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Table 2 Genes upregulated upon a temperature shift from 37°C to 25°C.

From: Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, Rickettsia typhi

Gene ID

Gene annotation

Fold Change (exp1, exp2, exp3)

Energy production and conversion

RT0308

hypothetical protein RT0308 [Rickettsia typhi str. Wilmington]

1.5 (2.2, 1.4, 1.0)

RT0346

NADH dehydrogenase alpha subunit [Rickettsia typhi str. Wilmington]

1.6 (1.2, 2.0, 1.8)

RT0419*

succinyl-CoA synthetase alpha subunit [Rickettsia typhi str. Wilmington]

1.9 (2.1, 1.7, 1.8)

Carbohydrate transport and metabolism

RT0478*

pyruvate phosphate dikinase [Rickettsia typhi str. Wilmington]

1.6 (1.9, 1.5, 1.6)

Coenzyme transport and metabolism

RT0867

lipoyltransferase [Rickettsia typhi str. Wilmington]

1.6 (1.3, 1.9, 1.7)

RT0530*

3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Rickettsia typhi str. Wilmington]

2.0 (2.0, 1.5, 2.3)

RT0675*

ubiquinone/menaquinone biosynthesis methyltransferase [Rickettsia typhi str. Wilmington]

2.8 (3.7, 2.4, 2.2)

Lipid transport and metabolism

RT0676*

hypothetical protein RT0676 [Rickettsia typhi str. Wilmington]

1.8 (3.0, 1.5, 1.6)

Translation

RT0337

16S rRNA-processing protein [Rickettsia typhi str. Wilmington]

1.9 (2, 1.3, 2.1)

RT0604*

30S ribosomal protein S21 [Rickettsia typhi str. Wilmington]

2.2 (2.1, 2.6, 2.2)

RT0014

NTP polymerase. [Rickettsia typhi str. Wilmington]

2.3 (5.6, 1.1, 1.5)

RT0870*

50S ribosomal protein L33 [Rickettsia typhi str. Wilmington]

2.3 (2.3, 1.9, 2.5)

RT0038

50S ribosomal protein L28 [Rickettsia typhi str. Wilmington]

2.5 (4.1, 1.7, 1.3)

RT0484

hypothetical protein RT0484 [Rickettsia typhi str. Wilmington]

1.6 (2.0, 1.6, 1.4)

Replication, recombination and repair

RT0339

exodeoxyribonuclease VII small subunit [Rickettsia typhi str. Wilmington]

1.6 (1.8,1.0,1.9)

Cell wall/membrane biogenesis

RT0815

possible outer surface protein [Rickettsia typhi str. Wilmington]

1.6 (2.3, 1.2, 1.2)

RT0083

hypothetical protein RT0083 [Rickettsia typhi str. Wilmington]

1.7 (2.8, 1.1, 1.1)

RT0694

hypothetical protein RT0694 [Rickettsia typhi str. Wilmington]

1.9 (2.6, 2.0, 1.3)

Cell motility

RT0457*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.9 (2.1, 1.9, 1.5)

Posttranslational modification, protein turnover, chaperones

RT0620

HSP-70 cofactor [Rickettsia typhi str. Wilmington]

1.6 (1.7, 1.5, 1.5)

RT0416

SsrA-binding protein [Rickettsia typhi str. Wilmington]

1.6 (1.5, 2.5, 1.0)

RT0195*

probable ATP binding cassette transporter [Rickettsia typhi str. Wilmington]

2.8 (2.1, 2.5, 5.2)

Inorganic ion transport and metabolism

RT0168

probable periplasmic divalent cation tolerance protein CutA [Rickettsia typhi str. Wilmington]

1.5 (1.3, 1.2, 2.1)

RT0013

probable zinc/manganese ABC transporter substrate binding protein

1.8 (2.5, 1.6, 1.3)

RT0523

superoxide dismutase [Rickettsia typhi str. Wilmington]

1.8 (1.8, 1.5, 2.0)

Secondary metabolites biosynthesis, transport and catabolism

RT0043*

hypothetical protein RT0043 [Rickettsia typhi str. Wilmington]

1.6 (1.8, 1.6, 1.3)

General function prediction only

RT0576

Sco2-like protein [Rickettsia typhi str. Wilmington]

1.6 (1.7, 1.5, 1.5)

RT0012

hypothetical protein RT0012 [Rickettsia typhi str. Wilmington]

1.6 (2.2, 1.3, 1.3)

RT0138

hypothetical protein RT0138 [Rickettsia typhi str. Wilmington]

1.6 (1.4, 1.0, 2.2)

