Draft Genome Sequence of Methylophaga aminisulfidivorans MP^T

Abstract

Methylophaga aminisulfidivorans MP^T is a restricted facultatively marine methylotrophic bacterium that grows on methanol, methylated amines, dimethyl sulfide, and dimethyl sulfoxide. Here we present the high-quality draft genome sequence of M. aminisulfidivorans MP^T (KCTC 12909^T = JCM 14647^T), consisting of a chromosome (3,092,085 bp) and a plasmid (16,875 bp).

GENOME ANNOUNCEMENT

The genus Methylophaga is a unique group of aerobic, halophilic, and non-methane-utilizing methylotrophs (6). Members of this genus have been isolated from various marine sediments and soda lakes and play an important role in the coastal environments participating in biogeochemical cycling of one-carbon substrates containing nitrogen, sulfur, or halogens (1, 7). They use the ribulose monophosphate pathway for one-carbon compound assimilation. The genus Methylophaga currently has seven species with validly published names, while only the genome sequence of Methylophaga thiooxydans (strain DMS010^T) has been reported (3).

Methylophaga aminisulfidivorans MP^T (KCTC 12909^T = JCM14647^T) was isolated from seawater at Mokpo, South Korea (7). The strain is aerobic, neutrophilic, and halophilic and grows well on methanol, methylated amines, dimethyl sulfide, and dimethyl sulfoxide. Only fructose is utilized as a multicarbon source.

The high-coverage genome sequence of M. aminisulfidivorans MP^T was determined using a combination of Illumina Genome Analyzer IIx (150-bp single-end shotgun sequencing, 33,762,341 sequencing reads, 1,365-fold coverage) and the Roche Genome Sequencer FLX system (paired ends with an insert size of 3 kb, 909,213 reads, 60-fold coverage). Assembly of the Illumina sequencing reads was carried out with CLC genomics wb4 (CLCbio), whereas Newbler assembler 2.3 (Roche) was used to generate scaffolds from a 454-paired-end library. The two assemblies were merged into a single assembly using the CodonCode Aligner software (CodonCode Co.). After multiple rounds of gap-closing steps based on standard PCR and Sanger sequencing, 2 contigs (2,266,798 and 825,287 bp, respectively, G+C content of 43.5 mol%) representing a chromosome and one circular plasmid (169,875 bp, G+C content of 41.20 mol%) were obtained. The resultant genome sequence was uploaded into the RAST server (2) to predict the open reading frames (ORFs), tRNAs, and rRNAs. The predicted ORFs were annotated by searching against clusters of orthologous groups (8) and SEED databases (5).

The chromosome of M. aminisulfidivorans MP^T harbors 2,984 protein coding genes, 3 rRNA operons, and 31 tRNAs, whereas 190 coding genes and 9 tRNAs were found in the plasmid. The gene clusters responsible for methanol oxidation (mxaFJGIRSACKL) and synthesis of the cofactor pyrroloquinoline quinone (pqqBCDE) were identified from the draft genome sequence. Five types of cytochromes and one cytochrome c oxidase (cbb₃) were also predicted. A gene encoding a novel bacterial flavin-containing monooxygenase (MAMP_00532), which catalyzes nitrogen-containing compounds or indole by use of oxygen through an NADPH-dependent pathway (4), was identified. At least four different gene clusters potentially encoding restriction modification (RM) systems, which include type I and type II, were predicted. A very low transformation efficiency of M. aminisulfidivorans MP^T may be due to these multiple RM systems. The information provided in the whole-genome sequence of M. aminisulfidivorans MP^T here should facilitate future studies of the metabolic diversity of the genus Methylophaga.

Nucleotide sequence accession number.

The genome sequence and annotation of M. aminisulfidivorans MP^T have been deposited in GenBank under accession number AFIG00000000.