bluuebunny/crossref_metadata_2025_split huggingface dataset:
UGE1
and
UGE2
Regulate the UDP-Glucose/UDP-Galactose Equilibrium in
Cryptococcus neoformans
Authors: Moyrand Frédérique , Lafontaine Ingrid , Fontaine Thierry , Janbon Guilhem 
Published: September 2008

ABSTRACT

The genome of the basidiomycete pathogenic yeast
Cryptococcus neoformans
carries two UDP-glucose epimerase genes (
UGE1
and
UGE2
).
UGE2
maps within a galactose cluster composed of a galactokinase homologue gene and a galactose-1-phosphate uridylyltransferase. This clustered organization of the
GAL
genes is similar to that in most of the hemiascomycete yeast genomes and in
Schizosaccharomyces pombe
but is otherwise not generally conserved in the fungal kingdom.
UGE1
has been identified as necessary for galactoxylomannan biosynthesis and virulence. Here, we show that
UGE2
is necessary for
C. neoformans
cells to utilize galactose as a carbon source at 30°C but is not required for virulence. In contrast, deletion of
UGE1
does not affect cell growth on galactose at this temperature. At 37°C, a
uge2Δ
mutant grows on galactose in a
UGE1
-dependent manner. This compensation by
UGE1
of
UGE2
mutation for growth on galactose at 37°C was not associated with upregulation of
UGE1
transcription or with an increase of the affinity of the enzyme for UDP-galactose at this temperature. We studied the subcellular localization of the two enzymes. Whereas at 30°C, Uge1p is at least partially associated with intracellular vesicles and Uge2p is on the plasma membrane, in cells growing on galactose at 37°C, Uge1p colocalizes with Uge2p to the plasma membrane, suggesting that its activity is regulated through subcellular localization.
KMP-11, a Basal Body and Flagellar Protein, Is Required for Cell Division in
Trypanosoma brucei
Authors: Li Ziyin , Wang Ching C. 
Published: September 2008

ABSTRACT

Kinetoplastid membrane protein 11 (KMP-11) has been identified as a flagellar protein and is conserved among kinetoplastid parasites, but its potential function remains unknown. In a recent study, we identified KMP-11 as a microtubule-bound protein localizing to the flagellum as well as the basal body in both procyclic and bloodstream forms of
Trypanosoma brucei
(Z. Li, J. H. Lee, F. Chu, A. L. Burlingame, A. Gunzl, and C. C. Wang, PLoS One 3:e2354, 2008). Silencing of KMP-11 by RNA interference inhibited basal body segregation and cytokinesis in both forms and resulted in multiple nuclei of various sizes, indicating a continuous, albeit somewhat defective, nuclear division while cell division was blocked. KMP-11 knockdown in the procyclic form led to severely compromised formation of the new flagellum attachment zone (FAZ) and detachment of the newly synthesized flagellum. However, a similar phenotype was not observed in the bloodstream form depleted of KMP-11. Thus, KMP-11 is a flagellar protein playing critical roles in regulating cytokinesis in both forms of the trypanosomes. Its distinct roles in regulating FAZ formation in the two forms may provide a clue to the different mechanisms of cytokinetic initiation in procyclic and bloodstream trypanosomes.
Changes in the
N
-Glycome, Glycoproteins with Asn-Linked Glycans, of
Giardia lamblia
with Differentiation from Trophozoites to Cysts
Authors: Ratner Daniel M. , Cui Jike , Steffen Martin , Moore Landon L. , Robbins Phillips W. , Samuelson John 
Published: September 2008

