bluuebunny/crossref_metadata_2025_split huggingface dataset:
The YeastCandida albicansBinds Complement Regulators Factor H and FHL-1
Authors: Meri T. , Hartmann A. , Lenk D. , Eck R. , Würzner R. , Hellwage J. , Meri S. , Zipfel P. F. 
Published: October 2002

ABSTRACTThe human facultative pathogenic yeastCandida albicanscauses mucocutaneous infections and is the major cause of opportunistic fungal infections in immunocompromised patients.C. albicansactivates both the alternative and classical pathway of the complement system. The aim of this study was to assay whetherC. albicansbinds human complement regulators in order to control complement activation at its surface. We observed binding of two central complement regulators, factor H and FHL-1, from normal human serum toC. albicansby adsorption assays, immunostaining, and fluorescence-activated cell sorter (FACS) analyses. Specificity of acquisition was further confirmed in direct binding assays with purified proteins. The surface-attached regulators maintained their complement regulatory activities and mediated factor I-dependent cleavage of C3b. Adsorption assays with recombinant deletion mutant proteins were used to identify binding domains. Two binding sites were localized. One binding domain common to both factor H and FHL-1 is located in the N-terminal short consensus repeat domains (SCRs) 6 and 7, and the other one located in C-terminal SCRs 19 and 20 is unique to factor H. These data indicate that by surface acquisition of host complement regulators, the human pathogenic yeastC. albicansis able to regulate alternative complement activation at its surface and to inactivate toxic complement activation products.
Borrelia burgdorferi erp
(
ospE
-Related) Gene Sequences Remain Stable during Mammalian Infection
Authors: Stevenson Brian 
Published: October 2002

ABSTRACT

A number of studies have indicated that
Borrelia burgdorferi erp
genes need not vary during vertebrate infection. However, it was recently reported that a
B. burgdorferi
bacterium reisolated from an infected mouse evidenced mutation and recombination events in several
erp
genes. Reexamination of that reisolate indicates that the previously reported changes were no doubt artifacts of the PCR processes originally used to clone those DNAs. Thus, no evidence has been found of
erp
gene variation during mammalian infection.
Shiga Toxin 2 Induces Macrophage-Granulocyte Colonies from Human Bone Marrow and Cord Blood Stem Cells
Authors: Chiyoda Shin , Takeda Tae , Aoki Yosuke 
Published: October 2002

ABSTRACT
Addition of Shiga toxin 2 to human bone marrow or cord blood cell culture induced macrophage-granulocyte colonies. Although Shiga toxin 2 alone induced colonies mainly composed of macrophages, it induced colonies mainly consisting of granulocytes when combined with physiological doses of interleukin-1β, granulocyte colony-stimulating factor, or stem cell factor with interleukin-3.
Neutrophil-Mediated Mycobacteriocidal Immunity in the Lung duringMycobacterium bovisBCG Infection in C57BL/6 Mice
Authors: Fulton S. A. , Reba S. M. , Martin T. D. , Boom W. H. 
Published: October 2002

ABSTRACTAlthough neutrophils have been identified as sources of inflammatory cytokines and chemokines, little is known about their immunologic function during mycobacterial infection in the lungs. In this study, we examined the growth ofMycobacterium bovisBCG in the lungs under experimental conditions that altered neutrophil recruitment to the lungs. Depletion and recruitment of neutrophils was associated with respective increases and decreases inM. bovisBCG growth. Thus, neutrophils may enhance mycobacteriocidal immunity in the lungs.
Comparison of Genome Structures of Vibrios, Bacteria Possessing Two Chromosomes
Authors: Tagomori Kenichi , Iida Tetsuya , Honda Takeshi 
Published: October 2002

