs), carbohydrates (n = 368), cofactors, vitamins, prosthetic groups, and pigments (n = 332), protein metabolism (n = 278), fatty acids, lipids, and isoprenoids (n = 161), RNA metabolism (n = 204), nucleosides and nucleotides (n = 115), virulence, disease, and defense (n = 129), stress response (n = 176), respiration (n = 148), DNA metabolism (n = 162), motility and chemotaxis (n = 129), membrane transport (n = 200), and cell wall and capsule (n = 183) were most abundant.

The NCBI PGAP predicted multiple genes involved in hydrocarbon degradation, including catechol 1,2-dioxygenase, homogentisate 1,2-dioxygenase, phenol monooxygenase, small and large subunits of benzoate 1,2-dioxygenase (benA and benB), alkane 1-monooxygenease, rubredoxin, alkene reductase, 2-alkenal reductase, P450, and a benzoate transporter protein, among others. BLAST analysis revealed two coding sequences with 99% homology to the alpha and beta subunits of toluene 1,2-dioxygenase of P. putida MT53 plasmid pWW53. Also, coding sequences with 96% homology to the xylene monooxygenase electron transfer subunit and 98% homology to the xylene monooxygenase hydrolase subunit of P. putida MT53 plasmid pWW53 were found. The presence of these enzymes explains the toluene and xylene degradation capacities of P. stutzeri 19. The genes for protocatechuate 3,4-dioxygenase, 3-carboxymuconate cycloisomerase, and 4-carboxymuconolactone decarboxylase of the central protocatechuate catabolic pathway for aromatic degradation were also present. A cluster of genes was observed with at least 78% homology to the ttg2 operon of P. putida that encodes an ABC transporter implicated in resistance to toluene (3, 4). The genome of P. stutzeri 19 encodes many multidrug and heavy-metal resistance-nodulation-division (RND) efflux transporters, some of which have been associated with hydrocarbon resistance (5). The genome of P. stutzeri strain 19 will help to understand the adaptive mechanisms deployed by Gram-negative bacteria for survival and proliferation in hydrocarbons.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number NFZU00000000. The version described in this paper is NFZU01000000.