Complete Genome of Pseudomonas mendocina NK-01, Which Synthesizes Medium-Chain-Length Polyhydroxyalkanoates and Alginate Oligosaccharides

Abstract

Pseudomonas mendocina NK-01 can synthesize medium-chain-length polyhydroxyalkanoate (PHA_MCL) and alginate oligosaccharides (AO) simultaneously from glucose under conditions of limited nitrogen. Here, we report the complete sequence of the 5.4-Mbp genome of Pseudomonas mendocina NK-01, which was isolated from farmland soil in Tianjin, China.

GENOME ANNOUNCEMENT

Polyhydroxyalkanoates (PHAs) are a family of biopolyesters produced by numerous bacteria as intracellular carbon and energy polymers under unfavorable growth conditions, such as limited nitrogen, phosphorus, oxygen, or magnesium, in the presence of excess carbon (1). Due to their biodegradability, biocompatibility, and thermoprocessibility, PHAs have been used in environmentally friendly bioplastics and biomedical materials (4, 14). Alginate oligosaccharides (AO) can be obtained from the degradation of alginate by alginate lyase (from Vibrio sp. 510) as described by Zhang et al. (15) or from mollusks in the natural world (3). In detailed studies, it was found that AO has many biological activities, such as antioxidation (13), anticoagulation (8), and immune regulation (10), and could be developed as a drug for enhancing human immunity. Pseudomonas mendocina NK-01 can synthesize medium-chain-length polyhydroxyalkanoate (PHA_MCL) and AO simultaneously from glucose under conditions of limited nitrogen (6).

The strain was grown in Luria-Bertani (LB) medium, and the genomic DNA was extracted from the cultured bacteria. We then sequenced the genome of Pseudomonas mendocina NK-01. The complete genome sequence of the strain was obtained using 454 pyrosequencing technology. The annotation was done by merging the results obtained from the RAST (Rapid Annotation using Subsystem Technology) server (2), the Glimmer 3.02 modeling software package (5), tRNAscan-SE 1.21 (9), and RNAmmer 1.2 (7).

The complete genome of P. mendocina NK-01 is made up of a circular chromosome of 5,434,353 bp with 62.51% G+C content and no plasmid. The genome size is bigger than that of P. mendocina ymp (5,072,807 bp; GenBank accession number NC_009439), and the genome's G+C content of P. mendocina NK-01 is lower than that of P. mendocina ymp (64%). The genome of P. mendocina NK-01 encodes 4,958 proteins, 65 tRNAs, and 12 rRNA operons which account for 89.04% of the genome. Among the 4,958 open reading frames (ORFs), 3,732 (75.27%) have a clear function, 1,077 (21.72%) have high similarity with putative proteins, and the remaining 149 (3.01%) have no match with the protein database of the National Center for Biotechnology Information (NCBI).

The genome of P. mendocina NK-01 encodes PHA_MCL and AO synthesis-related genes. Two putative PHA_MCL- and AO-biosynthetic pathways have been identified in this strain. The PHA_MCL production pathway has been very clearly described in Pseudomonas species (11). The genes encoding PHA_MCL synthases (PhaC1 and PhaC2) of P. mendocina NK-01, which are located at locus MDS_0568 and locus MDS_0566 of the genome, respectively, and flank the PhaZ gene (PHA_MCL depolymerase, locus MDS_0567), have been identified. The alginate production pathway in Pseudomonas species has also been clearly demonstrated (12). For P. mendocina NK-01, the key enzymes mannuronic acid polymerase (MP, encoded by alg8 at locus MDS_1081), mannuronan C-5 epimerase (AlgG, encoded by algG at locus MDS_1077), and alginate lyase (AlgL, encoded by algL at locus MDS_1075) have also been clearly confirmed.

Nucleotide sequence accession number.

The complete genome sequence of P. mendocina NK-01 is available in GenBank under accession number CP002620.