bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Genetic Analyses of Mating Pheromones Reveal Intervariety Mating or Hybridization in
Cryptococcus neoformans
Authors: Chaturvedi Vishnu , Fan Jinjiang , Stein Birgit , Behr Melissa J. , Samsonoff William A. , Wickes Brian L. , Chaturvedi Sudha 
Published: October 2002

ABSTRACT

The sexual mating of the pathogenic yeast
Cryptococcus neoformans
is important for pathogenesis studies because the fungal virulence is linked to the
α
mating type (
MATα
). We characterized
C. neoformans
mating pheromones (
MFα 1
and
MFa1
) from 122 strains to understand intervariety hybridization or mating and intervariety virulence.
MFα 1
in three
C. neoformans
varieties showed (a) specific nucleotide polymorphisms, (b) different copy numbers and chromosomal localizations, and (c) unique deduced amino acids in two geographic populations of
C. neoformans
var.
gattii. MFα 1
of different varieties cross-hybridized in Southern hybridizations. Their phylogenetic analyses showed purifying selection (neutral evolution). These observations suggested that
MATα
strains from any of the three
C. neoformans
varieties could mate or hybridize in nature with
MAT
a
strains of
C. neoformans
var.
neoformans
. A few serotype A/D diploid strains provided evidence for mating or hybridization, while a majority of A/D strains tested positive for haploid
MFα 1
identical to that of
C. neoformans
var.
grubii
.
MFα 1
sequence and copy numbers in diploids were identical to those of
C. neoformans
var.
grubii
, while their
MFa1
sequences were identical to those of
C. neoformans
var.
neoformans
; thus, these strains were hybrids. The mice survival curves and histological lesions revealed A/D diploids to be highly pathogenic, with pathogenicity levels similar to that of the
C. neoformans
var.
grubii
type strain and unlike the low pathogenicity levels of
C. neoformans
var.
neoformans
strains. In contrast to
MFα 1
in three varieties,
MFa1
amplicons and hybridization signals could be obtained only from two
C. neoformans
var.
neoformans
reference strains and eight A/D diploids. This suggested that a yet undiscovered
MFa
pheromone(s) in
C. neoformans
var.
gattii
and
C. neoformans
var.
grubii
is unrelated to, highly divergent from, or rarer than that in
C. neoformans
var.
neoformans
. These observations could form the basis for future studies on the role of intervariety mating in
C. neoformans
biology and virulence.
Identification and Disruption of the Gene Encoding the Third Member of the Low-Molecular-Mass Rhoptry Complex in
Plasmodium falciparum
Authors: Baldi Deborah L. , Good Robert , Duraisingh Manoj T. , Crabb Brendan S. , Cowman Alan F. 
Published: October 2002

ABSTRACT

The low-molecular-mass rhoptry complex of
Plasmodium falciparum
consists of three proteins, rhoptry-associated protein 1 (RAP1), RAP2, and RAP3. The genes encoding RAP1 and RAP2 are known; however, the
RAP3
gene has not been identified. In this study we identify the
RAP3
gene from the
P. falciparum
genome database and show that this protein is part of the low-molecular-mass rhoptry complex. Disruption of
RAP3
demonstrated that it is not essential for merozoite invasion, probably because RAP2 can complement the loss of RAP3. RAP3 has homology with RAP2, and the genes are encoded on chromosome 5 in a head-to-tail fashion. Analysis of the genome databases has identified homologous genes in all
Plasmodium
spp., suggesting that this protein plays a role in merozoite invasion. The region surrounding the
RAP3
homologue in the
Plasmodium yoelii
genome is syntenic with the same region in
P. falciparum
; however, there is a single gene. Phylogenetic comparison of the RAP2/3 protein family from
Plasmodium
spp. suggests that the RAP2/3 duplication occurred after divergence of these parasite species.
The Siderophore Iron Transporter ofCandida albicans(Sit1p/Arn1p) Mediates Uptake of Ferrichrome-Type Siderophores and Is Required for Epithelial Invasion
Authors: Heymann Petra , Gerads Michaela , Schaller Martin , Dromer Francoise , Winkelmann Günther , Ernst Joachim F. 
Published: October 2002

