bluuebunny/crossref_metadata_2025_split huggingface dataset:
Edwardsiella ictaluri
Encodes an Acid-Activated Urease That Is Required for Intracellular Replication in Channel Catfish (
Ictalurus punctatus
) Macrophages
Authors: Booth Natha J. , Beekman Judith B. , Thune Ronald L. 
Published: September 2009

ABSTRACT

Genomic analysis indicated that
Edwardsiella ictaluri
encodes a putative urease pathogenicity island containing the products of nine open reading frames, including urea and ammonium transporters. In vitro studies with wild-type
E. ictaluri
and a
ureG
::
kan
urease mutant strain indicated that
E. ictaluri
is significantly tolerant of acid conditions (pH 3.0) but that urease activity is not required for acid tolerance. Growth studies demonstrated that
E. ictaluri
is unable to grow at pH 5 in the absence of urea but is able to elevate the environmental pH from pH 5 to pH 7 and grow when exogenous urea is available. Substantial production of ammonia was observed for wild-type
E. ictaluri
in vitro in the presence of urea at low pH, and optimal activity occurred at pH 2 to 3. No ammonia production was detected for the urease mutant. Proteomic analysis with two-dimensional gel electrophoresis indicated that urease proteins are expressed at both pH 5 and pH 7, although urease activity is detectable only at pH 5. Urease was not required for initial invasion of catfish but was required for subsequent proliferation and virulence. Urease was not required for initial uptake or survival in head kidney-derived macrophages but was required for intracellular replication. Intracellular replication of wild-type
E. ictaluri
was significantly enhanced when urea was present, indicating that urease plays an important role in intracellular survival and replication, possibly through neutralization of the acidic environment of the phagosome.
Composition and Activity of an Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture
Authors: Blöthe Marco , Roden Eric E. 
Published: September 2009

ABSTRACT

16S rRNA gene libraries from the lithoautotrophic Fe(II)-oxidizing, nitrate-reducing enrichment culture described by Straub et al. (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl. Environ. Microbiol. 62:1458-1460, 1996) were dominated by a phylotype related (95% 16S rRNA gene homology) to the autotrophic Fe(II) oxidizer
Sideroxydans lithotrophicus
. The libraries also contained phylotypes related to known heterotrophic nitrate reducers
Comamonas badia
,
Parvibaculum lavamentivorans
, and
Rhodanobacter thiooxidans
. The three heterotrophs were isolated and found to be capable of only partial (12 to 24%) Fe(II) oxidation, suggesting that the
Sideroxydans
species has primary responsibility for Fe(II) oxidation in the enrichment culture.
l
-Ribose Production from
l
-Arabinose by Using Purified
l
-Arabinose Isomerase and Mannose-6-Phosphate Isomerase from
Geobacillus thermodenitrificans
Authors: Yeom Soo-Jin , Kim Nam-Hee , Park Chang-Su , Oh Deok-Kun 
Published: September 2009

ABSTRACT

Two enzymes,
l
-arabinose isomerase and mannose-6-phosphate isomerase, from
Geobacillus thermodenitrificans
produced 118 g/liter
l
-ribose from 500 g/liter
l
-arabinose at pH 7.0, 70°C, and 1 mM Co
2+
for 3 h, with a conversion yield of 23.6% and a volumetric productivity of 39.3 g liter
−1
h
−1
.
Reconstruction of Signaling Networks Regulating Fungal Morphogenesis by Transcriptomics
Authors: Meyer Vera , Arentshorst Mark , Flitter Simon J. , Nitsche Benjamin M. , Kwon Min Jin , Reynaga-Peña Cristina G. , Bartnicki-Garcia Salomon , van den Hondel Cees A. M. J. J. , Ram Arthur F. J. 
Published: September 2009

