Deinococcus as new chassis for industrial biotechnology: biology, physiology and tools

Deinococcus, originally identified as Micrococcus, are coccoid or rod-shaped nonsporulating bacteria known for their resistance to multiple stresses and their capacity to repair DNA damage with unparalleled efficiency compared to other known bacterial species. Deinococcus radiodurans strain R1 was the first discovered deinobacteria and was isolated in 1956 (Anderson et al. 1956) from X ray-irradiated canned meat. More than 60 different species have been isolated from very diverse environments, such as air dust (Weon et al. 2007; Yang et al. 2009, 2010) and air sample (Yoo et al. 2010), activated sludge (Im et al. 2008), desert soils (De Groot et al. 2005; Rainey et al. 2005), arsenic polluted water (Suresh et al. 2004), cold environments in Antarctica (Hirsch et al. 2004), hot springs or biofilms at the surface of paper machines (Ferreira et al. 1997; Kolari et al. 2002), radioactive sites (Siebert and Hirsch 1988) faeces (Brooks and Murray 1981), gut of a wood-feeding termite (Chen et al. 2012) and Phoenix spacecraft surface (Stepanov et al. 2014). These species grow at temperatures ranging from 4 to 55°C and have been regrouped in a distinct (Rainey et al. 2005) eubacterial phylogenetic lineage related to the Thermus genus. The closest Deinococcus relatives are Trueperaceae, Thermales (Marinithermus, Thermus, Oceanithermus and Vulcanithermus); no members of this genus have been implicated as pathogens. Robust cells that are able to assimilate all of the most common sugars and synthesize the biological macromolecules necessary for growth from cheap carbon sources without auxotrophy are of considerable interest for biotechnological applications. Indeed, several Deinococcus species meet this requirement because they are capable of growing on minimal media and metabolizing multiple sugars. Furthermore, the well-known robustness of this bacterium and its physiological specificities makes it an attractive chassis for future biotechnological applications. However, many bacteria with attractive properties are recalcitrant to genetic manipulation because of the lack of plasmids and shuttle vectors, the scarcity of selection markers, and low transformability or narrow host range. Approximately, 900 publications referenced in Medline describe the ability of D. radiodurans R1 to resist radiation and to overcome oxidative stress. Most of the genetic tools available for Deinococcus originate or were developed for this strain, and it can be easily engineered. The second most well-studied species is Deinococcus geothermalis, with approx. 50 publications referenced in Medline, but there is only one report describing the transformation of this strain with an autonomous plasmid originally constructed for D. radiodurans (Brim et al. 2003). In comparison, 300 000 publications mention Escherichia coli, and 100 000 publications discuss Saccharomyces cerevisiae. The focus on the resistance of Deinococcus to radiation has somewhat masked the potential interest in the industrial applications of this genus. In this review, we summarize the physiological and genomic properties of Deinococcus, the tools available to engineer the different species and the most recent applications.