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Shuffling and disruption of operons and horizontal gene transfer are major contributions …


Biology Articles » Microbiology » Microbial Genetics » Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ » Tables

Tables
- Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

Table 1
Examples of horizontally transferred operons
Operon
Recipient organism and correspondent genes
Probable source
Other probable recipients
Comment
Operon acquisition
Pyruvate:ferredoxin oxidoreductase
Thermotoga maritima TM0015-TM0018
Archaea
Aae, Hpy, Bha/Sau
Apparently, the related operon for 2-oxoisovalerate oxidoreductase (TM1758-TM1759) was also transferred from archaea
Sulfate/molybdate transport
Bacillus halodurans BH3128-BH3130
Gram-negative bacteria
-
No other such operons in Bacillus-Clostridium group members
Putative effector of murein hydrolase
Pyrococcus horikoshii PH1801-PH1802
Bacteria
Pab, Mac

Allophanate hydrolase subunits
Pyrococcus horikoshii PH0987-PH0988
Bacteria
Pab






Paralogous operon acquisition
Dipeptide transporter
Vibrio cholerae VC0620-VC0616
Thermotoga/Archaea
Tma
It has several another bacterial operons including VC1091-VC1095
Ribonucleotide reductase alpha and beta subunit
Halobacterium sp. VNG2384G VNG2383G
Bacteria
-
Additional to "archaeal:" Ribonucleotide reductase alpha subunit VNG1644G, beta subunit is apparently lost
Aromatic amino-acid biosynthesis
Halobacterium sp. VNG0384G VNG0386G
Bacteria
-
Paralogs of this pair are VNG1646G-VNG1647G





Xenologous operon displacement
Histidine biosynthesis suboperon
Pseudomonas aeruginosa PA3151-PA3152
Epsilon-Proteobacteria
-

Panthothenate synthesis
Campylobacter jejuni Cj0297c-Cj0298c
Gram-positive bacteria
-

DNA repair SbcDC
Vibrio cholerae VCA0520-VCA0521
Gram-positive bacteria
-

DNA gyrase A and B
Halobacterium sp. VNG0887G-VNG0889G
Bacteria
Hbs, Tac, Tvo, Afu,

Dipeptide transporter
Streptococcus pyogenes SPy2000-SPy2004
Gamma-Proteobacteria
-

Glutamate synthase complex
Thermotoga maritima TM0394-TM0398
Archaea
-
There is another homolog for gene TM0397 of possible archaeal origin
NADH:ubiquinone oxidoreductase
Halobacterium sp. VNG0635G-VNG0637G
Bacteria
-

Phosphate transporter
Methanothermobacter thermoautotrophicum MTH1727-MTH1734
Bacteria
-

Table 2
Examples of probable mosaic operons
Species
Predicted operon
General operon function
Horizontally acquired genes
Probable source of horizontally acquired genes
Functions of horizontally acquired genes
Cluster 1*





Rickettsia prowazekii Rickettsia conorii
RP633-661, RC0980-1008
Ribosomal operon
RP651 RC0998
Chlamydia
L29
Aquifex aeolicus
Aq001-021
Ribosomal operon
Aq018a
Archaea
L29






Cluster 2





Rickettsia prowazekii Rickettsia conorii
RP800-804, RC1234-1238
F0F1-type ATPase
RP804 RC1238 Gram-positive bacteria
Delta subunit

Ureaplasma urealyticum
UU128-138
F0F1-type ATPase
UU128, UU132_1, UU133, UU134
Gram-negative bacteria
Epsilon subunit, alpha subunit, delta subunit, delta subunit
Mycobacterium leprae
ML1139-1146
F0F1-type ATPase
ML1139
Gram-negative bacteria
A chain protein






Cluster 3





Rickettsia prowazekii Rickettsia conorii
RP134-139, RC175-180
Ribosomal proteins, transcription antiterminator, SecE
RP134 RC175
Gram-positive bacteria
Preprotein translocase subunit SecE






Cluster 5





Aquifex aeolicus
Aq1968_1_2 two domains
Histidine biosynthesis
Gram-negative bacteria
Phosphoribosyl-AMP cyclohydrolase







Cluster 8





Methanococcus jannaschii
MJ1037-1038
Tryptophan biosynthesis
MJ1037
Bacteria
Tryptophan synthase beta chain
Methanobacterium thermoautotrophicum
MTH1655-1661
Tryptophan biosynthesis
MTH1660
Gram-negative bacteria
Tryptophan synthase alpha chain
Halobacterium sp.
VNG0305-0309
Tryptophan biosynthesis
VNG0307G
Bacteria
Tryptophan synthase beta chain
Bacillus subtilis Bacillus halodurans
PabB-folK BH0090-0095
Tryptophan biosynthesis
PabB, BH0090
Gram-negative bacteria
Anthranilate/para-aminobenzoate synthases component I






Cluster 9





Halobacterium sp.
VNG0635G-0647G
NADH:ubiquinone oxidoreductase
VNG0640G
Gram-negative bacteria
NADH dehydrogenase-like protein






Cluster 18





Rickettsia prowazekii Rickettsia conorii
RP423-425, RC0588-0590
Lipid metabolism
RP425, RC0590
Spirochetes
Undecaprenyl pyrophosphate synthase






Cluster 27





Halobacterium sp.
VNG1306G-1310G
Succinate dehydrogenase/fumarate reductase
VNG1310G
Actinobacteria
Succinate dehydrogenase subunit C






