RIC: Research Interest Comparator

Smith, Alexandra, Ph.D.
Affiliation: Microbiology
Email: xandra.smith@utsouthwestern.edu
Home Page: not provided
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Expression of Borrelia burgdorferi OspC and DbpA is controlled by a RpoN-RpoS regulatory pathway.
A Hübner ... M V Norgard
Proc Natl Acad Sci U S A 2001 Oct; 98(22)12724-9.

Score: 0.941
Analysis of the ospC regulatory element controlled by the RpoN-RpoS regulatory pathway in Borrelia burgdorferi.
Xiaofeng F Yang ... Michael V Norgard
J Bacteriol 2005 Jul; 187(14)4822-9.

Score: 0.822
Mapping and characterization of the promoter elements of the regulatory nif genes rpoN, nifA1 and nifA2 in Rhodobacter capsulatus.
P Preker ... T A Bickle
Mol Microbiol 1992 Apr; 6(8)1035-47.

Score: 0.744
Control of gonococcal pilin-encoding gene expression in Escherichia coli.
J A Fyfe ... J K Davies
Gene 1993 Jan; 123(1)45-50.

Score: 0.714
Analysis of promoter elements involved in the transcriptional initiation of RpoS-dependent Borrelia burgdorferi genes.
Christian H Eggers ... Justin D Radolf
J Bacteriol 2004 Nov; 186(21)7390-402.

Score: 0.711
RpoS and RpoN are involved in the growth-dependent regulation of rfaH transcription and O antigen expression in Salmonella enterica serovar Typhi.
Mauricio Bittner ... Inés Contreras
Microb Pathog 2004 Jan; 36(1)19-24.

Score: 0.665
The -24/-12 promoter comes of age.
B Thöny ... H Hennecke
FEMS Microbiol Rev 1989 Dec; 5(4)341-57.

Score: 0.655
Azorhizobium caulinodans nitrogen fixation (nif/fix) gene regulation: mutagenesis of the nifA -24/-12 promoter element, characterization of a ntrA(rpoN) gene, and derivation of a model.
J Stigter ... F J de Bruijn
Mol Plant Microbe Interact 1993 Mar-Apr; 6(2)238-52.

Score: 0.655
RpoS is not central to the general stress response in Borrelia burgdorferi but does control expression of one or more essential virulence determinants.
Melissa J Caimano ... Justin D Radolf
Infect Immun 2004 Nov; 72(11)6433-45.

Score: 0.628
Compilation and analysis of sigma(54)-dependent promoter sequences.
H Barrios ... E Morett
Nucleic Acids Res 1999 Nov; 27(22)4305-13.

Score: 0.626
Alternate sigma factor RpoS is required for the in vivo-specific repression of Borrelia burgdorferi plasmid lp54-borne ospA and lp6.6 genes.
Melissa J Caimano ... Justin D Radolf
J Bacteriol 2005 Nov; 187(22)7845-52.

Score: 0.614
Structure and expression of the alternative sigma factor, RpoN, in Rhodobacter capsulatus; physiological relevance of an autoactivated nifU2-rpoN superoperon.
P J Cullen ... R G Kranz
Mol Microbiol 1994 Jan; 11(1)51-65.

Score: 0.589
Mutagenesis of the Bacillus subtilis "-12, -24" promoter of the levanase operon and evidence for the existence of an upstream activating sequence.
I Martin-Verstraete ... G Rapoport
J Mol Biol 1992 Jul; 226(1)85-99.

Score: 0.588
Regulation of the rpoN, ORF102 and ORF154 genes in Pseudomonas putida.
T Köhler ... S Harayama
FEMS Microbiol Lett 1994 Jan; 115(2-3)177-84.

Score: 0.578
Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the -24/-12 promoter element.
E M Souza ... M G Yates
Microbiology 2000 Jun; 146 ( Pt 6)()1407-18.

Score: 0.578
Altered stationary-phase response in a Borrelia burgdorferi rpoS mutant.
A F Elias ... P Rosa
J Bacteriol 2000 May; 182(10)2909-18.

Score: 0.576
Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli.
Y Takayanagi ... H Takahashi
Mol Gen Genet 1994 Jun; 243(5)525-31.

Score: 0.559
Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators.
V Shingler ... T Moore
J Bacteriol 1993 Mar; 175(6)1596-604.

