bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental Commitment in
Dictyostelium discoideum
Authors: Katoh Mariko , Chen Guokai , Roberge Emily , Shaulsky Gad , Kuspa Adam 
Published: September 2007

ABSTRACT

Upon starvation,
Dictyostelium discoideum
cells halt cell proliferation, aggregate into multicellular organisms, form migrating slugs, and undergo morphogenesis into fruiting bodies while differentiating into dormant spores and dead stalk cells. At almost any developmental stage cells can be forced to dedifferentiate when they are dispersed and diluted into nutrient broth. However, migrating slugs can traverse lawns of bacteria for days without dedifferentiating, ignoring abundant nutrients and continuing development. We now show that developing
Dictyostelium
cells revert to the growth phase only when bacteria are supplied during the first 4 to 6 h of development but that after this time, cells continue to develop regardless of the presence of food. We postulate that the cells’ inability to revert to the growth phase after 6 h represents a commitment to development. We show that the onset of commitment correlates with the cells’ loss of phagocytic function. By examining mutant strains, we also show that commitment requires extracellular cyclic AMP (cAMP) signaling. Moreover, cAMP pulses are sufficient to induce both commitment and the loss of phagocytosis in starving cells, whereas starvation alone is insufficient. Finally, we show that the inhibition of development by food prior to commitment is independent of contact between the cells and the bacteria and that small soluble molecules, probably amino acids, inhibit development during the first few hours and subsequently the cells become unable to react to the molecules and commit to development. We propose that commitment serves as a checkpoint that ensures the completion of cooperative aggregation of developing
Dictyostelium
cells once it has begun, dampening the response to nutritional cues that might inappropriately block development.
Alternative Modes of Organellar Segregation during Sporulation in
Saccharomyces cerevisiae
Authors: Suda Yasuyuki , Nakanishi Hideki , Mathieson Erin M. , Neiman Aaron M. 
Published: September 2007

ABSTRACT

Formation of ascospores in the yeast
Saccharomyces cerevisiae
is driven by an unusual cell division in which daughter nuclei are encapsulated within de novo-formed plasma membranes, termed prospore membranes. Generation of viable spores requires that cytoplasmic organelles also be captured along with nuclei. In mitotic cells segregation of mitochondria into the bud requires a polarized actin cytoskeleton. In contrast, genes involved in actin-mediated transport are not essential for sporulation. Instead, efficient segregation of mitochondria into spores requires Ady3p, a component of a protein coat found at the leading edge of the prospore membrane. Other organelles whose mitotic segregation is promoted by actin, such as the vacuole and the cortical endoplasmic reticulum, are not actively segregated during sporulation but are regenerated within spores. These results reveal that organellar segregation into spores is achieved by mechanisms distinct from those in mitotic cells.
Candida albicans
Sun41p, a Putative Glycosidase, Is Involved in Morphogenesis, Cell Wall Biogenesis, and Biofilm Formation
Authors: Hiller Ekkehard , Heine Sonja , Brunner Herwig , Rupp Steffen 
Published: September 2007

ABSTRACT

The SUN gene family has been defined in
Saccharomyces cerevisiae
and comprises a fungus-specific family of proteins which show high similarity in their C-terminal domains. Genes of this family are involved in different cellular processes, like DNA replication, aging, mitochondrial biogenesis, and cytokinesis. In
Candida albicans
the SUN family comprises two genes,
SUN41
and
SIM1
. We demonstrate that
C. albicans
mutants lacking
SUN41
show similar defects as found for
S. cerevisiae
, including defects in cytokinesis. In addition, the
SUN41
mutant showed a higher sensitivity towards the cell wall-disturbing agent Congo red, whereas no difference was observed in the presence of calcofluor white. Compared to the wild type,
SUN41
deletion strains exhibited a defect in biofilm formation, a reduced adherence on a Caco-2 cell monolayer, and were unable to form hyphae on solid medium under the conditions tested. Interestingly, Sun41p was found to be secreted in the medium of cells growing as blastospores as well as those forming hyphae. Our results support a function of SUN41p as a glycosidase involved in cytokinesis, cell wall biogenesis, adhesion to host tissue, and biofilm formation, indicating an important role in the host-pathogen interaction.
Genome-Wide Expression and Location Analyses of the
Candida albicans
Tac1p Regulon
Authors: Liu Teresa T. , Znaidi Sadri , Barker Katherine S. , Xu Lijing , Homayouni Ramin , Saidane Saloua , Morschhäuser Joachim , Nantel André , Raymond Martine , Rogers P. David 
Published: September 2007

