bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and Characterization of a Single-Stranded RNA Virus Infecting the Marine Planktonic Diatom
Chaetoceros tenuissimus
Meunier
Authors: Shirai Yoko , Tomaru Yuji , Takao Yoshitake , Suzuki Hidekazu , Nagumo Tamotsu , Nagasaki Keizo 
Published: May 2008

ABSTRACT

Diatoms are important components of the biological community and food web in the aquatic environment. Here, we report the characteristics of a single-stranded RNA (ssRNA) virus (CtenRNAV01) that infects the marine diatom
Chaetoceros tenuissimus
Meunier (Bacillariophyceae). The ca. 31-nm virus particle is icosahedral and lacks a tail. CtenRNAV01 forms crystalline arrays occupying most of the infected host's cytoplasm. By growth experiments, the lytic cycle and the burst size were estimated to be <24 h and ∼1 × 10
4
infectious units per host cell, respectively. Stationary-phase
C. tenuissimus
cultures were shown to be more sensitive to CtenRNAV01 than logarithmic-phase cultures. The most noticeable feature of this virus is its exceptionally high yields of ∼10
10
infectious units ml
−1
; this is much higher than those of any other algal viruses previously characterized. CtenRNAV01 has two molecules of ssRNA of approximately 8.9 and 4.3 kb and three major proteins (33.5, 31.5, and 30.0 kDa). Sequencing of the total viral genome has produced only one large contig [9,431 bases excluding the poly(A) tail], suggesting considerable overlapping between the two RNA molecules. The monophyly of CtenRNAV01 compared to another diatom-infecting virus,
Rhizosolenia setigera
RNA virus, was strongly supported in a maximum likelihood phylogenetic tree constructed based on the concatenated amino acid sequences of the RNA-dependent RNA polymerase domains. Although further analysis is required to determine the detailed classification and nomenclature of this virus, these data strongly suggest the existence of a diatom-infecting ssRNA virus group in natural waters.
Response of
Sinorhizobium meliloti
to Elevated Concentrations of Cadmium and Zinc
Authors: Rossbach Silvia , Mai Danielle J. , Carter Eric L. , Sauviac Laurent , Capela Delphine , Bruand Claude , de Bruijn Frans J. 
Published: May 2008

ABSTRACT

Whole-genome transcriptional profiling was used to identify genes in
Sinorhizobium meliloti
1021 that are differentially expressed during exposure to elevated concentrations of cadmium and zinc. Mutant strains with insertions in metal-regulated genes and in genes encoding putative metal efflux pumps were analyzed for their metal sensitivities, revealing a crucial role for the SMc04128-encoded P-type ATPase in the defense of
S. meliloti
against cadmium and zinc stress.
Involvement of Fumarase C and NADH Oxidase in Metabolic Adaptation ofPseudomonas fluorescensCells Evoked by Aluminum and Gallium Toxicity
Authors: Chenier Daniel , Beriault Robin , Mailloux Ryan , Baquie Mathurin , Abramia Gia , Lemire Joseph , Appanna Vasu 
Published: May 2008

ABSTRACTIron (Fe) is a critical element in all aerobic organisms as it participates in a variety of metabolic networks. In this study, aluminum (Al) and gallium (Ga), two Fe mimetics, severely impeded the ability of the soil microbePseudomonas fluorescensto perform oxidative phosphorylation. This was achieved by disrupting the activity and expression of complexes I, II, and IV. These toxic metals also inactivated aconitase (ACN) and fumarase A (FUM A), two tricarboxylic acid cycle enzymes dependent on Fe for their catalytic activity, while FUM C, an Fe-independent enzyme, displayed an increase in activity and expression under these stressed situations. Furthermore, in the Al- and Ga-exposed cells, the activity and expression of an H2O-forming NADH oxidase were markedly increased. The incubation of the Al- and Ga-challenged cells in an Fe-containing medium led to the recovery of the affected enzymatic activities. Taken together, these data provide novel insights into how environmental pollutants such as Al and Ga interfere with cellular Fe metabolism and also illustrate the ability ofPseudomonas fluorescensto modulate metabolic networks to combat this situation.
Eukaryotic Diversity in an Anaerobic Aquifer Polluted with Landfill Leachate
Authors: Brad Traian , Braster Martin , van Breukelen Boris M. , van Straalen Nico M. , Röling Wilfred F. M. 
Published: May 2008

