The OxyR Regulon in Nontypeable Haemophilus influenzae � †

The OxyR Regulon in Nontypeable Haemophilus influenzae � † (2006)

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by Alistair Harrison , William C. Ray , Beth D. Baker , David W , Lauren O. Bakaletz , Robert S. Munson , Alistair Harrison , William C. Ray , Beth D. Baker , David W. Armbruster , Lauren O. Bakaletz , Robert S. Munson

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236	A concise guide to cDNA microarray analysis. - Hegde, Qi, et al. - 2000 (Show Context) Citation Context ...g TRIZOL Reagent (Invitrogen Corporation, Carlsbad, CA) as outlined by Mason et al., (47). cDNA was synthesized and labeled using an indirect labeling method similar to that described by Hegde et al. =-=(30)-=-. Full microarray manufacturing, hybridization protocols, and data analysis methods are shown in the supplementary material. Quantitative RT-PCR. Quantitative RT-PCR was used to confirm the relative e...
180	Recombinational repair of DNA damage in Escherichia coli and bacteriophage λ, - Kuzminov - 1999 (Show Context) Citation Context ...RecA and RecN. RecA and RecN have important roles in the repair of DNA damage which have been extensively characterized in UV damage experiments in many organisms, including E. coli and H. influenzae =-=(43, 50, 51, 77, 82)-=-. Further repair mechanisms are potentially afforded by the gene products of NTHI0493 and NTHI0495, which encode homologues of the cochaperone proteins HscA and HscB, respectively, and that have roles...
133	DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. - Zheng, Wang, et al. - 2001 (Show Context) Citation Context ...n response protein that binds DNA and protects against H 2O 2-induced oxidative stress. Subsequently, H 2O 2 was found to induce Dps expression in actively growing E. coli in an OxyR-dependent manner =-=(3, 4, 92)-=-. Similarly, in Salmonella enterica serovar Typhimurium, Dps protects against H 2O 2-derived oxidative stress and is needed for bacterial survival after phagocytosis by macrophages, as shown in a mous...
129	A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev - Almiron, AJ, et al. - 1992 (Show Context) Citation Context ...ated iron binding protein 8 (4) 4 (4) 1 NTHI0477 hfeD Putative ABC type chelated iron transport system, 7 (6) 3 d ND e permease NTHI0479 hfeB Putative ABC type chelated iron transport system, 7 (5) 3 =-=(3)-=- ND ATPase NTHI0705 pgdX Peroxiredoxin/glutaredoxin 7 (9) 31 (35) 1 NTHI1794 Pseudogene for conserved hypothetical protein 7 0.5 ND NTHI0199 Conserved hypothetical protein 6 (1) 0.5 ND NTHI0478 hfeC P...
126	Activation of the OxyR transcription factor by reversible disulfide bond formation. - Zheng, Aslund, et al. - 1998 (Show Context) Citation Context ...w that the other functional domains in the OxyR protein from both organisms are well conserved. These include domains involved in tetramerization, disulfide bond formation, and RNA polymerase binding =-=(12, 41, 42, 83, 88, 90)-=-. Characterization of the 86-028NP oxyR mutant. The 86-028NP oxyR mutant strain was identified from a bank of random transposition mutants. The transposon insertion was between nucleotides 1242 and 12...
102	Superoxide accelerates DNA damage by elevating free-iron - Keyer, JA - 1996 (Show Context) Citation Context .... In the case of dihydroxy-acid dehydratase, this does not produce a loss of protein or induce the synthesis of new protein. It appears that the damage is reversible, and the clusters can be repaired =-=(19, 20, 39)-=-. Finally, the increased transcription of iron utilization genes in strain 86-028NP during a period of oxidative stress may also be related to 4Fe-4S cluster damage. The iron lost Downloaded from http...
98	Lethal oxidative damage and mutagenesis are generated by iron in delta fur mutants of Escherichia coli: protective role of superoxide dismutase - Touati, Jacques, et al. - 1995 (Show Context) Citation Context ...ve been previously described. A fur mutant of E. coli grown at increased oxygen tensions exhibited oxidative DNA damage possibly due to excess free iron generated by derepression of iron uptake genes =-=(85)-=-. Moreover, the promoter region of fldA, the cotranscribed gene upstream of fur in E. coli, exhibits a binding site for SoxS, the positive regulator of SOD (91). Furthermore, expression of both iron a...
93	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. - Altuvia, Almiron, et al. - 1994 (Show Context) Citation Context ...7) 0.5 1 NTHI1168 tbp1 Transferrin-binding protein 1 10 (8) 0.7 1 NTHI0782 hgpB Hemoglobin-haptoglobin binding protein B 8 (5) 1.5 2 NTHI0481 hfeA Putative periplasmic chelated iron binding protein 8 =-=(4)-=- 4 (4) 1 NTHI0477 hfeD Putative ABC type chelated iron transport system, 7 (6) 3 d ND e permease NTHI0479 hfeB Putative ABC type chelated iron transport system, 7 (5) 3 (3) ND ATPase NTHI0705 pgdX Per...
91	Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection. - Toledano - 1994 (Show Context) Citation Context ...w that the other functional domains in the OxyR protein from both organisms are well conserved. These include domains involved in tetramerization, disulfide bond formation, and RNA polymerase binding =-=(12, 41, 42, 83, 88, 90)-=-. Characterization of the 86-028NP oxyR mutant. The 86-028NP oxyR mutant strain was identified from a bank of random transposition mutants. The transposon insertion was between nucleotides 1242 and 12...
87	JA (2003) Pathways of oxidative damage - Imlay (Show Context) Citation Context ...xide (H 2O 2). The effects of ROS on cells can then be exacerbated by the presence of free iron which, via the Fenton reaction, can react with H 2O 2 to produce more highly reactive hydroxyl radicals =-=(34, 40, 52)-=-. Within a host, this problem is compounded by the release of extracellular ROS by phagocytes, which again, can have deleterious effects on invading pathogens (13). Thus, bacteria have evolved an arra...