RT0674

ubiquinone biosynthesis protein [Rickettsia typhi str. Wilmington]

1.6 (1.3, 1.4, 2.4)

RP031

no corresponding annotation for R. typhi

1.8 (1.1, 2.9, 1.4)

RP679

no corresponding annotation for R. typhi

2.1 (1.7, 1.9, 3.3)

RT0362*

Sec7-domain containing protein transport protein [Rickettsia typhi str. Wilmington]

2.6 (3.3, 5.6, 1.7)

Function unknown

RT0741

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.5 (1.0, 2.0, 1.7)

RT0716*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.6 (1.6, 1.8, 1.5)

RT0551

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.7 (1.4, 1.8, 1.6)

RP167

no corresponding annotation for R. typhi

1.9 (2.9, 1.7, 1.4)

RT0160

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.0 (2.4, 1.3, 2.1)

RT0222

hypothetical protein RT0222 [Rickettsia typhi str. Wilmington]

2.0 (2.8, 1.2, 1.7)

RT0069

iron-binding protein IscA/HesB [Rickettsia typhi str. Wilmington]

2.1 (2.2, 1.6, 2.1)

RT0743

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.1 (2.6, 1.1, 2.3)

RT0541

hypothetical protein RT0541 [Rickettsia typhi str. Wilmington]

2.4 (2.3, 3.5, 2.3)

Intracellular trafficking and secretion

RT0053

protein-export membrane protein [Rickettsia typhi str. Wilmington]

1.6 (1.8, 2.2, 0.9)

RT0164

signal recognition particle protein [Rickettsia typhi str. Wilmington]

1.7 (1.8, 1.2, 1.9)

RT0280

VirB8-like protein of the Type IV secretion system [Rickettsia typhi str. Wilmington]

1.8 (2.6, 1.4, 1.6)

RT0771*

VirB4 protein precursor [Rickettsia typhi str. Wilmington]

1.9 (1.9, 2.1, 1.7)

RT0278*

VirB8-like protein of type IV secretion system [Rickettsia typhi str. Wilmington]

2.6 (3.6, 2.8, 1.8)

not in COG

RT0351

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.5 (1.8, 1.0, 1.5)

RT0767*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.5 (1.6, 1.3, 1.7)

RT0861

hypothetical protein RT0861 [Rickettsia typhi str. Wilmington]

1.6 (1.2, 2.1, 1.4)

RT0080

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.6 (2.2, 1.0, 1.3)

RT0693

bicyclomycin resistance protein [Rickettsia typhi str. Wilmington]

1.6 (1.1, 1.8, 1.9)

RT0156

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.6 (2.4, 1.2, 1.5)

RT0461

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.6 (1.5, 1.6, 1.7)

RT0097

hypothetical protein RT0097 [Rickettsia typhi str. Wilmington]

1.8 (2.5, 1.4, 1.2)

RP084

no corresponding annotation for R. typhi

1.8 (2.7, 1.6, 1.5)

RT0052

190 kDa antigen precursor [Rickettsia typhi str. Wilmington]

1.8 (1.2, 1.6, 2.5)

RT0286

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

1.9 (1.4, 1.6, 3.3)

RT0443

50S ribosomal protein L36 [Rickettsia typhi str. Wilmington]

1.9 (1.9, 1.4, 2.2)

RT0206

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.0 (2.4, 1.6, 1.8)

RT0246*

UDP-3-O- [3-hydroxymyristoyl] N-acetylglucosamine deacetylase [Rickettsia typhi str. Wilmington]

2.1 (2.5, 1.8, 2.0)

RT0382

hypothetical protein RT0382 [Rickettsia typhi str. Wilmington]

2.2 (2.8, 2.0, 1.8)

RT0279

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.2 (5.2, 1.3, 1.3)

RT0710*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.3 (2.8, 1.7, 2.2)

RT0269

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.3 (1.8, 6.6, 1.3)

RT0692*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.7 (3.4, 1.7, 2.6)

RT0806*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.7 (2.3, 2.6, 3.3)

RT0709*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

2.9 (2.5, 3.1, 3.1)

RT0071

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

3.2 (2.9, 1.5, 6.0)

RT0268*

rickettsial conserved hypothetical protein [Rickettsia typhi str. Wilmington]

6.2 (9.0, 6.1, 4.0)

  1. Genes are grouped by functional categories. Gene IDs with asterisks and/or bold are statistically significant (see Methods). Fold change values in bold were obtained by comparing the normalized mean signal intensities of all three independent experiments using the Spotfire analysis program. Immediately following these values are the fold change values for each individual experiment (experiment 1, experiment 2 and experiment 3, respectively).