ABSTRACTEukaryotes may influence pollutant degradation processes in groundwater ecosystems by activities such as predation on bacteria and recycling of nutrients. Culture-independent community profiling and phylogenetic analysis of 18S rRNA gene fragments, as well as culturing, were employed to obtain insight into the sediment-associated eukaryotic community composition in an anaerobic sandy aquifer polluted with landfill leachate (Banisveld, The Netherlands). The microeukaryotic community at a depth of 1 to 5 m below the surface along a transect downgradient (21 to 68 m) from the landfill and at a clean reference location was diverse. Fungal sequences dominated most clone libraries. The fungal diversity was high, and most sequences were sequences of yeasts of theBasidiomycota. Sequences of green algae (Chlorophyta) were detected in parts of the aquifer close (<30 m) to the landfill. The bacterium-predating nanoflagellateHeteromita globosa(Cercozoa) was retrieved in enrichments, and its sequences dominated the clone library derived from the polluted aquifer at a depth of 5 m at a location 21 m downgradient from the landfill. The number of culturable eukaryotes ranged from 102to 103cells/g sediment. Culture-independent quantification revealed slightly higher numbers. Groundwater mesofauna was not detected. We concluded that the food chain in this polluted aquifer is short and consists of prokaryotes and fungi as decomposers of organic matter and protists as primary consumers of the prokaryotes.
Increased Respiration in the
sch9Δ
Mutant Is Required for Increasing Chronological Life Span but Not Replicative Life Span
Authors: Lavoie Hugo , Whiteway Malcolm 
Published: May 2008

ABSTRACT

Loss of the protein kinase Sch9p increases both the chronological life span (CLS) and the replicative life span (RLS) of
Saccharomyces cerevisiae
by mimicking calorie restriction, but the physiological consequences of
SCH9
deletion are poorly understood. By transcriptional profiling of an
sch9Δ
mutant, we show that mitochondrial electron transport chain genes are upregulated. Accordingly, protein levels of electron transport chain subunits are increased and the oxygen consumption rate is enhanced in the
sch9Δ
mutant. Deletion of
HAP4
and
CYT1
, both of which are essential for respiration, revert the
sch9Δ
mutant respiratory rate back to a lower-than-wild-type level. These alterations of the electron transport chain almost completely blocked CLS extension by the
sch9Δ
mutation but had a minor impact on the RLS.
SCH9
thus negatively regulates the CLS and RLS through inhibition of respiratory genes, but a large part of its action on life span seems to be respiration independent and might involve increased resistance to stress. Considering that
TOR1
deletion also increases respiration and that Sch9p is a direct target of TOR signaling, we propose that
SCH9
is one of the major effectors of TOR repression of respiratory activity in glucose grown cells.
Abnormal Micronuclear Telomeres Lead to an Unusual Cell Cycle Checkpoint and Defects in
Tetrahymena
Oral Morphogenesis
Authors: Kirk Karen E. , Christ Christina , McGuire Jennifer M. , Paul Arun G. , Vahedi Mithaq , Stuart Kathleen R. , Cole Eric S. 
Published: May 2008

ABSTRACT

Telomere mutants have been well studied with respect to telomerase and the role of telomere binding proteins, but they have not been used to explore how a downstream morphogenic event is related to the mutated telomeric DNA. We report that alterations at the telomeres can have profound consequences on organellar morphogenesis. Specifically, a telomerase RNA mutation termed
ter1-43AA
results in the loss of germ line micronuclear telomeres in the binucleate protozoan
Tetrahymena thermophila.
These cells also display a micronuclear mitotic arrest, characterized by an extreme delay in anaphase with an elongated, condensed chromatin and a mitotic spindle apparatus. This anaphase defect suggests telomere fusions and consequently a spindle rather than a DNA damage checkpoint. Most surprisingly, these mutants exhibit unique, dramatic defects in the formation of the cell's oral apparatus. We suggest that micronuclear telomere loss leads to a “dynamic pause” in the program of cortical development, which may reveal an unusual cell cycle checkpoint.
The CI Repressors of Shiga Toxin-Converting Prophages Are Involved in Coinfection of
Escherichia coli
Strains, Which Causes a Down Regulation in the Production of Shiga Toxin 2
Authors: Serra-Moreno R. , Jofre J. , Muniesa M. 
Published: May 2008

