Complete Genome Sequence of Thermus aquaticus Y51MC23

Abstract

Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser Basin of Yellowstone National Park. Remarkably, this T. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. Y51MC23 is a Gram-negative, rod-shaped organism that grows well between 50°C and 80°C with maximum growth rate at 65°C to 70°C. Growth studies suggest that Y51MC23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular proteases and peptidases as well as transporter systems for amino acids and peptides. The genome was assembled de novo using a 350 bp fragment library (paired end sequencing) and an 8 kb long span mate pair library. A closed and finished genome was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of 11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on megaplasmids were identified on the chromosome. The Y51MC23 genome contains two full and two partial prophage as well as numerous CRISPR loci. The high identity and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is interesting, given the 8,800 km separation of the two hot springs from which they were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple morphologies present in cultures. The use of fluorescence microscopy reveals new details about these unusual morphological features, including the presence of multiple types of large and small spheres, often forming a confluent layer of spheres. Many of the spheres appear to be formed not from cell envelope or outer membrane components as previously believed, but from a remodeled peptidoglycan cell wall. These complex morphological forms may serve multiple functions in the survival of the organism, including food and nucleic acid storage as well as colony attachment and organization.

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

“…Metabolism varies widely among thermophiles and general trends are hard to discern as it is extremely difficult to distinguish between the effect of speciation versus adjustment to extreme environments. For example, three main glycolytic pathways are used by bacteria in general: the traditional Embden-Meyerhof (EM) glycolysis, the Entner-Doudoroff pathway, and the pentose phosphate pathway; all three can also be found in different thermophilic bacteria (Counts et al 2017;Swarup et al 2014;Brumm et al 2015;Selig et al 1997) . In archaea, how ever, only modified variants of classical sugar degradation pathways were identified (Brasen et al 2014;Selig et al 1997) .…”

The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor

“…Examples of this include “rotund bodies” in Thermus aquaticus (Brumm P. J. et al, 2015), the outer membrane “toga” of Thermotoga maritima (Huber et al, 1986) and the multicellular spheres of D. turgidum (Svetlichny and Svetlichnaya, 1988). Regulation of these morphologies may be controlled by the action of SpoVS (Brumm P. J. et al, 2015).…”

“…Examples of this include “rotund bodies” in Thermus aquaticus (Brumm P. J. et al, 2015), the outer membrane “toga” of Thermotoga maritima (Huber et al, 1986) and the multicellular spheres of D. turgidum (Svetlichny and Svetlichnaya, 1988). Regulation of these morphologies may be controlled by the action of SpoVS (Brumm P. J. et al, 2015). D. turgidum possesses a gene coding for SpoVS (Rigden and Galperin, 2008) (Dtur_0800) similar to SpoVS proteins found in sporulating Firmicutes species as well as in the non-sporulating Thermus - Deinococcu s and Thermotoga groups, but not in non-sporulating Firmicutes species.…”

“…Thermotoga SpoVS orthologs have 53–78% identity, a Clostridium thermocellum ortholog has 74% identity, Caldicellulosiruptor orthologs have 65–71% identity, and Thermus orthologs have 56% identity to Dtur_0800. SpoVS may be an important regulator of cell morphology and differentiation in both sporulating thermophiles where it regulates the transition from vegetative growth to spore formation as well as the non-sporulating thermophiles where it regulates the transition from vegetative growth to formation of multiple morphologies (Brumm P. J. et al, 2015). …”

How can mate-pair sequencing be utilized for cancer patients?

“…There are also several other commercial available Mate Pair Library kits that have their own unique features. For example, the NxSeq Long Mate from Lucigen has shown that they could improve assembly quality [8]. Sage Science has improved the MP method using the SageELF, which lowers the needed sample input [9].…”