Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11T (= DSM 44721T)
© The Author(s) 2014
Published: 15 June 2014
Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium, which contains Gram-positive and non-spore forming bacteria with a high G+C content. C. terpenotabidum was isolated from soil based on its ability to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria. It displays tolerance to salts (up to 8%) and is related to Corynebacterium variabile involved in cheese ripening. As this is a type strain of Corynebacterium, this project describing the 2.75 Mbp long chromosome with its 2,369 protein-coding and 72 RNA genes will aid the Genomic Encyclopedia of Bacteria and Archaea project.
Strain Y-11T (= DSM 444721T) is the type strain of the species Corynebacterium terpenotabidum . It was originally isolated from soil, although the exact source has not been published [2,3]. The genus Corynebacterium is comprised of Gram-positive bacteria with a high G+C content. It currently contains over 80 members  isolated from diverse backgrounds like human clinical samples  and animals , but also from soil  and ripening cheese .
Within this diverse genus, C. terpenotabidum has been proposed to form a subclade together with C. variabile DSM 20132T and C. nuruki S6-4T, demonstrating 97.4% and 95.9% similarity respectively between the 16S rRNA gene sequences. Information on the strain is scarce. It was isolated for its ability to metabolize the linear triterpene squalene and classified as an Arthrobacter species [2,3], but no further information on the strain was supplied. Neither the origin nor the exact isolation procedures were reported. C. terpenotabidum can cleave squalene yielding geranylacetone  but also accepts some squalene derivatives .
Here we present a summary classification and a set of features for C. terpenotabidum DSM 44721T, together with the description of the genomic sequencing and annotation.
Classification and features
A representative genomic 16S rRNA sequence of C. terpenotabidum DSM 44721T was compared to the Ribosomal Database Project database . C. terpenotabidum shows highest similarity to C. variabile (97.4%).
Classification and general features of C. terpenotabidum Y-11T according to the MIGS recommendations .
Species Corynebacterium terpenotabidum
Type-strain Y-11T (=DSM 44721T)
0–8% (w/v) NaCl
fructose, galactose, mannose, lactate, ethanol
Terminal electron acceptor
Sample collection time
C. terpenotabidum was found to be able to utilize fructose, galactose, mannose, lactate, and ethanol as carbon source, while many others like arginine, aspartate, histidine, methylamine, ethylamine, methanol, galactose, lactose, maltose, sucrose, glycerol, sorbitol, mannitol, inositol, citrate, succinate, malonate, pimelate, m-hydroxybenzoate and p-hydroxybenzoate cannot be used. Optimal growth of strain Y-11T is reported at 28°C. C. terpenotabidum was shown to grow with a salinity between 0 and 8.0% (w/v NaCl), with no growth at 10% . The biochemical characterization revealed positive signals for urease, catalase, and hydrolysis of Tween 80.
The cell wall of C. terpenotabidum Y-11T contains alanine, glutamic acid, and meso-diaminopimelic acid in a molar ratio of 2.12: 1.00: 0.97. The main components of the cell wall sugars are described to be arabinose, galactose, and mannose in a molar ratio of 2.47: 1.71: 1.00. The glycan moiety of the cell wall was found to contain acetyl residues .
In C. terpenotabidum, cellular fatty acids are composed mainly of oleic acid (C18:1 ω9c, 31%), palmitic acid (C16:0, 28%), and tuberculostearic acid 10-methyl (C18:0, 21%). The whole-cell methanolysate of strain Y-11 contained mycolic esters . The predominant isoprenoid quinone is menaquinone MK-9(H2).
Genome sequencing and annotation
Genome project history
Genome sequencing project information
Two genomic libraries: one 454 pyrosequencing PE library (3.4 kb insert sizes), one Illumina library
454 GS FLX Titanium, Illumina MiSeq
29.52× Pyrosequencing; 61.71 × SBS
Newbler version 2.3
Gene calling method
GenBank Date of Release
September 1, 2013 / after publication
NCBI project ID
Source material identifier
Growth conditions and DNA isolation
C. terpenotabidum strain Y-11T, DSM 44721, was grown aerobically in LB broth (Carl Roth GmbH, Karlsruhe, Germany) at 30 °C. DNA was isolated from ∼ 108 cells using the protocol described by Tauch et al. 1995 .
Genome sequencing and assembly
The genome was sequenced using a 454 sequencing platform. A standard 3k paired end sequencing library was prepared according to the manufacturers protocol (Roche). The genome was sequenced using the GS-FLX platform with Titanium chemistry, yielding 384,252 total reads, providing 29.52× coverage of the genome. Pyrosequencing reads were assembled using the Newbler assembler v2.3 (Roche). The initial Newbler assembly consisted of 22 contigs in six scaffolds. Analysis of the six scaffolds revealed five that made up the chromosome, while the remaining one contained five copies of the RRN operon that caused the scaffold breaks. The scaffolds were ordered based on alignments to the complete genomes of C. variabile  and subsequent verification by restriction digestion, Southern blotting and hybridization with a 16S rDNA specific probe.
The Phred/Phrap/Consed software package [27–30] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, gaps between contigs were closed by editing in Consed (for repetitive elements) and by PCR with subsequent Sanger sequencing (IIT Biotech GmbH, Bielefeld, Germany). A total of 12 additional reactions were necessary to close gaps not caused by repetitive elements.
To raise the quality of the assembled sequence, Illumina reads were used to correct potential base errors and increase consensus quality. A WGS library was prepared using the Illumina-Compatible Nextera DNA Sample Prep Kit (Epicentre, WI, U.S.A) according to the manufacturer’s protocol. The library was sequenced in a 2x 120 bp paired read run on the MiSeq platform, yielding 2,307,926 total reads. Together, the combination of the Illumina and 454 sequencing platforms provided 91.2× coverage of the genome.
Gene prediction and annotation were done using the PGAAP pipeline . Genes were identified using GeneMark , GLIMMER , and Prodigal . For annotation, BLAST searches against the NCBI Protein Clusters Database  are performed and the annotation is enriched by searches against the Conserved Domain Database  and subsequent assignment of coding sequences to COGs. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE , Infernal , RNAMMer , Rfam , TMHMM , and SignalP .
% of totala
Genome size (bp)
DNA coding region (bp)
DNA G+C content (bp)
Genes with function prediction (protein)
Genes assigned to COGs
Genes in paralog clusters
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with the general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Christian Rückert acknowledges funding through a grant by the Federal Ministry for Education and Research (0316017) within the BioIndustry2021 initiative.
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