Extremely poor gene repertoire

Another remarkable feature of the genome is the complete loss of genes in many COG categories (Table 8 2) No genes for categories of nucleotide metabolism (F), lipid metabolism (I), coenzyme metabolism (H), defense mechanism (V), signal transduction (T), cell motil-ity (N), cell envelope biogenesis (M), and intracellular trafficking (U), representing a half of all COG categories, were found (Nakabachi et al , 2006), whereas other endosymbionts were demonstrated to have genes in almost all COG categories (Shigenobu et al , 2000; Tamas et al , 2002; Akman et al , 2002; van Ham et al , 2003; Gil et al , 2003; Degnan et al , 2005; Wu et al ., 2006; PĂ©rez-Brocal et al ., 2006) .

Carsonella-Pv completely lacks genes for biosynthesis of fatty acid, phospholipid, lipo-polysaccharide, and peptidoglycan The absence of these genes suggests that Carsonella is unable to synthesize its cell membrane and cell wall by their own mechanisms, whereas, of course, electron micrographs show the presence of cell envelopes (Chang and Musgrave, 1969; Waku and Endo, 1987; Thao et al , 2000) The genome also lacks genes for cell division, such as minCDE, ftsAZ, and ftsW. The mreBCD genes encoding cell-shape-determining proteins are missing as well Although the Carsonella cell is very elongated in shape in maternal bacteriocytes (Figure 8 1; Buchner, 1965; Chang and Musgrave, 1969; Nakabachi et al ., 2006), they need to divide to make short "infectious forms" before transmission to

