bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Biosynthetic Step in the Melanin Pathway ofWangiella(Exophiala)dermatitidis: Evidence for 2-Acetyl-1,3,6,8-Tetrahydroxynaphthalene as a Novel Precursor
Authors: Wheeler Michael H. , Abramczyk Dariusz , Puckhaber Lorraine S. , Naruse Michinori , Ebizuka Yutaka , Fujii Isao , Szaniszlo Paul J. 
Published: August 2008

ABSTRACTThe predominant cell wall melanin ofWangiella dermatitidis, a black fungal pathogen of humans, is synthesized from 1,8-dihydroxynaphthalene (D2HN). An early precursor, 1,3,6,8-tetrahydroxynaphthalene (T4HN), in the pathway leading to D2HN is reportedly produced directly as a pentaketide by an iterative type I polyketide synthase (PKS). In contrast, the bluish-green pigment inAspergillus fumigatusis produced after the enzyme Ayg1p converts the PKS product, the heptaketide YWA1, to T4HN. Previously, we created a new melanin-deficient mutant ofW. dermatitidis, WdBrm1, by random molecular insertion. From this strain, the altered gene WdYG1was cloned by a marker rescue strategy and found to encode WdYg1p, an ortholog of Ayg1p. In the present study, two gene replacement mutants devoid of the complete WdYG1gene were derived to eliminate the possibility that the phenotype of WdBrm1 was due to other mutations. Characterization of the new mutants showed that they were phenotypically identical to WdBrm1. Chemical analyses of mutant cultures demonstrated that melanin biosynthesis was blocked, resulting in the accumulation of 2-acetyl-1,3,6,8-tetrahydroxynaphthalene (AT4HN) and its oxidative product 3-acetylflaviolin in the culture media. When given to an albinoW. dermatitidisstrain with an inactivated WdPKS1gene, AT4HN was mostly oxidized to 3-acetylflaviolin and deacetylated to flaviolin. Under reduced oxygen conditions, cell-free homogenates of the albino converted AT4HN to D2HN. This is the first report of evidence that the hexaketide AT4HN is a melanin precursor for T4HN inW. dermatitidis.
Nucleus-Specific Importin Alpha Proteins and Nucleoporins Regulate Protein Import and Nuclear Division in the Binucleate
Tetrahymena thermophila
Authors: Malone Colin D. , Falkowska Katarzyna A. , Li Alanna Y. , Galanti Sarah E. , Kanuru Reshi C. , LaMont Elizabeth G. , Mazzarella Kate C. , Micev Alan J. , Osman Morwan M. , Piotrowski Nicholas K. , Suszko Jason W. , Timm Adam C. , Xu Ming-Ming , Liu Lucy , Chalker Douglas L. 
Published: August 2008

ABSTRACT

The ciliate
Tetrahymena thermophila
, having both germ line micronuclei and somatic macronuclei, must possess a specialized nucleocytoplasmic transport system to import proteins into the correct nucleus. To understand how
Tetrahymena
can target proteins to distinct nuclei, we first characterized FG repeat-containing nucleoporins and found that micro- and macronuclei utilize unique subsets of these proteins. This finding implicates these proteins in the differential permeability of the two nuclei and implies that nuclear pores with discrete specificities are assembled within a single cell. To identify the import machineries that interact with these different pores, we characterized the large families of karyopherin homologs encoded within the genome. Localization studies of 13 putative importin (imp) α- and 11 imp β-like proteins revealed that imp α-like proteins are nucleus specific—nine localized to the germ line micronucleus—but that most imp β-like proteins localized to both types of nuclei. These data suggest that micronucleus-specific proteins are transported by specific imp α adapters. The different imp α proteins exhibit substantial sequence divergence and do not appear to be simply redundant in function. Disruption of the
IMA10
gene encoding an imp α-like protein that accumulates in dividing micronuclei results in nuclear division defects and lethality. Thus, nucleus-specific protein import and nuclear function in
Tetrahymena
are regulated by diverse, specialized karyopherins.
Dissecting Colony Development ofNeurospora crassaUsing mRNA Profiling and Comparative Genomics Approaches
Authors: Kasuga Takao , Glass N. Louise 
Published: August 2008