ABSTRACT

Vibrios are gram-negative γ-proteobacteria which are ubiquitous in marine and estuarine environments. Recently, we demonstrated that some, if not all,
Vibrio
species have two circular chromosomes. The whole genome sequence of
Vibrio cholerae
N16961 has been reported. In this study, we constructed a physical and genetic map of the genome of Kanagawa phenomenon-positive
Vibrio parahaemolyticus
strain KX-V237 and compared it with those of
V. parahaemolyticus
AQ4673 and
V. cholerae
N16961. The genome of KX-V237 comprised two circular chromosomes (3.3 and 1.9 Mb), similar to the structure of the AQ4673 genome. The relative positions of the genes on the genomes were well conserved in the two strains, but a large inversion on the large chromosomes, probably symmetric around the replication origin, was suggested. Although the sizes of the large chromosomes of KX-V237 and
V. cholerae
N16961 were similar, the sizes of the small chromosomes were very different. Unlike N16961, the superintegron of KX-V237 was located on the large chromosome. Comparison of the genetic maps of the chromosomes of KX-V237 and
V. cholerae
N16961 revealed that most of the open reading frames (ORFs) present on the large chromosome of the
V. cholerae
strain had homologues on the large chromosome of the
V. parahaemolyticus
strain and that most of the ORFs on the small chromosome of N16961 were present on the small chromosome of KX-V237. The difference in the orders of the ORFs on the chromosomes of N16961 and KX-V237 implies that numerous and frequent genetic exchanges have occurred intrachromosomally rather than interchromosomally.
icaR
Encodes a Transcriptional Repressor Involved in Environmental Regulation of
ica
Operon Expression and Biofilm Formation in
Staphylococcus epidermidis
Authors: Conlon Kevin M. , Humphreys Hilary , O'Gara James P. 
Published: October 2002

ABSTRACT

Biofilm formation in
Staphylococcus epidermidis
is dependent upon the
ica
operon-encoded polysaccharide intercellular adhesin, which is subject to phase-variable and environmental regulation. The
icaR
gene, located adjacent to the
ica
operon, appears to be a member of the
tetR
family of transcriptional regulators. In the reference strain RP62A, reversible inactivation of the
ica
operon by IS
256
accounts for 25 to 33% of phase variants. In this study,
icaA
and
icaR
regulation were compared in RP62A and a biofilm-forming clinical isolate, CSF41498, in which IS
256
is absent. Predictably,
ica
operon expression was detected only in wild-type CSF41498 and RP62A but not in non-IS
256
-generated phase variants. In contrast, the
icaR
gene was not expressed in RP62A phase variants but was expressed in CSF41498 variants. An
icaR
::Em
r
insertion mutation in CSF41498 resulted in an at least a 5.8-fold increase in
ica
operon expression but did not significantly alter regulation of the
icaR
gene itself. Activation of
ica
operon transcription by ethanol in CSF41498 was
icaR
dependent. In contrast, a small but significant induction of
ica
by NaCl and glucose (NaCl-glucose) was observed in the
icaR
::Em
r
mutant. In addition, transcription of the
icaR
gene itself was not significantly affected by NaCl-glucose but was repressed by ethanol. Expression of the
ica
operon was induced by ethanol or NaCl-glucose in phase variants of CSF41498 (
icaR
+
) but not in RP62A variants (
icaR
deficient). These data indicate that
icaR
encodes a repressor of
ica
operon transcription required for ethanol but not NaCl-glucose activation of
ica
operon expression and biofilm formation.
Developmental Regulation of theStreptomyces lividans ramGenes: Involvement of RamR in Regulation of theramCSABOperon
Authors: Keijser Bart J. F. , van Wezel Gilles P. , Canters Gerard W. , Vijgenboom Erik 
Published: October 2002