ABSTRACTCoordinated control of hyphal elongation and branching is essential for sustaining mycelial growth of filamentous fungi. In order to study the molecular machinery ensuring polarity control in the industrial fungusAspergillus niger, we took advantage of the temperature-sensitive (ts) apical-branchingramosa-1mutant. We show here that this strain serves as an excellent model system to study critical steps of polar growth control during mycelial development and report for the first time a transcriptomic fingerprint of apical branching for a filamentous fungus. This fingerprint indicates that several signal transduction pathways, including TORC2, phospholipid, calcium, and cell wall integrity signaling, concertedly act to control apical branching. We furthermore identified the genetic locus affected in theramosa-1mutant by complementation of thetsphenotype. Sequence analyses demonstrated that a single amino acid exchange in the RmsA protein is responsible for induced apical branching of theramosa-1mutant. Deletion experiments showed that the correspondingrmsAgene is essential for the growth ofA. niger, and complementation analyses withSaccharomyces cerevisiaeevidenced that RmsA serves as a functional equivalent of the TORC2 component Avo1p. TORC2 signaling is required for actin polarization and cell wall integrity inS. cerevisiae. Congruently, our microscopic investigations showed that polarized actin organization and chitin deposition are disturbed in theramosa-1mutant. The integration of the transcriptomic, genetic, and phenotypic data obtained in this study allowed us to reconstruct a model for cellular events involved in apical branching.
A Contiguous Compartment Functions as Endoplasmic Reticulum and Endosome/Lysosome in
Giardia lamblia
Authors: Abodeely Marla , DuBois Kelly N. , Hehl Adrian , Stefanic Sasa , Sajid Mohammed , deSouza Wanderley , Attias Marcia , Engel Juan C. , Hsieh Ivy , Fetter Richard D. , McKerrow James H. 
Published: September 2009

ABSTRACT

The dynamic evolution of organelle compartmentalization in eukaryotes and how strictly compartmentalization is maintained are matters of ongoing debate. While the endoplasmic reticulum (ER) is classically envisioned as the site of protein cotranslational translocation, it has recently been proposed to have pluripotent functions. Using transfected reporter constructs, organelle-specific markers, and functional enzyme assays, we now show that in an early-diverging protozoan,
Giardia lamblia
, endocytosis and subsequent degradation of exogenous proteins occur in the ER or in an adjacent and communicating compartment. The
Giardia
endomembrane system is simple compared to those of typical eukaryotes. It lacks peroxisomes, a classical Golgi apparatus, and canonical lysosomes.
Giardia
orthologues of mammalian lysosomal proteases function within an ER-like tubulovesicular compartment, which itself can dynamically communicate with clathrin-containing vacuoles at the periphery of the cell to receive endocytosed proteins. These primitive characteristics support
Giardia
's proposed early branching and could serve as a model to study the compartmentalization of endocytic and lysosomal functions into organelles distinct from the ER. This system also may have functional similarity to the retrograde transport of toxins and major histocompatibility complex class I function in the ER of mammals.
Horizontal Chromosome Transfer, a Mechanism for the Evolution and Differentiation of a Plant-Pathogenic Fungus
Authors: Akagi Yasunori , Akamatsu Hajime , Otani Hiroshi , Kodama Motoichiro 
Published: September 2009

ABSTRACT

The tomato pathotype of
Alternaria alternata
produces host-specific AAL toxin and causes Alternaria stem canker on tomato. A polyketide synthetase (PKS) gene,
ALT1
, which is involved in AAL toxin biosynthesis, resides on a 1.0-Mb conditionally dispensable chromosome (CDC) found only in the pathogenic and AAL toxin-producing strains. Genomic sequences of
ALT1
and another PKS gene, both of which reside on the CDC in the tomato pathotype strains, were compared to those of tomato pathotype strains collected worldwide. This revealed that the sequences of both CDC genes were identical among five
A. alternata
tomato pathotype strains having different geographical origins. On the other hand, the sequences of other genes located on chromosomes other than the CDC are not identical in each strain, indicating that the origin of the CDC might be different from that of other chromosomes in the tomato pathotype. Telomere fingerprinting and restriction fragment length polymorphism analyses of the
A. alternata
strains also indicated that the CDCs in the tomato pathotype strains were identical, although the genetic backgrounds of the strains differed. A hybrid strain between two different pathotypes was shown to harbor the CDCs derived from both parental strains with an expanded range of pathogenicity, indicating that CDCs can be transmitted from one strain to another and stably maintained in the new genome. We propose a hypothesis whereby the ability to produce AAL toxin and to infect a plant could potentially be distributed among
A. alternata
strains by horizontal transfer of an entire pathogenicity chromosome. This could provide a possible mechanism by which new pathogens arise in nature.
Overexpression of MitochondrialLeishmania majorAscorbate Peroxidase Enhances Tolerance to Oxidative Stress-Induced Programmed Cell Death and Protein Damage
Authors: Dolai Subhankar , Yadav Rajesh K. , Pal Swati , Adak Subrata 
Published: September 2009

