Table 2

Genes with increased expression in LPS-deficient A. baumannii strain 19606R

Gene identifieraGene nameProtein descriptionFold change in expressionCOG categorySignal peptidecPredicted locationd
HMPREF0010_03216Phosphopantetheinyl transferasebHCyt
HMPREF0010_03059Transcriptional regulatorKCyt
HMPREF0010_00383Putative lipaseR
HMPREF0010_00724HypotheticalCM
HMPREF0010_01511HypotheticalSpII
HMPREF0010_03356Putative membrane protein168.9SSpI
HMPREF0010_02739Hypothetical137.2SpII
HMPREF0010_02733Putative membrane protein119.4SSpI
HMPREF0010_01945Hypothetical73.5SpII
HMPREF0010_03654Hypothetical68.6SpII
HMPREF0010_00185Hypothetical68.6SpI
HMPREF0010_03296Hypothetical64.0SpI
HMPREF0010_00181pgaCN-glycosyltransferase48.5MCM
HMPREF0010_03182Hypothetical42.2SpII
HMPREF0010_01712macAMacrolide transporter39.4MSpICM
HMPREF0010_03427cobWCobalamin synthesis29.9RCyt
HMPREF0010_01944Hypothetical29.9SpIICM
HMPREF0010_02579Hypothetical29.9SpI
HMPREF0010_02249Putative secreted protein27.9SSpI
HMPREF0010_02888lolAOuter membrane lipoprotein carrier protein27.9MSpIPer
HMPREF0010_01713macBMacrolide transporter ATP-binding protein27.9VCM
HMPREF0010_01714tolCOuter membrane efflux protein27.9MSpIIOM
HMPREF0010_00179pgaAOuter membrane protein26.0RSpIOM
HMPREF0010_00186Hypothetical22.6SpICM
HMPREF0010_00069Hypothetical22.6SpII
HMPREF0010_03655Hypothetical19.7SpII
HMPREF0010_00180pgaBOuter membrane N-deacetylase19.7RSpI
HMPREF0010_02462Hypothetical18.4
HMPREF0010_03406Hypothetical17.1SpI
HMPREF0010_00247Hypothetical17.1
HMPREF0010_01333lolBOuter membrane lipoprotein16.0MSpII
HMPREF0010_03425Hypothetical16.0SpII
HMPREF0010_00182pgaDPutative PNAG biosynthesis14.9R
HMPREF0010_02568Hypothetical14.9SpI
HMPREF0010_03355Putative membrane protein13.9SSpI
HMPREF0010_02269Hypothetical13.9SpI
HMPREF0010_01851rpmE250S ribosomal protein L31 type B13.9J
HMPREF0010_03241Hypothetical13.0CM
HMPREF0010_02727Putative glycosyltransferase13.0RCyt
HMPREF0010_03242Ferrichrome outer membrane transporter12.1PSpIOM
HMPREF0010_03516Hypothetical12.1SpIOM
HMPREF0010_02675Hypothetical12.1SpI
HMPREF0010_02288Hypothetical11.3
HMPREF0010_00814Hypothetical11.3SpII
HMPREF0010_02730TonB-dependent OM receptor10.6PSpIOM
HMPREF0010_00159Hypothetical9.8SpI
HMPREF0010_02077Putative transglycosylase9.8MOM
HMPREF0010_03295nadCNicotinate-nucleotide pyrophosphorylase8.6HCyt
HMPREF0010_01565Putative heat shock protein8.6OSpII
HMPREF0010_02779Hypothetical8.0S
HMPREF0010_00184Putative luciferase protein8.0CCyt
HMPREF0010_03631Hypothetical8.0
HMPREF0010_03357argAN-acetylglutamate synthase8.0ECyt
HMPREF0010_02071Multidrug efflux transport protein7.5VCM
HMPREF0010_01545nlpEPutative lipoprotein NlpE7.5SpII
HMPREF0010_02607mlaCToluene tolerance, Ttg2D7.5QSpI
HMPREF0010_02608mlaBAnti-anti-sigma factor7.0T
HMPREF0010_02815Entericidin A6.5SSpII
HMPREF0010_00263Mechanosensitive ion channel6.5MCM
HMPREF0010_02487Putative sulfate transporter6.5PCM
HMPREF0010_03607Hypothetical6.5
HMPREF0010_02248DNA-binding transcriptional activator LysR6.5KCyt
HMPREF0010_00610Hypothetical6.1SpII
HMPREF0010_01177Hypothetical6.1S
HMPREF0010_01282Hypothetical6.1Cyt
HMPREF0010_01271Hypothetical6.1
HMPREF0010_03351dsbADisulfide isomerase I6.1SpIPer
HMPREF0010_00396Hypothetical6.1Cyt
