Molecular Mechanisms of Ethanol-Induced Pathogenesis Revealed by RNA-Sequencing

1. BaumannP

DoudoroffM

StanierRY

1968 A study of the Moraxella group. II. Oxidative-negative species (genus Acinetobacter). J Bacteriol 95 1520 1541

2. JuniE

1978 Genetics and physiology of Acinetobacter. Annu Rev Microbiol 32 349 371

3. WaltermannM

StovekenT

SteinbuchelA

2007 Key enzymes for biosynthesis of neutral lipid storage compounds in prokaryotes: properties, function and occurrence of wax ester synthases/acyl-CoA: diacylglycerol acyltransferases. Biochimie 89 230 242

4. FagonJY

ChastreJ

DomartY

TrouilletJL

GibertC

1996 Mortality due to ventilator-associated pneumonia or colonization with Pseudomonas or Acinetobacter species: assessment by quantitative culture of samples obtained by a protected specimen brush. Clin Infect Dis 23 538 542

5. MetanG

AlpE

AygenB

SumerkanB

2007 Acinetobacter baumannii meningitis in post-neurosurgical patients: clinical outcome and impact of carbapenem resistance. J Antimicrob Chemother 60 197 199

6. WisplinghoffH

BischoffT

TallentSM

SeifertH

WenzelRP

2004 Nosocomial bloodstream infections in US hospitals: analysis of 24,179 cases from a prospective nationwide surveillance study. Clin Infect Dis 39 309 317

7. SeifertH

StrateA

PulvererG

1995 Nosocomial bacteremia due to Acinetobacter baumannii. Clinical features, epidemiology, and predictors of mortality. Medicine (Baltimore) 74 340 349

8. PoirelL

LebessiE

HeritierC

PatsouraA

FoustoukouM

2006 Nosocomial spread of OXA-58-positive carbapenem-resistant Acinetobacter baumannii isolates in a paediatric hospital in Greece. Clin Microbiol Infect 12 1138 1141

9. DijkshoornL

NemecA

SeifertH

2007 An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nat Rev Microbiol 5 939 951

10. HujerKM

HujerAM

HultenEA

BajaksouzianS

AdamsJM

2006 Analysis of antibiotic resistance genes in multidrug-resistant Acinetobacter sp. isolates from military and civilian patients treated at the Walter Reed Army Medical Center. Antimicrob Agents Chemother 50 4114 4123

11. TienHC

BattadA

BryceEA

FullerJ

MulveyM

2007 Multi-drug resistant Acinetobacter infections in critically injured Canadian forces soldiers. BMC Infect Dis 7 95

12. KnappS

WielandCW

FlorquinS

PantophletR

DijkshoornL

2006 Differential roles of CD14 and toll-like receptors 4 and 2 in murine Acinetobacter pneumonia. Am J Respir Crit Care Med 173 122 129

13. ErridgeC

Moncayo-NietoOL

MorganR

YoungM

PoxtonIR

2007 Acinetobacter baumannii lipopolysaccharides are potent stimulators of human monocyte activation via Toll-like receptor 4 signalling. J Med Microbiol 56 165 171

14. ChoiCH

LeeEY

LeeYC

ParkTI

KimHJ

2005 Outer membrane protein 38 of Acinetobacter baumannii localizes to the mitochondria and induces apoptosis of epithelial cells. Cell Microbiol 7 1127 1138

15. ChoiCH

HyunSH

LeeJY

LeeJS

LeeYS

2008 Acinetobacter baumannii outer membrane protein A targets the nucleus and induces cytotoxicity. Cell Microbiol 10 309 319

16. TomarasAP

DorseyCW

EdelmannRE

ActisLA

2003 Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system. Microbiology 149 3473 3484

17. ZimblerDL

PenwellWF

GaddyJA

MenkeSM

TomarasAP

2009 Iron acquisition functions expressed by the human pathogen Acinetobacter baumannii. Biometals 22 23 32

18. DorseyCW

TomarasAP

ConnerlyPL

TolmaskyME

CrosaJH

2004 The siderophore-mediated iron acquisition systems of Acinetobacter baumannii ATCC 19606 and Vibrio anguillarum 775 are structurally and functionally related. Microbiology 150 3657 3667

