Due to the oxygenase activity of the D-ribulose-1,5-bisphosphate carboxylase at low CO2 and high selleck chemicals llc O2 concentrations, the phosphoglycolate formed in these organisms is subsequently dephosphorylated to glycolate [8]. It is reported that no other organic or inorganic substrates are used [3], even though a total of 78 carbohydrate transport and metabolism genes are found the genome of this organism (COGS table). Neither sulfate, sulfite, thiosulfate, elemental sulfur, nor nitrate are reduced [3]. Figure 2 Scanning electron micrograph of S. glycolicus FlGlyRT Table 1 Classification and general features of S. glycolicus FlGlyRT according to the MIGS recommendations [22] and the NamesforLife database [23]. Chemotaxonomy Strain FlGlyRT has no cytochromes and the cells contain menaquinone-7-10, with MK-9 as major fraction [3].

Although the cells stain Gram-negative, the ultrastructural analysis shows a Gram-positive cell wall architecture [3]. Genome sequencing and annotation Genome project history This organism was selected for sequencing on the basis of its phylogenetic position [36], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [37]. The genome project is deposited in the Genome On Line Database [18] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2. Table 2 Genome sequencing project information Growth conditions and DNA isolation S. glycolicus FlGlyRT, DSM 8271, was grown anaerobically in DSMZ medium 298b (FlGlyM-medium) [38] at 28��C.

DNA was isolated from 0.5-1 g of cell paste using Jetflex Genomic DNA Purification kit (GENOMED 600100) following the standard protocol as recommended by the manufacturer, adding 10 ��L proteinase K to the standard lysis solution for 50 minutes at 58��C. DNA is available through the DNA Bank Network [39]. Genome sequencing and assembly The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [40]. Pyrosequencing reads were assembled using the Newbler assembler. The initial Newbler assembly consisting of 38 contigs in two scaffolds was converted into a phrap [41] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library.

Illumina sequencing Entinostat data (602.6 Mb) was assembled with Velvet [42] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. 454 draft assembly was based on 163.5 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [41] was used for sequence assembly and quality assessment in the subsequent finishing process.