bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candicidin Biosynthesis Gene Cluster Is Widely Distributed among
Streptomyces
spp. Isolated from the Sediments and the Neuston Layer of the Trondheim Fjord, Norway
Authors: Jørgensen Hanne , Fjærvik Espen , Hakvåg Sigrid , Bruheim Per , Bredholt Harald , Klinkenberg Geir , Ellingsen Trond E. , Zotchev Sergey B. 
Published: March 2009

ABSTRACT

A large number of
Streptomyces
bacteria with antifungal activity isolated from samples collected in the Trondheim fjord (Norway) were found to produce polyene compounds. Investigation of polyene-containing extracts revealed that most of the isolates produced the same compound, which had an atomic mass and UV spectrum corresponding to those of candicidin D. The morphological diversity of these isolates prompted us to speculate about the involvement of a mobile genetic element in dissemination of the candicidin biosynthesis gene cluster (
can
). Eight candicidin-producing isolates were analyzed by performing a 16S rRNA gene-based taxonomic analysis, pulsed-field gel electrophoresis, PCR, and Southern blot hybridization with
can
-specific probes. These analyses revealed that most of the isolates were related, although they were morphologically diverse, and that all of them contained
can
genes. The majority of the isolates studied contained large plasmids, and two
can
-specific probes hybridized to a 250-kb plasmid in one isolate. Incubation of the latter isolate at a high temperature resulted in loss of the
can
genes and candicidin production, while mating of the “cured” strain with a plasmid-containing donor restored candicidin production. The latter result suggested that the 250-kb plasmid contains the complete
can
gene cluster and could be responsible for conjugative transfer of this cluster to other streptomycetes.
Dual Role of the Oligopeptide Permease Opp3 during Growth of
Staphylococcus aureus
in Milk
Authors: Borezée-Durant Elise , Hiron Aurelia , Piard Jean-Christophe , Juillard Vincent 
Published: March 2009

ABSTRACT

Staphylococcus aureus
RN6390 presents a diauxic growth in milk, due to amino acid limitation. Inactivation of the oligopeptide permease Opp3 (dedicated to the nitrogen nutrition of the strain) not only affects the growth of the strain but also results in reduced expression levels of three major extracellular proteases.
Fusobacterium nucleatum
ATCC 10953 Requires
Actinomyces naeslundii
ATCC 43146 for Growth on Saliva in a Three-Species Community That Includes
Streptococcus oralis
34
Authors: Periasamy Saravanan , Chalmers Natalia I. , Du-Thumm Laurence , Kolenbrander Paul E. 
Published: March 2009

ABSTRACT

Formation of dental plaque is a developmental process involving initial and late colonizing species that form polymicrobial communities. Fusobacteria are the most numerous gram-negative bacteria in dental plaque, but they become prevalent after the initial commensal colonizers, such as streptococci and actinomyces, have established communities. The unusual ability of these bacteria to coaggregate with commensals, as well as pathogenic late colonizers, has been proposed to facilitate colonization by the latter organisms. We investigated the integration of
Fusobacterium nucleatum
into multispecies communities by employing two in vitro models with saliva as the sole nutritional source. In flow cell biofilms, numbers of cells were quantified using fluorescently conjugated antibodies against each species, and static biofilms were analyzed by quantitative real-time PCR (q-PCR) using species-specific primers. Unable to grow as single-species biofilms,
F. nucleatum
grew in two-species biofilms with
Actinomyces naeslundii
but not with
Streptococcus oralis
. However, enhanced growth of fusobacteria was observed in three-species biofilms, indicating that there was multispecies cooperation. Importantly, these community dynamics yielded an 18-fold increase in the
F. nucleatum
biomass between 4 h and 18 h in the flow cell inoculated with three species. q-PCR analysis of static biofilms revealed that maximum growth of the three species occurred at 24 h to 36 h. Lower numbers of cells were observed at 48 h, suggesting that saliva could not support higher cell densities as the sole nutrient. Integration of
F. nucleatum
into multispecies commensal communities was evident from the interdigitation of fusobacteria in coaggregates with
A. naeslundii
and
S. oralis
and from the improved growth of fusobacteria, which was dependent on the presence of
A. naeslundii
.
Microtubule-Nucleus Interactions in
Dictyostelium discoideum
Mediated by Central Motor Kinesins
Authors: Tikhonenko Irina , Nag Dilip K. , Robinson Douglas N. , Koonce Michael P. 
Published: March 2009