ABSTRACT

A major mechanism of azole resistance in
Candida albicans
is overexpression of the genes encoding the ATP binding cassette transporters Cdr1p and Cdr2p due to gain-of-function mutations in Tac1p, a transcription factor of the zinc cluster family. To identify the Tac1p regulon, we analyzed four matched sets of clinical isolates representing the development of
CDR1
- and
CDR2
-mediated azole resistance by using gene expression profiling. We identified 31 genes that were consistently up-regulated with
CDR1
and
CDR2
, including
TAC1
itself, and 12 consistently down-regulated genes. When a resistant strain deleted for
TAC1
was examined similarly, expression of almost all of these genes returned to levels similar to those in the matched azole-susceptible isolate. Using genome-wide location (ChIP-chip) analysis (a procedure combining chromatin immunoprecipitation with hybridization to DNA intergenic microarrays), we found 37 genes whose promoters were bound by Tac1p in vivo, including
CDR1
and
CDR2
. Sequence analysis identified nine new genes whose promoters contain the previously reported Tac1p drug-responsive element (CGGN
4
CGG), including
TAC1
. In total, there were eight genes whose expression was modulated in the four azole-resistant clinical isolates in a
TAC1
-dependent manner and whose promoters were bound by Tac1p, qualifying them as direct Tac1p targets:
CDR1, CDR2, GPX1
(putative glutathione peroxidase),
LCB4
(putative sphingosine kinase),
RTA3
(putative phospholipid flippase), and orf19.1887 (putative lipase), as well as
IFU5
and orf19.4898 of unknown function. Our results show that Tac1p binds under nonactivating conditions to the promoters of its targets, including to its own promoter. They also suggest roles for Tac1p in regulating lipid metabolism (mobilization and trafficking) and oxidative stress response in
C. albicans
.
Reassessment of the In Vivo Functions of DNA Polymerase I and RNase H in Bacterial Cell Growth
Authors: Fukushima Sanae , Itaya Mitsuhiro , Kato Hiroaki , Ogasawara Naotake , Yoshikawa Hirofumi 
Published: September 2007

ABSTRACT

A major factor in removing RNA primers during the processing of Okazaki fragments is DNA polymerase I (Pol I). Pol I is thought to remove the RNA primers and to fill the resulting gaps simultaneously. RNase H, encoded by
rnh
genes, is another factor in removing the RNA primers, and there is disagreement with respect to the essentiality of both the
polA
and
rnh
genes. In a previous study, we looked for the synthetic lethality of paralogs in
Bacillus subtilis
and detected several essential doublet paralogs, including the
polA ypcP
pair. YpcP consists of only the 5′-3′ exonuclease domain. In the current study, we first confirmed that the
polA
genes of both
Escherichia coli
and
B. subtilis
could be completely deleted. We found that the 5′-3′ exonuclease activity encoded by either
polA
or
ypcP xni
was required for the growth of
B. subtilis
and
E. coli
. Also, the 5′-3′ exonuclease activity of Pol I was indispensable in the cyanobacterium
Synechococcus elongatus
. These results suggest that a 5′-3′ exonuclease activity is essential in these organisms. Our success in constructing a
B. subtilis
strain that lacked all RNase H genes indicates that the enzymatic activity is dispensable, at least in the wild type. Increasing the 5′-3′ exonuclease activity partially compensated for a defective phenotype of an RNase H-deficient mutant, suggesting cooperative functions for the two enzyme systems. Our search for the distribution of the 5′-3′ exonuclease domain among 250 bacterial genomes resulted in the finding that all eubacteria, but not archaea, possess this domain.
Characterization of an Active Partition System for theEnterococcus faecalisPheromone-Responding Plasmid pAD1
Authors: Francia Maria Victoria , Weaver Keith E. , Goicoechea Patricia , Tille Patricia , Clewell Don B. 
Published: September 2007