ID

Start

Stop

Direction

Protein

COG

Gene

CR001

1

1317

+

tRNA_modification_GTPase

R

thdF

CR002

1314

2816

+

glucose_inhibited_division_protein_A

D

gidA

CR003

2785

3477

+

FOFl-type_ATP_synthase_A_subunit

C

atpB

CR004

3486

3719

+

FOFl-type_ATP_synthase_C_subunit

C

atpE

CR005

3721

4176

+

putative_FOFl-type_ATP_synthase_B_subunit

c

atpF

CR006

4169

4354

+

hypothetical_protein

CR007

4344

5789

+

FOFl-type_ATP_synthase_alpha_subunit

c

atpA

CR008

5786

6544

+

FOFl-type_ATP_synthase_gamma_subunit

c

atpG

CR009

6541

7884

+

FOFl-type_ATP_synthase_beta_subunit

c

atpD

CR010

7881

8123

+

hypothetical_protein

CR011

8110

8997

+

ornithine_carbamoyltransferase

E

argF

CR012

9521

9084

-

3-dehydroquinate_dehydratase

E

aroD

CR013

11407

9497

-

transketolase

G

tktB

CR014

11394

13061

+

hypothetical_protein

CR015

13048

13767

+

5,10-methylenetetrahydrofolate_reductase

E

metF

CR016

13892

13755

-

hypothetical_protein

tRNA-Ile

14011

14084

+

CR017

15115

14072

-

succinyl-diaminopimelate_desuccinylase

E

dapE

CR018

16080

15115

-

tetrahydrodipicolinate_N-succinyltransferase

E

dapD

CR019

16784

16074

-

methionine_aminopeptidase

J

map

CR020

16770

17420

+

ribosomal_protein_S2

J

rpsB

CR021

17414

18040

+

hypothetical_protein

CR022

18033

18563

+

hypothetical_protein

CR023

18556

21897

+

DNA_polymerase_III_alpha_subunit

L

dnaE

CR024

21894

22382

+

hypothetical_protein

CR025

22428

24530

+

5-methyltetrahydropteroyltriglutamate—homocysteine_S-methyltransferase

E

metE

CR026

24669

24857

+

ribosomal_protein_L31

J

rpmE

CR027

24835

25293

+

hypothetical_protein

E

CR028

25274

26320

+

3-dehydroquinate_synthase

E

aroB

CR029

26274

27923

+

dihydroxy-acid_dehydratase

E

ilvD

CR030

27916

29010

+

conserved_hypothetical_protein

CR031

29000

30196

+

serine_hydroxymethyltransferase

E

glyA

CR032

30317

31666

+

ABC_transporter_permease_component

O

CR033

31663

32328

+

ABC_transporter_ATP-binding_component

O

CR034

32319

33146

+

hypothetical_protein

CR035

33143

34297

+

selenocysteine_lyase

E

yfliO

CR036

35155

34259

-

putative_tRNA(5-methylaminomethyl-2-thiouridylate)_methyltransferase

J

trmU

CR037

35379

35155

-

translation_initiation_factor_IF-l

J

in/A

tRNA-Glu

35392

35462

+

tRNA-Gly

35463

35534

+

tRNA-Ser

35535

35619

+

CR038

35914

35618

-

putative_thioredoxin

O

CR039

37212

35911

-

6-phosphogluconate_dehydrogenase

G

gnd

tRNA-Asn

37565

37637

+

tRNA-Met

37710

37638

-

CR040

38177

37719

-

hypothetical_protein

CR041

38340

39029

+

putative_peptide_chain_release_factor_A

J

prfA

CR042

40130

39033

-

aspartyl / glutamyl-tRN A_amidotransferase_B_subunit

J

gatB

CR043

41478

40117

-

aspartyl / glutamyl-tRN A_amidotransferase_A_subunit

J

gatA

CR044

41675

41475

-

hypothetical_protein

CR045

41767

42060

+

ribosomal_protein_L13

J

rplM

CR046

42057

42437

+

ribosomal_protein_S9

J

rpsl

ID

Start

Stop

Direction

Protein

COG

Gene

CR047

42558

43139

+

hypothetical_protein

CR048

43129

43887

+

hypothetical_protein

CR049

43884

45107

+

3-phosphoshikimate_l-carboxyvinyltransferase

E

aroA

CR050

45091

46197

+

putative_ribosomal_protein_Sl

J

rpsA

CR051

47786

46194

-

chaperonin_GroEL

O

mopA

CR052

48069

47776

-

chaperonin_GroES

O

mopB

tRNA-Val

48215

48287

+

tRNA-Asp

48296

48369

+

CR053

48573

48971

+

hypothetical_protein

CR054

48961

49422

+

hypothetical_protein

CR055

49416

50561

+

putative_replicative_DNA_helicase

L

dnaB

CR056

50533

51102

+

hypothetical_protein

CR057

51080

51217

+

hypothetical_protein

CR058

51214

51987

