Abstract
Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.
Highlights
Dictyoglomus species are genetically distinct and divergent from known taxa, and have been assigned to their own phylum, Dictyoglomi (Saiki et al, 1985; Euzéby, 2012)
D. turgidum strain 6724T was obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ). 10G electrocompetent E. coli cells, pEZSeq, Thermus aquaticus (Taq) DNA polymerase and OmniAmp DNA polymerase were obtained from Lucigen, Middleton, WI
The fraction of the genes annotated as members of COG class G, carbohydrate transport and metabolism, 13.4%, is greater than the fraction observed for 95% of genomes in the MicrobesOnline database (Dehal et al, 2010)
Summary
Dictyoglomus species are genetically distinct and divergent from known taxa, and have been assigned to their own phylum, Dictyoglomi (Saiki et al, 1985; Euzéby, 2012) They have been cultivated from or detected in anaerobic, hyperthermophilic hot spring environments (Patel et al, 1987; Svetlichny and Svetlichnaya, 1988; Mathrani and Ahring, 1991; Kublanov et al, 2009; Gumerov et al, 2011; Kochetkova et al, 2011; Burgess et al, 2012; Sahm et al, 2013; Coil et al, 2014; Menzel et al, 2015) or isolated from paper-pulp factory effluent (Mathrani and Ahring, 1992), but only two Dictyoglomus species have been validly described in the literature (Saiki et al, 1985; Svetlichny and Svetlichnaya, 1988). We present functional analysis of its DNA Pol I gene and a number of novel carbohydrases
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