ABSTRACTEnterococcus faecalisplasmid pAD1 is a 60-kb conjugative, low-copy-number plasmid that encodes a mating response to the peptide sex pheromone cAD1 and a cytolytic exotoxin that contributes to virulence. Although aspects of conjugation have been studied extensively, relatively little is known about the control of pAD1 maintenance. Previous work on pAD1 identified a 5-kb region of DNA sufficient to support replication, copy control, and stable inheritance (K. E. Weaver, D. B. Clewell, and F. An, J. Bacteriol.175:1900-1909, 1993), and recently, the pAD1 replication initiator (RepA) and the origin of vegetative replication (oriV) were characterized (M. V. Francia, S. Fujimoto, P. Tille, K. E. Weaver, and D. B. Clewell, J. Bacteriol.186:5003-5016, 2004). The present study focuses on the adjacent determinantsrepBandrepC, as well as a group of 25 8-bp direct repeats (iterons with the consensus sequence TAGTARRR) located between the divergently transcribedrepAandrepB. Through mutagenesis andtrans-complementation experiments, RepB (a 33-kDa protein, a member of the ParA superfamily of ATPases) and RepC (a protein of 14.4 kDa) were shown to be required for maximal stabilization. Both were active intrans. The iteron region was shown to act as the pAD1 centromere-like site. Purified RepC was shown by DNA mobility shift and DNase I footprinting analyses to interact in a sequence-specific manner with the iteron repeats upstream of therepBClocus. The binding of RepC to the iteron region was shown to be modified by RepB in the presence of ATP via a possible interaction with the RepC-iteron complex. RepB did not bind to the iteron region in the absence of RepC.
Atomic Force Microscopy Study of the Effect of Lipopolysaccharides and Extracellular Polymers on Adhesion of
Pseudomonas aeruginosa
Authors: Atabek Arzu , Camesano Terri A. 
Published: September 2007

ABSTRACT

The roles of lipopolysaccharides (LPS) and extracellular polymers (ECP) on the adhesion of
Pseudomonas aeruginosa
PAO1 (expresses the A-band and B-band of O antigen) and AK1401 (expresses the A-band but not the B-band) to silicon were investigated with atomic force microscopy (AFM) and related to biopolymer physical properties. Measurement of macroscopic properties showed that strain AK1401 is more negatively charged and slightly more hydrophobic than strain PAO1 is. Microscopic AFM investigations of individual bacteria showed differences in how the biopolymers interacted with silicon. PAO1 showed larger decay lengths in AFM approach cycles, suggesting that the longer polymers on PAO1 caused greater steric repulsion with the AFM tip. For both bacterial strains, the long-range interactions we observed (hundreds of nanometers) were inconsistent with the small sizes of LPS, suggesting that they were also influenced by ECP, especially polysaccharides. The AFM retraction profiles provide information on the adhesion strength of the biopolymers to silicon (
F
adh
). For AK1401, the adhesion forces were only slightly lower (
F
adh
= 0.51 nN compared to 0.56 nN for PAO1), but the adhesion events were concentrated over shorter distances. More than 90% of adhesion events for AK1401 were at distances of <600 nm, while >50% of adhesion events for PAO1 were at distances of >600 nm. The sizes of the observed molecules suggest that the adhesion of
P. aeruginosa
to silicon was controlled by ECP, in addition to LPS. Steric and electrostatic forces each contributed to the interfacial interactions between
P. aeruginosa
and the silicon surface.
Anaplasma phagocytophilum p44
mRNA Expression Is Differentially Regulated in Mammalian and Tick Host Cells: Involvement of the DNA Binding Protein ApxR
Authors: Wang Xueqi , Cheng Zhihui , Zhang Chunbin , Kikuchi Takane , Rikihisa Yasuko 
Published: September 2007

ABSTRACT

The natural life cycle of
Anaplasma phagocytophilum
, an obligatory intracellular bacterium that causes human granulocytic anaplasmosis, consists of alternate infection of two distinct hosts, ticks and mammals, in which bacterial surface proteins are expected to have a critical role. The present study investigated regulation of
A. phagocytophilum p44
genes, which encode the P44 major surface proteins. Quantitative real-time reverse transcription-PCR analysis revealed that the amount of
p44
mRNA obtained from spleens of
A. phagocytophilum
-infected SCID mice was approximately 10-fold greater than the amount obtained from salivary glands of
A. phagocytophilum
-infected
Ixodes scapularis
nymphs. Similarly, the amount of
p44
mRNA obtained from
A. phagocytophilum
-infected HL-60 cells per bacterium was significantly greater than the amount obtained from infected ISE6 tick cells. The relative amount of
p44
mRNA was approximately threefold higher in
A. phagocytophilum
-infected HL-60 cells cultured at 37°C than in
A. phagocytophilum
-infected HL-60 cells cultured at 28°C. Although there are more than 100
p44
paralogs, we observed expression mainly from the
p44
expression locus (
p44E
) in various host environments. Interestingly, transcription of the
A. phagocytophilum
gene encoding the DNA binding protein ApxR was also significantly greater in
A. phagocytophilum
-infected HL-60 cells than in infected ISE6 tick cells. Gel mobility shift and DNase I protection assays revealed recombinant ApxR binding to the promoter regions of
p44E
and
apxR
. ApxR also transactivated the
p44E
and
apxR
promoter regions in a
lacZ
reporter assay. These results indicate that
p44
genes and
apxR
are specifically up-regulated in the mammalian host environment and suggest that ApxR not only is positively autoregulated but also acts as a transcriptional regulator of
p44E
.
TheMyxococcus xanthusNla4 Protein Is Important for Expression of Stringent Response-Associated Genes, ppGpp Accumulation, and Fruiting Body Development
Authors: Ossa Faisury , Diodati Michelle E. , Caberoy Nora B. , Giglio Krista M. , Edmonds Mick , Singer Mitchell , Garza Anthony G. 
Published: September 2007