19. MiharaK

TanabeT

YamakawaY

FunahashiT

NakaoH

2004 Identification and transcriptional organization of a gene cluster involved in biosynthesis and transport of acinetobactin, a siderophore produced by Acinetobacter baumannii ATCC 19606T. Microbiology 150 2587 2597

20. SmithMG

GianoulisTA

PukatzkiS

MekalanosJJ

OrnstonLN

2007 New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev 21 601 614

21. VallenetD

NordmannP

BarbeV

PoirelL

MangenotS

2008 Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS ONE 3 e1805 doi:10.1371/journal.pone.0001805

22. IaconoM

VillaL

FortiniD

BordoniR

ImperiF

2008 Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob Agents Chemother 52 2616 2625

23. AdamsMD

GoglinK

MolyneauxN

HujerKM

LavenderH

2008 Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii. J Bacteriol 190 8053 8064

24. SmithMG

Des EtagesSG

SnyderM

2004 Microbial synergy via an ethanol-triggered pathway. Mol Cell Biol 24 3874 3884

25. WannerBL

1987 Phosphate regulation of gene expression in Escherichia coli.

NeidhardtF

IngrahamJL

LowKB

MagasanikB

SchaechterM

UmbargerHE

Escherichia coli and Salmonella: cellular and molecular biology Washington, D.C. American Society for Microbiology 1326 1333

26. LamarcheMG

WannerBL

CrepinS

HarelJ

2008 The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis. FEMS Microbiol Rev 32 461 473

27. YuraT

NagaiH

MoriH

1993 Regulation of the heat-shock response in bacteria. Annu Rev Microbiol 47 321 350

28. LakhalF

Bury-MoneS

NomaneY

Le GoicN

PaillardC

2008 DjlA, a membrane-anchored DnaJ-like protein, is required for cytotoxicity of clam pathogen Vibrio tapetis to hemocytes. Appl Environ Microbiol 74 5750 5758

29. DuY

LenzJ

ArvidsonCG

2005 Global gene expression and the role of sigma factors in Neisseria gonorrhoeae in interactions with epithelial cells. Infect Immun 73 4834 4845

30. LinSN

AyadaK

ZhaoY

YokotaK

TakenakaR

2005 Helicobacter pylori heat-shock protein 60 induces production of the pro-inflammatory cytokine IL8 in monocytic cells. J Med Microbiol 54 225 233

31. HinodeD

YoshiokaM

TanabeS

MikiO

MasudaK

1998 The GroEL-like protein from Campylobacter rectus: immunological characterization and interleukin-6 and -8 induction in human gingival fibroblast. FEMS MicrobiolLett 167 1 6

32. MarioniJC

MasonCE

ManeSM

StephensM

GiladY

2008 RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18 1509 1517

33. FuX

FuN

GuoS

YanZ

XuY

2009 Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 10 161

34. KornbergHL

1966 The role and control of the glyoxylate cycle in Escherichia coli. Biochem J 99 1 11

35. KornbergHL

KrebsHA

1957 Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle. Nature 179 988 991

36. ArndtA

AuchterM

IshigeT

WendischVF

EikmannsBJ

2008 Ethanol catabolism in Corynebacterium glutamicum. J Mol Microbiol Biotechnol 15 222 233

37. GerstmeirR

WendischVF

SchnickeS

RuanH

FarwickM

2003 Acetate metabolism and its regulation in Corynebacterium glutamicum. J Biotechnol 104 99 122

38. WolfeAJ

2005 The acetate switch. Microbiol Mol Biol Rev 69 12 50

39. OhMK

RohlinL

KaoKC

LiaoJC

2002 Global expression profiling of acetate-grown Escherichia coli. J Biol Chem 277 13175 13183

40. KakudaH

HosonoK

ShiroishiK

IchiharaS

1994 Identification and characterization of the ackA (acetate kinase A)-pta (phosphotransacetylase) operon and complementation analysis of acetate utilization by an ackA-pta deletion mutant of Escherichia coli. J Biochem 116 916 922

