Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4

Abstract

Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.

High‐quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep‐branching lineages of the phylum Actinobacteria

“…No PTS‐type transporters were identified in G. occulta genome. By in large, S. soli and R. radiotolerans have similar ABC transporters for sugars (Egas et al, ).…”

“…Genes coding for enzymes involved in the synthesis of mannosylglycerate or di‐ myo ‐inositol‐phosphate were not identified in G. occulta . In R. radiotolerans , trehalose synthesis can proceed via four pathways namely TpS/TpP, TreS, TreT, and TreY/TreZ (Egas et al, ; Nobre et al, ). In G. occulta only the genes coding for TpS/TpP and TreS were detected in the genome ( tpS , EC 2.4.1.15, Gocc_2203, tpP , EC 3.1.3.12, Gocc_2154, treS , EC 5.4.99.16, Gocc_0097).…”

Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis

“…Results presented here show that homologs showing high degree of sequence similarity to the BchB and BchN proteins are present in two sequenced Rubrobacter species (R. xylanophilus and R. radiotolerans), belonging to the phylum Actinobacteria (family Rubrobaceteraceae, order Rubrobacterales) (Yarza et al 2008;Gao and Gupta 2012;Egas et al 2014;Albuquerque et al 2014). The phylum Actinobacteria is composed of high G?C Grampositive bacteria (Goodfellow et al 2011;Gao and Gupta 2012), and there is no prior indication of the presence of photosynthesis, or any evidence pertaining to it, in the members of this phylum.…”

“…These studies revealed that in BLASTp searches with the BchB and BchN proteins, in addition to the expected presence of homologs of these proteins in different photosynthetic organisms (Beale 1999;Raymond et al 2002;Mulkidjanian et al 2006;Gupta 2012), homologs exhibiting low expect values (E values), in the range of 2e -32 to 5e -53 , were also present in the two genome sequenced species from the genus Rubrobacter (viz. R. xylanophilus and R. radiotolerans) ( Table 1) (Egas et al 2014). The BchL, BchN, and BchB proteins are also known to exhibit sequence/structural similarity to the three subunits of chlorin reductase (viz.…”

“…Due to the unique presence of these three proteins in the chlorophototrophs, BLAST searches with their sequences provide important diagnostic tools to determine the presence of photosynthesis (or its remnants) in other bacterial lineages. The BLASTp searches with the sequences of these proteins reported in the present work have revealed that homologs showing high degree of sequence and structural similarity to the BchB and BchN proteins are present in members of the genus Rubrobacter, which is a part of the phylum Actinobacteria (Yarza et al 2008;Gao and Gupta 2012;Egas et al 2014;Albuquerque et al 2014). The branching pattern in phylogenetic trees and the sequence characteristics of the Rubrobacter BchB/BchN homologs indicate that the genes for these proteins are not derived by lateral gene transfers from other phyla of photosynthetic bacteria and that they likely represent ancestral forms of the BchB/ BchN proteins.…”