+

putative_DNA_primase

L

dnaG

CR059

51984

52946

+

putative_RNA_polymerase_sigma_factor_rpoD

K

rpoD

tRNA-Ala

52958

53029

+

tRNA-Phe

53154

53226

+

tRNA-Gln

53227

53298

+

tRNA-Thr

53302

53373

+

CR060

53892

53542

-

hypothetical_protein

CR061

53898

54353

+

chaperone_protein_GrpE

O

grpE

CR062

54408

56216

+

chaperone_protein_DnaK

O

dnaK

CR063

56273

56587

+

hypothetical_protein

CR064

56580

57278

+

dihydrodipicolinate_reductase

E

dapB

CR065

57272

57721

+

truncated_carbamoylphosphate_synthase_small_subunit

E

carA

CR066

57714

58253

+

truncated_carbamoylphosphate_synthase_small_subunitt

E

carA

CR067

58246

61143

+

carbamoylphosphate_synthase_large_subunit

E

carB

tRNA-Leu

61144

61216

+

CR068

61235

62845

+

putative_translation_initiation_factor_IF-2

J

infB

CR069

62817

63014

+

hypothetical_protein

CR070

63011

63988

+

tyrosyl-tRNA_synthetase

J

tyrS

CR071

63948

65123

+

glutaminyl-tRNA_synthetase

J

glnS

tRNA-Pro

65163

65236

+

tRNA-Arg

65237

65310

+

tRNA-His

65313

65385

+

CR072

65412

65996

+

ATP-dependent_Clp_protease_proteolytic_subunit

O

clpP

CR073

65971

67038

+

ATP-dependent_Clp_protease_ATP-binding_subunit

O

clpX

CR074

67801

68127

+

hypothetical_protein

CR075

68124

69401

+

aspartyl-tRNA_synthetase

J

aspS

tRNA-Ser

69415

69499

+

CR076

69553

70074

+

ribulose-phosphate_3-epimerase

G

rpe

CR077

73120

70076

-

delta-l-pyiToline-5-carboxylate_dehydrogenase

C

putA

CR078

73136

74479

+

2-isopropylmalate_synthase

E

leiiA

CR079

74472

75509

+

chorismate_synthase

E

aroC

CR080

75502

76872

+

3-isopropylmalate_dehydratase_large_subunit

E

leuC

CR081

76856

77422

+

3-isopropylmalate_dehydratase_small_subunit

E

leuD

CR082

77419

78468

+

3-isopropylmalate_dehydrogenase

C

leuB

CR083

78461

79486

+

aspartate-semialdehyde_dehydrogenase

E

asd

CR084

79497

80507

+

seryl-tRNA_synthetase

J

serS

tRNA-Leu

80487

80565

+

CR085

80599

80970

+

hypothetical_protein

CR086

81565

81029

-

hypothetical_protein

ID

Start

Stop

Direction

Protein

COG

Gene

CR087

82107

81562

-

DNA_polymerase_III_epsilon_subunit

L

dnaQ

CR088

83321

82104

-

hypothetical_protein

CR089

83577

83314

-

putative_phenylalanyl-tRNA_synthetase_alpha_subunit

J

pheS

CR090

84284

83979

-

ribosomal_protein_L20

J

rplT

CR091

84926

84402

-

translation_initiation_factor_IF-3

J

infC

CR092

85534

84926

-

superoxide_dismutase

P

sodA

CR093

86044

85571

-

hypothetical_protein

CR094

86949

86041

-

3-deoxy-7-phosphoheptulonate_synthase

E

aroH

CR095

87068

86937

-

hypothetical_protein

CR096

87069

88349

+

conserved_hypothetical_protein

J

yleA

CR097

88324

88617

+

hypothetical_protein

CR098

88604

90502

+

leucyl-tRNA_synthetase

J

leuS

CR099

91316

90492

-

succinyl-CoA_synthetase_alpha_subunit

C

sucD

CR100

92350

91313

-

succinyl-CoA_synthetase_beta_subunit

C

sucC

CR101

93345

92347

-

putative_glutamyl-tRNA_synthetase

J

gltX

tRNA-Met

93431

93359

-

CR102

93518

94816

+

methionyl-tRNA_synthetase

J

metG

CR103

94806

94991

+

hypothetical_protein

CR104

96165

94984

-

argininosuccinate_synthase

E

argG

tRNA-Cys

96209

96279

+

tRNA-Leu

96280

96361

+

CR105

97107

96343

-

dihydrodipicolinate_synthase

E

dapA

tRNA-Lys

97213

97140

-

CR106

97515

97204

-

hypothetical_protein

CR107

97509

98876

+

malate:quinone_oxidoreductase

R

mqo

tRNA-Arg

98940

98868

tRNA-Ser

99023

98942

CR108

100248

99010

aspartokinase

CR109

101231

100245

putative_alanyl-tRNA_synthetase

CR110

102118

101228

RecA_recombinase

CR111

102113

103993 +

valyl-tRNA_synthetase

CR112

103965