ABSTRACTThe human fungal pathogenCandida albicanscontains a close homologue of yeast siderophore transporters, designated Sit1p/Arn1p. We have characterized the function ofSIT1inC. albicansby constructingsit1deletion strains and testing their virulence and ability to utilize a range of siderophores and other iron complexes.sit1mutant strains are defective in the uptake of ferrichrome-type siderophores including ferricrocin, ferrichrysin, ferrirubin, coprogen, and triacetylfusarinine C. A mutation ofFTR1did not impair the use of these siderophores but did affect the uptake of ferrioxamines E and B, as well as of ferric citrate, indicating that their utilization was independent of Sit1p. Hemin was a source of iron for bothsit1andftr1mutants, suggesting a pathway of hemin uptake distinct from that of siderophores and iron salts. Heterologous expression ofSIT1in the yeastSaccharomyces cerevisiaeconfirmed the function of Sit1p as a transporter for ferrichrome-type siderophores. Thesit1mutant was defective in infection of a reconstituted human epithelium as a model for human oral mucosa, while theSIT1strain was invasive. In contrast, bothsit1andSIT1strains were equally virulent in the mouse model of systemic infection. These results suggest that siderophore uptake by Sit1p/Arn1p is required in a specific process ofC. albicansinfection, namely epithelial invasion and penetration, while in the blood or within organs other sources of iron, including heme, may be used.
Mixed Periodontal Th1-Th2 Cytokine Profile in
Actinobacillus actinomycetemcomitans
-Specific Osteoprotegerin Ligand (or RANK-L)- Mediated Alveolar Bone Destruction In Vivo
Authors: Teng Yen-Tung A. 
Published: October 2002

ABSTRACT

The Th1/Th2 cytokines involved in human periodontitis remain unclear; therefore, we established a humanized mouse model to investigate this issue in
Actinobacillus actinomycetemcomitans
-mediated periodontal infection. Quantitative-PCR analysis clearly demonstrates a predominantly mixed Th1 and Th2 expression profile associated with pathogen-specific cell-mediated immunity via osteoprotegerin ligand (or RANK-L)-mediated alveolar bone destruction in vivo.
β-1,2-Mannosylation of
Candida albicans
Mannoproteins and Glycolipids Differs with Growth Temperature and Serotype
Authors: Trinel P. A. , Jouault T. , Cutler J. E. , Poulain D. 
Published: October 2002

ABSTRACT

Increasing the growth temperature from 28 to 37°C reduced the expression of β-1,2-oligomannoside epitopes on mannoproteins of
Candida albicans
serotypes A and B. In contrast, β-1,2-mannosylation of phospholipomannan (PLM) remained constant despite a slight decrease in the relative molecular weight (
M
r
) of this compound. At all growth temperatures investigated, serotype A PLM displayed an
M
r
and an antigenicity different from those of serotype B PLM when they were tested with a panel of monoclonal antibodies.
Functional Domain of Bovine Milk Lactoferrin Which Inhibits the Adherence of
Streptococcus mutans
Cells to a Salivary Film
Authors: Oho Takahiko , Mitoma Morihide , Koga Toshihiko 
Published: October 2002

ABSTRACT

The bovine lactoferrin molecule and relatively long lactoferrin fragments containing residues 473 to 538 strongly inhibited adherence of
Streptococcus mutans
to saliva-coated hydroxyapatite beads. Each cysteine residue in Lf411 (residues 473 to 538) was replaced by a serine residue, and the mutants Lf411-C481S and Lf411-C532S strongly inhibited
S. mutans
adherence. These results suggest that the functional domain of lactoferrin that binds to a salivary film lies in residues 473 to 538 and that the region might be concealed by disulfide bond formation between Cys481 and Cys532 in the Lf411 fragment.
ADirofilaria immitisPolyprotein Up-Regulates Nitric Oxide Production
Authors: Tezuka Hiroyuki , Imai Shinjiro , Tsukidate Setsuko , Fujita Koichiro 
Published: October 2002

ABSTRACTWe investigated the effect of recombinantDirofilaria immitispolyprotein (rDiAg) on nitric oxide (NO) production by peritoneal macrophages. rDiAg induced NO production by macrophages from wild-type and lipopolysaccharide-hyporesponsive C3H/HeJ, but not CD40−/−, mice. These results suggest that CD40 is involved in rDiAg-driven NO production by murine macrophages.
Differential Expression of the p44 Gene Family in the Agent of Human Granulocytic Ehrlichiosis
Authors: IJdo Jacob W. , Wu Caiyun , Telford Sam R. , Fikrig Erol 
Published: October 2002

ABSTRACT
Using reverse transcription-PCR targeting of the p44 genes of the agent of human granulocytic ehrlichiosis (HGE) with primers flanking the hypervariable region, we show differential expression in a murine model of HGE infection and during tick transmission. The p44 genes were differentially expressed in salivary glands of infected nymphal ticks removed during transmission feeding but not in nonfeeding infected ticks. Similarly, the p44 genes were differentially expressed in infected C3H mice, in SCID mice, and in cultured HGE bacteria. Thus, differential p44 expression exists in vivo and in vitro and could provide a basis for antigenic variation.
Roles for the Two 1-Butanol Dehydrogenases ofPseudomonas butanovorain Butane and 1-Butanol Metabolism
Authors: Vangnai Alisa S. , Sayavedra-Soto Luis A. , Arp Daniel J. 
Published: October 2002

