Michael J. Daly Lab: Deinococcus radiodurans

D. radiodurans Genome

I. D. radiodurans Strain R1 Annotation

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

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
(Mycoplasma genitalium), 9.11 Mb
(Bradyrhizobium japonicum)

2

G+C content

66.6%

 

3

all ORFs

3192

Mycoplasma genitalium has 484 ORFs (min)
Bradyrhizobium japonicum has 8317 ORFs (max)

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 species


Table 2. Comparison of different genomes

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

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