ABSTRACTStreptomycetes are filamentous soil bacteria that produce spores through a complex process of morphological differentiation. Theramcluster plays an important part during the development. Theramgenes encode a membrane-bound kinase (RamC), a small protein (RamS), components of an ABC transporter (RamAB), and a response regulator (RamR). While the introduction of an extra copy of theramcluster accelerates development inStreptomyces lividans,ramABRdisruption mutants are unable to produce aerial hyphae and spores. The developmental regulation oframgene transcription was analyzed. Transcription of theramgenes occurred only on solid rich media and not on minimal media. TheramRgene is transcribed from a single promoter during all growth stages, with the highest levels during aerial growth. TheramCSABgenes comprise one operon and are transcribed from one principal promoter, P1, directly upstream oframC. Transcription oframCSABwas already observed during vegetative growth, but was strongly upregulated upon initiation of formation of aerial hyphae and was decreased during late stages of development. A large inverted repeat located downstream oframSterminated the majority of transcripts. The introduction oframRon a multicopy vector inS. lividansstrongly induced P1 activity, while disruption of this regulator eliminated all P1 promoter activity. This shows thatramRis a crucial activator oframCSABtranscription. Importantly, inbldA,bldB,bldD, orbldHmutants,ramRandramCSABare not transcribed, whileramgene transcription was observed in the earliestwhimutant,whiG. This indicates that the transcription of theramgenes marks the transition from vegetative to aerial growth.
Purification, Overproduction, and Partial Characterization of β-RFAP Synthase, a Key Enzyme in the Methanopterin Biosynthesis Pathway†
Authors: Scott Joseph W. , Rasche Madeline E. 
Published: October 2002

ABSTRACT

Methanopterin is a folate analog involved in the C
1
metabolism of methanogenic archaea, sulfate-reducing archaea, and methylotrophic bacteria. Although a pathway for methanopterin biosynthesis has been described in methanogens, little is known about the enzymes and genes involved in the biosynthetic pathway. The enzyme β-ribofuranosylaminobenzene 5′-phosphate synthase (β-RFAP synthase) catalyzes the first unique step to be identified in the pathway of methanopterin biosynthesis, namely, the condensation of
p
-aminobenzoic acid with phosphoribosylpyrophosphate to form β-RFAP, CO
2
, and inorganic pyrophosphate. The enzyme catalyzing this reaction has not been purified to homogeneity, and the gene encoding β-RFAP synthase has not yet been identified. In the present work, we report on the purification to homogeneity of β-RFAP synthase. The enzyme was purified from the methane-producing archaeon
Methanosarcina thermophila
, and the N-terminal sequence of the protein was used to identify corresponding genes from several archaea, including the methanogen
Methanococcus jannaschii
and the sulfate-reducing archaeon
Archaeoglobus fulgidus
. The putative β-RFAP synthase gene from
A. fulgidus
was expressed in
Escherichia coli
, and the enzymatic activity of the recombinant gene product was verified. A BLAST search using the deduced amino acid sequence of the β-RFAP synthase gene identified homologs in additional archaea and in a gene cluster required for C
1
metabolism by the bacterium
Methylobacterium extorquens
. The identification of a gene encoding a potential β-RFAP synthase in
M. extorquens
is the first report of a putative methanopterin biosynthetic gene found in the
Bacteria
and provides evidence that the pathways of methanopterin biosynthesis in
Bacteria
and
Archaea
are similar.
DksA Affects ppGpp Induction of RpoS at a Translational Level
Authors: Brown Larissa , Gentry Daniel , Elliott Thomas , Cashel Michael 
Published: October 2002