ABSTRACTPseudomonas butanovoragrown on butane or 1-butanol expresses two 1-butanol dehydrogenases, a quinoprotein (BOH) and a quinohemoprotein (BDH). BOH exhibited high affinity towards 1-butanol (Km= 1.7 ± 0.2 μM). BOH also oxidized butyraldehyde and 2-butanol (Km= 369 ± 85 μM andKm= 662 ± 98 μM, respectively). The mRNA induction profiles of BOH and BDH at three different levels of 1-butanol, a nontoxic level (0.1 mM), a growth-supporting level (2 mM), and a toxic level (40 mM), were similar. When cells were grown in citrate-containing medium in the presence of different levels of 1-butanol, wild-typeP. butanovoracould tolerate higher levels of 1-butanol than theP. butanovora boh::tetstrain and theP. butanovora bdh::kanstrain. A model is proposed in which the electrons from 1-butanol oxidation follow a branched electron transport chain. BOH may be coupled to ubiquinone, with the electrons being transported to a cyanide-sensitive terminal oxidase. In contrast, electrons from BDH may be transferred to a terminal oxidase that is less sensitive to cyanide. The former pathway may function primarily in energy generation, while the latter may be more important in the detoxification of 1-butanol.
ZntB Is a Novel Zn
2+
Transporter in
Salmonella enterica
Serovar Typhimurium
Authors: Worlock Ashley J. , Smith Ronald L. 
Published: October 2002

ABSTRACT

A Zn
2+
transport system encoded by the
zntB
locus of
Salmonella enterica
serovar Typhimurium has been identified. The protein encoded by this locus is homologous to the CorA family of Mg
2+
transport proteins and is widely distributed among the eubacteria. Mutations at
zntB
confer an increased sensitivity to the cytotoxic effects of Zn
2+
and Cd
2+
, a phenotype that suggests that the encoded protein mediates the efflux of both cations. A direct analysis of transport activity identified a capacity for Zn
2+
efflux. These data identify ZntB as a zinc efflux pathway in the enteric bacteria and assign a new function to the CorA family of cation transporters.
Tools for Characterization of
Escherichia coli
Genes of Unknown Function
Authors: Merlin Christophe , McAteer Sean , Masters Millicent 
Published: October 2002

ABSTRACT

Despite the power of sequencing and of emerging high-throughput technologies to collect data rapidly, the definitive functional characterization of unknown genes still requires biochemical and genetic analysis in case-by-case studies. This often involves the deletion of target genes and phenotypic characterization of the deletants. We describe here modifications of an existing deletion method which facilitates the deletion process and enables convenient analysis of the expression properties of the target gene by replacing it with an FRT-
lacZ
-
aph
-

P
lac

-FRT cassette. The
lacZ
gene specifically reports the activity of the deleted gene and therefore allows the determination of the conditions under which it is actively expressed. The
aph
gene, encoding resistance to kanamycin, provides a selectable means of transducing a deleted locus between strains so that the deletion can be combined with other relevant mutations. The
lac
promoter helps to overcome possible polar effects on downstream genes within an operon. Because the cassette is flanked by two directly repeated FRT sites, the cassette can be excised by the Flp recombinase provided in
trans
. Removing the cassette leaves an in-frame deletion with a short scar which should not interfere with downstream expression. Replacements of
yacF
,
yacG
,
yacH
,
yacK
(
cueO
),
yacL
,
ruvA
,
ruvB
,
yabB
, and
yabC
made with the cassette were used to verify its properties.
Genome Sequence of
Yersinia pestis
KIM
Authors: Deng Wen , Burland Valerie , Plunkett Guy , Boutin Adam , Mayhew George F. , Liss Paul , Perna Nicole T. , Rose Debra J. , Mau Bob , Zhou Shiguo , Schwartz David C. , Fetherston Jaqueline D. , Lindler Luther E. , Brubaker Robert R. , Plano Gregory V. , Straley Susan C. , McDonough Kathleen A. , Nilles Matthew L. , Matson Jyl S. , Blattner Frederick R. , Perry Robert D. 
Published: October 2002