ABSTRACT

Kinesins are a diverse superfamily of motor proteins that drive organelles and other microtubule-based movements in eukaryotic cells. These motors play important roles in multiple events during both interphase and cell division.
Dictyostelium discoideum
contains 13 kinesin motors, 12 of which are grouped into nine families, plus one orphan. Functions for 11 of the 13 motors have been previously investigated; we address here the activities of the two remaining kinesins, both isoforms with central motor domains. Kif6 (of the kinesin-13 family) appears to be essential for cell viability. The partial knockdown of Kif6 with RNA interference generates mitotic defects (lagging chromosomes and aberrant spindle assemblies) that are consistent with kinesin-13 disruptions in other organisms. However, the orphan motor Kif9 participates in a completely novel kinesin activity, one that maintains a connection between the microtubule-organizing center (MTOC) and nucleus during interphase.
kif9
null cell growth is impaired, and the MTOC appears to disconnect from its normally tight nuclear linkage. Mitotic spindles elongate in a normal fashion in
kif9

−

cells, but we hypothesize that this kinesin is important for positioning the MTOC into the nuclear envelope during prophase. This function would be significant for the early steps of cell division and also may play a role in regulating centrosome replication.
Phosphatidylethanolamine Is Required for Normal Cell Morphology and Cytokinesis in the Fission Yeast
Schizosaccharomyces pombe
Authors: Luo Jun , Matsuo Yasuhiro , Gulis Galina , Hinz Haylee , Patton-Vogt Jana , Marcus Stevan 
Published: March 2009

ABSTRACT

To investigate the contributions of phosphatidylethanolamine to the growth and morphogenesis of the fission yeast
Schizosaccharomyces pombe
, we have characterized three predicted genes in this organism, designated
psd1
,
psd2
, and
psd3
, encoding phosphatidylserine decarboxylases, which catalyze the conversion of phosphatidylserine to phosphatidylethanolamine in both eukaryotic and prokaryotic organisms.
S. pombe
mutants carrying deletions in any one or two
psd
genes are viable in complex rich medium and synthetic defined minimal medium. However, mutants carrying deletions in all three
psd
genes (
psd1-3
Δ mutants) grow slowly in rich medium and are inviable in minimal medium, indicating that the
psd1
to
psd3
gene products share overlapping essential cellular functions. Supplementation of growth media with ethanolamine, which can be converted to phosphatidylethanolamine by the Kennedy pathway, restores growth to
psd1-3
Δ cells in minimal medium, indicating that phosphatidylethanolamine is essential for
S. pombe
cell growth.
psd1-3
Δ cells produce lower levels of phosphatidylethanolamine than wild-type cells, even in medium supplemented with ethanolamine, indicating that the Kennedy pathway can only partially compensate for the loss of phosphatidylserine decarboxylase activity in
S. pombe
.
psd1-3Δ
cells appear morphologically indistinguishable from wild-type
S. pombe
cells in medium supplemented with ethanolamine, but when cultured in nonsupplemented medium, they produce high frequencies of abnormally shaped cells as well as cells exhibiting severe septation defects, including multiple, mispositioned, deformed, and misoriented septa. Our results demonstrate that phosphatidylethanolamine is essential for cell growth and for normal cytokinesis and cellular morphogenesis in
S. pombe
, and they illustrate the usefulness of this model eukaryote for investigating potentially conserved biological and molecular functions of phosphatidylethanolamine.
Altering Sphingolipid Metabolism in
Saccharomyces cerevisiae
Cells Lacking the Amphiphysin Ortholog Rvs161 Reinitiates Sugar Transporter Endocytosis
Authors: Morgan Jeanelle , McCourt Paula , Rankin Lauren , Swain Evelyn , Rice Lyndi M. , Nickels Joseph T. 
Published: March 2009

