I. D. radiodurans Strain R1 Annotation
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updated annotation (2003), Koonin's group (Excel, 0.7Mb);
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updated annotation (2004), Koonin's group (Excel, 1.03Mb)
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II. Deinococcus Features
The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. So far, D. radiodurans is the only representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Comparative genomic analysis of the Deinococcus genome revealed some special features (Tables 1, 2, 3), including expansions of several families such as phosphatases, proteases, and the Nudix (MutT) family of pyrophosphohydrolases; several unique protein families such as DR2457-like and DR2038-like (19 families in total); and unique multidomain proteins and proteins that were apparently horizontally transferred from eukaryotes and archaea (Table 3). The D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small noncoding repeats (SNRs) (Table 2). In combination, these observations suggest that several different biological mechanisms may contribute to the multiple stress resistant phenotypes of this organism. Perhaps the biggest surprise was that D. radiodurans encodes fewer genes known to be involved in DNA repair than E. coli. For Review, see Makarova et al., (2001).
Table 1. General features of D. radiodurans
|
# |
Feature |
D. radiodurans genome |
Comment |
|---|---|---|---|
|
1 |
Genome size |
3.25 Mb |
Range of the size of bacterial genomes: 0.58 Mb |
|
2 |
G+C content |
66.6% |
|
|
3 |
all ORFs |
3192 |
Mycoplasma genitalium has 484 ORFs (min) |
|
4 |
ORFs in COG |
2218 |
|
|
5 |
Ratio of proteins in COG/not in COG |
2.28 |
D. radiodurans (DR) has the highest number of proteins which are not related to any COGs compared to E. coli, B. subtilis,Synechocystis sp., and Mycobacterium tuberculosis |
|
6 |
Number of unknown (predicted) proteins |
604 |
>61% of predicted proteins have been confirmed by high throughput proteomics |
|
7 |
Repeats |
52-IS, 295-SNRs |
DR has the highest number of repeats compared to E. coli, B. subtilis, Synechocystis sp., Mycobacterium tuberculosis |
|
8 |
Specific expansions families |
20 |
Only 4 families have specific expansions in DR |
|
9 |
Unique protein families |
19 |
There are no homologs in other species |
|
10 |
Proteins with unique domain combinations |
DR1207, DRA0057, DRA0131, DR0603, DRB0033, DR2444, DR0329, DR0004, DR2611 |
Almost all fully sequenced bacteria have proteins with unique domain architectures that have not been detected in other specie |
Table 2. Comparison of different genomes
|
|
Genome size (Mb) |
G+C (%) |
ORFs (all) |
ORFs in COG |
Ratio of proteins in COG/not in COG |
Repeats |
|
|---|---|---|---|---|---|---|---|
|
IS |
SNRs |
||||||
|
D. radiodurans |
3.25 |
66.6 |
3192 |
2218 |
2.28 |
52 |
295 |
|
E. coli |
4.64 |
50.8 |
4279 |
3587 |
5.18 |
37 |
2635 |
|
B. subtilis |
4.21 |
43.5 |
4112 |
3079 |
2.98 |
0 |
36 |
|
Synechocystis |
3.57 |
47.7 |
3167 |
2315 |
2.71 |
NA |
118 |
|
M. tuberculosis |
4.41 |
65.6 |
3927 |
2.35 |
2756 |
32 |
252 |
Table 3. Expanded protein families
|
Specific expansions/families |
COG number and name |
Number of proteins/domains in DR vs. other bacteria |
|---|---|---|
|
MutT (Nudix hydrolases) |
COG0494 NTP pyrophosphohydrolases including oxidative damage repair enzymes |
17 (many other bacteria also have expansions) |
|
Alpha/beta hydrolases |
COG0596 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) |
10 (many other bacteria also have expansions) |
|
SAM-methyltransferases |
COG0500 SAM-dependent methyltransferases |
14 (many other bacteria also have expansions) |
|
NH2-acetyltransferases |
COG0454 Histone acetyltransferase HPA2 and related acetyltransferases |
26 (many other bacteria also have expansions) |
|
Zn-metallo-beta lactamases |
COG0491 Zn-dependent hydrolases, including glyoxylases |
10 (many other bacteria also have expansions) |
|
Calcineurin-like phosphoesterase |
COG0639 Diadenosine tetraphosphatase and related serine/threonine protein phosphatases |
9 (Eukaryotes also have expansions) |
|
Subtilisin-like proteases |
COG1404 Subtilisin-like serine proteases |
10 (B. halodurans-9, B. subtilis-7) |
|
Me-dependent enzymes, DinB homologs |
COG2318 Uncharacterized protein conserved in bacteria |
3 (B. subtilis-4, B. halodurans-4) |
|
Tellurium resistant/ cAMP-binding |
COG2310 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 |
7 (E. coli-Z-10) |
|
McrA family |
COG1403 Restriction endonuclease |
5 (Nostoc-15) |
|
Sugar deacetylases, PIG-L family |
COG2120 Uncharacterized proteins, LmbE homologs |
6 |
|
PR1 family |
COG2340 Uncharacterized protein with SCP/PR1 domains |
5 (Nostoc-5) |
|
Conserved archaeal family |
COG2018 Uncharacterized distant relative of homeotic protein bithoraxoid |
3 (M. thermoautotrophicum-3, M. jannaschii-4) |
|
DegV like protein family |
COG1307 Uncharacterized protein conserved in bacteria |
5 (C. acetobutylicum, L. lactis, S. pyogenes -4) |
|
WD40 repeats |
COG2319 FOG: WD40 repeat |
5 (Nostoc -25, Eukaryotes - many) |
|
YiiM_Ecoli family |
COG2258 Uncharacterized protein conserved in bacteria |
4 (P. aeruginosa-4) |
|
YgiH_Ecoli family |
COG0344 Predicted membrane protein |
3 |
|
Enterococcus VanW homolog |
COG2720 Uncharacterized vancomycin resistance protein |
3 |
|
Homolog of MTH747 |
COG2013 Uncharacterized conserved protein |
3 (Halobacterium, M. acetivorans,Synechocystis, C. acetobutylicum -3) |
|
Homolog of YNL094w |
COG4850 Uncharacterized conserved protein |
2
|