ABSTRACTThe RpoS sigma factor (also called σSor σ38) is known to regulate at least 50 genes in response to environmental sources of stress or during entry into stationary phase. Regulation of RpoS abundance and activity is complex, with many factors participating at multiple levels. One factor is the nutritional stress signal ppGpp. The absence of ppGpp blocks or delays the induction ofrpoSduring entry into stationary phase. Artificially inducing ppGpp, without starvation, is known to inducerpoSduring the log phase 25- to 50-fold. Induction of ppGpp is found to have only minor effects onrpoStranscript abundance or on RpoS protein stability; instead, the efficiency ofrpoSmRNA translation is increased by ppGpp as judged by both RpoS pulse-labeling and promoter-independent effects onlacZfusions. DksA is found to affect RpoS abundance in a manner related to ppGpp. DeletingdksAblocksrpoSinduction by ppGpp. Overproduction of DksA inducesrpoSbut not ppGpp. DeletingdksA neither alters regulation of ppGpp in response to amino acid starvation nor nullifies the inhibitory effects of ppGpp on stable RNA synthesis. Although this suggests thatdksAis epistatic to ppGpp, inducing ppGpp does not induce DksA. AdksAdeletion does display a subset of the same multiple-amino-acid requirements found for ppGpp0mutants, but overproducing DksA does not satisfy ppGpp0requirements. Sequenced spontaneous extragenic suppressors ofdksApolyauxotrophy are frequently the same T563PrpoBallele that suppresses a ppGpp0phenotype. We propose that DksA functions downstream of ppGpp but indirectly regulatesrpoSinduction.
Suppressive Subtractive Hybridization Detects Extensive Genomic Diversity in
Thermotoga maritima
Authors: Nesbø Camilla L. , Nelson Karen E. , Doolittle W. Ford 
Published: October 2002

ABSTRACT

Comparisons between genomes of closely related bacteria often show large variations in gene content, even between strains of the same species. Such studies have focused mainly on pathogens; here, we examined
Thermotoga maritima,
a free-living hyperthermophilic bacterium, by using suppressive subtractive hybridization. The genome sequence of
T. maritima
MSB8 is available, and DNA from this strain served as a reference to obtain strain-specific sequences from
Thermotoga
sp. strain RQ2, a very close relative (∼96% identity for orthologous protein-coding genes, 99.7% identity in the small-subunit rRNA sequence). Four hundred twenty-six RQ2 subtractive clones were sequenced. One hundred sixty-six had no DNA match in the MSB8 genome. These differential clones comprise, in sum, 48 kb of RQ2-specific DNA and match 72 genes in the GenBank database. From the number of identical clones, we estimated that RQ2 contains 350 to 400 genes not found in MSB8. Assuming a similar genome size, this corresponds to 20% of the RQ2 genome. A large proportion of the RQ2-specific genes were predicted to be involved in sugar transport and polysaccharide degradation, suggesting that polysaccharides are more important as nutrients for this strain than for MSB8. Several clones encode proteins involved in the production of surface polysaccharides. RQ2 encodes multiple subunits of a V-type ATPase, while MSB8 possesses only an F-type ATPase. Moreover, an RQ2-specific MutS homolog was found among the subtractive clones and appears to belong to a third novel archaeal type MutS lineage. Southern blot analyses showed that some of the RQ2 differential sequences are found in some other members of the order
Thermotogales
, but the distribution of these variable genes is patchy, suggesting frequent lateral gene transfer within the group.
Phosphorylation of thePseudomonas aeruginosaResponse Regulator AlgR Is Essential for Type IV Fimbria-Mediated Twitching Motility
Authors: Whitchurch Cynthia B. , Erova Tatiana E. , Emery Jacqui A. , Sargent Jennifer L. , Harris Jonathan M. , Semmler Annalese B. T. , Young Michael D. , Mattick John S. , Wozniak Daniel J. 
Published: October 2002