HMPREF0010_02938TonB dependent receptor5.7PSpIOM
HMPREF0010_01939Hypothetical5.7SSpI
HMPREF0010_02124lolEOuter membrane lipoprotein transporter5.7MCM
HMPREF0010_02166Hypothetical5.3SpIOM
HMPREF0010_02606mlaDABC transporter, substrate-binding protein5.3Q
HMPREF0010_00694Hypothetical5.3
HMPREF0010_01378OmpA family lipoprotein5.3MSpIIOM
HMPREF0010_02352OmpW family protein5.3SpI
HMPREF0010_03145Peptidase M48 family5.3OSpII
HMPREF0010_03538dcpADiguanylate cyclase5.3T
HMPREF0010_02583Hypothetical5.3SpI
HMPREF0010_02740baeSSignal transduction histidine-protein kinase4.9T
HMPREF0010_02125lolDLipoprotein transporter4.9VCM
HMPREF0010_01748Hypothetical4.9SSpI
HMPREF0010_02582Hypothetical4.9SpII
HMPREF0010_02025Putative lysine decarboxylase4.6R
HMPREF0010_02797Hypothetical4.6RSpI
HMPREF0010_02820Putative sulfite reductase4.3SCM
HMPREF0010_02553Hypothetical4.3Cyt
HMPREF0010_01798Hypothetical4.3SCM
HMPREF0010_00045mutTThiamine monophosphate synthase4.3HCyt
HMPREF0010_02558Hypothetical4.0SpII
HMPREF0010_01311Dethiobiotin synthetase4.0HCyt
HMPREF0010_03678Hypothetical4.0SCM
HMPREF0010_02741baeRDNA-binding transcriptional regulator3.7KCyt
HMPREF0010_02437gabDSuccinate-semialdehyde dehydrogenase I3.7CCyt
HMPREF0010_00264Hypothetical3.5Cyt
HMPREF0010_01938htpGHeat shock protein 903.5OCyt
HMPREF0010_02862Putative phospholipase3.5RSpIICM
HMPREF0010_03073Hypothetical3.5SpII
HMPREF0010_02162Hypothetical3.5SpI
HMPREF0010_00081htpXHeat shock protein HtpX3.5RSpI
HMPREF0010_00002Hypothetical3.2
HMPREF0010_00376Response regulator3.2TCyt
HMPREF0010_01233Hypothetical3.2
HMPREF0010_00046Hypothetical3.2SpII
HMPREF0010_02318ampCβ-Lactamase3.2VSpIPer
HMPREF0010_02681Hypothetical3.0SpI
HMPREF0010_02882adeIMultidrug efflux system protein3.0MSpIICM
HMPREF0010_00792Putative 6-pyruvoyl-tetrahydropterin synthase2.8HCyt
HMPREF0010_02881adeJMultidrug efflux protein2.8VCM
HMPREF0010_02674pyrEXanthine phosphoribosyltransferase2.8FCyt
HMPREF0010_02200Putative lipid binding protein2.8MSpI
HMPREF0010_00334fumCFumarate hydratase2.8CCyt
HMPREF0010_01332ipk4-Diphosphocytidyl-2-C-methyl-d-erythritol kinase2.8ICyt
HMPREF0010_02272nlpDOuter membrane lipoprotein, NlpD2.8MSpII
HMPREF0010_01850Hypothetical2.8RCyt
HMPREF0010_00333UDP-galactose-4-epimerase2.6MCyt
HMPREF0010_02068groESChaperonin, GroES2.6OCyt
HMPREF0010_01234metECobalamine-independent methionine synthase2.6ECyt
HMPREF0010_02178degPSerine protease, DegP2.6OSpIPer
HMPREF0010_00353Lysine family exporter2.6EOM
HMPREF0010_02883Putative membrane-associated lipid phosphatase2.5ICM
HMPREF0010_02142OmpA-like protein2.5MSpIIOM
HMPREF0010_02880adeKOuter membrane protein, AdeK2.5MSpIIOM
  • a Genes were considered to be differentially expressed if they displayed at least a 1.5-fold difference in gene expression at a confidence level of 95%.

  • b The infinity symbol (∞) indicates a gene where replicate samples from ATCC 19606 had zero read counts across the total gene length.

  • c Presence of signal peptide (signal peptidase I [spI] or signal peptidase II [spII] cleavage sites) as predicted by SignalP (7) and LipoP (20).

  • d Cellular localization predicted using PSORTB (17). Localization abbreviations: Cyt, cytoplasmic; CM, cytoplasmic membrane; Per, periplasmic; OM, outer membrane; Ext, extracellular.