ABSTRACT

Amphiphysins are proteins thought to be involved in synaptic vesicle endocytosis. Amphiphysins share a common BAR domain, which can sense and/or bend membranes, and this function is believed to be essential for endocytosis.
Saccharomyces cerevisiae
cells lacking the amphiphysin ortholog Rvs161 are inviable when starved for glucose. Altering sphingolipid levels in
rvs161
cells remediates this defect, but how lipid changes suppress remains to be elucidated. Here, we show that the sugar starvation-induced death of
rvs161
cells extends to other fermentable sugar carbon sources, and the loss of sphingolipid metabolism suppresses these defects. In all cases,
rvs161
cells respond to the starvation signal, elicit the appropriate transcriptional response, and properly localize the requisite sugar transporter(s). However, Rvs161 is required for transporter endocytosis.
rvs161
cells accumulate transporters at the plasma membrane under conditions normally resulting in their endocytosis and degradation. Transporter endocytosis requires the endocytosis (
endo
) domain of Rvs161. Altering sphingolipid metabolism by deleting the very-long-chain fatty acid elongase
SUR4
reinitiates transporter endocytosis in
rvs161
and
rvs161 endo
−
cells. The sphingolipid-dependent reinitiation of endocytosis requires the ubiquitin-regulating factors Doa1, Doa4, and Rsp5. In the case of Doa1, the phospholipase A
2
family ubiquitin binding motif is dispensable. Moreover, the conserved AAA-ATPase Cdc48 and its accessory proteins Shp1 and Ufd1 are required. Finally,
rvs161
cells accumulate monoubiquitin, and this defect is remediated by the loss of
SUR4
. These results show that defects in sphingolipid metabolism result in the reinitiation of ubiquitin-dependent sugar transporter endocytosis and suggest that this event is necessary for suppressing the nutrient starvation-induced death of
rvs161
cells.
Live-Cell Imaging and Measurement of Intracellular pH in Filamentous Fungi Using a Genetically Encoded Ratiometric Probe
Authors: Bagar Tanja , Altenbach Kirsten , Read Nick D. , Benčina Mojca 
Published: March 2009

ABSTRACT

A novel, genetically encoded, ratiometric pH probe (RaVC) was constructed to image and measure intracellular pH in living hyphae of
Aspergillus niger
. RaVC is a chimeric protein based on the pH-sensitive probe pHluorin, which was partially codon optimized for expression in
Aspergillus.
Intracellular pH imaging and measurement was performed by simultaneous, dual-excitation confocal ratio imaging. The mean cytoplasmic pH measured was 7.4 to 7.7 based on calibrating RaVC in situ within nigericin-treated hyphae. Pronounced, longitudinal cytoplasmic pH gradients were not observed in the apical 20 μm of actively growing hyphae at the periphery of 18-h-old colonies. The cytoplasmic pH remained unchanged after prolonged growth in buffered medium with pH values between 2.5 or 9.5. Sudden changes in external pH significantly changed cytoplasmic pH by <1.3 pH units, but it returned to its original value within 20 min following treatment. The weak acid and antifungal food preservative sorbic acid caused prolonged, concentration-dependent intracellular acidification. The inhibition of ATPases with
N
-ethylmaleimide, dicychlohexylcarbodimide, or sodium azide caused the cytoplasmic pH to decrease by <1 pH unit. Treatment with the protonophore carbonyl cyanide
m
-chlorophenylhydrazone or cyanide
p
-(trifluoromethoxy) phenylhydrazone reduced the cytoplasmic pH by <1 pH unit. In older hyphae from 32-h-old cultures, RaVC became sequestered within large vacuoles, which were shown to have pH values between 6.2 and 6.5. Overall, our study demonstrates that RaVC is an excellent probe for visualizing and quantifying intracellular pH in living fungal hyphae.
Nested Genes
CDA12
and
CDA13
Encode Proteins Associated with Membrane Trafficking in the Ciliate
Tetrahymena thermophila
Authors: Zweifel Erica , Smith Joshua , Romero Daniel , Giddings Thomas H. , Winey Mark , Honts Jerry , Dahlseid Jeff , Schneider Brent , Cole Eric S. 
Published: March 2009