ABSTRACT

Shiga toxins (Stx) are the main virulence factors associated with a form of
Escherichia coli
known as Shiga toxin-producing
E. coli
(STEC). They are encoded in temperate lambdoid phages located on the chromosome of STEC. STEC strains can carry more than one prophage. Consequently, toxin and phage production might be influenced by the presence of more than one Stx prophage on the bacterial chromosome. To examine the effect of the number of prophages on Stx production, we produced
E. coli
K-12 strains carrying either one Stx2 prophage or two different Stx2 prophages. We used recombinant phages in which an antibiotic resistance gene (
aph
,
cat
, or
tet
) was incorporated in the middle of the Shiga toxin operon. Shiga toxin was quantified by immunoassay and by cytotoxicity assay on Vero cells (50% cytotoxic dose). When two prophages were inserted in the host chromosome, Shiga toxin production and the rate of lytic cycle activation fell. The
c
I repressor seems to be involved in incorporation of the second prophage. Incorporation and establishment of the lysogenic state of the two prophages, which lowers toxin production, could be regulated by the CI repressors of both prophages operating in
trans
. Although the sequences of the
c
I genes of the phages studied differed, the CI protein conformation was conserved. Results indicate that the presence of more than one prophage in the host chromosome could be regarded as a mechanism to allow genetic retention in the cell, by reducing the activation of lytic cycle and hence the pathogenicity of the strains.
Functional Analysis of GlnE, an Essential Adenylyl Transferase in
Mycobacterium tuberculosis
Authors: Carroll Paul , Pashley Carey A. , Parish Tanya 
Published: May 2008

ABSTRACT

Glutamine synthetase (GS) plays an important role in nitrogen assimilation. The major GS of
Mycobacterium tuberculosis
is GlnA1, a type I GS whose activity is controlled by posttranscriptional modification by GlnE. GlnE is an adenylyl transferase comprised of an adenylylating domain and a deadenylylating domain which modulate GS activity. We previously demonstrated that GlnE is essential in
M. tuberculosis
in normal growth medium. In this study, we further show that GlnE is required under multiple medium conditions, including in nitrogen-limited medium. We demonstrate that adenylylation is the critical activity for
M. tuberculosis
survival, since we were able to delete the deadenylylation domain with no apparent effect on growth or GS activity. Furthermore, we identified a critical aspartate residue in the proposed nucleotidyltransferase motif. Temperature-sensitive mutants of GlnE were generated and shown to have a defect in growth and GS activity in nitrogen-limited medium. Finally, we were able to generate a GlnE null mutant in the presence of
l
-methionine sulfoximine, a GS inhibitor, and glutamine supplementation. In the presence of these supplements, the null mutant was able to grow similarly to the wild type. Surprisingly, the GlnE mutant was able to survive and grow for extended periods in liquid medium, but not on solid medium, in the absence of GS inhibition. Thus, we have confirmed that the unusual requirement of
M. tuberculosis
for GlnE adenylylation activity is linked to the activity of GS in the cell.
The Putative Hybrid Sensor Kinase SypF Coordinates Biofilm Formation inVibrio fischeriby Acting Upstream of Two Response Regulators, SypG and VpsR
Authors: Darnell Cynthia L. , Hussa Elizabeth A. , Visick Karen L. 
Published: May 2008

ABSTRACTColonization of the Hawaiian squidEuprymna scolopesby the marine bacteriumVibrio fischerirequires the symbiosis polysaccharide (syp) gene cluster, which contributes to symbiotic initiation by promoting biofilm formation on the surface of the symbiotic organ. We previously described roles for thesyp-encoded response regulator SypG and an unlinked gene encoding the sensor kinase RscS in controllingsyptranscription and inducingsyp-dependent cell-cell aggregation phenotypes. Here, we report the involvement of an additionalsyp-encoded regulator, the putative sensor kinase SypF, in promoting biofilm formation. Through the isolation of an increased activity allele,sypF1, we determined that SypF can function to inducesyptranscription as well as a variety of biofilm phenotypes, including wrinkled colony formation, adherence to glass, and pellicle formation. SypF1-mediated transcription of thesypcluster was entirely dependent on SypG. However, the biofilm phenotypes were reduced, not eliminated, in thesypGmutant. These phenotypes were also reduced in a mutant deleted forsypE, anothersyp-encoded response regulator. However, SypF1 still induced phenotypes in asypG sypEdouble mutant, suggesting that SypF1 might activate another regulator(s). Our subsequent work revealed that the residual SypF1-induced biofilm formation depended on VpsR, a putative response regulator, and cellulose biosynthesis. These data support a model in which a network of regulators and at least two polysaccharide loci contribute to biofilm formation inV. fischeri.
Characterization of
Clostridium perfringens
Spores That Lack SpoVA Proteins and Dipicolinic Acid
Authors: Paredes-Sabja Daniel , Setlow Barbara , Setlow Peter , Sarker Mahfuzur R. 
Published: May 2008