ABSTRACTThe response regulator AlgR is required for both alginate biosynthesis and type IV fimbria-mediated twitching motility inPseudomonas aeruginosa. In this study, the roles of AlgR signal transduction and phosphorylation in twitching motility and biofilm formation were examined. The predicted phosphorylation site of AlgR (aspartate 54) and a second aspartate (aspartate 85) in the receiver domain of AlgR were mutated to asparagine, and mutantalgRalleles were introduced into the chromosome ofP. aeruginosastrains PAK and PAO1. Assays of these mutants demonstrated that aspartate 54 but not aspartate 85 of AlgR is required for twitching motility and biofilm initiation. However, strains expressing AlgR D85N were found to be hyperfimbriate, indicating that both aspartate 54 and aspartate 85 are involved in fimbrial biogenesis and function.algDmutants were observed to have wild-type twitching motility, indicating that AlgR control of twitching motility is not mediated via its role in the control of alginate biosynthesis. In vitro phosphorylation assays showed that AlgR D54N is not phosphorylated by the enteric histidine kinase CheA. These findings indicate that phosphorylation of AlgR most likely occurs at aspartate 54 and that aspartate 54 and aspartate 85 of AlgR are required for the control of the molecular events governing fimbrial biogenesis, twitching motility, and biofilm formation inP. aeruginosa.
Microarray Transcription Profiling of a
Shewanella oneidensis etrA
Mutant
Authors: Beliaev Alex S. , Thompson Dorothea K. , Fields Matthew W. , Wu Liyou , Lies Douglas P. , Nealson Kenneth H. , Zhou Jizhong 
Published: October 2002

ABSTRACT

DNA microarrays were used to examine the effect of an insertional mutation in the
Shewanella oneidensis etrA
(electron transport regulator) locus on gene expression under anaerobic conditions. The mRNA levels of 69 genes with documented functions in energy and carbon metabolism, regulation, transport, and other cellular processes displayed significant alterations in transcript abundance in an
etrA
-mutant genetic background. This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in
S. oneidensis
MR-1.
One Repeat of the Cell Wall Binding Domain Is Sufficient for Anchoring the
Lactobacillus acidophilus
Surface Layer Protein
Authors: Smit Egbert , Pouwels Peter H. 
Published: October 2002

ABSTRACT

The N-terminal repeat (SAC1) of the S-protein of
Lactobacillus acidophilus
bound efficiently and specifically to cell wall fragments (CWFs) when fused to green fluorescent protein, whereas the C-terminal repeat (SAC2) did not. Treatment of CWFs with hydrofluoric acid, but not phenol, prevented binding. Apparently, SAC1 is necessary and sufficient for cell wall binding. Our data suggest that SAC anchors the S-protein to a cell wall teichoic acid.
Hierarchy of Carbon Source Selection inParacoccus pantotrophus: Strict Correlation between Reduction State of the Carbon Substrate and Aerobic Expression of thenapOperon
Authors: Ellington M. J. K. , Bhakoo K. K. , Sawers G. , Richardson D. J. , Ferguson S. J. 
Published: October 2002

ABSTRACTParacoccus pantotrophuscan express a periplasmic nitrate reductase (Nap) during aerobic growth. A proposed role for this enzyme is the dissipation of excess redox energy during oxidative metabolism of reduced carbon substrates. To investigate the regulation ofnapexpression, a transcriptional fusion between thenappromoter region ofP. pantotrophusand thelacZgene was constructed. When this fusion was used, analyses showed that transcription from thenappromoter increases as the average reduction state of the carbon atoms increases. Thus, β-galactosidase activities increase as the carbon source changes in the order succinate-acetate-butyrate. This result was obtained regardless of which of the three carbon sources was used for culture of the inoculum. If two carbon sources were presented together, the β-galactosidase activity was always the same as it was when the least-reduced carbon source was added alone. This suggests that the regulation is dependent upon metabolism of the more-reduced carbon sources rather than just their presence in the medium. Analysis of culture medium by1H nuclear magnetic resonance showed that for aerobic growthP. pantotrophusstrictly selected its carbon source in the order succinate-acetate-butyrate. This was reflected by diauxic growth kinetics on medium containing mixed carbon substrates. The regulatory mechanism underpinning such a selection is unknown but is likely to be related to the mechanism which controls the transcription of thenapoperon.
Identification by Heterologous Expression and Gene Disruption of VisA as
l
-Lysine 2-Aminotransferase Essential for Virginiamycin S Biosynthesis in
Streptomyces virginiae
Authors: Namwat Wises , Kinoshita Hiroshi , Nihira Takuya 
Published: October 2002