ABSTRACT

Giardia lamblia
is present in the intestinal lumen as a binucleate, flagellated trophozoite or a quadranucleate, immotile cyst. Here we used the plant lectin wheat germ agglutinin (WGA), which binds to the disaccharide di-
N
-acetyl-chitobiose (GlcNAc
2
), which is the truncated Asn-linked glycan (N-glycan) of
Giardia
, to affinity purify the
N
-glycomes (glycoproteins with N-glycans) of trophozoites and cysts. Fluorescent WGA bound to the perinuclear membranes, peripheral acidified vesicles, and plasma membranes of trophozoites. In contrast, WGA bound strongly to membranes adjacent to the wall of
Giardia
cysts and less strongly to the endoplasmic reticulum and acidified vesicles. WGA lectin-affinity chromatography dramatically enriched secreted and membrane proteins of
Giardia
, including proteases and acid phosphatases that retain their activities. With mass spectroscopy, we identified 91 glycopeptides with N-glycans and 194 trophozoite-secreted and membrane proteins, including 42 unique proteins. The
Giardia
oligosaccharyltransferase, which contains a single catalytic subunit, preferred N glycosylation sites with Thr to those with Ser in vivo but had no preference for flanking amino acids. The most-abundant glycoproteins in the
N
-glycome of trophozoites were lysosomal enzymes, folding-associated proteins, and unique transmembrane proteins with Cys-, Leu-, or Gly-rich repeats. We identified 157 secreted and membrane proteins in the
Giardia
cysts, including 20 unique proteins. Compared to trophozoites, cysts were enriched in Gly-rich repeat transmembrane proteins, cyst wall proteins, and unique membrane proteins but had relatively fewer Leu-rich repeat proteins, folding-associated proteins, and unique secreted proteins. In summary, there are major changes in the
Giardia N
-glycome with the differentiation from trophozoites to cysts.
Deletion of the
Plasmodium falciparum
Merozoite Surface Protein 7 Gene Impairs Parasite Invasion of Erythrocytes
Authors: Kadekoppala Madhusudan , O'Donnell Rebecca A. , Grainger Munira , Crabb Brendan S. , Holder Anthony A. 
Published: September 2008

ABSTRACT

Merozoite surface proteins have been implicated in the initial attachment to the host red blood cell membrane that begins the process of invasion, an important step in the life cycle of the malaria parasite. In
Plasmodium falciparum
, merozoite surface proteins include several glycosylphosphatidyl inositol-anchored proteins and peripheral proteins attached to the membrane through protein-protein interactions. The most abundant of these proteins is the merozoite surface protein 1 (MSP1) complex, encoded by at least three genes:
msp1
,
msp6
, and
msp7
. The
msp7 g
ene is part of a six-member multigene family in
Plasmodium falciparum
. We have disrupted
msp7
in the
Plasmodium falciparum
D10 parasite, as confirmed by Southern hybridization. Immunoblot and indirect immunofluorescence analyses confirmed the MSP7 null phenotype of D10ΔMSP7 parasites. The synthesis, distribution, and processing of MSP1 were not affected in this parasite line. The level of expression and cellular distribution of the proteins MSP1, MSP3, MSP6, MSP9, and SERA5 remained comparable to those for the parental line. Furthermore, no significant change in the expression of MSP7-related proteins, except for that of MSRP5, was detected at the transcriptional level. The lack of MSP7 was not lethal at the asexual blood stage, but it did impair invasion of erythrocytes by merozoites to a significant degree. Despite this reduction in efficiency, D10ΔMSP7 parasites did not show any obvious preference for alternate pathways of invasion.
Maintenance Role of a Glutathionyl-Hydroquinone Lyase (PcpF) in Pentachlorophenol Degradation by
Sphingobium chlorophenolicum
ATCC 39723
Authors: Huang Yan , Xun Randy , Chen Guanjun , Xun Luying 
Published: September 2008

ABSTRACT

Pentachlorophenol (PCP) is a toxic pollutant. Its biodegradation has been extensively studied in
Sphingobium chlorophenolicum
ATCC 39723. All enzymes required to convert PCP to a common metabolic intermediate before entering the tricarboxylic acid cycle have been characterized. One of the enzymes is tetrachloro-
p
-hydroquinone (TeCH) reductive dehalogenase (PcpC), which is a glutathione (GSH)
S
-transferase (GST). PcpC catalyzes the GSH-dependent conversion of TeCH to trichloro-
p
-hydroquinone (TriCH) and then to dichloro-
p
-hydroquinone (DiCH) in the PCP degradation pathway. PcpC is susceptible to oxidative damage, and the damaged PcpC produces glutathionyl (GS) conjugates, GS-TriCH and GS-DiCH, which cannot be further metabolized by PcpC. The fate and effect of GS-hydroquinone conjugates were unknown. A putative GST gene (
pcpF
) is located next to
pcpC
on the bacterial chromosome. The
pcpF
gene was cloned, and the recombinant PcpF was purified. The purified PcpF was able to convert GS-TriCH and GS-DiCH conjugates to TriCH and DiCH, respectively. The GS-hydroquinone lyase reactions catalyzed by PcpF are rather unusual for a GST. The disruption of
pcpF
in
S. chlorophenolicum
made the mutant lose the GS-hydroquinone lyase activities in the cell extracts. The mutant became more sensitive to PCP toxicity and had a significantly decreased PCP degradation rate, likely due to the accumulation of the GS-hydroquinone conjugates inside the cell. Thus, PcpF played a maintenance role in PCP degradation and converted the GS-hydroquinone conjugates back to the intermediates of the PCP degradation pathway.
Genome Sequence of a Nephritogenic and Highly Transformable M49 Strain ofStreptococcus pyogenes
Authors: McShan W. Michael , Ferretti Joseph J. , Karasawa Tadahiro , Suvorov Alexander N. , Lin Shaoping , Qin Biafang , Jia Honggui , Kenton Steve , Najar Fares , Wu Hongmin , Scott Julie , Roe Bruce A. , Savic Dragutin J. 
Published: September 2008