ABSTRACTColony development, which includes hyphal extension, branching, anastomosis, and asexual sporulation, is a fundamental aspect of the life cycle of filamentous fungi; genetic mechanisms underlying these phenomena are poorly understood. We conducted transcriptional profiling during colony development of the model filamentous fungusNeurospora crassa, using 70-mer oligonucleotide microarrays. Relative mRNA expression levels were determined for six sections of defined age excised from a 27-h-oldN. crassacolony. Functional category analysis showed that the expression of genes involved in cell membrane biosynthesis, polar growth, and cellular signaling was enriched at the periphery of the colony. The relative expression of genes involved in protein synthesis and energy production was enriched in the middle section of the colony, while sections of the colony undergoing asexual development (conidiogenesis) were enriched in expression of genes involved in protein/peptide degradation and unclassified proteins. A cross-examination of theN. crassadata set with a published data set ofAspergillus nigerrevealed shared patterns in the spatiotemporal regulation of gene orthologs during colony development. At present, less than 50% of genes inN. crassahave functional annotation, which imposes the chief limitation on data analysis. Using an evolutionary approach, we observed that the expression of phylogenetically conserved groups of genes was enriched in the middle section of anN. crassacolony whereas expression of genes unique to euascomycete species and ofN. crassaorphan genes was enriched at the colony periphery and in the older, conidiating sections of a fungal colony.
Protein Import into Hydrogenosomes ofTrichomonas vaginalisInvolves both N-Terminal and Internal Targeting Signals: a Case Study of Thioredoxin Reductases
Authors: Mentel Marek , Zimorski Verena , Haferkamp Patrick , Martin William , Henze Katrin 
Published: August 2008

ABSTRACTThe parabasalian flagellateTrichomonas vaginalisharbors mitochondrion-related and H2-producing organelles of anaerobic ATP synthesis, called hydrogenosomes, which harbor oxygen-sensitive enzymes essential to its pyruvate metabolism. In the human urogenital tract, however,T. vaginalisis regularly exposed to low oxygen concentrations and therefore must possess antioxidant systems protecting the organellar environment against the detrimental effects of molecular oxygen and reactive oxygen species. We have identified two closely related hydrogenosomal thioredoxin reductases (TrxRs), the hitherto-missing component of a thioredoxin-linked hydrogenosomal antioxidant system. One of the two hydrogenosomal TrxR isoforms, TrxRh1, carried an N-terminal extension resembling known hydrogenosomal targeting signals. Expression of hemagglutinin-tagged TrxRh1 in transfectedT. vaginaliscells revealed that its N-terminal extension was necessary to import the protein into the organelles. The second hydrogenosomal TrxR isoform, TrxRh2, had no N-terminal targeting signal but was nonetheless efficiently targeted to hydrogenosomes. N-terminal presequences from hydrogenosomal proteins with known processing sites, i.e., the alpha subunit of succinyl coenzyme A synthetase (SCSα) and pyruvate:ferredoxin oxidoreductase A, were investigated for their ability to direct mature TrxRh1 to hydrogenosomes. Neither presequence directed TrxRh1 to hydrogenosomes, indicating that neither extension is, by itself, sufficient for hydrogenosomal targeting. Moreover, SCSα lacking its N-terminal extension was efficiently imported into hydrogenosomes, indicating that this extension is not required for import of this major hydrogenosomal protein. The finding that some hydrogenosomal enzymes require N-terminal signals for import but that in others the N-terminal extension is not necessary for targeting indicates the presence of additional targeting signals within the mature subunits of several hydrogenosome-localized proteins.
A Protein with Similarity to PTEN Regulates Aggregation Territory Size by Decreasing Cyclic AMP Pulse Size during
Dictyostelium discoideum
Development
Authors: Tang Yitai , Gomer Richard H. 
Published: August 2008