ABSTRACT

The
visA
gene of
Streptomyces virginiae
has been thought to be a part of the virginiamycin S (VS) biosynthetic gene cluster based on its location in the middle of genes that encode enzymes highly similar to those participating in the biosynthesis of streptogramin-type antibiotics. Heterologous expression of the
visA
gene was achieved in
Escherichia coli
by an N-terminal fusion with thioredoxin (TrxA), and the intact recombinant VisA protein (rVisA) was purified after cleavage with enterokinase to remove the TrxA moiety. The purified rVisA showed clear
l
-lysine 2-aminotransferase activity with an optimum pH of around 8.0 and an optimum temperature at 35°C, with 2-oxohexanoate as the best amino acceptor, indicating that VisA converts
l
-lysine into Δ
1
-piperidine 2-carboxylic acid. A
visA
deletion mutant of
S. virginiae
was created by homologous recombination, and the in vivo function of the
visA
gene was studied by phenotypic comparison between the wild type and the
visA
deletion mutant. No differences in growth in liquid media or in morphological behavior on solid media were observed, indicating that
visA
is not involved in primary metabolism or morphological differentiation. However, the
visA
mutant failed to produce VS while maintaining the production of virginiamycin M
1
at a level comparable to that of the parental wild-type strain, demonstrating that
visA
is essential to VS biosynthesis. These results, together with the observed recovery of the defect in VS production by the external addition of 3-hydroxypicolinic acid (3-HPA), a starter molecule in VS biosynthesis, suggest that VisA is the first enzyme of the VS biosynthetic pathway and that it supplies 3-HPA from
l
-lysine.
Bacillus subtilis
Mutant LicT Antiterminators Exhibiting Enzyme I- and HPr-Independent Antitermination Affect Catabolite Repression of the
bglPH
Operon
Authors: Lindner Cordula , Hecker Michael , Le Coq Dominique , Deutscher Josef 
Published: October 2002

ABSTRACT

The
Bacillus subtilis
antiterminator LicT regulates the expression of
bglPH
and
bglS
, which encode the enzymes for the metabolism of aryl-β-glucosides and the β-glucanase BglS. The N-terminal domain of LicT (first 55 amino acids) prevents the formation of ρ-independent terminators on the respective transcripts by binding to target sites overlapping these terminators. Proteins of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) regulate the antitermination activity of LicT by phosphorylating histidines in its two PTS regulation domains (PRDs). Phosphorylation at His-100 in PRD-1 requires the PTS proteins enzyme I and HPr and the phosphorylated permease BglP and inactivates LicT. During transport and phosphorylation of aryl-β-glucosides, BglP is dephosphorylated, which renders LicT active and thus leads to
bglPH
and
bglS
induction. In contrast, phosphorylation at His-207 and/or His-269 in PRD-2, which requires only enzyme I and HPr, is absolutely necessary for LicT activity and
bglPH
and
bglS
expression. We isolated spontaneous
licT
mutants expressing
bglPH
even when enzyme I and HPr were absent (as indicated by the designation “Pia” [PTS-independent antitermination]). Introduced in a
ptsHI
+
strain, two classes of
licT
(Pia) mutations could be distinguished. Mutants synthesizing LicT(Pia) antiterminators altered in PRD-2 still required induction by aryl-β-glucosides, whereas mutations affecting PRD-1 caused constitutive
bglPH
expression. One of the two carbon catabolite repression (CCR) mechanisms operative for
bglPH
requires the ρ-independent terminator and is probably prevented when LicT is activated by P∼His-HPr-dependent phosphorylation in PRD-2 (where the prefix “P∼” stands for “phospho”). During CCR, the small amount of P∼His-HPr present in cells growing on repressing PTS sugars probably leads to insufficient phosphorylation at PRD-2 of LicT and therefore to reduced
bglPH
expression. In agreement with this concept, mutants synthesizing a P∼His-HPr-independent LicT(Pia) had lost LicT-modulated CCR.