ABSTRACT

We describe a novel pair of nested genes,
CDA12
and
CDA13
, from
Tetrahymena thermophila
. Both are implicated in membrane trafficking associated with cell division and conjugation. Green fluorescent protein localization reveals Cda12p decoration of diverse membrane-bound compartments, including mobile, subcortical tubulovesicular compartments; perinuclear vesicles; and candidates for recycling endosomes. Cda13p decorates intracellular foci located adjacent to cortically aligned mitochondria and their neighboring Golgi networks. The expression of antisense
CDA12
RNA in transformants produces defects in cytokinesis, macronuclear segregation, and the processing of pinosomes to downstream compartments. Antisense
CDA13
RNA expression produces a conjugation phenotype, resulting in the failure of mating pairs to separate, as well as failures in postconjugation cytokinesis and macronuclear fission. This study offers insight into the membrane trafficking events linking endosome and Golgi network activities, cytokinesis, and karyokinesis and the unique membrane-remodeling events that accompany conjugation in the ciliate
T. thermophila
. We also highlight an unusual aspect of genome organization in
Tetrahymena
, namely, the existence of nested, antisense genes.
A Comprehensive Survey of Single Nucleotide Polymorphisms (SNPs) across
Mycobacterium bovis
Strains and
M. bovis
BCG Vaccine Strains Refines the Genealogy and Defines a Minimal Set of SNPs That Separate Virulent
M. bovis
Strains and
M. bovis
BCG Strains
Authors: Garcia Pelayo M. Carmen , Uplekar Swapna , Keniry Andrew , Mendoza Lopez Pablo , Garnier Thierry , Nunez Garcia Javier , Boschiroli Laura , Zhou Xiangmei , Parkhill Julian , Smith Noel , Hewinson R. Glyn , Cole Stewart T. , Gordon Stephen V. 
Published: March 2009

ABSTRACT

To further unravel the mechanisms responsible for attenuation of the tuberculosis vaccine
Mycobacterium bovis
BCG, comparative genomics was used to identify single nucleotide polymorphisms (SNPs) that differed between sequenced strains of
Mycobacterium bovis
and
M. bovis
BCG. SNPs were assayed in
M. bovis
isolates from France and the United Kingdom and from different BCG vaccines in order to identify those that arose during the attenuation process which gave rise to BCG. Informative data sets were obtained for 658 SNPs from 21 virulent
M. bovis
strains and 13 BCG strains; these SNPs showed phylogenetic clustering that was consistent with the geographical origin of the strains and previous schemes for BCG genealogies. The data revealed a closer relationship between BCG Tice and BCG Pasteur than was previously appreciated, while we were able to position BCG Beijing within a grouping of BCG Denmark-derived strains. Only 186 SNPs were identified between virulent
M. bovis
strains and all BCG strains, with 115 nonsynonymous SNPs affecting important functions such as global regulators, transcriptional factors, and central metabolism, which might impact on virulence. We therefore refine previous genealogies of BCG vaccines and define a minimal set of SNPs between virulent
M. bovis
strains and the attenuated BCG strain that will underpin future functional analyses.
Whole-Genome Tiling Array Analysis of
Mycobacterium leprae
RNA Reveals High Expression of Pseudogenes and Noncoding Regions
Authors: Akama Takeshi , Suzuki Koichi , Tanigawa Kazunari , Kawashima Akira , Wu Huhehasi , Nakata Noboru , Osana Yasunori , Sakakibara Yasubumi , Ishii Norihisa 
Published: March 2009

ABSTRACT

Whole-genome sequence analysis of
Mycobacterium leprae
has revealed a limited number of protein-coding genes, with half of the genome composed of pseudogenes and noncoding regions. We previously showed that some
M. leprae
pseudogenes are transcribed at high levels and that their expression levels change following infection. In order to clarify the RNA expression profile of the
M. leprae
genome, a tiling array in which overlapping 60-mer probes cover the entire 3.3-Mbp genome was designed. The array was hybridized with
M. leprae
RNA from the SHR/NCrj-
rnu
nude rat, and the results were compared to results from an open reading frame array and confirmed by reverse transcription-PCR. RNA expression was detected from genes, pseudogenes, and noncoding regions. The signal intensities obtained from noncoding regions were higher than those from pseudogenes. Expressed noncoding regions include the
M. leprae
unique repetitive sequence RLEP and other sequences without any homology to known functional noncoding RNAs. Although the biological functions of RNA transcribed from
M. leprae
pseudogenes and noncoding regions are not known, RNA expression analysis will provide insights into the bacteriological significance of the species. In addition, our study suggests that
M. leprae
will be a useful model organism for the study of the molecular mechanism underlying the creation of pseudogenes and the role of microRNAs derived from noncoding regions.
Identification and Characterization of Inorganic Pyrophosphatase and PAP Phosphatase from
Thermococcus onnurineus
NA1
Authors: Lee Hyun Sook , Kim Yun Jae , Lee Jung-Hyun , Kang Sung Gyun 
Published: March 2009