ABSTRACTThe 1,815,783-bp genome of a serotype M49 strain ofStreptococcus pyogenes(group A streptococcus [GAS]), strain NZ131, has been determined. This GAS strain (FCT type 3;emmpattern E), originally isolated from a case of acute post-streptococcal glomerulonephritis, is unusually competent for electrotransformation and has been used extensively as a model organism for both basic genetic and pathogenesis investigations. As with the previously sequencedS. pyogenesgenomes, three unique prophages are a major source of genetic diversity. Two clustered regularly interspaced short palindromic repeat (CRISPR) regions were present in the genome, providing genetic information on previous prophage encounters. A unique cluster of genes was found in the pathogenicity island-likeemmregion that included a novel Nudix hydrolase, and, further, this cluster appears to be specific for serotype M49 and M82 strains. Nudix hydrolases eliminate potentially hazardous materials or prevent the unbalanced accumulation of normal metabolites; in bacteria, these enzymes may play a role in host cell invasion. Since M49S. pyogenesstrains have been known to be associated with skin infections, the Nudix hydrolase and its associated genes may have a role in facilitating survival in an environment that is more variable and unpredictable than the uniform warmth and moisture of the throat. The genome of NZ131 continues to shed light upon the evolutionary history of this human pathogen. Apparent horizontal transfer of genetic material has led to the existence of highly variable virulence-associated regions that are marked by multiple rearrangements and genetic diversification while other regions, even those associated with virulence, vary little between genomes. The genome regions that encode surface gene products that will interact with host targets or aid in immune avoidance are the ones that display the most sequence diversity. Thus, while natural selection favors stability in much of the genome, it favors diversity in these regions.
Processing of a Membrane Protein Required for Cell-to-Cell Signaling during Endospore Formation in
Bacillus subtilis
Authors: Serrano Mónica , Vieira Filipe , Moran Charles P. , Henriques Adriano O. 
Published: September 2008

ABSTRACT

Activation of the late prespore-specific RNA polymerase sigma factor σ
G
during
Bacillus subtilis
sporulation coincides with completion of the engulfment process, when the prespore becomes a protoplast fully surrounded by the mother cell cytoplasm and separated from it by a double membrane system. Activation of σ
G
also requires expression of
spoIIIJ
, coding for a membrane protein translocase of the YidC/Oxa1p/Alb3 family, and of the mother cell-specific
spoIIIA
operon. Here we present genetic and biochemical evidence indicating that SpoIIIAE, the product of one of the
spoIIIA
cistrons, and SpoIIIJ interact in the membrane, thereby linking the function of the
spoIIIJ
and
spoIIIA
loci in the activation of σ
G
. We also show that SpoIIIAE has a functional Sec-type signal peptide, which is cleaved during sporulation. Furthermore, mutations that reduce or eliminate processing of the SpoIIIAE signal peptide arrest sporulation following engulfment completion and prevent activation of σ
G
. SpoIIIJ-type proteins can function in cooperation with or independently of the Sec system. In one model, SpoIIIJ interacts with SpoIIIAE in the context of the Sec translocon to promote its correct localization and/or topology in the membrane, so that it can signal the activation of σ
G
following engulfment completion.
Phenotypic and Transcriptomic Characterization of
Bacillus subtilis
Mutants with Grossly Altered Membrane Composition
Authors: Salzberg Letal I. , Helmann John D. 
Published: September 2008

