Genome Sequence of Corynebacterium nuruki S6-4 ^T , Isolated from Alcohol Fermentation Starter

Abstract

Corynebacterium nuruki S6-4 T , isolated from Korean alcohol fermentation starter, is a strictly aerobic, nonmotile, Gram-positive, and rod-shaped bacterium belonging to the genus Corynebacterium and the actinomycete group. We report here the draft genome sequence of C. nuruki strain S6-4 T (3,106,595 bp, with a G؉C content of 69.5%).Corynebacterium nuruki strain S6-4 T was described as a Grampositive, strictly aerobic, irregular rod-shaped, and nonmotile bacterium (6). The strain was isolated from alcohol fermentation starter named "nuruk" in Korean, which is used for the manufacture of Korean traditional rice wine. Phylogenetic analysis based on 16S rRNA gene sequences showed that Corynebacterium nuruki strain S6-4T was most closely related to C. variabile DSM 20132 T , with 98.1% similarity. The genus Corynebacterium is currently composed of more than 100 type species, and 24 genome sequences have been reported to the NCBI database. The genetic information of the genus Corynebacterium has been enlarged over recent years, owing to its importance in the clinical aspect and food industry. The genome sequencing of C. diphtheriae NCTC13129, for instance, provided the knowledge about the etiology of diphtheria (2), and the genome sequencing of C. glutamicum ATCC 13032 confirmed the broad metabolic diversity related to fermentative production of L-amino acids for the food industry (3). To verify the role of the organism C. nuruki during alcohol fermentation, the sequencing project was initiated. Here, we present the genome of Corynebacterium nuruki strain S6-4 T in the family Corynebacteriaceae.The genome sequence of Corynebacterium nuruki strain S6-4 T was determined using paired-end sequencing technology (3-kb library) and performed with Roche 454 GS (FLX Titanium) pyrosequencing by Macrogen, Inc. (Seoul, Republic of Korea). The library preparation, sequencing reaction, and sequencing run were carried out with Roche software, according to the manufacturer's instructions. A total of 297,994 reads (81,128,322 bp) and 68 large contigs were generated to give 26-fold coverage. Assembly into scaffolds was performed using the GS Assembler software (version 2.5.3). The average size of the 9 scaffolds was 349,144 bp. The largest scaffold size was 1,619,955 bp, and the total assembly size was 3,142,299 bp.The unclosed draft genome was 3,106,595 bp in length and had a GϩC content of 69.5%. Two rRNA genes (5S-16S) and 56 tRNA genes in the draft assembly were identified by tRNAscan-SE 1.23 (5) and RNAmmer 1.2 (4), respectively. Open reading frames (ORFs) of large contigs were predicted by sixreading-frame translation (7) and annotated against the COG database (RPS-BLAST, E value of Ͻ10 Ϫ3

Chassis organism from Corynebacterium glutamicum – a top‐down approach to identify and delete irrelevant gene clusters

“…An intermediate degree of phylogenetic proximity was displayed by the subgroup core, which included gene overlaps from genomes of the subgroup within the genus Corynebacterium , such as: C. glutamicum ATCC 13032 (NC_006958) [ 13 ], C. deserti (unpublished genome), C. efficiens (NC_004369) [ 24 ] and C. callunae (unpublished genome). Finally, the widest core genome was called the genus core and included genes that were found in all of the following organisms: C. diphtheria (NC_002935) [ 25 ], C. halotolerans (NC_020302) [ 26 ], C. jeikeium (NC_007164) [ 27 ], C. nuruki (AFIZ00000000) [ 28 ], C. maris (NC_021915) [ 29 ], C. resistens (NC_015673) [ 30 ], C. terpenotabidum (NC_021663) [ 31 ], C. variabile (NC_015859) [ 32 ], and all genomes from the subgroup core. In order to evaluate the conservation for each gene, the information as to whether a gene belongs to a certain core genome was converted into a three-bit conservation code, with each bit representing a core genome group of the following order: genus, subgroup, and species.…”

The Family Corynebacteriaceae

“…The G+C content of the genomic DNA varies in a wide range between the species (> Table 12.1), as it can been expected when considering the taxonomic description of Corynebacterium species (Funke et al 1997b). However, some genome sequences of type strains revealed a significantly lower or higher G+C content of the genomic DNA than that deduced earlier from experimental taxonomic studies, for instance Corynebacterium kroppenstedtii (Tauch et al 2008a), Corynebacterium nuruki (Shin et al 2011b), and Corynebacterium resistens (Schröder et al 2012a) (> Table 12.1). The G+C content of the genomic DNA of Turicella otitidis is 71.35 mol% (Brinkrolf et al 2012) which is in the range of 65-72 mol% published previously (Funke et al 1994).…”

“…The latter section includes the additional species: Corynebacterium accolens, Corynebacterium ammoniagenes, Corynebacterium amycolatum, Corynebacterium glucuronolyticum, Corynebacterium lipophiloflavum, Corynebacterium matruchotii, Corynebacterium striatum, and Corynebacterium tuberculostearicum. The draft genome sequencing projects of Corynebacterium bovis (Schröder et al 2012b), Corynebacterium casei (Monnet et al 2012), Corynebacterium nuruki (Shin et al 2011b), and Turicella otitidis (Brinkrolf et al 2012) were published briefly as genome announcements.…”

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011

“…Kocuria rhizophila P7-4, sequence accession AFID00000000 [89] Streptomyces S4, sequence accession CADY01000000 [90] Corynebacterium nuruki S6-4 T , sequence accession AFIZ00000000 [91] Propionibacterium humerusii, sequence accession AFAM00000000.1 [92] Strain JDM601, sequence accession CP002329 [93] Streptomyces sp. strain Tü6071, sequence accession AFHJ01000000 [94] Bifidobacterium breve UCC2003, sequence accession CP000303 [95] Propionibacterium acnes, sequence accession CP002815 [96] Amycolicicoccus subflavus DQS3-9A1 T , sequence accession CP002786 (chromosome), CP002787 (plasmid pAS9A-1), and CP002788 (plasmid pAS9A-2).…”