Score: 0.539
Deletion analysis of the Klebsiella pneumoniae nitrogenase promoter: importance of spacing between conserved sequences around positions -12 and -24 for activation by the nifA and ntrC (glnG) products.
M Buck
J Bacteriol 1986 May; 166(2)545-51.

Score: 0.535
Insect saliva: an integrative approach.
Richard O Musser
Arch Insect Biochem Physiol 2005 Feb; 58(2)53.

Score: 0.533
Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440.
M I Ramos-González ... S Molin
J Bacteriol 1998 Jul; 180(13)3421-31.

Score: 0.530
Fis regulates transcriptional induction of RpoS in Salmonella enterica.
Matthew Hirsch ... Thomas Elliott
J Bacteriol 2005 Mar; 187(5)1568-80.

Score: 0.529
Ntr-like promoters and upstream regulatory sequence ftr are required for transcription of a developmentally regulated Caulobacter crescentus flagellar gene.
D A Mullin ... A Newton
J Bacteriol 1989 Jun; 171(6)3218-27.

Score: 0.528
Transcriptional and mutational analyses of the rpoN operon in Caulobacter crescentus.
R S Janakiraman ... Y V Brun
J Bacteriol 1997 Aug; 179(16)5138-47.

Score: 0.527
Identification of transcriptional start sites and the role of ppGpp in the expression of rpoS, the structural gene for the sigma S subunit of RNA polymerase in Escherichia coli.
R Lange ... R Hengge-Aronis
J Bacteriol 1995 Aug; 177(16)4676-80.

Score: 0.527
Involvement of the RpoN protein in the transcription of the oprE gene in Pseudomonas aeruginosa.
Y Yamano ... Y Komatsu
FEMS Microbiol Lett 1998 May; 162(1)31-7.

Score: 0.526
IHF- and RpoN-dependent regulation of hydrogenase expression in Bradyrhizobium japonicum.
L K Black ... R J Maier
Mol Microbiol 1995 May; 16(3)405-13.

Score: 0.525
Promoter substitution and deletion analysis of upstream region required for rpoS translational regulation.
C Cunning ... T Elliott
J Bacteriol 1998 Sep; 180(17)4564-70.

Score: 0.520
SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences.
Stephan Lacour ... Paolo Landini
J Bacteriol 2004 Nov; 186(21)7186-95.

Score: 0.520
Mapping sigma 54-RNA polymerase interactions at the -24 consensus promoter element.
Patricia C Burrows ... Siva R Wigneshweraraj
J Biol Chem 2003 Aug; 278(32)29728-43.

Score: 0.519
Regulation of the Caulobacter crescentus rpoN gene and function of the purified sigma 54 in flagellar gene transcription.
D K Anderson ... A Newton
Mol Gen Genet 1995 Mar; 246(6)697-706.

Score: 0.518
The Bradyrhizobium japonicum hsfA gene exhibits a unique developmental expression pattern in cowpea nodules.
H S Oh ... C I Cheon
Mol Plant Microbe Interact 2001 Nov; 14(11)1286-92.

Score: 0.517
In vivo genomic footprinting analysis reveals that the complex Bradyrhizobium japonicum fixRnifA promoter region is differently occupied by two distinct RNA polymerase holoenzymes.
H Barrios ... E Morett
Proc Natl Acad Sci U S A 1998 Feb; 95(3)1014-9.

Score: 0.515
RpoN of Rhizobium leguminosarum bv. viciae strain VF39SM plays a central role in FnrN-dependent microaerobic regulation of genes involved in nitrogen fixation.
S R Clark ... M F Hynes
Mol Gen Genet 2001 Jan; 264(5)623-33.

Score: 0.515
The symbiotic nitrogen fixation regulatory operon (fixRnifA) of Bradyrhizobium japonicum is expressed aerobically and is subject to a novel, nifA-independent type of activation.
B Thöny ... H Hennecke
Nucleic Acids Res 1987 Oct; 15(20)8479-99.

Score: 0.512
Regulation of expression of the paralogous Mlp family in Borrelia burgdorferi.
Xiaofeng F Yang ... Michael V Norgard
Infect Immun 2003 Sep; 71(9)5012-20.

Score: 0.511
Involvement of Pseudomonas putida RpoN sigma factor in regulation of various metabolic functions.
T Köhler ... K N Timmis
J Bacteriol 1989 Aug; 171(8)4326-33.

