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The authors analyzed the molecular evolution of the ribonuclease H (RNase H) …


Biology Articles » Microbiology » Microbial Genetics » Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes » Tables

Tables
- Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes

Table 1
Number of RNase H genes identified in the archaeal and bacterial species.
Kingdom
Type
No. of species
No. of RNase H genes






1
2
3
Archaea
RNase HI
9
6
3
0

RNase HII
27
27
0
0

RNase HIII
1
1
0
0






Bacteria
RNase HI
210
173
32
5

RNase HII
220
219
1
0

RNase HIII
40
40
0
0
Table 2
Combinations of the three RNase H genes found in the archaeal and bacterial genomes.
Kingdom
Subdivision
No. of species
Classification of RNase H combination






Group A
Group B
Group C
Group D
Group E
Group F
Group G
Archaea
Crenarchaeota
5
0
3
0
0
0
2
0

Euryarchaeota
21
0
6
1
0
0
14
0

Nanoarchaeota
1
0
0
0
0
0
1
0

Total
27
0
9
1
0
0
17
0










Bacteria
Acidobacteria
1
0
1
0
0
0
0
0

Actinobacteria
20
0
18
1
0
1
0
0

Aquificae
1
0
0
1
0
0
0
0

Bacteroidetes
4
0
4
0
0
0
0
0

Chlamydiae
7
0
0
7
0
0
0
0

Chlorobi
3
0
3
0
0
0
0
0

Chloroflexi
2
0
2
0
0
0
0
0

Cyanobacteria
8
0
8
0
0
0
0
0

Deinococcus-Thermus
3
0
3
0
0
0
0
0

Firmicutes
49
15
18
7
0
0
0
9

Fusobacteria
1
0
1
0
0
0
0
0

Planctomycetes
1
0
0
0
0
1
0
0

Alphaproteobacteria
38
0
38
0
0
0
0
0

Betaproteobacteria
23
0
23
0
0
0
0
0

Deltaproteobacteria
11
0
11
0
0
0
0
0

Epsilonproteobacteria
5
0
5
0
0
0
0
0

Gammaproteobacteria
52
0
49
0
0
3
0
0

Spirochaetes
5
0
4
0
0
1
0
0

Thermotogae
1
0
1
0
0
0
0
0











Total
235
15
189
16
0
6
0
9
All species were classified on the basis of the RNase H combinations shown in the Venn diagram in Figure 1.
Table 3
List of genes containing dsRHbd in complete genomes.
Kingdom
Species
Accession No.
ORF
Direction
Domain
Archaea
Euryarchaeota





      Methanococcus maripaludis
NC_005791
832383–832988
complement
dsRHbd (4–46), RNH (65–201)






Bacteria
Bacteroidetes





      Bacteroides fragilis NCTC 9343
NC_003228
207338–207967
complement
dsRHbd (6–48), RNH (79–197)

      Bacteroides fragilis YCH46
NC_006347
253987–254616
complement
dsRHbd (6–48), RNH (79–197)

      Bacteroides thetaiotaomicron
NC_004663
4371820–4372455
complement
dsRHbd (6–48), RNH (81–199)

      Porphyromonas gingivalis
NC_002950
1292573–1293223
direct
dsRHbd (5–47), RNH (85–199)







Cyanobacteria





      Gloeobacter violaceus
NC_005125
3808044–3808685
complement
RNH (1–138), dsRHbd (156–197)







Firmicutes





      Bacillus clausii
NC_006582
1399495–1400094
direct
dsRHbd (6–48), RNH (74–183)

      Bacillus halodurans
NC_002570
933504–934094
direct
dsRHbd (6–48), RNH (69–192)

      Clostridium acetobutylicum
NC_003030
2659515–2660237
complement
dsRHbd (6–48), RNH (103–238)

      Clostridium perfringens
NC_003366
1707913–1708542
complement
dsRHbd (5–49), RNH (70–207)

      Clostridium tetani
NC_004557
2281472–2282092
complement
dsRHbd (5–47), RNH (68–203)

      Desulfitobacterium hafniense
NC_007907
2075150–2075770
complement
dsRHbd (8–50), RNH (71–203)

      Lactobacillus acidophilus
NC_006814
116459–117205
direct
dsRHbd (3–45), RNH (91–245)

      Lactobacillus delbrueckii
NC_008054
146497–147264
direct
dsRHbd (4–45), RNH (93–253)



978609–979283
complement
Resolvase (1–106), dsRHbd (127–168)

      Lactobacillus johnsonii
NC_005362
118550–119281
direct
dsRHbd (3–45), RNH (86–240)

      Lactobacillus plantarum
NC_004567
2310574–2311470
direct
dsRHbd (5–47), RNH (70–225)

      Lactobacillus salivarius
NC_007929
459722–460381
direct
dsRHbd (4–46), RNH (59–216)

      Mesoplasma florum
NC_006055
559864–560484
complement
dsRHbd (3–45), RNH (63–199)

      Mycoplasma capricolum
NC_007633
382602–383222
direct
dsRHbd (5–47), RNH (63–198)

      Mycoplasma mycoides
NC_005364
375791–376408
direct
dsRHbd (5–47), RNH (62–198)

      Mycoplasma penetrans
NC_004432
1267458–1268120
complement
dsRHbd (5–47), RNH (73–216)







Fusobacteria





      Fusobacterium nucleatum
NC_003454
1651474–1652124
complement
dsRHbd (6–48), RNH (70–215)







Deltaproteobacteria





      Bdellovibrio bacteriovorus
NC_005363
3036447–3037238
complement
RNH (18–164), dsRHbd (207–248)

      Desulfotalea psychrophila
NC_006138
1023218–1024003
direct
dsRHbd (28–70), RNH (105–247)

      Myxococcus xanthus
NC_008095
2628106–2628873
complement
RNH (3–154), dsRHbd (199–240)







Gammaproteobacteria





      Colwellia psychrerythraea
NC_003910
1743847–1744665
complement
dsRHbd (5–47), RNH (98–247)

      Photobacterium profundum
NC_006370
2161121–2161870
complement
dsRHbd (5–47), RNH (77–225)

      Saccharophagus degradans
NC_007912
82187–82945
complement
dsRHbd (5–47), RNH (81–228)

      Shewanella denitrificans
NC_007954
880428–881219
direct
dsRHbd (5–47), RNH (91–239)







Spirochaetes





      Borrelia burgdorferi
NC_001318
897096–897740
complement
dsRHbd (19–62), RNH (74–211)

      Borrelia garinii
NC_006156
899069–899668
complement
dsRHbd (4–47), RNH (88–196)







Thermotogae





      Thermotoga maritima
NC_000853
1322788–1323459
complement
dsRHbd (7–49), RNH (63–197)
dsRHbd sequences were found in 32 complete genomes (31 species, one with two strains). Open reading frame (ORF) numbers indicate the genomic positions of the genes that encode dsRHbd. Domain numbers indicate the amino acid positions relative to the start of each protein sequence. RNH represents the RNase H group.

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