ABSTRACT

We present the complete genome sequence of
Yersinia pestis
KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of
Escherichia coli
K-12. The KIM genome sequence was compared with that of
Y. pestis
CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and
E. coli
K-12 genome proteins were also compared, exposing surprising amounts of locally colinear “backbone,” or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of
E. coli
pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.
Mutational Analysis of the TolA C-Terminal Domain ofEscherichia coliand Genetic Evidence for an Interaction between TolA and TolB
Authors: Dubuisson Jean François , Vianney Anne , Lazzaroni Jean Claude 
Published: October 2002

ABSTRACTThe Tol proteins are involved in the outer membrane stability of gram-negative bacteria. The C-terminal domain of TolA was mutagenized to identify residues important for its functions. The isolation of suppressor mutants oftolAmutations in thetolBgene confirmed an interaction between TolAIII and the N-terminal domain of TolB.
Recombination-Promoting Activity of the Bacteriophage λ Rap Protein in
Escherichia coli
K-12
Authors: Poteete Anthony R. , Fenton Anita C. , Wang Hsinju R. 
Published: October 2002

ABSTRACT

The
rap
gene of bacteriophage λ was placed in the chromosome of an
Escherichia coli
K-12 strain in which the
recBCD
gene cluster had previously been replaced by the λ
red
genes and in which the
recG
gene had been deleted. Recombination between linear double-stranded DNA molecules and the chromosome was tested in variants of the
recG
Δ
red
+
rap
+
strain bearing mutations in genes known to affect recombination in other cellular pathways. The linear DNA was a 4-kb fragment containing the
cat
gene, with flanking
lac
sequences, released from an infecting phage chromosome by restriction enzyme cleavage in the cell. Replacement of wild-type
lacZ
with
lacZ
::
cat
was monitored by measuring the production of Lac-deficient chloramphenicol-resistant bacterial progeny. The results of these experiments indicated that the λ
rap
gene could functionally substitute for the
E. coli ruvC
gene in Red-mediated recombination.
Genomic Variability of O Islands Encoding Tellurite Resistance in Enterohemorrhagic
Escherichia coli
O157:H7 Isolates
Authors: Taylor Diane E. , Rooker Michelle , Keelan Monika , Ng Lai-King , Martin Irene , Perna Nicole T. , Burland N. T. Valerie , Blattner Fredrick R. 
Published: October 2002

ABSTRACT

Strains of
Escherichia coli
causing enterohemorrhagic colitis belonging to the O157:H7 lineage are reported to be highly related. Fifteen strains of
E. coli
O157:H7 and 1 strain of
E. coli
O46:H
−
(nonflagellated) were examined for the presence of potassium tellurite resistance (Te
r
). Te
r
genes comprising
terABCDEF
were shown previously to be part of a pathogenicity island also containing integrase, phage, and urease genes. PCR analysis, both conventional and light cycler based, demonstrated that about one-half of the Te
r
E. coli
O157:H7 strains (6 of 15), including the Sakai strain, which has been sequenced, carried a single copy of the Te
r
genes. Five of the strains, including EDL933, which has also been sequenced, contained two copies. Three other O157:H7 strains and the O46:H
−
strain did not contain the Te
r
genes. In strains containing two copies, the Te
r
genes were associated with the
serW
and
serX
tRNA genes. Five O157:H7 strains resembled the O157 Sakai strain whose sequence contained one copy, close to
serX
, whereas in one isolate the single copy was associated with
serW
. There was no correlation between Te
r
and the ability to produce Shiga toxin ST1 or ST2. The Te
r
MIC for most strains, containing either one or two copies, was 1,024 μg/ml, although for a few the MIC was intermediate, 64 to 128 μg/ml, which could be increased to 512 μg/ml by pregrowth of strains in subinhibitory concentrations of potassium tellurite. Reverse transcriptase PCR analysis confirmed that in most strains Te
r
was constitutive but that in the rest it was inducible and involved induction of
terB
and
terC
genes. Only the
terB
, -
C
, -
D
, and -
E
genes are required for Te
r
. The considerable degree of homology between the
ter
genes on IncH12 plasmid R478, which originated in
Serratia marcescens
, and pTE53, from an
E. coli
clinical isolate, suggests that the pathogenicity island was acquired from a plasmid. This work demonstrates diversity among
E. coli
O157:H7 isolates, at least as far as the presence of Te
r
genes is concerned.
Roles of RecJ, RecO, and RecR in RecET-Mediated Illegitimate Recombination in
Escherichia coli
Authors: Shiraishi Kouya , Hanada Katsuhiro , Iwakura Yoichiro , Ikeda Hideo 
Published: October 2002