Cluster 29





Mycoplasma genitalium Mycoplasma pneumoniae
MG461-466 MPN677-682
Housekeeping
MG466 MPN682
Gram-negative bacteria
Ribosomal protein L34






Cluster 34





Thermotoga maritima
TM0548-0556
Leucine/isoleucine biosynthesis
TM0552 TM0555 TM0554
2-Isopropylmalate synthase 3-Isopropylmalate dehydratase, small subunit 3-Isopropylmalate dehydratase, large subunit

Pyrococcus abyssi
PAB888-895
PAB0890 PAB0893
Bacteria
2-Isopropylmalate synthase (LeuA-1) 3-Isopropylmalate dehydrogenase (LeuB)

Clostridium acetobutylicum
CAC3169-3174
Leucine/isoleucine biosynthesis
CAC3172 CAC3173 CAC3174 Archaea
3-Isopropylmalate dehydratase, small subunit 3-Isopropylmalate dehydratase, large subunit 2-Isopropylmalate synthase







Cluster 41





Thermotoga maritima
TM1243-1251
Nucleotide metabolism
TM1243
Archaea
Phosphoribosylaminoimidazole-succinocarboxamide synthase






Cluster 42





Lactococcus lactis
L0104-0108
Arginine biosynthesis
L0107
Gram-negative bacteria
Acetylglutamate kinase
Thermotoga maritima
TM1780-1785
Arginine biosynthesis TM1784
Archaea
Acetylglutamate kinase







Cluster 48





Borrelia burgdorferi
BB0054-0061
Carbohydrate metabolism (glycolysis, gluconeogenesis)
BB0057
Gram-positive bacteria
Glyceraldehyde-3-phosphate dehydrogenase






Cluster 54





Thermotoga maritima
TM1780-1785
Arginine biosynthesis
TM1780
Gram-negative bacteria
Argininosuccinate synthase






Cluster 63





Mycoplasma pneumoniae Mycoplasma genitalium
MPN573-574 MG391-392
Molecular chaperones
MPN574 MG393
Gram-negative bacteria
Heat shock protein (groES)






Cluster 82





Mycoplasma pneumoniae, Mycoplasma genitalium
MPN535-536 MG358-359
DNA replication, recombination and repair
MPN536 MG359
Gram-negative bacteria
Holliday junction resolvasome helicase subunit
Ureaplasma urealyticum
UU448-449
DNA replication, recombination and repair
UU448
Gram-negative bacteria
Holliday junction resolvasome helicase subunit






Cluster 86





Halobacterium sp.
VNG6305CC-6306C
Tetrahydrobiopterin biosynthesis
VNG6305C
Gram-negative bacteria
Organic radical activating enzyme






Cluster 87





Halobacterium sp.
VNG0582C-0586C
Energy production and conversion
VNG0582, VNG0583G
Bacteria
Cytochrome b subunit of the bc complex Cytochrome b subunit of the bc complex






Cluster 103





Archaeoglobus fulgidus
AF0321-0325
Lipopolysaccharide biosynthesis
AF0323b
Bacteria
dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes
Deinococcus radiodurans
DRA0037-DRA0044
Lipopolysaccharide biosynthesis
DRA0044
Archaea
dTDP-4-dehydrorhamnose epimerase
Methanothermobacter thermoautotrophicus
MTH1789-1792
Lipopolysaccharide biosynthesis
MTH1789, MTH1790, MTH1791
Gram-positive bacteria Bacteria Bacteria
dTDP-D-glucose 4,6-dehydratase dTDP-4-dehydrorhamnose 3,5-epimerase dTDP-glucose pyrophosphorylase
*The numbering of gene clusters is from the previously published analysis of gene neighborhoods in prokaryotic genomes [25].
Table 3
Kishino-Hasegawa test for the analyzed cases of apparent xenologous gene displacement in situ
Tree*
Diff lnL
S.E.
RELL-BP§
L19 original
0.0
ML
0.8004
1R2
-12.6
7.7
0.0480
3R4
-6.6
6.6
0.1516
RuvB original
0.00
ML
0.9631
1R2
-27.1
15.4
0.0369
UppS original
0.00
ML
0.9883
1R2
-29.3
12.8
0.0117
NuoH original
0.00
ML
0.8336
1R2
-7.4
7.9
0.1664
RfbA original
0.00
ML
1.0000
1R2
-151.1
25.0
0.0000
RfbD original
0.00
ML
0.9005
1R2
-17.0
13.3
0.0995
LeuA original
0.00
ML
1.0000
1R2
-150.2
25.8
0.0000
3R4
-418.6
31.5
0.0000
5R6
-245.0
27.8
0.0000
LeuB original
0.00
ML
0.9847
1R2
-52.9
18.1
0.0007
3R4
-31.7
14.9
0.0146
LeuC original
0.00
ML
1.0000
1R2
-302.7
31.6
0.0000
3R4
-439.1
32.1
0.0000
LeuD original
0.00
ML
1.0000
1R2
-66.6
17.2
0.0000
3R4
-76.7
16.8
0.0000
*The numbers refer to local rearrangements of the tree as indicated on the corresponding figures. Difference of the Log-likelihoods relative to the best tree. Standard error of Diff lnL. §Bootstrap probability of the given tree calculated using the RELL method (Resampling of Estimated Log-likelihoods).

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