Score: 0.509
Allelic exchange mutagenesis of rpoN encoding RNA-polymerase sigma54 subunit in Helicobacter pylori.
R Fujinaga ... M Shirai
J Infect Chemother 2001 Sep; 7(3)148-55.

Score: 0.507
Stationary-phase regulation of RpoS translation in Escherichia coli.
Matthew Hirsch ... Thomas Elliott
J Bacteriol 2005 Nov; 187(21)7204-13.

Score: 0.504
Central regulatory role for the RpoS sigma factor in expression of Salmonella dublin plasmid virulence genes.
C Y Chen ... D G Guiney
J Bacteriol 1995 Sep; 177(18)5303-9.

Score: 0.504
RpoN (sigma 54) is required for conversion of phenol to catechol in Acinetobacter calcoaceticus.
S Ehrt ... W Hillen
J Bacteriol 1994 Jun; 176(12)3493-9.

Score: 0.500
Bradyrhizobium japonicum has two differentially regulated, functional homologs of the sigma 54 gene (rpoN).
I Kullik ... H M Fischer
J Bacteriol 1991 Feb; 173(3)1125-38.

Score: 0.500
Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium.
L Brown ... T Elliott
J Bacteriol 1997 Feb; 179(3)656-62.

Score: 0.497
Positive selection for loss of RpoS function in Escherichia coli.
Guozhu Chen ... Herb E Schellhorn
Mutat Res 2004 Oct; 554(1-2)193-203.

Score: 0.496
TetR family member psrA directly binds the Pseudomonas rpoS and psrA promoters.
Milan Kojic ... Vittorio Venturi
J Bacteriol 2002 Apr; 184(8)2324-30.

Score: 0.493
Cascade regulation of the toluene-3-monooxygenase operon (tbuA1UBVA2C) of Burkholderia pickettii PKO1: role of the tbuA1 promoter (PtbuA1) in the expression of its cognate activator, TbuT.
A M Byrne ... R H Olsen
J Bacteriol 1996 Nov; 178(21)6327-37.

Score: 0.493
Regulation of quorum sensing by RpoS in Pseudomonas aeruginosa.
M Whiteley ... E P Greenberg
J Bacteriol 2000 Aug; 182(15)4356-60.

Score: 0.484
Enterobacter cloacae rpoS promoter and gene organization.
Juana María Navarro-Lloréns ... Antonio Tormo
Arch Microbiol 2002 Dec; 179(1)33-41.

Score: 0.484
The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing.
Martin Schuster ... E P Greenberg
Mol Microbiol 2004 Feb; 51(4)973-85.

Score: 0.484
Cloning, analysis and expression of an rpoS homologue gene from Pseudomonas aeruginosa PAO1.
K Tanaka ... H Takahashi
Gene 1994 Dec; 150(1)81-5.

Score: 0.482
Current aspects of Lyme disease and other Borrelia burgdorferi infections.
B W Berger
Dermatol Clin 1997 Apr; 15(2)247-55.

Score: 0.481
Identification of cis-acting DNA sequences involved in the transcription of the virulence regulatory gene spvR in Salmonella typhimurium.
L Kowarz ... F Norel
Mol Gen Genet 1996 May; 251(2)225-35.

Score: 0.478
Role of rpoS in stress survival and virulence of Vibrio cholerae.
F H Yildiz ... G K Schoolnik
J Bacteriol 1998 Feb; 180(4)773-84.

Score: 0.477
The alternative sigma factor RpoN regulates the quorum sensing gene rhlI in Pseudomonas aeruginosa.
Lyndal S Thompson ... Staffan Kjelleberg
FEMS Microbiol Lett 2003 Mar; 220(2)187-95.

Score: 0.473
Overlapping promoters for two different RNA polymerase holoenzymes control Bradyrhizobium japonicum nifA expression.
H Barrios ... E Morett
J Bacteriol 1995 Apr; 177(7)1760-5.

Score: 0.472
The Legionella pneumophila rpoS gene is required for growth within Acanthamoeba castellanii.
L M Hales ... H A Shuman
J Bacteriol 1999 Aug; 181(16)4879-89.

Score: 0.472
DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription.
N Majdalani ... S Gottesman
Proc Natl Acad Sci U S A 1998 Oct; 95(21)12462-7.