84	OxyR and SoxRS regulation of fur. - Zheng, Doan, et al. - 1999 (Show Context) Citation Context ...ed by derepression of iron uptake genes (85). Moreover, the promoter region of fldA, the cotranscribed gene upstream of fur in E. coli, exhibits a binding site for SoxS, the positive regulator of SOD =-=(91)-=-. Furthermore, expression of both iron and manganese cofactored SOD is positively regulated by Fur in multiple species of bacteria (reviewed by Touati [84]). Finally, with regard to OxyR regulation of...
80	Alkyl hydroperoxide reductase is the primary scavenger of endogenous hydrogen peroxide in Escherichia coli. - Seaver, Imlay - 2001 (Show Context) Citation Context ...s indistinguishable from that of the parent strain (results not shown). This is contrary to what was found for AhpC, E. coli’s homologue of TsaA, which has a major role in the decomposition of H 2O 2 =-=(75, 76)-=-. Homologues of TsaA are utilized in the decomposition of other ROS. For example, mutations in ahp in both E. coli and S. enterica serovar Typhimurium increase sensitivity to cumene hydroperoxide (80)...
67	Inhibitory and bactericidal effects of hydrogen peroxide production by Streptococcus pneumoniae on other inhabitants of the upper respiratory tract. Infect. Immun - Pericone, Overweg, et al. - 2000 (Show Context) Citation Context ...clear leukocytes, with the attendant possibility of insult by ROS (36, 37, 58). Also, S. pneumoniae produces extracellular H 2O 2 at concentrations that are bactericidal toward H. influenzae in vitro =-=(64)-=-. Despite these attentions, the ability of NTHi to successfully infect the middle ear space suggests that NTHi have multiple robust mechanisms in place to withstand the effects of oxidative stress. Ho...
59	The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. - Sauer, Canonaco, et al. - 2004 (Show Context) Citation Context ..., respectively. In E. coli, PntAB has a role in the generation of NADPH; treatment of E. coli with H 2O 2 induces both this activity and an increase in NADPH-dependent oxidase and peroxidase activity =-=(11, 73)-=-. Both the thioredoxin and glutaredoxin systems utilize the reducing power of NADPH to reduce disulfide bonds, so this process will likely be important during periods of oxidative stress. Also, NADPH ...
55	2003. Touch and go: tying TonB to transport - Postle, Kadner (Show Context) Citation Context ...lex with hemopexin (14–16). The TonB-ExbBD system has a vital role in transducing the energy of the proton motor force to generate conformational changes in TonB-dependent outer membrane transporters =-=(68)-=-. If the upregulation of outer membrane-associated iron uptake system proteins is functionally relevant to the conditions induced by treatment of strain 86-028NP with H 2O 2, then the concomitant upre...
55	An alkyl hydroperoxide reductase induced by oxidative stress in Salmonella typhimurium and Escherichia coli: genetic characterization and cloning of ahp,” - Storz, Jacobson, et al. - 1989 (Show Context) Citation Context ... 76). Homologues of TsaA are utilized in the decomposition of other ROS. For example, mutations in ahp in both E. coli and S. enterica serovar Typhimurium increase sensitivity to cumene hydroperoxide =-=(80)-=-. Our data suggest that TsaA in strain 86-028NP may have a yet-unidentified role in protection against oxidative stress. (ii) DNA and protein repair. All genes with roles in DNA and protein repair aft...
54	Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for DNA binding and multimerization. - Kullik, Stevens, et al. - 1995 (Show Context) Citation Context ...e in strain 86-028NP encodes a protein that is 73% identical to the E. coli OxyR protein. Nineteen of twenty residues in the helix-turn-helix motif thought to be involved in DNA binding are identical =-=(41)-=-. Further comparisons of the amino acid sequences of OxyR from strain 86-028NP and those from E. coli show that the other functional domains in the OxyR protein from both organisms are well conserved....
50	A gene cluster involved in the utilization of both free heme and heme:hemopexin by Haemophilus influenzae type b - Cope, Yogev, et al. - 1995
48	The inactivation of Fe-S cluster containing hydro-lyases by superoxide - Flint, Tuminello, et al. - 1993 (Show Context) Citation Context .... In the case of dihydroxy-acid dehydratase, this does not produce a loss of protein or induce the synthesis of new protein. It appears that the damage is reversible, and the clusters can be repaired =-=(19, 20, 39)-=-. Finally, the increased transcription of iron utilization genes in strain 86-028NP during a period of oxidative stress may also be related to 4Fe-4S cluster damage. The iron lost Downloaded from http...
48	Superoxide sensitivity of the Escherichia coli aconitase - Gardner, Fridovich - 1991
46	Redox-operated genetic switches: the SoxR and OxyR transcription factors,” - Pomposiello, Demple - 2001 (Show Context) Citation Context ...er free iron and bind to DNA, thus protecting DNA from damage (27, 33, 45, 53, 59, 60, 67). In addition, many bacterial species possess genes encoding OxyR, a global regulator of antioxidant defenses =-=(24, 66)-=-. Protection against oxidative stress is especially important to nontypeable Haemophilus influenzae (NTHi). NTHi is one of three bacterial commensal organisms, the others being Streptococcus pneumonia...
40	IscU as a scaffold for iron-sulfur cluster biosynthesis: sequential assembly of [2Fe-2S] and [4Fe-4S] clusters in IscU. - Agar, Krebs, et al. - 2000 (Show Context) Citation Context ...hfeC Putative ABC-type chelated iron transport system, 6 (4) 3 (3) 1 permease NTHI0736 hgpD Hemoglobin-haptoglobin binding protein D 6 1 ND NTHI0179 hitB Iron(III) transport system permease protein 5 =-=(2)-=- 2 d ND NTHI1817 dps Conserved hypothetical DNA-binding ferritin-like 4 (1) 7 (5) 0.4 protein NTHI0681 gnd 6-phosphogluconate dehydrogenase 4 (4) 6 (8) 1 NTHI0358 tonB Energizer of iron uptake systems...