ABSTRACT

Spores of
Clostridium perfringens
possess high heat resistance, and when these spores germinate and return to active growth, they can cause gastrointestinal disease. Work with
Bacillus subtilis
has shown that the spore's dipicolinic acid (DPA) level can markedly influence both spore germination and resistance and that the proteins encoded by the
spoVA
operon are essential for DPA uptake by the developing spore during sporulation. We now find that proteins encoded by the
spoVA
operon are also essential for the uptake of Ca
2+
and DPA into the developing spore during
C. perfringens
sporulation. Spores of a
spoVA
mutant had little, if any, Ca
2+
and DPA, and their core water content was approximately twofold higher than that of wild-type spores. These DPA-less spores did not germinate spontaneously, as DPA-less
B. subtilis
spores do. Indeed, wild-type and
spoVA C. perfringens
spores germinated similarly with a mixture of
l
-asparagine and KCl (AK), KCl alone, or a 1:1 chelate of Ca
2+
and DPA (Ca-DPA). However, the viability of
C. perfringens spoVA
spores was 20-fold lower than the viability of wild-type spores. Decoated wild-type and
spoVA
spores exhibited little, if any, germination with AK, KCl, or exogenous Ca-DPA, and their colony-forming efficiency was 10
3
- to 10
4
-fold lower than that of intact spores. However, lysozyme treatment rescued these decoated spores. Although the levels of DNA-protective α/β-type, small, acid-soluble spore proteins in
spoVA
spores were similar to those in wild-type spores,
spoVA
spores exhibited markedly lower resistance to moist heat, formaldehyde, HCl, hydrogen peroxide, nitrous acid, and UV radiation than wild-type spores did. In sum, these results suggest the following. (i) SpoVA proteins are essential for Ca-DPA uptake by developing spores during
C. perfringens
sporulation. (ii) SpoVA proteins and Ca-DPA release are not required for
C. perfringens
spore germination. (iii) A low spore core water content is essential for full resistance of
C. perfringens
spores to moist heat, UV radiation, and chemicals.
Clusters of Charged Residues at the C Terminus of MotA and N Terminus of MotB Are Important for Function of the
Escherichia coli
Flagellar Motor
Authors: Hosking Edan R. , Manson Michael D. 
Published: May 2008

ABSTRACT
MotA contains a conserved C-terminal cluster of negatively charged residues, and MotB contains a conserved N-terminal cluster of positively charged residues. Charge-altering mutations affecting these residues impair motility but do not diminish Mot protein levels. The motility defects are reversed by second-site mutations targeting the same or partner protein.
CpcM Posttranslationally Methylates Asparagine-71/72 of Phycobiliprotein Beta Subunits in
Synechococcus
sp. Strain PCC 7002 and
Synechocystis
sp. Strain PCC 6803
Authors: Shen Gaozhong , Leonard Heidi S. , Schluchter Wendy M. , Bryant Donald A. 
Published: May 2008

