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Results: 7

1.
Figure 4

Figure 4. IR resistance of wild-type (ATCC BAA-816) and D. radiodurans mutants lacking orthologs in D. geothermalis (DSM 11300).. From: Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.

Survival values following 9 kGy (60Co) are from three independent trials with standard deviations shown. The structure of the homozygous mutants DRB0100, DR2221, DR105 and DR0140 are presented in Figure S6.

Kira S. Makarova, et al. PLoS ONE. 2007;2(9):e955.
2.
Figure 6

Figure 6. Sequence signature of a predicted site of a radiation response regulator.. From: Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.

Four different nucleotides are shown by four letters (A, G, C, T) in different colors. The height of the letter is proportional to its contribution to the information content in the corresponding position of the multiple alignment used for “sequence logo” construction. The figure was constructed by the “sequence logo” program described previously [160].

Kira S. Makarova, et al. PLoS ONE. 2007;2(9):e955.
3.
Figure 2

Figure 2. Whole genome evolutionary reconstructions for D. radiodurans, D. geothermalis, T. thermophilus (HB8) and T. thermophilus (HB27).. From: Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.

For each internal node of tree (open boxes), the inferred number of tdCOGs is shown. For each tree branch the inferred number of tdCOGs lost (minus sign) and gained (plus sign) is shown. For the deep ancestor of the Cyanobacteria, Actinobacteria and Deinococcus-Thermus group (shaded box), the inferred number of COGs is shown. For the extant species, the number of tdCOGs, the number of proteins in tdCOGs (in parentheses), and the number of “free” (not assigned to tdCOGs) proteins (plus sign) are shown.

Kira S. Makarova, et al. PLoS ONE. 2007;2(9):e955.
4.
Figure 7

Figure 7. X-ray fluorescence (XRF) microprobe element distribution maps [142].. From: Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.

A, D. geothermalis (diplococcus). B, D. radiodurans (tetracocus). Cells were harvested from mid-logarithmic cultures in undefined rich medium, imaged, and quantified as described previously [17]. The element distribution images are plotted to different scales designated by a single color-box, where red represents the highest concentration and black the lowest. ppm values in parentheses next to the element symbol correspond to red. XRF microprobe analysis measurements were made at beamline 2ID-D at the Advanced Photon Source, Argonne National Laboratory as described recently [17].

Kira S. Makarova, et al. PLoS ONE. 2007;2(9):e955.
5.
Figure 3

Figure 3. Gene-gain and gene-loss for different functional groups for D. radiodurans and D. geothermalis.. From: Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.

Designations of functional groups (from the COG database): J–Translation, ribosomal structure and biogenesis; K–Transcription; L–DNA replication, recombination and repair; D–Cell division and chromosome partitioning; O–Posttranslational modification, protein turnover, chaperones; M–Cell envelope and outer membrane biogenesis; N–Cell motility and secretion; P–Inorganic ion transport and metabolism; T–Signal transduction mechanisms; C–Energy production and conversion; G–Carbohydrate transport and metabolism; E–Amino acid transport and metabolism; F–Nucleotide transport and metabolism; H–Coenzyme metabolism; I–Lipid metabolism; Q–Secondary metabolites biosynthesis, transport and catabolism; V–genes involved in stress response and microbial defense.

Kira S. Makarova, et al. PLoS ONE. 2007;2(9):e955.
6.
Figure 1

Figure 1. Radiation resistance and genome structure of D. geothermalis and D. radiodurans. A, IR (60Co, 5.5 kGy/h).. From: Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.

B, UV (254 nm) (3 J/m2 s−1). Open circle, D. radiodurans (32°C); open triangle, D. geothermalis (50°C); and open square, D. geothermalis (32°C). Values are from three independent trials with standard deviations shown. At near-optimal growth temperatures, the 10% survival values (D10) following IR for D. radiodurans (32°C) and D. geothermalis (50°C) are 15 kGy; for E. coli, 0.7 kGy (37°C) [5]; and for T. thermophilus (HB27) 0.8 kGy (65°C) [27]. C, PFGE of genomic DNA prepared from irradiated (0.2 kGy) D. radiodurans (DR+IR) and D. geothermalis (DG+IR); and genomic DNA from non-irradiated D. geothermalis digested with SpeI (DG+SpeI). (M) PFGE DNA size markers. PFGE was as described previously [77].

Kira S. Makarova, et al. PLoS ONE. 2007;2(9):e955.
7.
Figure 5

Figure 5. Multiple alignments of selected families conserved in two Deinococcus species.. From: Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks.

The multiple alignments were constructed for selected representative sets of sequences by the MUSCLE program [154]. Where necessary, alignments were modified manually on the basis of PSI-BLAST outputs [94]. The positions of the first and the last residue of the aligned region in the corresponding protein are indicated for each sequence. The numbers within the alignment refer to the length of inserts that are poorly conserved between all the families. Secondary structure elements are denoted as follows: E-β-strand; and H-α-helix. The coloring scheme is as follows: predominantly hydrophobic residues are high-lighted in yellow; positions with small residues are in green; positions with turn-promoting residues are in cyan; positions with polar residues are in red; hydroxyl-group containing residues are in blue; aromatic residues are in magenta; and invariant, highly conserved groups are in boldface. A, DR0644-Dgeo_0284 conserved pair of orthologs belong to the copper/Zinc superoxide dismutase family; shaded letters refer to amino acids that play an important role in the Cu2+/Zn2+ coordination environment and in the active site region. The bottom line shows the correspondence between the most conserved regions corresponding to the β-stand structural core and conserved in most family members as denoted in Bordo et al [157]. B, Dgeo_0137-DR0449 are highly specific for the Deinococcus lineage proteins that have an RNAse H-related domain. Catalytic residues conserved in the RNAse H family are shaded. Secondary structure elements are shown for E. coli RNase HI (PDB:2rn2). C, DR0041-Dgeo_0188 is another conserved pair (DdrA-related) of proteins belonging to the Rad52 family of DNA single-strand annealing proteins [97]. Secondary structure elements are shown for human RAD52 (PDB:1KN0) [158]. sak is a phage gene described previously [159]; D, DR0381-Dgeo_0373 are diverged homologs of NADPH-dependent nitrile reductase (GTP cyclohydrolase I family) that might be involved in nucleotide metabolism. The conserved Cys and Glu found in the substrate binding pocket of both protein families and specific zinc-binding and catalytic residues in the FolE family are shaded. The QueF family motif is boxed. Other catalytic residues in FolE not found in QueF are in yellow. Genbank Identifier (gi) numbers are listed on the right.

Kira S. Makarova, et al. PLoS ONE. 2007;2(9):e955.

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