40	Iron and oxidative stress in - Touati (Show Context) Citation Context ...site for SoxS, the positive regulator of SOD (91). Furthermore, expression of both iron and manganese cofactored SOD is positively regulated by Fur in multiple species of bacteria (reviewed by Touati =-=[84]-=-). Finally, with regard to OxyR regulation of Fur, microarray analyses of hydrogen peroxide-treated E. coli indicated that fur expression was slightly upregulated compared to that of the untreated sam...
39	The human neutrophil respiratory burst oxidase - Clark - 1990 (Show Context) Citation Context ...y reactive hydroxyl radicals (34, 40, 52). Within a host, this problem is compounded by the release of extracellular ROS by phagocytes, which again, can have deleterious effects on invading pathogens =-=(13)-=-. Thus, bacteria have evolved an array of increasingly well-defined mechanisms to abrogate the effects of oxidative stress. Proteins involved in such processes include catalase, which decomposes H 2O ...
37	Superoxide and the production of oxidative DNA damage. - Keyer, AS, et al. - 1995 (Show Context) Citation Context ...(61). Binding of free iron may thus help abrogate the toxic effects of the Fenton reaction. In E. coli, Fe 2� , a substrate for the Fenton reaction, may be generated by the reduction of Fe 3� by NADH =-=(38)-=-. Thus, in the case of strain 86-028NP, the increased expression of homologues of proteins such as HitA may help mitigate the effects of the Fenton reaction due to a reduction in concentration of intr...
36	Hydrogen peroxide fluxes and compartmentalization inside growing Escherichia coli,” - Seaver, Imlay - 2001 (Show Context) Citation Context ...s indistinguishable from that of the parent strain (results not shown). This is contrary to what was found for AhpC, E. coli’s homologue of TsaA, which has a major role in the decomposition of H 2O 2 =-=(75, 76)-=-. Homologues of TsaA are utilized in the decomposition of other ROS. For example, mutations in ahp in both E. coli and S. enterica serovar Typhimurium increase sensitivity to cumene hydroperoxide (80)...
36	Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells. A ferritin-like DNA-binding protein of Escherichia coli - Zhao, Ceci, et al. - 2002 (Show Context) Citation Context ...o bind Fe 2� and abrogate H 2O 2-induced hydroxy radical production via the Fenton reaction; H 2O 2 treatment of Fe 2� -DNA complexes, in the absence of Dps, leads to the total degradation of the DNA =-=(89)-=-. The final members of the OxyR regulon with a proposed role in mitigating oxidative stress in strain 86-028NP are NTHI1802 and NTHI1801. Both genes have FDRs higher than the set cutoff (0.06 and 0.09...
35	Genomic sequence of an otitis media isolate of nontypeable Haemophilus influenzae: comparative study with H. influenzae serotype d, strain KW20 - Harrison - 2005 (Show Context) Citation Context ... of ROS in clinical isolates of NTHi have been elucidated through our laboratory’s investigations of strain differences between strain Rd and two NTHi isolates recovered from children with chronic OM =-=(29, 55)-=-. Microarray comparisons between the genomes of strain Rd and that of the NTHi OM isolate 1885MEE revealed a homologue of the gene encoding the alkylhydroperoxidase TsaA in the OM isolate (55). Genes ...
32	Identi®cation of a locus involved in the utilization of iron by Haemophilus in¯uenzae. - Sanders, Cope, et al. - 1994 (Show Context) Citation Context ...f iron utilization proteins include NTHI0177, NTHI0179, and NTHI0180, which are homologues of genes encoding components of the Hit system, an ABC transport system that imports free iron into the cell =-=(1, 72)-=-. Strain 86-028NP also possesses genes which are homologues of genes encoding hemoglobin and hemoglobin-haptoglobin binding proteins (HgpB, HgpC, and HgpD). H 2O 2 treatment upregulated the expression...
29	The identification of primary sites of superoxide and hydrogen peroxide formation in the aerobic respiratory chain and sulfite reductase complex of Escherichia coli. The Journal of biological chemistry 274 - Messner, Imlay - 1999 (Show Context) Citation Context ...xide (H 2O 2). The effects of ROS on cells can then be exacerbated by the presence of free iron which, via the Fenton reaction, can react with H 2O 2 to produce more highly reactive hydroxyl radicals =-=(34, 40, 52)-=-. Within a host, this problem is compounded by the release of extracellular ROS by phagocytes, which again, can have deleterious effects on invading pathogens (13). Thus, bacteria have evolved an arra...
28	An ABC transport system of Yersinia pestis allows utilization of chelated iron by Escherichia coli SAB11. - Bearden, Staggs, et al. - 1998 (Show Context) Citation Context ...ative ABC type chelated iron transport system, 7 (6) 3 d ND e permease NTHI0479 hfeB Putative ABC type chelated iron transport system, 7 (5) 3 (3) ND ATPase NTHI0705 pgdX Peroxiredoxin/glutaredoxin 7 =-=(9)-=- 31 (35) 1 NTHI1794 Pseudogene for conserved hypothetical protein 7 0.5 ND NTHI0199 Conserved hypothetical protein 6 (1) 0.5 ND NTHI0478 hfeC Putative ABC-type chelated iron transport system, 6 (4) 3 ...
28	Substantial DNA damage from submicromolar intracellular hydrogen peroxide detected in Hpx-mutants of Escherichia coli. - Park, You, et al. - 2005 (Show Context) Citation Context ...ation and DNA damage. An hpx dps double mutant also exhibited greater levels of DNA damage, again indicating both the damaging effects of iron and the role Dps plays in protecting against such damage =-=(61)-=-. Binding of free iron may thus help abrogate the toxic effects of the Fenton reaction. In E. coli, Fe 2� , a substrate for the Fenton reaction, may be generated by the reduction of Fe 3� by NADH (38)...
27	Effect of multiple mutations in the hemoglobin- and hemoglobin-haptoglobin-binding proteins, HgpA, HgpB, and HgpC, of Haemophilus influenzae type b. Infect Immun 67 - Morton, Whitby, et al. - 1999 (Show Context) Citation Context ...of the genes encoding HgpB and HgpD but not that of the gene encoding HgpC. The three encoded hemoglobin and hemoglobin-haptoglobin binding proteins in H. influenzae type b have overlapping functions =-=(35, 54, 69)-=-, which suggests that if the upregulation of hemoglobin and hemoglobin-haptoglobin binding proteins is needed during oxidative stress, it is not vital that expression of all three proteins is upregula...