ABSTRACTChanges in gene expression are important for the landmark morphological events that occur duringMyxococcus xanthusfruiting body development. Enhancer binding proteins (EBPs), which are transcriptional activators, play prominent roles in the coordinated expression of developmental genes. A mutation in the EBP genenla4affects the timing of fruiting body formation, the morphology of mature fruiting bodies, and the efficiency of sporulation. In this study, we showed that thenla4mutant accumulates relatively low levels of the stringent nucleotide ppGpp. We also found that thenla4mutant is defective for early developmental events and for vegetative growth, phenotypes that are consistent with a deficiency in ppGpp accumulation. Further studies revealed thatnla4cells produce relatively low levels of GTP, a precursor of RelA-dependent synthesis of (p)ppGpp. In addition, the normal expression patterns of all stringent response-associated genes tested, including theM. xanthusppGpp synthetase generelA, are altered innla4mutant cells. These findings indicate that Nla4 is part of regulatory pathway that is important for mounting a stringent response and for initiating fruiting body development.
Polymerization of the Actin-Like Protein MamK, Which Is Associated with Magnetosomes
Authors: Taoka Azuma , Asada Ryuji , Wu Long-Fei , Fukumori Yoshihiro 
Published: September 2007

ABSTRACT

The recombinant actin-like protein MamK was purified from
Escherichia coli
and used as an antigen to generate the anti-MamK antibody. Immunostaining studies showed a linear distribution of MamK in
Magnetospirillum magnetotacticum
cells and of MamK in association with magnetosomes. Moreover, we demonstrated that MamK polymerizes into filamentous bundles in vitro.
The Wetting Agent Required for Swarming in
Salmonella enterica
Serovar Typhimurium Is Not a Surfactant
Authors: Chen Bryan G. , Turner Linda , Berg Howard C. 
Published: September 2007

ABSTRACT

We compared the abilities of media from agar plates surrounding swarming and nonswarming cells of
Salmonella enterica
serovar Typhimurium to wet a nonpolar surface by measuring the contact angles of small drops. The swarming cells were wild type for chemotaxis, and the nonswarming cells were nonchemotactic mutants with motor biases that were counterclockwise (
cheY
) or clockwise (
cheZ
). The latter strains have been shown to be defective for swarming because the agar remains dry (Q. Wang, A. Suzuki, S. Mariconda, S. Porwollik, and R. M. Harshey, EMBO J. 24:2034-2042, 2005). We found no differences in the abilities of the media surrounding these cells, either wild type or mutant, to wet a low-energy surface (freshly prepared polydimethylsiloxane); although, their contact angles were smaller than that of the medium harvested from the underlying agar. So the agent that promotes wetness produced by wild-type cells is not a surfactant; it is an osmotic agent.
Population Genetic Structure of the
Staphylococcus intermedius
Group: Insights into
agr
Diversification and the Emergence of Methicillin-Resistant Strains
Authors: Bannoehr Jeanette , Ben Zakour Nouri L. , Waller Andrew S. , Guardabassi Luca , Thoday Keith L. , van den Broek Adri H. M. , Fitzgerald J. Ross 
Published: September 2007

