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Table 1 Pseudomonas aeruginosa PAO1 genes targeted by growth-impairing inserts including a single locus

From: A shotgun antisense approach to the identification of novel essential genes in Pseudomonas aeruginosa

Insert namea

Insert-included locus

Gene name and product annotationb

Function classb

Orthologous proteins in DEGc

S2F1

PA0577

dnaG - DNA primase (2)

DNA replication, recombination, modification and repair

Bs, Sa, Ec, Hi, Sp, Mt, Fn, Ab, Mp, Se, Cc, Ss

S3D3

S11F7

PA4269

rpoC - DNA-directed RNA polymerase beta chain (2)

Transcription, RNA processing and degradation

Bs, Sa, Ec, Mg, Sp, Mt, St, Fn, Ab, Mp, Se, Ss, Pg

B1

PA4270

rpoB - DNA-directed RNA polymerase beta chain (2)

Transcription, RNA processing and degradation

Bs, Sa, Vc, Ec, Hi, Mg, Mt, St, Fn, Ab, Mp, Pa, Se, Cc, Ss, Pg, Bt

S6A10

PA4744

infB - translation initiation factor IF-2 (2)

Translation, post-translational modification, degradation

Bs, Sa, Vc, Ec, Mg, Mt, St, Fn Ab, Mp, Pa, Se, Cc, Pg, Bt

S2F6

PA4743

rbfA - ribosome-binding factor A (2)

Translation, post-translational modification, degradation

Sa, Vc, Mg, Hp, Fn, Ab, Se

S6E7

PA3820

secF - secretion protein SecF (2)

Protein secretion/export apparatus

Ec, Hi, St, Fn, Ab, Pa, Se

S5A10

PA1709d

popD - Translocator outer membrane protein (1)

Protein secretion/export apparatus

 

S11B13

PA4669

ipk - isopentenyl monophosphate kinase(2)

Biosynthesis of cofactors, prosthetic groups and carriers

Vc, Se, Pa

G2

PA2951

etfA - electron transfer flavoprotein alpha-subunit (2)

Energy metabolism

Ab, Cc

H2

S10F8

PA5186

probable iron-containing alcohol dehydrogenase (3)

Energy metabolism

 

F1

PA1554

ccoN1\ fixN \ Cytochrome c oxidase, cbb3-type, CcoN subunit (1)

Energy metabolism

 

S11G10

PA3687

ppc - phosphoenolpyruvate carboxylase (2)

Energy metabolism

Hi

S86C

PA3758

nagA - probable N-acetylglucosamine-6-phosphate deacetylase (3)

Central intermediary metabolism

Hi, Mt

E5

PA1183

dctA - C4-dicarboxylate transport protein (2)

Transport of small molecules

Ab

S11C9

PA3382

phnE - phosphonate transport protein PhnE (2)

Transport of small molecules

 

S4E6

PA4903

vanK - probable major facilitator superfamily (MFS) transporter (3)

Transport of small molecules

 

B3

PA5548

probable major facilitator superfamily (MFS) transporter (3)

Transport of small molecules

 

S4H12

A5

PA1590

braB - branched chain amino acid transporter (1)

Transport of small molecules

 

S3D4

PA1805

ppiD - peptidyl-prolyl cis-trans isomerase D - Rotamase D (2)

Translation, post-translational modification, degradation

Cc, Bs

S9G5

PA2402

Probable non-ribosomal peptide synthetase (3)

Putative enzymes

 

S5D4

S5A4

PA5238

probable O-antigen acetylase (3)

Membrane proteins, Cell wall/LPS/capsule

 

S5G6

S4B10

PA3433

ywbI - probable transcriptional regulator (3)

Transcriptional regulators

 

S5A1

PA2220

oprR - probable transcriptional regulator (3)

Transcriptional regulators

 

M4G6

PA2873e

tgpA - transglutaminase protein A TgpA (1)

Adaptation, Protection, Membrane proteins

 

S10A3

PA0307

hypothetical protein (4)

Hypothetical, unclassified, unknown

 

S841F

PA4926

conserved hypothetical protein (4)

Hypothetical, unclassified, unknown

 

S9A9

PA0262

conserved hypothetical protein (4)

Hypothetical, unclassified, unknown

 

F2

PA5264

hypothetical protein (4)

Hypothetical, unclassified, unknown

 
  1. aInserts with antisense orientation are in bold.
  2. bAnnotations according to the Pseudomonas Genome Database (http://www.pseudomonas.com) [27]. Numbers inside parenthesis indicate the classes of product name confidence. Class1: Function experimentally demonstrated in P. aeruginosa; Class 2: Function of highly similar gene experimentally demonstrated in another organism; Class 3: Function proposed based on presence of conserved amino acid motif, structural feature or limited sequence similarity to an experimentally studied gene. Class 4: Homologs of previously reported genes of unknown function, or no similarity to any previously reported sequences.
  3. cDEG: Database of Essential Genes (DEG 7.0) (http://www.essentialgene.org) [20]. For each hit, the orthologue proteins, extracted from the Ortholuge DB [30], that were found in DEG are indicated with the abbreviation of the harboring bacterial species. Bacterial species: Ab (Acinetobacter baylyi), Bs (Bacillus subtilis), Bt (Bacteroides thetaiotaomicron), Cc (Caulobacter crescentus), Ec (Escherichia coli), Fn (Francisella novicida), Hi (Haemophilus influenzae), Hp (Helicobacter pylori), Mt (Mycobacterium tuberculosis), Mp (Mycoplasma pulmonis), Mg (Mycoplasma genitalium), Pg (Porphyromonas gingivalis), Pa (Pseudomonas aeruginosa), Se (Salmonella enterica), St (Salmonella typhimurium), Sp (Streptococcus pneumoniae), Ss (Streptococcus sanguinis), Sa (Staphylococcus aureus), Vc (Vibrio cholerae).
  4. dPrevious reports [2426] did not mention growth defects associated to deletion of popD gene.
  5. eHit not present in DEG whose essentiality was experimentally demonstrated in P. aeruginosa[21].