27	Reading of DNA sequence logos: prediction of major groove binding by information theory. - Schneider - 1996 (Show Context) Citation Context ...set from the 11-bp repeat of the presumed primary binding motifs. A similar phenomenon, suggestive of a minorgroove contact in the binding geometry, has been observed among E. coli OxyR binding sites =-=(74)-=-. Of note, initially no similar patterns were identified upstream of the putative OxyR regulon members NTHI0681 and NTHI0481. However, if OxyR binding tolerates misspacing of the highly conserved pres...
27	Synergistic effect of adenovirus type 1 and nontypeable Haemophilus influenzae in a chinchilla model of experimental otitis media - Suzuki, Bakaletz - 1994 (Show Context) Citation Context ... media used. NTHi strain 86-028NP was recovered from the nasopharynx of a child with chronic otitis media. This strain has been well characterized both in vitro (8, 32) and in chinchilla models of OM =-=(7, 47, 81)-=-. The genome sequence has been published (29). For routine culturing, strain 86-028NP and the strain 86-028NP oxyR mutant were grown on chocolate II plates (Fisher Scientific, Pittsburgh, PA). For tes...
26	Frequency of fimbriation of nontypable Haemophilus influenzae and its ability to adhere to chinchilla and human respiratory epithelium. Infect. Immun - Bakaletz, Tallan, et al. - 1988 (Show Context) Citation Context ...D METHODS Bacterial strains and culture media used. NTHi strain 86-028NP was recovered from the nasopharynx of a child with chronic otitis media. This strain has been well characterized both in vitro =-=(8, 32)-=- and in chinchilla models of OM (7, 47, 81). The genome sequence has been published (29). For routine culturing, strain 86-028NP and the strain 86-028NP oxyR mutant were grown on chocolate II plates (...
26	Genome-wide transcriptional profiling of the steady-state response of Pseudomonas aeruginosa to hydrogen peroxide - Salunkhe, Topfer, et al. - 2005 (Show Context) Citation Context ...identified genes with roles in protection against oxidative stress and repair of oxidative damage, while only the last organism exhibits the induction of multiple genes with roles in iron utilization =-=(71, 79, 92)-=-. Thus, identification of a major category of genes, whose expression was upregulated during H 2O 2 treatment, which encode proteins that have roles in the 86-028NP strain’s iron utilization systems i...
23	Biochemical characterization of a Haemophilus influenzae periplasmic iron transport operon. - Adhikari, Kirby, et al. - 1995 (Show Context) Citation Context ...nsport system, 7 (5) 3 (3) ND ATPase NTHI0705 pgdX Peroxiredoxin/glutaredoxin 7 (9) 31 (35) 1 NTHI1794 Pseudogene for conserved hypothetical protein 7 0.5 ND NTHI0199 Conserved hypothetical protein 6 =-=(1)-=- 0.5 ND NTHI0478 hfeC Putative ABC-type chelated iron transport system, 6 (4) 3 (3) 1 permease NTHI0736 hgpD Hemoglobin-haptoglobin binding protein D 6 1 ND NTHI0179 hitB Iron(III) transport system pe...
23	hgpB, a gene encoding a second Haemophilus influenzae hemoglobin- and hemoglobinhaptoglobin-binding protein. Infect Immun 66:4733–4741 - Ren, Jin, et al. - 1998 (Show Context) Citation Context ...of the genes encoding HgpB and HgpD but not that of the gene encoding HgpC. The three encoded hemoglobin and hemoglobin-haptoglobin binding proteins in H. influenzae type b have overlapping functions =-=(35, 54, 69)-=-, which suggests that if the upregulation of hemoglobin and hemoglobin-haptoglobin binding proteins is needed during oxidative stress, it is not vital that expression of all three proteins is upregula...
21	Molecular design and functional organization of the RecA protein - McGrew, Knight (Show Context) Citation Context ...RecA and RecN. RecA and RecN have important roles in the repair of DNA damage which have been extensively characterized in UV damage experiments in many organisms, including E. coli and H. influenzae =-=(43, 50, 51, 77, 82)-=-. Further repair mechanisms are potentially afforded by the gene products of NTHI0493 and NTHI0495, which encode homologues of the cochaperone proteins HscA and HscB, respectively, and that have roles...
20	Relative immunogenicity and efficacy of two synthetic chimeric peptides of fimbrin as vaccinogens against nasopharyngeal colonization by nontypeable Haemophilus influenzae in the chinchilla. Vaccine 15:955–961 - Bakaletz, Leake, et al. - 1997 (Show Context) Citation Context ... media used. NTHi strain 86-028NP was recovered from the nasopharynx of a child with chronic otitis media. This strain has been well characterized both in vitro (8, 32) and in chinchilla models of OM =-=(7, 47, 81)-=-. The genome sequence has been published (29). For routine culturing, strain 86-028NP and the strain 86-028NP oxyR mutant were grown on chocolate II plates (Fisher Scientific, Pittsburgh, PA). For tes...
20	Lack of expression of the global regulator OxyR in Haemophilus influenzae has a profound effect on growth phenotype. - Maciver, Hansen - 1996 (Show Context) Citation Context ...mutant. The 86-028NP oxyR mutant strain was identified from a bank of random transposition mutants. The transposon insertion was between nucleotides 1242 and 1250 of the oxyR gene. Maciver and Hansen =-=(46)-=- showed that a mutation in oxyR inhibited the growth of a H. influenzae type b strain on medium in which heme was replaced with the heme precursor PPIX. Nakahigashi et al. showed that a ferrochelatase...