41. ReinscheidDJ

SchnickeS

RittmannD

ZahnowU

SahmH

1999 Cloning, sequence analysis, expression and inactivation of the Corynebacterium glutamicum pta-ack operon encoding phosphotransacetylase and acetate kinase. Microbiology 145(Pt 2) 503 513

42. SerranoJA

CamachoM

BoneteMJ

1998 Operation of glyoxylate cycle in halophilic archaea: presence of malate synthase and isocitrate lyase in Haloferax volcanii. FEBS Lett 434 13 16

43. LohWH

RandlesCI

SharpWR

MillerRH

1984 Intermediary carbon metabolism of Azospirillum brasilense. J Bacteriol 158 264 268

44. MolinaI

PellicerMT

BadiaJ

AguilarJ

BaldomaL

1994 Molecular characterization of Escherichia coli malate synthase G. Differentiation with the malate synthase A isoenzyme. Eur J Biochem 224 541 548

45. OrnstonLN

OrnstonMK

1969 Regulation of glyoxylate metabolism in Escherichia coli K-12. J Bacteriol 98 1098 1108

46. CozzoneAJ

1998 Regulation of acetate metabolism by protein phosphorylation in enteric bacteria. Annu Rev Microbiol 52 127 164

47. SauerU

EikmannsBJ

2005 The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev 29 765 794

48. FleckCB

BrockM

2009 Re-characterisation of Saccharomyces cerevisiae Ach1p: fungal CoA-transferases are involved in acetic acid detoxification. Fungal Genet Biol 46 473 485

49. van der RestME

FrankC

MolenaarD

2000 Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli. J Bacteriol 182 6892 6899

50. MolenaarD

van der RestME

DryschA

YucelR

2000 Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum. J Bacteriol 182 6884 6891

51. ItohT

MatsudaH

MoriH

1999 Phylogenetic analysis of the third hsp70 homolog in Escherichia coli; a novel member of the Hsc66 subfamily and its possible co-chaperone. DNA Res 6 299 305

52. KluckCJ

PatzeltH

GenevauxP

BrehmerD

RistW

2002 Structure-function analysis of HscC, the Escherichia coli member of a novel subfamily of specialized Hsp70 chaperones. J Biol Chem 277 41060 41069

53. CipakA

JaganjacM

TehlivetsO

KohlweinSD

ZarkovicN

2008 Adaptation to oxidative stress induced by polyunsaturated fatty acids in yeast. Biochim Biophys Acta 1781 283 287

54. AllakhverdievSI

KinoshitaM

InabaM

SuzukiI

MurataN

2001 Unsaturated fatty acids in membrane lipids protect the photosynthetic machinery against salt-induced damage in Synechococcus. Plant Physiol 125 1842 1853

55. AlexandreH

RousseauxI

CharpentierC

1994 Ethanol adaptation mechanisms in Saccharomyces cerevisiae. Biotechnol Appl Biochem 20(Pt 2) 173 183

56. ZhangYM

RockCO

2008 Membrane lipid homeostasis in bacteria. Nat Rev Microbiol 6 222 233

57. MarchandI

Damier-PiolleL

CourvalinP

LambertT

2004 Expression of the RND-type efflux pump AdeABC in Acinetobacter baumannii is regulated by the AdeRS two-component system. Antimicrob Agents Chemother 48 3298 3304

58. BinaXR

LavineCL

MillerMA

BinaJE

2008 The AcrAB RND efflux system from the live vaccine strain of Francisella tularensis is a multiple drug efflux system that is required for virulence in mice. FEMS Microbiol Lett 279 226 233

59. O'TooleR

WilliamsHD

2003 Universal stress proteins and Mycobacterium tuberculosis. Res Microbiol 154 387 392

60. KvintK

NachinL

DiezA

NystromT

2003 The bacterial universal stress protein: function and regulation. Curr Opin Microbiol 6 140 145

61. NachinL

NannmarkU

NystromT

2005 Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol 187 6265 6272

62. NonakaG

BlankschienM

HermanC

GrossCA

RhodiusVA

2006 Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress. Genes Dev 20 1776 1789