ABSTRACT

Two hypothetical genes were functionally verified to be a pyrophosphatase and a PAP phosphatase in
Thermococcus onnurineus
NA1. This is the first report of the pyrophosphatases and the PAP phosphatases being organized in the gene clusters of the sulfate activation system only in
T. onnurineus
NA1 and “
Pyrococcus abyssi
.”
Competence for Genetic Transformation in
Streptococcus pneumoniae
: Termination of Activity of the Alternative Sigma Factor ComX Is Independent of Proteolysis of ComX and ComW
Authors: Piotrowski Andrew , Luo Ping , Morrison Donald A. 
Published: March 2009

ABSTRACT

Competence for genetic transformation in
Streptococcus pneumoniae
is a transient physiological state whose development is coordinated by a peptide pheromone (CSP) and its receptor, which activates transcription of two downstream genes,
comX
and
comW
, and 15 other “early” genes. ComX, a transient alternative sigma factor, drives transcription of “late” genes, many of which are essential for transformation. In vivo, ComW both stabilizes ComX against proteolysis by the ClpE-ClpP protease and stimulates its activity. Interestingly, stabilization of ComX by deletion of the gene encoding the ClpP protease did not extend the period of competence. We considered the hypothesis that the rapid decay of competence arises from a rapid loss of ComW and thus of its ComX stimulating activity, so that ComX might persist but lose its transcriptional activity. Western analysis revealed that ComW is indeed a transient protein, which is also stabilized by deletion of the gene encoding the ClpP protease. However, stabilizing both ComX and ComW did not prolong either ComX activity or the period of transformation, indicating that termination of the transcriptional activity of ComX is not dependent on proteolysis of ComW.
Cytoskeletal Asymmetrical Dumbbell Structure of a Gliding Mycoplasma,
Mycoplasma gallisepticum
, Revealed by Negative-Staining Electron Microscopy
Authors: Nakane Daisuke , Miyata Makoto 
Published: March 2009

ABSTRACT

Several mycoplasma species feature a membrane protrusion at a cell pole, and unknown mechanisms provide gliding motility in the direction of the pole defined by the protrusion.
Mycoplasma gallisepticum
, an avian pathogen, is known to form a membrane protrusion composed of bleb and infrableb and to glide. Here, we analyzed the gliding motility of
M. gallisepticum
cells in detail. They glided in the direction of the bleb at an average speed of 0.4 μm/s and remained attached around the bleb to a glass surface, suggesting that the gliding mechanism is similar to that of a related species,
Mycoplasma pneumoniae
. Next, to elucidate the cytoskeletal structure of
M. gallisepticum
, we stripped the envelopes by treatment with Triton X-100 under various conditions and observed the remaining structure by negative-staining transmission electron microscopy. A unique cytoskeletal structure, about 300 nm long and 100 nm wide, was found in the bleb and infrableb. The structure, resembling an asymmetrical dumbbell, is composed of five major parts from the distal end: a cap, a small oval, a rod, a large oval, and a bowl. Sonication likely divided the asymmetrical dumbbell into a core and other structures. The cytoskeletal structures of
M. gallisepticum
were compared with those of
M. pneumoniae
in detail, and the possible protein components of these structures were considered.
Mechanism for Sortase Localization and the Role of Sortase Localization in Efficient Pilus Assembly in
Enterococcus faecalis
Authors: Kline Kimberly A. , Kau Andrew L. , Chen Swaine L. , Lim Adeline , Pinkner Jerome S. , Rosch Jason , Nallapareddy Sreedhar R. , Murray Barbara E. , Henriques-Normark Birgitta , Beatty Wandy , Caparon Michael G. , Hultgren Scott J. 
Published: March 2009

ABSTRACT

Pathogenic streptococci and enterococci primarily rely on the conserved secretory (Sec) pathway for the translocation and secretion of virulence factors out of the cell. Since many secreted virulence factors in gram-positive organisms are subsequently attached to the bacterial cell surface via sortase enzymes, we sought to investigate the spatial relationship between secretion and cell wall attachment in
Enterococcus faecalis
. We discovered that sortase A (SrtA) and sortase C (SrtC) are colocalized with SecA at single foci in the enterococcus. The SrtA-processed substrate aggregation substance accumulated in single foci when SrtA was deleted, implying a single site of secretion for these proteins. Furthermore, in the absence of the pilus-polymerizing SrtC, pilin subunits also accumulate in single foci. Proteins that localized to single foci in
E. faecalis
were found to share a positively charged domain flanking a transmembrane helix. Mutation or deletion of this domain in SrtC abolished both its retention at single foci and its function in efficient pilus assembly. We conclude that this positively charged domain can act as a localization retention signal for the focal compartmentalization of membrane proteins.