19	A peroxide/ascorbateinducible catalase from Haemophilus influenzae is homologous to the Escherichia coli katE gene product - Bishai, Smith, et al. - 1994 (Show Context) Citation Context ... three categories. (i) Oxidative stress. Proteins can have a direct role in controlling the effects of oxidative stress by detoxifying reactive oxygen species. NTHI1099 (htkE), which encodes catalase =-=(10)-=-, was the most highly upregulated gene, with an approximate 60-fold induction in the H 2O 2-treated parent compared to that in the untreated parent. NTHI1099 was not induced in the H 2O 2-treated oxyR...
19	Binding of heme-hemopexin complexes by soluble HxuA protein allows utilization of this complexed heme by Haemophilus influenzae. Infect Immun 66 - Cope, Thomas, et al. - 1998
19	Adherence of non-typeable Haemophilus influenzae promotes reorganization of the actin cytoskeleton in human or chinchilla epithelial cells in vitro - Holmes, Bakaletz - 1997 (Show Context) Citation Context ...D METHODS Bacterial strains and culture media used. NTHi strain 86-028NP was recovered from the nasopharynx of a child with chronic otitis media. This strain has been well characterized both in vitro =-=(8, 32)-=- and in chinchilla models of OM (7, 47, 81). The genome sequence has been published (29). For routine culturing, strain 86-028NP and the strain 86-028NP oxyR mutant were grown on chocolate II plates (...
19	Nontypeable Haemophilus influenzae gene expression induced in vivo in a chinchilla model of otitis media. Infect Immun - Mason, Munson, et al. - 2003 (Show Context) Citation Context ... media used. NTHi strain 86-028NP was recovered from the nasopharynx of a child with chronic otitis media. This strain has been well characterized both in vitro (8, 32) and in chinchilla models of OM =-=(7, 47, 81)-=-. The genome sequence has been published (29). For routine culturing, strain 86-028NP and the strain 86-028NP oxyR mutant were grown on chocolate II plates (Fisher Scientific, Pittsburgh, PA). For tes...
18	Bacterial defenses against oxidants: Mechanistic features of cysteinebased peroxidases and their flavoprotein reductases. Archives of Biochemistry and Biophysics 433 - Poole - 2005 (Show Context) Citation Context ...e organic hydroperoxide resistance proteins (Ohr) that decompose organic peroxides. Also, DNA-binding ferritin-like proteins (Dps) sequester free iron and bind to DNA, thus protecting DNA from damage =-=(27, 33, 45, 53, 59, 60, 67)-=-. In addition, many bacterial species possess genes encoding OxyR, a global regulator of antioxidant defenses (24, 66). Protection against oxidative stress is especially important to nontypeable Haemo...
17	The transcriptome response of Neisseria gonorrhoeae to hydrogen peroxide reveals genes with previously uncharacterized roles in oxidative damage protection - Stohl, Criss, et al. - 2005 (Show Context) Citation Context ...identified genes with roles in protection against oxidative stress and repair of oxidative damage, while only the last organism exhibits the induction of multiple genes with roles in iron utilization =-=(71, 79, 92)-=-. Thus, identification of a major category of genes, whose expression was upregulated during H 2O 2 treatment, which encode proteins that have roles in the 86-028NP strain’s iron utilization systems i...
16	Antimicrobial activity of innate immune molecules against Streptococcus pneumoniae, Moraxella catarrhalis and nontypeable Haemophilus influenzae. - HY, Andalibi, et al. - 2004 (Show Context) Citation Context ...d cause otitis media (OM) in the normally sterile middle ear space (5). During this process, the bacteria are subject to multiple innate host defenses. These include assault by antimicrobial peptides =-=(28, 44, 49)-=-, as well as invasion of the middle ear by polymorphonuclear leukocytes, with the attendant possibility of insult by ROS (36, 37, 58). Also, S. pneumoniae produces extracellular H 2O 2 at concentratio...
16	Partial analysis of the genomes of two nontypeable Haemophilus influenzae otitis media isolates. Infect Immun - Munson, Harrison, et al. - 2004 (Show Context) Citation Context ... of ROS in clinical isolates of NTHi have been elucidated through our laboratory’s investigations of strain differences between strain Rd and two NTHi isolates recovered from children with chronic OM =-=(29, 55)-=-. Microarray comparisons between the genomes of strain Rd and that of the NTHi OM isolate 1885MEE revealed a homologue of the gene encoding the alkylhydroperoxidase TsaA in the OM isolate (55). Genes ...
15	Genetic and physiological characterization of ohr, encoding a protein involved in organic hydroperoxide resistance in Pseudomonas aeruginosa - Ochsner, Hassett, et al. - 2001 (Show Context) Citation Context ...e organic hydroperoxide resistance proteins (Ohr) that decompose organic peroxides. Also, DNA-binding ferritin-like proteins (Dps) sequester free iron and bind to DNA, thus protecting DNA from damage =-=(27, 33, 45, 53, 59, 60, 67)-=-. In addition, many bacterial species possess genes encoding OxyR, a global regulator of antioxidant defenses (24, 66). Protection against oxidative stress is especially important to nontypeable Haemo...
14	Effects of hydrogen peroxide upon nicotinamide nucleotide metabolism in Escherichia coli. Changes in enzyme levels and nicotinamide nucleotide pools and studies on the oxidation of NAD(P)H by Fe(III - Brumaghim, Li, et al. - 2003 (Show Context) Citation Context ..., respectively. In E. coli, PntAB has a role in the generation of NADPH; treatment of E. coli with H 2O 2 induces both this activity and an increase in NADPH-dependent oxidase and peroxidase activity =-=(11, 73)-=-. Both the thioredoxin and glutaredoxin systems utilize the reducing power of NADPH to reduce disulfide bonds, so this process will likely be important during periods of oxidative stress. Also, NADPH ...
13	Demonstration of type IV pilus expression and a twitching phenotype by Haemophilus influenzae. Infect. Immun - Bakaletz, Baker, et al. - 2005 (Show Context) Citation Context ...cloned into pGEM-T Easy (Promega Co., Madison, WI), and then moved into pSPEC1, a derivative of the Escherichia coli-Haemophilus shuttle vector pGZRS-39A that contains a spectinomycin resistance gene =-=(6)-=-. The pSPEC1-oxyR construct was transformed into the 86-028NP oxyR::Tn5 mutant strain, and transformants were selected on chocolate agar containing 200 �g spectinomycin/ml. Complemented clones were id...
