Rubrobacter radiotolerans

Classification

Higher order taxa

Domain: Bacteria

Phylum: Actinobacteria

Class: Actinobacteria

Subclass: Rubrobacteridae

Order: Rubrobacterales

Family: Rubrobacteraceae

Genus: Rubrobacter

Species

Rubrobacter radiotolerans RSPS-4 (Type Strain RRD 42256)

Description and significance

The strain RSPS-4 of Rubrobacter radiotolerans was isolated from hot spring runoff in São Pedro do Sul, Portugal (Egas, et al., 2014). The spring was at the surface and had a pH of 8.9 and a temperature of 50℃. From this and isolation it seems to have optimal conditions in semi-salty water with temperatures of 45℃ (hot springs). The strain was warranted to the the Spanish Type Culture Collection (CETC) under the code CETC 8386 (Egas, et al., 2014). Rubrobacter radiotolerans (at first, Arthrobacter radiotolerans) was originally found in a water sample taken from a hot spring in Tottori Prefecture, Japan. It was discovered after putting the sample through gamma-irradiation (Strain P-1) (Yoshinaka, Yano, and Yamaguchi, 1973). It is a gram-positive bacterium high in G+C content that is non-sporulating and non-motile. In earlier stages the bacteria seems to be shaped mostly as pleomorphic rods and in late stages seems to be mostly coccoid-shaped or shaped as short rods (Yoshinaka, Yano, and Yamaguchi, 1973). R. radiotolerans are smooth, opaque, and contain pinkish to red pigmented carotenoids. The major pigmented components are bacterioruberin and monoanhydrobacterioruberin which have 13 conjugated double bonds that are characteristic of halophilic bacteria. Bacterioruberin has four tertiary OH groups and monoanhydrobacterioruberin has three tertiary OH groups (Saito et al., 1994). A third major component, deinoxanthin, has also been identified in contributing to their reddish pigment (Asgarani et al., 2000).

R.radiotolerans are extremely resistant to UV, thermal, and gamma radiation, even more so than its relative Rubrobacter xylanophilus (Ferreira et al., 1999). Gamma radiation is typically restricted to locations contaminated with nuclear waste as high doses are not naturally found in the biosphere. One hypothesis for such a characteristic is that it evolved in response to environmental challenges such as desiccation or reactive oxidative stress. In addition, such radiation resistance is often found in organisms that do not produce spores, such as R.radiotolerans (Egas et al., 2014).

The ability to recover from such high doses of radiation seems to result from a combination of several mechanisms. Within its carotenoids, the components deinoxanthin and bacterioruberin are attributed to radiation resistance and act as an effective antioxidant in vitro. Additionally, bacterioruberin has also been attributed to resistance to hydrogen peroxide. A DNA repair enzyme, known as R-endonuclease, aids in DNA repair activity by recognizing radiation-induced DNA lesions. Thymine glycol and ring fragmentation products such as urea residues, which blocks DNA replication and is premutagenic, and abasic sites, which can be lethal and mutagenic, are cleaved by this repair enzyme in order to prevent their cytotoxic and mutagenic effects on cells (Asgarani et al., 2000). A third mechanism involves the manganese superoxide dismutase (SOD), an enzyme that forms homo-tetramerization of 24,000 Da-monomer while maintaining enzymatic activity against potassium cyanide and hydrogen peroxide.

16S Ribosomal RNA Gene Information

The strains RSPS-4 and P-1 (Type strain DSM 5868) have extremely similar 16s rRNA sequences, with only two components differing (Egas, et. al, 2014).. The sequencing of the 16s ribosomal RNA data of DSM 5858 can be found at:

NCBI database

(ncbi database) https://www.ncbi.nlm.nih.gov/nuccore/NR_119230.1

Genome Structure (if the genome exists)

The total complete genome size is 3,267,233 bp. The genome consists of a one circular chromosome of 2,875,491 bp with a G+C content of 66.91% and three circular plasmids of 190,889 bp, 149,806 bp, 51,047 bp, holding 3,214 predicted protein coding genes, 46 tRNA genes, and one rRNA operon (strain RSPS 4) (Egas, et al., 2014).

The sequencing was conducted in Penzberg, Germany at Roche Diagnostics GmbH (Egas, et al., 2014).

Cell structure and metabolism

R. radiotolerans are a smooth, opaque bacterium shaped as pleomorphic rods and, later in life, is coccoid-shaped or shaped as short rods (Yoshinaka, Yano, and Yamaguchi, 1973). Their pigmented carotenoids are pinkish to red colored. The major pigmented components are bacterioruberin and monanhydrobacterioruberin, which contain 13 conjugated double bonds that are a characteristic of halophilic bacteria. There are four tertiary OH groups in bacterioruberin and three in monanhydrobacterioruberin (Saito, et al., 1994). Deinoxanthin, a third pigmented component, has been identified (Asgarani, et. al, 2000).

Rubrobacter radiotolerans have multiple different mechanisms that result in it being radiotolerant. Deinoxanthin and bacterioberin link to radiation resistance as an antioxidant. Bacterioruberin has been linked to hydrogen peroxide resistance (Asgarani, et al., 2000). R-endonuclease, a DNA repair enzyme, helps by recognizing radiation-induced lesions. Manganese supreroxide dismutase maintains enzymatic activity against potassium cyanide and hydrogen peroxide (Asgarani, et al., 2000).

You can find a table of different metabolic pathways, including unique gene counts and which genes that belong to certain pathways at:

https://www.patricbrc.org/portal/portal/patric/CompPathwayTable?cType=genome&cId=42256.3&algorithm=PATRIC&ec_number=.

(Wattam et al., 2014).

Author

Amber Parcel Katie McCullough