Score: 0.469
An upstream element containing an ETS binding site is crucial for transcription of the human presenilin-1 gene.
M Pastorcic ... H K Das
J Biol Chem 1999 Aug; 274(34)24297-307.

Score: 0.469
Regulation of rpoS gene expression in Pseudomonas: involvement of a TetR family regulator.
M Kojic ... V Venturi
J Bacteriol 2001 Jun; 183(12)3712-20.

Score: 0.467
Negative control of rpoS expression by phosphoenolpyruvate: carbohydrate phosphotransferase system in Escherichia coli.
C Ueguchi ... T Mizuno
J Bacteriol 2001 Jan; 183(2)520-7.

Score: 0.467
Stationary phase-specific expression of the fic gene in Escherichia coli K-12 is controlled by the rpoS gene product (sigma 38).
R Utsumi ... M Kawamukai
FEMS Microbiol Lett 1993 Nov; 113(3)273-8.

Score: 0.466
Controlled induction of the RpoS regulon in Escherichia coli, using an RpoS-expressing plasmid.
Guozhu Chen ... Herb E Schellhorn
Can J Microbiol 2003 Dec; 49(12)733-40.

Score: 0.466
Nucleotide sequence of the rpoN (hno) gene region of Alcaligenes eutrophus: evidence for a conserved gene cluster.
J Warrelmann ... B Friedrich
Arch Microbiol 1992 ; 158(2)107-14.

Score: 0.466
m-xylene-responsive Pu-PnifH hybrid sigma54 promoters that overcome physiological control in Pseudomonas putida KT2442.
Manuel Carmona ... Víctor de Lorenzo
J Bacteriol 2005 Jan; 187(1)125-34.

Score: 0.465
Interdependence of environmental factors influencing reciprocal patterns of gene expression in virulent Borrelia burgdorferi.
X Yang ... M V Norgard
Mol Microbiol 2000 Sep; 37(6)1470-9.

Score: 0.465
Characterizing wild-type and mutant promoters of the tetracycline resistance gene in pBR313.
R L Rodriguez ... H W Boyer
Nucleic Acids Res 1979 Jul; 6(10)3267-87.

Score: 0.465
Analysis of rpoS mRNA in Salmonella dublin: identification of multiple transcripts with growth-phase-dependent variation in transcript stability.
G Paesold ... M Krause
J Bacteriol 1999 Feb; 181(4)1264-8.

Score: 0.464
Transcriptional control of gonococcal pilE expression: involvement of an alternate sigma factor.
S Boyle-Vavra ... H S Seifert
Gene 1993 Dec; 137(2)233-6.

Score: 0.463
The Escherichia coli SOS gene sbmC is regulated by H-NS and RpoS during the SOS induction and stationary growth phase.
T J Oh ... I G Kim
Biochem Biophys Res Commun 2001 Nov; 288(4)1052-8.

Score: 0.463
Molecular cloning and functional analysis of an rpoS homologue gene from Vibrio cholerae N86.
K Hiratsu ... K Makino
Genes Genet Syst 1997 Apr; 72(2)115-8.

Score: 0.462
Identification of conserved, RpoS-dependent stationary-phase genes of Escherichia coli.
H E Schellhorn ... L Chang
J Bacteriol 1998 Dec; 180(23)6283-91.

Score: 0.461
Efficient translation of the RpoS sigma factor in Salmonella typhimurium requires host factor I, an RNA-binding protein encoded by the hfq gene.
L Brown ... T Elliott
J Bacteriol 1996 Jul; 178(13)3763-70.

Score: 0.460
The Lyme disease vaccine candidate outer surface protein A (OspA) in a formulation compatible with human use protects mice against natural tick transmission of B. burgdorferi.
W T Golde ... Y Lobet
Vaccine 1995 Apr; 13(5)435-41.

Score: 0.459
Differential spectrum of mutations that activate the Escherichia coli bgl operon in an rpoS genetic background.
Sudha Moorthy ... S Mahadevan
J Bacteriol 2002 Jul; 184(14)4033-8.

Score: 0.459
Regulation of RpoS proteolysis in Escherichia coli: the response regulator RssB is a recognition factor that interacts with the turnover element in RpoS.
G Becker ... R Hengge-Aronis
Proc Natl Acad Sci U S A 1999 May; 96(11)6439-44.