ABSTRACT

An interesting but largely unanswered biological question is how eukaryotic organisms regulate the size of multicellular tissues. During development, a lawn of
Dictyostelium
cells breaks up into territories, and within the territories the cells aggregate in dendritic streams to form groups of ∼20,000 cells. Using random insertional mutagenesis to search for genes involved in group size regulation, we found that an insertion in the
cnrN
gene affects group size. Cells lacking CnrN (
cnrN
−
) form abnormally small groups, which can be rescued by the expression of exogenous CnrN. Relayed pulses of extracellular cyclic AMP (cAMP) direct cells to aggregate by chemotaxis to form aggregation territories and streams.
cnrN
−
cells overaccumulate cAMP during development and form small territories. Decreasing the cAMP pulse size by treating
cnrN
−
cells with cAMP phosphodiesterase or starving
cnrN
−
cells at a low density rescues the small-territory phenotype. The predicted CnrN sequence has similarity to phosphatase and tensin homolog (PTEN), which in
Dictyostelium
inhibits cAMP-stimulated phosphatidylinositol 3-kinase signaling pathways. CnrN inhibits cAMP-stimulated phosphatidylinositol 3,4,5-trisphosphate accumulation, Akt activation, actin polymerization, and cAMP production. Our results suggest that CnrN is a protein with some similarities to PTEN and that it regulates cAMP signal transduction to regulate territory size.
β1,2-Xylosyltransferase Cxt1p Is Solely Responsible for Xylose Incorporation into
Cryptococcus neoformans
Glycosphingolipids
Authors: Castle Sherry A. , Owuor Elizabeth A. , Thompson Stephanie H. , Garnsey Michelle R. , Klutts J. Stacey , Doering Tamara L. , Levery Steven B. 
Published: August 2008

ABSTRACT

The Manα1,3(Xylβ1,2)Manα structural motif is common to both capsular polysaccharides of
Cryptococcus neoformans
and to cryptococcal glycosphingolipids. Comparative analysis of glycosphingolipid structural profiles in wild-type and mutant strains showed that the Xylβ1,2-transferase (Cxt1p) that participates in capsular polysaccharide biosynthesis is also the sole transferase responsible for adding xylose to
C. neoformans
glycosphingolipids.
Regulation of CorA Mg
2+
Channel Function Affects the Virulence of
Salmonella enterica
Serovar Typhimurium
Authors: Papp-Wallace Krisztina M. , Maguire Michael E. 
Published: August 2008

ABSTRACT

The CorA Mg
2+
channel is the primary source of intracellular Mg
2+
in
Salmonella enterica
serovar Typhimurium. In another study, we found that a strain lacking
corA
was attenuated in mice and also defective for invasion and replication within Caco-2 epithelial cells (K. M. Papp-Wallace, M. Nartea, D. G. Kehres, S. Porwollik, M. McClelland, S. J. Libby, F. C. Fang, and M. E. Maguire, J. Bacteriol. 190:6517-6523, 2008). Therefore, we further examined
Salmonella
interaction with Caco-2 epithelial cells. Inhibiting CorA acutely or chronically with a high concentration of a selective inhibitor, Co(III) hexaammine, had no effect on
S. enterica
serovar Typhimurium invasion of Caco-2 epithelial cells. Complementing the
corA
mutation with
corA
from various species rescued the invasion defect only if the complementing allele was functional and if it was evolutionarily similar to
S. enterica
serovar Typhimurium CorA. One explanation for these results could be that regulation of CorA function is needed for optimal virulence. Further experiments examining
corA
transcription, CorA protein content, CorA transport, and cell Mg
2+
content indicated that both CorA expression and CorA function are differentially regulated. Moreover, the rates of Mg
2+
influx via CorA are not closely correlated with either protein levels or Mg
2+
content. We conclude that loss of the CorA protein disrupts a regulatory network(s) with the ultimate phenotype of decreased virulence. This conclusion is compatible with the microarray results in our other study, which showed that loss of
corA
resulted in changes in transcription (and protein expression) in multiple metabolic pathways (Papp-Wallace et al., J. Bacteriol. 190:6517-6523, 2008). Further study of the regulation of CorA expression and function provides an opportunity to dissect the complexity of Mg
2+
homeostasis and its ties to virulence within the bacterium.
Transition State Regulator AbrB Inhibits Transcription of
Bacillus amyloliquefaciens
FZB45 Phytase through Binding at Two Distinct Sites Located within the Extended
phyC
Promoter Region
Authors: Makarewicz Oliwia , Neubauer Svetlana , Preusse Corinna , Borriss Rainer 
Published: August 2008

