bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Profiling of Cross Pathway Control in
Neurospora crassa
and Comparative Analysis of the Gcn4 and CPC1 Regulons
Authors: Tian Chaoguang , Kasuga Takao , Sachs Matthew S. , Glass N. Louise 
Published: April 2007

ABSTRACT

Identifying and characterizing transcriptional regulatory networks is important for guiding experimental tests on gene function. The characterization of regulatory networks allows comparisons among both closely and distantly related species, providing insight into network evolution, which is predicted to correlate with the adaptation of different species to particular environmental niches. One of the most intensely studied regulatory factors in the yeast
Saccharomyces cerevisiae
is the bZIP transcription factor Gcn4p. Gcn4p is essential for a global transcriptional response when
S. cerevisiae
experiences amino acid starvation. In the filamentous ascomycete
Neurospora crassa
, the ortholog of
GCN4
is called the
c
ross
p
athway
c
ontrol-1 (
cpc-1
) gene; it is required for the ability of
N. crassa
to induce a number of amino acid biosynthetic genes in response to amino acid starvation. Here, we deciphered the CPC1 regulon by profiling transcription in wild-type and
cpc-1
mutant strains with full-genome
N. crassa
70-mer oligonucleotide microarrays. We observed that at least 443 genes were direct or indirect CPC1 targets; these included 67 amino acid biosynthetic genes, 16 tRNA synthetase genes, and 13 vitamin-related genes. Comparison among the
N. crassa
CPC1 transcriptional profiling data set and the Gcn4/CaGcn4 data sets from
S. cerevisiae
and
Candida albicans
revealed a conserved regulon of 32 genes, 10 of which are predicted to be directly regulated by Gcn4p/CPC1. The 32-gene conserved regulon comprises mostly amino acid biosynthetic genes. The comparison of regulatory networks in species with clear orthology among genes sheds light on how gene interaction networks evolve.
Cryptococcus neoformans
Mates on Pigeon Guano: Implications for the Realized Ecological Niche and Globalization
Authors: Nielsen Kirsten , De Obaldia Anna L. , Heitman Joseph 
Published: April 2007

ABSTRACT

The ecological niche that a species can occupy is determined by its resource requirements and the physical conditions necessary for survival. The niche to which an organism is most highly adapted is the realized niche, whereas the complete range of habitats that an organism can occupy represents the fundamental niche. The growth and development of
Cryptococcus neoformans
and
Cryptococcus gattii
on pigeon guano were examined to determine whether these two species occupy the same or different ecological niches.
C. neoformans
is a cosmopolitan pathogenic yeast that infects predominantly immunocompromised individuals, exists in two varieties (
grubii
[serotype A] and
neoformans
[serotype D]), and is commonly isolated from pigeon guano worldwide. By contrast,
C. gattii
often infects immunocompetent individuals and is associated with geographically restricted environments, most notably, eucalyptus trees. Pigeon guano supported the growth of both species, and a brown pigment related to melanin, a key virulence factor, was produced.
C. neoformans
exhibited prolific mating on pigeon guano, whereas
C. gattii
did not. The observations that
C. neoformans
completes the life cycle on pigeon guano but that
C. gattii
does not indicates that pigeon guano could represent the realized ecological niche for
C. neoformans
. Because
C. gattii
grows on pigeon guano but cannot sexually reproduce, pigeon guano represents a fundamental but not a realized niche for
C. gattii
. Based on these studies, we hypothesize that an ancestral
Cryptococcus
strain gained the ability to sexually reproduce in pigeon guano and then swept the globe.
Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon
Pyrococcus furiosus
: Characterization of a Coenzyme A- Dependent NAD(P)H Sulfur Oxidoreductase
Authors: Schut Gerrit J. , Bridger Stephanie L. , Adams Michael W. W. 
Published: April 2007