Score: 0.459
bptA (bbe16) is essential for the persistence of the Lyme disease spirochete, Borrelia burgdorferi, in its natural tick vector.
Andrew T Revel ... Michael V Norgard
Proc Natl Acad Sci U S A 2005 May; 102(19)6972-7.

Score: 0.458
The live oral typhoid vaccine Ty21a is a rpoS mutant and is susceptible to various environmental stresses.
V Robbe-Saule ... F Norel
FEMS Microbiol Lett 1995 Feb; 126(2)171-6.

Score: 0.457
Molecular analysis of the operon which encodes the RNA polymerase sigma factor sigma 54 of Escherichia coli.
D H Jones ... C M Thomas
Microbiology 1994 May; 140 ( Pt 5)()1035-43.

Score: 0.456
Active recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and alphaCTD.
G Bertoni ... V de Lorenzo
EMBO J 1998 Sep; 17(17)5120-8.

Score: 0.454
The Escherichia coli histone-like protein HU regulates rpoS translation.
A Balandina ... J Rouviere-Yaniv
Mol Microbiol 2001 Feb; 39(4)1069-79.

Score: 0.454
Role of rpoS in the regulation of Salmonella plasmid virulence (spv) genes.
P Heiskanen ... M Rhen
FEMS Microbiol Lett 1994 Oct; 123(1-2)125-30.

Score: 0.453
The LysR-like regulator LeuO in Escherichia coli is involved in the translational regulation of rpoS by affecting the expression of the small regulatory DsrA-RNA.
E Klauck ... R Hengge-Aronis
Mol Microbiol 1997 Aug; 25(3)559-69.

Score: 0.453
Cloning and characterization of Planctomyces limnophilus rpoN: complementation of a Salmonella typhimurium rpoN mutant strain.
B A Leary ... T R Hoover
Gene 1998 Oct; 221(1)151-7.

Score: 0.453
Transcriptional activation of the Klebsiella pneumoniae nifLA promoter by NTRC is face-of-the-helix dependent and the activator stabilizes the interaction of sigma 54-RNA polymerase with the promoter.
S D Minchin ... R A Dixon
EMBO J 1989 Nov; 8(11)3491-9.

Score: 0.453
The RpoN-box motif of the RNA polymerase sigma factor sigma N plays a role in promoter recognition.
M Taylor ... M Merrick
Mol Microbiol 1996 Dec; 22(5)1045-54.

Score: 0.451
Characterization of the promoter and upstream activating sequence from the Pseudomonas alcaligenes lipase gene.
M Cox ... W J Quax
J Biotechnol 2001 Mar; 86(1)9-17.

Score: 0.451
Role of GacA, LasI, RhlI, Ppk, PsrA, Vfr and ClpXP in the regulation of the stationary-phase sigma factor rpoS/RpoS in Pseudomonas.
Iris Bertani ... Vittorio Venturi
Arch Microbiol 2003 Oct; 180(4)264-71.

Score: 0.451
Isolation and characterization of the nifUSVW-rpoN gene cluster from Rhodobacter sphaeroides.
W G Meijer ... F R Tabita
J Bacteriol 1992 Jun; 174(12)3855-66.

Score: 0.451
The rpoS gene of Erwinia carotovora: gene organization and functional expression in E. coli.
M J Calcutt ... A Eisenstark
FEMS Microbiol Lett 1998 Feb; 159(2)275-81.

Score: 0.451
The pathogenic neisseriae contain an inactive rpoN gene and do not utilize the pilE sigma54 promoter.
L Laskos ... J K Davies
Gene 1998 Feb; 208(1)95-102.

Score: 0.450
Relationships between H-NS, sigma S, SpvR and growth phase in the control of spvR, the regulatory gene of the Salmonella plasmid virulence operon.
V Robbe-Saule ... F Norel
Mol Gen Genet 1997 Oct; 256(4)333-47.

Score: 0.449
Essential role for OspA/B in the life cycle of the Lyme disease spirochete.
Xiaofeng F Yang ... Michael V Norgard
J Exp Med 2004 Mar; 199(5)641-8.

Score: 0.448
Identification and characterization of the Erwinia amylovora rpoS gene: RpoS is not involved in induction of fireblight disease symptoms.
M Anderson ... J A Eastgate
J Bacteriol 1998 Dec; 180(24)6789-92.