ABSTRACT

We have previously identified the
phyC
gene of
Bacillus amyloliquefaciens
FZB45, encoding extracellular phytase, as a member of the PhoP regulon, which is expressed only during phosphate starvation. Its σ
A
-dependent promoter is positively and negatively regulated by the phosphorylated PhoP response regulator in a phosphate-dependent manner (O. Makarewicz, S. Dubrac, T. Msadek, and R. Borriss, J. Bacteriol. 188:6953-6965, 2006). Here, we provide experimental evidence that the transcription of
phyC
underlies a second control mechanism exerted by the global transient-phase regulator protein, AbrB, which hinders its expression during exponential growth. Gel mobility shift and DNase I footprinting experiments demonstrated that AbrB binds to two different regions in the
phyC
promoter region that are separated by about 200 bp. One binding site is near the divergently orientated
yodU
gene, and the second site is located downstream of the
phyC
promoter and extends into the coding region of the
phyC
gene. Cooperative binding to the two distant binding regions is necessary for the AbrB-directed repression of
phyC
transcription. AbrB does not affect the transcription of the neighboring
yodU
gene.
A Defect in Menadione Biosynthesis Induces Global Changes in Gene Expression in
Staphylococcus aureus
Authors: Kohler Christian , von Eiff Christof , Liebeke Manuel , McNamara Peter J. , Lalk Michael , Proctor Richard A. , Hecker Michael , Engelmann Susanne 
Published: August 2008

ABSTRACT

Both the high-resolution two-dimensional protein gel electrophoresis technique and full-genome DNA microarrays were used for identification of
Staphylococcus aureus
genes whose expression was changed by a mutation in
menD
. Because the electron transport chain is interrupted, the mutant should be unable to use oxygen and nitrate as terminal electron acceptors. Consistent with this, a mutation in
menD
was found to cause a gene expression pattern typically detected under anaerobic conditions in wild-type cells: proteins involved in glycolytic as well as in fermentation pathways were upregulated, whereas tricarboxylic acid (TCA) cycle enzymes were significantly downregulated. Moreover, the expression of genes encoding enzymes for nitrate respiration and the arginine deiminase pathway was strongly increased in the mutant strain. These results indicate that the
menD
mutant, just as the site-directed
S. aureus hemB
mutant, generates ATP from glucose or fructose mainly by substrate phosphorylation and might be defective in utilizing a variety of carbon sources, including TCA cycle intermediates and compounds that generate ATP only via electron transport phosphorylation. Of particular interest is that there are also differences in the gene expression patterns between
hemB
and
menD
mutants. While some anaerobically active enzymes were present in equal amounts in both strains (Ldh1, SACOL2535), other classically anaerobic enzymes seem to be present in higher amounts either in the
hemB
mutant (e.g., PflB, Ald1, IlvA1) or in the
menD
mutant (
arc
operon). Only genes involved in nitrate respiration and the
ald1
operon seem to be additionally regulated by a depletion of oxygen in the
hemB
and/or
menD
mutant.
X-Ray Absorption Spectroscopy as a Probe of Microbial Sulfur Biochemistry: the Nature of Bacterial Sulfur Globules Revisited
Authors: George Graham N. , Gnida Manuel , Bazylinski Dennis A. , Prince Roger C. , Pickering Ingrid J. 
Published: August 2008

ABSTRACT

The chemical nature of the sulfur in bacterial sulfur globules has been the subject of controversy for a number of years. Sulfur K-edge X-ray absorption spectroscopy (XAS) is a powerful technique for probing the chemical forms of sulfur in situ, but two groups have used it with very different conclusions. The root of the controversy lies with the different detection strategies used by the two groups, which result in very different spectra. This paper seeks to resolve the controversy. We experimentally demonstrate that the use of transmittance detection for sulfur K-edge XAS measurements is highly prone to spectroscopic distortions and that much of the published work on sulfur bacteria is very likely based on distorted data. We also demonstrate that all three detection methods used for X-ray absorption experiments yield essentially identical spectra when the measurements are carried out under conditions where no experimental distortions are expected. Finally, we turn to the original question—the chemical nature of bacterial sulfur. We examine isolated sulfur globules of
Allochromatium vinosum
and intact cells of a strain of magnetotactic coccus and show that XAS indicates the presence of a chemical form of sulfur resembling S
8
.
The
Vibrio cholerae
Hybrid Sensor Kinase VieS Contributes to Motility and Biofilm Regulation by Altering the Cyclic Diguanylate Level
Authors: Martinez-Wilson Hector F. , Tamayo Rita , Tischler Anna D. , Lazinski David W. , Camilli Andrew 
Published: August 2008