ABSTRACT

The hyperthermophilic archaeon
Pyrococcus furiosus
uses carbohydrates as a carbon source and produces acetate, CO
2
, and H
2
as end products. When S
0
is added to a growing culture, within 10 min the rate of H
2
production rapidly decreases and H
2
S is detected. After 1 hour cells contain high NADPH- and coenzyme A-dependent S
0
reduction activity (0.7 units/mg, 85°C) located in the cytoplasm. The enzyme responsible for this activity was purified to electrophoretic homogeneity (specific activity, 100 units/mg) and is termed NAD(P)H elemental sulfur oxidoreductase (NSR). NSR is a homodimeric flavoprotein (
M
r
, 100,000) and is encoded by PF1186. This designation was previously assigned to the gene encoding an enzyme that reduces coenzyme A disulfide, which is a side reaction of NSR. Whole-genome DNA microarray and quantitative PCR analyses showed that the expression of NSR is up-regulated up to sevenfold within 10 min of S
0
addition. This primary response to S
0
also involves the up-regulation (>16-fold) of a 13-gene cluster encoding a membrane-bound oxidoreductase (MBX). The cluster encoding MBX is proposed to replace the homologous 14-gene cluster that encodes the ferredoxin-oxidizing, H
2
-evolving membrane-bound hydrogenase (MBH), which is down-regulated >12-fold within 10 min of S
0
addition. Although an activity for MBX could not be demonstrated, it is proposed to conserve energy by oxidizing ferredoxin and reducing NADP, which is used by NSR to reduce S
0
. A secondary response to S
0
is observed 30 min after S
0
addition and includes the up-regulation of genes encoding proteins involved in amino acid biosynthesis and iron metabolism, as well as two so-called sulfur-induced proteins termed SipA and SipB. This novel S
0
-reducing system involving NSR and MBX has been found so far only in the heterotrophic
Thermococcales
and is in contrast to the cytochrome- and quinone-based S
0
-reducing system in autotrophic archaea and bacteria.
Environmental Regulation of
Pseudomonas aeruginosa
PAO1 Las and Rhl Quorum-Sensing Systems
Authors: Duan Kangmin , Surette Michael G. 
Published: April 2007

ABSTRACT

The
lasI
-
lasR
and the
rhlI
-
rhlR
quorum-sensing systems in
Pseudomonas aeruginosa
regulate the expression of numerous cellular and secreted virulence factor genes and play important roles in the development of biofilms. The
las
and
rhl
systems themselves are known to be directly or indirectly regulated by a number of transcriptional regulators, and consequently, their expression is sensitive to environmental conditions. In this report, the activities of these two quorum-sensing systems have been examined systematically under 46 growth conditions, and the regulation by environmental conditions has been investigated. The relative timing and strength of expression of these two systems varied significantly under different conditions, which contrasts with the notion of a preset hierarchy with these two systems in
P. aeruginosa
. Depending on the growth conditions, the correlation between each synthase and its cognate transcriptional regulator also varied, suggesting that the transcription of these genes independently allows for further fine tuning of each system. Finally, we observe that the activities of both the
lasI
-
lasR
and the
rhlI
-
rhlR
quorum-sensing systems were dramatically enhanced in the presence of extracts of sputum samples from cystic fibrosis patients.
A Copper-Activated Two-Component System Interacts with Zinc and Imipenem Resistance in
Pseudomonas aeruginosa
Authors: Caille Olivier , Rossier Claude , Perron Karl 
Published: April 2007

ABSTRACT

The effects of copper (Cu) on trace metal and antibiotic resistance of
Pseudomonas aeruginosa
have been investigated. Cu treatments induced resistance not only to this metal but also, surprisingly, to zinc (Zn). Quantitative reverse transcription-PCR (qRT-PCR) revealed that after Cu treatment the transcription of the
czcRS
two-component system (TCS) operon was enhanced as well as that of the
czcCBA
operon encoding an efflux pump specific for zinc, cadmium, and cobalt. Cu treatments at the same time caused a decrease in the production of OprD porin, resulting in resistance to the carbapenem antibiotic imipenem. The CzcR regulator was known to repress
oprD
. However, Cu was still able to decrease the production of OprD and induce imipenem resistance in a
czcRS
knockout mutant. This strongly suggested that another Cu-dependent regulatory system was acting negatively on
oprD
expression. TCS regulator genes
copR-copS
have been shown to be involved in Cu tolerance in
P. aeruginosa
. qRT-PCR showed that overproduction of the CopR or of the CzcR regulator resulted in increased transcription of the
czcC
gene as well as in a decrease in
oprD
gene transcription, either in the wild-type strain or in the
czcRS
knockout mutant. Overproduction experiments suggest that a metal-dependent mechanism operates at the posttranscriptional level to control the production of the CzcCBA efflux pump. This study shows that CopR is a new negative regulator of OprD porin and that it links Zn, Cu, and imipenem resistances by interacting with the CzcRS TCS.
Structure-Based Functional Analysis of the Replication Protein of Plasmid R6K: Key Amino Acids at the π/DNA Interface
Authors: Kunnimalaiyaan Selvi , Rakowski Sheryl A. , Filutowicz Marcin 
Published: April 2007