Score: 0.448
Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli.
Matthew Hirsch ... Thomas Elliott
J Bacteriol 2002 Sep; 184(18)5077-87.

Score: 0.447
The rpoS mutant allele of Salmonella typhi Ty2 is identical to that of the live typhoid vaccine Ty21a.
V Robbe-Saule ... F Norel
FEMS Microbiol Lett 1999 Jan; 170(1)141-3.

Score: 0.446
Vaccination against Lyme borreliosis.
P Wahlberg
Ann Med 1999 Aug; 31(4)233-5.

Score: 0.445
Analysis of the rpoN locus in the plant pathogenic bacterium, Pseudomonas syringae pv. glycinea.
F J Alarcón-Chaidez ... C L Bender
DNA Seq 2001 Jul; 12(1)77-84.

Score: 0.443
Borrelia burgdorferi sigma54 is required for mammalian infection and vector transmission but not for tick colonization.
Mark A Fisher ... Frank C Gherardini
Proc Natl Acad Sci U S A 2005 Apr; 102(14)5162-7.

Score: 0.443
Upstream regulatory sequence for transcriptional activator XylR in the first operon of xylene metabolism on the TOL plasmid.
S Inouye ... T Nakazawa
J Mol Biol 1990 Nov; 216(2)251-60.

Score: 0.442
Control of Escherichia coli type 1 fimbrial gene expression in stationary phase: a negative role for RpoS.
S L Dove ... C J Dorman
Mol Gen Genet 1997 Mar; 254(1)13-20.