ABSTRACT

The
Bacillus subtilis
membrane contains diacylglycerol-based lipids with at least five distinct headgroups that together help to define the physical and chemical properties of the lipid bilayer. Here, we describe the phenotypic characterization of mutant strains lacking one or more of the following lipids: glycolipids (
ugtP
mutants), phosphatidylethanolamine (
pssA
and
psd
mutants), lysylphosphatidylglycerol (
mprF
), and cardiolipin (
ywnE
and
ywjE
). Alterations of membrane lipid headgroup composition are generally well-tolerated by the cell, and even severe alterations lead to only modest effects on growth proficiency. Mutants with decreased levels of positively charged lipids display an increased sensitivity to cationic antimicrobial compounds, and cells lacking glycolipids are more sensitive to the peptide antibiotic sublancin and are defective in swarming motility. A quadruple mutant strain (
ugtP pssA mprF ywnE
), with a membrane comprised predominantly of phosphatidylglycerol, is viable and grows at near-wild-type rates, although it forms long, coiled filaments. Transcriptome comparisons identified numerous regulons with altered expression in cells of the
ugtP
mutant, the
pssA mprF ywnE
triple mutant, and the
ugtP pssA mprF ywnE
quadruple mutant. These effects included a general decrease in expression of the SigD and FapR regulons and increased expression of cell envelope stress responses mediated by σ
M
and the YvrGHb two-component system.
Tricarboxylic Acid Cycle-Dependent Regulation of
Staphylococcus epidermidis
Polysaccharide Intercellular Adhesin Synthesis
Authors: Sadykov Marat R. , Olson Michael E. , Halouska Steven , Zhu Yefei , Fey Paul D. , Powers Robert , Somerville Greg A. 
Published: September 2008

ABSTRACT

Staphylococcus epidermidis
is a major nosocomial pathogen primarily infecting immunocompromised individuals or those with implanted biomaterials (e.g., catheters). Biomaterial-associated infections often involve the formation of a biofilm on the surface of the medical device. In
S. epidermidis
, polysaccharide intercellular adhesin (PIA) is an important mediator of biofilm formation and pathogenesis. Synthesis of PIA is regulated by at least three DNA binding proteins (IcaR, SarA, and σ
B
) and several environmental and nutritional conditions. Previously, we observed the environmental conditions that increased PIA synthesis decreased tricarboxylic acid (TCA) cycle activity. In this study,
S. epidermidis
TCA cycle mutants were constructed, and the function of central metabolism in PIA biosynthesis was examined. TCA cycle inactivation altered the metabolic status of
S. epidermidis
, resulting in a massive derepression of PIA biosynthetic genes and a redirection of carbon from growth into PIA biosynthesis. These data demonstrate that the bacterial metabolic status is a critical regulatory determinant of PIA synthesis. In addition, these data lead us to propose that the TCA cycle acts as a signal transduction pathway to translate external environmental cues into intracellular metabolic signals that modulate the activity of transcriptional regulators.
Frequent Homologous Recombination Events in
Mycobacterium tuberculosis
PE/PPE Multigene Families: Potential Role in Antigenic Variability
Authors: Karboul Anis , Mazza Alberto , Gey van Pittius Nicolaas C. , Ho John L. , Brousseau Roland , Mardassi Helmi 
Published: September 2008

ABSTRACT

The PE and PPE (PE/PPE) multigene families of
Mycobacterium tuberculosis
are particularly GC-rich and share extensive homologous repetitive sequences. We hypothesized that they may undergo homologous recombination events, a mechanism rarely described in the natural evolution of mycobacteria. To test our hypothesis, we developed a specific oligonucleotide-based microarray targeting nearly all of the PE/PPE genes, aimed at detecting signals for homologous recombination. Such a microarray has never before been reported due to the multiplicity and highly repetitive and homologous nature of these sequences. Application of the microarray to a collection of
M. tuberculosis
clinical isolates (
n
= 33) representing prevalent spoligotype strain families in Tunisia allowed successful detection of six deleted genomic regions involving a total of two PE and seven PPE genes. Some of these deleted genes are known to be immunodominant or involved in virulence. The four precisely determined deletions were flanked by 400- to 500-bp stretches of nearly identical sequences lying mainly at the conserved N-terminal region of the PE/PPE genes. These highly homologous sequences thus serve as substrates to mediate both intergenic and intragenic homologous recombination events, indicating an important function in generating strain variation. Importantly, all recombination events yielded a new in-frame fusion chimeric gene. Hence, homologous recombination within and between PE/PPE genes likely increased their antigenic variability, which may have profound implications in pathogenicity and/or host adaptation. The finding of high prevalence (∼45% and ∼58%) for at least two of the genomic deletions suggests that they likely confer advantageous biological attributes.
Suppression of ΔbipAPhenotypes inEscherichia coliby Abolishment of Pseudouridylation at Specific Sites on the 23S rRNA
Authors: Krishnan Karthik , Flower Ann M. 
Published: September 2008