ABSTRACT

The population genetic structure of the animal pathogen
Staphylococcus intermedius
is poorly understood. We carried out a multilocus sequence phylogenetic analysis of isolates from broad host and geographic origins to investigate inter- and intraspecies diversity. We found that isolates phenotypically identified as
S. intermedius
are differentiated into three closely related species,
S. intermedius
,
Staphylococcus pseudintermedius
, and
Staphylococcus delphini. S. pseudintermedius
, not
S. intermedius
, is the common cause of canine pyoderma and occasionally causes zoonotic infections of humans. Over 60 extant STs were identified among the
S. pseudintermedius
isolates examined, including several that were distributed on different continents. As the
agr
quorum-sensing system of staphylococci is thought to have evolved along lines of speciation within the genus, we examined the allelic variation of
agrD
, which encodes the autoinducing peptide (AIP). Four AIP variants were encoded by
S. pseudintermedius
isolates, and identical AIP variants were shared among the three species, suggesting that a common quorum-sensing capacity has been conserved in spite of species differentiation in largely distinct ecological niches. A lack of clonal association of
agr
alleles suggests that assortive recombination may have contributed to the distribution of
agr
diversity. Finally, we discovered that the recent emergence of methicillin-resistant strains was due to multiple acquisitions of the
mecA
gene by different
S. pseudintermedius
clones found on different continents. Taken together, these data have resolved the population genetic structure of the
S. intermedius
group, resulting in new insights into its ancient and recent evolution.
DNA Bending in the Mycobacterial Plasmid pAL5000 Origin-RepB Complex
Authors: Chatterjee Sujoy , Basu Arnab , Basu Abhijit , Das Gupta Sujoy K. 
Published: September 2007

ABSTRACTPlasmid pAL5000 represents a family of relatively newly discovered cryptic plasmids in gram-positiveActinomycetesbacteria. The replication regions of these plasmids comprise a bicistronic operon,repA-repB, encoding two replication proteins. Located upstream is acis-acting element that functions as the origin of replication. It comprises an ∼200-bp segment spanning two binding sites for the replication protein RepB, a low-affinity (L) site and a high-affinity (H) site separated by an ∼40-bp spacer sequence. The trajectory of the DNA in the RepB-origin complex has been investigated, and it has been found that the origin undergoes significant bending movements upon RepB binding. RepB binding not only led to local bending effects but also caused a long-range polar curvature which affected the DNA sequences 3′ to the H site. These movements appear to be essential for the in-phase alignment of the L and H sites that leads to the formation of a looped structure. A novel property of RepB unearthed in this study is its ability to form multimers. This property may be an important factor that determines the overall trajectory of the DNA in the RepB-origin complex. The results presented in this study suggest that the origins of replication of pAL5000 and related plasmids are highly flexible and that multimeric, RepB-like initiator proteins bind the origin and induce local deformations and long-range curvatures which are probably necessary for the proper functioning of the origin.
The GATC-Binding Protein SeqA Is Required for Bile Resistance and Virulence inSalmonella entericaSerovar Typhimurium
Authors: Prieto Ana I. , Jakomin Marcello , Segura Ignacio , Pucciarelli M. Graciela , Ramos-Morales Francisco , García-del Portillo Francisco , Casadesús Josep 
Published: September 2007

ABSTRACTDisruption of theseqAgene ofSalmonella entericaserovar Typhimurium causes defects similar to those described inE. coli: filament formation, aberrant nucleoid segregation, induction of the SOS response, envelope instability, and increased sensitivity to membrane-damaging agents. Differences between SeqA−mutants ofE. coliandS. enterica, however, are found. SeqA−mutants ofS. entericaform normal colonies and do not exhibit alterations in phage plaquing morphology. Lack of SeqA causes attenuation ofS. entericavirulence by the oral route but not by the intraperitoneal route, suggesting a virulence defect in the intestinal stage of infection. However, SeqA−mutants are fully proficient in the invasion of epithelial cells. We hypothesize that attenuation of SeqA−mutants by the oral route may be caused by bile sensitivity, which in turn may be a consequence of envelope instability.
Phenotypic Characterization of Pore Mutants of theVibrio choleraePorin OmpU
Authors: Pagel Melissa , Simonet Valérie , Li Jie , Lallemand Mathilde , Lauman Brian , Delcour Anne H. 
Published: September 2007

ABSTRACTGeneral-diffusion porins form large β-barrel channels that control the permeability of the outer membrane of gram-negative bacteria to nutrients, some antibiotics, and external signals. Here, we have analyzed the effects of mutations in the OmpU porin ofVibrio choleraeat conserved residues that are known to affect pore properties in theEscherichia coliporins OmpF and OmpC. Various phenotypes were investigated, including sensitivity to β-lactam antibiotics, growth on large sugars, and sensitivity to and biofilm induction by sodium deoxycholate, a major bile component that acts as an external signal for multiple cellular responses of this intestinal pathogen. Overall, our results indicate that specific residues play different roles in controlling the passage of various compounds. Mutations of barrel wall arginine residues that protrude in the pore affect pore size and growth in the presence of large sugars or sodium deoxycholate. Sensitivity to large cephalosporins is mostly affected by D116, located on the L3 loop, whose homolog inE. coli, OmpF, is a known binding determinant for these drugs. L3 loop residues also affect biofilm induction. The results are interpreted in terms of a homology model based on the structures ofE. coliporins.