11	RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks - Meddows, Savory, et al. - 2005 (Show Context) Citation Context ...RecA and RecN. RecA and RecN have important roles in the repair of DNA damage which have been extensively characterized in UV damage experiments in many organisms, including E. coli and H. influenzae =-=(43, 50, 51, 77, 82)-=-. Further repair mechanisms are potentially afforded by the gene products of NTHI0493 and NTHI0495, which encode homologues of the cochaperone proteins HscA and HscB, respectively, and that have roles...
10	Involvement of HxuC outer membrane protein in utilization of hemoglobin by Haemophilus influenza. Infect. Immun - Cope, Love, et al. - 2001
10	How to flip the (redox) switch. Cell 111: 607–610 - Georgiou - 2002 (Show Context) Citation Context ...er free iron and bind to DNA, thus protecting DNA from damage (27, 33, 45, 53, 59, 60, 67). In addition, many bacterial species possess genes encoding OxyR, a global regulator of antioxidant defenses =-=(24, 66)-=-. Protection against oxidative stress is especially important to nontypeable Haemophilus influenzae (NTHi). NTHi is one of three bacterial commensal organisms, the others being Streptococcus pneumonia...
9	Hsc66 substrate specificity is directed toward a discrete region of the iron-sulfur cluster template protein IscU - Hoff, Ta, et al. - 2002 (Show Context) Citation Context ...otentially afforded by the gene products of NTHI0493 and NTHI0495, which encode homologues of the cochaperone proteins HscA and HscB, respectively, and that have roles in iron-sulfur cluster assembly =-=(2, 31, 78)-=-. NTHI1588 is a homologue of a gene that encodes ImpA, an error-prone DNA polymerase originally identified in the incompatibility group plasmid TP110. Possession of this plasmid increases a cell’s res...
9	Detection and quantification of superoxide formed within the periplasm of Escherichia coli - Korshunov, Imlay - 2006 (Show Context) Citation Context ...xide (H 2O 2). The effects of ROS on cells can then be exacerbated by the presence of free iron which, via the Fenton reaction, can react with H 2O 2 to produce more highly reactive hydroxyl radicals =-=(34, 40, 52)-=-. Within a host, this problem is compounded by the release of extracellular ROS by phagocytes, which again, can have deleterious effects on invading pathogens (13). Thus, bacteria have evolved an arra...
9	2001 Effects of mutations involving cell division, recombination and chromosome dimer resolution on a priA2::kan mutant - McCool, Sandler (Show Context) Citation Context ...FtsK in both DNA replication and cell division has been well established. In E. coli, FtsK is presumed to have a role in resolving chromosome dimers caused by crossovers during chromosome replication =-=(17, 48)-=-. (iii) Iron utilization. The most strongly upregulated genes in this class were NTHI1168 and NTHI1169, which are homologues of genes encoding transferrin-binding proteins 1 and 2, respectively, (65)....
9	Photosensitivity of a protoporphyrin-accumulating, light-sensitive mutant (visA) of Escherichia coli K-12 - Nakahigashi, Nishimura, et al. - 1991 (Show Context) Citation Context ...eplaced with the heme precursor PPIX. Nakahigashi et al. showed that a ferrochelatase mutant of E. coli was sensitive to light. They postulated that ROS was generated as a result of PPIX accumulation =-=(57)-=-. This suggested to Maciver and Hansen that the differential growth of an oxyR mutant on PPIX-containing medium was due to the generation of superoxide that, in turn, could spontaneously undergo dismu...
9	Iron transport systems in Neisseria meningitidis - Perkins-Balding, Ratliff-Griffin, et al. - 2004 (Show Context) Citation Context ..., 48). (iii) Iron utilization. The most strongly upregulated genes in this class were NTHI1168 and NTHI1169, which are homologues of genes encoding transferrin-binding proteins 1 and 2, respectively, =-=(65)-=-. Other OxyR-independent upregulated genes encoding homologues of iron utilization proteins include NTHI0177, NTHI0179, and NTHI0180, which are homologues of genes encoding components of the Hit syste...
9	Mechanisms of iron acquisition by the human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. Front - Rohde, Dyer (Show Context) Citation Context ...cates alternative oxidative-stress-responsive regulation of these genes. The best-characterized global regulator of iron utilization genes is Fur (for a review of Fur in Neisseria, see Rohde and Dyer =-=[70]-=-), and the interrelatedness of Fur regulation and oxidative stress responses have been previously described. A fur mutant of E. coli grown at increased oxygen tensions exhibited oxidative DNA damage p...
9	Beeumen, Exogenous Glutathione Completes the Defense against Oxidative Stress in Haemophilus influenza - Vergauwen, Pauwels, et al. (Show Context) Citation Context ... has a role in protection1008 HARRISON ET AL. J. BACTERIOL. against H 2O 2 and alkylhydroperoxidase; the glutathione-dependent reducing action of the glutaredoxin domain allows the system to recycle =-=(62, 63, 86, 87)-=-. The expression of PGdx was subsequently found to be upregulated during in vitro biofilm formation by multiple isolates of NTHi from patients with chronic obstructive pulmonary disease (56). NTHI1817...
8	The inactivation of dihydroxy-acid dehydratase in Escherichia coli treated with hyperbaric oxygen occurs because of the destruction of its Fe-S cluster, but the enzyme remains in the cell in a form that can be reactivated - Flint, Smyk-Randall, et al. - 1993 (Show Context) Citation Context .... In the case of dihydroxy-acid dehydratase, this does not produce a loss of protein or induce the synthesis of new protein. It appears that the damage is reversible, and the clusters can be repaired =-=(19, 20, 39)-=-. Finally, the increased transcription of iron utilization genes in strain 86-028NP during a period of oxidative stress may also be related to 4Fe-4S cluster damage. The iron lost Downloaded from http...