ABSTRACTAscorbate peroxidase fromLeishmania major(LmAPX) is one of the key enzymes for scavenging of reactive oxygen species generated from the mitochondrial respiratory chain. We have investigated whether mitochondrial LmAPX has any role in oxidative stress-induced apoptosis. The measurement of reduced glutathione (GSH) and protein carbonyl contents in cellular homogenates indicates that overexpression of LmAPX protectsLeishmaniacells against depletion of GSH and oxidative damage of proteins by H2O2or camptothecin (CPT) treatment. Confocal microscopy and fluorescence spectroscopy data have revealed that the intracellular elevation of Ca2+attained by the LmAPX-overexpressing cells was always below that attained in control cells. Flow cytometry assay data and confocal microscopy observation strongly suggest that LmAPX overexpression protects cells from H2O2-induced mitochondrial membrane depolarization as well as ATP decrease. Western blot data suggest that overexpression of LmAPX shields against H2O2- or CPT-induced cytochromecand endonuclease G release from mitochondria and subsequently their accumulation in the cytoplasm. Caspase activity assay by flow cytometry shows a lower level of caspase-like protease activity in LmAPX-overexpressing cells under apoptotic stimuli. The data on phosphatidylserine exposed on the cell surface and DNA fragmentation results show that overexpression of LmAPX renders theLeishmaniacells more resistant to apoptosis provoked by H2O2or CPT treatment. Taken together, these results indicate that constitutive overexpression of LmAPX in the mitochondria ofL. majorprevents cells from the deleterious effects of oxidative stress, that is, mitochondrial dysfunction and cellular death.
Distinct Subsets of Sit4 Holophosphatases Are Required for Inhibition ofSaccharomyces cerevisiaeGrowth by Rapamycin and Zymocin
Authors: Jablonowski Daniel , Täubert Jens-Eike , Bär Christian , Stark Michael J. R. , Schaffrath Raffael 
Published: September 2009

ABSTRACTProtein phosphatase Sit4 is required for growth inhibition ofSaccharomyces cerevisiaeby the antifungals rapamycin and zymocin. Here, we show that the rapamycin effector Tap42, which interacts with Sit4, is dispensable for zymocin action. Although Tap42 binding-deficientsit4mutants are resistant to zymocin, these mutations also block interaction between Sit4 and the Sit4-associating proteins Sap185 and Sap190, previously shown to mediate zymocin toxicity. Among the four differentSAPgenes, we found thatSAP190deletions specifically induce rapamycin resistance but that this phenotype is reversed in the additional absence ofSAP155. Similarly, the rapamycin resistance of anrrd1Δ mutant lacking the Sit4 interactor Rrd1 specifically requires the Sit4/Sap190 complex. Thus, Sit4/Sap190 and Sit4/Sap155 holophosphatases apparently play opposing roles following rapamycin treatment, although rapamycin inhibition is operational in the absence of all Sap family members or Sit4. We further identified a Sit4-interacting region on Sap185 insap190Δ cells that mediates Sit4/Sap185 complex formation and is essential for dephosphorylation of Elp1, a subunit of the Elongator complex. This suggests that Sit4/Sap185 and Sit4/Sap190 holophosphatases promote Elongator functions, a notion supported by data showing that their inactivation eliminates Elongator-dependent processes, including tRNA suppression bySUP4and tRNA cleavage by zymocin.
Conservation of the Sterol Regulatory Element-Binding Protein Pathway and Its Pathobiological Importance in
Cryptococcus neoformans
Authors: Chang Yun C. , Ingavale Susham S. , Bien Clara , Espenshade Peter , Kwon-Chung Kyung J. 
Published: September 2009