ABSTRACT

Phosphorelay systems are important mediators of signal transduction during bacterial adaptation to new environments. Previously we described the
vieSAB
operon, encoding a putative three-protein component phosphorelay involved in regulating
Vibrio cholerae
virulence gene expression. At least part of the regulatory activity of VieSAB is exerted through the cyclic diguanylate (c-di-GMP)-degrading activity of the putative response regulator VieA. So far no direct evidence that VieSAB encodes a phosphorelay system exists. In addition, the role VieS plays in modulating VieA activity remains unclear. To address these questions, we expressed and purified VieA and a soluble cytoplasmic portion of VieS and used them in autophosphorylation and phosphotransfer assays. These assays showed that VieS has kinase activity in vitro and is able to selectively phosphorylate VieA. A phenotypic comparison revealed that deletion of
vieS
results in increased biofilm production comparable to that seen for deletion of
vieA
, whereas motility was decreased only slightly in the Δ
vieS
mutant compared to the profound defect observed in a Δ
vieA
mutant. We also found that the Δ
vieS
strain has a lower level of
vieA
transcript and, similar to a Δ
vieA
mutant, an increased intracellular level of c-di-GMP. Further analysis using site-directed
vieA
mutants showed that some of the phenotypes observed were due to the phosphorylation status of VieA. The evidence presented in this report is the first to link VieS and VieA biochemically and genetically, lending support to the hypothesis that these proteins function together in a signaling system.
The Pangenome Structure ofEscherichia coli: Comparative Genomic Analysis ofE. coliCommensal and Pathogenic Isolates
Authors: Rasko David A. , Rosovitz M. J. , Myers Garry S. A. , Mongodin Emmanuel F. , Fricke W. Florian , Gajer Pawel , Crabtree Jonathan , Sebaihia Mohammed , Thomson Nicholas R. , Chaudhuri Roy , Henderson Ian R. , Sperandio Vanessa , Ravel Jacques 
Published: August 2008

ABSTRACTWhole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content ofEscherichia coli. Six distinctE. colipathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenicE. coli, enteropathogenicE. coli, and enteroaggregativeE. coli. We also determined the first genome sequence of a human commensalE. coliisolate,E. coliHS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenicE. coli. Comparison of 17E. coligenomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate thatE. coligenomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the speciesE. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.
Characterization of the
traD
Operon of Naphthalene-Catabolic Plasmid NAH7: a Host-Range Modifier in Conjugative Transfer
Authors: Miyazaki Ryo , Ohtsubo Yoshiyuki , Nagata Yuji , Tsuda Masataka 
Published: August 2008

ABSTRACT

Pseudomonas putida
G7 carries a naphthalene-catabolic and self-transmissible plasmid, NAH7, which belongs to the IncP-9 incompatibility group. Adjacent to the putative origin of conjugative transfer (
oriT
) of NAH7 are three genes,
traD
,
traE
, and
traF
, whose functions and roles in conjugation were previously unclear. These three genes were transcribed monocistronically and thus were designated the
traD
operon. Mutation of the three genes in the
traD
operon resulted in 10- to 10
5
-fold decreases in the transfer frequencies of the plasmids from
Pseudomonas
to
Pseudomonas
and
Escherichia coli
and from
E. coli
to
E. coli
. On the other hand, the
traD
operon was essential for the transfer of NAH7 from
E. coli
to
Pseudomonas
strains. These results indicated that the
traD
operon is a host-range modifier in the conjugative transfer of NAH7. The TraD, TraE, and TraF proteins were localized in the cytoplasm, periplasm, and membrane, respectively, in strain G7 cells. Our use of a bacterial two-hybrid assay system showed that TraE interacted in vivo with other essential components for conjugative transfer, including TraB (coupling protein), TraC (relaxase), and MpfH (a channel subunit in the mating pair formation system).