8	Aeppli D. Pathophysiology of Streptococcus pneumoniae otitis media: kinetics of the middle ear biochemical and cytologic host responses. Ann Otol Rhinol Laryngol 1991; 100:236-43. at Pennsylvania State U niversity on Septem ber 15, 2016 http://jid.oxfordj - Nonomura, GS, et al. (Show Context) Citation Context ...ate host defenses. These include assault by antimicrobial peptides (28, 44, 49), as well as invasion of the middle ear by polymorphonuclear leukocytes, with the attendant possibility of insult by ROS =-=(36, 37, 58)-=-. Also, S. pneumoniae produces extracellular H 2O 2 at concentrations that are bactericidal toward H. influenzae in vitro (64). Despite these attentions, the ability of NTHi to successfully infect the...
7	DpsA protects the human pathogen Burkholderia pseudomallei against organic hydroperoxide - Loprasert, Whangsuk, et al. - 2004 (Show Context) Citation Context ...e organic hydroperoxide resistance proteins (Ohr) that decompose organic peroxides. Also, DNA-binding ferritin-like proteins (Dps) sequester free iron and bind to DNA, thus protecting DNA from damage =-=(27, 33, 45, 53, 59, 60, 67)-=-. In addition, many bacterial species possess genes encoding OxyR, a global regulator of antioxidant defenses (24, 66). Protection against oxidative stress is especially important to nontypeable Haemo...
7	Expression of a peroxiredoxin-glutaredoxin by Haemophilus influenzae in biofilms and during human respiratory tract infection. - TF, Kirkham, et al. - 2005 (Show Context) Citation Context ...2, 63, 86, 87). The expression of PGdx was subsequently found to be upregulated during in vitro biofilm formation by multiple isolates of NTHi from patients with chronic obstructive pulmonary disease =-=(56)-=-. NTHI1817, encoding Dps, a conserved hypothetical DNAbinding ferritin-like protein, is a further member of the OxyR regulon in strain 86-028NP. Dps was identified in E. coli as a starvation response ...
6	Quinolinate synthetase: the oxygen-sensitive site of de novo NAD(P)+ biosynthesis - Gardner, Fridovich - 1991
6	Helicobacter hepaticus DPS protein plays an important role in protecting DNA from oxidative damage - Hong, Wang, et al. - 2006 (Show Context) Citation Context ...e organic hydroperoxide resistance proteins (Ohr) that decompose organic peroxides. Also, DNA-binding ferritin-like proteins (Dps) sequester free iron and bind to DNA, thus protecting DNA from damage =-=(27, 33, 45, 53, 59, 60, 67)-=-. In addition, many bacterial species possess genes encoding OxyR, a global regulator of antioxidant defenses (24, 66). Protection against oxidative stress is especially important to nontypeable Haemo...
6	Characterization of hgpA, a gene encoding a haemoglobin/haemoglobin-haptoglobin-binding protein of Haemophilus influenzae - Jin, Ren, et al. - 1999 (Show Context) Citation Context ...BC type chelated iron transport system, 7 (6) 3 d ND e permease NTHI0479 hfeB Putative ABC type chelated iron transport system, 7 (5) 3 (3) ND ATPase NTHI0705 pgdX Peroxiredoxin/glutaredoxin 7 (9) 31 =-=(35)-=- 1 NTHI1794 Pseudogene for conserved hypothetical protein 7 0.5 ND NTHI0199 Conserved hypothetical protein 6 (1) 0.5 ND NTHI0478 hfeC Putative ABC-type chelated iron transport system, 6 (4) 3 (3) 1 pe...
6	Penicillin treatment accelerates middle ear inflammation in experimental pneumococcal otitis media. Infect. Immun - Kawana, Kawana, et al. - 1992 (Show Context) Citation Context ...ate host defenses. These include assault by antimicrobial peptides (28, 44, 49), as well as invasion of the middle ear by polymorphonuclear leukocytes, with the attendant possibility of insult by ROS =-=(36, 37, 58)-=-. Also, S. pneumoniae produces extracellular H 2O 2 at concentrations that are bactericidal toward H. influenzae in vitro (64). Despite these attentions, the ability of NTHi to successfully infect the...
5	Rapid identification of EZ:Tn transposon insertion sites in the genome of Neisseria gonorrhoeae. Epicentre Forum 9:6–7 - Ducey, Dyer - 2002 (Show Context) Citation Context ...8NP, and kanamycin-resistant mutants were selected. Mutations in individual clones were mapped by DNA sequencing of amplicons generated using a single primer PCR method as described by Ducey and Dyer =-=(18)-=-. Complementation of the oxyR mutation in strain 86-028NP. The oxyR gene, its 122-bp upstream intergenic region, and the first 23 bp of the 5� end of the downstream gene were amplified by PCR, TA clon...
5	Regulation of the HscA ATPase reaction cycle by the co-chaperone HscB and the iron-sulfur cluster assembly protein IscU - Silberg, Tapley, et al. - 2004 (Show Context) Citation Context ...otentially afforded by the gene products of NTHI0493 and NTHI0495, which encode homologues of the cochaperone proteins HscA and HscB, respectively, and that have roles in iron-sulfur cluster assembly =-=(2, 31, 78)-=-. NTHI1588 is a homologue of a gene that encodes ImpA, an error-prone DNA polymerase originally identified in the incompatibility group plasmid TP110. Possession of this plasmid increases a cell’s res...
4	Tn7 mutagenesis of Haemophilus influenzae Rd and characterization of the role of atpA in transformation - vitro
4	A member of the cathelicidin family of antimicrobial peptides is produced in the upper airway of the chinchilla and its mRNA expression is altered by common viral and bacterial co-pathogens of otitis - McGillivary, Ray, et al. - 2007 (Show Context) Citation Context ...d cause otitis media (OM) in the normally sterile middle ear space (5). During this process, the bacteria are subject to multiple innate host defenses. These include assault by antimicrobial peptides =-=(28, 44, 49)-=-, as well as invasion of the middle ear by polymorphonuclear leukocytes, with the attendant possibility of insult by ROS (36, 37, 58). Also, S. pneumoniae produces extracellular H 2O 2 at concentratio...