104492 +

alkyl_hydroperoxide_reductase

CR113

105386

104493

transaldolase

1-RNA-5S

105557

105446

1-RNA-23S

108398

105572

1-RNA-16S

109973

108444

CR114

110920

110048

tryptophanyl-tRNA_synthetase

CR115

111066

110917

ribosomal_protein_L33

CR116

111242

111054

ribosomal_protein_L28

CRH 7

111563

111243

hypothetical_protein

CR118

112711

111566

lysyl-tRNA_synthetase

CR119

113520

112708

peptide_chain_release_factor_B

CR120

114821

113517

threonine_synthase

CR121

115951

114821

homoserine_dehydrogenase

CR122

116151

115948

hypothetical_protein

CR123

116314

116120

hypothetical_protein

CR124

116532

116311

ribosomal_protein_Sl 6

tRNA-Met

116581

116653 +

CR125

117669

116674

ketol-acid_reductoisomerase

CR126

118073

117687

hypothetical_protein

CR127

119709

118045

acetolactate_synthase_large_subunit

CR128

120320

119706

ribosomal_large_subunit_pseudouridine_

thrA

alaS

recA

valS

ahpC

talA

trpS

rpmG

rpmB

lysS prfB thrC thrA

rpsP

ilvC

ilvl rluD

ID

Start

Stop

Direction Protein

CR129

122787

120313

isoleucyl-tRNA_synthetase

CR130

122923

122777

- hypothetical_protein

CR131

123672

122908

- putative_GTPase

CR132

123916

123662

ribosomal_protein_L27

CR133

124227

123919

- hypothetical_protein

CR134

124460

124224

- hypothetical_protein

CR135

125418

124450

RNA_polymerase_alpha_subunit

CR136

126008

125415

- ribosomal_protein_S4

CR137

126361

126005

- ribosomal_protein_SH

CR138

126704

126348

ribosomal_protein_Sl 3

CR139

126814

126701

- ribosomal_protein_L36

CR140

127047

126811

- putative_ribosomal_protein_L15

CR141

127466

127047

- ribosomal_protein_S5

CR142

127674

127438

hypothetical_protein

CR143

128216

127671

- ribosomal_protein_L6

CR144

128539

128168

- ribosomal_protein_S8

CR145

128820

128533

ribosomal_protein_Sl 4

CR146

129322

128822

- ribosomal_protein_L5

CR147

129687

129319

- ribosomal_protein_L14

CR148

129935

129684

ribosomal_protein_Sl 7

CR149

130335

129928

ribosomal_protein_Ll 6

CR150

130936

130325

- ribosomal_protein_S3

CR151

131234

130920

putative_ribosomal_protein_L22

CR152

131497

131231

- ribosomal_protein_S19

CR153

132201

131494

- ribosomal_protein_L2

COG Gene

J ileS

R yhbZ

J rpmA

rpoA

rpsD

rpsK

rpsM

rpmj rplO

rpsE

rplF

rpsH

rpsN

rplE

rplN

rpsQ

rplP

rpsC

rplV

rpsS

rplB

CR154

132716

132198

-

ribosomal_protein_L4

J

rplD

CR155

133123

132713

-

ribosomal_protein_L3

J

rplC

CR156

133416

133120

-

ribosomal_protein_Sl 0

J

rpsJ

CR157

134605

133409

-

elongation_factor_Tu

J

tufB

CR158

136653

134608

-

elongation_factor_G

J

fits A

CR159

137120

136650

-

ribosomal_protein_S7

J

rpsG

CR160

137482

137120

-

ribosomal_protein_Sl 2

J

rpsL

CR161

141362

137484

-

RN A_polymerase_beta '_subunit

K

rpoC

CR162

145162

141359

-

RNA_polymerase_beta_subunit

K

rpoB

CR163

145500

145159

-

ribosomal_protein_L7/ LI 2

J

rplL

CR164

145918

145478

-

hypothetical_protein

CR165

146490

145915

-

hypothetical_protein

CR166

146899

146471

-

ribosomal_protein_Lll

J

rplK

tRNA-Trp

147001

146931

-

tRNA-Gly

147094

147024

-

tRNA-Tyr

147179

147099

-

CR167

147530

147249

-

putative_cytochrome_0_ubiquinol_oxidase_subunit_IV

c

cyoD

CR168

148012

147497

-

cytochrome_0_ubiquinol_oxidase_subunit_III

c

ajoC

CR169

149825

148005

-

cytochrome_0_ubiquinol_oxidase_subunit_I

c

cyoB

CR170

150580

149822

-

cytochrome_0_ubiquinol_oxidase_subunit_II

c

cyoA

CR171

150557

151297

+

hypothetical_protein

CR172

151290

152183

+

branched-chain_amino_acid_aminotransferase

E

ilvE

CR173

152194

153258

+

histidyl-tRNA_synthetase

J

hisS

CR174

153236

153562

+