ABSTRACT

We analyzed effects of overexpression of RecE and RecT on illegitimate recombination during prophage induction in
Escherichia coli
and found that frequencies of spontaneous and UV-induced illegitimate recombination are enhanced by coexpression of RecE and RecT in the wild type, but the enhanced recombination was reduced by
recJ, recO
, or
recR
mutation. The results indicated that RecET-mediated illegitimate recombination depends on the functions of RecJ, RecO, and RecR, suggesting that the RecE and RecJ exonucleases play different roles in this recombination pathway and that the RecO and RecR proteins also play important roles in the recombination. On the other hand, the frequency of the RecET-mediated illegitimate recombination was enhanced by a
recQ
mutation, implying that the RecQ protein plays a role in suppression of RecET-mediated illegitimate recombination. It was also found that RecET-mediated illegitimate recombination is independent of the RecA function with UV irradiation, but it is enhanced by the
recA
mutation without UV irradiation. Based on these results, we propose a model for the roles of RecJOR on RecET-mediated illegitimate recombination.
Tet(L) and Tet(K) Tetracycline-Divalent Metal/H
+
Antiporters: Characterization of Multiple Catalytic Modes and a Mutagenesis Approach to Differences in Their Efflux Substrate and Coupling Ion Preferences
Authors: Jin Jie , Guffanti Arthur A. , Bechhofer David H. , Krulwich Terry A. 
Published: October 2002

ABSTRACT

The Tet(L) protein encoded in the
Bacillus subtilis
chromosome and the closely related Tet(K) protein from
Staphylococcus aureus
plasmids are multifunctional antiporters that have three cytoplasmic efflux substrates: a tetracycline-divalent metal (TC-Me
2+
) complex that bears a net single positive charge, Na
+
, and K
+
. Tet(L) and Tet(K) had been shown to couple efflux of each of these substrates to influx of H
+
as the coupling ion. In this study, competitive cross-inhibition between K
+
and other cytoplasmic efflux substrates was demonstrated. Tet(L) and Tet(K) had also been shown to use K
+
as an alternate coupling ion in support of Na
+
or K
+
efflux. Here they were shown to couple TC-Me
2+
efflux to K
+
uptake as well, exhibiting greater use of K
+
as a coupling ion as the external pH increased. The substrate and coupling ion preferences of the two Tet proteins differed, especially in the higher preference of Tet(K) than Tet(L) for K
+
, both as a cytoplasmic efflux substrate and as an external coupling ion. Site-directed mutagenesis was employed to test the hypothesis that some feature of the putative “antiporter motif,” motif C, of Tet proteins would be involved in these characteristic preferences. Mutation of the A157 in Tet(L) to a hydroxyamino acid resulted in a more Tet(K)-like K
+
preference both as coupling ion and efflux substrate. A reciprocal S157A mutant of Tet(K) exhibited reduced K
+
preference. Competitive inhibition among substrates and the parallel effects of the single mutation upon K
+
preference, as both an efflux substrate and coupling ion, are compatible with a model in which a single translocation pathway through the Tet(L) and Tet(K) transporters is used both for the cytoplasmic efflux substrates and for the coupling ions, in an alternating fashion. However, the effects of the A157 and other mutations of Tet(L) indicate that even if there are a shared binding site and translocation pathway, some elements of that pathway are used by all substrates and others are important only for particular substrates.
Genome-Wide Analysis of the Stationary-Phase Sigma Factor (Sigma-H) Regulon ofBacillus subtilis
Authors: Britton Robert A. , Eichenberger Patrick , Gonzalez-Pastor Jose Eduardo , Fawcett Paul , Monson Rita , Losick Richard , Grossman Alan D. 
Published: October 2002

ABSTRACTSigma-H is an alternative RNA polymerase sigma factor that directs the transcription of many genes that function at the transition from exponential growth to stationary phase inBacillus subtilis. Twenty-three promoters, which drive transcription of 33 genes, are known to be recognized by sigma-H-containing RNA polymerase. To identify additional genes under the control of sigma-H on a genome-wide basis, we carried out transcriptional profiling experiments using a DNA microarray containing >99% of the annotatedB.subtilisopen reading frames. In addition, we used a bioinformatics-based approach aimed at the identification of promoters recognized by RNA polymerase containing sigma-H. This combination of approaches was successful in confirming most of the previously described sigma-H-controlled genes. In addition, we identified 26 putative promoters that drive expression of 54 genes not previously known to be under the direct control of sigma-H. Based on the known or inferred function of most of these genes, we conclude that, in addition to its previously known roles in sporulation and competence, sigma-H controls genes involved in many physiological processes associated with the transition to stationary phase, including cytochrome biogenesis, generation of potential nutrient sources, transport, and cell wall metabolism.