ABSTRACT

The mammalian sterol regulatory element-binding protein (SREBP) homolog, Sre1, is important for adaptation and growth of
Cryptococcus neoformans
in the mouse brain, where oxygen concentration and nutritional conditions are suboptimal for fungal growth. The extent of conservation of the SREBP pathway in
C. neoformans
or in any other fungi, however, has not been investigated. We generated mutants susceptible to low oxygen and identified six genes that play a role in the SREBP pathway. Three of these genes (
SFB2
,
KAP123
, and
GSK3
) are not known to be involved in the SREBP pathway in other fungi. Furthermore, we show that
C. neoformans
contains an additional gene,
DAM1
, which functions in the SREBP pathway but is yet to be described. Mutants associated with the steps prior to formation of the nuclear Sre1 form dramatically reduced accumulation of the nuclear form under low-oxygen conditions. Concurrently, two mutant strains,
scp1Δ
and
stp1Δ
, and the previously isolated
sre1Δ
strain showed reduction in ergosterol levels, hypersensitivity to several chemical agents, including azole antifungals, CoCl
2
, and compounds producing reactive oxygen or nitrogen species, and most importantly, reduced virulence in mice. Mutants affecting genes involved in later steps of the Sre1 pathway, such as those required for import and phosphorylation of proteins in the nucleus, showed less compelling phenotypes. These findings suggest that the SREBP pathway is highly conserved in
C. neoformans
and it serves as an important link between sterol biosynthesis, oxygen sensing, CoCl
2
sensitivity, and virulence in
C. neoformans
.
Depletion of the Signal Recognition Particle Receptor Inactivates Ribosomes in
Escherichia coli
Authors: Bürk Jonas , Weiche Benjamin , Wenk Meike , Boy Diana , Nestel Sigrun , Heimrich Bernd , Koch Hans-Georg 
Published: September 2009

ABSTRACT

The signal recognition particle (SRP)-dependent cotranslational targeting of proteins to the cytoplasmic membrane in bacteria or the endoplasmic reticulum membrane in eukaryotes is an essential process in most living organisms. Eukaryotic cells have been shown to respond to an impairment of the SRP pathway by (i) repressing ribosome biogenesis, resulting in decreased protein synthesis, and (ii) by increasing the expression of protein quality control mechanisms, such as chaperones and proteases. In the current study, we have analyzed how bacteria like
Escherichia coli
respond to a gradual depletion of FtsY, the bacterial SRP receptor. Our analyses using cell-free transcription/translation systems showed that FtsY depletion inhibits the translation of both SRP-dependent and SRP-independent proteins. This synthesis defect is the result of a multifaceted response that includes the upregulation of the ribosome-inactivating protein ribosome modulation factor (RMF). Although the consequences of these responses in
E. coli
are very similar to some of the effects also observed in eukaryotic cells, one striking difference is that
E. coli
obviously does not reduce the rate of protein synthesis by downregulating ribosome biogenesis. Instead, the upregulation of RMF leads to a direct and reversible inhibition of translation.
Functional Characterization of Flagellin Glycosylation in
Campylobacter jejuni
81-176
Authors: Ewing Cheryl P. , Andreishcheva Ekaterina , Guerry Patricia 
Published: September 2009

ABSTRACT

The major flagellin of
Campylobacter jejuni
strain 81-176, FlaA, has been shown to be glycosylated at 19 serine or threonine sites, and this glycosylation is required for flagellar filament formation. Some enzymatic components of the glycosylation machinery of
C. jejuni
81-176 are localized to the poles of the cell in an FlhF-independent manner. Flagellin glycosylation could be detected in flagellar mutants at multiple levels of the regulatory hierarchy, indicating that glycosylation occurs independently of the flagellar regulon. Mutants were constructed in which each of the 19 serine or threonines that are glycosylated in FlaA was converted to an alanine. Eleven of the 19 mutants displayed no observable phenotype, but the remaining 8 mutants had two distinct phenotypes. Five mutants (mutations S417A, S436A, S440A, S457A, and T481A) were fully motile but defective in autoagglutination (AAG). Three other mutants (mutations S425A, S454A, and S460A) were reduced in motility and synthesized truncated flagellar filaments. The data implicate certain glycans in mediating filament-filament interactions resulting in AAG and other glycans appear to be critical for structural subunit-subunit interactions within the filament.
Repeat-Associated Plasticity in the
Helicobacter pylori
RD Gene Family
Authors: Shak Joshua R. , Dick Jonathan J. , Meinersmann Richard J. , Perez-Perez Guillermo I. , Blaser Martin J. 
Published: September 2009