Score: 0.442
Abstract:
Lyme borreliosis (Lyme disease), caused by Borrelia burgdorferi, remains the most prevalent arthropod-borne infection in the United States. In addition to its clinical importance, many features of Lyme disease continue to be poorly understood, including those traits of B. burgdorferi that allow it to subsist in nature in both ticks and mammals. It is now widely held that the spirochete must undergo profound adaptive changes in order to accommodate its two very diverse niches in nature. Clearly, elucidating key aspects of such adaptive responses is critical for understanding many enigmatic features of B. burgdorferi related to vector colonization, spirochete transmission, mammalian infection, Lyme disease progression (pathogenesis), and bacterial chronicity. It is now well documented that key membrane lipoproteins of B. burgdorferi are vital for maintaining the spirochete in its enzootic transmission cycle between ticks and mammals. We were the first to report that the alternative sigma factor RpoS regulates the expression of a number of these lipoproteins, two of which are outer surface protein C (OspC) and A (OspA). However, we also have contended that RpoS first must be activated by another transcription factor, RpoN (resulting in an RpoN-RpoS regulatory network), before RpoS can promote the expression of these virulence-associated lipoproteins. In this regard, we have hypothesized that RpoN directly controls the expression of RpoS by binding to the rpoS promoter. Bases -78 to -63 upstream of the rpoS open reading frame comprise a theoretical RpoN-dependent -24/-12 promoter (5'-TGGCACAGTTTTTGCA-3'). However, to date there have been little experimental data to substantiate such predictions. 5'-RACE (Rapid amplification of cDNA 5' ends) was used to determine the transcriptional initiation site for rpoS. 5'-RACE experiments have revealed that the initiation of transcription for rpoS is located at residue -50 upstream of rpoS and 13 base pairs downstream of the putative promoter. This is the region we had predicted to be involved, inasmuch as in most cases, initiation of transcription tends to be at nucleotides 11, 12, or 13 downstream of the promoter. To further confirm the significance of the predicted RpoN binding site we determined the effect of mutations in the promoter sequence on rpoS transcription. Site-directed mutagenesis of plasmids containing the wild-type rpoS promoter was carried out to yield the following mutations: G -76 T and C -64 A. An RpoS-deficient mutant of B. burgdorferi was complemented with the mutant plasmids, and the rpoS transcripts within the resulting borrelial strains were assessed by quantitative real-time RT-PCR. Complementation of the RpoS-deficient mutant with the wild-type rpoS promoter resulted in rpoS transcript levels of 77% (0.62-0.95%) relative to normal expression (87-116%). The G -76 T mutation in the -24 region of the rpoS promoter resulted in decreased rpoS transcription of 36% (23-55%). This latter result agreed with our hypothesis, in that the -24 region appears to be essential for binding of RpoN (i.e., a mutation in this region should result in decreased RpoN binding). Although not anticipated, the C -64 A mutation in the -12 region of the rpoS promoter resulted in increased rpoS transcription of 146% (124-171%). This -12 region is involved in early melting of the DNA, thereby resulting in an open complex form, from which transcription can then proceed. Although not universal, mutations in this region have been shown in some circumstances to result in increased transcription of RpoN-dependent genes of enteric bacteria. There appears to be a stringent requirement for the -24/-12 elements to be on the same face of the DNA helix, inasmuch as deletions of one or more nucleotides in enteric bacteria abolish RpoN-dependent promoter function. Recently, we have constructed two such deletion mutations in the rpoS promoter, and complementation experiments using the RpoS-deficient mutant of B. burgdorferi are in progress. We have expended significant efforts towards preparing soluble recombinant RpoN protein. Recombinant borrelial RpoN protein is necessary for experiments to show evidence of direct binding of the RpoN protein to the rpoS promoter region. Previous results from our lab have shown that E. coli RpoN protein specifically binds to the borrelial rpoS promoter in a dose-dependent fashion (in electrophoretic mobility gel shift assays [EMSAs]). Success in the purification of borrelial RpoN, however, has been problematic, inasmuch as borrelial RpoN tends to be insoluble and also negatively affects the growth of the E. coli host harboring the borrelial rpoN gene for hyperexpression. To circumvent this obstacle, we have recently had success in constructing an MBP fusion containing the C-terminal portion of borrelial RpoN. In this truncated fusion protein, the activator-interacting domain is not present, but both the putative core-binding and presumptive DNA-binding domains remain intact. EMSAs are now being developed and performed using this fusion protein to assess the direct binding of borrelial RpoN to the borrelial rpoS promoter. Understanding the molecular details of the RpoN-RpoS regulatory pathway has far reaching implications for elucidating many aspects of B. burgdorferi gene regulation, particularly as it pertains to governing infectivity and virulence expression. Discerning the elements of this pathway, and the molecular mechanisms involved, also has the potential to uncover regulatory and virulence-associated genes that contribute to many as yet unknown aspects of B. burgdorferi's complex parasitic strategy. All of these issues relate directly to efforts towards vaccine development, inasmuch as the regulation of virulence-associated genes needs to be understood before a rational approach to vaccine development can be realized.