63. ThomasJ

CronanJE

2005 The enigmatic acyl carrier protein phosphodiesterase of Escherichia coli: genetic and enzymological characterization. J Biol Chem 280 34675 34683

64. AudiaJP

PattonMC

WinklerHH

2008 DNA microarray analysis of the heat shock transcriptome of the obligate intracytoplasmic pathogen Rickettsia prowazekii. Appl Environ Microbiol 74 7809 7812

65. SlamtiL

LivnyJ

WaldorMK

2007 Global gene expression and phenotypic analysis of a Vibrio cholerae rpoH deletion mutant. J Bacteriol 189 351 362

66. QinJH

ShengYY

ZhangZM

ShiYZ

HeP

2006 Genome-wide transcriptional analysis of temperature shift in L. interrogans serovar lai strain 56601. BMC Microbiol 6 51

67. GreenHA

DonohueTJ

2006 Activity of Rhodobacter sphaeroides RpoHII, a second member of the heat shock sigma factor family. J Bacteriol 188 5712 5721

68. Asadulghani

SuzukiY

NakamotoH

2003 Light plays a key role in the modulation of heat shock response in the cyanobacterium Synechocystis sp PCC 6803. Biochem Biophys Res Commun 306 872 879

69. Martinez-SalazarJM

Sandoval-CalderonM

GuoX

Castillo-RamirezS

ReyesA

2009 The Rhizobium etli RpoH1 and RpoH2 sigma factors are involved in different stress responses. Microbiology 155 386 397

70. GrossC

NeidhardtFC

CurtissRIII

IngrahamJL

LinECC

1996 Function and regulation of the heat shock proteins. Eschericha coli and Salmonella: cellular and Molecular Biology. Washington, D.C. ASM Press 1382 1399

71. GurE

SauerRT

2008 Recognition of misfolded proteins by Lon, a AAA(+) protease. Genes Dev 22 2267 2277

72. ShelburneCE

CoopamahMD

SweierDG

AnFY

LopatinDE

2007 HtpG, the Porphyromonas gingivalis HSP-90 homologue, induces the chemokine CXCL8 in human monocytic and microvascular vein endothelial cells. Cell Microbiol 9 1611 1619

73. XuH

LeeHY

AhnJ

2008 Cross-protective effect of acid-adapted Salmonella enterica on resistance to lethal acid and cold stress conditions. Lett Appl Microbiol 47 290 297

74. GunasekeraTS

CsonkaLN

PaliyO

2008 Genome-wide transcriptional responses of Escherichia coli K-12 to continuous osmotic and heat stresses. J Bacteriol 190 3712 3720

75. KogaT

SakamotoF

YamotoA

TakumiK

1999 Acid adaptation induces cross-protection against some environmental stresses in Vibrio parahaemolyticus. J Gen Appl Microbiol 45 155 161

76. VolkerU

MachH

SchmidR

HeckerM

1992 Stress proteins and cross-protection by heat shock and salt stress in Bacillus subtilis. J Gen Microbiol 138 2125 2135

77. SongerJG

1997 Bacterial phospholipases and their role in virulence. Trends Microbiol 5 156 161

78. KorbsrisateS

TomarasAP

DamninS

CkumdeeJ

SrinonV

2007 Characterization of two distinct phospholipase C enzymes from Burkholderia pseudomallei. Microbiology 153 1907 1915

79. PoussinMA

LeitgesM

GoldfineH

2009 The ability of Listeria monocytogenes PI-PLC to facilitate escape from the macrophage phagosome is dependent on host PKCbeta. Microb Pathog 46 1 5

80. AnsteyNM

CurrieBJ

HassellM

PalmerD

DwyerB

2002 Community-acquired bacteremic Acinetobacter pneumonia in tropical Australia is caused by diverse strains of Acinetobacter baumannii, with carriage in the throat in at-risk groups. J Clin Microbiol 40 685 686