ABSTRACT

In previous work, we characterized the bases in an iteron of plasmid R6K that are important for the binding of π protein monomers and dimers. Here we investigate the following six amino acids of π, encoded by
pir
, hypothesized to be important for DNA contact: Ser71, Try74, Gly131, Gly211, Arg225, and Arg254.
A Polyomic Approach To Elucidate the Fluoranthene-Degradative Pathway inMycobacterium vanbaaleniiPYR-1
Authors: Kweon Ohgew , Kim Seong-Jae , Jones Richard C. , Freeman James P. , Adjei Michael D. , Edmondson Ricky D. , Cerniglia Carl E. 
Published: April 2007

ABSTRACTMycobacterium vanbaaleniiPYR-1 is capable of degrading a wide range of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs), including fluoranthene. We used a combination of metabolomic, genomic, and proteomic technologies to investigate fluoranthene degradation in this strain. Thirty-seven fluoranthene metabolites including potential isomers were isolated from the culture medium and analyzed by high-performance liquid chromatography, gas chromatography-mass spectrometry, and UV-visible absorption. Total proteins were separated by one-dimensional gel and analyzed by liquid chromatography-tandem mass spectrometry in conjunction with theM. vanbaaleniiPYR-1 genome sequence (http://jgi.doe.gov), which resulted in the identification of 1,122 proteins. Among them, 53 enzymes were determined to be likely involved in fluoranthene degradation. We integrated the metabolic information with the genomic and proteomic results and proposed pathways for the degradation of fluoranthene. According to our hypothesis, the oxidation of fluoranthene is initiated by dioxygenation at the C-1,2, C-2,3, and C-7,8 positions. The C-1,2 and C-2,3 dioxygenation routes degrade fluoranthene via fluorene-type metabolites, whereas the C-7,8 routes oxidize fluoranthene via acenaphthylene-type metabolites. The major site of dioxygenation is the C-2,3 dioxygenation route, which consists of 18 enzymatic steps via 9-fluorenone-1-carboxylic acid and phthalate with the initial ring-hydroxylating oxygenase, NidA3B3, oxidizing fluoranthene to fluoranthenecis-2,3-dihydrodiol. Nonspecific monooxygenation of fluoranthene with subsequent O methylation of dihydroxyfluoranthene also occurs as a detoxification reaction.
Variability and Expression of Ankyrin Domain Genes in
Wolbachia
Variants Infecting the Mosquito
Culex pipiens
Authors: Duron Olivier , Boureux Anthony , Echaubard Pierre , Berthomieu Arnaud , Berticat Claire , Fort Philippe , Weill Mylène 
Published: April 2007

ABSTRACT

Wolbachia
strains are maternally inherited endosymbiotic bacteria that infect many arthropod species and have evolved several different ways of manipulating their hosts, the most frequent way being cytoplasmic incompatibility (CI). CI leads to embryo death in crosses between infected males and uninfected females as well as in crosses between individuals infected by incompatible
Wolbachia
strains. The mosquito
Culex pipiens
exhibits the highest crossing type variability reported so far. Our crossing data support the notion that CI might be driven by at least two distinct genetic units that control the CI functions independently in males and females. Although the molecular basis of CI remains unknown, proteins with ankyrin (ANK) domains represent promising candidates since they might interact with a wide range of host proteins. Here we searched for sequence variability in the 58 ANK genes carried in the genomes of
Wolbachia
variants infecting
Culex pipiens
. Only five ANK genes were polymorphic in the genomes of incompatible
Wolbachia
variants, and none correlated with the CI pattern obtained with 15 mosquito strains (representing 14
Wolbachia
variants). Further analysis of ANK gene expression evidenced host- and sex-dependent variations, which did not improve the correlation. Taken together, these data do not support the direct implication of ANK genes in CI determinism.
Augmented Expression of Polysaccharide Intercellular Adhesin in a DefinedStaphylococcus epidermidisMutant with the Small-Colony-Variant Phenotype
Authors: Al Laham Nahed , Rohde Holger , Sander Gunnar , Fischer Andreas , Hussain Muzaffar , Heilmann Christine , Mack Dietrich , Proctor Richard , Peters Georg , Becker Karsten , von Eiff Christof 
Published: April 2007