Keywords extracted from the abstract: [ eliminated words list ]
Count Word
19.481 -12
19.481 -24
6.000 -50
6.000 -63
12.198 -64
12.198 -76
6.000 -78
8.665 -race
6.000 -tggcacagtttttgca-3
6.000 124-171
6.000 23-55
6.000 62-0
6.000 87-116
6.000 [emsas]
3.087 abolish
3.211 accommodate
1.675 activated
6.000 activator-interacting
4.968 adaptive
1.265 addition
2.206 affects
2.732 agreed
2.025 allow
1.777 alternative
2.132 amplification
2.838 anticipated
3.338 appears
1.396 approach
4.387 arthropod-borne
4.695 aspects
Count Word
1.813 assays
1.668 assess
1.542 assessed
3.289 bacteria
1.148 bacterial
1.420 base
2.376 bases
4.065 binding
2.104 binds
2.845 borrelia
21.066 borrelial
3.503 borreliosis
12.983 burgdorferi
2.160 c-terminal
1.721 carried
0.984 cases
1.399 caused
1.805 cdna
1.053 changes
3.424 chronicity
2.559 circumstances
3.472 circumvent
1.992 clearly
0.816 clinical
2.765 coli
2.565 colonization
5.130 complementation
3.110 complemented
2.525 complex
2.845 comprise
Count Word
2.128 confirm
2.169 constructed
3.238 constructing
3.004 containing
4.448 contended
2.400 continue
1.831 contribute
1.388 controls
4.566 core-binding
1.660 critical
1.557 cycle
0.847 data
2.231 date
2.535 decreased
1.834 deletion
2.433 deletions
2.565 details
1.359 determine
1.283 determined
1.308 developed
2.033 development
3.130 direct
3.580 directly
4.203 discerning
2.168 disease
2.273 diverse
1.664 dna
1.757 dna-binding
2.114 documented
1.563 domain
Count Word
1.874 domains
2.064 dose-dependent
4.694 downstream
1.222 early
0.890 effect
4.629 efforts
2.385 electrophoretic
3.517 elements
6.458 elucidating
4.383 emsas
2.512 ends
3.669 enigmatic
5.440 enteric
3.605 enzootic
1.630 essential
3.858 expended
1.303 experimental
4.130 experiments
3.315 expression
2.163 face
1.973 factor
2.039 far
2.331 fashion
3.199 features
2.254 first
1.204 following
1.398 form
2.348 frame
1.313 further
4.396 fusion
Count Word
1.515 gel
1.825 gene
3.114 genes
2.907 governing
0.909 growth
2.995 harboring
2.499 held
2.480 helix
1.776 host
4.351 hyperexpression
1.717 hypothesis
2.355 hypothesized
1.803 implications
1.705 importance
11.660 inasmuch
1.327 including
1.897 increased
2.396 infection
2.798 infectivity
5.226 initiation
2.846 insoluble
1.794 intact
3.737 involved
1.930 issues
3.816 key
2.175 lab
1.919 latter
0.931 levels
4.823 lipoproteins
1.709 little
Count Word
1.773 located
8.996 lyme
2.393 maintaining
1.879 mammalian
4.681 mammals
2.759 mbp
1.429 mechanisms
2.949 melting
1.050 membrane
2.140 mobility
1.923 molecular
0.902 more
2.157 most
3.522 must
1.979 mutagenesis
5.124 mutant
3.856 mutation
5.101 mutations
3.442 nature
1.717 necessary
1.924 needs
2.343 negatively
2.040 network
3.886 niches
1.028 normal
4.944 now
3.799 nucleotides
3.319 obstacle
3.556 open
1.503 order
Count Word
3.694 ospa
4.019 ospc
2.006 outer
2.107 pairs
2.470 parasitic
1.752 particularly
1.848 pathogenesis
3.215 pathway
1.222 performed
4.032 pertains
3.684 plasmids
2.168 poorly
2.123 portion
1.292 potential
3.787 predicted
2.553 predictions
2.982 preparing
2.982 presumptive
2.476 prevalent
1.550 previous
2.970 problematic
3.031 proceed
2.514 profound
2.146 progress
1.766 progression
2.216 promote
9.164 promoter
3.024 protein
1.218 purification
4.124 putative
Count Word
1.718 quantitative
1.579 rapid
2.657 rational
2.503 reaching
2.044 reading
2.540 real-time
2.967 realized
3.435 recently
2.721 recombinant
2.108 regard
5.919 region
2.349 regulates
2.674 regulation
4.902 regulatory
2.659 relate
1.284 related
1.501 relative
2.078 remain
1.835 remains
0.947 report
2.301 requirement
2.088 residue
1.318 responses
4.183 resulted
4.682 resulting
0.741 results
1.318 revealed
22.536 rpon
15.234 rpon-dependent
11.899 rpon-rpos
Count Word
22.701 rpos
15.472 rpos-deficient
2.279 rt-pcr
1.283 same
0.904 sequence
2.030 shift
2.342 sigma
1.765 significance
0.990 significant
2.796 site
2.291 site-directed
1.931 soluble
1.887 specifically
10.115 spirochete
0.575 states
1.285 strains
1.997 strategy
3.152 stringent
5.131 subsist
3.437 substantiate
4.158 success
1.231 surface
6.096 tends
1.972 theoretical
2.236 thereby
5.537 ticks
4.141 towards
2.503 traits
2.328 transcript
6.060 transcription
Count Word
1.961 transcriptional
2.141 transcripts
3.270 transmission
1.881 truncated
3.549 uncover
2.245 undergo
3.638 understanding
4.592 understood
0.576 united
2.600 universal
1.878 unknown
4.575 upstream
0.946 used
1.801 using
3.520 vaccine
2.098 vector
2.097 virulence
10.959 virulence-associated
2.321 vital
2.045 widely
3.757 wild-type
2.047 yield
RIC Statistics:
Extraction Method: Keyword Count with Lexical Variants Added
Eliminated words list: MedlinePlus List
Similarity Method: Weighted keyword count
Weighting Method: Term Frequency * Inverse Document Frequency
Database: Medline abstracts (1967 - Present)
Publication Type: All
Score Calculation Method: Cosine Similarity Method
Sort by: Score
Submission date and time: 3-8-2006, 13:21:40
Computation time: 00:00:04
Last updated: Wednesday, 08-Mar-2006 13:21:44 CST