81. ChenM-Z

HsuehPo-Ren

LeeLi-Na

YuC-J

YangP-C

LuhK-T

2001 Severe Community-Acquired Pneumonia due to Acinetobacter baumannii. Chest 120 1072 1077

82. FalagasME

KarveliEA

KelesidisI

KelesidisT

2007 Community-acquired Acinetobacter infections. Eur J Clin Microbiol Infect Dis 26 857 868

83. BaileyKL

WyattTA

RombergerDJ

SissonJH

2009 Alcohol functionally upregulates Toll-like receptor 2 in airway epithelial cells. Alcohol Clin Exp Res 33 499 504

84. VulicM

KolterR

2002 Alcohol-induced delay of viability loss in stationary-phase cultures of Escherichia coli. J Bacteriol 184 2898 2905

85. OchsnerUA

SnyderA

VasilAI

VasilML

2002 Effects of the twin-arginine translocase on secretion of virulence factors, stress response, and pathogenesis. Proc Natl Acad Sci USA 99 8312 8317

86. RossierO

CianciottoNP

2005 The Legionella pneumophila tatB gene facilitates secretion of phospholipase C, growth under iron-limiting conditions, and intracellular infection. Infect Immun 73 2020 2032

87. LeeJC

OhJY

KimKS

JeongYW

ParkJC

2001 Apoptotic cell death induced by Acinetobacter baumannii in epithelial cells through caspase-3 activation. APMIS 109 679 684

88. TitballRW

1993 Bacterial phospholipases C. Microbiol Rev 57 347 366

89. VasilML

StonehouseMJ

VasilAI

WadsworthSJ

GoldfineH

2009 A complex extracellular sphingomyelinase of Pseudomonas aeruginosa inhibits angiogenesis by selective cytotoxicity to endothelial cells. PLoS Pathog 5 e1000420 doi:10.1371/journal.ppat.1000420

90. CamilliA

TilneyLG

PortnoyDA

1993 Dual roles of plcA in Listeria monocytogenes pathogenesis. Mol Microbiol 8 143 157

91. MarquisH

DoshiV

PortnoyDA

1995 The broad-range phospholipase C and a metalloprotease mediate listeriolysin O-independent escape of Listeria monocytogenes from a primary vacuole in human epithelial cells. Infect Immun 63 4531 4534

92. GrundlingA

GonzalezMD

HigginsDE

2003 Requirement of the Listeria monocytogenes broad-range phospholipase PC-PLC during infection of human epithelial cells. J Bacteriol 185 6295 6307

93. QuandtJ

HynesMF

1993 Versatile suicide vectors which allow direct selection for gene replacement in gram-negative bacteria. Gene 127 15 21

94. HungerM

SchmuckerR

KishanV

HillenW

1990 Analysis and nucleotide sequence of an origin of DNA replication in Acinetobacter calcoaceticus and its use for Escherichia coli shuttle plasmids. Gene 87 45 51

95. SpainkHP

OkkerRJH

WijffelmanCA

PeesE

LugtenbergBJJ

1987 Promoters in the nodulation region of the Rhizobium leguminosarum symbiotic plasmid pRL1JI. Plant Mol Biol 9 27 39

96. AusubelFM

BrentR

KingstonRE

MooreDD

SeidmanJG

1987 Current Protocols in Molecular Biology. New York John Wiley

97. DorseyCW

TomarasAP

ActisLA

2002 Genetic and phenotypic analysis of Acinetobacter baumannii insertion derivatives generated with a transposome system. Appl Environ Microbiol 68 6353 6360

98. RozenS

SkaletskyH

2000 Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132 365 386

99. LivakKJ

SchmittgenTD

2001 Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25 402 408

100. MillerJ

1972 Experiments in molecular genetics. Cold Spring Harbor, N.Y. Cold Spring Harbor Laboratory

101. PatonJC

RogersTJ

MoronaR

PatonAW

2001 Oral administration of formaldehyde-killed recombinant bacteria expressing a mimic of the Shiga toxin receptor protects mice from fatal challenge with Shiga-toxigenic Escherichia coli. Infect Immun 69 1389 1393