ABSTRACT

Cyanobacteria produce phycobilisomes, which are macromolecular light-harvesting complexes mostly assembled from phycobiliproteins. Phycobiliprotein beta subunits contain a highly conserved γ-
N
-methylasparagine residue, which results from the posttranslational modification of Asn71/72. Through comparative genomic analyses, we identified a gene, denoted
cpcM
, that (i) encodes a protein with sequence similarity to other
S
-adenosylmethionine-dependent methyltransferases, (ii) is found in all sequenced cyanobacterial genomes, and (iii) often occurs near genes encoding phycobiliproteins in cyanobacterial genomes. The
cpcM
genes of
Synechococcus
sp. strain PCC 7002 and
Synechocystis
sp. strain PCC 6803 were insertionally inactivated. Mass spectrometric analyses of phycobiliproteins isolated from the mutants confirmed that the CpcB, ApcB, and ApcF were 14 Da lighter than their wild-type counterparts. Trypsin digestion and mass analyses of phycobiliproteins isolated from the mutants showed that tryptic peptides from phycocyanin that included Asn72 were also 14 Da lighter than the equivalent peptides from wild-type strains. Thus, CpcM is the methyltransferase that modifies the amide nitrogen of Asn71/72 of CpcB, ApcB, and ApcF. When cells were grown at low light intensity, the
cpcM
mutants were phenotypically similar to the wild-type strains. However, the mutants were sensitive to high-light stress, and the
cpcM
mutant of
Synechocystis
sp. strain PCC 6803 was unable to grow at moderately high light intensities. Fluorescence emission measurements showed that the ability to perform state transitions was impaired in the
cpcM
mutants and suggested that energy transfer from phycobiliproteins to the photosystems was also less efficient. The possible functions of asparagine N methylation of phycobiliproteins are discussed.
Substrate Specificity of the 3-Methylcrotonyl Coenzyme A (CoA) and Geranyl-CoA Carboxylases from
Pseudomonas aeruginosa
Authors: Aguilar J. A. , Díaz-Pérez C. , Díaz-Pérez A. L. , Rodríguez-Zavala J. S. , Nikolau B. J. , Campos-García J. 
Published: May 2008

ABSTRACT

Biotin-containing 3-methylcrotonyl coenzyme A (MC-CoA) carboxylase (MCCase) and geranyl-CoA (G-CoA) carboxylase (GCCase) from
Pseudomonas aeruginosa
were expressed as His-tagged recombinant proteins in
Escherichia coli
. Both native and recombinant MCCase and GCCase showed pH and temperature optima of 8.5 and 37°C. The apparent
K
0.5
(affinity constant for non-Michaelis-Menten kinetics behavior) values of MCCase for MC-CoA, ATP, and bicarbonate were 9.8 μM, 13 μM, and 0.8 μM, respectively. MCCase activity showed sigmoidal kinetics for all the substrates and did not carboxylate G-CoA. In contrast, GCCase catalyzed the carboxylation of both G-CoA and MC-CoA. GCCase also showed sigmoidal kinetic behavior for G-CoA and bicarbonate but showed Michaelis-Menten kinetics for MC-CoA and the cosubstrate ATP. The apparent
K
0.5
values of GCCase were 8.8 μM and 1.2 μM for G-CoA and bicarbonate, respectively, and the apparent

K
m

values of GCCase were 10 μM for ATP and 14 μM for MC-CoA. The catalytic efficiencies of GCCase for G-CoA and MC-CoA were 56 and 22, respectively, indicating that G-CoA is preferred over MC-CoA as a substrate. The enzymatic properties of GCCase suggest that it may substitute for MCCase in leucine catabolism and that both the MCCase and GCCase enzymes play important roles in the leucine and acyclic terpene catabolic pathways.
Role of Dipicolinic Acid in the Germination, Stability, and Viability of Spores of
Bacillus subtilis
Authors: Magge Anil , Granger Amanda C. , Wahome Paul G. , Setlow Barbara , Vepachedu Venkata R. , Loshon Charles A. , Peng Lixin , Chen De , Li Yong-qing , Setlow Peter 
Published: May 2008

ABSTRACT

Spores of
Bacillus subtilis spoVF
strains that cannot synthesize dipicolinic acid (DPA) but take it up during sporulation were prepared in medium with various DPA concentrations, and the germination and viability of these spores as well as the DPA content in individual spores were measured. Levels of some other small molecules in DPA-less spores were also measured. These studies have allowed the following conclusions. (i) Spores with no DPA or low DPA levels that lack either the cortex-lytic enzyme (CLE) SleB or the receptors that respond to nutrient germinants could be isolated but were unstable and spontaneously initiated early steps in spore germination. (ii) Spores that lacked SleB and nutrient germinant receptors and also had low DPA levels were more stable. (iii) Spontaneous germination of spores with no DPA or low DPA levels was at least in part via activation of SleB. (iv) The other redundant CLE, CwlJ, was activated only by the release of high levels of DPA from spores. (v) Low levels of DPA were sufficient for the viability of spores that lacked most α/β-type small, acid-soluble spore proteins. (vi) DPA levels accumulated in spores prepared in low-DPA-containing media varied greatly between individual spores, in contrast to the presence of more homogeneous DPA levels in individual spores made in media with high DPA concentrations. (vii) At least the great majority of spores of several
spoVF
strains that contained no DPA also lacked other major spore small molecules and had gone through some of the early reactions in spore germination.