ABSTRACTWhile coagulase-negative staphylococci (CoNS), with their ability to form a thick, multilayered biofilm on foreign bodies, have been identified as the major cause of implant-associated infections, no data are available about biofilm formation by staphylococcal small-colony variants (SCVs). In the past years, a number of device-associated infections due to staphylococcal SCVs were described, among them, several pacemaker infections due to SCVs of CoNS auxotrophic to hemin. To test the characteristics of SCVs of CoNS, in particular, to study the ability of SCVs to form a biofilm on foreign bodies, we generated a stable mutant in electron transport by interrupting one of the hemin biosynthetic genes,hemB, inStaphylococcus epidermidis. In fact, this mutant displayed a stable SCV phenotype with tiny colonies showing strong adhesion to the agar surface. When the incubation time was extended to 48 h or a higher inoculum concentration was used, the mutant produced biofilm amounts on polystyrene similar to those produced by the parent strain. When grown under planktonic conditions, the mutant formed markedly larger cell clusters than the parental strain which were completely disintegrated by the specific β-1,6-hexosaminidase dispersin B but were resistant to trypsin treatment. In a dot blot assay, the mutant expressed larger amounts of polysaccharide intercellular adhesin (PIA) than the parent strain. In conclusion, interrupting a hemin biosynthetic gene inS. epidermidisresulted in an SCV phenotype. Markedly larger cell clusters and the ability of thehemBmutant to form a biofilm are related to the augmented expression of PIA.
Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in
Methanocaldococcus jannaschii
Authors: Drevland Randy M. , Waheed Abdul , Graham David E. 
Published: April 2007

ABSTRACT

The archaeon
Methanocaldococcus jannaschii
uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme B biosyntheses. In each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. The genome sequence of
M. jannaschii
encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. The genes are more similar to each other than to previously characterized isopropylmalate isomerase or homoaconitase enzyme genes. To identify the functions of these homologs, the four combinations of subunits were heterologously expressed in
Escherichia coli
, purified, and reconstituted to generate the iron-sulfur center of the holoenzyme. Only the combination of MJ0499 and MJ1277 proteins catalyzed isopropylmalate and citramalate isomerization reactions. This pair also catalyzed hydration half-reactions using citraconate and maleate. Another broad-specificity enzyme, isopropylmalate dehydrogenase (MJ0720), catalyzed the oxidative decarboxylation of β-isopropylmalate, β-methylmalate, and
d
-malate. Combined with these results, phylogenetic analysis suggests that the pyruvate pathway to 2-oxobutyrate (an alternative to threonine dehydratase in isoleucine biosynthesis) evolved several times in bacteria and archaea. The enzymes in the isopropylmalate pathway of leucine biosynthesis facilitated the evolution of 2-oxobutyrate biosynthesis through the introduction of a citramalate synthase, either by gene recruitment or gene duplication and functional divergence.
The Oxidoreductase DsbA Plays a Key Role in the Ability of the Crohn's Disease-Associated Adherent-Invasive
Escherichia coli
Strain LF82 To Resist Macrophage Killing
Authors: Bringer Marie-Agnès , Rolhion Nathalie , Glasser Anne-Lise , Darfeuille-Michaud Arlette 
Published: April 2007

ABSTRACT

Adherent-invasive
Escherichia coli
(AIEC) isolated from Crohn's disease patients is able to adhere to and invade intestinal epithelial cells and to replicate in mature phagolysosomes within macrophages. Here, we show that the
dsbA
gene, encoding a periplasmic oxidoreductase, was required for AIEC strain LF82 to adhere to intestinal epithelial cells and to survive within macrophages. The LF82-Δ
dsbA
mutant did not express flagella and, probably as a consequence of this, did not express type 1 pili. The role of DsbA in adhesion is restricted to the loss of flagella and type 1 pili, as forced contact between bacteria and cells and induced expression of type 1 pili restored the wild-type phenotype. In contrast, the
dsbA
gene is essential for AIEC LF82 bacteria to survive within macrophages, irrespective of the loss of flagella and type 1 pilus expression, and the survival ability of LF82-Δ
dsbA
was as low as that of the nonpathogenic
E. coli
K-12, which was efficiently killed by macrophages. We also provide evidence that the
dsbA
gene is needed for LF82 bacteria to grow and survive in an acidic and nutrient-poor medium that partly mimics the harsh environment of the phagocytic vacuole. In addition, under such stress conditions
dsbA
transcription is highly up-regulated. Finally, the CpxRA signaling pathway does not play a role in regulation of
dsbA
expression in AIEC LF82 bacteria under conditions similar to those of mature phagolysosomes.
Genetic Dissection of Specificity Determinants in the Interaction of HPr with Enzymes II of the Bacterial Phosphoenolpyruvate:Sugar Phosphotransferase System inEscherichia coli
Authors: Reichenbach Birte , Breustedt Daniel A. , Stülke Jörg , Rak Bodo , Görke Boris 
Published: April 2007