ABSTRACTThe BipA protein ofEscherichia colihas intriguing similarities to the elongation factor subfamily of GTPases, including EF-Tu, EF-G, and LepA. In addition, phenotypes of abipAdeletion mutant suggest that BipA is involved in regulation of a variety of pathways. These two points have led to speculation that BipA may be a novel regulatory protein that affects efficient translation of target genes through direct interaction with the ribosome. We isolated and characterized suppressors of the cold-sensitive growth phenotype exhibited by ΔbipAstrains and identified insertion mutations inrluC. TherluCgene encodes a pseudouridine synthase responsible for pseudouridine modification of 23S rRNA at three sites, all located near the peptidyl transferase center. Deletion ofrluCnot only suppressed cold sensitivity but also alleviated the decrease in capsule synthesis exhibited bybipAmutants, suggesting that the phenotypic effects of BipA are manifested through an effect on the ribosome. The suppressor effect is specific torluC, as deletion of otherrlugenes did not relieve cold sensitivity, and further, more than a single pseudouridine residue is involved, as alteration of single residues did not produce suppressors. These results are consistent with a role for BipA in either the structure or the function of the ribosome and imply that wild-type ribosomes are dependent on BipA for efficient expression of target mRNAs and that the lack of pseudouridylation at these three sites renders the ribosomes BipA independent.
A Two-Component Regulatory System Integrates Redox State and Population Density Sensing in
Pseudomonas putida
Authors: Fernández-Piñar Regina , Ramos Juan Luis , Rodríguez-Herva José Juan , Espinosa-Urgel Manuel 
Published: September 2008

ABSTRACT

A two-component system formed by a sensor histidine kinase and a response regulator has been identified as an element participating in cell density signal transduction in
Pseudomonas putida
KT2440. It is a homolog of the
Pseudomonas aeruginosa
RoxS/RoxR system, which in turn belongs to the RegA/RegB family, described in photosynthetic bacteria as a key regulatory element. In KT2440, the two components are encoded by PP_0887 (
roxS
) and PP_0888 (
roxR
), which are transcribed in a single unit. Characterization of this two-component system has revealed its implication in redox signaling and cytochrome oxidase activity, as well as in expression of the cell density-dependent gene
ddcA
, involved in bacterial colonization of plant surfaces. Whole-genome transcriptional analysis has been performed to define the
P. putida
RoxS/RoxR regulon. It includes genes involved in sugar and amino acid metabolism and the sulfur starvation response and elements of the respiratory chain (a
cbb3
cytochrome oxidase, Fe-S clusters, and cytochrome
c
-related proteins) or genes participating in the maintenance of the redox balance. A putative RoxR recognition element containing a conserved hexamer (TGCCAG) has also been identified in promoters of genes regulated by this two-component system.
Characterization of the Oxygen-Responsive NreABC Regulon of
Staphylococcus aureus
Authors: Schlag Steffen , Fuchs Stephan , Nerz Christiane , Gaupp Rosmarie , Engelmann Susanne , Liebeke Manuel , Lalk Michael , Hecker Michael , Götz Friedrich 
Published: September 2008

ABSTRACT

Here, we investigate the functionality of the oxygen-responsive nitrogen regulation system NreABC in the human pathogen
Staphylococcus aureus
and evaluate its role in anaerobic gene regulation and virulence factor expression. Deletion of
nreABC
resulted in severe impairment of dissimilatory nitrate and nitrite reduction and led to a small-colony phenotype in the presence of nitrate during anaerobic growth. For characterization of the NreABC regulon, comparative DNA microarray and proteomic analyses between the wild type and
nreABC
mutant were performed under anoxic conditions in the absence and presence of nitrate. A reduced expression of virulence factors was not observed in the mutant. However, both the transcription of genes involved in nitrate and nitrite reduction and the accumulation of corresponding proteins were highly decreased in the
nreABC
mutant, which was unable to utilize nitrate as a respiratory oxidant and, hence, was forced to use fermentative pathways. These data were corroborated by the quantification of the extracellular metabolites lactate and acetate. Using an
Escherichia coli
-compatible two-plasmid system, the activation of the promoters of the nitrate and nitrite reductase operons and of the putative nitrate/nitrite transporter gene
narK
by NreBC was confirmed. Overall, our data indicate that NreABC is very likely a specific regulation system that is essential for the transcriptional activation of genes involved in dissimilatory reduction and transport of nitrate and nitrite. The study underscores the importance of NreABC as a fitness factor for
S. aureus
in anoxic environments.