hypothetical_protein

CR175

153547

154011

+

peptide_deformylase

J

def

CR176

154008

155216

+

hypothetical_protein

CR177

155213

156409

+

diaminopimelate_decarboxylase

E

lysA

ID

Start

Stop

Direction

Protein

COG

Gene

CR178

156402

157157

+

diaminopimelate_epimerase

E

dapF

CR179

157154

157897

+

glycyl-tRNA_synthetase_alpha_subunit

J

giyQ

CR180

157894

158382

+

hypothetical_protein

CR181

158603

158400

-

cold_shock_protein

K

cspE

CR182

159662

158649

-

hypothetical_protein

oocytes (Buchner, 1965; Waku and Endo, 1987), raising a question as to how they achieve it with the complete lack of genes for cell division .

All known genes necessary for glycolysis and tricarboxylic acid (TCA) cycle are missing except those encoding succinyl-CoA synthetase subunits (CR099 and CR100) (Table 8 . 2) . In Carsonella-Pv, six genes (CR003-CR005, CR007-CR009) for F0F1 type ATP synthase sub-units (except delta and epsilon) are conserved with the same gene organization as in other related bacteria, whereas ydiC, which seems essential for proper integration of the ATP synthase into the membrane, is absent. Four genes (CR167-CR170) encoding cytochrome O ubiquinol oxidase subunits are identified, but the genes for ubiquinone biosynthesis are missing in Carsonella Further studies are required to know whether Carsonella can produce ATP by carrying out oxidative respirations or whether it imports ATP from its host In general, it appears that bacteriocyte-restricted primary symbionts are unable to synthesize many of the essential metabolites and, thus, must rely on the host bacterio-cyte to obtain them (Zientz et al ., 2004; Nakabachi et al ., 2005) . Whereas Carsonella-Pv has the most limited biosynthetic capacities as mentioned above, the genome encodes only a single transporter (ABC transporter), which consists of a permease (CR032) and an ATP-binding component (CR033) but no substrate-binding component (Table 8 2) The genome completely lacks genes for the flagellar apparatus, which might serve as an alternative to transporters in some other symbiotic bacteria (Shigenobu et al ., 2000) .

The extreme AT-richness in the genome may result from the loss of DNA repair functions in Carsonella. The genome of Carsonella-Pv lacks uracil-DNA glycosylase (ung), which removes uracil residues from DNA, and dUTPase (dut), which prevents dUTP from being misincorporated into DNA. The dut gene is conserved in all other sequenced endosym-bionts, and the ung gene is retained in them except Buchnera-Sg The lack of these two enzymes is the only substantial difference in repair gene sets between Carsonella and other bacteriocyte endosymbionts and might underlie the extreme AT-richness of the Carsonella genome The genome also lacks other genes for DNA repair, such as polA, nth, mutT, mutS, mutY, and mutL. Moreover, Carsonella-Pv has lost most other genes involved in DNA metabolism With respect to DNA replication, the genome retains recA (CR110), dnaB (CR055), dnaG (CR058), and genes encoding alpha (dnaE, CR023) and epsilon (dnaQ, CR087) subunits of DNA polymerase III, but lacks dnaA, dnaN, dnaX, priA, recBCD, sbcB, gyrAB, lig, and topA (Table 8 2) As for transcription, genes for the alpha (rpoA, CR135), beta (rpoB, CR162) and beta' (rpoC, CR161) subunits of the core RNA polymerase are retained . Carsonella-Pv has only one sigma factor (rpoD, CR059), whereas other sequenced bacteriocyte symbionts retain two sigma factors (rpoD and rpoH). Genes for transcription elongation and termination, such as nusA, nusB, nusG, greA, deaD, and rho are missing The genome retains 15 genes for aminoacyl-tRNA synthetase, but lacks argS, asnS, cysS, glyS, pheT, pros, and thrS.

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