ABSTRACTThe histidine protein (HPr) is the energy-coupling protein of the phosphoenolpyruvate (PEP)-dependent carbohydrate:phosphotransferase system (PTS), which catalyzes sugar transport in many bacteria. In its functions, HPr interacts with a number of evolutionarily unrelated proteins. Mainly, it delivers phosphoryl groups from enzyme I (EI) to the sugar-specific transporters (EIIs). HPr proteins of different bacteria exhibit almost identical structures, and, where known, they use similar surfaces to interact with their target proteins. Here we studied the in vivo effects of the replacement of HPr and EI ofEscherichia coliwith the homologous proteins fromBacillus subtilis, a gram-positive bacterium. This replacement resulted in severe growth defects on PTS sugars, suggesting that HPr ofB. subtilis cannot efficiently phosphorylate the EIIs ofE. coli. In contrast, activation of theE. coliBglG regulatory protein by HPr-catalyzed phosphorylation works well with theB. subtilisHPr protein. Random mutations were introduced intoB. subtilisHPr, and a screen for improved growth on PTS sugars yielded amino acid changes in positions 12, 16, 17, 20, 24, 27, 47, and 51, located in the interaction surface of HPr. Most of the changes restore intermolecular hydrophobic interactions and salt bridges normally formed by the corresponding residues inE. coliHPr. The residues present at the targeted positions differ between HPrs of gram-positive and -negative bacteria, but within each group they are highly conserved. Therefore, they may constitute a signature motif that determines the specificity of HPr for either gram-negative or -positive EIIs.
Conversion of Flavodoxin from Holoenzyme to Apoprotein during Growth Phase Changes inHelicobacter pylori
Authors: Shimomura Hirofumi , Hayashi Shunji , Yokota Kenji , Oguma Keiji , Hirai Yoshikazu 
Published: April 2007

ABSTRACTThe catabolic pathway for flavodoxin has yet to be clarified for any bacterial species. In this study, we found that the flavin mononucleotide in the flavodoxin ofHelicobacter pyloriis degraded to riboflavin via the phosphomonoesterase activity of class C acid phosphatase. The result is a conversion of holoflavodoxin to apoflavodoxin.
Quorum Sensing Regulates Denitrification in
Pseudomonas aeruginosa
PAO1
Authors: Toyofuku Masanori , Nomura Nobuhiko , Fujii Tatsuya , Takaya Naoki , Maseda Hideaki , Sawada Isao , Nakajima Toshiaki , Uchiyama Hiroo 
Published: April 2007

ABSTRACT

Anaerobic growth of
Pseudomonas aeruginosa
PAO1 was affected by quorum sensing. Deletion of genes that produce
N
-acyl-
l
-homoserine lactone signals resulted in an increase in denitrification activity, which was repressed by exogenous signal molecules. The effect of the
las
quorum-sensing system was dependent on the
rhl
quorum-sensing system in regulating denitrification.
Characterization of a Novel Bile-Inducible Operon Encoding a Two-Component Regulatory System inLactobacillus acidophilus
Authors: Pfeiler Erika A. , Azcarate-Peril M. Andrea , Klaenhammer Todd R. 
Published: April 2007

ABSTRACTLactobacillus acidophilusNCFM is an industrially important strain used extensively as a probiotic culture. Tolerance of the presence of bile is an attribute important to microbial survival in the intestinal tract. A whole-genome microarray was employed to examine the effects of bile on the global transcriptional profile of this strain, with the intention of elucidating genes contributing to bile tolerance. Genes involved in carbohydrate metabolism were generally induced, while genes involved in other aspects of cellular growth were mostly repressed. A 7-kb eight-gene operon encoding a two-component regulatory system (2CRS), a transporter, an oxidoreductase, and four hypothetical proteins was significantly upregulated in the presence of bile. Deletion mutations were constructed in six genes of the operon. Transcriptional analysis of the 2CRS mutants showed that mutation of the histidine protein kinase (HPK) had no effect on the induction of the operon, whereas the mutated response regulator (RR) showed enhanced induction when the cells were exposed to bile. These results indicate that the 2CRS plays a role in bile tolerance and that the operon it resides in is negatively controlled by the RR. Mutations in the transporter, the HPK, the RR, and a hypothetical protein each resulted in loss of tolerance of bile. Mutations in genes encoding another hypothetical protein and a putative oxidoreductase resulted in significant increases in bile tolerance. This functional analysis showed that the operon encoded proteins involved in both bile tolerance and bile sensitivity.