ABSTRACT

The bacterium
Helicobacter pylori
is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two
H. pylori
strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the
H. pylori
RD gene family. Each gene of this family is composed of a conserved 3′ region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5′ region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42
H. pylori
strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject's stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by
H. pylori
-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding
H. pylori
persistence in its natural host.
Envelope Proteins of the CsmB/CsmF and CsmC/CsmD Motif Families Influence the Size, Shape, and Composition of Chlorosomes in
Chlorobaculum tepidum
Authors: Li Hui , Bryant Donald A. 
Published: September 2009

ABSTRACT

The chlorosome envelope of
Chlorobaculum tepidum
contains 10 proteins that belong to four structural motif families. A previous mutational study (N.-U. Frigaard, H. Li, K. J. Milks, and D. A. Bryant, J. Bacteriol. 186:646-653, 2004) suggested that some of these proteins might have redundant functions. Six multilocus mutants were constructed to test the effects of eliminating the proteins of the CsmC/CsmD and CsmB/CsmF motif families, and the resulting strains were characterized physiologically and biochemically. Mutants lacking all proteins of either motif family still assembled functional chlorosomes, and as measured by growth rates of the mutant strains, light harvesting was affected only at the lowest light intensities tested (9 and 32 μmol photons m
−2
s
−1
). The size, composition, and biogenesis of the mutant chlorosomes differed from those of wild-type chlorosomes. Mutants lacking proteins of the CsmC/CsmD motif family produced smaller chlorosomes than did the wild type, and the

Q
y

absorbance maximum for the bacteriochlorophyll
c
aggregates in these chlorosomes was strongly blueshifted. Conversely, the chlorosomes of mutants lacking proteins of the CsmB/CsmF motif family were larger than wild-type chlorosomes, and the

Q
y

absorption for their bacteriochlorophyll
c
aggregates was redshifted. When CsmH was eliminated in addition to other proteins of either motif family, chlorosomes had smaller diameters. These data show that the chlorosome envelope proteins of the CsmB/CsmF and CsmC/CsmD families play important roles in determining chlorosome size as well as the assembly and supramolecular organization of the bacteriochlorophyll
c
aggregates within the chlorosome.
Identification of Direct Transcriptional Target Genes of ExoS/ChvI Two-Component Signaling in
Sinorhizobium meliloti
Authors: Chen Esther J. , Fisher Robert F. , Perovich Virginia M. , Sabio Erich A. , Long Sharon R. 
Published: September 2009

ABSTRACT

The
Sinorhizobium meliloti
ExoS/ChvI two-component signaling pathway is required for the development of a nitrogen-fixing symbiosis between
S. meliloti
and its plant hosts. ExoS/ChvI also has important roles in regulating succinoglycan production, biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. Previous microarray experiments with an
exoS96
::Tn
5
mutant indicated that ExoS/ChvI influences the expression of a few hundred genes, complicating the investigation of which downstream genes respond directly or indirectly to ExoS/ChvI regulation. To focus our study of ExoS/ChvI transcriptional target genes, we performed transcriptional profiling with
chvI
gain-of-function and reduced-function strains. The
chvI
gain-of-function strain that we used contains a dominant gain-of-function
chvI
allele in addition to wild-type
chvI
. We identified genes that, relative to their expression level in the wild type, are both upregulated in the
chvI
gain-of-function strain and downregulated in the reduced-function strain or vice versa. Guided by this focused set of genes, we performed gel mobility shift assays and demonstrated that ChvI directly binds the intergenic regions upstream of
ropB1
, SMb21440, and SMc01580. Furthermore, DNase I footprint analysis of the region upstream of SMc01580 identified a specific DNA sequence bound by ChvI and allowed the discovery of a possible motif for ChvI binding. Our results provide insight into the mechanism of how ExoS/ChvI regulates its downstream targets and lay a foundation for studying this conserved pathway with critical roles in free-living and symbiotic bacteria.