4	Characterization of the rec-1 gene of Haemophilus influenzae and behavior of the gene in Escherichia coli - Setlow, Spikes, et al. - 1988 (Show Context) Citation Context ...RecA and RecN. RecA and RecN have important roles in the repair of DNA damage which have been extensively characterized in UV damage experiments in many organisms, including E. coli and H. influenzae =-=(43, 50, 51, 77, 82)-=-. Further repair mechanisms are potentially afforded by the gene products of NTHI0493 and NTHI0495, which encode homologues of the cochaperone proteins HscA and HscB, respectively, and that have roles...
4	Hydrogen peroxide scavenging is not a virulence determinant in the pathogenesis of Haemophilus influenzae type b strain Eagan - Vergauwen, Herbert, et al. - 2006 (Show Context) Citation Context ... has a role in protection1008 HARRISON ET AL. J. BACTERIOL. against H 2O 2 and alkylhydroperoxidase; the glutathione-dependent reducing action of the glutaredoxin domain allows the system to recycle =-=(62, 63, 86, 87)-=-. The expression of PGdx was subsequently found to be upregulated during in vitro biofilm formation by multiple isolates of NTHi from patients with chronic obstructive pulmonary disease (56). NTHI1817...
4	Mutational analysis to define an activating region on the redox-sensitive transcriptional regulator OxyR - Wang - 2006 (Show Context) Citation Context ...w that the other functional domains in the OxyR protein from both organisms are well conserved. These include domains involved in tetramerization, disulfide bond formation, and RNA polymerase binding =-=(12, 41, 42, 83, 88, 90)-=-. Characterization of the 86-028NP oxyR mutant. The 86-028NP oxyR mutant strain was identified from a bank of random transposition mutants. The transposon insertion was between nucleotides 1242 and 12...
3	FtsK: Maxwell’s demon? Mol. Cell 9:206–207 - Donachie - 2002 (Show Context) Citation Context ...FtsK in both DNA replication and cell division has been well established. In E. coli, FtsK is presumed to have a role in resolving chromosome dimers caused by crossovers during chromosome replication =-=(17, 48)-=-. (iii) Iron utilization. The most strongly upregulated genes in this class were NTHI1168 and NTHI1169, which are homologues of genes encoding transferrin-binding proteins 1 and 2, respectively, (65)....
3	Molecular analysis of the UV protection and mutation genes carried by the I incompatibility group plasmid TP110 - Glazebrook, Grewal, et al. - 1986 (Show Context) Citation Context ...s ImpA, an error-prone DNA polymerase originally identified in the incompatibility group plasmid TP110. Possession of this plasmid increases a cell’s resistance to both UV and UV-mediated mutagenesis =-=(25)-=-. In E. coli, impA is a member of the impCAB operon but, as with the H. influenzae Rd strain, strain 86-028NP lacks homologues of impB and impC. The sixth OxyR-independent gene in this group was NTHI1...
3	The dps gene of symbiotic “Candidatus Legionella jeonii” in Amoeba proteus responds to hydrogen peroxide and phagocytosis - Park, ST, et al. (Show Context) Citation Context ...e organic hydroperoxide resistance proteins (Ohr) that decompose organic peroxides. Also, DNA-binding ferritin-like proteins (Dps) sequester free iron and bind to DNA, thus protecting DNA from damage =-=(27, 33, 45, 53, 59, 60, 67)-=-. In addition, many bacterial species possess genes encoding OxyR, a global regulator of antioxidant defenses (24, 66). Protection against oxidative stress is especially important to nontypeable Haemo...
2	Oxidative metabolic products released from polymorphonuclear leukocytes in middle ear during experimental otitis media. Infect. Immun - Kawana, Kawana, et al. - 1991 (Show Context) Citation Context ...ate host defenses. These include assault by antimicrobial peptides (28, 44, 49), as well as invasion of the middle ear by polymorphonuclear leukocytes, with the attendant possibility of insult by ROS =-=(36, 37, 58)-=-. Also, S. pneumoniae produces extracellular H 2O 2 at concentrations that are bactericidal toward H. influenzae in vitro (64). Despite these attentions, the ability of NTHi to successfully infect the...
2	Physiological characterization of Haemophilus influenzae Rd deficient in its glutathione-dependent peroxidase PGdx - Pauwels, Vergauwen, et al. - 2004 (Show Context) Citation Context ... has a role in protection1008 HARRISON ET AL. J. BACTERIOL. against H 2O 2 and alkylhydroperoxidase; the glutathione-dependent reducing action of the glutaredoxin domain allows the system to recycle =-=(62, 63, 86, 87)-=-. The expression of PGdx was subsequently found to be upregulated during in vitro biofilm formation by multiple isolates of NTHi from patients with chronic obstructive pulmonary disease (56). NTHI1817...
1	Purification and characterization of a chimeric enzyme from Downloaded from http://jb.asm.org - Pauwels, Vergauwen, et al. - 2003 (Show Context) Citation Context ... has a role in protection1008 HARRISON ET AL. J. BACTERIOL. against H 2O 2 and alkylhydroperoxidase; the glutathione-dependent reducing action of the glutaredoxin domain allows the system to recycle =-=(62, 63, 86, 87)-=-. The expression of PGdx was subsequently found to be upregulated during in vitro biofilm formation by multiple isolates of NTHi from patients with chronic obstructive pulmonary disease (56). NTHI1817...
1	Induction of the SOS regulon of Haemophilus influenzae does not affect phase variation rates at tetranucleotide or dinucleotide repeats - Sweetman, Moxon, et al. - 2005 (Show Context) Citation Context ...RecA and RecN. RecA and RecN have important roles in the repair of DNA damage which have been extensively characterized in UV damage experiments in many organisms, including E. coli and H. influenzae =-=(43, 50, 51, 77, 82)-=-. Further repair mechanisms are potentially afforded by the gene products of NTHI0493 and NTHI0495, which encode homologues of the cochaperone proteins HscA and HscB, respectively, and that have roles...