Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream.

Caldanaerobacter yonseiensis is a strictly anaerobic, thermophilic, spore-forming bacterium, which was isolated from a geothermal hot stream in Indonesia. This bacterium utilizes xylose and produces a variety of proteases. Here, we report the draft genome sequence of C. yonseiensis, which reveals insights into the pentose phosphate pathway and protein degradation metabolism in thermophilic microorganisms.

GENOME ANNOUNCEMENT

Caldanaerobacter yonseiensis was isolated from a geothermal hot stream at Sileri, Java Island, in Indonesia (1). Previously, this strain was classified as a new species of the genus Thermoanaerobacter, designated Thermoanaerobacter yonseiensis, but reassigned as a novel genus and species, Caldanaerobacter yonseiensis (2). This strain is a strictly anaerobic, extremely thermophilic, spore-forming, and xylose-utilizing bacterium. C. yonseiensis can grow in the temperature range of 50 to 85°C, with an optimum at 75°C, and a pH range for growth of 4.5 to 9.0, with an optimum at pH 6.5 (1). These properties indicated that C. yonseiensis might be a good source for the isolation of thermostable and acidophilic d-xylose isomerase, which is suitable for the production of high fructose corn syrup in the food industry (3–5). Moreover, C. yonseiensis produces a novel subtilisin-like protease, thermicin, that showed maximum proteolytic activity at 92.5°C and pH 9.0, indicating that this enzyme will be applicable for the hydrolysis of collagens at elevated temperatures without contamination (6). Thus, C. yonseiensis is of great interest as a potential industrial microorganism, which led us to sequence the whole genome of this microorganism.

The genome of C. yonseiensis was sequenced via the Ion Torrent personal genome machine (PGM) sequencer system using a 316 D sequencing chip (7). The sequence was assembled using MIRA 3.4.0. The assembled genome consists of 102 contigs (>500 bp), with a genome size of 2,700,546 bp at 34.96-fold coverage, with a G+C content of 36.6%. The assembled contigs were submitted to the RAST annotation server (http://rast.nmpdr.org/) for subsystem classification and functional annotation. There were a total of 2,905 predicted protein-coding sequences (CDS), with 49% assigned to recognizable functional genes. While the 16S rRNA gene sequencing of C. yonseiensis showed the similarity of this bacterium to C. tengcongensis strain MB4 (99% sequence identity) and C. keratinophilus strain 2KXI (99% sequence identity), RAST analysis suggested that C. tengcongensis MB4 was actually the closet neighbor in terms of sequence similarity.

Consequently, we confirmed 13 genes from the draft sequence that encode proteins related to xylose utilization, including two xylose isomerase-coding genes that are involved in xylose metabolism in the C. yonseiensis genome. Also identified were genes that encode glucose-6-phosphate 1-dehydrogenase and 6-phosphogluconate dehydrogenase, which are among the key enzymes for the generation of reducing power (NADPH) in the pentose phosphate pathway. Another feature of C. yonseiensis is the ability to hydrolyze glycine- and proline-rich collagens (6). Based on our data, a gene encoding a subtilicin-like serine protease, designated thermicin, was identified, together with another four genes encoding serine proteases. Moreover, four genes encoding cysteine proteases and 27 genes encoding a variety of proteases were identified. Given these results, the draft genome sequence of C. yonseiensis will not only provide insights into the metabolism of monomeric and polymeric carbohydrates under extremely thermophilic conditions, but it will also encourage further study of a variety of proteases potentially applicable for their use in detergents and in the leather and textile industries.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AXDC00000000. The version described in this paper is the first version, AXDC01000000.